1887

International Journal of Systematic and Evolutionary Microbiology

Volume 70, Issue 1

gen. nov., sp. nov., a nonphotosynthetic bacterium isolated from oil-contaminated soil Free

Abstract

A nonphotosynthetic, Gram-stain-negative, rod-shaped and motile strain, designated Pet-1, was isolated from oil-contaminated soil collected from Daqing oil field in China. Optimal growth occurred at 37 °C, pH 5.5 and in 1 % (w/v) NaCl. Q-10 was the sole respiratory quinone. The most abundant fatty acid was Cɷ7/Cɷ6 (67.4 %). The major polar lipids were phosphatidylglycerol, aminolipid, phosphatidylethanolaine, phosphatidycholine, two unidentified lipids and two unidentified phospholipids. The genomic DNA G+C content was 69.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that Pet-1 shared the highest similarity (95.1 %) to DSM 18714, followed by sk2b1 (95.0 %) and CCUG 47968 (95.0 %). In the phylogenetic tree, strain Pet-1 formed a separate branch from the closely related genera and within the family . Based on the data from the current polyphasic study, it is proposed that the isolate is a novel species of a novel genus within the family , with the name gen. nov., sp. nov. The type strain of the type species is Pet-1 (=KCTC 72074 =CCTCC AB 2018368).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): nonphotosynthetic bacterium , oil-contaminated soil , Rhodobacteraceae , Solirhodobacter and Solirhodobacter olei
Funding
This study was supported by the:
  • Natural Science Foundation of China (Award No. 31800097)
  • Sciency and Technology Agency of Henan (Award No. 192102310493)
  • Education Department of Henan Province, http://dx.doi.org/10.13039/501100009101 (Award No. 19A180010)
© 2020 The Authors
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2020-02-03
2021-10-24
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References

