1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 64, Issue Pt_4

sp. nov., a methanotroph isolated from manure and a denitrification tank Free

Abstract

Two methanotrophic bacteria, strains R-45377 and R-45370, were respectively isolated from a slurry pit of a cow stable and from a denitrification tank of a wastewater treatment plant in Belgium. The strains showed 99.9 % 16S rRNA gene sequence similarity. Cells were Gram-negative, motile rods containing type I methanotroph intracytoplasmic membranes. Colonies and liquid cultures appeared white to pale pink. The gene encoding particulate methane monooxygenase (pMMO) and the gene encoding nitrogenase were present. Soluble methane monooxygenase (sMMO) activity, the presence of the gene encoding sMMO and the presence of the gene encoding a sequence-divergent pMMO were not detected. Methane and methanol were utilized as sole carbon sources. The strains grew optimally at 20 °C (range 15–28 °C) and at pH 6.8–7.3 (range pH 6.3–7.8). The strains grew in media supplemented with up to 1.2 % NaCl. The major cellular fatty acids were Cω8, Cω5, Cω7, C, C and C and the DNA G+C content was 47 mol%. 16S rRNA gene- and -based phylogenetic analyses showed that the isolates cluster among members of the genus within the class , with pairwise 16S rRNA gene sequence similarities of 97.5 and 97.2 % between R-45377 and the closest related type strains, SR5 and MG30, respectively. Based on phenotypic characterization of strains R-45377 and R-45370, their low 16S rRNA gene sequence similarities and the formation of a separate phylogenetic lineage compared with existing species of the genus , we propose to classify these strains in a novel species, sp. nov., with R-45377 ( = LMG 26260 = JCM 19378) as the type strain.

