@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{SchaeferEtAl2002a,
year = {2002},
journal = {Int J Syst Evol Microbiol},
volume = {52},
pages = {851-859},
author = {Schaefer, J.K. and Goodwin, K.D. and McDonald, I.R. and Murrell, J.C. and Oremland, R.S.},
title = {Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide.},
abstract = {A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the alpha-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov..},
doi = {10.1099/00207713-52-3-851},
issue = {3},
pmid = {12054249}
}
@article{VandecandelaereEtAl2008b,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2788-2793},
author = {Vandecandelaere, I. and Segaert, E. and Mollica, A. and Faimali, M. and Vandamme, P.},
title = {Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al. 2006.},
abstract = {Strain LMG 24366T was isolated from a marine electroactive biofilm grown on a stainless steel cathode (Genova, Italy) and was investigated by using a polyphasic taxonomic approach. This study demonstrated that strain LMG 24366T represents a novel species within the genus Leisingera, which shared 98.9 % 16S rRNA gene similarity with its nearest phylogenetic neighbour, Leisingera methylohalidivorans. Strain LMG 24366T grew on betaine (1 mM) as a sole carbon source, whereas no growth was observed on L-methionine (10 mM). The phenotypic and genotypic analyses showed that strain LMG 24366T could be differentiated from established Leisingera species and that it represented a novel species, for which the name Leisingera aquimarina sp. nov. is proposed. The type strain is LMG 24366T (=CCUG 55860T) and has a DNA G+C content of 61.4 mol%.},
doi = {10.1099/ijs.0.65844-0},
issue = {Pt 12},
pmid = {19060059}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LeeEtAl2007k,
year = {2007},
journal = {Int J Syst Evol Microbiol},
volume = {57},
pages = {1815-1818},
author = {Lee, K. and Choo, Y.J. and Giovannoni, S.J. and Cho, J.C.},
title = {Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean.},
abstract = {Gram-negative, facultatively aerobic, chemoheterotrophic, short rod-shaped marine bacterial strains HTCC2662T and HTCC2663, isolated from the Sargasso Sea by using a dilution-to-extinction culturing method, were investigated to determine their taxonomic position. Characterization of the two strains by phenotypic and phylogenetic analyses revealed that they belonged to the same species. The DNA G+C content of strain HTCC2662T was 58.4 mol% and the predominant cellular fatty acids were C(18 : 1) omega 7c (52.5 %), C(16 : 0) 2-OH (13.5 %) and C(18 : 1) 11-methyl omega 7c (12.2 %). Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains represented a distinct line of descent within the genus Ruegeria, with highest sequence similarities to Ruegeria atlantica DSM 5823T (97.2 %), Ruegeria lacuscaerulensis DSM 11314T (96.5 %) and Ruegeria pomeroyi DSM 15171T (95.6 %). Several phenotypic characteristics, including facultatively requiring NaCl and oxygen for growth, together with the cellular fatty acid composition, differentiated strain HTCC2662T from other members of the genus Ruegeria. Based on phenotypic, chemotaxonomic and phylogenetic traits, it is suggested that strains HTCC2662T and HTCC2663 represent a novel species of the genus Ruegeria, for which the name Ruegeria pelagia sp. nov. is proposed. The type strain is HTCC2662T (=KCCM 42378T=NBRC 102038T).},
doi = {10.1099/ijs.0.65032-0},
issue = {8},
pmid = {17684263}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{MuramatsuEtAl2007a,
year = {2007},
journal = {Int J Syst Evol Microbiol},
volume = {57},
pages = {1304-1309},
author = {Muramatsu, Y. and Uchino, Y. and Kasai, H. and Suzuki, K. and Nakagawa, Y.},
title = {Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau.},
abstract = {The taxonomic positions of two bacterial strains, MBIC01146T and MBIC01099, isolated from marine environments of Japan and Palau, respectively, were determined by using a polyphasic approach. The bacteria were aerobic, motile, Gram-negative rods and formed star-shaped aggregations. The G+C content of the genomic DNA ranged from 58.5 to 58.7 mol%. The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acids were C(16 : 0), C(18 : 1)omega6c and C(18 : 1)omega7c. 16S rRNA gene sequence analyses based on both neighbour-joining and maximum-parsimony methods revealed that strains MBIC01146T and MBIC01099 were positioned within the cluster comprising Ruegeria atlantica and Silicibacter lacuscaerulensis within subgroup alpha-3 of the Proteobacteria. The phenotypic and chemotaxonomic characteristics of the novel strains were similar to those of Ruegeria atlantica; however, DNA-DNA hybridization tests showed that the isolates represented an independent species. The isolates could be differentiated from Ruegeria atlantica based on several characteristics. Therefore, strains MBIC01146T and MBIC01099 are considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria mobilis sp. nov. is proposed. The type strain is MBIC01146T (=NBRC 101030T=CIP 109181T). An emended description of Ruegeria atlantica Uchino et al. 1999 is also given.},
doi = {10.1099/ijs.0.64572-0},
issue = {6},
pmid = {17551047}
}
@article{RugerHofle1992a,
year = {1992},
journal = {Int J Syst Bacteriol},
volume = {42},
pages = {133-143},
author = {Ruger, H.J. and Hofle, M.G.},
title = {Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev.},
abstract = {Two new species of aerobic, gram-negative, peritrichously flagellated or nonmotile marine bacteria usually forming star-shaped aggregates were isolated from northeastern Atlantic Ocean bottom sediments. These organisms resembled eight star-shaped-aggregate-forming bacterial species from the Baltic Sea originally ascribed to the genus Agrobacterium but not included on the Approved Lists of Bacterial Names because of their questionable relationships to true agrobacteria. These two sets of star-shaped-aggregate-forming bacteria were compared by means of phenotypic data, DNA base compositions, DNA-DNA relatedness, and one-dimensional electrophoretic analysis of low-molecular-weight RNAs (5S rRNA and tRNA). According to the results of genotyping, the northeastern Atlantic Ocean isolates and three of the Baltic Sea species formed a group of closely related bacteria that could not be excluded from the genus Agrobacterium with certainty. Until more genotypic data are available, these five marine species are regarded as a distinct subdivision of the genus Agrobacterium consisting of Agrobacterium atlanticum sp. nov. (type strain, 1480T = DSM 5823T), A. meteori sp. nov. (type strain, 1513T = DSM 5824T), A. ferrugineum sp. nov. nom. rev. emend. (type strain, ATCC 25652T), A. gelatinovorum sp. nov. nom. rev. emend. (type strain, ATCC 25655T), and A. stellulatum sp. nov. nom. rev. emend. (type strain, ATCC 15215T). "A. aggregatum" proved to be a later subjective synonym of A. stellulatum, which had priority. The remaining four Baltic Sea species, "A. agile," "A. kieliense," "A. luteum," and "A. sanguineum," could not be placed in the new subdivision of Agrobacterium.},
doi = {10.1099/00207713-42-1-133},
issue = {1},
pmid = {1371058}
}
@article{UchinoEtAl1998c,
year = {1998},
journal = {J Gen Appl Microbiol},
volume = {44},
pages = {201-210},
author = {Uchino, Y. and Hirata, A. and Yokota, A. and Sugiyama, J.},
title = {Reclassification of marine Agrobacterium species: Proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev.},
abstract = {The bootstrapped 16S rDNA sequence-based neighbor-joining phylogeny has suggested that the marine species of the genus Agrobacterium have no relation to the terrestrial Agrobacterium species. Agrobacterium atlanticum IAM 14463T (a superscript T=type strain), Agrobacterium ferrugineum IAM 12616T, Agrobacterium gelatinovorum IAM 12617T, Agrobacterium meteori IAM 14464T, Agrobacterium stellulatum IAM 12621T and IAM 12614, and the invalidly published marine species "Agrobacterium kieliense" IAM 12618 occupy an independent position in the a-subclass of the Proteobacteria. Based on 16S rDNA sequencing and on chemotaxonomic, morphological, and physiological studies, we propose the transfer of A. atlanticum, A. gelatinovorum, and Roseobacter algicola to the genus Ruegeria gen. nov. as Ruegeria atlantica comb. nov., Ruegeria gelatinovora comb. nov., and Ruegeria algicola comb. nov., respectively; of strains of A. stellulatum to the genus Stappia gen. nov. as Stappia stellulata comb. nov. and Stappia aggregata sp. nov., nom. rev., respectively; and of "A. kieliense" to the genus Ahrensia gen. nov. as Ahrensia kieliense sp. nov., nom. rev. Agrobacterium meteori is assigned to be a synonym of A. atlanticum.},
doi = {10.2323/jgam.44.201},
issue = {3},
pmid = {12501429}
}
@article{VandecandelaereEtAl2008a,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2726-2733},
author = {Vandecandelaere, I. and Nercessian, O. and Segaert, E. and Achouak, W. and Faimali, M. and Vandamme, P.},
title = {Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm.},
abstract = {Seventy isolates were obtained from a marine electroactive biofilm that was generated on a cathodically polarized stainless steel electrode (Genoa, Italy). The genetic diversity was investigated by means of BOX-PCR fingerprinting and two clusters of isolates with similar BOX-PCR profiles were delineated. Whole-cell fatty acid methyl ester analysis and 16S rRNA gene sequence analysis showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. DNA-DNA hybridization experiments and a biochemical analysis demonstrated that four isolates belonged to the species Ruegeria mobilis. However, 66 isolates from the second BOX-PCR cluster constituted a novel species within the genus Ruegeria, for which the name Ruegeria scottomollicae sp. nov. is proposed. The DNA G+C content was 61.0+/-0.4 %. The type strain is LMG 24367T (=CCUG 55858T).},
doi = {10.1099/ijs.0.65843-0},
issue = {12},
pmid = {19060048}
}
@article{YiEtAl2007b,
year = {2007},
journal = {Int J Syst Evol Microbiol},
volume = {57},
pages = {815-819},
author = {Yi, H. and Lim, Y.W. and Chun, J.},
title = {Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999.},
abstract = {The taxonomic positions of the genera Ruegeria and Silicibacter were evaluated by a polyphasic investigation. It was evident from 16S rRNA gene sequence analysis that both genera are closely related as they formed a monophyletic clade with high sequence similarities (96.9-98.2 %). Several properties commonly found in these taxa strongly suggest that they should be classified in the same genus. Further, a comparative study based on DNA-DNA hybridization, phenotypic characterization and chemotaxonomic analysis indicated that the members of this clade, namely Ruegeria atlantica, Silicibacter lacuscaerulensis and Silicibacter pomeroyi, can be readily differentiated from each other. On the basis of the polyphasic data obtained in this study, all species of the genus Silicibacter should be transferred to the genus Ruegeria, since the latter has nomenclatural priority. It is therefore proposed that Silicibacter lacuscaerulensis and Silicibacter pomeroyi are transferred to the genus Ruegeria as Ruegeria lacuscaerulensis comb. nov. and Ruegeria pomeroyi comb. nov.},
doi = {10.1099/ijs.0.64568-0},
issue = {4},
pmid = {17392212}
}
@article{BreiderEtAl2017a,
year = {2017},
journal = {Int J Syst Evol Microbiol},
volume = {67},
pages = {2153-2159},
author = {Breider, S. and Freese, H.M. and Sproer, C. and Simon, M. and Overmann, J. and Brinkhoff, T.},
title = {Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour.},
abstract = {Three heterotrophic, aerobic, brown-pigmented strains, designated P97T, P100 and P104, were isolated from a harbour in the southern North Sea. Phylogenetic analysis of 16S rRNA gene sequences revealed that the isolates are affiliated to the genus Phaeobacter. In silico DNA-DNA hybridization of the genome of strain P97T against those of existing type species indicated that P97T represents a novel species within the genus Phaeobacter, with Phaeobacter inhibens T5T as the closest described organism (29.6 % DNA-DNA relatedness) followed by P. gallaeciensis CIP 105210T (26.4 %). DNA-DNA hybridization demonstrated that the three new strains belong to the same species. The new isolates inhibited Pseudoalteromonas tunicata DSM 14096T, and were Gram-stain-negative, catalase- and oxidase-positive, chemo-organoheterotrophic and motile. Growth occurred at pH 6.5-9.5 (optimum 7.0-8.0) and at 4-30 degrees C (optimum 20-28 degrees C). The strains required NaCl for growth. The salinity range was 0.5-6.0 % (w/v) NaCl for P97T and P100, and 0.5-5.0 % for P104, lower than values described for Phaeobacter gallaeciensis and Phaeobacter inhibens. The optimum NaCl concentration for strains P97T and P104 was 2.0-4.0 %, and for P100 was 2.0-3.0 %. Fatty acids (>1 %) comprised 18 : 1omega7c, 16 : 0, 18 : 1 omega7c 11-methyl, 18 : 0, 12 :1, 18 : 2omega7c,12, 10 : 0 3-OH and 12 : 0 3-OH. Polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, one unknown lipid and one additional unknown lipid in strain P97T. The major respiratory quinone was Q10. Based on phylogenetic and phenotypic differences, the strains represent a novel species in the genus Phaeobacter, for which the name Phaeobacter porticola sp. nov. is proposed. The type strain is P97T (=DSM 103148T=LMG 29594T).},
doi = {10.1099/ijsem.0.001879},
issue = {7},
pmid = {28699865}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{RaineyEtAl1999b,
year = {1999},
journal = {Int J Syst Bacteriol},
volume = {49},
pages = {645-651},
author = {Rainey, F.A. and Kelly, D.P. and Stackebrandt, E. and Burghardt, J. and Hiraishi, A. and Katayama, Y. and Wood, A.P.},
title = {A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov.},
abstract = {Comparison of both 16S rRNA coding sequences and DNA-DNA hybridization of ten strains of alpha-subclass of Proteobacteria currently classified as strains of Paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. Comparison with published data on the cytochrome c profiles and other 16S rRNA coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups. Group A comprises strains ATCC 17741T (the type strain of P. denitrificans), LMD 22.21T, DSM 413T, ATCC 19367, ATCC 13543, DSM 1404, DSM 1405, Pd 1222 (a genetic modification of DSM 413T) and NCIMB 8944. Group B comprises ATCC 35512T (the original type strain of Thiosphaera pantotropha), LMD 82.5T, LMD 92.63, DSM 65, LMG 4218, IAM 12479, JCM 6892, DSM 11072, DSM 11073 and DSM 11104. In light of these findings, it is proposed that: (1) strains of group A are retained as P. denitrificans, with ATCC 17741T as the type strain of the type species; and (2) all strains of group B are assigned to the new species combination Paracoccus pantotrophus comb. nov., with strain ATCC 35512T as the type strain. Comparative 16S rRNA sequence analysis and DNA-DNA hybridization of strains of Paracoccus versutus confirm that this species is distinct from both P. denitrificans and P. pantotrophus, but that its nearest phylogenetic neighbour is P. pantotrophus.},
doi = {10.1099/00207713-49-2-645},
issue = {2},
pmid = {10319488}
}
@article{RobertsonKuenen1983a,
year = {1983},
journal = {J. Gen. Microbiol.},
volume = {129},
pages = {2847-2855},
author = {Robertson, L.A. and Kuenen, J.G.},
title = {Thiosphaera pantotropha gen. nov., sp. nov., a facultatively anaerobic, facultatively autotrophic sulphur bacterium.},
doi = {10.1099/00221287-129-9-2847}
}
@article{KlotzEtAl2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {736-744},
author = {Klotz, F. and Brinkhoff, T. and Freese, H.M. and Wietz, M. and Teske, A. and Simon, M. and Giebel, H.A.},
title = {Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill.},
abstract = {A heterotrophic, Gram-stain-negative, aerobic, sodium-requiring and motile bacterium was isolated from oil-contaminated surface water of the Gulf of Mexico during the Deepwater Horizon oil spill. Strain O3.65T showed highest 16S rRNA gene sequence similarity to Phaeobacter gallaeciensis BS107T and Phaeobacter inhibens T5T, both with 98.3 %, respectively. Based on complete genome analysis, highest similarity was observed to species of the genus Ruegeria. Strain O3.65T exhibited a broad salinity, temperature and pH range of 0.5-10 % NaCl, 4-45 degrees C and 5.5-9.0, respectively. The DNA G+C content of strain O3.65T was 61.5 mol%. The major respiratory lipoquinone was ubiquinone-10 (Q-10), the most dominant fatty acids (>1 %) comprised 18 : 1omega7c and 18 : 1omega7c 11-methyl, 10 : 0 3OH, 12 : 1 3OH, 14 : 1 3OH/3-oxo-14 : 0, 16 : 0, 16 : 0 2OH, 18 : 1 2OH and 12 : 1. The polar lipid pattern indicated presence of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, two unidentified phospholipids and seven unidentified lipids. On Difco marine broth agar, strain O3.65T formed smooth, shiny white to beige and convex colonies with regular edges. Phylogenetic, phylogenomic and phenotypic differences revealed that strain O3.65T represents a new species of a novel genus within the family Rhodobacteraceae, for which we propose the name Tritonibacter horizontis gen. nov., sp. nov. The type strain of the type species is O3.65T (=DSM 101689T=LMG 29740T).},
doi = {10.1099/ijsem.0.002573},
issue = {3},
pmid = {29458459}
}
@article{LiangEtAl2021j,
year = {2021},
journal = {Front Microbiol},
volume = {12},
pages = {683109},
author = {Liang, K.Y.H. and Orata, F.D. and Boucher, Y.F. and Case, R.J.},
title = {Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov.},
abstract = {The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.},
doi = {10.3389/fmicb.2021.683109},
pmid = {34248901}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LiuEtAl2014h,
year = {2014},
journal = {Int J Syst Evol Microbiol},
volume = {64},
pages = {66-71},
author = {Liu, J.J. and Zhang, X.Q. and Chi, F.T. and Pan, J. and Sun, C. and Wu, M.},
title = {Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds.},
abstract = {A Gram-stain-negative, non-motile and aerobic bacterium, designated CF17T, was isolated from coastal planktonic seaweeds, East China Sea. The isolate grew at 18-37 degrees C (optimum 25-28 degrees C), pH 6.5-9.0 (optimum 7.0-8.0) and with 0-5 % NaCl (optimum 1-2 %, w/v) and 0.5-10 % sea salts (optimum 2-3 %, w/v). Growth of strain CF17T could be stimulated prominently by supplementing the growth medium with the autoclaved supernatant of a culture of strain CF5, which was isolated from the same sample along with strain CF17T. The cell morphology of strain CF17T was a bean-shaped rod consisting of a swollen end and a long prostheca. The phylogenetic analysis of 16S rRNA gene sequences indicated that strain CF17T clustered with Gemmobacter nectariphilus DSM 15620T within the genus Gemmobacter. The DNA G+C content of strain CF17T was 61.4 mol%. The respiratory quinone was ubiquinone Q-10. The major fatty acids included C18 : 1omega7c and C18 : 0. The polar lipids of strain CF17T consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two uncharacterized phospholipids, one uncharacterized aminolipid, three uncharacterized glycolipids and one uncharacterized lipid. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain CF17T ( = CGMCC 1.11024T = JCM 18498T) is considered to represent a novel species of the genus Gemmobacter, for which the name Gemmobacter megaterium sp. nov. is proposed.},
doi = {10.1099/ijs.0.050955-0},
issue = {1},
pmid = {24014623}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{SrinivasEtAl2007b,
year = {2007},
journal = {Int J Syst Evol Microbiol},
volume = {57},
pages = {1984-1987},
author = {Srinivas, T.N. and Kumar, P.A. and Sasikala, C.h. and Ramana, C.h.V. and Imhoff, J.F.},
title = {Rhodobacter vinaykumarii sp. nov., a marine phototrophic alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter.},
abstract = {A rod-shaped, phototrophic, purple non-sulfur bacterium was isolated in pure culture from seawater collected from the seashore of Visakhapatnam, on the east coast of India, in a medium that contained 2 % NaCl (w/v). Strain JA123T was Gram-negative and non-motile and had a requirement for NaCl. Photo-organoheterotrophic and chemo-organoheterotrophic growth occurred with organic compounds as carbon sources and electron donors. Photolithoautotrophic, chemolithoautotrophic and fermentative growth could not be demonstrated. Strain JA123T contained vesicular intracellular photosynthetic membrane structures. Bacteriochlorophyll a and probably carotenoids of the spheroidene series were present as photosynthetic pigments. Biotin was required for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA123T clustered with species of the genus Rhodobacter. Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA123T is sufficiently different from other Rhodobacter species to propose a novel species, Rhodobacter vinaykumarii sp. nov., to accommodate this strain; the type strain is JA123T (=DSM 18714T =JCM 14544T =CCUG 54311T).},
doi = {10.1099/ijs.0.65077-0},
issue = {Pt 9},
pmid = {17766859}
}
@article{SureshEtAl2019a,
year = {2019},
journal = {Front Microbiol},
volume = {10},
pages = {2480},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.},
doi = {10.3389/fmicb.2019.02480},
pmid = {31736915}
}
@article{KatayamaEtAl1995a,
year = {1995},
journal = {Microbiology (Reading)},
volume = {141},
pages = {1469-1477},
