Metagenome-assembled genomes from northern West Siberia: insights into microbial diversity in permafrost and contemporary soils.

AIMS: Permafrost thawing due to global warming threatens to release long-preserved microbial communities, including potentially novel bacterial lineages. Despite the importance of West Siberian permafrost for climate models, genome-resolved studies of its microbial diversity remain limited. This study aimed to recover and characterize metagenome-assembled genomes (MAGs) from permafrost and contemporary soils of northern West Siberia, and to assess their biosynthetic and antibiotic resistance potential.

METHODS AND RESULTS: We reconstructed 117 MAGs from soil samples collected from northern West Siberia, including ancient permafrost deposits (∼10 000 and ∼ 39 000 years old) and contemporary soils. Permafrost deposits exhibited significantly higher biosynthetic gene cluster (BGC) diversity compared to contemporary soils (Shannon H' = 4.15 vs. 3.36-3.59) with terpenes, RiPP-like and NRPS-like clusters being the most abundant. Notably, Vulcanimicrobiota and Verrucomicrobiota were recovered exclusively from permafrost in this dataset. A total of 14 unique antibiotic resistance genes conferring resistance to eight drug classes were detected. The RND efflux pump gene, adeF, dominated the resistome across all biomes, while Van family genes were largely restricted to permafrost at the phylum level. Verrucomiocota showed the highest adeF load followed by Planctomicrobiota and Pseudomonodota. A strong correlation was observed between bacterial genes and antibiotic resistance genes across biomes (Spearman's ρ = 0.893, p = 0.007).

CONCLUSIONS: This genome-resolved study reveals a high level of undiscovered bacterial diversity in West Siberian permafrost including habitat-specific lineages. Our findings highlight permafrost as a rich repository of novel biosynthetic potential and emphasize the importance of metagenomic exploration of Arctic ecosystems under climate change.