1887

Abstract

An obligate aerobic and bacteriochlorophyll -containing bacterium, designated strain AI77, was isolated from a fish farm in Uwa Sea, Japan. Cells were Gram-stain-negative, coccoid- to oval-shaped, and showed no motility. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AI77 is a member of the genus and closely related to MM-7 (97.8 %), OCh 114 (97.3 %) and OCh 149 (97.3 %). The G+C content of strain AI77 was 61.0 mol%. The average amino acid identity values of the genome in strain AI77 with those in OCh 114 and OCh 149 were 73.26 % (SD 16.46) and 72.63 % (SD 16.76), respectively. The digital DNA–DNA hybridization values of strain AI77 with the type strains OCh 114 and OCh 149 were 18.70 and 18.50 %, respectively. The dominant fatty acids (>10 % of total fatty acids) of AI77 were summed feature 8 (C ω7 and/or C ω6) and saturated fatty acid C. The sole respiratory quinone was ubiquinone-10. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. Based on the genetic and phenotypic data obtained herein, we conclude that strain AI77 represents a new species of the genus , for which we propose the name sp. nov.; the type strain is AI77 (=DSM 110091=NBRC 114115).

Funding
This study was supported by the:
  • So Muramatsu , the Institute for Fermentation, Osaka
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2020-07-30
2020-12-01
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References

  1. Beatty JT. On the natural selection and evolution of the aerobic phototrophic bacteria. Photosynth Res 2002; 73:109–114 [CrossRef][PubMed]
    [Google Scholar]
  2. Lami R, Cottrell MT, Ras J, Ulloa O, Obernosterer I et al. High abundances of aerobic anoxygenic photosynthetic bacteria in the South Pacific Ocean. Appl Environ Microbiol 2007; 73:4198–4205 [CrossRef][PubMed]
    [Google Scholar]
  3. Ritchie AE, Johnson ZI. Abundance and genetic diversity of aerobic anoxygenic phototrophic bacteria of coastal regions of the Pacific Ocean. Appl Environ Microbiol 2012; 78:2858–2866 [CrossRef][PubMed]
    [Google Scholar]
  4. Lamy D, Jeanthon C, Cottrell MT, Kirchman DL, Van Wambeke F et al. Ecology of aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean sea. Biogeosciences 2011; 8:973–985 [CrossRef]
    [Google Scholar]
  5. Kolber ZS, Plumley FG, Lang AS, Beatty JT, Blankenship RE et al. Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 2001; 292:2492–2495 [CrossRef][PubMed]
    [Google Scholar]
  6. Cottrell MT, Kirchman DL. Photoheterotrophic microbes in the Arctic Ocean in summer and winter. Appl Environ Microbiol 2009; 75:4958–4966 [CrossRef][PubMed]
    [Google Scholar]
  7. Yurkov V, Csotonyi JT. New Light on Aerobic Anoxygenic Phototrophs. In Dordrecht C, Hunter Neil, Daldal Fevzi, Thurnauer MarionC, Thomas Beatty J. (editors) The Purple Phototrophic Bacteria Advances in Photosynthesis and Respiration Springer; 2008 pp 31–55
    [Google Scholar]
  8. Yurkov V, Hughes E. Aerobic anoxygenic phototrophs: Four decades of mystery. In: Modern Topics in the Phototrophic Prokaryotes: Environmental and Applied Aspects . Springer International Publishing 2017 pp. 193–214
    [Google Scholar]
  9. Zeng Y, Feng F, Medová H, Dean J, Koblížek M. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes . Proc Natl Acad Sci U S A 2014; 111:7795–7800 [CrossRef][PubMed]
    [Google Scholar]
  10. Sato-Takabe Y, Nakao H, Kataoka T, Yokokawa T, Hamasaki K et al. Abundance of common aerobic anoxygenic phototrophic bacteria in a coastal aquaculture area. Front Microbiol 1996; 2016:7
    [Google Scholar]
  11. Woese CR. Bacterial evolution. Microbiol Rev 1987; 51:221–271 [CrossRef][PubMed]
    [Google Scholar]
  12. Shiba T. Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a. Syst Appl Microbiol 1991; 14:140–145 [CrossRef]
    [Google Scholar]
  13. Jung Y-T, Park S, Lee J-S, Yoon J-H. Roseobacter ponti sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:2189–2194 [CrossRef][PubMed]
    [Google Scholar]
  14. Zobelle CE. Studies on marine bacteria. I-The cultural requirements of heterotrophic aerobes. J Mar Res 1941; 4:42–75
    [Google Scholar]
  15. Hirose S, Matsuura K, Haruta S. Phylogenetically diverse aerobic anoxygenic phototrophic bacteria isolated from epilithic biofilms in TamA river, Japan. Microbes Environ 2016; 31:299–306 [CrossRef][PubMed]
    [Google Scholar]
  16. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406-25 [CrossRef][PubMed]
    [Google Scholar]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783 [CrossRef][PubMed]
    [Google Scholar]
  21. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  22. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  23. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [CrossRef][PubMed]
    [Google Scholar]
  24. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: the United States department of energy systems biology knowledgebase. Nat Biotechnol 2018; 36:566–569 [CrossRef][PubMed]
    [Google Scholar]
  25. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [CrossRef][PubMed]
    [Google Scholar]
  26. Hamada M, Iino T, Iwami T, Harayama S, Tamura T et al. Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., two new members of the family Dermatophilaceae, and reclassification of Dermatophilus chelonae (masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov. J Gen Appl Microbiol 2010; 56:427–436 [CrossRef]
    [Google Scholar]
  27. Takaichi S, Shimada K. Characterization of carotenoids in photosynthetic bacteria. Methods Enzymol 1992; 213:374–385
    [Google Scholar]
  28. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [CrossRef]
    [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  30. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e7312 [CrossRef][PubMed]
    [Google Scholar]
  31. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  32. Hahnke S, Tindall BJ, Schumann P, Simon M, Brinkhoff T. Pelagimonas varians gen. nov., sp. nov., isolated from the southern North sea. Int J Syst Evol Microbiol 2013; 63:835–843 [CrossRef][PubMed]
    [Google Scholar]
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