author = {Katayama, Y. and Hiraishi, A. and Kuraishi, H.},
title = {Paracoccus thiocyanatus sp. nov., a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of Thiobacillus versutus to the genus Paracoccus as Paracoccus versutus comb. nov. with emendation of the genus.},
abstract = {A facultatively chemolithotrophic thiocyanate-degrading bacterium, strain THI 011T, which was previously isolated from activated sludge and tentatively named Thiobacillus sp., was studied taxonomically and phylogenetically. This bacterium utilizes thiocyanate as sole energy source and the specific growth rate for chemolithoautotrophic growth with thiocyanate was 0.059 h-1. Molecular phylogenetic relationships of strain THI 011T to Thiobacillus versutus and members of the genus Paracoccus were elucidated by comparing 16S rRNA gene sequences. Binary sequence comparisons showed that strain THI 011T was most related to Paracoccus aminophilus, at a similarity level of 97.0%, and T. versutus was most similar to Paracoccus denitrificans, at a level of 99.1%. A neighbour-joining phylogenetic tree showed that strain THI 011T formed a cluster together with T. versutus and known species of the genus Paracoccus within the alpha-3 subclass of the Proteobacteria. DNA-DNA hybridization assays and phenotypic studies indicated that strain THI 011T differed from T. versutus and known species of the genus Paracoccus. On the basis of these results, we propose to classify strain THI 011T into a new species of the genus Paracoccus with the name Paracoccus thiocyanatus sp. nov. We also propose to transfer T. versutus to the genus Paracoccus and present an emended description of the genus.},
doi = {10.1099/13500872-141-6-1469},
issue = {6},
pmid = {7545513}
}
@article{ArunasriEtAl2008a,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {1792-1796},
author = {Arunasri, K. and Venkata Ramana, V. and Sproer, C. and Sasikala, C.h. and Ramana, C.h.V.},
title = {Rhodobacter megalophilus sp. nov., a phototroph from the Indian Himalayas possessing a wide temperature range for growth.},
abstract = {Two strains of phototrophic, purple non-sulfur bacteria capable of growing at low temperatures (5 degrees C) were isolated from the Himalayas. The two strains showed positive phototaxis and grew over a relatively wide temperature range (5-40 degrees C). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA194T clustered with members of the genus Rhodobacter. Strain JA194T showed highest 16S rRNA gene sequence similarity with Rhodobacter sphaeroides DSM 158T (99 %). However, DNA-DNA hybridization experiments between Rba. sphaeroides DSM 158T and strain JA194T revealed a level of relatedness of only 67 %. The DNA base composition of strain JA194T was 66.67 mol% G+C (by HPLC). Based on 16S rRNA gene sequence analysis, morphological, physiological, Fourier transform infrared fingerprinting and DNA-DNA hybridization studies, strain JA194T (=KCTC 5602T =JCM 14598T) is sufficiently different from other Rhodobacter species to merit its description as the type strain of a novel species, for which the name Rhodobacter megalophilus sp. nov. is proposed.},
doi = {10.1099/ijs.0.65642-0},
issue = {8},
pmid = {18676458}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{SureshEtAl2019a,
year = {2019},
journal = {Front Microbiol},
volume = {10},
pages = {2480},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.},
doi = {10.3389/fmicb.2019.02480},
pmid = {31736915}
}
@article{SureshEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {1111},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Corrigendum: Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.02480.].},
doi = {10.3389/fmicb.2020.01111},
pmid = {32582079}
}
@article{ArahalEtAl2005a,
year = {2005},
journal = {Int J Syst Evol Microbiol},
volume = {55},
pages = {2371-2376},
author = {Arahal, D.R. and Macian, M.C. and Garay, E. and Pujalte, M.J.},
title = {Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov.},
abstract = {A Gram-negative, slightly halophilic, non-pigmented, strictly aerobic, chemo-organotrophic bacterium was isolated from sea water off the western Mediterranean coast near Valencia (Spain). This strain was able to grow on several organic acids and amino acids added to a minimal medium as carbon sources, but used few carbohydrates or yielded slight growth when sugars were used. Phylogenetic analysis based on an almost complete 16S rRNA gene sequence revealed that strain XSM19T was a member of the Roseobacter group within the 'Alphaproteobacteria', with its closest phylogenetic neighbour being Ruegeria gelatinovorans (97.6 % sequence similarity). Following a polyphasic approach, it was concluded that strain XSM19T represents a new genus and novel species, for which the name Thalassobius mediterraneus sp. nov. is proposed. The type strain is XSM19T (=CECT 5383T=CIP 108400T=CCUG 49438T). It is also proposed that R. gelatinovorans (Ruger & Hofle 1992) Uchino et al. 1999 is reclassified as Thalassobius gelatinovorus comb. nov.},
doi = {10.1099/ijs.0.63842-0},
issue = {6},
pmid = {16280499}
}
@article{DeshmukhOren2023aaaj,
year = {2023},
journal = {Int J Syst Evol Microbiol},
volume = {73},
pages = {6025},
author = {Deshmukh, U.B. and Oren, A.},
title = {Proposal of Thalassovita gen. nov. and Alloyangia gen. nov. as replacement names for the illegitimate prokaryotic generic names Thalassobius and Yangia, respectively.},
abstract = {The prokaryotic generic names Thalassobius Arahal et al. 2005 and Yangia Dai et al. 2006 are illegitimate because they are later homonyms of the genus names Thalassobius Solier 1849 (Coleoptera) and Yangia Zheng 1997 (fossil Rodentia), respectively Principle two and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes]. We therefore propose the replacement generic names Thalassovita and Alloyangia, with type species Thalassovita gelatinovora and Alloyangia pacifica, respectively.},
doi = {10.1099/ijsem.0.006025},
issue = {9},
pmid = {37695726}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{HameedEtAl2014a,
year = {2014},
journal = {Int J Syst Evol Microbiol},
volume = {64},
pages = {2729-2737},
author = {Hameed, A. and Shahina, M. and Lin, S.Y. and Nakayan, P. and Liu, Y.C. and Lai, W.A. and Hsu, Y.H.},
title = {Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007.},
abstract = {A Gram-staining-negative, non-pigmented, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, devoid of bacteriochlorophyll, designated strain CC-AMW-ET, was isolated from surface seawater off the coast at Kending, Taiwan. Strain CC-AMW-ET shared 95.7 and 93.9% 16S rRNA gene sequence similarity, respectively, with the type strains of the type species of the genera Donghicola (Donghicola eburneus SW-277T) and Roseovarius (Roseovarius tolerans EL-172T). The predominant (>75% of the total) fatty acid was summed feature 8 (C(18 : 1)omega6c and/or C(18 : 1)omega7c). The polar lipid profile included major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified aminolipid. In addition, moderate amounts of an unidentified lipid and trace amounts of an unidentified phospholipid were detected. The DNA G+C content was 67.9 mol%. Ubiquinone Q-10 was the sole respiratory quinone. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics (in particular its polar lipid pattern), we conclude that strain CC-AMW-ET represents a novel genus and species of the family Rhodobacteraceae, for which the name Youngimonas vesicularis gen. nov., sp. nov. is proposed. The type strain of Youngimonas vesicularis is CC-AMW-ET ( = JCM 18819T = BCRC 80549T). In addition, an emended description of the genus Donghicola Yoon et al. 2007 and the reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. (type strain Y-2T = MCCC 1A00107T = LMG 24574T = CGMCC 1.7081T) are proposed.},
doi = {10.1099/ijs.0.060962-0},
issue = {8},
pmid = {24844264}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{TanEtAl2009a,
year = {2009},
journal = {Int J Syst Evol Microbiol},
volume = {59},
pages = {1143-1147},
author = {Tan, T. and Wang, B. and Shao, Z.},
title = {Donghicola xiamenensis sp. nov., a marine bacterium isolated from seawater of the Taiwan Strait in China.},
abstract = {A Gram-negative, ovoid rod-shaped bacterium that lacked bacteriochlorophyll a, designated strain Y-2T, was isolated from seawater of the Taiwan Strait, China. The strain was oxidase- and catalase-positive, and reduced nitrate to nitrite. Optimal growth occurred at around pH 7.0 and 25 degrees C in the presence of 1-3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Y-2T belonged to the class Alphaproteobacteria and formed a coherent cluster with Donghicola eburneus SW-277T (96.2 % sequence similarity). The major whole-cell fatty acid was C(18 : 1)omega7c (75.42 %). Other characteristic fatty acids were C(18 : 0) (9.16 %) and C(16 : 0) (7.32 %). The DNA G+C content of strain Y-2T was 62.4 mol%. Therefore, based on phenotypic properties, phylogeny and genomic data, strain Y-2T should be placed in the genus Donghicola as representing a novel species, for which the name Donghicola xiamenensis sp. nov. is proposed. The type strain is Y-2T (=MCCC 1A00107T=LMG 24574T=CGMCC 1.7081T).},
doi = {10.1099/ijs.0.000901-0},
issue = {5},
pmid = {19406808}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{RohEtAl2009a,
year = {2009},
journal = {Int J Syst Evol Microbiol},
volume = {59},
pages = {790-794},
author = {Roh, S.W. and Nam, Y.D. and Chang, H.W. and Kim, K.H. and Kim, M.S. and Shin, K.S. and Yoon, J.H. and Oh, H.M. and Bae, J.W.},
title = {Paracoccus aestuarii sp. nov., isolated from tidal flat sediment.},
abstract = {A Gram-negative micro-organism, designated strain B7T, was isolated from tidal flat sediment and subjected to a polyphasic taxonomic study involving morphological, physiological, biochemical and 16S rRNA gene sequence analyses. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain B7T belonged to the genus Paracoccus and was closely related phylogenetically to Paracoccus marcusii MH1T (97.5 % sequence similarity), Paracoccus marinus KKL-A5T (97.5 %), Paracoccus haeundaensis BC74171T (97.3 %), Paracoccus carotinifaciens E-396T (97.3 %), Paracoccus homiensis DD-R11T (97.2 %), Paracoccus seriniphilus MBT-A4T (96.9 %) and other type strains of the genus Paracoccus (95.2-96.7 %). The G+C content of the genomic DNA and the major isoprenoid quinone of the type strain were 62.0 mol% and ubiquinone-10, respectively. The major fatty acid components were C(18 : 1)omega7c (68.9 %) and C(18 : 0) (18.1 %); this profile, with C(18 : 1)omega7c as the predominant fatty acid, was characteristic of members of the genus Paracoccus. The 16S rRNA gene sequence analysis, DNA-DNA hybridization studies and physiological and biochemical tests identified genotypic and phenotypic differences between strain B7T and recognized Paracoccus species. On the basis of these data, therefore, strain B7T represents a novel species of the genus Paracoccus, for which the name Paracoccus aestuarii sp. nov. is proposed. The type strain is B7T (=KCTC 22049T=DSM 19484T=JCM 15119T).},
doi = {10.1099/ijs.0.65759-0},
issue = {4},
pmid = {19329608}
}
@article{ChenEtAl2013c,
year = {2013},
journal = {Int J Syst Evol Microbiol},
volume = {63},
pages = {470-478},
author = {Chen, W.M. and Cho, N.T. and Huang, W.C. and Young, C.C. and Sheu, S.Y.},
title = {Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis.},
abstract = {A light-yellow-pigmented bacterial strain designated JS43T was isolated from a freshwater spring in Taiwan and was characterized using a polyphasic taxonomic approach. Cells of strain JS43T were Gram-negative-staining, facultatively anaerobic, rod-shaped, non-motile and non-spore-forming. Growth occurred at 10-30 degrees C (optimum, 25 degrees C), at pH 7.0-10.0 (optimum, pH 7.0-8.0) and with 0-0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JS43T was a member of the family Rhodobacteraceae of the class Alphaproteobacteria. Sequence similarities to type strains of the genera Gemmobacter and Catellibacterium were between 94.6 and 98.1 %. The highest sequence similarity was found with Gemmobacter aquatilis DSM 3857T. Strain JS43T contained C(18 : 1)omega7c as the predominant fatty acid (74.4 %). The major isoprenoid quinone was Q-10 and the DNA G+C content was 69.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two uncharacterized aminolipids and three uncharacterized phospholipids. The DNA-DNA relatedness values of strain JS43T with respect to the phylogenetically related Gemmobacter aquatilis DSM 3857T, Catellibacterium aquatile A1-9T and Catellibacterium caeni DCA-1T were less than 70 %. The taxonomic relationship between members of the genera Gemmobacter and Catellibacterium was clarified by means of a direct experimental comparison. Based on phylogenetic, chemotaxonomic and phenotypic data, we propose that all species currently classified in the genus Catellibacterium should be transferred to the genusGemmobacter. The following new combinations are proposed: Catellibacterium nectariphilum is reclassified as Gemmobacter nectariphilus comb. nov. (type strain, AST4T = DSM 15620T = JCM 11959T = NBRC 100046T), Catellibacterium changlense as Gemmobacter changlensis comb. nov. (type strain, JA139T = CCUG 53722T = DSM 18774T = JCM 14338T), Catellibacterium aquatile as Gemmobacter aquaticus nom. nov. (type strain, A1-9T = CGMCC 1.7029T = NBRC 104254T), Catellibacterium caeni as Gemmobacter caeni comb. nov. (type strain, DCA-1T = CGMCC 1.7745T = DSM 21823T) and Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov. (type strain, Y12T = CCTCC AB 2010218T = KCTC 23298T). Emended descriptions of the genus Gemmobacter and of Gemmobacter aquatilis are also presented. Strain JS43T could be distinguished from recognized species of the genera Gemmobacter and Catellibacterium. It is suggested, on the basis of genotypic and phenotypic characteristics, that strain JS43T ( = BCRC 80082T = LMG 25376T) represents a novel species for which the name Gemmobacter fontiphilus is proposed.},
doi = {10.1099/ijs.0.042051-0},
issue = {2},
pmid = {22493172}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{TanakaEtAl2004a,
year = {2004},
journal = {Int J Syst Evol Microbiol},
volume = {54},
pages = {955-959},
author = {Tanaka, Y. and Hanada, S. and Manome, A. and Tsuchida, T. and Kurane, R. and Nakamura, K. and Kamagata, Y.},
title = {Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth.},
abstract = {A bacterial strain, designated AST4T, was isolated from activated sludge. The bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. Culture filtrate of a strain related to the genus Sphingomonas in particular increased the cell yield and growth rate of strain AST4T. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AST4T is located within the 'Rhodobacter group' in the alpha-3 subclass of Proteobacteria, but is clearly distant from related genera in this group such as Paracoccus, Rhodobacter and Rhodovulum. Strain AST4T is a Gram-negative, non-motile, rod-shaped (0.6-0.8x1.3-2.0 micro m) and aerobic bacterium. It was not able to reduce nitrate to nitrite or N(2). No phototrophic growth was observed. Optimal growth occurred at 30 degrees C and pH 6.5-7.5. The dominant cellular fatty acid in the isolate was C(18 : 1)cis11. Ubiquinone-10 was the major respiratory quinone. The G+C content was 64.5 mol% (by HPLC). Based on the phylogenetic and phenotypic traits, the name Catellibacterium nectariphilum gen. nov., sp. nov. is proposed for this isolate; the type strain is AST4T (=NBRC 100046T=JCM 11959T=DSM 15620T).},
doi = {10.1099/ijs.0.02750-0},
issue = {3},
pmid = {15143049}
}
@article{BerryEtAl2003a,
year = {2003},
journal = {Int J Syst Evol Microbiol},
volume = {53},
pages = {231-238},
author = {Berry, A. and Janssens, D. and Humbelin, M. and Jore, J.P. and Hoste, B. and Cleenwerck, I. and Vancanneyt, M. and Bretzel, W. and Mayer, A.F. and Lopez-Ulibarri, R. and Shanmugam, B. and Swings, J. and Pasamontes, L.},
title = {Paracoccus zeaxanthinifaciens sp. nov., a zeaxanthin-producing bacterium.},
abstract = {A comprehensive taxonomic re-evaluation was performed on the marine, zeaxanthin-producing bacterium formerly classified as [Favobacterium] sp. strain R-1 512 (ATCC 21588). This strain, together with two other previously described marine isolates, [Flavobacterium] strain R-1506 and Paracoccus sp. strain MBIC 3966, were found to comprise a new species of the genus Paracoccus. The name Paracoccus zeaxanthinifaciens sp. nov. is proposed, with ATCC 21588T (= R-1512T =LMG 21293T) designated as the type strain.},
doi = {10.1099/ijs.0.02368-0},
issue = {1},
pmid = {12656178}
}
@article{DaneshvarEtAl2003c,
year = {2003},
journal = {J Clin Microbiol},
volume = {41},
pages = {1289-1294},
author = {Daneshvar, M.I. and Hollis, D.G. and Weyant, R.S. and Steigerwalt, A.G. and Whitney, A.M. and Douglas, M.P. and Macgregor, J.P. and Jordan, J.G. and Mayer, L.W. and Rassouli, S.M. and Barchet, W. and Munro, C. and Shuttleworth, L. and Bernard, K.},
title = {Paracoccus yeeii sp. nov. (formerly CDC group EO-2), a novel bacterial species associated with human infection.},
abstract = {CDC eugonic oxidizer group 2 (EO-2) is a group of unclassified gram-negative bacterial strains isolated from various human sources. As determined by biochemical tests and analyses of fatty acid compositions, these organisms form a homogeneous group that appears to be distinct from but related to other Paracoccus species. Molecular studies were performed on a set of 13 EO-2 strains from various clinical sources and geographic locations in the United States and Canada to determine their relationship to the Paracoccus genus. Control strains were Paracoccus denitrificans ATCC 17741T, P. versutus ATCC 25364T, P. aminophilus ATCC 49673T, P. solventivorans ATCC 700252T, and Psychrobacter immobilis ATCC 43116T, which are phenotypically similar to EO-2. Nearly complete (1,500-base) 16S rRNA gene sequencing of eight EO-2 strains showed a high level of sequence similarity (>99.3%) within the group, and a BLAST search of GenBank placed the EO-2 cluster in close proximity to Paracoccus species (95 to 97% similarity). DNA-DNA hybridization studies of 13 of the EO-2 strains showed all to be related at the species level, with >70% relatedness under stringent conditions and a divergence within the group of less than 2%. None of the Paracoccus control strains hybridized at >54% with any of the EO-2 strains. These results indicate that EO-2 represents a new Paracoccus species, the first isolated from human clinical specimens. A new species, Paracoccus yeeii, is proposed for the EO-2 strains. The type strain of P. yeeii is CDCG1212 (ATCC BAA-599 and CCUG 46822), isolated in Pennsylvania from dialysate of a 77-year-old male with peritonitis.},
doi = {10.1128/jcm.41.3.1289-1294.2003},
issue = {3},
pmid = {12624070}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{DoroninaEtAl2000e,
year = {2000},
journal = {Int J Syst Evol Microbiol},
volume = {50},
pages = {1849-1859},
author = {Doronina, N.V. and Trotsenko, Y.A. and Tourova, T.P.},
title = {Methylarcula marina gen. nov., sp. nov. and Methylarcula terricola sp. nov.: novel aerobic, moderately halophilic, facultatively methylotrophic bacteria from coastal saline environments.},
abstract = {A new genus, Methylarcula, with two new species, Methylarcula marina and Methylarcula terricola, are proposed for strains h1T and h37T of moderately halophilic facultatively methylotrophic bacteria isolated from the coastal saline habitats. These methylobacteria are aerobic, Gram-negative, asporogenous, non-motile, colourless rods that multiply by binary fission. Their cellular fatty acids profiles consist primarily of straight-chain unsaturated (C18:1; 70-80%), saturated (C18:0; 14-16%) and cyclopropane (C19:0; 5-6%) acids. The major ubiquinone is Q-10. The dominant phospholipids are phosphatidylethanolamine and phosphatidylcholine. Both strains could use methylamine, some sugars and organic acids as carbon and energy sources. They grew well under optimal conditions (29-35 degrees C, pH 7.5-8.5, 0.5-1.0 M NaCl) and accumulated intracellularly poly-beta-hydroxybutyrate and the compatible solute ectoine. The ectoine pool was found to increase upon increasing the external NaCl concentration and accounted for 18% of the dry cellular weight. Both strains oxidized methylamine by the N-methylglutamate (N-MG) pathway enzymes (gamma-glutamylmethylamide synthetase/lyase and N-MG synthetase/lyase) to formaldehyde and assimilated it via the icl- serine pathway. The DNA G+C content was 60-4 mol% for Methylarcula marina h1T and 57.1 mol% for Methylarcula terricola h37T. The DNA-DNA hybridization value between strains hl and h37 was 25-30%, although they had a low level of DNA relatedness (5-7%) with the type strains of the serine pathway methylobacteria belonging to the genera Methylobacterium, Aminobacter, Methylorhabdus and Methylopila. A comparative 16S rDNA sequence-based phylogenetic analysis placed the two species of Methylarcula into a separate branch of the alpha-3 subclass of the Proteobacteria. The type strains of the new species are Methylarcula marina h1T (= VKM B-2159T) and Methylarcula terricola h37T (= VKM B-2160T).},
doi = {10.1099/00207713-50-5-1849},
issue = {5},
pmid = {11034496}
}
@article{DoroninaEtAl2020d,
year = {2020},
journal = {Microbiology},
volume = {89},
pages = {197-204},
