1887

Abstract

A novel mesophilic, hydrogenotrophic methanogen, designated strain TNR, was isolated from an anaerobic, propionate-degradation enrichment culture that was originally established from a rice field soil sample from Taiwan. Cells were non-motile rods, 2.0–6.5 µm long by 0.3 µm wide. Filamentous (up to about 100 µm) and coccoid (about 1 µm in diameter) cells were also observed in cultures in the late exponential phase of growth. Strain TNR grew at 20–40 °C (optimally at 37 °C), at pH 6.5–7.4 (optimally at pH 7.0) and in the presence of 0–25 g NaCl l (optimally at 0 g NaCl l). The strain utilized H/CO and formate for growth and produced methane. The G+C content of the genomic DNA was 56.4 mol%. Based on sequences of both the 16S rRNA gene and the methanogen-specific marker gene , strain TNR was related most closely to NOBI-1; levels of sequence similarities were 94.8 and 86.4 %, respectively. The 16S rRNA gene sequence similarity indicates that strain TNR and NOBI-1 represent different species within the same genus. This is supported by shared phenotypic properties, including substrate usage and cell morphology, and differences in growth temperature. Based on these genetic and phenotypic properties, strain TNR is considered to represent a novel species of the genus , for which the name sp. nov. is proposed; the type strain is TNR ( = NBRC 105659 = DSM 23604). In addition, we also suggest family status for the E1/E2 group within the order , for which the name fam. nov. is proposed; the type genus of family is .

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2012-06-01
2019-08-25
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References

  1. Bräuer S. L. , Cadillo-Quiroz H. , Yashiro E. , Yavitt J. B. , Zinder S. H. . ( 2006a; ). Isolation of a novel acidiphilic methanogen from an acidic peat bog. . Nature 442:, 192–194. [CrossRef] [PubMed]
    [Google Scholar]
  2. Bräuer S. L. , Yashiro E. , Ueno N. G. , Yavitt J. B. , Zinder S. H. . ( 2006b; ). Characterization of acid-tolerant H2/CO2-utilizing methanogenic enrichment cultures from an acidic peat bog in New York State. . FEMS Microbiol Ecol 57:, 206–216. [CrossRef] [PubMed]
    [Google Scholar]
  3. Bräuer S. L. , Cadillo-Quiroz H. , Ward R. J. , Yavitt J. B. , Zinder S. H. . ( 2011; ). Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog. . Int J Syst Evol Microbiol 61:, 45–52. [CrossRef] [PubMed]
    [Google Scholar]
  4. Cadillo-Quiroz H. , Bräuer S. , Yashiro E. , Sun C. , Yavitt J. , Zinder S. . ( 2006; ). Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA. . Environ Microbiol 8:, 1428–1440. [CrossRef] [PubMed]
    [Google Scholar]
  5. Cadillo-Quiroz H. , Yashiro E. , Yavitt J. B. , Zinder S. H. . ( 2008; ). Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. . Appl Environ Microbiol 74:, 2059–2068. [CrossRef] [PubMed]
    [Google Scholar]
  6. Cadillo-Quiroz H. , Yavitt J. B. , Zinder S. H. . ( 2009; ). Methanosphaerula palustris gen. nov., sp. nov., a hydrogenotrophic methanogen isolated from a minerotrophic fen peatland. . Int J Syst Evol Microbiol 59:, 928–935. [CrossRef] [PubMed]
    [Google Scholar]
  7. Chen C.-L. , Macarie H. , Ramirez I. , Olmos A. , Ong S. L. , Monroy O. , Liu W.-T. . ( 2004; ). Microbial community structure in a thermophilic anaerobic hybrid reactor degrading terephthalate. . Microbiology 150:, 3429–3440. [CrossRef] [PubMed]
    [Google Scholar]