  • Published Online:
Funding
This study was supported by the:
  • Geconcerteerde Onderzoeksactie (GOA) of Ghent University (Award BOF09/GOA/005)
  • Flemish Fund for Scientific Research (Award FWO11/PDO/084)
© 2014 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.057794-0
2014-04-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/4/1210.html?itemId=/content/journal/ijsem/10.1099/ijs.0.057794-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. ( 1990 ). Basic local alignment search tool. . J Mol Biol 215, 403–410.[PubMed] [CrossRef]
    [Google Scholar]
  2. Anthony C. ( 1982 ). Biochemistry of Methylotrophs. London:: Academic Press;.
     [Google Scholar]
  3. Auman A. J., Stolyar S., Costello A. M., Lidstrom M. E. ( 2000 ). Molecular characterization of methanotrophic isolates from freshwater lake sediment. . Appl Environ Microbiol 66, 5259–5266. [View Article] [PubMed]
    [Google Scholar]
  4. Auman A. J., Speake C. C., Lidstrom M. E. ( 2001 ). nifH sequences and nitrogen fixation in type I and type II methanotrophs. . Appl Environ Microbiol 67, 4009–4016. [View Article] [PubMed]
    [Google Scholar]
  5. Boulygina E. S., Kuznetsov B. B., Marusina A. I., Turova T. P., Kravchenko I. K., Bykova S. A., Kolganova T. V., Gal’chenko V. F. ( 2002 ). [Study of nucleotide sequences of nifH genes in methanotrophic bacteria]. . Mikrobiologiia 71, 500–508 (in Russian).[PubMed]
    [Google Scholar]
  6. Bowman J. ( 2006 ). The methanotrophs – the families Methylococcaceae and Methylocystaceae . . In The Prokaryotes, , 3rd edn., pp. 266–289. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. . New York:: Springer;. [View Article]
    [Google Scholar]
  7. Bowman J. P., Sly L. I., Cox J. M., Hayward A. C. ( 1990 ). Methylomonas fodinarum sp. nov. and Methylomonas aurantiaca sp. nov.: two closely related type I obligate methanotrophs. . Syst Appl Microbiol 13, 279–287. [View Article]
    [Google Scholar]
  8. Bowman J. P., Sly L. I., Nichols P. D., Hayward A. C. ( 1993 ). Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. . Int J Syst Bacteriol 43, 735–753. [View Article]
    [Google Scholar]
  9. Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. ( 2002 ). Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov.. Int J Syst Evol Microbiol 52, 1551–1558. [View Article] [PubMed]
    [Google Scholar]
  10. Cole J. R., Chai B., Farris R. J., Wang Q., Kulam S. A., McGarrell D. M., Garrity G. M., Tiedje J. M. ( 2005 ). The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. . Nucleic Acids Res 33, D294–D296. [View Article] [PubMed]
    [Google Scholar]
  11. Costello A. M., Lidstrom M. E. ( 1999 ). Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. . Appl Environ Microbiol 65, 5066–5074.[PubMed]
    [Google Scholar]
  12. Danilova O. V., Kulichevskaya I. S., Rozova O. N., Detkova E. N., Bodelier P. L., Trotsenko Y. A., Dedysh S. N. ( 2013 ). Methylomonas paludis sp. nov., the first acid-tolerant member of the genus Methylomonas, from an acidic wetland. . Int J Syst Evol Microbiol 63, 2282–2289. [View Article] [PubMed]
    [Google Scholar]
  13. De Meyer S. E., van Hoorde K., Vekeman B., Braeckman T., Willems A. ( 2011 ). Genetic diversity of rhizobia associated with indigenous legumes in different regions of Flanders (Belgium). . Soil Biol Biochem 43, 2384–2396. [View Article]
    [Google Scholar]
  14. Dedysh S. N. ( 2009 ). Exploring methanotroph diversity in acidic northern wetlands: molecular and cultivation-based studies. . Microbiology (English translation of Mikrobiologiia) 78, 655–669. [View Article]
    [Google Scholar]
  15. Dunfield P. F., Khmelenina V. N., Suzina N. E., Trotsenko Y. A., Dedysh S. N. ( 2003 ). Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. . Int J Syst Evol Microbiol 53, 1231–1239. [View Article] [PubMed]
    [Google Scholar]
  16. Ettwig K. F., Butler M. K., Le Paslier D., Pelletier E., Mangenot S., Kuypers M. M., Schreiber F., Dutilh B. E., Zedelius J. & other authors ( 2010 ). Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. . Nature 464, 543–548. [View Article] [PubMed]
    [Google Scholar]
  17. Geymonat E., Ferrando L., Tarlera S. E. ( 2011 ). Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field. . Int J Syst Evol Microbiol 61, 2568–2572. [View Article] [PubMed]
    [Google Scholar]
  18. Hanson R. S., Hanson T. E. ( 1996 ). Methanotrophic bacteria. . Microbiol Rev 60, 439–471.[PubMed]
    [Google Scholar]
  19. Heimbrook M. E., Wang W. L. L., Campbell G. ( 1989 ). Staining bacterial flagella easily. . J Clin Microbiol 27, 2612–2615.[PubMed]
    [Google Scholar]
  20. Hoefman S., van der Ha D., De Vos P., Boon N., Heylen K. ( 2012a ). Miniaturized extinction culturing is the preferred strategy for rapid isolation of fast-growing methane-oxidizing bacteria. . Microb Biotechnol 5, 368–378. [View Article] [PubMed]
    [Google Scholar]