  1. Garrity G, Bel IJ. Family I. Rhodobacteraceae fam. nov.. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology The Proteobacteria, Part C, The Alpha, -Beta, -Delta and Epsilonproteobacteria 2, 2nd ed. New York: Springer; 2005 pp 161–229
     [Google Scholar]
  2. Parte AC. LPSN – list of prokaryotic names with standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
     [Google Scholar]
  3. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC et al. The family Rhodobacteraceae . The Prokaryotes–Alphaproteobacteria and Betaproteobacteria Berlin: Springer Verlag; 2014 pp 439–512
     [Google Scholar]
  4. Li N, Chen T, Cheng D, Xu XJ, He J. Chitinophaga sedimenti sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2017; 67:3485–3489 [View Article]
     [Google Scholar]
  5. Moore DD, Dowhan D. Preparation and analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD. eds Current Protocols in Molecular Biology New York: Wiley; 1995 pp 2–11
     [Google Scholar]
  6. Lane DL. 16S/23S rRNA sequencing. In Stackebrandt ER, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–175
     [Google Scholar]
  7. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article]
     [Google Scholar]
  8. 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]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  10. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  11. 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]
  12. 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]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  14. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  15. Lakshmi KVNS, Sasikala C, Ramana CV. Rhodoplanes pokkaliisoli sp. nov., a phototrophic alphaproteobacterium isolated from a waterlogged brackish paddy soil. Int J Syst Evol Microbiol 2009; 59:2153–2157 [View Article]
     [Google Scholar]
  16. Biebl H, Pfennig N. Isolation of members of the family Rhodospirillaceae . In Starr MP, Stolp H, Tru¨per HG, Balows A. eds The Prokaryotes 1 New York: Springer; 1981 pp 267–273
     [Google Scholar]
  17. Albuquerque L, Santos J, Travassos P, Nobre MF, Rainey FA et al. Albidovulum inexpectatum gen. nov., sp. nov., a nonphotosynthetic and slightly thermophilic bacterium from a marine hot spring that is very closely related to members of the photosynthetic genus Rhodovulum . Appl Environ Microbiol 2002; 68:4266–4273 [View Article]
     [Google Scholar]
  18. Uchino Y, Hamada T, Yokota A. Proposal of Pseudorhodobacter ferrugineus gen. nov., comb. nov., for a non-photosynthetic marine bacterium, Agrobacterium ferrugineum, related to the genus Rhodobacter . J Gen Appl Microbiol 2002; 48:309–319 [View Article]
     [Google Scholar]
  19. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586
     [Google Scholar]
  20. Kuykendall LD, Roy MA, O'NEILL JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  21. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990a; 13:128–130 [View Article]
     [Google Scholar]
  22. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990b; 66:199–202 [View Article]
     [Google Scholar]
  23. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Marzluf JA, Schmidt TM. eds Methods for General and Molecular Microbiology, 3rd edn. Washington, DC: American Society of Microbiology; 2007 pp 330–393
     [Google Scholar]
  24. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
     [Google Scholar]
  25. Xu GT, Piao C, Chang JP, Guo LM, Yang XQ et al. Sinorhodobacter populi sp. nov., isolated from the symptomatic bark tissue of Populus × euramericana canker. Int J Syst Evol Microbiol 2019; 69:1220–1224 [View Article]
     [Google Scholar]
  26. Wang D, Liu H, Zheng S, Wang G. Paeni rhodobacter 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]
  27. Srinivas TNR, Kumar PA, 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]
  28. 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]
  29. 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]
  30. Subhash Y, Lee SS. Rhodobacter sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:2965–2970 [View Article]
     [Google Scholar]
  31. Yang G, Chen M, Zhou S, Liu Z, Yuan Y. Sinorhodobacter ferrireducens gen. nov., sp. nov., a non-phototrophic iron-reducing bacterium closely related to phototrophic Rhodobacter species. Antonie van Leeuwenhoek 2013; 104:715–724 [View Article]
     [Google Scholar]
  32. Xi L, Qiao N, Zhang Z, Yan L, Li F et al. Sinorhodobacter hungdaonensis sp. nov. isolated from activated sludge collected from a municipal wastewater treatment plant. Antonie van Leeuwenhoek 2017; 110:27–32 [View Article]
     [Google Scholar]
  33. Helsel LO, Hollis D, Steigerwalt AG, Morey RE, Jordan J et al. 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.". J Clin Microbiol 2007; 45:1238–1243 [View Article]
     [Google Scholar]
  34. Zhang S, Sun C, Xie J, Wei H, Hu Z et al. Defluviimonas pyrenivorans sp. nov. a novel bacterium capable of degrading polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 2018; 69:1220–1224
     [Google Scholar]
  35. Foesel BU, Drake HL, Schramm A. Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture. Syst Appl Microbiol 2011; 34:498–502 [View Article]
     [Google Scholar]
  36. Liu Y, Lai Q, Wang W, Shao Z. Defluviimonas nitratireducens sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:2752–2757 [View Article]
     [Google Scholar]
  37. Pan XC, Geng S, Lv XL, Mei R, Jiangyang JH et al. Defluviimonas alba sp. nov., isolated from an oilfield. Int J Syst Evol Microbiol 2015; 65:1805–1811 [View Article]
     [Google Scholar]
  38. Jiang L, Xu H, Shao Z, Long M. Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment. Int J Syst Evol Microbiol 2014; 64:2084–2088 [View Article]
     [Google Scholar]
  39. Jung YT, Park S, Lee JS, Yoon JH. Defluviimonas aquaemixtae sp. nov., isolated from the junction between a freshwater spring and the ocean. Int J Syst Evol Microbiol 2014; 64:4191–4197 [View Article]
     [Google Scholar]
  40. Divyasree B, Lakshmi KVNS, Bharti D, Sasikala C, Ramana CV. Rhodovulum aestuarii sp. nov., isolated from a brackish water body. Int J Syst Evol Microbiol 2016; 66:165–171 [View Article]
     [Google Scholar]
  41. Ramaprasad EVV, Tushar L, Dave B, Sasikala C, Ramana CV. Rhodovulum algae sp. nov., isolated from an algal mat. Int J Syst Evol Microbiol 2016; 66:3367–3371 [View Article]
     [Google Scholar]
  42. Srinivas A, Vinay Kumar B, Divya Sree B, Tushar L, Sasikala C et al. Rhodovulum salis sp. nov. and Rhodovulum viride sp. nov., phototrophic Alphaproteobacteria isolated from marine habitats. Int J Syst Evol Microbiol 2014; 64:957–962 [View Article]
     [Google Scholar]
  43. Lai Q, Liu X, Yuan J, Xie S, Shao Z. Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean. Int J Syst Evol Microbiol 2019; 69:932–936 [View Article]
     [Google Scholar]
  44. Wang XL, Zhao YN, Wang K, Du ZJ. Pararhodobacter oceanensis sp. nov., isolated from marine intertidal sediment and emended description of the genus Pararhodobacter . Int J Syst Evol Microbiol 2019; 69:866–870 [View Article]
     [Google Scholar]
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Solirhodobacter olei gen. nov., sp. nov., a nonphotosynthetic bacterium isolated from oil-contaminated soil
Int J Syst Evol Microbiol 70, 582 (2020); https://doi.org/10.1099/ijsem.0.003795
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