Articles | Volume 13, issue 7
https://doi.org/10.5194/bg-13-2207-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-13-2207-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Metagenomic analyses of the late Pleistocene permafrost – additional tools for reconstruction of environmental conditions
Elizaveta Rivkina
CORRESPONDING AUTHOR
Institute of Physicochemical and Biological Problems in Soil Science,
Russian Academy of Sciences, Pushchino, Russia
Lada Petrovskaya
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian
Academy of Sciences, Moscow, Russia
Tatiana Vishnivetskaya
Institute of Physicochemical and Biological Problems in Soil Science,
Russian Academy of Sciences, Pushchino, Russia
University of Tennessee, Center for Environmental Biotechnology,
Knoxville, USA
Kirill Krivushin
Institute of Physicochemical and Biological Problems in Soil Science,
Russian Academy of Sciences, Pushchino, Russia
Lyubov Shmakova
Institute of Physicochemical and Biological Problems in Soil Science,
Russian Academy of Sciences, Pushchino, Russia
Maria Tutukina
Bioinformatics and Genomics Programme, Centre for Genomic
Regulation (CRG), Barcelona, Spain
Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino,
Russia
Arthur Meyers
University of Tennessee, Center for Environmental Biotechnology,
Knoxville, USA
Fyodor Kondrashov
Bioinformatics and Genomics Programme, Centre for Genomic
Regulation (CRG), Barcelona, Spain
Universitat Pompeu Fabra (UPF), Barcelona, Spain
Institució Catalana de Recerca i Estudis Avançats (ICREA),
Barcelona, Spain
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Cited
46 citations as recorded by crossref.
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- Earth's perennially frozen environments as a model of cryogenic planet ecosystems E. Rivkina et al. 10.1002/ppp.1987
- The biotechnological potential of microbial communities from Antarctic soils and sediments: Application to low temperature biogenic methane production P. Aguilar-Muñoz et al. 10.1016/j.jbiotec.2022.04.014
- Prokaryotic community in Pleistocene ice wedges of Mammoth Mountain A. Rakitin et al. 10.1007/s00792-019-01138-z
- Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates O. Müller et al. 10.1111/1462-2920.14348
- Biogeochemical Characteristics of Earth's Volcanic Permafrost: An Analog of Extraterrestrial Environments T. Vishnivetskaya et al. 10.1089/ast.2021.0137
- Geochemical Features of Ground Ice from the Faddeevsky Peninsula Eastern Coast (Kotelny Island, East Siberian Arctic) as a Key to Understand Paleoenvironmental Conditions of Its Formation A. Pismeniuk et al. 10.3390/land12020324
- New member of the hormone-sensitive lipase family from the permafrost microbial community L. Petrovskaya et al. 10.1080/21655979.2016.1230571
- Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau Y. Chen et al. 10.1111/mec.14396
- Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients M. Waldrop et al. 10.1038/s41396-023-01429-6
- Life at the Frozen Limit: Microbial Carbon Metabolism Across a Late Pleistocene Permafrost Chronosequence M. Leewis et al. 10.3389/fmicb.2020.01753
- Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost R. Liang et al. 10.1128/AEM.00560-19
- Permafrost Microbial Community Structure Changes Across the Pleistocene-Holocene Boundary A. Saidi-Mehrabad et al. 10.3389/fenvs.2020.00133
- Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities E. Bottos et al. 10.1093/femsec/fiy110
- Frozen Zoo: a collection of permafrost samples containing viable protists and their viruses S. Malavin et al. 10.3897/BDJ.8.e51586
- Free Iron and Iron-Reducing Microorganisms in Permafrost and Permafrost-Affected Soils of Northeastern Siberia E. Rivkina et al. 10.1134/S1064229320100166
- Microeukaryotes in the Metagenomes of Late Pleistocene Permafrost Deposits L. Shmakova et al. 10.1134/S003103012008016X
- Insights into community of photosynthetic microorganisms from permafrost T. Vishnivetskaya et al. 10.1093/femsec/fiaa229
- Simple kinetics, assay, and trends for soil microbial catalases M. Chabot et al. 10.1016/j.ab.2020.113901
- First evidence for cold-adapted anaerobic oxidation of methane in deep sediments of thermokarst lakes M. Winkel et al. 10.1088/2515-7620/ab1042
- Microbial Community Changes in 26,500-Year-Old Thawing Permafrost M. Scheel et al. 10.3389/fmicb.2022.787146
- Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico B. Moguel et al. 10.1038/s41598-021-92981-8
