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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 3

sp. nov., a thermophilic bacterium isolated from a hot spring Free

Abstract

A thermophilic bacterium, designated SYSU G03088, was isolated from Moincer hot spring, Tibet, PR China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position and genomic profiles of the strain. Phylogenetic analysis using 16S rRNA gene sequence indicated that SYSU G03088 showed highest sequence similarity to CGMCC 1.3365 (96.0 % sequence identity). The strain could be differentiated from most recognized species of the genus by its slightly purple colony colour, distinct phenotypic characters and low ANI values. Cells were Gram-staining negative, and oval-to-rod shaped. Poly-β-hydroxybutyrate and vesicular intracytoplasmic membrane structures were formed inside cells. Growth occurred optimally at 45 °C and pH 7.0. Ubiquinone 10 was the only respiratory quinone. The major fatty acids (>10 %) were C, Cω7 11-methyl and summed feature 8 (Cω7 and/or Cω6). The detected polar lipids of SYSU G03088 included diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmethylethanolamine. The DNA G+C content of SYSU G03088 was 67.7 % (genome). On the basis of the differences in the phenotypic characteristics and phylogenetic analyses, SYSU G03088 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU G03088 (=CGMCC 1.16876=KCTC 72354).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): Genome sequencing , hot spring , Polyphasic taxonomy , Rhodobacter flagellatus sp. nov. and Tibet
Funding
This study was supported by the:
  • Guangdong Province Introduction of Innovative R&D Team (CN) (Award 2018B020206001)
    • Principle Award Recipient: Wen-Jun Li
  • Science and Technology Program of Guangzhou, China (Award 201803030030)
    • Principle Award Recipient: Wen-Jun Li
  • National Natural Science Foundation of China (Award 91951205)
    • Principle Award Recipient: Wen-Jun Li
© 2020 Sun Yat-Sen University, PR China
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2019-12-20
2024-04-19
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References

