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Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing

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Abstract

Archaeal communities of permafrost deposits of King George Island and Bunger Hills Oasis (Antarctica) differing in the content of biogenic methane were analyzed using the clone libraries of two 16S rRNA gene regions. Phylotypes belonging to methanogenic archaea were identified in all horizons.

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References

  1. Abramov, A.A., Sletten, R.S., Rivkina, E.M., Mironov, V.A., and Gilichinskii, D.A., Geocryological conditions of Antarctica, Kriosfera Zemli, 2011, vol. 15, no. 3, pp. 3–19.

    Google Scholar 

  2. Anisimov, M.A., Ezhikov, I.S., Verkulich, S.R., and Stepanova, O.V., Glaciological monitoring of Antarctic edge zone: first results and prospects, in Prirodnye riski: analiz, otsenka, kartografirovanie (Environmental Risks: Analysis, Assessment, and Mapping), Proc. Int. Sci. Conf., Moscow: Mos. Gos. Univ., 2013, pp. 13–17.

    Google Scholar 

  3. Verkulich, S.R., Pushina, Z.V., and Demidov, N.E., Interstadial conditions (MIS3) and glaciation patterns of the last glacial maximum in Antarctic edge zone, in Prirodnye riski: analiz, otsenka, kartografirovanie (Environmental Risks: Analysis, Assessment, and Mapping), Proc. Int. Sci. Conf., Moscow: Mos. Gos. Univ., 2013, pp. 53–57.

    Google Scholar 

  4. Mironov, V.A., Scherbakova, V.A., Rivkina, E.M., and Gilichinsky D.A., Thermophilic bacteria of the genus Geobacillus from permafrost volcanic sedimentary rocks, Microbiology (Moscow), 2013, vol. 82, no. 3, pp. 389–392.

    Article  CAS  Google Scholar 

  5. Cameron, R.E. and Morelli, F.A., Viable microorganisms from ancient Ross Island and Taylor Valley drill core, Antarctic J. U.S., 1974, vol. 9, no. 4, pp. 113–116.

    Google Scholar 

  6. Gilichinsky, D.A., Wilson, G.S., Friedmann, E.I., McKay, C.P., Slattem, R.S., Rivkina, E.M., Vishnivetskaya, T.A., Erocjina, L.G., Ivanushkina, N.E., Kochkina, G.A., Scherbakova, V.A., Soina, V.S., Spirina, E.V., Vorobyova, E.A., Fyodorov-Davydov, D.G., Hallet, B., Ozerskaya, S.M., Sorokovikov, V.A., Laurinavichyus, K.S., Shatilovich, A.V., Chanton, J.P., Ostroumov, V.E., and Tidje, J.M., Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology, Astrobiology, 2007, vol. 7, no. 2, pp. 275–311.

    Article  CAS  PubMed  Google Scholar 

  7. Vorobyova, E., Soina, V., Gorlenko, M., Minkovskaya, N., Zalinova, N., Mamukelashvili, A., Gilichinsky, D., Rivkina, E., and Vishnivetskaya, T., The deep cold biosphere: facts and hypothesis. Microorganisms and biomarkers in permafrost, FEMS Microbiol. Rev., 1997, vol. 20, pp. 277–290.

    Article  CAS  Google Scholar 

  8. Demidov, N.E., Verkulich, S.R., Zanina, O.G., Karaevskaya, E.S., Pushina, Z.V., Rivkina, E.M., and Shmelev, D.G., Terminal moraine and lake-lagoon deposits in the section of Quaternary deposits of the Larcemann Hills oasis, East Antarctica, Problemy Arktiki i Antarktiki, AANII, 2013, vol. 97, no. 3, pp. 79–90.

    Google Scholar 

  9. Rivkina, E., Shcherbakova, V., Laurinavichius, K., Petrovskaya, L., Krivushin, K., Kraev, G., Pecheritsina, S., and Gilichinsky, D., Biogeochemistry of methane and methanogenic archaea in permafrost, FEMS Microbiol. Ecol., 2007, vol. 61, no. 1, pp. 1–15.

    Article  CAS  PubMed  Google Scholar 

  10. Chuvochina, M.S., Marie, D., Chevaillier, S., Petit, J.R., Normand, P., Alekhina, I.A., and Bulat, S.A., Community variability of bacteria in alpine snow (Mont Blanc) containing Saharan dust deposition and their snow colonisation potential, Microbes Environ., 2011, vol. 26, no. 3, pp. 237–247.