- Bacterial Communities of Novaya Zemlya Archipelago Ice and Permafrost A. Belov et al. 10.3390/geosciences10020067
- Archaeal communities of Arctic methane-containing permafrost V. Shcherbakova et al. 10.1093/femsec/fiw135
- Abiotic factors affecting the bacterial and fungal diversity of permafrost in a rock glacier in the Stelvio Pass (Italian Central Alps) C. Sannino et al. 10.1016/j.apsoil.2021.104079
- Methanogenic response to long-term permafrost thaw is determined by paleoenvironment S. Holm et al. 10.1093/femsec/fiaa021
- Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost R. Liang et al. 10.1186/s40168-021-01057-2
- Microbiological Study of Yamal Lakes: A Key to Understanding the Evolution of Gas Emission Craters A. Savvichev et al. 10.3390/geosciences8120478
- Mycoplasma Diversity in Arctic Permafrost I. Vishnyakov et al. 10.1007/s12668-016-0280-3
- Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia) S. Zaitseva et al. 10.3390/microorganisms10112202
- A New Methanogenic, Hydrogenotrophic Archaeon from Spitsbergen Permafrost V. Trubitsyn et al. 10.31857/S002636562260064X
- Biotechnological perspectives of microorganisms isolated from the Polar Regions V. Shcherbakova & O. Troshina 10.1071/MA18042
- A New Methanogenic, Hydrogenotrophic Archaeon from Spitsbergen Permafrost V. Trubitsyn et al. 10.1134/S0026261722603256
- Microbial survival strategies in ancient permafrost: insights from metagenomics R. Mackelprang et al. 10.1038/ismej.2017.93
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- Effects of a long‐term anoxic warming scenario on microbial community structure and functional potential of permafrost‐affected soil S. Yang et al. 10.1002/ppp.2131
- Geomorphological and Climatic Drivers of Thermokarst Lake Area Increase Trend (1999–2018) in the Kolyma Lowland Yedoma Region, North-Eastern Siberia A. Veremeeva et al. 10.3390/rs13020178
- Ecological Characteristics of Antarctic Fungi D. Nikitin 10.1134/S0012496622700120
- Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost K. Sipes et al. 10.1128/AEM.00972-21
- Microbial and Geochemical Evidence of Permafrost Formation at Mamontova Gora and Syrdakh, Central Yakutia M. Cherbunina et al. 10.3389/feart.2021.739365
- Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics X. Wu et al. 10.1186/s40793-023-00487-9
- Are permafrost microorganisms as old as permafrost? A. Abramov et al. 10.1093/femsec/fiaa260
- Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples A. Saidi-Mehrabad et al. 10.1038/s41598-020-71234-0
- Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia) A. Brouchkov et al. 10.1016/j.gene.2017.09.021
44 citations as recorded by crossref.
- Cryogenic Displacement and Accumulation of Biogenic Methane in Frozen Soils G. Kraev et al. 10.3390/atmos8060105
- Earth's perennially frozen environments as a model of cryogenic planet ecosystems E. Rivkina et al. 10.1002/ppp.1987
- The biotechnological potential of microbial communities from Antarctic soils and sediments: Application to low temperature biogenic methane production P. Aguilar-Muñoz et al. 10.1016/j.jbiotec.2022.04.014
- Prokaryotic community in Pleistocene ice wedges of Mammoth Mountain A. Rakitin et al. 10.1007/s00792-019-01138-z
- Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates O. Müller et al. 10.1111/1462-2920.14348
- Biogeochemical Characteristics of Earth's Volcanic Permafrost: An Analog of Extraterrestrial Environments T. Vishnivetskaya et al. 10.1089/ast.2021.0137
- Geochemical Features of Ground Ice from the Faddeevsky Peninsula Eastern Coast (Kotelny Island, East Siberian Arctic) as a Key to Understand Paleoenvironmental Conditions of Its Formation A. Pismeniuk et al. 10.3390/land12020324
- New member of the hormone-sensitive lipase family from the permafrost microbial community L. Petrovskaya et al. 10.1080/21655979.2016.1230571
- Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau Y. Chen et al. 10.1111/mec.14396
- Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients M. Waldrop et al. 10.1038/s41396-023-01429-6
- Life at the Frozen Limit: Microbial Carbon Metabolism Across a Late Pleistocene Permafrost Chronosequence M. Leewis et al. 10.3389/fmicb.2020.01753
- Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost R. Liang et al. 10.1128/AEM.00560-19
- Permafrost Microbial Community Structure Changes Across the Pleistocene-Holocene Boundary A. Saidi-Mehrabad et al. 10.3389/fenvs.2020.00133
- Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities E. Bottos et al. 10.1093/femsec/fiy110
