gen. nov., sp. nov., a thermophilic, strictly anaerobic bacterium of the phylum isolated from a deep subsurface oil reservoir Free

Abstract

A novel thermophilic, anaerobic, chemoheterotrophic, acetate-oxidizing and iron(III)-, manganese(IV)-, nitrate- and sulfate-reducing bacterium, designated strain ANA, was isolated from a deep subsurface oil field in Japan (Yabase oil field, Akita Pref.). Cells of strain ANA were Gram-stain-negative, non-motile, non-spore forming and slightly curved or twisted rods (1.5–5.0 µm long and 0.6–0.7 µm wide). The isolate grew at 25–60 °C (optimum 55 °C) and pH 6.0–8.0 (optimum pH 7.0). The isolate was capable of reducing iron(III), manganese(IV), nitrate and sulfate as an electron acceptor. The isolate utilized a limited range of electron donors such as acetate, lactate, pyruvate and yeast extract for iron reduction. Strain ANA also used pyruvate, fumarate, succinate, malate, yeast extract and peptone for fermentative growth. The major respiratory quinones were menaquinone-7(H8) and menaquinone-8. The strain contained C, iso-C and C as the major cellular fatty acids. The G+C content of the genomic DNA was 34.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ANA was closely related to in the phylum with low sequence similarities (89.5 %), and formed a distinct clade within the family . In addition, the isolate is the first sulfate-reducing member of the phylum . Based on phenotypic, chemotaxonomic and phylogenetic properties, a novel genus and species, gen. nov., sp. nov., is proposed for the isolate (type strain=ANA= NBRC 112621=DSM 105015).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002234
2017-10-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/10/3982.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002234&mimeType=html&fmt=ahah

