Christo-Foroux, E. | Search bioRxiv

bioRxiv2021

High prevalence and diversity of beta-lactamase-encoding bacteria in cryosoils and ancient permafrost

BackgroundAntimicrobial resistance is one of the major challenges affecting public health. It is mostly due to the continuous emergence of extended-spectrum {beta}-lactamase from various environments followed by their rapid dissemination and selection in clinical settings. The warming of Earths climate is the other global threat facing human society, in particular with the Arctic regions experiencing a twice faster warming than the global average and permafrost affected by widespread thawing. A potentially dreadful combination of these two threats would be the release and dispersion of harmful microbes that have remained confined to largely uninhabited Arctic regions, or are stored dormant in permafrost. MethodsEnvironmental DNA was isolated from 12 soil samples from various Arctic and subarctic pristine regions in Siberia (Yakutia and Kamchatka), including nine permafrost samples collected at various depths. The large datasets obtained from high throughput sequencing was assembled in contigs and their protein-gene contents predicted. We used exhaustive similarity searches to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. In addition, we specifically identified {beta}-lactamase genes and their prevalence per bacterial genome estimated through the detection of two universal single copy genes. FindingsA total of 9.217 1011 bp were exploited, leading to a total of 525,313 contigs at least 5kb in size. The DNA content of the various samples was found to be highly variable, not strictly correlated with the depth or radio-carbon-based deposit age, and most likely linked to the global density of microbes trapped in the corresponding permafrost layers. Bacteria account for more than 90% of the contigs in most samples, followed by Eukaryotes and Archaea (always lower than 10%). Viruses represented less than 2% of all contigs in all samples. The taxonomic profiles of surface cryosoils and deep permafrost samples exhibited a high diversity, including between permafrost samples originating from various depths in the same borehole. In all samples, bacterial contigs carrying different {beta}-lactamases from class A to D were identified. InterpretationNo clear common taxonomic feature could be found shared by surface cryosoils or ancient permafrost layers. However, most samples (9/12) exhibited a high frequency of {beta}-lactamase genes, with an estimated average close to 1 copy/bacterial genome. In addition to the well-documented reactivation of infectious ancient pathogens (bacteria, viruses, protozoa), we show now that global warming could contribute to the emergence of new antibiotic resistances through the mobilization by contemporary bacteria of ancient DNA released from thawing permafrost. FundingCNRS PRC research grant (PRC1484-2018) to C.A. E C-F was supported by a PhD grant (DGA/DS/MRIS) #2017 60 0004. GG and JS were funded by ERC PETA-CARB (#338335) and the HGF Impulse and Networking Fund (ERC-0013).

microbiology↗

bioRxiv2019

Characterization of Mollivirus kamchatka, the first modern representative of the proposed Molliviridae family of giant viruses

Microbes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing researches in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky river in Kamchatka. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleo-cytoplasmic replication cycle identical to that of M. sibericum. Its spherical particle (0.6-m in diameter) encloses a 648-kb GC-rich double stranded DNA genome coding for 480 proteins of which 61 % are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92 % identical residues in average) despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to the virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry. ImportanceVirology has long been viewed through the prism of human, cattle or plant diseases leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under light microscopy (i.e., >0.3m in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenomes analyses have shown the presence of giant viruses in most terrestrial and aquatic environments including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae. We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year old arctic permafrost.

microbiology↗