Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols

• Published in: microLife
• Main Authors: Rigou, Sofia, Christo-Foroux, Eugène, Santini, Sébastien, Goncharov, Artemiy, Strauss, Jens, Grosse, Guido, Fedorov, Alexander, Labadie, Karine, Abergel, Chantal, Claverie, Jean-Michel
• Other Authors: 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
• Language: English
• Published: HAL CCSD 2022
• Subjects: metagenomics; Kamchatka; Yakutia; Siberia; permafrost thaw; antibiotic resistance genes; [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology; Arctic; Chukotka; Global warming; permafrost; Subarctic
• 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

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.