author = {Doronina, N.V. and Shmareva, M.N. and Kaparullina, E.N. and Vasilenko, O.V. and Tarlachkov, S.V. and et al},
title = {Reclassification of Methylarcula marina Doronina et al. 2000 as Paracoccus methylarcula nom. nov.},
doi = {10.1134/s0026261720020034}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{EckersleyDow1980a,
year = {1980},
journal = {J. Gen. Microbiol.},
volume = {119},
pages = {465-473},
author = {Eckersley, K. and Dow, C.S.},
title = {Rhodopseudomonas blastica sp. nov.: a member of the Rhodospirillaceae.},
doi = {10.1099/00221287-119-2-465}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{KawasakiEtAl1993a,
year = {1993},
journal = {Arch Microbiol},
volume = {160},
pages = {358-362},
author = {Kawasaki, H. and Hoshino, Y. and Hirata, A. and Yamasato, K.},
title = {Is intracytoplasmic membrane structure a generic criterion? It does not coincide with phylogenetic interrelationships among phototrophic purple nonsulfur bacteria.},
abstract = {The 16S rRNA or rRNA gene sequences of the type strains of 5 species of Rhodobacter, Rhodopseudomonas blastica and Paracoccus denitrificans were determined. The sequence analysis revealed that Rhodobacter species, whose intracytoplasmic membrane systems were characteristically vesicular, composed a sole cluster. Rhodopseudomonas blastica, whose intracytoplasmic membrane system was lamellar, was included in the cluster of Rhodobacter. The phylogenetic co-clustering of these bacteria conformed to their possessing of the identical types of carotenoids. Paracoccus denitrificans, which is nonphototrophic, is a right member of the Rhodobacter cluster. Rhodobacter species, Rhodopseudomonas blastica and Paracoccus denitrificans are apart from the other phototrophic bacteria and have the common deletions of 21 bases at the positions 1258 to 1278 (Escherichia coli numbering system). It was demonstrated that the morphological character "intracytoplasmic membrane structure", that has been regarded as a generic criterion does not reflect the phylogeny in the phototrophic bacteria. The transfer of Rhodopseudomonas blastica to the genus Rhodobacter is proposed.},
doi = {10.1007/bf00252221},
issue = {5},
pmid = {8257281}
}
@article{SureshEtAl2019a,
year = {2019},
journal = {Front Microbiol},
volume = {10},
pages = {2480},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.},
doi = {10.3389/fmicb.2019.02480},
pmid = {31736915}
}
@article{LiangEtAl2021j,
year = {2021},
journal = {Front Microbiol},
volume = {12},
pages = {683109},
author = {Liang, K.Y.H. and Orata, F.D. and Boucher, Y.F. and Case, R.J.},
title = {Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov.},
abstract = {The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.},
doi = {10.3389/fmicb.2021.683109},
pmid = {34248901}
}
@article{LucenaEtAl2013a,
year = {2013},
journal = {Syst Appl Microbiol},
volume = {36},
pages = {325-329},
author = {Lucena, T. and Ruvira, M.A. and Macian, M.C. and Pujalte, M.J. and Arahal, D.R.},
title = {Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov.},
abstract = {Four strains (M15slashed circle_3, M17T, M49 and R37T) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellon, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8-96.4%), Phaeobacter inhibens (95.9-96.3%) and Phaeobacter gallaeciensis (95.9-96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF) data proved: (i) non clonality among the strains, and (ii) the existence of two genospecies, one consisting of strains M15slashed circle_3, M17T, M49 and 2OM6 and another one consisting of strain R37T. Phenotypic traits determined allow differentiating both genospecies from each other and from closely related taxa. In view of all data collected we propose to accommodate these isolates in two species as members of the genus Tropicibacter, Tropicibacter mediterraneus sp. nov. (type strain M17T=CECT 7615T=KCTC 23058T) and Tropicibacter litoreus sp. nov. (type strain R37T=CECT 7639T=KCTC 23353T).},
doi = {10.1016/j.syapm.2013.04.001},
issue = {5},
pmid = {23706913}
}
@article{WirthWhitman2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2393-2411},
author = {Wirth, J.S. and Whitman, W.B.},
title = {Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera.},
abstract = {Roseobacters are a diverse and globally abundant group of Alphaproteobacteria within the Rhodobacteraceae family. Recent studies and the cophenetic correlations suggest that the 16S rRNA genes are poor phylogenetic markers within this group. In contrast, the cophenetic correlation coefficients of the core-gene average amino acid identity (cAAI) and RpoC protein sequences are high and likely more predictive of relationships. A maximum-likelihood phylogenetic tree calculated from 53 core genes demonstrated that some of the current genera were either polyphyletic or paraphyletic. The boundaries of bacterial genera were redefined based upon the cAAI, the percentage of conserved proteins, and phenotypic characteristics and resulted in the following taxonomic proposals. Loktanella vestfoldensis, Loktanella litorea, Loktanella maricola, Loktanella maritima, Loktanella rosea, Loktanella sediminilitoris, Loktanella tamlensis, and Roseobacter sp. CCS2 should be reclassified into the novel genus Yoonia. Loktanella hongkongensis, Loktanella aestuariicola, Loktanella cinnabarina, Loktanella pyoseonensis, Loktanellasoe soekkakensis and Loktanella variabilis should be reclassified in the novel genus Limimaricola. Loktanella koreensis and Loktanella sediminum should be reclassified in the novel genus Cognatiyoonia. Loktanella marina should be reclassified in the novel genus Flavimaricola. Aestuariivita atlantica should be reclassified in the novel genus Pseudaestuariivita. Thalassobius maritima should be reclassified in the novel genus Cognatishimia. Similarly, Ruegeria mobilis, Ruegeria scottomollicae, Ruegeria sp. TM1040 and Tropicibacter multivorans should be reclassified in the genus Epibacterium. Tropicibacter litoreus and Tropicibacter mediterraneus should be reclassified in the genus Ruegeria. Thalassobius abyssi and Thalassobius aestuarii should be reclassified in the genus Shimia. Citreicella aestuarii, Citreicella manganoxidans, Citreicella marina, Citreicella thiooxidans, Pelagibaca bermudensis and Thiobacimonas profunda should be reclassified in the genus Salipiger. Nautella italica should be reclassified in the genus Phaeobacter. Because these proposals to reclassify the type and all others species of Citreicella, Nautella, Pelagibaca and Thiobacimonas, these genera are not used in this taxonomy.},
doi = {10.1099/ijsem.0.002833},
issue = {7},
pmid = {29809121}
}
@article{ArahalEtAl2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2515-2522},
author = {Arahal, D.R. and Lucena, T. and Rodrigo-Torres, L. and Pujalte, M.J.},
title = {Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis.},
abstract = {Strain CECT 5091T, an aerobic, marine, Gram-reaction- and Gram-stain-negative, chemoheterotrophic bacterium was isolated from oysters harvested off the Spanish Mediterranean coast. Analysis of the 16S rRNA gene sequence placed the strain within the genus Ruegeria, in the family Rhodobacteraceae, with 16S rRNA gene similarities of 98.7, 98.7 and 98.4 % to Ruegeria conchae, Ruegeria atlanticaand Ruegeria arenilitoris, respectively. Average nucleotide identities (ANI) and in silico DNA-DNA hybridization (DDH) were determined, comparing the genome sequence of CECT 5091T with those of the type strains of 12 species of the genus Ruegeria: the values obtained were always below the thresholds (95-96 % ANI, 70 % in silico DDH) used to define genomic species, proving that CECT 5091T represents a novel species of the genus Ruegeria. The strain was slightly halophilic and mesophilic, with optimum growth at 26 degrees C, pH 7.0 and 3 % salinity, it required sodium and magnesium ions for growth and was able to reduce nitrate to dinitrogen. Carbon sources for growth include some carbohydrates (d-ribose, d-glucose, l-rhamnose, N-acetyl-d-glucosamine) and multiple organic acids and amino acids. The major cellular fatty acid was summed feature 8 (C18 : 1omega7c and/or C18 : 1omega6c), representing 70 % of the total fatty acids. Carbon monoxide oxidation, cyanophycin synthetic ability and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine production are predicted from genome annotation, while bacteriochlorophyll a production was absent. The DNA G+C content of the genome was 56.7 mol%. We propose the name Ruegeriadenitrificans sp. nov. and strain CECT 5091T (=5OM10T=LMG 29896T) as the type strain for the novel species.},
doi = {10.1099/ijsem.0.002867},
issue = {8},
pmid = {29944092}
}
@article{JungEtAl2014f,
year = {2014},
journal = {Int J Syst Evol Microbiol},
volume = {64},
pages = {2763-2769},
author = {Jung, Y.T. and Park, S. and Lee, J.S. and Yoon, J.H.},
title = {Paracoccus lutimaris sp. nov., isolated from a tidal flat sediment.},
abstract = {A Gram-negative, coccoid or oval-shaped and gliding bacterial strain, designated HDM-25T, belonging to the Alphaproteobacteria, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HDM-25T grew optimally at pH 7.0-8.0, at 30 degrees C and in the presence of 2-3% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HDM-25T fell within the clade comprising the species of the genus Paracoccus, clustering with the type strain of Paracoccus aminophilus, with which it exhibited the highest 16S rRNA gene sequence similarity (97.7%). The 16S rRNA gene sequence similarity between strain HDM-25T and the type strains of the other species of Paracoccus was 93.6-97.0%. The DNA G+C content was 65.9 mol% and the mean DNA-DNA relatedness between strain HDM-25T and the type strain of P. aminophilus was 10.7+/-2.7% (9.9+/-4.0%, reciprocal analysis). Strain HDM-25T contained Q-10 as the predominant ubiquinone and summed feature 8 (C(18 : 1)omega7c and/or C(18 : 1)omega6c) and C(16 : 0) as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain HDM-25T is distinguishable from other species of the genus Paracoccus. On the basis of the data presented, strain HDM-25T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus lutimaris sp. nov. is proposed. The type strain is HDM-25T ( = KCTC 42007T = CECT 8525T).},
doi = {10.1099/ijs.0.064865-0},
issue = {8},
pmid = {24860114}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{ImhoffEtAl1984j,
year = {1984},
journal = {Int. J. Syst. Bacteriol.},
volume = {34},
pages = {340-343},
author = {Imhoff, J.F. and Trüper, H.G. and Pfennig, N.},
title = {Rearrangement of the species and genera of the phototrophic "purple nonsulfur bacteria".},
doi = {10.1099/00207713-34-3-340},
issue = {3}
}
@article{Vanniel1944a,
year = {1944},
journal = {Bacteriol Rev},
volume = {8},
pages = {1-118},
author = {van Niel, C.B.},
title = {THE CULTURE, GENERAL PHYSIOLOGY, MORPHOLOGY, AND CLASSIFICATION OF THE NON-SULFUR PURPLE AND BROWN BACTERIA.},
doi = {10.1128/br.8.1.1-118.1944},
issue = {1},
pmid = {16350090}
}
@book{Molisch1907a,
author = {Molisch, H.},
year = {1907},
title = {Die Purpurbakterien nach neuen Untersuchungen I-VII},
publisher = {G. Fischer},
address = {Jena}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{PanEtAl2014a,
year = {2014},
journal = {Int J Syst Evol Microbiol},
volume = {64},
pages = {2512-2516},
author = {Pan, J. and Sun, C. and Zhang, X.Q. and Huo, Y.Y. and Zhu, X.F. and Wu, M.},
title = {Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment.},
abstract = {Strain CMB17T was a short rod-shaped bacterium isolated from marine sediment of the Pacific Ocean. Cells were Gram-stain-negative and non-motile. Optimal growth occurred at 25-30 degrees C, pH 6.5-7 and 0.5-1% (w/v) NaCl. The major fatty acid was C(18 : 1)omega7c (87.59%), and ubiquinone-10 was detected as the only isoprenoid quinone. The DNA G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CMB17T is most closely related to Paracoccus stylophorae KTW-16T (96.7%), P. solventivorans DSM 6637T (96.4%) and P. saliphilus YIM 90738T (96.4%). Based on phenotypic, genotypic and phylogenetic characteristics, strain CMB17T is proposed to represent a novel species, denominated Paracoccus sediminis sp. nov. (type strain CMB17T = JCM 18467T = DSM 26170T = CGMCC 1.12681T).},
doi = {10.1099/ijs.0.051318-0},
issue = {8},
pmid = {24812365}
}
@article{Nakamura2015a,
year = {2015},
journal = {Int J Syst Evol Microbiol},
volume = {65},
pages = {3878-3884},
author = {Nakamura, A.},
title = {Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil.},
abstract = {Strain 43PT was isolated as an l-glucose-utilizing bacterium from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic and non-motile cocci. The 16S rRNA gene sequence of the strain showed high similarity to that of Paracoccus limosus (98.5 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that this strain belongs to the genus Paracoccus. Strain 43PT contained Q-10 as the sole isoprenoid quinone. The major cellular fatty acids were C18: 1omega7c or C18: 1omega6c and C16: 0, and C18: 0, C18: 1omega9c, C10: 0 3-OH and summed feature 2 were detected as minor components. The DNA G+C content of strain 43PT was 64.1 mol%. Strain 43PT contained the major polar lipids phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and two unknown glycolipids. The DNA-DNA relatedness between strain 43PT and the six related type strains of the genus Paracoccus, including P. limosus, was below 23 %. Based on the chemotaxonomic and physiological data and the values of DNA-DNA relatedness, especially the ability to assimilate l-glucose, this strain should be classified as a representative of a novel species of the genus Paracoccus, for which the name Paracoccus laeviglucosivorans sp. nov. (type strain 43PT = JCM 30587T = DSM 100094T) is proposed.},
doi = {10.1099/ijsem.0.000508},
issue = {11},
pmid = {26243274}
}
@article{BeijerinckMinkman1910b,
year = {1910},
journal = {Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene, Abteilung II},
volume = {25},
pages = {30-63},
author = {Beijerinck, M.W. and Minkman, D.C.J.},
title = {Bildung und Verbrauch von Stickstoffoxydul durch Bakterien.}
}
@article{DavisEtAl1969a,
year = {1969},
journal = {International Journal of Systematic Bacteriology},
volume = {19},
pages = {375-390},
author = {Davis, D.H. and Doudoroff, M. and Stanier, R.Y. and Mandel, M.},
title = {Proposal to reject the genus Hydrogenomonas: taxonomic implications.},
doi = {10.1099/00207713-19-4-375},
issue = {4}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LudwigEtAl1993a,
year = {1993},
journal = {Int J Syst Bacteriol},
volume = {43},
pages = {363-367},
author = {Ludwig, W. and Mittenhuber, G. and Friedrich, C.G.},
title = {Transfer of Thiosphaera pantotropha to Paracoccus denitrificans.},
abstract = {Comparative sequence analysis of in vitro-amplified 16S rRNA genes of Thiosphaera pantotropha GB17T (T = type strain) and Paracoccus denitrificans LMG 4218T revealed identical 16S rRNA primary structures for the two organisms. The level of overall DNA similarity of Thiosphaera pantotropha GB17T and P. denitrificans DSM 65T is 85%, as determined by quantitative DNA-DNA hybridization. Therefore, we propose the transfer of Thiosphaera pantotropha to P. denitrificans. The closest relative of Thiosphaera pantotropha and P. denitrificans is Thiobacillus versutus, as revealed by comparative 16S rRNA sequence analysis. These organisms are members of the alpha subclass of the Proteobacteria. Within this subclass, Thiosphaera pantotropha, P. denitrificans, and Thiobacillus versutus form a phylogenetic group with Rhodobacter sphaeroides, Rhodobacter capsulatus, and "Erythrobacter longus."},
doi = {10.1099/00207713-43-2-363},
issue = {2},
pmid = {8494744}
}
@article{NokhalSchlegel1983a,
year = {1983},
journal = {Int. J. Syst. Bacteriol.},
volume = {33},
pages = {26-37},
author = {Nokhal, T.H. and Schlegel, H.G.},
title = {Taxonomic study of Paracoccus denitrificans.},
doi = {10.1099/00207713-33-1-26},
issue = {1}
}
@article{RaineyEtAl1999b,
year = {1999},
journal = {Int J Syst Bacteriol},
volume = {49},
pages = {645-651},
author = {Rainey, F.A. and Kelly, D.P. and Stackebrandt, E. and Burghardt, J. and Hiraishi, A. and Katayama, Y. and Wood, A.P.},
title = {A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov.},
abstract = {Comparison of both 16S rRNA coding sequences and DNA-DNA hybridization of ten strains of alpha-subclass of Proteobacteria currently classified as strains of Paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. Comparison with published data on the cytochrome c profiles and other 16S rRNA coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups. Group A comprises strains ATCC 17741T (the type strain of P. denitrificans), LMD 22.21T, DSM 413T, ATCC 19367, ATCC 13543, DSM 1404, DSM 1405, Pd 1222 (a genetic modification of DSM 413T) and NCIMB 8944. Group B comprises ATCC 35512T (the original type strain of Thiosphaera pantotropha), LMD 82.5T, LMD 92.63, DSM 65, LMG 4218, IAM 12479, JCM 6892, DSM 11072, DSM 11073 and DSM 11104. In light of these findings, it is proposed that: (1) strains of group A are retained as P. denitrificans, with ATCC 17741T as the type strain of the type species; and (2) all strains of group B are assigned to the new species combination Paracoccus pantotrophus comb. nov., with strain ATCC 35512T as the type strain. Comparative 16S rRNA sequence analysis and DNA-DNA hybridization of strains of Paracoccus versutus confirm that this species is distinct from both P. denitrificans and P. pantotrophus, but that its nearest phylogenetic neighbour is P. pantotrophus.},
doi = {10.1099/00207713-49-2-645},
issue = {2},
pmid = {10319488}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{KampferEtAl2016c,
year = {2016},
journal = {Int J Syst Evol Microbiol},
volume = {66},
pages = {5101-5105},
author = {Kampfer, P. and Aurass, P. and Karste, S. and Flieger, A. and Glaeser, S.P.},
title = {Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm.},
abstract = {A beige-pigmented, oxidase-positive bacterial strain (WPAn02T), isolated as a presumably airborne contaminant of an axenic bacterial microcosm, was studied using a polyphasic taxonomic approach. Cells of the isolate were coccoid and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain WPAn02T with sequences of type strains of the most closely related species of the genus Paracoccus showed highest sequence similarities to Paracoccus chinensis (97.7 %), Paracoccus marinus (97.1 %), Paracoccus niistensis (97.4 %) and 'Paracoccus zhejiangensis' (97.0 %). 16S rRNA gene sequence similarities to all other species of the genus Paracoccuswere below 97 %. The fatty acid profile of the strain consisted of the major fatty acids C18 : 1omega7c/omega9t/omega12t and C18 : 0. DNA-DNA hybridizations between WPAn02T and type strains of P. chinensis, P. marinus, P. niistensis, and 'P. zhejiangensis' resulted in similarity values of 49 % (reciprocal 22 %), 16 % (reciprocal 10 %), 30 % (reciprocal 32 %), and 18 % (reciprocal 7 %), respectively. DNA-DNA hybridization results together with the differentiating biochemical and chemotaxonomic properties indicated that WPAn02T represents a novel species of the genus Paracoccus, for which the name Paracoccus contaminans sp. nov. (type strain WPAn02T=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T), is proposed.},
doi = {10.1099/ijsem.0.001478},
issue = {12},
pmid = {27599853}
}
@article{KimEtAl2014d,
year = {2014},
journal = {Antonie Van Leeuwenhoek},
volume = {105},
pages = {551-558},
author = {Kim, Y.O. and Park, S. and Nam, B.H. and Jung, Y.T. and Kim, D.G. and Yoon, J.H.},
title = {Ruegeria meonggei sp. nov., an alphaproteobacterium isolated from ascidian Halocynthia roretzi.},
abstract = {A Gram-negative, strictly aerobic, non-flagellated and rod-shaped bacterial strain, designated MA-E2-3T, was isolated from an ascidian (Halocynthia roretzi) collected from the South Sea, South Korea. Strain MA-E2-3T was found to grow optimally at 30 degrees C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MA-E2-3T fell within the clade comprising Ruegeria species, clustering consistently with the type strain of Ruegeria halocynthiae, with which it exhibited 98.2 % sequence similarity. Sequence similarities to the type strains of the other recognized Ruegeria species were 94.7-97.7 %. Strain MA-E2-3T was found to contain Q-10 as the predominant ubiquinone and C18:1 omega7c as the predominant fatty acid. The major polar lipids of strain MA-E2-3T were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA-E2-3T was determined to be 58.0 mol%. Mean DNA-DNA relatedness values between strain MA-E2-3T and the type strains of four phylogenetically closely related Ruegeria species were in the range of 13-23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain MA-E2-3T is separated from other Ruegeria species. On the basis of the data presented, strain MA-E2-3T (=KCTC 32450T = CECT 8411T) represents a novel species of the genus Ruegeria, for which the name Ruegeria meonggei sp. nov. is proposed.},
doi = {10.1007/s10482-013-0107-y},
issue = {3},
pmid = {24380959}
}
@article{YoonEtAl2008m,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {1198-1202},
author = {Yoon, J.H. and Kang, S.J. and Oh, T.K.},
title = {Roseovarius aestuarii sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.},
