The phylogeny of purple bacteria: The alpha subdivision

Woese, Carl R.; Stackebrandt, Erko; Weisburg, William G.; Paster, Bruce J.; Madigan, Michael T.; Fowler, Valerie J.; Hahn, Christoph; Blanz, Paul; Gupta, Ramesh C.; Nealson, Kenneth H.; Fox, George E.

doi:10.1016/s0723-2020(84)80034-x

Cited by 387 publications

(183 citation statements)

References 23 publications

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“…However, attention should be paid to the fact that the genus Rhodopseudomonas itself is an assemblage of phylogenetically heterogeneous species. The present study and other phylogenetic studies by 16s rRNA cataloging (29,34) and sequencing (24,33,35) demonstrate that the type species R. palustris is more closely related to some chemotrophic taxa, i.e., Ajipia felis, Bradyrhizobium japonicum, Blastobacter denitrijicans, and Nitrobacter winogradskyi, than to any of the other Rhodopseudomonas species for which sequence formation is available. Our data also show that the new isolates and R. rosea belong to a lineage distinct from that of R. palushis and all other Rhodopseudomonas species compared.…”

Section: Discussionsupporting

confidence: 68%

“…In spite of their morphological and structural similarities, Rhodopseudomonas species are phylogenetically quite diverse. Comparisons of rRNA, i.e., DNA-rRNA hybridization and 16s rRNA cataloging and sequencing, have demonstrated that these bacteria belong to several different lines of descent within the alpha-2 subclass of the Proteobacteria (2,33,34). Exceptionally, Rhodopseudomonas blastica is a member of the alpha-3 subclass, closely related to Rhodobacter species (14,18), and this situation has led to the proposal for transfer of R. blastica to the genus Rhodobacter (18).…”

mentioning

confidence: 99%

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Rhodoplanes gen. nov., a New Genus of Phototrophic Bacteria Including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov.

Hiraishi¹,

Ueda²

1994

International Journal of Systematic Bacteriology

106

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Section: Discussionsupporting

confidence: 68%

mentioning

confidence: 99%

Rhodoplanes gen. nov., a New Genus of Phototrophic Bacteria Including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov.

Hiraishi¹,

Ueda²

1994

International Journal of Systematic Bacteriology

106

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“…However, the 16S rRNA gene sequence of Beijerinckia indica subsp. indica (Woese et al, 1984) has until now been the only Beijerinckia sequence available in public-domain databases. We have determined the 16S rRNA gene sequences for four other representatives of this genus: Beijerinckia indica subsp.…”

Section: Phylogeny Of Acidophilic Mb Based On the 16s Rrna Genementioning

confidence: 99%

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

2004

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The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus Beijerinckia. To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98?5 and 96?6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition. This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M. acidiphila B2 and Beijerinckia spp. are capable of active growth on nitrogen-free media under fully aerobic conditions.

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“…The a-Proteobacteria have been divided into four groups (a1, a2, a3 and a4) that have been historically used in the taxonomy of a-Proteobacteria (Woese et al, 1984;Bhat et al, 1991;Kosako et al, 2000;Ruiz et al, 2000). Recently, the second edition of Bergey's Manual of Systematic Bacteriology proposed that the class a-Proteobacteria should be divided into six orders: Rhodospirillales, Rickettsiales, Caulobacterales, 'Rhodobacterales', 'Sphingomonadales' and 'Rhizobiales', on the basis of 16S rRNA gene sequences (Garrity & Holt, 2001).…”

Section: Polyphasic Taxonomy Of the Novel Strainsmentioning

confidence: 99%

Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria

Cho

Giovannoni

2003

International Journal of Systematic and Evolutionary Microbiology

126

123

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Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the a-Proteobacteria Jang-Cheon Cho and Stephen J. Giovannoni CorrespondenceStephen J. Giovannoni steve.giovannoni@orst.edu Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA Two bacterial strains, HTCC2503 T and HTCC2517, were isolated from the Bermuda Atlantic Time Series Station in the western Sargasso Sea, Atlantic Ocean, by new high-throughput culture methods that rely on dilution to extinction in very-low-nutrient media. Characterization of the two strains by polyphasic approaches revealed that they belonged to the same species. These isolates are Gram-negative, strictly aerobic, chemoheterotrophic, slightly motile short rods with a single flagellum. The temperature, pH and NaCl concentration ranges for growth were 10-37˚C, 6?0-9?0 and 0?75-20 % (w/v), respectively. Colonies on marine agar were very small (0?3-0?8 mm in diameter), yellowish-brown and very hard. Carotenoid pigments were synthesized but bacteriochlorophyll a was not. Several kinds of pentose, hexose, sugar alcohol, oligosaccharide and amino acid were utilized as sole carbon sources. Oxidase was produced, but catalase was not. All cellular fatty acids were even-numbered monounsaturated or saturated fatty acids and the major fatty acid was cis-7-octadecenoic acid (73?3 %). The DNA G+C content of strain HTCC2503 T was 60?8 mol%. Phylogenetic analyses of 16S rRNA gene sequences clearly indicated that the strains formed a distinct lineage, allied with activated sludge environmental clone H9, in the a-Proteobacteria. The clade containing strains HTCC2503 T and HTCC2517 and clone H9 could not be phylogenetically associated with any of the six known orders of the a-Proteobacteria. From this polyphasic evidence, it is proposed that the novel strains should be classified as Parvularcula bermudensis gen. nov., sp. nov. The type strain is HTCC2503 T (=ATCC BAA-594 T =KCTC 12087 T ) and the reference strain is HTCC2517. INTRODUCTIONIt is generally accepted that standard plate-count methods on solid-surface media recover <1 % of all microbial cells from marine environments (Kogure et al., 1979;Ferguson et al., 1984). Molecular biological tools, such as 16S rRNA gene cloning and sequencing, have elucidated this issue for a decade (Giovannoni et al., 1990;DeLong, 1992;Suzuki et al., 1997; Béjà et al., 2000), and have led to the conclusion that the most abundant marine microbial groups are as yet uncultivated and probably play a significant role in marine biogeochemical cycling (Giovannoni & Rappé, 2000). Acquisition of pure cultures for the study of their physiology, ecology and taxonomy is an important goal of research in this field. Recently, high-throughput culture (HTC) methods were developed, which allowed large numbers of microbial isolates to be recovered by dilution to extinction in natural sea-water media . The first cultured representative of the SAR11 clade (Rappé et al., 2002) and many novel strains in the Proteobacteria were ...

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The phylogeny of purple bacteria: The alpha subdivision

Cited by 387 publications

References 23 publications

Rhodoplanes gen. nov., a New Genus of Phototrophic Bacteria Including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov.

Rhodoplanes gen. nov., a New Genus of Phototrophic Bacteria Including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov.

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria

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