    Article  PubMed  Google Scholar 

  11. Karlov, D.S., Chuvochina, M.S., Alekhina, I.A., Bulat, S.A., and Marie, D., Microbial communities of water column of Lake Radok, East Antarctica, dominated by abundant actinobacterium “Candidatus Planktophila limnetica,” Microbiology (Moscow), 2011, vol. 80, no. 4, pp. 576–579.

    Article  CAS  Google Scholar 

  12. Alperin, M.J. and Reeburgh, W.S., Inhibition experiments on anaerobic methane oxidation, Appl. Environ. Microbiol., 1985, vol. 50, no. 4, pp. 940–945.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Coplen, T.B., Reporting of stable hydrogen, carbon, and oxygen isotopic abundances, Pure Appl. Chem., 1994, vol. 66, pp. 273–276.

    Article  CAS  Google Scholar 

  14. Shcherbakova, V., Rivkina, E., Pecheritsyna, S., Laurinavichius, K., Suzina, N., and Gilichinsky, D., Methanobacterium arcticum sp. nov., a methanogenic archaeon from Holocene Arctic permafrost, Int. J. Syst. Evol. Microbiol., 2011, vol. 61, no. 1, pp. 144–147.

    Article  CAS  PubMed  Google Scholar 

  15. Bulat, S.A., Alekhina, I.A., Blot, M., Petit, J.R., de Angelis, M., Wagenbach, D., Lipenkov, V.Ya., Vasilyeva, L.P., Wloch, D., Raynaud, D., and Lukin, V.V., DNA signature of thermophilic bacteria from the aged accretion ice of Lake Vostok, Antarctica: implications for searching for life in extreme icy environmentals, Int. J. Astrobiol., 2004, vol. 3, pp. 1–7.

    Article  CAS  Google Scholar 

  16. Murray, P.A. and Zinder, S.S., Nutritional requirements of Methanosarcina sp. strain TM-1, Appl. Environ. Microbiol., 1985, vol. 50, no. 1, pp. 49–55.

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Miller, T.L. and Lin, C., Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov., Int. J. Syst. Evol. Microbiol., 2002, no. 52, pp. 819–822.

    Google Scholar 

  18. Hatzenpichler, R., Lebedeva, E.V., Spieck, E., Stoecker, K., Richter, A., Daims, H., and Wagner, M., A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring, PNAS, 2007, vol. 105, no. 6, pp. 2134–2139.

    Article  Google Scholar 

  19. Segerer, A., Langworthy, T.A., and Stetter, K.O., Thermoplasma acidophilum and Thermoplasma volcanium sp. nov. from solfatara fields, Syst. Appl. Microbiol., 1988, vol. 10, no. 2, pp. 161–171.

    Article  Google Scholar 

  20. Zyakun, A.M., Potential of 13C/12C variations in bacterial methane in assessing origin of environmental methane, in Hydrocarbon Migration and Its Near-Surface Expression, Schumacher, D. and Abrams, M., Eds., AAPG Memoir, Fairbanks, AL: Alaska Quaternary Center, 1996, vol. 66, pp. 341–352.

    Google Scholar 

  21. Simankova, M.V., Parshina, S.N., Tourova, T.P., Kolganova, T.V., Zehnder, A.J.B., and Nozhevnikova, A.N., Methanosarcina lacustris sp. nov., a new psychrotolerant methanogenic archaeon from anoxic lake sediments, Syst. Appl. Microbiol., 2001, vol. 4, no. 3, pp. 362–367.

    Article  Google Scholar 

  22. Lomans, B.P., Maas, R., Luderer, R., Op den Camp, H.J.M., Pol, A., Van der Drift, C., and Vogels, G.D., 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., 1999, vol. 65, no. 8, pp. 3641–3650.

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Kim, J.G., Jung, M.Y., Park, S.J., and Rijpstra, W.I., Sinninghe Damsté, J.S., Madsen, E.L., Min, D., Kim, J.S., Kim, G.J., and Rhee, S.K., Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I. 1b from an agricultural soil, Environ. Microbiol., 2012, vol. 14, no. 6, pp. 1528–1543.

    Article  CAS  PubMed  Google Scholar 

  24. Lynch, R.C., King, A.J., Farias, M.E., Sowell, P., Vitry, C., and Schmidt, S.K., The potential for microbial life in the highest elevation (>6000 m.a.s.l.) mineral soils of the Atacama region, J. Geophys. Res., 2012, vol. 117, p. G02028.