  1. Garrity GM, Bell JA, Lilburn T. Family I. Rhodobacteraceae fam. nov. Bergey’s Manual of Systematic Bacteriology 2, 2nd edn. New York: Springer; 2005 pp 161–228
     [Google Scholar]
  2. 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 [View Article]
     [Google Scholar]
  3. Hansen TA, Imhoff JF. Rhodobacter veldkampii, a new species of phototrophic purple nonsulfur bacteria. Int J Syst Bacteriol 1985; 35:115–116 [View Article]
     [Google Scholar]
  4. Suresh G, Sailaja B, Ashif A, Dave BP, Sasikala C et al. Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov. Int J Syst Evol Microbiol 2017; 67:3289–3295 [View Article]
     [Google Scholar]
  5. Raj PS, Ramaprasad EVV, Vaseef S, Sasikala C, Ramana CV. Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream. Int J Syst Evol Microbiol 2013; 63:181–186 [View Article]
     [Google Scholar]
  6. van Niel CB. The culture, general physiology, morphology, and classification of the non-sulfur purple and brown bacteria. Bacteriol Rev 1944; 8:1–118
     [Google Scholar]
  7. Subhash Y, Lee S-S. Rhodobacter sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:2965–2970 [View Article]
     [Google Scholar]
  8. Srinivas TNR, Anil Kumar P, Sasikala C, Spröer C, Ramana CV. Rhodobacter ovatus sp. nov., a phototrophic alphaproteobacterium isolated from a polluted pond. Int J Syst Evol Microbiol 2008; 58:1379–1383 [View Article]
     [Google Scholar]
  9. Girija KR, Sasikala C, Ramana CV, Spröer C, Takaichi S et al. Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils. Int J Syst Evol Microbiol 2010; 60:2099–2107 [View Article]
     [Google Scholar]
  10. Venkata Ramana V, Sasikala C, Ramana CV. Rhodobacter maris sp. nov., a phototrophic alphaproteobacterium isolated from a marine habitat of India. Int J Syst Evol Microbiol 2008; 58:1719–1722 [View Article]
     [Google Scholar]
  11. Venkata Ramana V, Anil Kumar P, Srinivas TNR, Sasikala C, Ramana CV. Rhodobacter aestuarii sp. nov., a phototrophic alphaproteobacterium isolated from an estuarine environment. Int J Syst Evol Microbiol 2009; 59:1133–1136 [View Article]
     [Google Scholar]
  12. Hiraishi A, Muramatsu K, Ueda Y. Molecular genetic analyses of Rhodobacter azotoformans sp. nov. and related species of phototrophic bacteria. Syst Appl Microbiol 1996; 19:168–177 [View Article]
     [Google Scholar]
  13. Srinivas TNR, Anil Kumar P, Sasikala C, Ramana CV, Imhoff JF. Rhodobacter vinaykumarii sp. nov., a marine phototrophic alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter . Int J Syst Evol Microbiol 2007; 57:1984–1987 [View Article]
     [Google Scholar]
  14. Gandham S, Lodha T, Chintalapati S, Chintalapati VR. Rhodobacter alkalitolerans sp. nov., isolated from an alkaline brown pond. Arch Microbiol 2018; 200:1487–1492 [View Article]
     [Google Scholar]
  15. Kawasaki H, Hoshino Y, Hirata A, Yamasato K. Is intracytoplasmic membrane structure a generic criterion? it does not coincide with phylogenetic interrelationships among phototrophic purple nonsulfur bacteria. Arch Microbiol 1993; 160:358–362 [View Article]
     [Google Scholar]
  16. Arunasri K, Venkata Ramana V, Spröer C, Sasikala C, Ramana CV. Rhodobacter megalophilus sp. nov., a phototroph from the Indian Himalayas possessing a wide temperature range for growth. Int J Syst Evol Microbiol 2008; 58:1792–1796 [View Article]
     [Google Scholar]
  17. Wang D, Liu H, Zheng S, Wang G. Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter . Int J Syst Evol Microbiol 2014; 64:551–558 [View Article]
     [Google Scholar]
  18. Khan IU, Habib N, Xiao M, Li M-M, Xian W-D et al. Rhodobacter thermarum sp. nov., a novel phototrophic bacterium isolated from sediment of a hot spring. Antonie Van Leeuwenhoek 2019; 112:867–875 [View Article]
     [Google Scholar]
  19. Visvesvara GS, Balamuth W. Comparative studies on related free-living and pathogenic amebae with special reference to Acanthamoeba . Journal of Eukaryotic Microbiology 1975; 22:245–256
     [Google Scholar]
  20. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993
     [Google Scholar]
  21. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
     [Google Scholar]
  22. Smibert RA, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, D.C: American Society of Microbiology; 1994 pp 607–654
     [Google Scholar]
  23. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
     [Google Scholar]
  24. Groth I, Schumann P, Rainey FA, Martin K, Schuetze B et al. Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 1997; 47:1129–1133 [View Article]
     [Google Scholar]
  25. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  26. Pfennig N, Trüper HG. Isolation of members of the families Chromatiaceae and Chlorobiaceae . In Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG. (editors) The Prokaryotes: A Handbook on Habitats, Isolation, and Identification of Bacteria Berlin, Heidelberg: Springer Berlin Heidelberg; 1981 pp 279–289
     [Google Scholar]
  27. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article]
     [Google Scholar]
  28. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article]
     [Google Scholar]
  29. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
     [Google Scholar]
  30. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75:7537–7541 [View Article]
     [Google Scholar]
  31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  33. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  34. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  35. 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 [View Article]
     [Google Scholar]
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  37. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article]
     [Google Scholar]
  38. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article]
     [Google Scholar]
  39. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article]
     [Google Scholar]
  40. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  41. 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 [View Article]
     [Google Scholar]
  42. Wu Y-W. ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes. BMC Genomics 2018; 19:8–16 [View Article]
     [Google Scholar]
  43. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article]
     [Google Scholar]
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Rhodobacter flagellatus sp. nov., a thermophilic bacterium isolated from a hot spring
Int J Syst Evol Microbiol 70, 1541 (2020); https://doi.org/10.1099/ijsem.0.003929
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