abstract = {A Gram-negative, motile, ovoid to rod-shaped bacterial strain, designated strain SMK-122T, was isolated from a Yellow Sea tidal flat located on the coast of Korea. Strain SMK-122T grew optimally at pH 7.0-8.0 and 30 degrees C. It contained Q-10 as the predominant ubiquinone and possessed C18 : 1omega7c and C16 : 0 as the major fatty acids. The DNA G+C content was 58.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain SMK-122T fell within the genus Roseovarius, being closest to Roseovarius nubinhibens ISMT; the sequence similarities with respect to Roseovarius species ranged from 94.9 to 97.3 %. The mean value for DNA-DNA relatedness between strain SMK-122T and Rva. nubinhibens DSM 15170T was 13 %. Differential phenotypic properties of SMK-122T, together with its phylogenetic and genetic distinctiveness, revealed that this strain is distinct from recognized Roseovarius species. On this basis, strain SMK-122T represents a novel species of the genus Roseovarius, for which the name Roseovarius aestuarii sp. nov. is proposed. The type strain is SMK-122T (=KCTC 22174T =CCUG 55325T).},
doi = {10.1099/ijs.0.65657-0},
issue = {5},
pmid = {18450713}
}
@article{ChenEtAl2011f,
year = {2011},
journal = {Int J Syst Evol Microbiol},
volume = {61},
pages = {823-827},
author = {Chen, M.H. and Sheu, S.Y. and Chen, C.A. and Wang, J.T. and Chen, W.M.},
title = {Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera.},
abstract = {A bacterial strain, designated SW6T, was isolated from the reef-building coral Isopora palifera, collected from seawater off the coast of southern Taiwan, and characterized using a polyphasic taxonomic approach. Strain SW6T was Gram-negative, aerobic, beige coloured, rod-shaped and motile by monopolar flagella. 16S rRNA gene sequence studies showed that the strain clustered closely with Shimia marina JCM 13038T (97.9 % 16S rRNA gene sequence similarity). Strain SW6T required NaCl for growth and exhibited optimal growth at 25-30 degrees C and 3-4 % NaCl. The predominant cellular fatty acid was summed feature 8 (C(18 : 1)omega7c/C(18 : 1)omega6c; 64.1 %). The major respiratory quinone was ubiquinone Q-10 and the DNA G+C content was 54.9 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from previously described species of the genus Shimia. It is evident from the genotypic, phenotypic and chemotaxonomic data that the new strain should be classified as a representative of a novel species in the genus Shimia. The name proposed for this taxon is Shimia isoporae sp. nov.; the type strain is SW6T ( = LMG 25377T = BCRC 80085T).},
doi = {10.1099/ijs.0.022848-0},
issue = {4},
pmid = {20453104}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{VandecandelaereEtAl2008a,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2726-2733},
author = {Vandecandelaere, I. and Nercessian, O. and Segaert, E. and Achouak, W. and Faimali, M. and Vandamme, P.},
title = {Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm.},
abstract = {Seventy isolates were obtained from a marine electroactive biofilm that was generated on a cathodically polarized stainless steel electrode (Genoa, Italy). The genetic diversity was investigated by means of BOX-PCR fingerprinting and two clusters of isolates with similar BOX-PCR profiles were delineated. Whole-cell fatty acid methyl ester analysis and 16S rRNA gene sequence analysis showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. DNA-DNA hybridization experiments and a biochemical analysis demonstrated that four isolates belonged to the species Ruegeria mobilis. However, 66 isolates from the second BOX-PCR cluster constituted a novel species within the genus Ruegeria, for which the name Ruegeria scottomollicae sp. nov. is proposed. The DNA G+C content was 61.0+/-0.4 %. The type strain is LMG 24367T (=CCUG 55858T).},
doi = {10.1099/ijs.0.65843-0},
issue = {12},
pmid = {19060048}
}
@article{WirthWhitman2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2393-2411},
author = {Wirth, J.S. and Whitman, W.B.},
title = {Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera.},
abstract = {Roseobacters are a diverse and globally abundant group of Alphaproteobacteria within the Rhodobacteraceae family. Recent studies and the cophenetic correlations suggest that the 16S rRNA genes are poor phylogenetic markers within this group. In contrast, the cophenetic correlation coefficients of the core-gene average amino acid identity (cAAI) and RpoC protein sequences are high and likely more predictive of relationships. A maximum-likelihood phylogenetic tree calculated from 53 core genes demonstrated that some of the current genera were either polyphyletic or paraphyletic. The boundaries of bacterial genera were redefined based upon the cAAI, the percentage of conserved proteins, and phenotypic characteristics and resulted in the following taxonomic proposals. Loktanella vestfoldensis, Loktanella litorea, Loktanella maricola, Loktanella maritima, Loktanella rosea, Loktanella sediminilitoris, Loktanella tamlensis, and Roseobacter sp. CCS2 should be reclassified into the novel genus Yoonia. Loktanella hongkongensis, Loktanella aestuariicola, Loktanella cinnabarina, Loktanella pyoseonensis, Loktanellasoe soekkakensis and Loktanella variabilis should be reclassified in the novel genus Limimaricola. Loktanella koreensis and Loktanella sediminum should be reclassified in the novel genus Cognatiyoonia. Loktanella marina should be reclassified in the novel genus Flavimaricola. Aestuariivita atlantica should be reclassified in the novel genus Pseudaestuariivita. Thalassobius maritima should be reclassified in the novel genus Cognatishimia. Similarly, Ruegeria mobilis, Ruegeria scottomollicae, Ruegeria sp. TM1040 and Tropicibacter multivorans should be reclassified in the genus Epibacterium. Tropicibacter litoreus and Tropicibacter mediterraneus should be reclassified in the genus Ruegeria. Thalassobius abyssi and Thalassobius aestuarii should be reclassified in the genus Shimia. Citreicella aestuarii, Citreicella manganoxidans, Citreicella marina, Citreicella thiooxidans, Pelagibaca bermudensis and Thiobacimonas profunda should be reclassified in the genus Salipiger. Nautella italica should be reclassified in the genus Phaeobacter. Because these proposals to reclassify the type and all others species of Citreicella, Nautella, Pelagibaca and Thiobacimonas, these genera are not used in this taxonomy.},
doi = {10.1099/ijsem.0.002833},
issue = {7},
pmid = {29809121}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LucenaEtAl2012a,
year = {2012},
journal = {Int J Syst Evol Microbiol},
volume = {62},
pages = {844-848},
author = {Lucena, T. and Pujalte, M.J. and Ruvira, M.A. and Garay, E. and Macian, M.C. and Arahal, D.R.},
title = {Tropicibacter multivorans sp. nov., an aerobic alphaproteobacterium isolated from surface seawater.},
abstract = {Strain MD5T, an aerobic marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized in a polyphasic study and was placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MD5T is related to Tropicibacter naphthalenivorans C02T, Phaeobacter inhibens T5T, P. gallaeciensis BS107T and P. daeponensis TF-218T, with 96.9, 96.2, 96.1 and 96.1 % sequence similarity, respectively. Phylogenetic analyses also showed that strain MD5T forms a stable clade only with T. naphthalenivorans C02T. Strain MD5T requires Na+ plus a divalent cation (either Mg2+ or Ca2+) to grow, does not reduce nitrate to nitrite and uses a large number of carbohydrates as sole carbon sources. It is positive for beta-galactosidase and urease activities and aesculin hydrolysis. Enzyme activities displayed in the API ZYM strip were alkaline phosphatase, leucine arylamidase, acid phosphatase and alpha-glucosidase. Major cellular fatty acids were summed feature 8 (C18:1omega7c and/or C18:1omega6c; 70.9 %) and C16:0 (8.2 %). The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from the only described species of the genus Tropicibacter. It is evident from the genotypic and phenotypic data obtained that the strain should be classified in a novel species in the genus Tropicibacter. The name Tropicibacter multivorans sp. nov. is proposed, with the type strain MD5T (=CECT 7557T=KCTC 23350T).},
doi = {10.1099/ijs.0.030973-0},
issue = {4},
pmid = {21602360}
}
@article{WirthWhitman2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2393-2411},
author = {Wirth, J.S. and Whitman, W.B.},
title = {Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera.},
abstract = {Roseobacters are a diverse and globally abundant group of Alphaproteobacteria within the Rhodobacteraceae family. Recent studies and the cophenetic correlations suggest that the 16S rRNA genes are poor phylogenetic markers within this group. In contrast, the cophenetic correlation coefficients of the core-gene average amino acid identity (cAAI) and RpoC protein sequences are high and likely more predictive of relationships. A maximum-likelihood phylogenetic tree calculated from 53 core genes demonstrated that some of the current genera were either polyphyletic or paraphyletic. The boundaries of bacterial genera were redefined based upon the cAAI, the percentage of conserved proteins, and phenotypic characteristics and resulted in the following taxonomic proposals. Loktanella vestfoldensis, Loktanella litorea, Loktanella maricola, Loktanella maritima, Loktanella rosea, Loktanella sediminilitoris, Loktanella tamlensis, and Roseobacter sp. CCS2 should be reclassified into the novel genus Yoonia. Loktanella hongkongensis, Loktanella aestuariicola, Loktanella cinnabarina, Loktanella pyoseonensis, Loktanellasoe soekkakensis and Loktanella variabilis should be reclassified in the novel genus Limimaricola. Loktanella koreensis and Loktanella sediminum should be reclassified in the novel genus Cognatiyoonia. Loktanella marina should be reclassified in the novel genus Flavimaricola. Aestuariivita atlantica should be reclassified in the novel genus Pseudaestuariivita. Thalassobius maritima should be reclassified in the novel genus Cognatishimia. Similarly, Ruegeria mobilis, Ruegeria scottomollicae, Ruegeria sp. TM1040 and Tropicibacter multivorans should be reclassified in the genus Epibacterium. Tropicibacter litoreus and Tropicibacter mediterraneus should be reclassified in the genus Ruegeria. Thalassobius abyssi and Thalassobius aestuarii should be reclassified in the genus Shimia. Citreicella aestuarii, Citreicella manganoxidans, Citreicella marina, Citreicella thiooxidans, Pelagibaca bermudensis and Thiobacimonas profunda should be reclassified in the genus Salipiger. Nautella italica should be reclassified in the genus Phaeobacter. Because these proposals to reclassify the type and all others species of Citreicella, Nautella, Pelagibaca and Thiobacimonas, these genera are not used in this taxonomy.},
doi = {10.1099/ijsem.0.002833},
issue = {7},
pmid = {29809121}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LafayEtAl1995a,
year = {1995},
journal = {Int J Syst Bacteriol},
volume = {45},
pages = {290-296},
author = {Lafay, B. and Ruimy, R. and de Traubenberg, C.R. and Breittmayer, V. and Gauthier, M.J. and Christen, R.},
title = {Roseobacter algicola sp. nov., a new marine bacterium isolated from the phycosphere of the toxin-producing dinoflagellate Prorocentrum lima.},
abstract = {We describe a new species on the basis of phenotypic characteristics and the results of an analysis of small-subunit rRNA sequences. Three strains of this organism were isolated from a culture of the toxin-producing dinoflagellate Prorocentrum lima. These bacteria are gram-negative, strictly aerobic, ovoid organisms that are motile by means of one or two subpolar flagella. They grow at temperatures ranging from 10 to 37 degrees C and in the presence of NaCl concentrations ranging from 0.1 to 2 M and have an absolute requirement for sodium ions. They are strictly aerobic with a nonfermentative type of metabolism and are not able to grow anaerobically in presence or absence of nitrate. They do not denitrify. They exhibit oxidase, catalase, gelatinase, esculinase, beta-galactosidase, and (to a lesser extent) amylase activities. The three strains which we examined require thiamine and biotin for growth. They grow only when glucose, trehalose, saccharose, fructose, maltose, pyruvate, malate, citrate, esculin, 2-ketoglutarate, 5-ketogluconate, glutamate, or shikimate is present as a sole carbon source. The three strains have identical small-subunit rRNA sequences. A phylogenetic analysis of these sequences revealed that these bacteria belong to the alpha subdivision of the Proteobacteria and that they form a distinct and robust monophyletic group with Roseobacter denitrificans and Roseobacter litoralis. This result and the general phenotypic characteristics of the organisms place them in the genus Roseobacter, although they do not produce bacteriochlorophyll a, in contrast to previously described Roseobacter species.(ABSTRACT TRUNCATED AT 250 WORDS)},
doi = {10.1099/00207713-45-2-290},
issue = {2},
pmid = {7537061}
}
@article{MartensEtAl2006a,
year = {2006},
journal = {Int J Syst Evol Microbiol},
volume = {56},
pages = {1293-1304},
author = {Martens, T. and Heidorn, T. and Pukall, R. and Simon, M. and Tindall, B.J. and Brinkhoff, T.},
title = {Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera.},
abstract = {A heterotrophic, antibiotic-producing bacterium, strain T5T, was isolated from the German Wadden Sea, located in the southern region of the North Sea. Sequence analysis of the 16S rRNA gene of this strain demonstrated close affiliation with Roseobacter gallaeciensis BS107T (99 % similarity), but the results of genotypic (DNA-DNA hybridization and DNA G + C content) and phenotypic characterization revealed that strain T5T represents a novel species. The novel organism is strictly aerobic, Gram-negative, rod-shaped, motile and forms brown-pigmented colonies. Strain T5T produces the antibiotic tropodithietic acid throughout the exponential phase which inhibits the growth of bacteria from different taxa, as well as marine algae. Strain T5T requires sodium ions and utilizes a wide range of substrates, including oligosaccharides, sugar alcohols, organic acids and amino acids. The DNA G + C content is 55.7 mol%. Comparative 16S rRNA gene sequence analysis revealed that strains T5T and Roseobacter gallaeciensis BS107T group with Leisingera methylohalidivorans as their closest described relative within the Roseobacter clade (97.9 and 97.6 % sequence similarity, respectively) and with Ruegeria algicola (96.6 and 96.5 % similarity, respectively) of the Alphaproteobacteria. Comparison of strains T5T and Roseobacter gallaeciensis BS107T with Roseobacter denitrificans and Roseobacter litoralis showed striking differences in 16S rRNA gene sequence similarities, chemical composition, pigmentation, presence of bacteriochlorophyll a and antibiotic production. On the basis of these results, it is proposed that Roseobacter gallaeciensis is reclassified as the type species of a new genus, Phaeobacter, as Phaeobacter gallaeciensis comb. nov. (type strain BS107T = CIP 105210T = ATCC 700781T = NBRC 16654T = DSM 17395T). Strain T5T (=LMG 22475T = DSM 16374T) is proposed as the type strain of a novel species of this genus, Phaeobacter inhibens sp. nov. At the same time, emended descriptions are provided of the genera Roseobacter, Ruegeria and Leisingera, as well as reclassifying Ruegeria algicola as the type species of a new genus, Marinovum, with the name Marinovum algicola comb. nov.},
doi = {10.1099/ijs.0.63724-0},
issue = {6},
pmid = {16738106}
}
@article{UchinoEtAl1998c,
year = {1998},
journal = {J Gen Appl Microbiol},
volume = {44},
pages = {201-210},
author = {Uchino, Y. and Hirata, A. and Yokota, A. and Sugiyama, J.},
title = {Reclassification of marine Agrobacterium species: Proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev.},
abstract = {The bootstrapped 16S rDNA sequence-based neighbor-joining phylogeny has suggested that the marine species of the genus Agrobacterium have no relation to the terrestrial Agrobacterium species. Agrobacterium atlanticum IAM 14463T (a superscript T=type strain), Agrobacterium ferrugineum IAM 12616T, Agrobacterium gelatinovorum IAM 12617T, Agrobacterium meteori IAM 14464T, Agrobacterium stellulatum IAM 12621T and IAM 12614, and the invalidly published marine species "Agrobacterium kieliense" IAM 12618 occupy an independent position in the a-subclass of the Proteobacteria. Based on 16S rDNA sequencing and on chemotaxonomic, morphological, and physiological studies, we propose the transfer of A. atlanticum, A. gelatinovorum, and Roseobacter algicola to the genus Ruegeria gen. nov. as Ruegeria atlantica comb. nov., Ruegeria gelatinovora comb. nov., and Ruegeria algicola comb. nov., respectively; of strains of A. stellulatum to the genus Stappia gen. nov. as Stappia stellulata comb. nov. and Stappia aggregata sp. nov., nom. rev., respectively; and of "A. kieliense" to the genus Ahrensia gen. nov. as Ahrensia kieliense sp. nov., nom. rev. Agrobacterium meteori is assigned to be a synonym of A. atlanticum.},
doi = {10.2323/jgam.44.201},
issue = {3},
pmid = {12501429}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{SorokinEtAl2005a,
year = {2005},
journal = {Syst Appl Microbiol},
volume = {28},
pages = {679-687},
author = {Sorokin, D.Y. and Tourova, T.P. and Muyzer, G.},
title = {Citreicella thiooxidans gen. nov., sp. nov., a novel lithoheterotrophic sulfur-oxidizing bacterium from the Black Sea.},
abstract = {Four strains of obligately heterotrophic bacteria isolated from the oxygen-sulfide interface of the Black Sea are characterized. The bacteria are aerobic, Gram-negative, with lemon-like, nonmotile cells. Bacteriochlorophyll a is not detected. They are mesophilic and neutrophilic with a temperature range of 8-35 degrees C (optimum 25) and pH range of 6.5-8.5 (optimum 7.8). Their growth is NaCl dependent within a range of 5 and 60 (optimum 20) g l(-1). They are able to oxidize thiosulfate, sulfide and elemental sulfur to sulfate and to use metabolic energy from these reactions (lithoheterotrophy). According to the level of DNA reassociation of more than 40%, all isolates represent a single generic group. The G+C content of the DNA was in the range of 67.5-69.2mol%. According to phylogenetic analysis, the new isolates form a separate branch in the alpha-3 subdivision of the Proteobacteria together with two undescribed marine bacterial strains. On the basis of phenotypical and genomic properties, the new isolates are described as a new genus and species Citreicella thiooxidans gen. nov., sp. nov. The type strain is CHLG 1T ( = DSM 10146, UNIQEM U 228).},
doi = {10.1016/j.syapm.2005.05.006},
issue = {8},
pmid = {16261857}
}
@article{WirthWhitman2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2393-2411},
author = {Wirth, J.S. and Whitman, W.B.},
title = {Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera.},
abstract = {Roseobacters are a diverse and globally abundant group of Alphaproteobacteria within the Rhodobacteraceae family. Recent studies and the cophenetic correlations suggest that the 16S rRNA genes are poor phylogenetic markers within this group. In contrast, the cophenetic correlation coefficients of the core-gene average amino acid identity (cAAI) and RpoC protein sequences are high and likely more predictive of relationships. A maximum-likelihood phylogenetic tree calculated from 53 core genes demonstrated that some of the current genera were either polyphyletic or paraphyletic. The boundaries of bacterial genera were redefined based upon the cAAI, the percentage of conserved proteins, and phenotypic characteristics and resulted in the following taxonomic proposals. Loktanella vestfoldensis, Loktanella litorea, Loktanella maricola, Loktanella maritima, Loktanella rosea, Loktanella sediminilitoris, Loktanella tamlensis, and Roseobacter sp. CCS2 should be reclassified into the novel genus Yoonia. Loktanella hongkongensis, Loktanella aestuariicola, Loktanella cinnabarina, Loktanella pyoseonensis, Loktanellasoe soekkakensis and Loktanella variabilis should be reclassified in the novel genus Limimaricola. Loktanella koreensis and Loktanella sediminum should be reclassified in the novel genus Cognatiyoonia. Loktanella marina should be reclassified in the novel genus Flavimaricola. Aestuariivita atlantica should be reclassified in the novel genus Pseudaestuariivita. Thalassobius maritima should be reclassified in the novel genus Cognatishimia. Similarly, Ruegeria mobilis, Ruegeria scottomollicae, Ruegeria sp. TM1040 and Tropicibacter multivorans should be reclassified in the genus Epibacterium. Tropicibacter litoreus and Tropicibacter mediterraneus should be reclassified in the genus Ruegeria. Thalassobius abyssi and Thalassobius aestuarii should be reclassified in the genus Shimia. Citreicella aestuarii, Citreicella manganoxidans, Citreicella marina, Citreicella thiooxidans, Pelagibaca bermudensis and Thiobacimonas profunda should be reclassified in the genus Salipiger. Nautella italica should be reclassified in the genus Phaeobacter. Because these proposals to reclassify the type and all others species of Citreicella, Nautella, Pelagibaca and Thiobacimonas, these genera are not used in this taxonomy.},
doi = {10.1099/ijsem.0.002833},
issue = {7},
pmid = {29809121}
}
@article{UrakamiEtAl1990b,
year = {1990},
journal = {Int J Syst Bacteriol},
