1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 61, Issue 1

sp. nov., a methane-producing archaeon isolated from methanogenic sludge Free

Abstract

A novel methane-producing archaeon, strain SMSP, was isolated from an anaerobic, propionate-degrading enrichment culture that was originally obtained from granular sludge in a mesophilic upflow anaerobic sludge blanket (UASB) reactor used to treat a beer brewery effluent. Cells were non-motile, blunt-ended, straight rods, 1.0–2.6 μm long by 0.5 μm wide; cells were sometimes up to 7 μm long. Asymmetrical cell division was observed in rod-shaped cells. Coccoid cells (0.5–1.0 μm in diameter) were also observed in mid- to late-exponential phase cultures. Growth was observed between 10 and 40 °C (optimum, 30–33 °C) and pH 7.0 and 7.6 (optimum, pH 7.4). The G+C content of the genomic DNA was 56.2 mol%. The strain utilized formate and hydrogen for growth and methane production. Based on comparative sequence analyses of the 16S rRNA and (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-producing pathway) genes, strain SMSP was affiliated with group E1/E2 within the order . The closest relative based on both 16S rRNA and gene sequences was 6A8 (96.3 % 16S rRNA gene sequence similarity, 85.4 % deduced McrA amino acid sequence similarity). The percentage of 16S rRNA gene sequence similarity indicates that strain SMSP and 6A8 represent different species within the same genus. This is supported by our findings of shared phenotypic properties, including cell morphology and growth temperature range, and phenotypic differences in substrate usage and pH range. Based on these genetic and phenotypic properties, we propose that strain SMSP represents a novel species of the genus , for which we propose the name sp. nov., with the type strain SMSP (=NBRC 105244 =DSM 22288).

  • Published Online:
Keyword(s): FISH, fluorescence in situ hybridization and UASB, upflow anaerobic sludge blanket
SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.014811-0
2011-01-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/1/53.html?itemId=/content/journal/ijsem/10.1099/ijs.0.014811-0&mimeType=html&fmt=ahah

References

  1. Amann R. I., Binder B. J., Olson R. J., Chisholm S. W., Devereux R., Stahl D. A. 1990; Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919–1925
     [Google Scholar]
  2. 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]
     [Google Scholar]
  3. 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]
     [Google Scholar]
  4. 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]
     [Google Scholar]
  5. 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]
     [Google Scholar]
  6. 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]
     [Google Scholar]
  7. 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]
     [Google Scholar]
  8. Chan O. C., Wolf M., Hepperle D., Casper P. 2002; Methanogenic archaeal community in the sediment of an artificially partitioned acidic bog lake. FEMS Microbiol Ecol 42:119–129 [CrossRef]
     [Google Scholar]
  9. Chan O. C., Claus P., Casper P., Ulrich A., Lueders T., Conrad R. 2005; Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment. Environ Microbiol 7:1139–1149 [CrossRef]
     [Google Scholar]
  10. 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]
     [Google Scholar]
  11. 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]
     [Google Scholar]
  12. Daims H., Brühl A., Amann R., Schleifer K. H., Wagner M. 1999; The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22:434–444 [CrossRef]
     [Google Scholar]
  13. DeLong E. F. 1992; Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89:5685–5689 [CrossRef]
     [Google Scholar]
  14. Dojka M. A., Hugenholtz P., Haack S. K., Pace N. R. 1998; Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877
     [Google Scholar]
  15. Ficker M., Krastel K., Orlicky S., Edwards E. 1999; Molecular characterization of a toluene-degrading methanogenic consortium. Appl Environ Microbiol 65:5576–5585
     [Google Scholar]
  16. 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]
     [Google Scholar]
  17. Großkopf R., Janssen P. H., Liesack W. 1998; Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S RNA gene sequence retrieval. Appl Environ Microbiol 64:960–969
     [Google Scholar]
  18. 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
     [Google Scholar]
  19. Hatamoto M., Imachi H., Ohashi A., Harada H. 2007; Identification and cultivation of anaerobic, syntrophic long-chain fatty acid-degrading microbes from mesophilic and thermophilic methanogenic sludges. Appl Environ Microbiol 73:1332–1340 [CrossRef]
     [Google Scholar]
  20. 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]
     [Google Scholar]
  21. 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]
     [Google Scholar]
  22. 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]
     [Google Scholar]
  23. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism vol 3 pp 21–132 Edited by Munro H. N. New York: Academic Press;
     [Google Scholar]
  24. Jurgens G., Glöckner F., Amann R., Saano A., Montonen L., Likolammi M., Münster U. 2000; Identification of novel archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol Ecol 34:45–56
     [Google Scholar]
  25. 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
     [Google Scholar]
  26. 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]
     [Google Scholar]
  27. Lueders T., Friedrich M. 2000; Archaeal population dynamics during sequential reduction processes in rice field soil. Appl Environ Microbiol 66:2732–2742 [CrossRef]
     [Google Scholar]
  28. Macbeth T. W., Cummings D. E., Spring S., Petzke L. M., Sorenson K. S. 2004; Molecular characterization of a dechlorinating community resulting from in situ biostimulation in a trichloroethene-contaminated deep, fractured basalt aquifer and comparison to a derivative laboratory culture. Appl Environ Microbiol 70:7329–7341 [CrossRef]
     [Google Scholar]
  29. 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]
     [Google Scholar]
  30. 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]
     [Google Scholar]
  31. Nüsslein B., Chin K.-J., Eckert W., Conrad R. 2001; Evidence for anaerobic syntrophic acetate oxidation during methane production in the profundal sediment of subtropical Lake Kinneret (Israel). Environ Microbiol 3:460–470 [CrossRef]
     [Google Scholar]
  32. Purdy K. J., Munson M. A., Nedwell D. B., Embley T. M. 2002; Comparison of the molecular diversity of the methanogenic community at the brackish and marine ends of a UK estuary. FEMS Microbiol Ecol 39:17–21 [CrossRef]
     [Google Scholar]
  33. 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]
     [Google Scholar]
  34. Sekiguchi Y., Kamagata Y., Syutsubo K., Ohashi A., Harada H., Nakamura K. 1998; Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144:2655–2665 [CrossRef]
     [Google Scholar]
  35. 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]
  36. van Hoek A. H. A. M., van Alen T. A., Sprakel V. S. I., Leunissen J. A. M., Brigge T., Vogels G. D., Hackstein J. H. P. 2000; Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates. Mol Biol Evol 17:251–258 [CrossRef]
     [Google Scholar]
  37. Watanabe K., Kodama Y., Hamamura N., Kaku N. 2002; Diversity, abundance, and activity of archaeal populations in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Appl Environ Microbiol 68:3899–3907 [CrossRef]
     [Google Scholar]
  38. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
     [Google Scholar]
  39. Wu X. L., Friedrich M. W., Conrad R. 2006; Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils. Environ Microbiol 8:394–404 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.014811-0
Loading
Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge
Int J Syst Evol Microbiol 61, 53 (2011); https://doi.org/10.1099/ijs.0.014811-0
/content/journal/ijsem/10.1099/ijs.0.014811-0
/content/journal/ijsem/10.1099/ijs.0.014811-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error