1887

Abstract

A mesophilic deltaproteobacterium, designated strain SPR, was isolated from a methanogenic consortium capable of degrading long-chain paraffins. Cells were motile, vibrio-shaped, and occurred singly, in pairs or in clusters. Strain SPR did not metabolize hydrocarbons but grew fermentatively on pyruvate and oxaloacetate and autotrophically with H and CO. Thiosulfate served as a terminal electron acceptor, but sulfate or sulfite did not. The organism required at least 10 g NaCl l and a small amount of yeast extract (0.001%) for growth. Optimal growth was observed between 30 and 37 °C and a pH range from 6.0 to 7.2. The DNA G+C content of SPR's genome was 52.02 mol%. Based on 16S rRNA gene sequence analysis, strain SPR was distinct from previously described , exhibiting the closest affiliation to DSM 2075 and SCBM, with only 91% similarity between their respective 16S gene sequences. genome comparison supported the distinctiveness between strain SPR and both SCBM and DSM 2075. Based on physiological differences, as well as phylogenetic and genomic comparisons, we propose to classify SPR as the type strain ( = DSM 100305 = JCM 30857) of a novel species of a new genus with the name gen. nov., sp. nov.

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2016-03-01
2020-01-18
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References

  1. An T. T., Picardal F. W.. 2014; Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed. Int J Syst Evol Microbiol64:2907–2914 [CrossRef][PubMed]
    [Google Scholar]
  2. Anderson R. T., Lovley D. R.. 2000; Hexadecane decay by methanogenesis. Nature404:722–723 [CrossRef][PubMed]
    [Google Scholar]
  3. Auch A. F., von Jan M., Klenk H.-P., Göker M.. 2010; Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  4. Boetzer M., Henkel C. V., Jansen H. J., Butler D., Pirovano W.. 2011; Scaffolding pre-assembled contigs using SSPACE. Bioinformatics27:578–579 [CrossRef][PubMed]
    [Google Scholar]
  5. Caldwell M. E., Garrett R. M., Prince R. C., Suflita J. M.. 1998; Anaerobic biodegradation of long-chain n-alkanes under sulfate-reducing conditions. Environ Sci Technol32:2191–2195 [CrossRef]
    [Google Scholar]
  6. Callaghan A. V., Davidova I. A., Savage-Ashlock K., Parisi V. A., Gieg L. M., Suflita J. M., Kukor J. J., Wawrik B.. 2010; Diversity of benzyl- and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures. Environ Sci Technol44:7287–7294 [CrossRef][PubMed]
    [Google Scholar]
  7. Cole J. R., Wang Q., Fish J. A., Chai B., McGarrell D. M., Sun Y., Brown C. T., Porras-Alfaro A., Kuske C. R., Tiedje J. M.. 2014; Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res42:(D1)D633–D642 [CrossRef][PubMed]
    [Google Scholar]
  8. Davidova I. A., Callaghan A. V., Duncan K. E., Sunner J., Biri B., Wawrik B., Suflita J. M.. 2011; Long-chain paraffin metabolism by a methanogenic bacterial consortium enriched from marine sediments (poster presentation). In Proceedings of the 8th International Symposium of Subsurface Microbiology (ISSM-8) Garmisch-Partenkirchen; Germany. S7-P3; p.66:
    [Google Scholar]
  9. Davidova I. A., Duncan K. E., Perez-Ibarra B. M., Suflita J. M.. 2012; Involvement of thermophilic archaea in the biocorrosion of oil pipelines. Environ Microbiol14:1762–1771 [CrossRef][PubMed]
    [Google Scholar]
  10. Embree M., Nagarajan H., Movahedi N., Chitsaz H., Zengler K.. 2014; Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. ISME J8:757–767 [CrossRef][PubMed]
    [Google Scholar]
  11. Foght J.. 2008; Anaerobic biodegradation of aromatic hydrocarbons: pathways and prospects. J Mol Microbiol Biotechnol15:93–120 [CrossRef][PubMed]
    [Google Scholar]
  12. Fuchs G.. 2008; Anaerobic metabolism of aromatic compounds. Ann N Y Acad Sci1125:82–99 [CrossRef][PubMed]
    [Google Scholar]
  13. Gieg L. M., Duncan K. E., Suflita J. M.. 2008; Bioenergy production via microbial conversion of residual oil to natural gas. Appl Environ Microbiol74:3022–3029 [CrossRef][PubMed]
    [Google Scholar]
  14. Gottschalk G., Barker H. A.. 1966; Synthesis of glutamate and citrate by Clostridium kluyveri. A new type of citrate synthase. Biochemistry5:1125–1133 [CrossRef][PubMed]
    [Google Scholar]
  15. Gray N. D., Sherry A., Grant R. J., Rowan A. K., Hubert C. R., Callbeck C. M., Aitken C. M., Jones D. M., Adams J. J., other authors. 2011; The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes. Environ Microbiol13:2957–2975 [CrossRef][PubMed]