volume = {40},
pages = {287-291},
author = {Urakami, T. and Araki, H. and Oyanagi, H. and Suzuki, K. and Komagata, K.},
title = {Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov., which utilize N,N-dimethylformamide.},
abstract = {Two methylamine- and N,N-dimethylformamide-utilizing Paracoccus spp. are described. These bacteria are gram-negative, nonsporeforming, nonmotile, coccoid or short rod-shaped organisms. Their DNA base composition is 62 to 68 mol% G + C. Their cellular fatty acids include large amounts of C18:1 acid. Their major hydroxy acids are 3-OH C10:0 and 3-OH C14:0 acids. The major ubiquinone is Q-10. These bacteria are distinguished from Paracoccus denitrificans and Paracoccus alcaliphilus by physiological characteristics and by DNA-DNA-homology. Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov. are proposed. The type strain of P. aminophilus is DM-15 (= JCM 7686), and the type strain of P. aminovorans is DM-82 (= JCM 7685). Paracoccus halodenitrificans is distinguished from other Paracoccus species on the basis of cellular fatty acid composition, hydroxy fatty acid composition, and DNA-DNA homology. It may not be a valid member of the genus Paracoccus.},
doi = {10.1099/00207713-40-3-287},
issue = {3},
pmid = {2397196}
}
@article{ChenEtAl2013c,
year = {2013},
journal = {Int J Syst Evol Microbiol},
volume = {63},
pages = {470-478},
author = {Chen, W.M. and Cho, N.T. and Huang, W.C. and Young, C.C. and Sheu, S.Y.},
title = {Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis.},
abstract = {A light-yellow-pigmented bacterial strain designated JS43T was isolated from a freshwater spring in Taiwan and was characterized using a polyphasic taxonomic approach. Cells of strain JS43T were Gram-negative-staining, facultatively anaerobic, rod-shaped, non-motile and non-spore-forming. Growth occurred at 10-30 degrees C (optimum, 25 degrees C), at pH 7.0-10.0 (optimum, pH 7.0-8.0) and with 0-0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JS43T was a member of the family Rhodobacteraceae of the class Alphaproteobacteria. Sequence similarities to type strains of the genera Gemmobacter and Catellibacterium were between 94.6 and 98.1 %. The highest sequence similarity was found with Gemmobacter aquatilis DSM 3857T. Strain JS43T contained C(18 : 1)omega7c as the predominant fatty acid (74.4 %). The major isoprenoid quinone was Q-10 and the DNA G+C content was 69.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two uncharacterized aminolipids and three uncharacterized phospholipids. The DNA-DNA relatedness values of strain JS43T with respect to the phylogenetically related Gemmobacter aquatilis DSM 3857T, Catellibacterium aquatile A1-9T and Catellibacterium caeni DCA-1T were less than 70 %. The taxonomic relationship between members of the genera Gemmobacter and Catellibacterium was clarified by means of a direct experimental comparison. Based on phylogenetic, chemotaxonomic and phenotypic data, we propose that all species currently classified in the genus Catellibacterium should be transferred to the genusGemmobacter. The following new combinations are proposed: Catellibacterium nectariphilum is reclassified as Gemmobacter nectariphilus comb. nov. (type strain, AST4T = DSM 15620T = JCM 11959T = NBRC 100046T), Catellibacterium changlense as Gemmobacter changlensis comb. nov. (type strain, JA139T = CCUG 53722T = DSM 18774T = JCM 14338T), Catellibacterium aquatile as Gemmobacter aquaticus nom. nov. (type strain, A1-9T = CGMCC 1.7029T = NBRC 104254T), Catellibacterium caeni as Gemmobacter caeni comb. nov. (type strain, DCA-1T = CGMCC 1.7745T = DSM 21823T) and Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov. (type strain, Y12T = CCTCC AB 2010218T = KCTC 23298T). Emended descriptions of the genus Gemmobacter and of Gemmobacter aquatilis are also presented. Strain JS43T could be distinguished from recognized species of the genera Gemmobacter and Catellibacterium. It is suggested, on the basis of genotypic and phenotypic characteristics, that strain JS43T ( = BCRC 80082T = LMG 25376T) represents a novel species for which the name Gemmobacter fontiphilus is proposed.},
doi = {10.1099/ijs.0.042051-0},
issue = {2},
pmid = {22493172}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{RotheEtAl1987b,
year = {1987},
journal = {Arch. Microbiol.},
volume = {147},
pages = {92-99},
author = {Rothe, B. and Fisher, A. and Hirsch, P. and Sittig, M. and Stackebrandt, E.},
title = {The phylogenetic position of the budding bacteria Blustobacter aggregatus and Gemmobacter aquatilis gen. nov., sp. nov.},
doi = {10.1007/bf00492911}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LipskiEtAl1998b,
year = {1998},
journal = {Int J Syst Bacteriol},
volume = {48},
pages = {529-536},
author = {Lipski, A. and Reichert, K. and Reuter, B. and Sproer, C. and Altendorf, K.},
title = {Identification of bacterial isolates from biofilters as Paracoccus alkenifer sp. nov. and Paracoccus solventivorans with emended description of Paracoccus solventivorans.},
abstract = {Two groups of strains isolated from biofilters for the treatment of waste gases were assigned to the genus Paracoccus by phylogenetic and chemotaxonomic methods. All type strains of the genus Paracoccus were compared with these groups using 16S rDNA sequence analysis, fatty acid patterns and physiological reaction profiles. For both groups, the nearest related reference species was Paracoccus solventivorans based on 16S rDNA sequence similarity. However, whereas one group of isolates was identified as a member of this species by fatty acid analysis and DNA-DNA hybridization, the other group was proposed as a new species, Paracoccus alkenifer sp. nov. Fatty acid analysis showed the unusual fatty acid 20:1cis13 instead of 19:0 cyclo11-12 for P. alkenifer and P. solventivorans, and 14:1cis7 instead of 12:1cis5 for P. alkenifer and Paracoccus kocurii. By means of a GC-MS method, diaminopimelic acid was detected for P. solventivorans. Based on these results we propose an emended description for the species P. solventivorans.},
doi = {10.1099/00207713-48-2-529},
issue = {2},
pmid = {9731294}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{PukallEtAl2003a,
year = {2003},
journal = {Int J Syst Evol Microbiol},
volume = {53},
pages = {443-447},
author = {Pukall, R. and Laroche, M. and Kroppenstedt, R.M. and Schumann, P. and Stackebrandt, E. and Ulber, R.},
title = {Paracoccus seriniphilus sp. nov., an L-serine-dehydratase-producing coccus isolated from the marine bryozoan Bugula plumosa.},
abstract = {A novel marine Gram-negative, non-motile, non-spore-forming, aerobic bacterium, associated with the bryozoan Bugula plumosa, was isolated in a screening programme for strains containing enzymes able to convert the amino acid L-serine. Strain MBT-A4T produced L-serine dehydratase and was able to grow on L-serine as the sole carbon and nitrogen source. The nearest phylogenetic neighbour was Paracoccus marcusii, as determined by 16S rDNA sequence analysis (97.8% similarity). The DNA-DNA reassociation value obtained for Paracoccus marcusii DSM11574T and MBT-A4T was 32.6%. The major ubiquinone was 0-10. Based on genotypic, chemotaxonomic and physiological characteristics, a new species of the genus Paracoccus is proposed, Paracoccus seriniphilus sp. nov., the type strain being strain MBT-A4T (=DSM 14827T =CIP 107400T).},
doi = {10.1099/ijs.0.02352-0},
issue = {2},
pmid = {12710610}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{SrinivasEtAl2008a,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {1379-1383},
author = {Srinivas, T.N. and Anil Kumar, P. and Sasikala, C.h. and Sproer, C. and Ramana, C.h.V.},
title = {Rhodobacter ovatus sp. nov., a phototrophic alphaproteobacterium isolated from a polluted pond.},
abstract = {A novel ovoid, phototrophic, purple non-sulfur bacterium was isolated in pure culture from a sample of sediment from an industrially polluted pond (Noor Mohammad Kunta) in Hyderabad, India. Strain JA234T was found to be Gram-negative and non-motile and grew photoheterotrophically with a number of organic compounds serving as carbon source/electron donor. Photo-organoheterotrophic and chemo-organoheterotrophic growth were demonstrated. Biotin and thiamine were required for growth of strain JA234T. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA234T is most closely related to Rhodobacter azotoformans (97.3 % sequence similarity) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA-DNA hybridization with Rba. azotoformans JCM 9340T showed a relatedness of only 31.3 % with respect to strain JA234T. On the basis of 16S rRNA gene sequence analysis, DNA-DNA hybridization data and morphological and physiological characteristics, strain JA234T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter ovatus sp. nov. is proposed. The type strain is JA234T (=JCM 14779T=CCUG 55049T).},
doi = {10.1099/ijs.0.65619-0},
issue = {6},
pmid = {18523181}
}
@article{SureshEtAl2019a,
year = {2019},
journal = {Front Microbiol},
volume = {10},
pages = {2480},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.},
doi = {10.3389/fmicb.2019.02480},
pmid = {31736915}
}
@article{SureshEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {1111},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Corrigendum: Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.02480.].},
doi = {10.3389/fmicb.2020.01111},
pmid = {32582079}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{VandecandelaereEtAl2009a,
year = {2009},
journal = {Int J Syst Evol Microbiol},
volume = {59},
pages = {811-817},
author = {Vandecandelaere, I. and Nercessian, O. and Segaert, E. and Achouak, W. and Mollica, A. and Faimali, M. and Vandamme, P.},
title = {Nautella italica gen. nov., sp. nov., isolated from a marine electroactive biofilm.},
abstract = {Five isolates obtained from a marine electroactive biofilm grown on a stainless steel cathode were investigated by using a polyphasic taxonomic approach. Analyses of whole-cell fatty acid methyl esters and 16S rRNA gene sequences showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. Both phenotypic and genotypic analyses demonstrated that the five new isolates constituted a single species that did not represent a recognized member of the Roseobacter lineage. Therefore the five isolates represent a novel genus and species, for which the name Nautella italica gen. nov., sp. nov. is proposed. The type strain is LMG 24365T (=CCUG 55857T). The DNA G+C content of the type strain is 61 mol%.},
doi = {10.1099/ijs.0.002683-0},
issue = {4},
pmid = {19329612}
}
@article{WirthWhitman2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2393-2411},
author = {Wirth, J.S. and Whitman, W.B.},
title = {Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera.},
abstract = {Roseobacters are a diverse and globally abundant group of Alphaproteobacteria within the Rhodobacteraceae family. Recent studies and the cophenetic correlations suggest that the 16S rRNA genes are poor phylogenetic markers within this group. In contrast, the cophenetic correlation coefficients of the core-gene average amino acid identity (cAAI) and RpoC protein sequences are high and likely more predictive of relationships. A maximum-likelihood phylogenetic tree calculated from 53 core genes demonstrated that some of the current genera were either polyphyletic or paraphyletic. The boundaries of bacterial genera were redefined based upon the cAAI, the percentage of conserved proteins, and phenotypic characteristics and resulted in the following taxonomic proposals. Loktanella vestfoldensis, Loktanella litorea, Loktanella maricola, Loktanella maritima, Loktanella rosea, Loktanella sediminilitoris, Loktanella tamlensis, and Roseobacter sp. CCS2 should be reclassified into the novel genus Yoonia. Loktanella hongkongensis, Loktanella aestuariicola, Loktanella cinnabarina, Loktanella pyoseonensis, Loktanellasoe soekkakensis and Loktanella variabilis should be reclassified in the novel genus Limimaricola. Loktanella koreensis and Loktanella sediminum should be reclassified in the novel genus Cognatiyoonia. Loktanella marina should be reclassified in the novel genus Flavimaricola. Aestuariivita atlantica should be reclassified in the novel genus Pseudaestuariivita. Thalassobius maritima should be reclassified in the novel genus Cognatishimia. Similarly, Ruegeria mobilis, Ruegeria scottomollicae, Ruegeria sp. TM1040 and Tropicibacter multivorans should be reclassified in the genus Epibacterium. Tropicibacter litoreus and Tropicibacter mediterraneus should be reclassified in the genus Ruegeria. Thalassobius abyssi and Thalassobius aestuarii should be reclassified in the genus Shimia. Citreicella aestuarii, Citreicella manganoxidans, Citreicella marina, Citreicella thiooxidans, Pelagibaca bermudensis and Thiobacimonas profunda should be reclassified in the genus Salipiger. Nautella italica should be reclassified in the genus Phaeobacter. Because these proposals to reclassify the type and all others species of Citreicella, Nautella, Pelagibaca and Thiobacimonas, these genera are not used in this taxonomy.},
doi = {10.1099/ijsem.0.002833},
issue = {7},
pmid = {29809121}
}
@article{KimEtAl2006g,
year = {2006},
journal = {Int J Syst Evol Microbiol},
volume = {56},
pages = {2387-2390},
author = {Kim, B.Y. and Weon, H.Y. and Yoo, S.H. and Kwon, S.W. and Cho, Y.H. and Stackebrandt, E. and Go, S.J.},
title = {Paracoccus homiensis sp. nov., isolated from a sea-sand sample.},
abstract = {Strain DD-R11T, isolated from a sea-sand sample from Homi Cape, Pohang city, South Korea, was a Gram-negative, aerobic, motile, non-spore-forming, rod- to ovoid-shaped bacterium. Colonies grown on marine agar were circular, convex and colourless to creamy white. Growth occurred between 10 and 40 degrees C (optimum 25-30 degrees C) and at pH 5.0-9.0 (optimum pH 6.0-8.0). The strain could grow in up to 15 % NaCl (optimum 3-5 % NaCl). According to 16S rRNA gene sequence analysis, the strain was a member of the genus Paracoccus in the Alphaproteobacteria. Sequence similarities to type strains of the genus Paracoccus were between 94.6 and 98.3 %, showing the highest sequence similarity to Paracoccus zeaxanthinifaciens ATCC 21588T. The DNA-DNA relatedness value of strain DD-R11T and P. zeaxanthinifaciens ATCC 21588T was 27 %. Strain DD-R11T was characterized by having ubiquinone 10 as the major respiratory quinone and C(18 : 1)omega7c as the predominant fatty acid. The DNA G+C content was 63.0 mol%. On the basis of its phenotypic and genotypic characteristics, it is suggested that DD-R11T represents a novel species of the genus Paracoccus, for which the name Paracoccus homiensis sp. nov. is proposed, with DD-R11T (=KACC 11518T=DSM 17862T) as the type strain.},
doi = {10.1099/ijs.0.64275-0},
issue = {10},
pmid = {17012567}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{UrakamiEtAl1989a,
year = {1989},
journal = {Int. J. Syst. Bacteriol.},
volume = {39},
pages = {116-121},
author = {Urakami, T. and Tamaoka, J. and Suzuki, K.I. and Komagata, K.},
title = {Paracoccus alcaliphilus sp. nov., an alkaliphilic and facultatively methylotrophic bacterium.},
doi = {10.1099/00207713-39-2-116},
issue = {2}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{HyunEtAl2013a,
year = {2013},
journal = {Int J Syst Evol Microbiol},
volume = {63},
pages = {4248-4253},
author = {Hyun, D.W. and Kim, M.S. and Shin, N.R. and Kim, J.Y. and Kim, P.S. and Whon, T.W. and Yun, J.H. and Bae, J.W.},
title = {Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai.},
abstract = {A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain WM35T, was isolated from the intestinal tract of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The cells of the isolate grew optimally at 30 degrees C, pH 7, and with 3 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity comparisons, strain WM35T was grouped in the genus Shimia and was closely related to the type strains of Shimia isoporae (98.7 % similarity) and Shimia marina (97.8 % similarity). The major cellular fatty acids were summed feature 8 and C16 : 0 2-OH. Ubiquinone Q-10 was the predominant respiratory quinone. The polar lipids of strain WM35T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of the isolate was 53.8 mol%. DNA-DNA hybridization values indicated <16 % genomic relatedness with members of the genus Shimia. The physiological, chemical and genotypic analyses indicated that strain WM35T represents a novel species of the genus Shimia, for which the name Shimia haliotis sp. nov. is proposed. The type strain is WM35T ( = KACC 17212T = JCM 18870T).},
doi = {10.1099/ijs.0.053140-0},
issue = {11},
pmid = {23811138}
}
@article{BreiderEtAl2014a,
year = {2014},
journal = {Front Microbiol},
volume = {5},
pages = {416},
author = {Breider, S. and Scheuner, C. and Schumann, P. and Fiebig, A. and Petersen, J. and Pradella, S. and Klenk, H.P. and Brinkhoff, T. and Goker, M.},
title = {Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.},
abstract = {Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.},
doi = {10.3389/fmicb.2014.00416},
pmid = {25157246}
}
@article{VandecandelaereEtAl2009b,
year = {2009},
journal = {Int J Syst Evol Microbiol},
volume = {59},
pages = {1209-1214},
author = {Vandecandelaere, I. and Segaert, E. and Mollica, A. and Faimali, M. and Vandamme, P.},
title = {Phaeobacter caeruleus sp. nov., a blue-coloured, colony-forming bacterium isolated from a marine electroactive biofilm.},
abstract = {Three isolates (LMG 24369T, LMG 24370 and R-26156) obtained from a marine electroactive biofilm that was grown on a cathodically polarized electrode were investigated by using a polyphasic taxonomic approach. Whole-cell fatty acid methyl ester and 16S rRNA gene sequence analyses indicated that the isolates were members of the genus Phaeobacter, class Alphaproteobacteria. Genotypic and phenotypic analyses demonstrated that the three isolates represent a novel species of the genus Phaeobacter, for which the name Phaeobacter caeruleus sp. nov. is proposed. The type strain is LMG 24369T (=CCUG 55859T). The DNA G+C content of strain LMG 24369T is 63.6 mol%.},
doi = {10.1099/ijs.0.002642-0},
issue = {5},
pmid = {19406821}
}
@article{BreiderEtAl2014a,
year = {2014},
journal = {Front Microbiol},
volume = {5},
pages = {416},
author = {Breider, S. and Scheuner, C. and Schumann, P. and Fiebig, A. and Petersen, J. and Pradella, S. and Klenk, H.P. and Brinkhoff, T. and Goker, M.},
title = {Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.},
abstract = {Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.},
doi = {10.3389/fmicb.2014.00416},
pmid = {25157246}
}
@article{DogsEtAl2013b,
year = {2013},
journal = {Stand Genomic Sci},
volume = {9},
pages = {142-159},
author = {Dogs, M. and Teshima, H. and Petersen, J. and Fiebig, A. and Chertkov, O. and Dalingault, H. and Chen, A. and Pati, A. and Goodwin, L.A. and Chain, P. and Detter, J.C. and Ivanova, N. and Lapidus, A. and Rohde, M. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Simon, M. and Goker, M. and Klenk, H.P. and Brinkhoff, T.},
title = {Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis.},
abstract = {TF-218T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.},
doi = {10.4056/sigs.4287962},
issue = {1},
pmid = {24501652}
}
@article{VandecandelaereEtAl2008b,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2788-2793},
author = {Vandecandelaere, I. and Segaert, E. and Mollica, A. and Faimali, M. and Vandamme, P.},
title = {Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al. 2006.},
abstract = {Strain LMG 24366T was isolated from a marine electroactive biofilm grown on a stainless steel cathode (Genova, Italy) and was investigated by using a polyphasic taxonomic approach. This study demonstrated that strain LMG 24366T represents a novel species within the genus Leisingera, which shared 98.9 % 16S rRNA gene similarity with its nearest phylogenetic neighbour, Leisingera methylohalidivorans. Strain LMG 24366T grew on betaine (1 mM) as a sole carbon source, whereas no growth was observed on L-methionine (10 mM). The phenotypic and genotypic analyses showed that strain LMG 24366T could be differentiated from established Leisingera species and that it represented a novel species, for which the name Leisingera aquimarina sp. nov. is proposed. The type strain is LMG 24366T (=CCUG 55860T) and has a DNA G+C content of 61.4 mol%.},
doi = {10.1099/ijs.0.65844-0},
issue = {Pt 12},
pmid = {19060059}
}
@article{YoonEtAl2007v,
year = {2007},
journal = {Int J Syst Evol Microbiol},
volume = {57},
pages = {856-861},
author = {Yoon, J.H. and Kang, S.J. and Lee, S.Y. and Oh, T.K.},
title = {Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.},
abstract = {A Gram-negative, motile and egg-shaped bacterium, strain TF-218T, was isolated from a tidal flat at Daepo Beach (Yellow Sea), Korea, and subjected to a polyphasic taxonomic analysis. Strain TF-218T grew optimally at pH 7.0-8.0 and 37 degrees C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C(18 : 1)omega7c and 11-methyl C(18 : 1)omega7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and an aminolipid. The DNA G+C content was 64.9 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain TF-218T is phylogenetically closely related to the genera Phaeobacter, Leisingera and Marinovum of the Alphaproteobacteria. The phylogenetic and chemotaxonomic similarities suggest that strain TF-218T represents a member of the genus Phaeobacter. DNA-DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain TF-218T differs from the recognized Phaeobacter species. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain TF-218T represents a novel species of the genus Phaeobacter, for which the name Phaeobacter daeponensis sp. nov. is proposed. The type strain is TF-218T (=KCTC 12794T=JCM 13606T).},
