1887

Abstract

A methanogenic archaeon, strain MK4, was isolated from ancient permafrost after long-term selective anaerobic cultivation. The cells were rods, 2.0–8.0 μm long and 0.40–0.45 μm wide, and stained Gram-negative. Optimal growth was observed at 28 °C and pH 7.0–7.2 and in 0.05 M NaCl. The isolate used H plus CO, methylamine plus H and methanol plus H as sources for growth and methanogenesis. Phylogenetic analysis of the 16S rRNA gene sequence of the strain showed close affinity with (similarity >99 % to the type strain). On the basis of the level of DNA–DNA hybridization (62 %) between strain MK4 and VKM B-1629 and phenotypic and phylogenetic differences, strain MK4 was assigned to a novel species of the genus , sp. nov., with the type strain MK4 (=DSM 19849 =VKM B-2440).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.011205-0
2010-02-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/2/455.html?itemId=/content/journal/ijsem/10.1099/ijs.0.011205-0&mimeType=html&fmt=ahah

References

  1. Balch W. E., Fox G. E., Magrum L. J., Wolfe R. S. 1979; Methanogens: reevalution of a unique biological group. Microbiol Rev 43:260–296
    [Google Scholar]
  2. Boone D. R. 1987; Replacement of the type strain of Methanobacterium formicicum and reinstatement of Methanobacterium bryantii sp. nov., nom. rev. (ex Balch and Wolfe 1981) with M.o.H. (DSM 863) as the type strain. Int J Syst Bacteriol 37:172–173 [CrossRef]
    [Google Scholar]
  3. Boone D. R., Whitman W. B. 1988; Proposal of minimal standards for describing new taxa of methanogenic bacteria. Int J Syst Bacteriol 38:212–219 [CrossRef]
    [Google Scholar]
  4. Bryant M. P., Boone D. R. 1987; Isolation and characterization of Methanobacterium formicicum MF. Int J Syst Bacteriol 37: 171 [CrossRef]
    [Google Scholar]
  5. Bryant M. P., Wolin E. A., Wolin M. J., Wolfe R. S. 1967; Methanobacillus omelianskii , a symbiotic association of two species of bacteria. Arch Mikrobiol 59:20–31 [CrossRef]
    [Google Scholar]
  6. Corradi C., Kolle O., Walter K., Zimov S. A., Schulze E.-D. 2005; Carbon dioxide and methane exchange of a north-east Siberian tussock tundra. Glob Chang Biol 11:1910–1925
    [Google Scholar]
  7. Cuzin N., Ouattara A. S., Labat M., Garcia J.-L. 2001; Methanobacterium congolense sp. nov., from a methanogenic fermentation of cassava peel. Int J Syst Evol Microbiol 51:489–493
    [Google Scholar]
  8. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [CrossRef]
    [Google Scholar]
  9. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  10. Franzmann P. D., Springer N., Ludwig W., Conway de Macario E., Rohde M. 1992; A methanogenic archaeon from Ace Lake, Antarctica – Methanococcoides burtonii sp. nov. Syst Appl Microbiol 15:573–581 [CrossRef]
    [Google Scholar]
  11. Franzmann P. D., Liu Y., Balkwill D. L., Aldrich H. C., Conway de Macario E., Boone D. R. 1997; Methanogenium frigidum sp. nov., a psychrophilic, H2-using methanogen from Ace Lake, Antarctica. Int J Syst Bacteriol 47:1068–1072 [CrossRef]
    [Google Scholar]
  12. Gilichinsky D., Khlebnikova G., Zvyagintsev D., Fyodorov-Davydov D., Kudryavtseva N. 1989; Microbiology of sedimentary materials in the permafrost zone. Int Geol Rev 31:847–858 [CrossRef]
    [Google Scholar]
  13. Hungate R. E. 1969; A roll tube method for cultivation of strict anaerobes. Methods Microbiol 3B:117–132
    [Google Scholar]
  14. Joulian C., Patel B. K. C., Ollivier B., Garcia J.-L., Roger P. A. 2000; Methanobacterium oryzae sp. nov., a novel methanogenic rod isolated from a Philippines ricefield. Int J Syst Evol Microbiol 50:525–528 [CrossRef]