    [Google Scholar]
  16. Jansen K., Thauer R. K., Widdel F., Fuchs G.. 1984; Carbon assimilation pathways in sulfate reducing bacteria: formate, carbon-dioxide, carbon-monoxide, and acetate assimilation by Desulfovibrio baarsii. Arch Microbiol138:257–262 [CrossRef]
    [Google Scholar]
  17. Kämpfer P., Glaeser S. P.. 2012; Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited. Environ Microbiol14:291–317 [CrossRef][PubMed]
    [Google Scholar]
  18. Kim M., Le H., McInerney M. J., Buckel W.. 2013; Identification and characterization of re-citrate synthase in Syntrophus aciditrophicus. J Bacteriol195:1689–1696 [CrossRef][PubMed]
    [Google Scholar]
  19. Kuever J., Rainey F. A., Widdel F.. 2005; Order IV Desulfarcales ord. nov. Family I Desulfarculaceae fam. nov. In Bergey's Manual of Systematic Bacteriology pp1003–1005Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M.. New York: Springer;
    [Google Scholar]
  20. Li F., Hagemeier C. H., Seedorf H., Gottschalk G., Thauer R. K.. 2007; Re-citrate synthase from Clostridium kluyveri is phylogenetically related to homocitrate synthase and isopropylmalate synthase rather than to Si-citrate synthase. J Bacteriol189:4299–4304 [CrossRef][PubMed]
    [Google Scholar]
  21. Miller C. S., Baker B. J., Thomas B. C., Singer S. W., Banfield J. F.. 2011; emirge: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol12:R44 [CrossRef][PubMed]
    [Google Scholar]
  22. Nakatsu C. H., Marsh T. L.. 2007; Analysis of microbial communities with denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism. In Methods for General and Molecular Microbiology, 3rd edn. pp909–923Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC: American Society for Microbiology; [CrossRef]
    [Google Scholar]
  23. Pires R. H., Lourenço A. I., Morais F., Teixeira M., Xavier A. V., Saraiva L. M., Pereira I. A. C.. 2003; A novel membrane-bound respiratory complex from Desulfovibrio desulfuricans ATCC 27774. Biochim Biophys Acta1605:67–82 [CrossRef][PubMed]
    [Google Scholar]
  24. Qin Q. L., Xie B. B., Zhang X. Y., Chen X. L., Zhou B. C., Zhou J., Oren A., Zhang Y. Z.. 2014; A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol196:2210–2215 [CrossRef][PubMed]
    [Google Scholar]
  25. Siddique T., Fedorak P. M., Foght J. M.. 2006; Biodegradation of short-chain n-alkanes in oil sands tailings under methanogenic conditions. Environ Sci Technol40:5459–5464 [CrossRef][PubMed]
    [Google Scholar]
  26. Siddique T., Penner T., Semple K., Foght J. M.. 2011; Anaerobic biodegradation of longer-chain n-alkanes coupled to methane production in oil sands tailings. Environ Sci Technol45:5892–5899 [CrossRef][PubMed]
    [Google Scholar]
  27. Stackebrandt E., Ebers J.. 2006; Taxonomic parameters revisited: tarnished gold standards. Microbiol Today33:152
    [Google Scholar]
  28. Sun H., Spring S., Lapidus A., Davenport K., Del Rio T. G., Tice H., Nolan M., Copeland A., Cheng J. F., other authors. 2010; Complete genome sequence of Desulfarculus baarsii type strain (2st14T). Stand Genomic Sci3:276–284 [CrossRef][PubMed]
    [Google Scholar]
  29. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; mega6: molecular evolutionary genetics analysis version 6.0.Mol Biol Evol30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  30. Townsend G. T., Prince R. C., Suflita J. M.. 2003; Anaerobic oxidation of crude oil hydrocarbons by the resident microorganisms of a contaminated anoxic aquifer. Environ Sci Technol37:5213–5218 [CrossRef][PubMed]
    [Google Scholar]
  31. Trüper H. G., Schlegel H. G.. 1964; Sulphur metabolism in Thiorhodaceae 1. Quantitative measurements on growing cells of Chromatium okenii. Antonie van Leeuwenhoek30:225–238 [CrossRef][PubMed]
    [Google Scholar]
  32. Widdel F., Bak F.. 1992; Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes pp3352–3378Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H.. New York: [CrossRef] Springer;
    [Google Scholar]
  33. Zengler K., Richnow H. H., Rosselló-Mora R., Michaelis W., Widdel F.. 1999; Methane formation from long-chain alkanes by anaerobic microorganisms. Nature401:266–269 [CrossRef][PubMed]
    [Google Scholar]
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