    Google Scholar 

  25. Spang, A., Hatzenpichler, R., Brochier-Armanet, C., Rattei, T., Tischler, P., Spieck, E., Streit, W., Stahl, D.A., Wagner, M., and Schleper, C., Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota, Trends Microbiol., 2010, vol. 18, no. 8, pp. 331–340.

    Article  CAS  PubMed  Google Scholar 

  26. Bouali, M., Zrafi-Nouira, I., Bakhrouf, A., Le Paslier, D., Chaussonnerie, S., Ammar, E., and Sghir, A., The structure and spatio-temporal distribution of the “Archaea” in a horizontal subsurface flow constructed wetland, Sci. Total Environ., 2012, vol. 435, pp. 465–471.

    Article  PubMed  Google Scholar 

  27. Nakamura, K., Takahashi, A., Mori, C., Tamaki, H., Mochimaru, H., Nakamura, K., Takamizawa, K., and Kamagata, Y., Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field, Int. J. Syst. Evol. Microbiol., 2013, vol. 63, no. 2, pp. 715–722.

    Article  CAS  PubMed  Google Scholar 

  28. Ohkuma, M., Noda, S., and Kudo, T., Phylogenetic relationships of symbiotic methanogens in diverse termites, FEMS Microbiol. Lett., 1999, vol. 171, no. 2, pp. 147–153.

    Article  CAS  PubMed  Google Scholar 

  29. Beal, E.J., House, C.H., and Orphan, V.J., Manganese-and iron-dependent marine methane oxidation, Science, 2009, vol. 325, no. 5937, pp. 184–187.

    Article  CAS  PubMed  Google Scholar 

  30. Wang, T., He, J., and Li, S., Isolation and characterization of methanogens from biogas fermentation reactor, Direct Genbank submission, 2005.

    Google Scholar 

  31. Zeikus, J.G. and Henning, D.L., Methanobacterium arbophilicum sp. nov. an obligate anaerobe isolated from wetwood of living trees, Antonie van Leeuwenhoek, 1975, vol. 41, no. 1, pp. 543–552.

    Article  CAS  PubMed  Google Scholar 

  32. Dridi, B., Richet, H., Cohen-Bacrie, S., Raoult, D., and Drancourt, M., Archaeal diversity of the human gut, Direct Genbank submission, 2010.

    Google Scholar 

  33. Iino, T., Tamaki, H., Tamazawa, S., Ueno, Y., Ohkuma, M., Suzuki, K., Igarashi, Y., and Haruta, S., Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata, Microbes Environ., 2012, vol. 28, no. 2, pp. 244–250.

    Article  Google Scholar 

  34. Gao, Y., Li, F., and Qin, S., Vertical distribution and diversity of bacteria and archaea in methane-rich cold seep sediments located at the base of the Okhotsk Sea, Direct NCBI submission, 2009.

    Google Scholar 

  35. Anderson, I.J., Sun, H., Lapidus, A., Copeland, A., Glavina, DelRioT., Tice, H., Dalin, E., Lucas, S., Barry, K., Land, M., Richardson, P., Huber, H., and Kyrpides, N.C., Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1, Standards Genomic Sci., 2009, vol. 1, no. 2, p. 183.

    Article  Google Scholar 

  36. Dang, H., Luan, X.W., Chen, R., Zhang, X., Guo, L., and Klotz, M.G., Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea, FEMS Microbiol. Ecol., 2010, vol. 72, no. 3, pp. 370–385.

    Article  CAS  PubMed  Google Scholar 

  37. Lyimo, T.J., Pol, A., Op den Camp, H.J., Harhangi, H.R., and Vogels, G.D., Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment, Int. J. Syst. Evol. Microbiol., 2000, vol. 50, no. 1, pp. 171–178.

    Article  CAS  PubMed  Google Scholar 

  38. Wright, A.D.G. and Pimm, C., Improved strategy for presumptive identification of methanogens using 16S riboprinting, J. Microbiol. Methods, 2003, vol. 55, no. 2, pp. 337–349.

    Article  CAS  PubMed  Google Scholar 

  39. Qiu, T., Cheng, L., Zhang, H., and Deng, Y., Direct Genbank Submission, 2012.

    Google Scholar 

  40. Rouviere, P., Mandelco, L., Winker, S., and Woese, C.R., A detailed phylogeny for the “Methanomicrobiales,” Syst. Appl. Microbiol., 1992, vol. 15, no. 3, pp. 363–371.

