publication . Article . 2016

Stable and variable parts of microbial community in Siberian deep subsurface thermal aquifer system revealed in a long-term monitoring study

Frank, Yulia A.; Kadnikov, Vitaly V.; Gavrilov, Sergei N.; Banks, David; Gerasimchuk, Anna L.; Podosokorskaya, Olga A.; Merkel, Alexander Y.; Chernyh, Nikolai A.; Mardanov, Andrey V.; Ravin, Nikolai V.; ...
Open Access English
  • Published: 27 Dec 2016 Journal: Frontiers in Microbiology, volume 7 (issn: 1664-302X, eissn: 1664-302X, Copyright policy)
  • Publisher: Frontiers Media
Abstract
The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of five years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50oC. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surfac...
Subjects
free text keywords: QR, phylogenetic analysis, element cycles and biogeochemical processes, QE, deep subsurface, Western Siberia, Microbiology, Original Research, thermophilic microbial communities
88 references, page 1 of 6

Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nuclic Acids Res. 25, 389-402. doi: 10.1093/nar/25.17.3389

Banks, D. (2012). An Introduction to Thermogeology: Ground Source Heating and Cooling, 2nd Edn. Chichester: John Wiley and Sons.

Banks, D., Frank, Y. A., Kadnikov, V. V., Watts, M., Boyce, A., and Frengstad, B. S. (2014). Hydrochemical Data Report from Sampling of Two Deep Abandoned Hydrocarbon Exploration Wells: Byelii Yar and Parabel', Tomsk oblast', Western Siberia, Russian Federation, NGU Report 2014.034, Geological Survey of Norway, Trondheim.

Banks, D., Parnachev, V. P., Karnachuk, O. V., Arkhipov, A. L., Gundersen, P., and Davis, J. (2011). Hydrogeochemical Data Report: The Sampling of Selected Localities in Kemerovo oblast' and Tomsk oblast', Siberia, Russian Federation, NGU Report 2011.054, Geological Survey of Norway, Trondheim.

Batzke, A., Engelen, B., Sass, H., and Cypionka, H. (2007). Phylogenetic and physiological diversity of cultured deep-biosphere bacteria from equatorial Pacific ocean and Peru margin sediments. Geomicrobiol. J. 24, 261-273. doi: 10.1080/01490450701456453

Beeder, J., Nilsen, R. K., Rosnes, J. T., Torsvik, T., and Lien, T. (1994). Archaeoglobus fulgidus isolated from hot North Sea oil field waters. Appl. Environ. Microbiol. 60, 1227-1231. [OpenAIRE]

Behnke, A., Engel, M., Christen, R., Nebel, M., Klein, R. R., and Stoeck, T. (2011). Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ. Microbiol. 13, 340-349. doi: 10.1111/j.1462-2920.2010.02332.x

Biddle, J. F., White, J. R., Teske, A. P., and House, C. H. (2011). Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes. ISME J. 5, 1038-1047. doi: 10.1038/ismej.2010.199

Bomberg, M., Nyyssönen, M., Pitkänen, P., Lehtinen, A., and Itävaara, M. (2015). Active microbial communities inhabit sulphate-methane interphase in deep bedrock fracture fluids in Olkiluoto, Finland. BioMed Res. Int. 2015:979530. doi: 10.1155/2015/979530 [OpenAIRE]

Bonch-Osmolovskaya, E. A., Miroshnichenko, M. L., Lebedinsky, A. V., Chernyh, N. A., Nazina, T. N., Ivoilov, V. S., et al. (2003). Radioisotopic, culturebased, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir. Appl. Environ. Microbiol. 69, 6143-6151. doi: 10.1128/AEM.69.10.6143-6151.2003 [OpenAIRE]

Castelle, C. J., Hug, L. A., Wrighton, K. C., Thomas, B. C., Williams, K. H., and Wu, D. (2013). Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat. Commun. 4:2120. doi: 10.1038/ncomms3120

Chen, S. L., Blomberg, M. R., and Siegbahn, P. E. (2012). How is methane formed and oxidized reversibly when catalyzed by Ni-containing methyl-coenzyme M reductase? Chemistry 18, 6309-6315. doi: 10.1002/chem.201200274

Cline, J. D. (1969). Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol. Oceanogr. 14, 454-458. doi: 10.4319/lo.1969.14.3.0454

Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., et al. (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, 141-145. doi: 10.1093/nar/gkn879 [OpenAIRE]

Coolen, M. J. L., Hopmans, E. C., Rijpstra, W. I. C., Muyzer, G., Schouten, S., Volkman, J. K., et al. (2004). Evolution of the methane cycle in Ace Lake (Antarctica) during the Holocene: response of methanogens and methanotrophs to environmental change. Org. Geochem. 35, 1151-1167. doi: 10.1016/j.orggeochem.2004.06.009 [OpenAIRE]

88 references, page 1 of 6
Abstract
The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of five years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50oC. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surfac...
Subjects
free text keywords: QR, phylogenetic analysis, element cycles and biogeochemical processes, QE, deep subsurface, Western Siberia, Microbiology, Original Research, thermophilic microbial communities
88 references, page 1 of 6

Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nuclic Acids Res. 25, 389-402. doi: 10.1093/nar/25.17.3389

Banks, D. (2012). An Introduction to Thermogeology: Ground Source Heating and Cooling, 2nd Edn. Chichester: John Wiley and Sons.