- Frozen Zoo: a collection of permafrost samples containing viable protists and their viruses S. Malavin et al. 10.3897/BDJ.8.e51586
- Free Iron and Iron-Reducing Microorganisms in Permafrost and Permafrost-Affected Soils of Northeastern Siberia E. Rivkina et al. 10.1134/S1064229320100166
- Microeukaryotes in the Metagenomes of Late Pleistocene Permafrost Deposits L. Shmakova et al. 10.1134/S003103012008016X
- Insights into community of photosynthetic microorganisms from permafrost T. Vishnivetskaya et al. 10.1093/femsec/fiaa229
- Simple kinetics, assay, and trends for soil microbial catalases M. Chabot et al. 10.1016/j.ab.2020.113901
- First evidence for cold-adapted anaerobic oxidation of methane in deep sediments of thermokarst lakes M. Winkel et al. 10.1088/2515-7620/ab1042
- Microbial Community Changes in 26,500-Year-Old Thawing Permafrost M. Scheel et al. 10.3389/fmicb.2022.787146
- Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico B. Moguel et al. 10.1038/s41598-021-92981-8
- Bacterial Communities of Novaya Zemlya Archipelago Ice and Permafrost A. Belov et al. 10.3390/geosciences10020067
- Archaeal communities of Arctic methane-containing permafrost V. Shcherbakova et al. 10.1093/femsec/fiw135
- Abiotic factors affecting the bacterial and fungal diversity of permafrost in a rock glacier in the Stelvio Pass (Italian Central Alps) C. Sannino et al. 10.1016/j.apsoil.2021.104079
- Methanogenic response to long-term permafrost thaw is determined by paleoenvironment S. Holm et al. 10.1093/femsec/fiaa021
- Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost R. Liang et al. 10.1186/s40168-021-01057-2
- Microbiological Study of Yamal Lakes: A Key to Understanding the Evolution of Gas Emission Craters A. Savvichev et al. 10.3390/geosciences8120478
- Mycoplasma Diversity in Arctic Permafrost I. Vishnyakov et al. 10.1007/s12668-016-0280-3
- Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia) S. Zaitseva et al. 10.3390/microorganisms10112202
- A New Methanogenic, Hydrogenotrophic Archaeon from Spitsbergen Permafrost V. Trubitsyn et al. 10.31857/S002636562260064X
- Biotechnological perspectives of microorganisms isolated from the Polar Regions V. Shcherbakova & O. Troshina 10.1071/MA18042
- A New Methanogenic, Hydrogenotrophic Archaeon from Spitsbergen Permafrost V. Trubitsyn et al. 10.1134/S0026261722603256
- Microbial survival strategies in ancient permafrost: insights from metagenomics R. Mackelprang et al. 10.1038/ismej.2017.93
- Selective Isolation of a Eucalyptus spp. Woodchip Bacterial Community and Its Taxonomic and Metabolic Profiling C. Nnadozie et al. 10.1007/s12155-017-9816-9
- The potential science and engineering value of samples delivered to Earth by Mars sample return D. Beaty et al. 10.1111/maps.13242
- Metagenomes from Late Pleistocene Ice Complex Sediments of the Siberian Arctic T. Vishnivetskaya et al. 10.1128/MRA.01010-19
- Effects of a long‐term anoxic warming scenario on microbial community structure and functional potential of permafrost‐affected soil S. Yang et al. 10.1002/ppp.2131
- Geomorphological and Climatic Drivers of Thermokarst Lake Area Increase Trend (1999–2018) in the Kolyma Lowland Yedoma Region, North-Eastern Siberia A. Veremeeva et al. 10.3390/rs13020178
- Ecological Characteristics of Antarctic Fungi D. Nikitin 10.1134/S0012496622700120
- Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost K. Sipes et al. 10.1128/AEM.00972-21
- Microbial and Geochemical Evidence of Permafrost Formation at Mamontova Gora and Syrdakh, Central Yakutia M. Cherbunina et al. 10.3389/feart.2021.739365
- Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics X. Wu et al. 10.1186/s40793-023-00487-9
- Are permafrost microorganisms as old as permafrost? A. Abramov et al. 10.1093/femsec/fiaa260
2 citations as recorded by crossref.
- Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples A. Saidi-Mehrabad et al. 10.1038/s41598-020-71234-0
- Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia) A. Brouchkov et al. 10.1016/j.gene.2017.09.021
Saved (final revised paper)
Latest update: 13 Dec 2024
Short summary
A comparative analysis of the metagenomes from two 30,000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which are characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed both a low abundance of methanogenic archaea and enzymes from the carbon, nitrogen, and sulfur cycles.
A comparative analysis of the metagenomes from two 30,000-year-old permafrost samples, one of...
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