  8. Chen C.-L. , Wu J.-H. , Tseng I.-C. , Liang T.-M. , Liu W.-T. . ( 2009; ). Characterization of active microbes in a full-scale anaerobic fluidized bed reactor treating phenolic wastewater. . Microbes Environ 24:, 144–153. [CrossRef] [PubMed]
    [Google Scholar]
  9. Díaz E. E. , Stams A. J. M. , Amils R. , Sanz J. L. . ( 2006; ). Phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater. . Appl Environ Microbiol 72:, 4942–4949. [CrossRef] [PubMed]
    [Google Scholar]
  10. Felsenstein J. . ( 1985; ). Confidence limits of phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  11. Ferry J. G. , Smith P. H. , Wolfe R. S. . ( 1974; ). Methanospirillum, a new genus of methanogenic bacteria, and characterization of Methanospirillum hungatei sp. nov. . Int J Syst Bacteriol 24:, 465–469. [CrossRef]
    [Google Scholar]
  12. Galand P. E. , Saarnio S. , Fritze H. , Yrjälä K. . ( 2002; ). Depth related diversity of methanogen Archaea in Finnish oligotrophic fen. . FEMS Microbiol Ecol 42:, 441–449. [CrossRef] [PubMed]
    [Google Scholar]
  13. Hales B. A. , Edwards C. , Ritchie D. A. , Hall G. , Pickup R. W. , Saunders J. R. . ( 1996; ). Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. . Appl Environ Microbiol 62:, 668–675.[PubMed]
    [Google Scholar]
  14. Imachi H. , Sekiguchi Y. , Kamagata Y. , Loy A. , Qiu Y.-L. , Hugenholtz P. , Kimura N. , Wagner M. , Ohashi A. , Harada H. . ( 2006; ). Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments. . Appl Environ Microbiol 72:, 2080–2091. [CrossRef] [PubMed]
    [Google Scholar]
  15. Imachi H. , Sakai S. , Sekiguchi Y. , Hanada S. , Kamagata Y. , Ohashi A. , Harada H. . ( 2008; ). Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge. . Int J Syst Evol Microbiol 58:, 294–301. [CrossRef] [PubMed]
    [Google Scholar]
  16. Imachi H. , Sakai S. , Nagai H. , Yamaguchi T. , Takai K. . ( 2009; ). Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field. . Int J Syst Evol Microbiol 59:, 800–805. [CrossRef] [PubMed]
    [Google Scholar]
  17. Keswani J. , Whitman W. B. . ( 2001; ). Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. . Int J Syst Evol Microbiol 51:, 667–678.[PubMed]
    [Google Scholar]
  18. Ludwig W. , Strunk O. , Westram R. , Richter L. , Meier H. , Yadhukumar , Buchner A. , Lai T. , Steppi S. . & other authors ( 2004; ). ARB: a software environment for sequence data. . Nucleic Acids Res 32:, 1363–1371. [CrossRef] [PubMed]
    [Google Scholar]
  19. Lykidis A. , Chen C.-L. , Tringe S. G. , McHardy A. C. , Copeland A. , Kyrpides N. C. , Hugenholtz P. , Macarie H. , Olmos A. . & other authors ( 2011; ). Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. . ISME J 5:, 122–130. [CrossRef] [PubMed]
    [Google Scholar]
  20. Nakagawa S. , Takai K. , Horikoshi K. , Sako Y. . ( 2003; ). Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney. . Int J Syst Evol Microbiol 53:, 863–869. [CrossRef] [PubMed]
    [Google Scholar]
  21. Narihiro T. , Terada T. , Ohashi A. , Wu J.-H. , Liu W.-T. , Araki N. , Kamagata Y. , Nakamura K. , Sekiguchi Y. . ( 2009; ). Quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rRNA cleavage method. . ISME J 3:, 522–535. [CrossRef] [PubMed]
    [Google Scholar]
  22. Ollivier B. M. , Mah R. A. , Garcia J. L. , Boone D. R. . ( 1986; ). Isolation and characterization of Methanogenium bourgense sp. nov. . Int J Syst Bacteriol 36:, 297–301. [CrossRef]
    [Google Scholar]