doi = {10.1099/ijs.0.64779-0},
issue = {Pt 4},
pmid = {17392219}
}
@article{DogsEtAl2013a,
year = {2013},
journal = {Stand Genomic Sci},
volume = {9},
pages = {334-350},
author = {Dogs, M. and Voget, S. and Teshima, H. and Petersen, J. and Davenport, K. and Dalingault, H. and Chen, A. and Pati, A. and Ivanova, N. and Goodwin, L.A. and Chain, P. and Detter, J.C. and Standfest, S. and Rohde, M. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Simon, M. and Klenk, H.P. and Goker, M. and Brinkhoff, T.},
title = {Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens.},
abstract = {Strain T5T is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5T was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5T comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5T possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5T a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.},
doi = {10.4056/sigs.4448212},
issue = {2},
pmid = {24976890}
}
@article{MartensEtAl2006a,
year = {2006},
journal = {Int J Syst Evol Microbiol},
volume = {56},
pages = {1293-1304},
author = {Martens, T. and Heidorn, T. and Pukall, R. and Simon, M. and Tindall, B.J. and Brinkhoff, T.},
title = {Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera.},
abstract = {A heterotrophic, antibiotic-producing bacterium, strain T5T, was isolated from the German Wadden Sea, located in the southern region of the North Sea. Sequence analysis of the 16S rRNA gene of this strain demonstrated close affiliation with Roseobacter gallaeciensis BS107T (99 % similarity), but the results of genotypic (DNA-DNA hybridization and DNA G + C content) and phenotypic characterization revealed that strain T5T represents a novel species. The novel organism is strictly aerobic, Gram-negative, rod-shaped, motile and forms brown-pigmented colonies. Strain T5T produces the antibiotic tropodithietic acid throughout the exponential phase which inhibits the growth of bacteria from different taxa, as well as marine algae. Strain T5T requires sodium ions and utilizes a wide range of substrates, including oligosaccharides, sugar alcohols, organic acids and amino acids. The DNA G + C content is 55.7 mol%. Comparative 16S rRNA gene sequence analysis revealed that strains T5T and Roseobacter gallaeciensis BS107T group with Leisingera methylohalidivorans as their closest described relative within the Roseobacter clade (97.9 and 97.6 % sequence similarity, respectively) and with Ruegeria algicola (96.6 and 96.5 % similarity, respectively) of the Alphaproteobacteria. Comparison of strains T5T and Roseobacter gallaeciensis BS107T with Roseobacter denitrificans and Roseobacter litoralis showed striking differences in 16S rRNA gene sequence similarities, chemical composition, pigmentation, presence of bacteriochlorophyll a and antibiotic production. On the basis of these results, it is proposed that Roseobacter gallaeciensis is reclassified as the type species of a new genus, Phaeobacter, as Phaeobacter gallaeciensis comb. nov. (type strain BS107T = CIP 105210T = ATCC 700781T = NBRC 16654T = DSM 17395T). Strain T5T (=LMG 22475T = DSM 16374T) is proposed as the type strain of a novel species of this genus, Phaeobacter inhibens sp. nov. At the same time, emended descriptions are provided of the genera Roseobacter, Ruegeria and Leisingera, as well as reclassifying Ruegeria algicola as the type species of a new genus, Marinovum, with the name Marinovum algicola comb. nov.},
doi = {10.1099/ijs.0.63724-0},
issue = {6},
pmid = {16738106}
}
@article{VandecandelaereEtAl2008b,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2788-2793},
author = {Vandecandelaere, I. and Segaert, E. and Mollica, A. and Faimali, M. and Vandamme, P.},
title = {Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al. 2006.},
abstract = {Strain LMG 24366T was isolated from a marine electroactive biofilm grown on a stainless steel cathode (Genova, Italy) and was investigated by using a polyphasic taxonomic approach. This study demonstrated that strain LMG 24366T represents a novel species within the genus Leisingera, which shared 98.9 % 16S rRNA gene similarity with its nearest phylogenetic neighbour, Leisingera methylohalidivorans. Strain LMG 24366T grew on betaine (1 mM) as a sole carbon source, whereas no growth was observed on L-methionine (10 mM). The phenotypic and genotypic analyses showed that strain LMG 24366T could be differentiated from established Leisingera species and that it represented a novel species, for which the name Leisingera aquimarina sp. nov. is proposed. The type strain is LMG 24366T (=CCUG 55860T) and has a DNA G+C content of 61.4 mol%.},
doi = {10.1099/ijs.0.65844-0},
issue = {Pt 12},
pmid = {19060059}
}
@article{BreiderEtAl2014a,
year = {2014},
journal = {Front Microbiol},
volume = {5},
pages = {416},
author = {Breider, S. and Scheuner, C. and Schumann, P. and Fiebig, A. and Petersen, J. and Pradella, S. and Klenk, H.P. and Brinkhoff, T. and Goker, M.},
title = {Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.},
abstract = {Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.},
doi = {10.3389/fmicb.2014.00416},
pmid = {25157246}
}
@article{ZhangEtAl2008g,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {1384-1387},
author = {Zhang, D.C. and Li, H.R. and Xin, Y.H. and Liu, H.C. and Chi, Z.M. and Zhou, P.J. and Yu, Y.},
title = {Phaeobacter arcticus sp. nov., a psychrophilic bacterium isolated from the Arctic.},
abstract = {A Gram-negative, psychrophilic, motile, rod-shaped bacterium, designated strain 20188T, was isolated from marine samples collected from the Arctic (7 degrees 00' 24'' N 16 degrees 59' 37'' W), and was identified taxonomically by means of a polyphasic study. On the basis of 16S rRNA gene sequence similarity, strain 20188T was closely related to members of the genera Phaeobacter. 16S rRNA gene sequence similarities between strain 20188T and the type strains of Phaeobacter inhibens, Phaeobacter gallaeciensis and Phaeobacter daeponensis were 97.0, 96.8 and 96.2 %, respectively. The temperature range for growth was 0-25 degrees C, with optimum growth occurring at 19-20 degrees C and at approximately pH 6.0-9.0. Strain 20188T had ubiquinone-10 as the major respiratory quinone and C(18 : 1)omega7c and 11-methyl C(18 : 1)omega7c as major fatty acids. The genomic DNA G+C content was 59.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain 20188T is considered to represent a novel species of the genus Phaeobacter, for which the name Phaeobacter arcticus sp. nov. is proposed. The type strain is 20188T (=CGMCC 1.6500T=JCM 14644T).},
doi = {10.1099/ijs.0.65708-0},
issue = {6},
pmid = {18523182}
}
@article{VandecandelaereEtAl2008b,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2788-2793},
author = {Vandecandelaere, I. and Segaert, E. and Mollica, A. and Faimali, M. and Vandamme, P.},
title = {Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al. 2006.},
abstract = {Strain LMG 24366T was isolated from a marine electroactive biofilm grown on a stainless steel cathode (Genova, Italy) and was investigated by using a polyphasic taxonomic approach. This study demonstrated that strain LMG 24366T represents a novel species within the genus Leisingera, which shared 98.9 % 16S rRNA gene similarity with its nearest phylogenetic neighbour, Leisingera methylohalidivorans. Strain LMG 24366T grew on betaine (1 mM) as a sole carbon source, whereas no growth was observed on L-methionine (10 mM). The phenotypic and genotypic analyses showed that strain LMG 24366T could be differentiated from established Leisingera species and that it represented a novel species, for which the name Leisingera aquimarina sp. nov. is proposed. The type strain is LMG 24366T (=CCUG 55860T) and has a DNA G+C content of 61.4 mol%.},
doi = {10.1099/ijs.0.65844-0},
issue = {Pt 12},
pmid = {19060059}
}
@article{GonzalezEtAl2003a,
year = {2003},
journal = {Int J Syst Evol Microbiol},
volume = {53},
pages = {1261-1269},
author = {Gonzalez, J.M. and Covert, J.S. and Whitman, W.B. and Henriksen, J.R. and Mayer, F. and Scharf, B. and Schmitt, R. and Buchan, A. and Fuhrman, J.A. and Kiene, R.P. and Moran, M.A.},
title = {Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments.},
abstract = {Three Gram-negative, rod-shaped, aerobic bacteria that were capable of degrading dimethylsulfoniopropionate (DMSP) were isolated from marine waters. These isolates (DSS-3T, DSS-10 and ISMT) exhibited the ability to demethylate and cleave DMSP, as well as to degrade other sulfur compounds related to DMSP that are cycled in marine environments. Intracellular poly-beta-hydroxybutyrate inclusions, surface blebs and one polar, complex flagellum that rotated exclusively in the clockwise direction were observed for DSS-3T. The outer membrane of ISMT was separated from the cytoplasm at the poles in a toga-like morphology. The primary fatty acid in both strains was C(18 : 1)omega7c. DNA G+C contents for the isolates were 68.0+/-0.1, 68.1+/-0.1 and 66.0+/-0.2 mol% for DSS-3T, DSS-10 and ISMT, respectively. 16S rRNA gene sequence analyses placed these organisms within the Roseobacter lineage of the alpha-PROTEOBACTERIA: Closely related species were Silicibacter lacuscaerulensis and Ruegeria atlantica (DSS-3T and DSS-10) and Roseovarius tolerans (ISMT). Neither DSS-3T nor ISMT exhibited 16S rRNA similarity >97 % or DNA-DNA hybridization values >45 % to their nearest described relatives. Genotypic and phenotypic analyses support the creation of two novel species: Silicibacter pomeroyi sp. nov. with strain DSS-3T (=ATCC 700808T=DSM 15171T) as the type strain, and Roseovarius nubinhibens sp. nov. with strain ISMT (=ATCC BAA-591T=DSM 15170T) as the type strain.},
doi = {10.1099/ijs.0.02491-0},
issue = {Pt 5},
pmid = {13130004}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{MartensEtAl2006a,
year = {2006},
journal = {Int J Syst Evol Microbiol},
volume = {56},
pages = {1293-1304},
author = {Martens, T. and Heidorn, T. and Pukall, R. and Simon, M. and Tindall, B.J. and Brinkhoff, T.},
title = {Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera.},
abstract = {A heterotrophic, antibiotic-producing bacterium, strain T5T, was isolated from the German Wadden Sea, located in the southern region of the North Sea. Sequence analysis of the 16S rRNA gene of this strain demonstrated close affiliation with Roseobacter gallaeciensis BS107T (99 % similarity), but the results of genotypic (DNA-DNA hybridization and DNA G + C content) and phenotypic characterization revealed that strain T5T represents a novel species. The novel organism is strictly aerobic, Gram-negative, rod-shaped, motile and forms brown-pigmented colonies. Strain T5T produces the antibiotic tropodithietic acid throughout the exponential phase which inhibits the growth of bacteria from different taxa, as well as marine algae. Strain T5T requires sodium ions and utilizes a wide range of substrates, including oligosaccharides, sugar alcohols, organic acids and amino acids. The DNA G + C content is 55.7 mol%. Comparative 16S rRNA gene sequence analysis revealed that strains T5T and Roseobacter gallaeciensis BS107T group with Leisingera methylohalidivorans as their closest described relative within the Roseobacter clade (97.9 and 97.6 % sequence similarity, respectively) and with Ruegeria algicola (96.6 and 96.5 % similarity, respectively) of the Alphaproteobacteria. Comparison of strains T5T and Roseobacter gallaeciensis BS107T with Roseobacter denitrificans and Roseobacter litoralis showed striking differences in 16S rRNA gene sequence similarities, chemical composition, pigmentation, presence of bacteriochlorophyll a and antibiotic production. On the basis of these results, it is proposed that Roseobacter gallaeciensis is reclassified as the type species of a new genus, Phaeobacter, as Phaeobacter gallaeciensis comb. nov. (type strain BS107T = CIP 105210T = ATCC 700781T = NBRC 16654T = DSM 17395T). Strain T5T (=LMG 22475T = DSM 16374T) is proposed as the type strain of a novel species of this genus, Phaeobacter inhibens sp. nov. At the same time, emended descriptions are provided of the genera Roseobacter, Ruegeria and Leisingera, as well as reclassifying Ruegeria algicola as the type species of a new genus, Marinovum, with the name Marinovum algicola comb. nov.},
doi = {10.1099/ijs.0.63724-0},
issue = {6},
pmid = {16738106}
}
@article{RuizponteEtAl1998b,
year = {1998},
journal = {Int J Syst Bacteriol},
volume = {48},
pages = {537-542},
author = {Ruiz-Ponte, C. and Cilia, V. and Lambert, C. and Nicolas, J.L.},
title = {Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus.},
abstract = {Four bacterial strains were isolated from larval cultures and collectors of the scallop Pecten maximus. They showed a high level of intragroup genomic relatedness (84-95%) as determined by DNA-DNA hybridization. The cells were Gram-negative, strictly aerobic, motile, ovoid rods. They grew at temperatures from 15 to 37 degrees C and from pH 7.0 to 10, but did not grow in the absence of NaCl and required growth factors. They had the ability to use a wide variety of compounds as sole carbon source: D-mannose, D-galactose, D-fructose, D-glucose, D-xylose, melibiose, trehalose, maltose, cellobiose, sucrose, mesoerythritol, D-mannitol, glycerol, D-sorbitol, meso-inositol, succinate, propionate, butyrate, gamma-aminobutyrate, DL-hydroxybutyrate, 2-ketoglutarate, pyruvate, fumarate, glycine, L-alpha-alanine, beta-alanine, L-glutamate, L-arginine, L-lysine, L-ornithine and L-proline. They exhibited oxidase and catalase activities but no denitrification activity. The isolates did not contain bacteriochlorophyll a. The G + C content ranged from 57.6 to 58 mol%. Phylogenetic analyses of the 16S rRNA sequence revealed that these isolates belong to the genus Roseobacter. On the basis of quantitative hybridization data, it is proposed that these isolates should be placed in a new species, Roseobacter gallaeciensis. The type strain is Roseobacter gallaeciensis BS107T (= CIP 105210T).},
doi = {10.1099/00207713-48-2-537},
issue = {2},
pmid = {9731295}
}
@article{UrakamiEtAl1990b,
year = {1990},
journal = {Int J Syst Bacteriol},
volume = {40},
pages = {287-291},
author = {Urakami, T. and Araki, H. and Oyanagi, H. and Suzuki, K. and Komagata, K.},
title = {Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov., which utilize N,N-dimethylformamide.},
abstract = {Two methylamine- and N,N-dimethylformamide-utilizing Paracoccus spp. are described. These bacteria are gram-negative, nonsporeforming, nonmotile, coccoid or short rod-shaped organisms. Their DNA base composition is 62 to 68 mol% G + C. Their cellular fatty acids include large amounts of C18:1 acid. Their major hydroxy acids are 3-OH C10:0 and 3-OH C14:0 acids. The major ubiquinone is Q-10. These bacteria are distinguished from Paracoccus denitrificans and Paracoccus alcaliphilus by physiological characteristics and by DNA-DNA-homology. Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov. are proposed. The type strain of P. aminophilus is DM-15 (= JCM 7686), and the type strain of P. aminovorans is DM-82 (= JCM 7685). Paracoccus halodenitrificans is distinguished from other Paracoccus species on the basis of cellular fatty acid composition, hydroxy fatty acid composition, and DNA-DNA homology. It may not be a valid member of the genus Paracoccus.},
doi = {10.1099/00207713-40-3-287},
issue = {3},
pmid = {2397196}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{PetursdottirKristjansson1997a,
year = {1997},
journal = {Extremophiles},
volume = {1},
pages = {94-99},
author = {Petursdottir, S.K. and Kristjansson, J.K.},
title = {Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland.},
abstract = {Mesophilic, moderately halophilic bacteria were isolated from a silica-rich geothermal lake, the Blue Lagoon in Iceland. The isolates are strictly aerobic, but reduce nitrate to nitrite, and are oxidase- and catalase-positive. The nonsporeforming and nonmotile Gram negative rods are 0.6-0.8 microm in diameter and variable in length (9-18 microm), and contain gas vacuoles. The GC content in their DNA is 66.15%. The minimum, optimum, and maximum temperatures for growth are 22 degrees C, 45 degrees C, and 50 degrees C, respectively. The isolates do not grow without added salt in the medium and can grow at up to 7% NaCl (w/v). The optimal salinity for growth is 3.5%-4% NaCl. The pH range for growth is 6.5-8.5, with the optimal pH at 7.0. At optimal conditions the bacterium has a doubling time of 80 min. The main cytochrome is a membrane-bound cytochrome c with an alpha-peak at 549nm. Sequencing of 16S rRNA from the type strain ITI-1157 revealed it to be a proteobacterium of the alpha-subclass with the closest relatives being Roseobacter litoralis and Paracoccuss kocuri. The new isolates do not contain bacteriochlorophyll a and are considered to represent a new genus and a new species, Silicibacter lacuscaerulensis.},
doi = {10.1007/s007920050020},
issue = {2},
pmid = {9680308}
}
@article{VandecandelaereEtAl2008a,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2726-2733},
author = {Vandecandelaere, I. and Nercessian, O. and Segaert, E. and Achouak, W. and Faimali, M. and Vandamme, P.},
title = {Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm.},
abstract = {Seventy isolates were obtained from a marine electroactive biofilm that was generated on a cathodically polarized stainless steel electrode (Genoa, Italy). The genetic diversity was investigated by means of BOX-PCR fingerprinting and two clusters of isolates with similar BOX-PCR profiles were delineated. Whole-cell fatty acid methyl ester analysis and 16S rRNA gene sequence analysis showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. DNA-DNA hybridization experiments and a biochemical analysis demonstrated that four isolates belonged to the species Ruegeria mobilis. However, 66 isolates from the second BOX-PCR cluster constituted a novel species within the genus Ruegeria, for which the name Ruegeria scottomollicae sp. nov. is proposed. The DNA G+C content was 61.0+/-0.4 %. The type strain is LMG 24367T (=CCUG 55858T).},
doi = {10.1099/ijs.0.65843-0},
issue = {12},
pmid = {19060048}
}
@article{YiEtAl2007b,
year = {2007},
journal = {Int J Syst Evol Microbiol},
volume = {57},
pages = {815-819},
author = {Yi, H. and Lim, Y.W. and Chun, J.},
title = {Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999.},
abstract = {The taxonomic positions of the genera Ruegeria and Silicibacter were evaluated by a polyphasic investigation. It was evident from 16S rRNA gene sequence analysis that both genera are closely related as they formed a monophyletic clade with high sequence similarities (96.9-98.2 %). Several properties commonly found in these taxa strongly suggest that they should be classified in the same genus. Further, a comparative study based on DNA-DNA hybridization, phenotypic characterization and chemotaxonomic analysis indicated that the members of this clade, namely Ruegeria atlantica, Silicibacter lacuscaerulensis and Silicibacter pomeroyi, can be readily differentiated from each other. On the basis of the polyphasic data obtained in this study, all species of the genus Silicibacter should be transferred to the genus Ruegeria, since the latter has nomenclatural priority. It is therefore proposed that Silicibacter lacuscaerulensis and Silicibacter pomeroyi are transferred to the genus Ruegeria as Ruegeria lacuscaerulensis comb. nov. and Ruegeria pomeroyi comb. nov.},
doi = {10.1099/ijs.0.64568-0},
issue = {4},
pmid = {17392212}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{ImhoffEtAl1984j,
year = {1984},
journal = {Int. J. Syst. Bacteriol.},
volume = {34},
pages = {340-343},
author = {Imhoff, J.F. and Trüper, H.G. and Pfennig, N.},
title = {Rearrangement of the species and genera of the phototrophic "purple nonsulfur bacteria".},
doi = {10.1099/00207713-34-3-340},
issue = {3}
}
@article{SureshEtAl2019a,
year = {2019},
journal = {Front Microbiol},
volume = {10},
pages = {2480},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.},
doi = {10.3389/fmicb.2019.02480},
pmid = {31736915}
}
@article{SureshEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {1111},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Corrigendum: Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.02480.].},
doi = {10.3389/fmicb.2020.01111},
pmid = {32582079}
}
@article{Vanniel1944a,
year = {1944},
journal = {Bacteriol Rev},
volume = {8},
pages = {1-118},
author = {van Niel, C.B.},
title = {THE CULTURE, GENERAL PHYSIOLOGY, MORPHOLOGY, AND CLASSIFICATION OF THE NON-SULFUR PURPLE AND BROWN BACTERIA.},
doi = {10.1128/br.8.1.1-118.1944},
issue = {1},
pmid = {16350090}
}
@article{BreiderEtAl2014a,
year = {2014},
journal = {Front Microbiol},
volume = {5},
pages = {416},
author = {Breider, S. and Scheuner, C. and Schumann, P. and Fiebig, A. and Petersen, J. and Pradella, S. and Klenk, H.P. and Brinkhoff, T. and Goker, M.},