    [Google Scholar]
  15. Kotelnikova S. V., Obraztsova A. Ya., Gongadze G. M., Laurinavichius K. S. 1993; Methanobacterium thermoflexum sp. nov. and Methanobacterium defluvii sp. nov.: thermophilic rod-shaped methanogens isolated from anaerobic digester sludge. Syst Appl Microbiol 16:427–435 [CrossRef]
    [Google Scholar]
  16. Kotelnikova S., Macario A. J. L., Pedersen K. 1998; Methanobacterium subterraneum sp. nov., a new alkaliphilic, eurythermic and halotolerant methanogen isolated from deep granitic groundwater. Int J Syst Bacteriol 48:357–367 [CrossRef]
    [Google Scholar]
  17. Lomans B. P., Maas R., Luderer R., Op den Camp H. J. M., Pol A., van der Drift C., Vogels G. D. 1999; Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl Environ Microbiol 65:3641–3650
    [Google Scholar]
  18. Ma K., Liu X., Dong X. 2005; Methanobacterium beijingense sp. nov., a novel methanogen isolated from anaerobic digesters. Int J Syst Evol Microbiol 55:325–329 [CrossRef]
    [Google Scholar]
  19. Morita R. Y. 1975; Psychrophilic bacteria. Bacteriol Rev 39:144–167
    [Google Scholar]
  20. Müller V., Blaut M., Gottschalk G. 1986; Utilization of methanol plus hydrogen by Methanosarcina barkeri for methanogenesis and growth. Appl Environ Microbiol 52:269–274
    [Google Scholar]
  21. Powell G. E. 1983; Interpreting gas kinetics of batch culture. Biotechnol Lett 5:437–440 [CrossRef]
    [Google Scholar]
  22. Rivkina E., Gilichinsky D., Wagener S., Tiedje J., McGrath J. 1998; Biogeochemical activity of anaerobic microorganisms from buried permafrost sediments. Geomicrobiol J 15:187–193 [CrossRef]
    [Google Scholar]
  23. Rivkina E., Gilichinsky D., McKay C., Dallimore S. 2001; Methane distribution in permafrost: evidence for an interpore pressure methane hydrate. In Permafrost Response on Economic Development, Environmental Security and Natural Resources pp 487–497 Edited by Paepe R., Melnikov V. P. Dordrecht: Kluwer Academic;
    [Google Scholar]
  24. Rivkina E., Shcherbakova V., Laurinavichuis K., Petrovskaya L., Krivushin K., Kraev G., Pecheritsina S., Gilichinsky D. 2007; Biogeochemistry of methane and methanogenic archaea in permafrost. FEMS Microbiol Ecol 61:1–15 [CrossRef]
    [Google Scholar]
  25. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  26. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual , 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  27. Schirrmeister L., Siegert C., Kuznetsova T., Kuzmina S., Andreev A., Kienast F., Meyer H., Bobrov A. A. 2002; Paleoenvironmental and paleoclimatic records from permafrost deposits in the Arctic region of Northern Siberia. Quat Int 89:97–118 [CrossRef]
    [Google Scholar]
  28. Shcherbakova V. A., Chyvilskya N. A., Rivkina E. M., Pecheritsyna S. A., Laurinavichius K. S., Suzina N. E., Osipov Yu. A., Lysenko A. M., Gilichinsky D. A., Akimenko V. K. 2005; Novel psychrophilic anaerobic spore-forming bacterium from the overcooled water brine in permafrost: description Clostridium algoriphilum sp. nov. Extremophiles 9:239–246 [CrossRef]
    [Google Scholar]
  29. Sher A. V. 1974; Pleistocene mammals and stratigraphy of the Far Northeast USSR and North America. Int Geol Rev 16:1–284 [CrossRef]
    [Google Scholar]
  30. Sher A. V. 1997; A brief overview of the Late-Cenozoic history of the Western Beringian lowlands. In Terrestrial Paleoenvironmental Studies in Beringia pp 3–6 Edited by Edwards M. E., Sher A. V., Guthrie R. D. Fairbanks, AK: University of Alaska Museum;
