Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols
International audience In the context of global warming, the melting of arctic permafrost raises the threat of a re-emergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acqui...
Published in: | microLife |
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Main Authors: | , , , , , , , , , |
Other Authors: | , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2022
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Subjects: | |
Online Access: | https://amu.hal.science/hal-03640343 https://amu.hal.science/hal-03640343/document https://amu.hal.science/hal-03640343/file/Metagenomic%20survey_uqac003.pdf https://doi.org/10.1093/femsml/uqac003 |
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ftceafr:oai:HAL:hal-03640343v1 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
HAL-CEA (Commissariat à l'énergie atomique et aux énergies alternatives) |
op_collection_id |
ftceafr |
language |
English |
topic |
metagenomics Kamchatka Yakutia Siberia permafrost thaw antibiotic resistance genes [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology |
spellingShingle |
metagenomics Kamchatka Yakutia Siberia permafrost thaw antibiotic resistance genes [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology Rigou, Sofia Christo-Foroux, Eugène Santini, Sébastien Goncharov, Artemiy Strauss, Jens Grosse, Guido Fedorov, Alexander Labadie, Karine Abergel, Chantal Claverie, Jean-Michel Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols |
topic_facet |
metagenomics Kamchatka Yakutia Siberia permafrost thaw antibiotic resistance genes [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology |
description |
International audience In the context of global warming, the melting of arctic permafrost raises the threat of a re-emergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here we present a metagenomics analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia, and Kamchatka, including 9 permafrost samples collected at various depths. These large datasets (9.2 1011 total bp) were assembled (525,313 contigs > 5kb), their encoded protein contents predicted, then used to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition of known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations. |
author2 |
Information génomique et structurale (IGS) Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS) Northwestern State Medical Mechnikov University Alfred Wegener Institute Potsdam Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung = Alfred Wegener Institute for Polar and Marine Research = Institut Alfred-Wegener pour la recherche polaire et marine (AWI) Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association North-Eastern Federal University Institut de Biologie François JACOB (JACOB) Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010) European Project: 338335,EC:FP7:ERC,ERC-2013-StG,PETA-CARB(2013) |
format |
Article in Journal/Newspaper |
author |
Rigou, Sofia Christo-Foroux, Eugène Santini, Sébastien Goncharov, Artemiy Strauss, Jens Grosse, Guido Fedorov, Alexander Labadie, Karine Abergel, Chantal Claverie, Jean-Michel |
author_facet |
Rigou, Sofia Christo-Foroux, Eugène Santini, Sébastien Goncharov, Artemiy Strauss, Jens Grosse, Guido Fedorov, Alexander Labadie, Karine Abergel, Chantal Claverie, Jean-Michel |
author_sort |
Rigou, Sofia |
title |
Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols |
title_short |
Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols |
title_full |
Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols |
title_fullStr |
Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols |
title_full_unstemmed |
Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols |
title_sort |
metagenomic survey of the microbiome of ancient siberian permafrost and modern kamchatkan cryosols |
publisher |
HAL CCSD |
publishDate |
2022 |
url |
https://amu.hal.science/hal-03640343 https://amu.hal.science/hal-03640343/document https://amu.hal.science/hal-03640343/file/Metagenomic%20survey_uqac003.pdf https://doi.org/10.1093/femsml/uqac003 |
genre |
Arctic Chukotka Global warming Kamchatka permafrost Subarctic Yakutia Siberia |
genre_facet |
Arctic Chukotka Global warming Kamchatka permafrost Subarctic Yakutia Siberia |
op_source |
EISSN: 2633-6693 microLife https://amu.hal.science/hal-03640343 microLife, 2022, pp.uqac003. ⟨10.1093/femsml/uqac003⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1093/femsml/uqac003 info:eu-repo/grantAgreement/EC/FP7/338335/EU/Rapid Permafrost Thaw in a Warming Arctic and Impacts on the Soil Organic Carbon Pool/PETA-CARB hal-03640343 https://amu.hal.science/hal-03640343 https://amu.hal.science/hal-03640343/document https://amu.hal.science/hal-03640343/file/Metagenomic%20survey_uqac003.pdf doi:10.1093/femsml/uqac003 |
op_rights |
http://creativecommons.org/licenses/by-nc/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1093/femsml/uqac003 |
container_title |
microLife |
_version_ |
1810293139018088448 |
spelling |
ftceafr:oai:HAL:hal-03640343v1 2024-09-15T17:51:16+00:00 Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols Rigou, Sofia Christo-Foroux, Eugène Santini, Sébastien Goncharov, Artemiy Strauss, Jens Grosse, Guido Fedorov, Alexander Labadie, Karine Abergel, Chantal Claverie, Jean-Michel Information génomique et structurale (IGS) Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS) Northwestern State Medical Mechnikov University Alfred Wegener Institute Potsdam Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung = Alfred Wegener Institute for Polar and Marine Research = Institut Alfred-Wegener pour la recherche polaire et marine (AWI) Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association North-Eastern Federal University Institut de Biologie François JACOB (JACOB) Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010) European Project: 338335,EC:FP7:ERC,ERC-2013-StG,PETA-CARB(2013) 2022-04-07 https://amu.hal.science/hal-03640343 https://amu.hal.science/hal-03640343/document https://amu.hal.science/hal-03640343/file/Metagenomic%20survey_uqac003.pdf https://doi.org/10.1093/femsml/uqac003 en eng HAL CCSD Oxford University Press info:eu-repo/semantics/altIdentifier/doi/10.1093/femsml/uqac003 info:eu-repo/grantAgreement/EC/FP7/338335/EU/Rapid Permafrost Thaw in a Warming Arctic and Impacts on the Soil Organic Carbon Pool/PETA-CARB hal-03640343 https://amu.hal.science/hal-03640343 https://amu.hal.science/hal-03640343/document https://amu.hal.science/hal-03640343/file/Metagenomic%20survey_uqac003.pdf doi:10.1093/femsml/uqac003 http://creativecommons.org/licenses/by-nc/ info:eu-repo/semantics/OpenAccess EISSN: 2633-6693 microLife https://amu.hal.science/hal-03640343 microLife, 2022, pp.uqac003. ⟨10.1093/femsml/uqac003⟩ metagenomics Kamchatka Yakutia Siberia permafrost thaw antibiotic resistance genes [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology info:eu-repo/semantics/article Journal articles 2022 ftceafr https://doi.org/10.1093/femsml/uqac003 2024-07-22T13:11:47Z International audience In the context of global warming, the melting of arctic permafrost raises the threat of a re-emergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here we present a metagenomics analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia, and Kamchatka, including 9 permafrost samples collected at various depths. These large datasets (9.2 1011 total bp) were assembled (525,313 contigs > 5kb), their encoded protein contents predicted, then used to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition of known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations. Article in Journal/Newspaper Arctic Chukotka Global warming Kamchatka permafrost Subarctic Yakutia Siberia HAL-CEA (Commissariat à l'énergie atomique et aux énergies alternatives) microLife |