Banks, D., Frank, Y. A., Kadnikov, V. V., Watts, M., Boyce, A., and Frengstad, B. S. (2014). Hydrochemical Data Report from Sampling of Two Deep Abandoned Hydrocarbon Exploration Wells: Byelii Yar and Parabel', Tomsk oblast', Western Siberia, Russian Federation, NGU Report 2014.034, Geological Survey of Norway, Trondheim.

Banks, D., Parnachev, V. P., Karnachuk, O. V., Arkhipov, A. L., Gundersen, P., and Davis, J. (2011). Hydrogeochemical Data Report: The Sampling of Selected Localities in Kemerovo oblast' and Tomsk oblast', Siberia, Russian Federation, NGU Report 2011.054, Geological Survey of Norway, Trondheim.

Batzke, A., Engelen, B., Sass, H., and Cypionka, H. (2007). Phylogenetic and physiological diversity of cultured deep-biosphere bacteria from equatorial Pacific ocean and Peru margin sediments. Geomicrobiol. J. 24, 261-273. doi: 10.1080/01490450701456453

Beeder, J., Nilsen, R. K., Rosnes, J. T., Torsvik, T., and Lien, T. (1994). Archaeoglobus fulgidus isolated from hot North Sea oil field waters. Appl. Environ. Microbiol. 60, 1227-1231. [OpenAIRE]

Behnke, A., Engel, M., Christen, R., Nebel, M., Klein, R. R., and Stoeck, T. (2011). Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ. Microbiol. 13, 340-349. doi: 10.1111/j.1462-2920.2010.02332.x

Biddle, J. F., White, J. R., Teske, A. P., and House, C. H. (2011). Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes. ISME J. 5, 1038-1047. doi: 10.1038/ismej.2010.199

Bomberg, M., Nyyssönen, M., Pitkänen, P., Lehtinen, A., and Itävaara, M. (2015). Active microbial communities inhabit sulphate-methane interphase in deep bedrock fracture fluids in Olkiluoto, Finland. BioMed Res. Int. 2015:979530. doi: 10.1155/2015/979530 [OpenAIRE]

Bonch-Osmolovskaya, E. A., Miroshnichenko, M. L., Lebedinsky, A. V., Chernyh, N. A., Nazina, T. N., Ivoilov, V. S., et al. (2003). Radioisotopic, culturebased, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir. Appl. Environ. Microbiol. 69, 6143-6151. doi: 10.1128/AEM.69.10.6143-6151.2003 [OpenAIRE]

Castelle, C. J., Hug, L. A., Wrighton, K. C., Thomas, B. C., Williams, K. H., and Wu, D. (2013). Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat. Commun. 4:2120. doi: 10.1038/ncomms3120

Chen, S. L., Blomberg, M. R., and Siegbahn, P. E. (2012). How is methane formed and oxidized reversibly when catalyzed by Ni-containing methyl-coenzyme M reductase? Chemistry 18, 6309-6315. doi: 10.1002/chem.201200274

Cline, J. D. (1969). Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol. Oceanogr. 14, 454-458. doi: 10.4319/lo.1969.14.3.0454

Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., et al. (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, 141-145. doi: 10.1093/nar/gkn879 [OpenAIRE]

Coolen, M. J. L., Hopmans, E. C., Rijpstra, W. I. C., Muyzer, G., Schouten, S., Volkman, J. K., et al. (2004). Evolution of the methane cycle in Ace Lake (Antarctica) during the Holocene: response of methanogens and methanotrophs to environmental change. Org. Geochem. 35, 1151-1167. doi: 10.1016/j.orggeochem.2004.06.009 [OpenAIRE]

88 references, page 1 of 6
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publication . Article . 2016

Stable and variable parts of microbial community in Siberian deep subsurface thermal aquifer system revealed in a long-term monitoring study

Frank, Yulia A.; Kadnikov, Vitaly V.; Gavrilov, Sergei N.; Banks, David; Gerasimchuk, Anna L.; Podosokorskaya, Olga A.; Merkel, Alexander Y.; Chernyh, Nikolai A.; Mardanov, Andrey V.; Ravin, Nikolai V.; ...