1887

Abstract

A strictly anaerobic Gram-stain-negative bacterium, designated strain SEBR 4223, was isolated from the production water of an offshore Congolese oil field. Cells were non-motile, pleomorphic and had spherical, annular or budding shapes, often exhibiting long stalks. Strain SEBR 4223 grew on a range of carbohydrates, optimally at 37 °C and pH 7, in a medium containing 40 g l NaCl. Predominant fatty acids were C, C DMA, C and Cω and the major polar lipids were phosphoglycolipids, phospholipids, glycolipids and diphosphatidylglycerol. The G+C content of the DNA was 28.7 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain SEBR 4223 and MO-SPC2 formed a cluster with similarity to other species of the genus of of less than 86 %. On the basis of the phenotypic characteristics and taxonomic analyses, we propose a novel genus, gen. nov., to accommodate the novel species sp. nov., with SEBR 4223 (=DSM 103077=JCM 31 475) as the type strain. We also propose the reclassification of MO SPC2 as MO-SPC2 comb. nov., the type strain of this novel genus and emend description of the genus .

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2017-02-01
2024-03-29
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References

  1. Magot M, Ollivier B, Patel BK. Microbiology of petroleum reservoirs. Antonie van Leeuwenhoek 2000; 77:103–116[PubMed] [CrossRef]
    [Google Scholar]
  2. Head IM, Jones DM, Larter SR. Biological activity in the deep subsurface and the origin of heavy oil. Nature 2003; 426:344–352 [View Article][PubMed]
    [Google Scholar]
  3. Huang H, Bowler BFJ, Zhang Z, Oldenburg TBP, Larter SR. Influence of biodegradation on carbazole and benzocarbazole distributions in oil columns from the Liaohe basin, NE China. Org Geochem 2003; 34:951–969 [View Article]
    [Google Scholar]
  4. Hallmann C, Schwark L, Grice K. Community dynamics of anaerobic bacteria in deep petroleum reservoirs. Nat Geosci 2008; 1:588–591 [View Article]
    [Google Scholar]
  5. Youssef N, Elshahed MS, McInerney MJ. Microbial processes in oil fields: culprits, problems, and opportunities. Adv Appl Microbiol 2009; 66:141–251 [View Article][PubMed]
    [Google Scholar]
  6. Gray ND, Sherry A, Hubert C, Dolfing J, Head IM. Methanogenic degradation of petroleum hydrocarbons in subsurface environments remediation, heavy oil formation, and energy recovery. Adv Appl Microbiol 2010; 72:137–161 [View Article][PubMed]
    [Google Scholar]
  7. Nazina TN, Shestakova NM, Pavlova NK, Tatarkin YV, Ivoilov VS et al. Functional and phylogenetic microbial diversity in formation waters of a low-temperature carbonate petroleum reservoir. Int Biodeterior Biodegradation 2013; 81:71–81 [View Article]
    [Google Scholar]
  8. Ollivier B, Cayol JL. The fermentative, iron-reducing, and nitrate-reducing microorganisms. In Ollivier B, Magot M. (editors) Petroleum Microbiology Washington, DC: American Society for Microbiology; 2005 pp. 71–88 [CrossRef]
    [Google Scholar]
  9. Davey ME, Wood WA, Key R, Nakamura K, Stahl DA. Isolation of three species of Geotoga and Petrotoga: Two new genera, representing a new lineage in the bacterial line of descent distantly related to the “Thermotogales”. Syst Appl Microbiol 1993; 16:191–200 [View Article]
    [Google Scholar]
  10. Miranda-Tello E, Fardeau ML, Thomas P, Ramirez F, Casalot L et al. Petrotoga mexicana sp. nov., a novel thermophilic, anaerobic and xylanolytic bacterium isolated from an oil-producing well in the Gulf of Mexico. Int J Syst Evol Microbiol 2004; 54:169–174 [View Article][PubMed]
    [Google Scholar]
  11. Cayol JL, Ollivier B, Patel BK, Ravot G, Magot M et al. Description of Thermoanaerobacter brockii subsp. lactiethylicus subsp. nov., isolated from a deep subsurface French oil well, a proposal to reclassify Thermoanaerobacter finnii as Thermoanaerobacter brockii subsp. finnii comb. nov., and an emended description of Thermoanaerobacter brockii. Int J Syst Bacteriol 1995; 45:783–789 [View Article][PubMed]
    [Google Scholar]
  12. Ravot G, Magot M, Fardeau ML, Patel BK, Prensier G et al. Thermotoga elfii sp. nov., a novel thermophilic bacterium from an African oil-producing well. Int J Syst Bacteriol 1995; 45:308–314 [View Article][PubMed]
    [Google Scholar]
  13. Ravot G, Magot M, Ollivier B, Patel BK, Ageron E et al. Haloanaerobium congolense sp. nov., an anaerobic, moderately halophilic, thiosulfate- and sulfur-reducing bacterium from an African oil field. FEMS Microbiol Lett 1997; 147:81–88 [View Article][PubMed]
    [Google Scholar]
  14. Fardeau ML, Ollivier B, Patel BK, Magot M, Thomas P et al. Thermotoga hypogea sp. nov., a xylanolytic, thermophilic bacterium from an oil-producing well. Int J Syst Bacteriol 1997; 47:1013–1019 [View Article][PubMed]
    [Google Scholar]
  15. Fardeau ML, Magot M, Patel BK, Thomas P, Garcia JL et al. Thermoanaerobacter subterraneus sp. nov., a novel thermophile isolated from oilfield water. Int J Syst Evol Microbiol 2000; 50:2141–2149 [View Article][PubMed]
    [Google Scholar]
  16. Grabowski A, Nercessian O, Fayolle F, Blanchet D, Jeanthon C. Microbial diversity in production waters of a low-temperature biodegraded oil reservoir. FEMS Microbiol Ecol 2005; 54:427–443 [View Article][PubMed]
    [Google Scholar]