    Article  CAS  PubMed  Google Scholar 

  41. Yanagawa, K., Nunoura, T., McAllister, S.M., Hirai, M., Breuker, A., Brandt, L., House, C.H., Moyer, C.L., Birrien, J.L., Aoike, K., Sunamura, M., Urabe, T., Mottl, M.J., and Takai, K., The first microbiological contamination assessment by deep-sea drilling and coring by the D/V Chikyu at the Iheya North hydrothermal field in the Mid-Okinawa Trough (IODP expedition 331), Front. Microbiol., 2013, no. 4, p. 327.

    Google Scholar 

  42. Tourna, M., Stieglmeier, M., Spang, A., Könneke, M., Schintlmeister, A., Urich, T., Engel, M., Schloter, M., Wagner, M., Richter, A., and Schleper, C., Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil, Proc. Natl. Acad. Sci. U. S. A., 2011, vol. 108, no. 20, pp. 8420–8425.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Chan, Y.-K., McCormick, W.A., and Ma, B.L., Effects of inorganic fertilizer and manure on soil archaeal abundance at two experimental farms during three consecutive rotation-cropping seasons, Agric. Ecosyst. Environ. Appl. Soil Ecol., 2013, vol. T. 68, pp. 26–35.

    Article  Google Scholar 

  44. Herrmann, M., Saunders, A.M., and Schramm, A., Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora, Appl. Environ. Microbiol., 2008, vol. 74, no. 10, pp. 3279–3283.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Imachi, H., Aoi, K., Tasumi, E., Saito, Y., Yamanaka, Y., Saito, Y., Yamaguchi, T., Tomaru, H., Takeuchi, R., Morono, Y., Inagaki, F., and Takai, K., Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor, ISME J., 2011, vol. 5, no. 12, pp. 1913–1925.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Yarza, P., Euzeby, J., Sproeer, C., Klenk, H.P., and Crouch, A., Taxonomic note: SOS, Sequencing Orphan Species: filling the gaps in the 16S rRNA gene sequence database for all classified species with validly published names, Direct Genbank submission, 2013.

    Google Scholar 

  47. Zengler, K., Richnow, H.H., Rosselló-Mora, R., Michaelis, W., and Widdel, F., Methane formation from long-chain alkanes by anaerobic microorganisms, Nature, 1999, vol. 401, no. 6750, pp. 266–269.

    Article  CAS  PubMed  Google Scholar 

  48. Kuhlman, K.R., Fusco, W.G., La Duc, M.T., Allenbach, L.B., Ball, C.L., Kuhlman, G.M., Anderson, R.C., Erickson, I.K., Stuecker, T., Benardini, J., Strap, J.L., and Crawford, R.L., Diversity of microorganisms within rock varnish in the Whipple Mountains, California, Appl. Environ. Microbiol., 2006, vol. 72, no. 2, pp. 1708–1715.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Boyd, E.S., Skidmore, M., Mitchell, A.C., Bakermans, C., and Peters, J.W., Methanogenesis in subglacial sediments, Environ. Microbiol. Rep., 2010, vol. 2, no. 5, pp. 685–692.

    Article  CAS  PubMed  Google Scholar 

  50. Flynn, T.M., Sanford, R.A., Ryu, H., Bethke, C.M., Levine, A.D., Ashbolt, N.J., and Santo Domingo, J.W., Functional microbial diversity explains groundwater chemistry in a pristine aquifer, BMC Microbiol., 2013, vol. 13, no. 1, p. 146.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Institute of Physicochemical and Biological Problems of Soil Science, Russian Academy of Sciences, Pushchino, Russia

    E. S. Karaevskaya, N. E. Demidov, E. M. Rivkina & D. A. Gilichinsky

  2. Konstantinov Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, Gatchina, Russia

    L. S. Demchenko & S. A. Bulat

Authors
  1. E. S. Karaevskaya
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  2. L. S. Demchenko
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  3. N. E. Demidov
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  4. E. M. Rivkina
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  5. S. A. Bulat
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  6. D. A. Gilichinsky
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Correspondence to E. S. Karaevskaya.

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Original Russian Text © E.S. Karaevskaya, L.S. Demchenko, N.E. Demidov, E.M. Rivkina, S.A. Bulat, D.A. Gilichinsky, 2014, published in Mikrobiologiya, 2014, Vol. 83, No. 4, pp. 475–483.

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Karaevskaya, E.S., Demchenko, L.S., Demidov, N.E. et al. Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing. Microbiology 83, 398–406 (2014). https://doi.org/10.1134/S0026261714040092

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