title = {Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.},
abstract = {Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.},
doi = {10.3389/fmicb.2014.00416},
pmid = {25157246}
}
@article{ParkEtAl2014ab,
year = {2014},
journal = {Int J Syst Evol Microbiol},
volume = {64},
pages = {1378-1383},
author = {Park, S. and Park, D.S. and Bae, K.S. and Yoon, J.H.},
title = {Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring.},
abstract = {A Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped or ovoid bacterial strain, designated SSK6-1T, was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain SSK6-1T grew optimally at 30 degrees C, at pH 7.0-7.5 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSK6-1T clustered with Phaeobacter daeponensis TF-218T and Phaeobacter caeruleus LMG 24369T, exhibiting sequence similarities of 98.6 and 98.3 %, respectively. The novel strain exhibited sequence similarities of 94.6-97.8 % to the type strains of other recognized species of the genera Phaeobacter and Leisingera. Strain SSK6-1T contained Q-10 as the predominant ubiquinone and C18 : 1omega7c and 11-methyl C18 : 1omega7c as the major fatty acids. The major polar lipids of strain SSK6-1T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain SSK6-1T was 64.6 mol% and its DNA-DNA relatedness values with P. daeponensis TF-218T and P. caeruleus were 21 and 25 %, respectively. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SSK6-1T is separate from recognized Phaeobacter species. On the basis of the data presented, strain SSK6-1T is considered to represent a novel species of the genus Phaeobacter, for which the name Phaeobacter aquaemixtae sp. nov. is proposed. The type strain is SSK6-1T ( = KCTC 32538T = CECT 8399T).},
doi = {10.1099/ijs.0.057646-0},
issue = {4},
pmid = {24449788}
}
@article{ArahalEtAl2005a,
year = {2005},
journal = {Int J Syst Evol Microbiol},
volume = {55},
pages = {2371-2376},
author = {Arahal, D.R. and Macian, M.C. and Garay, E. and Pujalte, M.J.},
title = {Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov.},
abstract = {A Gram-negative, slightly halophilic, non-pigmented, strictly aerobic, chemo-organotrophic bacterium was isolated from sea water off the western Mediterranean coast near Valencia (Spain). This strain was able to grow on several organic acids and amino acids added to a minimal medium as carbon sources, but used few carbohydrates or yielded slight growth when sugars were used. Phylogenetic analysis based on an almost complete 16S rRNA gene sequence revealed that strain XSM19T was a member of the Roseobacter group within the 'Alphaproteobacteria', with its closest phylogenetic neighbour being Ruegeria gelatinovorans (97.6 % sequence similarity). Following a polyphasic approach, it was concluded that strain XSM19T represents a new genus and novel species, for which the name Thalassobius mediterraneus sp. nov. is proposed. The type strain is XSM19T (=CECT 5383T=CIP 108400T=CCUG 49438T). It is also proposed that R. gelatinovorans (Ruger & Hofle 1992) Uchino et al. 1999 is reclassified as Thalassobius gelatinovorus comb. nov.},
doi = {10.1099/ijs.0.63842-0},
issue = {6},
pmid = {16280499}
}
@article{DeshmukhOren2023aaaj,
year = {2023},
journal = {Int J Syst Evol Microbiol},
volume = {73},
pages = {6025},
author = {Deshmukh, U.B. and Oren, A.},
title = {Proposal of Thalassovita gen. nov. and Alloyangia gen. nov. as replacement names for the illegitimate prokaryotic generic names Thalassobius and Yangia, respectively.},
abstract = {The prokaryotic generic names Thalassobius Arahal et al. 2005 and Yangia Dai et al. 2006 are illegitimate because they are later homonyms of the genus names Thalassobius Solier 1849 (Coleoptera) and Yangia Zheng 1997 (fossil Rodentia), respectively Principle two and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes]. We therefore propose the replacement generic names Thalassovita and Alloyangia, with type species Thalassovita gelatinovora and Alloyangia pacifica, respectively.},
doi = {10.1099/ijsem.0.006025},
issue = {9},
pmid = {37695726}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{HelselEtAl2007a,
year = {2007},
journal = {J Clin Microbiol},
volume = {45},
pages = {1238-1243},
author = {Helsel, L.O. and Hollis, D. and Steigerwalt, A.G. and Morey, R.E. and Jordan, J. and Aye, T. and Radosevic, J. and Jannat-Khah, D. and Thiry, D. and Lonsway, D.R. and Patel, J.B. and Daneshvar, M.I. and Levett, P.N.},
title = {Identification of "Haematobacter," a new genus of aerobic Gram-negative rods isolated from clinical specimens, and reclassification of Rhodobacter massiliensis as "Haematobacter massiliensis comb. nov.".},
abstract = {Twelve strains of gram-negative, nonfermenting rods recovered mainly from septicemic patients were studied using conventional and molecular methods. The phenotypic profiles of these strains most closely resembled Psychrobacter phenylpyruvicus. They produced catalase, oxidase, urease, and H(2)S (lead acetate paper) but did not produce indole, reduce nitrate or nitrite, or hydrolyze gelatin or esculin. No acid production was observed in a King's oxidation-fermentation base containing d-glucose, d-xylose, d-mannitol, sucrose, lactose, or maltose. All strains were nonmotile and nonpigmented. Most strains produced green discoloration on blood agar. All strains grew at 25 degrees C and 35 degrees C and most grew on MacConkey agar. They shared a common cellular fatty acid (CFA) profile characterized by large amounts (56% to 90%) of 18:1omega7c and the presence of 3-OH-10:0, 16:1omega7c, 16:0, and 19:0cycomega8c that overall was most similar to that of Rhodobacter species but was quite distinct from that of P. phenylpyruvicus. The MICs for most beta-lactams, fluoroquinolones, aminoglycosides, and carbapenems were low. MICs for aztreonam and piperacillin were higher, with MICs for some strains of > 64 mg/liter and > 128 mg/liter, respectively. Polyphasic analysis of these strains, including morphological, biochemical, CFA composition, DNA-DNA hybridization, 16S rRNA gene sequencing, and percent guanine-plus-cytosine (G+C) content analysis, demonstrated that these strains and Rhodobacter massiliensis represent a new genus, "Haematobacter" (proposed name), with the species H. missouriensis (type strain H1892T = CCUG 52307T = CIP 109176T) and H. massiliensis comb. nov. (type strain FramboiseT = CCUG 47968T = CIP 107725T) and an unnamed genomospecies.},
doi = {10.1128/JCM.01188-06},
issue = {4},
pmid = {17287332}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{RugerHofle1992a,
year = {1992},
journal = {Int J Syst Bacteriol},
volume = {42},
pages = {133-143},
author = {Ruger, H.J. and Hofle, M.G.},
title = {Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev.},
abstract = {Two new species of aerobic, gram-negative, peritrichously flagellated or nonmotile marine bacteria usually forming star-shaped aggregates were isolated from northeastern Atlantic Ocean bottom sediments. These organisms resembled eight star-shaped-aggregate-forming bacterial species from the Baltic Sea originally ascribed to the genus Agrobacterium but not included on the Approved Lists of Bacterial Names because of their questionable relationships to true agrobacteria. These two sets of star-shaped-aggregate-forming bacteria were compared by means of phenotypic data, DNA base compositions, DNA-DNA relatedness, and one-dimensional electrophoretic analysis of low-molecular-weight RNAs (5S rRNA and tRNA). According to the results of genotyping, the northeastern Atlantic Ocean isolates and three of the Baltic Sea species formed a group of closely related bacteria that could not be excluded from the genus Agrobacterium with certainty. Until more genotypic data are available, these five marine species are regarded as a distinct subdivision of the genus Agrobacterium consisting of Agrobacterium atlanticum sp. nov. (type strain, 1480T = DSM 5823T), A. meteori sp. nov. (type strain, 1513T = DSM 5824T), A. ferrugineum sp. nov. nom. rev. emend. (type strain, ATCC 25652T), A. gelatinovorum sp. nov. nom. rev. emend. (type strain, ATCC 25655T), and A. stellulatum sp. nov. nom. rev. emend. (type strain, ATCC 15215T). "A. aggregatum" proved to be a later subjective synonym of A. stellulatum, which had priority. The remaining four Baltic Sea species, "A. agile," "A. kieliense," "A. luteum," and "A. sanguineum," could not be placed in the new subdivision of Agrobacterium.},
doi = {10.1099/00207713-42-1-133},
issue = {1},
pmid = {1371058}
}
@article{LiEtAl2015ag,
year = {2015},
journal = {Int J Syst Evol Microbiol},
volume = {65},
pages = {3281-3285},
author = {Li, G. and Lai, Q. and Du, Y. and Liu, X. and Sun, F. and Shao, Z.},
title = {Aestuariivita atlantica sp. nov., isolated from deep-sea sediment.},
abstract = {A novel strain, 22II-S11-z3T, was isolated from the deep-sea sediment of the Atlantic Ocean. The bacterium was aerobic, Gram-staining-negative, oxidase-positive and catalase-negative, oval- to rod-shaped, and non-motile. Growth was observed at salinities of 1-9 % NaCl and temperatures of 10-45 degrees C. The isolate could hydrolyse aesculin and Tweens 20, 40 and 80, but not gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S11-z3T belonged to the genus Aestuariivita, with highest sequence similarity to Aestuariivita boseongensis KCTC 42052T (97.5 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain 22II-S11-z3T and A. boseongensis KCTC 42052T were 71.5 % and 20.0 +/- 2.3 %, respectively. The G+C content of the chromosomal DNA was 65.5 mol%. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1omega7c/omega6c) (35.2 %), C19 : 0 cyclo omega8c (20.9 %), C16 : 0 (11.8 %), 11-methyl C18 : 1omega7c (11.4 %) and C12 : 1 3-OH (9.4 %). The respiratory quinone was determined to be Q-10. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, nine unidentified phospholipids, one unidentified aminolipid and two unidentified lipids were present. The combined genotypic and phenotypic data show that strain 22II-S11-z3T represents a novel species of the genus Aestuariivita, for which the name Aestuariivita atlantica sp. nov. is proposed, with the type strain 22II-S11-z3T ( = KCTC 42276T = MCCC 1A09432T).},
doi = {10.1099/ijsem.0.000406},
issue = {10},
pmid = {26297013}
}
@article{WirthWhitman2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2393-2411},
author = {Wirth, J.S. and Whitman, W.B.},
title = {Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera.},
abstract = {Roseobacters are a diverse and globally abundant group of Alphaproteobacteria within the Rhodobacteraceae family. Recent studies and the cophenetic correlations suggest that the 16S rRNA genes are poor phylogenetic markers within this group. In contrast, the cophenetic correlation coefficients of the core-gene average amino acid identity (cAAI) and RpoC protein sequences are high and likely more predictive of relationships. A maximum-likelihood phylogenetic tree calculated from 53 core genes demonstrated that some of the current genera were either polyphyletic or paraphyletic. The boundaries of bacterial genera were redefined based upon the cAAI, the percentage of conserved proteins, and phenotypic characteristics and resulted in the following taxonomic proposals. Loktanella vestfoldensis, Loktanella litorea, Loktanella maricola, Loktanella maritima, Loktanella rosea, Loktanella sediminilitoris, Loktanella tamlensis, and Roseobacter sp. CCS2 should be reclassified into the novel genus Yoonia. Loktanella hongkongensis, Loktanella aestuariicola, Loktanella cinnabarina, Loktanella pyoseonensis, Loktanellasoe soekkakensis and Loktanella variabilis should be reclassified in the novel genus Limimaricola. Loktanella koreensis and Loktanella sediminum should be reclassified in the novel genus Cognatiyoonia. Loktanella marina should be reclassified in the novel genus Flavimaricola. Aestuariivita atlantica should be reclassified in the novel genus Pseudaestuariivita. Thalassobius maritima should be reclassified in the novel genus Cognatishimia. Similarly, Ruegeria mobilis, Ruegeria scottomollicae, Ruegeria sp. TM1040 and Tropicibacter multivorans should be reclassified in the genus Epibacterium. Tropicibacter litoreus and Tropicibacter mediterraneus should be reclassified in the genus Ruegeria. Thalassobius abyssi and Thalassobius aestuarii should be reclassified in the genus Shimia. Citreicella aestuarii, Citreicella manganoxidans, Citreicella marina, Citreicella thiooxidans, Pelagibaca bermudensis and Thiobacimonas profunda should be reclassified in the genus Salipiger. Nautella italica should be reclassified in the genus Phaeobacter. Because these proposals to reclassify the type and all others species of Citreicella, Nautella, Pelagibaca and Thiobacimonas, these genera are not used in this taxonomy.},
doi = {10.1099/ijsem.0.002833},
issue = {7},
pmid = {29809121}
}
@article{GirijaEtAl2010a,
year = {2010},
journal = {Int J Syst Evol Microbiol},
volume = {60},
pages = {2099-2107},
author = {Girija, K.R. and Sasikala, C.h. and Ramana, C.h.V. and Sproer, C. and Takaichi, S. and Thiel, V. and Imhoff, J.F.},
title = {Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils.},
abstract = {An oval to rod-shaped, phototrophic, purple non-sulfur bacterium, strain JA192T, was isolated from an enrichment culture of a pasteurized rhizosphere soil sample from a field cultivated with jowar (sorghum) collected from Godumakunta village near Hyderabad, India. Strain JA192T is Gram-negative, motile and produces endospores. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain JA192T is closely related to Rhodobacter sphaeroides 2.4.1T (99.9 % sequence similarity), Rba. megalophilus JA194T (99.8 %) and Rba. azotoformans KA25T (98.1 %) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA-DNA hybridization with Rba. sphaeroides DSM 158T, Rba. megalophilus JA194T and Rba. azotoformans JCM 9340T showed relatedness of only 38-57 % with respect to strain JA192T. On the basis of 16S rRNA gene sequence analysis, DNA-DNA hybridization data and morphological, physiological and chemotaxonomic characters, strain JA192T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter johrii sp. nov. is proposed. The type strain is JA192T (=DSM 18678T =JCM 14543T =MTCC 8172T).},
doi = {10.1099/ijs.0.011718-0},
issue = {9},
pmid = {19854875}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{SureshEtAl2019a,
year = {2019},
journal = {Front Microbiol},
volume = {10},
pages = {2480},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.},
doi = {10.3389/fmicb.2019.02480},
pmid = {31736915}
}
@article{SureshEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {1111},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Corrigendum: Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.02480.].},
doi = {10.3389/fmicb.2020.01111},
pmid = {32582079}
}
@article{ChenEtAl2011e,
year = {2011},
journal = {Int J Syst Evol Microbiol},
volume = {61},
pages = {1138-1143},
author = {Chen, M.H. and Sheu, S.Y. and Chen, C.A. and Wang, J.T. and Chen, W.M.},
title = {Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera.},
abstract = {A bacterial strain, designated SW-3T, was isolated from the reef-building coral Isopora palifera, from Southern Taiwan, and was characterized by using a polyphasic taxonomic approach. Cells of strain SW-3T were Gram-reaction-negative, aerobic, rod-shaped and motile by means of monopolar flagella and formed cream-white colonies. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-3T belonged to the genus Paracoccus and its most closely related neighbours were P. aestuarii B7T, P. homiensis DD-R11T, P. marinus KKL-A5T, P. denitrificans DSM 413T and P. zeaxanthinifaciens R-1512T, with sequence similarities of 96.8, 96.6, 96.1, 95.8 and 94.9 %, respectively. Strain SW-3T exhibited optimal growth at 25-30 degrees C and pH 9-10 and in 3-5 % (w/v) NaCl. The predominant cellular fatty acid was summed feature 8 (C(18 : 1)omega7c and/or C(18 : 1)omega6c; 75 %). The major respiratory quinone was Q-10. The polar lipid profile consisted of a mixture of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and several uncharacterized polar lipids. The DNA G+C content of strain SW-3T was 63.7 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from recognized species of the genus Paracoccus. It is evident from the genotypic, phenotypic and chemotaxonomic data that strain SW-3T represents a novel species of the genus Paracoccus, for which the name Paracoccus isoporae sp. nov. is proposed. The type strain is SW-3T ( = LMG 25205T = BCRC 17967T).},
doi = {10.1099/ijs.0.023333-0},
issue = {5},
pmid = {20543151}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{McginnisEtAl2015a,
year = {2015},
journal = {Int J Syst Evol Microbiol},
volume = {65},
pages = {1877-1882},
author = {McGinnis, J.M. and Cole, J.A. and Dickinson, M.C. and Mingle, L.A. and Lapierre, P. and Musser, K.A. and Wolfgang, W.J.},
title = {Paracoccus sanguinis sp. nov., isolated from clinical specimens of New York State patients.},
abstract = {Eight independent isolates of a Gram-reaction-negative, non-motile rod, were recovered from clinical specimens of New York State patients between the years 2005 and 2013. Four of these isolates were characterized in a taxonomic study using a polyphasic approach that involved phenotypic, phylogenetic and genotypic methodologies. Based on 16S rRNA gene sequence similarity and phylogenetic analysis, the closest relative type strain of the isolates is Paracoccus sphaerophysae HAMBI 3106T (97.7 % 16S rRNA gene sequence similarity). Among the four isolates, the 16S rRNA gene sequence similarity is 100 %. In silico genomic comparisons, including average nucleotide identity (ANI) and the genome-to-genome distance calculator (GGDC), were used as an alternative to DNA-DNA hybridization in this study to support designation of the four isolates as a novel species of the genus Paracoccus. Mass spectrometry profiles were also obtained for the novel isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The predominant cellular fatty acids of the novel isolates were C18 : 1omega7c and C18 : 0. Biochemical analysis and morphological characteristics further contribute to designation of the four isolates as a novel species of the genus Paracoccus, for which the name Paracoccus sanguinis sp. nov. is proposed. The type strain is 05503T( = DSM 29303T = LMG 28451T).},
doi = {10.1099/ijs.0.000193},
issue = {6},
pmid = {25792366}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{MuramatsuEtAl2007a,
year = {2007},
journal = {Int J Syst Evol Microbiol},
volume = {57},
pages = {1304-1309},
author = {Muramatsu, Y. and Uchino, Y. and Kasai, H. and Suzuki, K. and Nakagawa, Y.},
title = {Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau.},
abstract = {The taxonomic positions of two bacterial strains, MBIC01146T and MBIC01099, isolated from marine environments of Japan and Palau, respectively, were determined by using a polyphasic approach. The bacteria were aerobic, motile, Gram-negative rods and formed star-shaped aggregations. The G+C content of the genomic DNA ranged from 58.5 to 58.7 mol%. The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acids were C(16 : 0), C(18 : 1)omega6c and C(18 : 1)omega7c. 16S rRNA gene sequence analyses based on both neighbour-joining and maximum-parsimony methods revealed that strains MBIC01146T and MBIC01099 were positioned within the cluster comprising Ruegeria atlantica and Silicibacter lacuscaerulensis within subgroup alpha-3 of the Proteobacteria. The phenotypic and chemotaxonomic characteristics of the novel strains were similar to those of Ruegeria atlantica; however, DNA-DNA hybridization tests showed that the isolates represented an independent species. The isolates could be differentiated from Ruegeria atlantica based on several characteristics. Therefore, strains MBIC01146T and MBIC01099 are considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria mobilis sp. nov. is proposed. The type strain is MBIC01146T (=NBRC 101030T=CIP 109181T). An emended description of Ruegeria atlantica Uchino et al. 1999 is also given.},
doi = {10.1099/ijs.0.64572-0},
issue = {6},
pmid = {17551047}
}
@article{VandecandelaereEtAl2008a,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2726-2733},
author = {Vandecandelaere, I. and Nercessian, O. and Segaert, E. and Achouak, W. and Faimali, M. and Vandamme, P.},
title = {Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm.},
abstract = {Seventy isolates were obtained from a marine electroactive biofilm that was generated on a cathodically polarized stainless steel electrode (Genoa, Italy). The genetic diversity was investigated by means of BOX-PCR fingerprinting and two clusters of isolates with similar BOX-PCR profiles were delineated. Whole-cell fatty acid methyl ester analysis and 16S rRNA gene sequence analysis showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. DNA-DNA hybridization experiments and a biochemical analysis demonstrated that four isolates belonged to the species Ruegeria mobilis. However, 66 isolates from the second BOX-PCR cluster constituted a novel species within the genus Ruegeria, for which the name Ruegeria scottomollicae sp. nov. is proposed. The DNA G+C content was 61.0+/-0.4 %. The type strain is LMG 24367T (=CCUG 55858T).},
doi = {10.1099/ijs.0.65843-0},
issue = {12},