  21. Hoefman S., Van Hoorde K., Boon N., Vandamme P., De Vos P., Heylen K. ( 2012b ). Survival or revival: long-term preservation induces a reversible viable but non-culturable state in methane-oxidizing bacteria. . PLoS ONE 7, e34196. [View Article] [PubMed]
    [Google Scholar]
  22. Horz H. P., Yimga M. T., Liesack W. ( 2001 ). Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. . Appl Environ Microbiol 67, 4177–4185. [View Article] [PubMed]
    [Google Scholar]
  23. Hutchens E., Radajewski S., Dumont M. G., McDonald I. R., Murrell J. C. ( 2004 ). Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. . Environ Microbiol 6, 111–120. [View Article] [PubMed]
    [Google Scholar]
  24. Kalyuzhnaya M. G., Khmelenina V. N., Kotelnikova S., Holmquist L., Pedersen K., Trotsenko Y. A. ( 1999 ). Methylomonas scandinavica sp. nov., a new methanotrophic psychrotrophic bacterium isolated from deep igneous rock ground water of Sweden. . Syst Appl Microbiol 22, 565–572. [View Article] [PubMed]
    [Google Scholar]
  25. Kip N., Ouyang W., van Winden J., Raghoebarsing A., van Niftrik L., Pol A., Pan Y., Bodrossy L., van Donselaar E. G. & other authors ( 2011 ). Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses. . Appl Environ Microbiol 77, 5643–5654. [View Article] [PubMed]
    [Google Scholar]
  26. Logan N. A., Lebbe L., Hoste B., Goris J., Forsyth G., Heyndrickx M., Murray B. L., Syme N., Wynn-Williams D. D., De Vos P. ( 2000 ). Aerobic endospore-forming bacteria from geothermal environments in northern Victoria Land, Antarctica, and Candlemas Island, South Sandwich archipelago, with the proposal of Bacillus fumarioli sp. nov.. Int J Syst Evol Microbiol 50, 1741–1753.[PubMed]
    [Google Scholar]
  27. 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. [View Article] [PubMed]
    [Google Scholar]
  28. McDonald I. R., Kenna E. M., Murrell J. C. ( 1995 ). Detection of methanotrophic bacteria in environmental samples with the PCR. . Appl Environ Microbiol 61, 116–121.[PubMed]
    [Google Scholar]
  29. Mesbah M., Premachandran U., Whitman W. B. ( 1989 ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39, 159–167. [View Article]
    [Google Scholar]
  30. Ogiso T., Ueno C., Dianou D., Huy T. V., Katayama A., Kimura M., Asakawa S. ( 2012 ). Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field. . Int J Syst Evol Microbiol 62, 1832–1837. [View Article] [PubMed]
    [Google Scholar]
  31. Op den Camp H. J. M., Islam T., Stott M. B., Harhangi H. R., Hynes A., Schouten S., Jetten M. S. M., Birkeland N. K., Pol A., Dunfield P. F. ( 2009 ). Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia . . Environ Microbiol Rep 1, 293–306. [View Article] [PubMed]
    [Google Scholar]
  32. Semrau J. D., DiSpirito A. A., Yoon S. ( 2010 ). Methanotrophs and copper. . FEMS Microbiol Rev 34, 496–531.[PubMed]
    [Google Scholar]
  33. Söhngen N. L. ( 1906 ). Uber Bakterien, welche Methan ab Kohlenstoffnahrung und Energiequelle gerbrauchen. . Z Bakteriol Parasitenkd Infectionsk 15, 513–517 (in German).
     [Google Scholar]
  34. Spieck E., Lipski A. ( 2011 ). Cultivation, growth physiology, and chemotaxonomy of nitrite-oxidizing bacteria. . Methods Enzymol 486, 109–130.[PubMed]
    [Google Scholar]
  35. 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. [View Article] [PubMed]
    [Google Scholar]
  36. Tavormina P. L., Ussler W. III, Orphan V. J. ( 2008 ). Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin. . Appl Environ Microbiol 74, 3985–3995. [View Article] [PubMed]
    [Google Scholar]
  37. Tavormina P. L., Orphan V. J., Kalyuzhnaya M. G., Jetten M. S. M., Klotz M. G. ( 2011 ). A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. . Environ Microbiol Rep 3, 91–100. [View Article] [PubMed]
    [Google Scholar]
  38. Vancanneyt M., Witt S., Abraham W. R., Kersters K., Fredrickson H. L. ( 1996 ). Fatty acid content in whole-cell hydrolysates and phospholipid fractions of pseudomonads: a taxonomic evaluation. . Syst Appl Microbiol 19, 528–540. [View Article]
    [Google Scholar]
  39. Vela G. R., Wyss O. ( 1964 ). Improved stain for visualization of Azotobacter encystment. . J Bacteriol 87, 476–477.[PubMed]
    [Google Scholar]
  40. Vorobev A. V., Baani M., Doronina N. V., Brady A. L., Liesack W., Dunfield P. F., Dedysh S. N. ( 2011 ). Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase. . Int J Syst Evol Microbiol 61, 2456–2463. [View Article] [PubMed]
    [Google Scholar]
  41. Whittenbury R., Phillips K. C., Wilkinson J. F. ( 1970 ). Enrichment, isolation and some properties of methane-utilizing bacteria. . J Gen Microbiol 61, 205–218. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.057794-0
Loading
Methylomonas lenta sp. nov., a methanotroph isolated from manure and a denitrification tank
Int J Syst Evol Microbiol 64, 1210 (2014); https://doi.org/10.1099/ijs.0.057794-0
/content/journal/ijsem/10.1099/ijs.0.057794-0
/content/journal/ijsem/10.1099/ijs.0.057794-0
Loading

Data & Media loading...

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