Antimicrobial resistance varies with warming in active layer soil and permafrost

Although antimicrobial resistance is a contemporary public health concern, antimicrobial resistance genes (ARGs) have existed long before human use of antimicrobials, and recent attention has focused on whether permafrost thaw could release ARGs as the resistome shifts. We present a metagenomic analysis of permafrost samples from four sites in Alaska and Sweden, thawed under laboratory conditions. We used ABRicate, an alignment-based tool, and DeepARG, a deep learning tool, to identify ARGs, assessed their abundances under experimental thaw, measured taxonomic shifts, and examined metagenome-assembled genomes (MAGs) carrying ARGs. ARG abundance varied with depth, with some permafrost containing more ARGs than the seasonally thawed active layer. ARG abundance increased with soil carbon and decreased with pH across sites, suggesting site-specific influences. The majority of 164 high-quality MAGs contained ARGs, including 80 out of 105 species identified. This included bacteria from nine phyla, demonstrating widespread distribution across microbial taxa. Laboratory thaw experiments revealed that ARG abundances did not change significantly in two of the sites, but declined with thaw in the remaining two sites. Together, these findings demonstrate that ARGs are consistently present in permafrost microbiomes across multiple sites, but relative abundances generally do not increase during thaw. While ARGs that persist may pose potential risks, our results suggest that permafrost thaw may not substantially elevate environmental or public health risks.