References

  1. Head IM, Jones DM, Larter SR. Biological activity in the deep subsurface and the origin of heavy oil. Nature 2003; 426:344352 [View Article][PubMed]
    [Google Scholar]
  2. Aitken CM, Jones DM, Larter SR. Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs. Nature 2004; 431:291–294 [View Article][PubMed]
    [Google Scholar]
  3. Gittel A, Kofoed MV, Sørensen KB, Ingvorsen K, Schramm A. Succession of Deferribacteres and Epsilonproteobacteria through a nitrate-treated high-temperature oil production facility. Syst Appl Microbiol 2012; 35:165–174 [View Article][PubMed]
    [Google Scholar]
  4. Mayumi D, Dolfing J, Sakata S, Maeda H, Miyagawa Y et al. Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs. Nat Commun 2013; 4:1998 [View Article][PubMed]
    [Google Scholar]
  5. Orphan VJ, Taylor LT, Hafenbradl D, Delong EF. Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microbiol 2000; 66:700–711 [View Article][PubMed]
    [Google Scholar]
  6. Mayumi D, Mochimaru H, Yoshioka H, Sakata S, Maeda H et al. Evidence for syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis in the high-temperature petroleum reservoir of Yabase oil field (Japan). Environ Microbiol 2011; 13:1995–2006 [View Article][PubMed]
    [Google Scholar]
  7. Li D, Midgley DJ, Ross JP, Oytam Y, Abell GC et al. Microbial biodiversity in a Malaysian oil field and a systematic comparison with oil reservoirs worldwide. Arch Microbiol 2012; 194:513–523 [View Article][PubMed]
    [Google Scholar]
  8. Fiala G, Woese CR, Langworthy TA, Stetter KO. Flexistipes sinusarabici, a novel genus and species of eubacteria occurring in the Atlantis II Deep brines of the Red Sea. Arch Microbiol 1990; 154:120–126 [View Article]
    [Google Scholar]
  9. Caccavo F, Coates JD, Rossello-Mora RA, Ludwig W, Schleifer KH et al. Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium. Arch Microbiol 1996; 165:370–376 [View Article][PubMed]
    [Google Scholar]
  10. Greene AC, Patel BK, Sheehy AJ. Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir. Int J Syst Bacteriol 1997; 47:505–509 [View Article][PubMed]
    [Google Scholar]
  11. Myhr S, Torsvik T. Denitrovibrio acetiphilus, a novel genus and species of dissimilatory nitrate-reducing bacterium isolated from an oil reservoir model column. Int J Syst Evol Microbiol 2000; 50:1611–1619 [View Article][PubMed]
    [Google Scholar]
  12. Janssen PH, Liesack W, Schink B. Geovibrio thiophilus sp. nov., a novel sulfur-reducing bacterium belonging to the phylum Deferribacteres . Int J Syst Evol Microbiol 2002; 52:1341–1347 [View Article][PubMed]
    [Google Scholar]
  13. Takai K, Kobayashi H, Nealson KH, Horikoshi K. Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2003; 53:839–846 [View Article][PubMed]
    [Google Scholar]
  14. Miroshnichenko ML, Slobodkin AI, Kostrikina NA, L'Haridon S, Nercessian O et al. Deferribacter abyssi sp. nov., an anaerobic thermophile from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. Int J Syst Evol Microbiol 2003; 53:1637–1641 [View Article][PubMed]
    [Google Scholar]
  15. Robertson BR, O'Rourke JL, Neilan BA, Vandamme P, On SL et al. Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents. Int J Syst Evol Microbiol 2005; 55:1199–1204 [View Article][PubMed]
    [Google Scholar]
  16. Iino T, Nakagawa T, Mori K, Harayama S, Suzuki K. Calditerrivibrio nitroreducens gen. nov., sp. nov., a thermophilic, nitrate-reducing bacterium isolated from a terrestrial hot spring in Japan. Int J Syst Evol Microbiol 2008; 58:1675–1679 [View Article][PubMed]
    [Google Scholar]
  17. Slobodkina GB, Kolganova TV, Chernyh NA, Querellou J, Bonch-Osmolovskaya EA et al. Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2009; 59:1508–1512 [View Article][PubMed]
    [Google Scholar]
  18. Rauschenbach I, Posternak V, Cantarella P, Mcconnell J, Starovoytov V et al. Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the Deferribacteraceae . Int J Syst Evol Microbiol 2013; 63:3659–3665 [View Article][PubMed]
    [Google Scholar]
  19. Nakamura K, Takahashi A, Mori C, Tamaki H, Mochimaru H et al. Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field. Int J Syst Evol Microbiol 2013; 63:715–722 [View Article][PubMed]
    [Google Scholar]
  20. Widdel F, Bak F. Gram-negative mesophilic sulfate-reducing bacteria. The Prokaryotes New York: Springer; 1992 pp. 3352–3378 [Crossref]
    [Google Scholar]
  21. Tamaki H, Hanada S, Sekiguchi Y, Tanaka Y, Kamagata Y. Effect of gelling agent on colony formation in solid cultivation of microbial community in lake sediment. Environ Microbiol 2009; 11:1827–1834 [View Article][PubMed]
    [Google Scholar]
  22. Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng XY et al. Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int J Syst Evol Microbiol 2011; 61:1442–1447 [View Article][PubMed]
    [Google Scholar]
  23. Takeuchi M, Kamagata Y, Oshima K, Hanada S, Tamaki H et al. Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum . Int J Syst Evol Microbiol 2014; 64:3240–3246 [View Article][PubMed]
    [Google Scholar]
  24. Kanno M, Katayama T, Morita N, Tamaki H, Hanada S et al. Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester. Int J Syst Evol Microbiol 2015; 65:805–810 [View Article][PubMed]
    [Google Scholar]
  25. Hanada S, Takaichi S, Matsuura K, Nakamura K. Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Microbiol 2002; 52:187–193 [View Article][PubMed]
    [Google Scholar]
  26. Yamada K, Okuno Y, Meng XY, Tamaki H, Kamagata Y et al. Granulicella cerasi sp. nov., an acidophilic bacterium isolated from cherry bark. Int J Syst Evol Microbiol 2014; 64:2781–2785 [View Article][PubMed]
    [Google Scholar]
  27. Cline JD. Spectrophotometric determination of hydrogen sulfide in natural waters1. Limnol Oceanogr 1969; 14:454–458 [View Article]
    [Google Scholar]
  28. Nakagawa T, Fukui M. Phylogenetic characterization of microbial mats and streamers from a Japanese alkaline hot spring with a thermal gradient. J Gen Appl Microbiol 2002; 48:211–222 [View Article][PubMed]
    [Google Scholar]
  29. Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N et al. Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol 2005; 71:2162–2169 [View Article][PubMed]
    [Google Scholar]
  30. Tamazawa S, Takasaki K, Tamaki H, Kamagata Y, Hanada S. Metagenomic and biochemical characterizations of sulfur oxidation metabolism in uncultured large sausage-shaped bacterium in hot spring microbial mats. PLoS One 2012; 7:e49793 [View Article][PubMed]
    [Google Scholar]
  31. 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][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002234
Loading
/content/journal/ijsem/10.1099/ijsem.0.002234
Loading

Data & Media loading...

Most cited Most Cited RSS feed