  23. Ollivier B. , Fardeau M.-L. , Cayol J.-L. , Magot M. , Patel B. K. C. , Prensier G. , Garcia J.-L. . ( 1998; ). Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well. . Int J Syst Bacteriol 48:, 821–828. [CrossRef] [PubMed]
    [Google Scholar]
  24. Paynter M. J. B. , Hungate R. E. . ( 1968; ). Characterization of Methanobacterium mobilis, sp. n., isolated from the bovine rumen. . J Bacteriol 95:, 1943–1951.[PubMed]
    [Google Scholar]
  25. Rivard C. J. , Henson J. M. , Thomas M. V. , Smith P. H. . ( 1983; ). Isolation and characterization of Methanomicrobium paynteri sp. nov., a mesophilic methanogen isolated from marine sediments. . Appl Environ Microbiol 46:, 484–490.[PubMed]
    [Google Scholar]
  26. Romesser J. A. , Wolfe R. S. , Mayer F. , Spiess E. , Walther-Mauruschat A. . ( 1979; ). Methanogenium, a new genus of marine methanogenic bacteria, and characterization of Methanogenium cariaci sp. nov. and Methanogenium marisnigri sp. nov. . Arch Mikrobiol 121:, 147–153.[CrossRef]
    [Google Scholar]
  27. Sakai S. , Imachi H. , Sekiguchi Y. , Ohashi A. , Harada H. , Kamagata Y. . ( 2007; ). Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster rice cluster I. . Appl Environ Microbiol 73:, 4326–4331. [CrossRef] [PubMed]
    [Google Scholar]
  28. Sakai S. , Imachi H. , Hanada S. , Ohashi A. , Harada H. , Kamagata Y. . ( 2008; ). Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage ‘Rice Cluster I’, and proposal of the new archaeal order Methanocellales ord. nov.. Int J Syst Evol Microbiol 58:, 929–936. [CrossRef] [PubMed]
    [Google Scholar]
  29. Sakai S. , Imachi H. , Sekiguchi Y. , Tseng I.-C. , Ohashi A. , Harada H. , Kamagata Y. . ( 2009; ). Cultivation of methanogens under low-hydrogen conditions by using the coculture method. . Appl Environ Microbiol 75:, 4892–4896. [CrossRef] [PubMed]
    [Google Scholar]
  30. Stackebrandt E. , Goebel B. M. . ( 1994; ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  31. Tamura K. , Peterson D. , Peterson N. , Stecher G. , Nei M. , Kumar S. . ( 2011; ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef] [PubMed]
    [Google Scholar]
  32. Wildgruber G. , Thomm M. , König H. , Ober K. , Ricchiuto T. , Stetter K. O. . ( 1982; ). Methanoplanus limicola, a plate-shaped methanogen representing a novel family, the Methanoplanaceae. . Arch Microbiol 132:, 31–36. [CrossRef]
    [Google Scholar]
  33. Yashiro Y. , Sakai S. , Ehara M. , Miyazaki M. , Yamaguchi T. , Imachi H. . ( 2011; ). Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge. . Int J Syst Evol Microbiol 61:, 53–59. [CrossRef] [PubMed]
    [Google Scholar]
  34. Ye W. , Liu X. , Lin S. , Tan J. , Pan J. , Li D. , Yang H. . ( 2009; ). The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. . FEMS Microbiol Ecol 70:, 107–120. [CrossRef] [PubMed]
    [Google Scholar]
  35. Zabel H. P. , König H. , Winter J. . ( 1984; ). Isolation and characterization of a new coccoid methanogen, Methanogenium tatii spec. nov. from a solfataric field on Mount Tatio. . Arch Microbiol 137:, 308–315. [CrossRef]
    [Google Scholar]
  36. Zellner G. , Alten C. , Stackebrandt E. , Conway de Macario E. , Winter J. . ( 1987; ). Isolation and characterization of Methanocorpusculum parvum gen. nov., spec. nov., a new tungsten requiring, coccoid methanogen. . Arch Microbiol 147:, 13–20. [CrossRef]
    [Google Scholar]
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