    [Google Scholar]
  31. Sher A. V., Kuzmina S. A., Kuznetsova T. V., Sulerzhitsky L. D. 2005; New insights into the Weichselian environment and climate of the East Siberian Arctic, derived from fossil insects, plants, and mammals. Quat Sci Rev 24:533–569 [CrossRef]
    [Google Scholar]
  32. Shi T., Reeves R. H., Gilichinsky D. A., Friedmann E. I. 1997; Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing. Microb Ecol 33:169–179 [CrossRef]
    [Google Scholar]
  33. Shlimon A. G., Friedrich M. W., Niemann H., Ramsing N. B., Finster K. 2004; Methanobacterium aarhusense sp. nov., a novel methanogen isolated from a marine sediment (Aarhus Bay, Denmark). Int J Syst Evol Microbiol 54:759–763 [CrossRef]
    [Google Scholar]
  34. Tamura K., Nei M., Kumar S. 2004; Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035 [CrossRef]
    [Google Scholar]
  35. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [CrossRef]
    [Google Scholar]
  36. Vatsurina A., Badrutdinova D., Schumann P., Spring S., Vainshtein M. 2008; Desulfosporosinus hippei sp. nov., a mesophilic sulfate-reducing bacterium isolated from permafrost. Int J Syst Evol Microbiol 58:1228–1232 [CrossRef]
    [Google Scholar]
  37. Virina E. I. 1997; Paleomagnetic stratigraphy of Pliocene/Pleistocene sediments of the Kolyma lowland and some problems of correlation with the Alaska record. In Terrestrial Paleoenvironmental Studies in Beringia pp 19–24 Edited by Edwards M. E., Sher A. V., Guthrie R. D. Fairbanks, AK: University of Alaska Museum;
    [Google Scholar]
  38. Vishnivetskaya T., Kathariou S., McGrath J., Gilichinsky D., Tiedje J. 2000; Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments. Extremophiles 3:165–173
    [Google Scholar]
  39. Vorobyova E., Soina V., Gorlenko M., Minkovskaya N., Mamukelashvili A., Zalinova N., Gilichinsky D., Rivkina E., Vishnivetskaya T. 1997; The deep cold biosphere: facts and hypothesis. FEMS Microbiol Rev 20:277–290 [CrossRef]
    [Google Scholar]
  40. Worakit S., Boone D. R., Mah R. A., Abdel-Samie M.-E., El-Halwagi M. M. 1986; Methanobacterium alcaliphilum sp. nov., an H2-utilizing methanogen that grows at high pH values. Int J Syst Bacteriol 36:380–382 [CrossRef]
    [Google Scholar]
  41. Zazhigin V. S. 1997; Late-Pliocene and Pleistocene rodent faunas in the Kolyma lowland: possible correlations with North America. In Terrestrial Paleoenvironmental Studies in Beringia pp 25–29 Edited by Edwards M. E., Sher A. V., Guthrie R. D. Fairbanks, AK: University of Alaska Museum;
    [Google Scholar]
  42. Zellner G., Winter J. 1987; Secondary alcohols as hydrogen donors for CO2-reduction by methanogens. FEMS Microbiol Lett 44:323–328 [CrossRef]
    [Google Scholar]
  43. Zellner G., Bleicher K., Braun E., Kneifel H., Tindall B. J., Conway de Macario E., Winter J. 1989; Characterization of a new mesophilic, secondary alcohol-utilizing methanogen, Methanobacterium palustre spec. nov. from a peat bog. Arch Microbiol 151:1–9
    [Google Scholar]
  44. Zvyagintsev D. G., Gilichinsky D. A., Blagodatsky S. A., Vorobyova E. A., Khlebnikova G. M., Arkhangelov A. A., Kudryavtseva N. N. 1985; The time of microbial preservation in constantly frozen sedimentary rocks and buried soils. Mikrobiologiia 54:155–163 (in Russian)
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.011205-0
Loading
/content/journal/ijsem/10.1099/ijs.0.011205-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF
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