  17. Tang YQ, Li Y, Zhao JY, Chi CQ, Huang LX et al. Microbial communities in long-term, water-flooded petroleum reservoirs with different in situ temperatures in the Huabei oilfield, China. PLoS One 2012; 7:e33535 [View Article][PubMed]
    [Google Scholar]
  18. Kobayashi H, Endo K, Sakata S, Mayumi D, Kawaguchi H et al. Phylogenetic diversity of microbial communities associated with the crude-oil, large-insoluble-particle and formation-water components of the reservoir fluid from a non-flooded high-temperature petroleum reservoir. J Biosci Bioeng 2012; 113:204–210 [View Article][PubMed]
    [Google Scholar]
  19. Gao P, Tian H, Li G, Sun H, Ma T. Microbial diversity and abundance in the Xinjiang Luliang long-term water-flooding petroleum reservoir. Microbiologyopen 2015; 4:332–342 [View Article]
    [Google Scholar]
  20. You J, Wu G, Ren F, Chang Q, Yu B et al. Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing. Appl Microbiol Biotechnol 2016; 100:1469–1478 [View Article]
    [Google Scholar]
  21. Magot M, Fardeau ML, Arnauld O, Lanau C, Ollivier B et al. Spirochaeta smaragdinae sp. nov., a new mesophilic strictly anaerobic spirochete from an oil field. FEMS Microbiol Lett 1997; 155:185–191 [View Article][PubMed]
    [Google Scholar]
  22. Ritalahti KM, Justicia-Leon SD, Cusick KD, Ramos-Hernandez N, Rubin M et al. Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes. Int J Syst Evol Microbiol 2012; 62:210–216 [View Article][PubMed]
    [Google Scholar]
  23. Abt B, Han C, Scheuner C, Lu M, Lapidus A et al. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci 2012; 6:194–209 [View Article][PubMed]
    [Google Scholar]
  24. Miyazaki M, Sakai S, Ritalahti KM, Saito Y, Yamanaka Y et al. Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta. Int J Syst Evol Microbiol 2014; 64:4147–4154 [View Article][PubMed]
    [Google Scholar]
  25. Troshina O, Oshurkova V, Suzina N, Machulin A, Ariskina E et al. Sphaerochaeta associata sp. nov., a spherical spirochaete isolated from cultures of Methanosarcina mazei JL01. Int J Syst Evol Microbiol 2015; 65:4315–4322 [View Article][PubMed]
    [Google Scholar]
  26. Caro-Quintero A, Ritalahti KM, Cusick KD, Löffler FE, Konstantinidis KT. The chimeric genome of Sphaerochaeta: nonspiral spirochetes that break with the prevalent dogma in spirochete biology. MBio 2012; 3:e00025-12 [View Article][PubMed]
    [Google Scholar]
  27. Charon NW, Cockburn A, Li C, Liu J, Miller KA et al. The unique paradigm of spirochete motility and chemotaxis. Annu Rev Microbiol 2012; 66:349–370 [View Article][PubMed]
    [Google Scholar]
  28. Dröge S, Fröhlich J, Radek R, König H. Spirochaeta coccoides sp. nov., a novel coccoid spirochete from the hindgut of the termite Neotermes castaneus. Appl Environ Microbiol 2006; 72:392–397 [View Article][PubMed]
    [Google Scholar]
  29. Bernard FP, Connan J, Magot M. Indigenous microorganisms in connate water of many oil fields: a new tool in exploration and production techniques. In Proceedings of the 67th Annual Technical Conference and Exhibition of the Society of Petroleum Engineers Paper SPE 24811 Richardson, TX: SPE; 1992 pp. 1–10
    [Google Scholar]
  30. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260–296[PubMed]
    [Google Scholar]
  31. Pfennig N, Widdel F, Truper HG. The dissimilatory sulfate-reducing bacteria. In Starr MP, Stolp H, Truper HG, Balows A, Schlegel HG. (editors) The Prokaryotes vol. 1 Berlin: Springer; 1981 pp. 926–940 [CrossRef]
    [Google Scholar]
  32. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp. 115–175
    [Google Scholar]
  33. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC et al. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 1998; 64:795–799[PubMed]
    [Google Scholar]
  34. 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][PubMed]
    [Google Scholar]
  35. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  36. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  37. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [CrossRef]
    [Google Scholar]
  38. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  39. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  40. Cline JD. Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol Oceanogr 1969; 14:454–458 [View Article]
    [Google Scholar]
  41. Schumann P. Peptidoglycan structure. Method Microbiol 2011; 38:101–129 [CrossRef]
    [Google Scholar]
  42. Jeske O, Schüler M, Schumann P, Schneider A, Boedeker C et al. Planctomycetes do possess a peptidoglycan cell wall. Nat Commun 2015; 6:7116 [View Article][PubMed]
    [Google Scholar]
  43. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  44. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM. et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp. 330–393
    [Google Scholar]
  45. Miller LT. A single derivatization method for bacterial fatty acid methyl esters including hydroxy acids. J Clin Microbiol 1982; 16:584–586
    [Google Scholar]
  46. 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]
  47. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
    [Google Scholar]
  48. 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]
  49. Hirsch P. Budding bacteria. Annu Rev Microbiol 1974; 28:391–440 [View Article][PubMed]
    [Google Scholar]
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