Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw

Abstract

Understanding the distribution and mobility of antibiotic resistance genes (ARGs) in soil bacteria from diverse ecological niches is critical in assessing their impacts on the global spread of antibiotic resistance. In permafrost associated soils, climate and human driven forces augment near-surface thaw altering the overlying active layer. Physiochemical changes shift bacterial community composition and metabolic functioning, however, it is unknown if permafrost thaw will affect ARGs comprising the boreal soil resistome. To assess how thaw shifts the resistome, we performed susceptibility testing and whole genome sequencing on soil isolates from a disturbance-induced thaw gradient in Interior Alaska. We found resistance was widespread in the Alaskan isolates, with 87% of the 90 isolates resistant to at least one of the five antibiotics. We also observed positive trends in both the proportion of resistant isolates and the abundance of ARGs with permafrost thaw. However, the number of ARGs per genome and types of genes present were shown to cluster more strongly by bacterial taxa rather than thaw emphasizing the evolutionary origins of resistance and the role vertical gene transfer has in shaping the predominantly chromosomally encoded ARGs. The observed higher proportion of plasmid-borne and distinct ARGs in our isolates compared to RefSoil+ suggests local conditions affect the composition of the resistome along with selection for ARG mobility. Overall taxonomy and geography shape the resistome, suggesting that as microbial communities shift in response to permafrost thaw so will the ARGs in the boreal active layer.