pmid = {19060048}
}
@article{WirthWhitman2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2393-2411},
author = {Wirth, J.S. and Whitman, W.B.},
title = {Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera.},
abstract = {Roseobacters are a diverse and globally abundant group of Alphaproteobacteria within the Rhodobacteraceae family. Recent studies and the cophenetic correlations suggest that the 16S rRNA genes are poor phylogenetic markers within this group. In contrast, the cophenetic correlation coefficients of the core-gene average amino acid identity (cAAI) and RpoC protein sequences are high and likely more predictive of relationships. A maximum-likelihood phylogenetic tree calculated from 53 core genes demonstrated that some of the current genera were either polyphyletic or paraphyletic. The boundaries of bacterial genera were redefined based upon the cAAI, the percentage of conserved proteins, and phenotypic characteristics and resulted in the following taxonomic proposals. Loktanella vestfoldensis, Loktanella litorea, Loktanella maricola, Loktanella maritima, Loktanella rosea, Loktanella sediminilitoris, Loktanella tamlensis, and Roseobacter sp. CCS2 should be reclassified into the novel genus Yoonia. Loktanella hongkongensis, Loktanella aestuariicola, Loktanella cinnabarina, Loktanella pyoseonensis, Loktanellasoe soekkakensis and Loktanella variabilis should be reclassified in the novel genus Limimaricola. Loktanella koreensis and Loktanella sediminum should be reclassified in the novel genus Cognatiyoonia. Loktanella marina should be reclassified in the novel genus Flavimaricola. Aestuariivita atlantica should be reclassified in the novel genus Pseudaestuariivita. Thalassobius maritima should be reclassified in the novel genus Cognatishimia. Similarly, Ruegeria mobilis, Ruegeria scottomollicae, Ruegeria sp. TM1040 and Tropicibacter multivorans should be reclassified in the genus Epibacterium. Tropicibacter litoreus and Tropicibacter mediterraneus should be reclassified in the genus Ruegeria. Thalassobius abyssi and Thalassobius aestuarii should be reclassified in the genus Shimia. Citreicella aestuarii, Citreicella manganoxidans, Citreicella marina, Citreicella thiooxidans, Pelagibaca bermudensis and Thiobacimonas profunda should be reclassified in the genus Salipiger. Nautella italica should be reclassified in the genus Phaeobacter. Because these proposals to reclassify the type and all others species of Citreicella, Nautella, Pelagibaca and Thiobacimonas, these genera are not used in this taxonomy.},
doi = {10.1099/ijsem.0.002833},
issue = {7},
pmid = {29809121}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LiuEtAl2008f,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {257-261},
author = {Liu, Z.P. and Wang, B.J. and Liu, X.Y. and Dai, X. and Liu, Y.H. and Liu, S.J.},
title = {Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969.},
abstract = {An aerobic bacterial isolate, strain HN-182T, was isolated from sediments of the South China Sea. Cells of strain HN-182T are coccoid to short rods, Gram-negative, non-spore-forming and non-motile. Strain HN-182T is heterotrophic and grows well on marine broth (Difco 2216), and is not capable of growing autotrophically on reduced sulfur. Grows at temperatures ranging from 7 to 42 degrees C (optimum at 25 degrees C), but not at 4 or 45 degrees C, and at pH 5.0-9.0 (optimum at pH 7.0), but not at pH 4.5 or 9.5. NaCl is required for growth [0.5-8.5% (w/v)] with an optimum of 4.5%. Cells are positive for catalase, oxidase and urease activities. Nitrate is not reduced. Strain HN-182T contains ubiquinone-10 as sole respiratory quinone. The major polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid and an unidentified glycolipid. Major cellular fatty acids are C18:1omega7c (60.7 %), C16:0 (12.5%) and C18:0 (8.1%). DNA G+C content is 67.2 mol% (by T(m)). The analysis of 16S rRNA gene sequences indicated that strain HN-182T was related to members of the genus Paracoccus, with similarities ranging from 91.2 to 96.7% (highest to Paracoccus versutus) and a close relationship with Paracoccus sulfuroxidans, indicating that strain HN-182T is a member of Paracoccus. Based on these results, it is concluded that strain HN-182T represents a novel species of the genus Paracoccus, for which the name Paracoccus halophilus sp. nov. is proposed. The type strain is HN-182T (=CGMCC 1.6117T=JCM 14014T).},
doi = {10.1099/ijs.0.65237-0},
issue = {1},
pmid = {18175718}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LeeEtAl2016u,
year = {2016},
journal = {Int J Syst Evol Microbiol},
volume = {66},
pages = {1068-1073},
author = {Lee, Y.M. and Yang, J.Y. and Baek, K. and Han, S.J. and Shin, S.C. and Hwang, C.Y. and Hong, S.G. and Lee, H.K.},
title = {Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter.},
abstract = {A Gram-stain-negative, facultatively aerobic, cream-coloured, ovoid-shaped, non-motile and psychrotolerant bacterial strain, PAMC 27389T, was isolated from terrestrial soil collected on King George Island, Antarctica. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain PAMC 27389T belongs to the genus Pseudorhodobacter, sharing highest similarities with the type strains of Pseudorhodobacter wandonensis (96.9 %), Pseudorhodobacter antarcticus (96.8 %), Pseudorhodobacter ferrugineus (96.5 %) and Pseudorhodobacter aquimaris (95.4 %). Average nucleotide identity values between strain PAMC 27389T and the type strains of P. wandonensis, P. antarcticus, P. ferrugineus and P. aquimaris were 70.8, 70.9, 71.0 and 70.5 %, respectively and the genome-to-genome distances were 18.4-19.1 %, indicating PAMC 27389T is clearly distinguished from the most closely related Pseudorhodobacter species. The genomic DNA G+C content was 60.1 mol%. Strain PAMC 27389T grew at 0-37 degrees C (optimally at 15-20 degrees C), at pH 5.5-9.0 (optimally at pH 6.5-7.0) and in the presence of 0.5-3.0 % (w/v) sea salt (optimally with 0.5 %). It lacked bacteriochlorophyll a. The major fatty acids (>5 %) were summed feature 8 (C18 : 1omega7c and/or C18 : 1omega6c) and C18 : 1omega7c 11-methyl. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid, an unidentified lipid and three unidentified aminophospholipids. The major respiratory quinone was Q-10. Based on the phenotypic, chemotaxonomic and genomic data presented, we propose the name Pseudorhodobacter psychrotolerans sp. nov. with the type strain PAMC 27389T ( = KCTC 42640T = JCM 30764T).},
doi = {10.1099/ijsem.0.000841},
issue = {2},
pmid = {26653106}
}
@article{LiEtAl2009g,
year = {2009},
journal = {Int J Syst Evol Microbiol},
volume = {59},
pages = {2670-2674},
author = {Li, H.F. and Qu, J.H. and Yang, J.S. and Li, Z.J. and Yuan, H.L.},
title = {Paracoccus chinensis sp. nov., isolated from sediment of a reservoir.},
abstract = {A Gram-negative, short ovoid- to coccus-shaped, aerobic, motile, non-spore-forming bacterium (designated strain KS-11T) was isolated from sediment of the eutrophic Guanting reservoir in Beijing, China. Colonies grown on R2A agar plates were circular, convex and colourless to orange. The strain grew in the presence of up to 1 % NaCl (optimum, 0 % NaCl). Growth occurred at 25-40 degrees C (optimum, 28-37 degrees C) and at pH 6.0-9.5 (optimum, pH 7.5-9.0). On the basis of 16S rRNA gene sequence similarity, strain KS-11T was shown to belong to the class Alphaproteobacteria, being closely related to Paracoccus marinus (96.9 % 16S rRNA gene sequence similarity), followed by Paracoccus koreensis (96.8 %), Paracoccus solventivorans (96.8 %), Paracoccus alkenifer (96.2 %) and Paracoccus kocurii (95.8 %). The major fatty acids of strain KS-11T were summed feature 7 (C(18 : 1)omega7c/omega9t/omega12t) (83.8 %) and C(18 : 0) (6.5 %) and the G+C content of the genomic DNA was 69.0 mol%. Based on comparative analysis of physiological and chemotaxonomic data, it is proposed that strain KS-11T represents a novel species of the genus Paracoccus, named Paracoccus chinensis sp. nov. The type strain is KS-11T (=CGMCC 1.7655T=NBRC 104937T).},
doi = {10.1099/ijs.0.004705-0},
issue = {11},
pmid = {19625438}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{LipskiEtAl1998b,
year = {1998},
journal = {Int J Syst Bacteriol},
volume = {48},
pages = {529-536},
author = {Lipski, A. and Reichert, K. and Reuter, B. and Sproer, C. and Altendorf, K.},
title = {Identification of bacterial isolates from biofilters as Paracoccus alkenifer sp. nov. and Paracoccus solventivorans with emended description of Paracoccus solventivorans.},
abstract = {Two groups of strains isolated from biofilters for the treatment of waste gases were assigned to the genus Paracoccus by phylogenetic and chemotaxonomic methods. All type strains of the genus Paracoccus were compared with these groups using 16S rDNA sequence analysis, fatty acid patterns and physiological reaction profiles. For both groups, the nearest related reference species was Paracoccus solventivorans based on 16S rDNA sequence similarity. However, whereas one group of isolates was identified as a member of this species by fatty acid analysis and DNA-DNA hybridization, the other group was proposed as a new species, Paracoccus alkenifer sp. nov. Fatty acid analysis showed the unusual fatty acid 20:1cis13 instead of 19:0 cyclo11-12 for P. alkenifer and P. solventivorans, and 14:1cis7 instead of 12:1cis5 for P. alkenifer and Paracoccus kocurii. By means of a GC-MS method, diaminopimelic acid was detected for P. solventivorans. Based on these results we propose an emended description for the species P. solventivorans.},
doi = {10.1099/00207713-48-2-529},
issue = {2},
pmid = {9731294}
}
@article{SillerEtAl1996a,
year = {1996},
journal = {Int J Syst Bacteriol},
volume = {46},
pages = {1125-1130},
author = {Siller, H. and Rainey, F.A. and Stackebrandt, E. and Winter, J.},
title = {Isolation and characterization of a new gram-negative, acetone-degrading, nitrate-reducing bacterium from soil, Paracoccus solventivorans sp. nov.},
abstract = {An acetone-degrading, nitrate-reducing, coccoid to rod-shaped bacterium, strain L1, was isolated from soil on the site of a natural gas company. Cells of the logarithmic growth phase reacted gram positive, while those of the stationary growth phase were gram negative. Single organisms were 0.4 to 0.5 by 0.9 to 1.5 microns in size, nonmotile, and non-spore forming and had poly-beta-hydroxybutyrate inclusions. The doubling time of strain L1 on acetone-CO2-nitrate at the optimal pH of 7 to 8 and the optimal temperature of 30 to 37 degrees C was 12 h. More than 0.2% NaCl or 10 mM thiosulfate inhibited growth. For oxygen or nitrate respiration, acetone and a few organic chemicals were utilized as carbon sources whereas many others could not be used (for details, see Results). Bicarbonate (or CO2) was essential for growth on acetone but not for growth on acetoacetate. The growth yields for acetone-CO2 and acetoacetate were 28.3 and 27.3 g/mol, respectively. With acetone as the carbon source, poly-beta-hydroxybutyrate accounted for up to 40% of the cellular dry weight. The DNA of strain L1 had a G + C content of 68.5 mol% (as determined by high-performance liquid chromatography of nucleotides) or 70 mol% (as determined by the TM method). The sequence of the gene coding for the 16S rRNA led to the classification of strain L1 in the paracoccus group of the alpha subclass of the Proteobacteria. The new isolate is named Paracoccus solventivorans sp. nov. DSM 6637.},
doi = {10.1099/00207713-46-4-1125},
issue = {4},
pmid = {8863446}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{PetursdottirKristjansson1997a,
year = {1997},
journal = {Extremophiles},
volume = {1},
pages = {94-99},
author = {Petursdottir, S.K. and Kristjansson, J.K.},
title = {Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland.},
abstract = {Mesophilic, moderately halophilic bacteria were isolated from a silica-rich geothermal lake, the Blue Lagoon in Iceland. The isolates are strictly aerobic, but reduce nitrate to nitrite, and are oxidase- and catalase-positive. The nonsporeforming and nonmotile Gram negative rods are 0.6-0.8 microm in diameter and variable in length (9-18 microm), and contain gas vacuoles. The GC content in their DNA is 66.15%. The minimum, optimum, and maximum temperatures for growth are 22 degrees C, 45 degrees C, and 50 degrees C, respectively. The isolates do not grow without added salt in the medium and can grow at up to 7% NaCl (w/v). The optimal salinity for growth is 3.5%-4% NaCl. The pH range for growth is 6.5-8.5, with the optimal pH at 7.0. At optimal conditions the bacterium has a doubling time of 80 min. The main cytochrome is a membrane-bound cytochrome c with an alpha-peak at 549nm. Sequencing of 16S rRNA from the type strain ITI-1157 revealed it to be a proteobacterium of the alpha-subclass with the closest relatives being Roseobacter litoralis and Paracoccuss kocuri. The new isolates do not contain bacteriochlorophyll a and are considered to represent a new genus and a new species, Silicibacter lacuscaerulensis.},
doi = {10.1007/s007920050020},
issue = {2},
pmid = {9680308}
}
@article{VandecandelaereEtAl2008a,
year = {2008},
journal = {Int J Syst Evol Microbiol},
volume = {58},
pages = {2726-2733},
author = {Vandecandelaere, I. and Nercessian, O. and Segaert, E. and Achouak, W. and Faimali, M. and Vandamme, P.},
title = {Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm.},
abstract = {Seventy isolates were obtained from a marine electroactive biofilm that was generated on a cathodically polarized stainless steel electrode (Genoa, Italy). The genetic diversity was investigated by means of BOX-PCR fingerprinting and two clusters of isolates with similar BOX-PCR profiles were delineated. Whole-cell fatty acid methyl ester analysis and 16S rRNA gene sequence analysis showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. DNA-DNA hybridization experiments and a biochemical analysis demonstrated that four isolates belonged to the species Ruegeria mobilis. However, 66 isolates from the second BOX-PCR cluster constituted a novel species within the genus Ruegeria, for which the name Ruegeria scottomollicae sp. nov. is proposed. The DNA G+C content was 61.0+/-0.4 %. The type strain is LMG 24367T (=CCUG 55858T).},
doi = {10.1099/ijs.0.65843-0},
issue = {12},
pmid = {19060048}
}
@article{YiEtAl2007b,
year = {2007},
journal = {Int J Syst Evol Microbiol},
volume = {57},
pages = {815-819},
author = {Yi, H. and Lim, Y.W. and Chun, J.},
title = {Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999.},
abstract = {The taxonomic positions of the genera Ruegeria and Silicibacter were evaluated by a polyphasic investigation. It was evident from 16S rRNA gene sequence analysis that both genera are closely related as they formed a monophyletic clade with high sequence similarities (96.9-98.2 %). Several properties commonly found in these taxa strongly suggest that they should be classified in the same genus. Further, a comparative study based on DNA-DNA hybridization, phenotypic characterization and chemotaxonomic analysis indicated that the members of this clade, namely Ruegeria atlantica, Silicibacter lacuscaerulensis and Silicibacter pomeroyi, can be readily differentiated from each other. On the basis of the polyphasic data obtained in this study, all species of the genus Silicibacter should be transferred to the genus Ruegeria, since the latter has nomenclatural priority. It is therefore proposed that Silicibacter lacuscaerulensis and Silicibacter pomeroyi are transferred to the genus Ruegeria as Ruegeria lacuscaerulensis comb. nov. and Ruegeria pomeroyi comb. nov.},
doi = {10.1099/ijs.0.64568-0},
issue = {4},
pmid = {17392212}
}
@article{HiraishiEtAl1996a,
year = {1996},
journal = {Syst. Appl. Microbiol.},
volume = {19},
pages = {168-177},
author = {Hiraishi, A. and Muramatsu, K. and Ueda, Y.},
title = {Molecular genetic analyses of Rhodobacter azotoformans sp. nov. and related species of phototrophic bacteria.},
doi = {10.1016/s0723-2020(96)80042-7}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{SureshEtAl2019a,
year = {2019},
journal = {Front Microbiol},
volume = {10},
pages = {2480},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.},
doi = {10.3389/fmicb.2019.02480},
pmid = {31736915}
}
@article{SureshEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {1111},
author = {Suresh, G. and Lodha, T.D. and Indu, B. and Sasikala, C. and Ramana, C.V.},
title = {Corrigendum: Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.02480.].},
doi = {10.3389/fmicb.2020.01111},
pmid = {32582079}
}
@article{ChoGiovannoni2006a,
year = {2006},
journal = {Int J Syst Evol Microbiol},
volume = {56},
pages = {855-859},
author = {Cho, J.C. and Giovannoni, S.J.},
title = {Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales.},
abstract = {A Gram-negative, chemoheterotrophic, facultatively anaerobic, slightly halophilic, oval-shaped marine bacterium, designated HTCC2601T, was isolated from the western Sargasso Sea by high-throughput culturing involving dilution to extinction. Although the 16S rRNA gene sequence similarity between the isolate and Salipiger mucosus was 96.5 %, phylogenetic analyses using different treeing algorithms clearly indicated that the strain forms a distinct lineage within a clade containing the recently classified genera Salipiger and Palleronia in the order Rhodobacterales of the Alphaproteobacteria. The DNA-DNA relatedness between strain HTCC2601T and S. mucosus was 26.3 %. Strain HTCC2601T utilized a wide range of carbohydrates, including hexose monomers, sugar alcohols, organic acids and amino acids, as sole carbon sources. The DNA G+C content of strain HTCC2601T was 65.4 mol%, and the predominant constituents of the cellular fatty acids were 18 : 1omega7c (79.7 %) and 11-methyl 18 : 1omega7c (7.5 %). The strain differed from members of the closely related genera Salipiger and Palleronia in its morphological, biochemical and ecological characteristics. On the basis of the taxonomic data obtained in this study, a novel genus and species, Pelagibaca bermudensis gen. nov., sp. nov., is proposed; HTCC2601T (=KCTC 12554T = JCM 13377T) is the type strain of Pelagibaca bermudensis.},
doi = {10.1099/ijs.0.64063-0},
issue = {4},
pmid = {16585706}
}
@article{HordtEtAl2020a,
year = {2020},
journal = {Front Microbiol},
volume = {11},
pages = {468},
author = {Hordt, A. and Lopez, M.G. and Meier-Kolthoff, J.P. and Schleuning, M. and Weinhold, L.M. and Tindall, B.J. and Gronow, S. and Kyrpides, N.C. and Woyke, T. and Goker, M.},
title = {Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.},
abstract = {The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.},
doi = {10.3389/fmicb.2020.00468},
pmid = {32373076}
}
@article{WirthWhitman2018a,
year = {2018},
journal = {Int J Syst Evol Microbiol},
volume = {68},
pages = {2393-2411},
author = {Wirth, J.S. and Whitman, W.B.},
title = {Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera.},
abstract = {Roseobacters are a diverse and globally abundant group of Alphaproteobacteria within the Rhodobacteraceae family. Recent studies and the cophenetic correlations suggest that the 16S rRNA genes are poor phylogenetic markers within this group. In contrast, the cophenetic correlation coefficients of the core-gene average amino acid identity (cAAI) and RpoC protein sequences are high and likely more predictive of relationships. A maximum-likelihood phylogenetic tree calculated from 53 core genes demonstrated that some of the current genera were either polyphyletic or paraphyletic. The boundaries of bacterial genera were redefined based upon the cAAI, the percentage of conserved proteins, and phenotypic characteristics and resulted in the following taxonomic proposals. Loktanella vestfoldensis, Loktanella litorea, Loktanella maricola, Loktanella maritima, Loktanella rosea, Loktanella sediminilitoris, Loktanella tamlensis, and Roseobacter sp. CCS2 should be reclassified into the novel genus Yoonia. Loktanella hongkongensis, Loktanella aestuariicola, Loktanella cinnabarina, Loktanella pyoseonensis, Loktanellasoe soekkakensis and Loktanella variabilis should be reclassified in the novel genus Limimaricola. Loktanella koreensis and Loktanella sediminum should be reclassified in the novel genus Cognatiyoonia. Loktanella marina should be reclassified in the novel genus Flavimaricola. Aestuariivita atlantica should be reclassified in the novel genus Pseudaestuariivita. Thalassobius maritima should be reclassified in the novel genus Cognatishimia. Similarly, Ruegeria mobilis, Ruegeria scottomollicae, Ruegeria sp. TM1040 and Tropicibacter multivorans should be reclassified in the genus Epibacterium. Tropicibacter litoreus and Tropicibacter mediterraneus should be reclassified in the genus Ruegeria. Thalassobius abyssi and Thalassobius aestuarii should be reclassified in the genus Shimia. Citreicella aestuarii, Citreicella manganoxidans, Citreicella marina, Citreicella thiooxidans, Pelagibaca bermudensis and Thiobacimonas profunda should be reclassified in the genus Salipiger. Nautella italica should be reclassified in the genus Phaeobacter. Because these proposals to reclassify the type and all others species of Citreicella, Nautella, Pelagibaca and Thiobacimonas, these genera are not used in this taxonomy.},
doi = {10.1099/ijsem.0.002833},
issue = {7},
pmid = {29809121}
}