1887

Abstract

The genus , containing purple nonsulfur photosynthetic Proteobacteria, has a number of strains that belong to different species, although many of them are collectively called . The type species and closely related species are the focus of this paper. The comparison of available genome sequences indicate that the following species are well recognized: (strains ATH 2.1.6=DSM 123=NBRC 100419 and BisB5), (strains R1, DSM 126, CGA009, ATH 2.1.37, Eli 1980, ATCC 17001 and TIE1), JA575 and JCM 11668. Other strains for which genome sequences are available are distinct from these four species. Evidence is presented that strain ATH 2.1.6–KCM as obtained directly from the van Niel collection by one of us (T.E.M.) is identical to the DSMZ deposit DSM 123 of ATH 2.1.6, but not to the deposit at ATCC 17001. The amino acid sequences of the cytochromes C2 and C556 from strain ATH 2.1.6–KCM are in complete agreement with the translated genome sequences of DSM 123. In addition, the 16S rRNA gene sequence of NBRC 100419 completely matches that of strain DSM 123. In conclusion, the type strain of ATH 2.1.6 is correctly represented by DSM 123 and NBRC 100419. However, the deposit at ATCC 17001 has properties that do not conform with properties of authentic , but rather indicate that this is a strain of . The previously suggested assignment of the type strain of DSM 123 to the new species was incorrect because strain DSM 123 is the authentic type strain of .

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2020-06-04
2020-07-02
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References

  1. van Niel CB. The culture, general physiology, morphology, and classification of the non-sulfur purple and brown bacteria. Bacteriol Rev 1944; 8:1–118 [CrossRef][PubMed]
    [Google Scholar]
  2. Pfennig N, Trüper HG. Type and neotype strains of the species of phototrophic bacteria maintained in pure culture. Int J Syst Bacteriol 1971; 21:19–24 [CrossRef]
    [Google Scholar]
  3. Imhoff JF, Trüper HG, Pfennig N. Rearrangement of the species and genera of the phototrophic "Purple Nonsulfur Bacteria". Int J Syst Bacteriol 1984; 34:340–343 [CrossRef]
    [Google Scholar]
  4. Imhoff JF. The phototrophic alpha-Proteobacteria. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. (editors) The Prokaryotes. an Evolving Electronic Resource for the Microbiological Community, 3rd ed. New York: Springer Verlag; 2001
    [Google Scholar]
  5. Imhoff JF. Genus Rhodopseudomonas. Bergey’s Manual of Systematic Bacteriology 2, Part C, 2nd ed. 2005 pp 473–476
    [Google Scholar]
  6. Akiba T, Usami R, Horikoshi K. Rhodopseudomonas rutila, a new species of nonsulfur purple photosynthetic bacteria.. Int J Syst Bacteriol 1983; 33:551–556 [CrossRef]
    [Google Scholar]
  7. Zhang D, Yang H, Huang Z, Zhang W, Liu S-J. Rhodopseudomonas faecalis sp. nov., a phototrophic bacterium isolated from an anaerobic reactor that digests chicken faeces. Int J Syst Evol Microbiol 2002; 52:2055–2060 [CrossRef][PubMed]
    [Google Scholar]
  8. Kumar BV, Ramprasad EVV, Sasikala C, Ramana CV. Rhodopseudomonas pentothenatexigens sp. nov. and Rhodopseudomonas thermotolerans sp. nov., isolated from paddy soils. Int J Syst Evol Microbiol 2013; 63:200–207 [CrossRef][PubMed]
    [Google Scholar]
  9. Ramana VV, Chakravarthy SK, Raj PS, Kumar BV, Shobha E et al. Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris . Int J Syst Evol Microbiol 2012; 62:1790–1798 [CrossRef][PubMed]
    [Google Scholar]
  10. Hiraishi A, Santos TS, Sugiyama J, Komagata K. Rhodopseudomonas rutila is a later subjective synonym of Rhodopseudomonas palustris . Int J Syst Bacteriol 1992; 42:186–188 [CrossRef]
    [Google Scholar]
  11. Okamura K, Takata K, Hiraishi A. Intrageneric relationships of members of the genus Rhodopseudomonas . J Gen Appl Microbiol 2009; 55:469–478 [CrossRef][PubMed]
    [Google Scholar]
  12. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  13. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [CrossRef][PubMed]
    [Google Scholar]
  14. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef]
    [Google Scholar]
  15. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758–771 [CrossRef][PubMed]
    [Google Scholar]
  16. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  17. Letunic I, Bork P. Interactive tree of life (iTOL) V4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [CrossRef][PubMed]
    [Google Scholar]
  18. Adessi A, Spini G, Presta L, Mengoni A, Viti C et al. Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL. Stand Genomic Sci 2016; 11:24 [CrossRef][PubMed]
    [Google Scholar]
  19. Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S et al. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris . Nat Biotechnol 2004; 22:55–61 [CrossRef][PubMed]
    [Google Scholar]
  20. Robertson S, Rayyan A, Meyer T, Kyndt J. Draft whole-genome sequence of the purple nonsulfur photosynthetic bacterium, Rhodopseudomonas rutila R1. Microbiol Resour Announc 2018; 7:e01267–18 [CrossRef][PubMed]
    [Google Scholar]
  21. Göker M, Huntemann M, Clum A, Pillay M, Palaniappan K et al. Rhodopseudomonas faecalis strain JCM 11668. Whole genome shotgun sequence, unpublished; 2018
  22. Ambler RP, Daniel M, Hermoso J, Meyer TE, Bartsch RG et al. Cytochrome c2 sequence variation among the recognised species of purple nonsulphur photosynthetic bacteria. Nature 1979; 278:659–660 [CrossRef][PubMed]
    [Google Scholar]
  23. Ambler RP, Bartsch RG, Daniel M, Kamen MD, McLellan L et al. Amino acid sequences of bacterial cytochromes c' and c-556. Proc Natl Acad Sci U S A 1981; 78:6854–6857 [CrossRef][PubMed]
    [Google Scholar]
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