Antibiotic resistance in a changing North: unearthing the effects of disturbance-induced permafrost thaw on the Alaskan soil resistome

Abstract

The evolution of antibiotic resistance in pathogenic bacteria is a major threat at the forefront of public health today. By studying soils, one of the ancestral origins of antibiotic production and resistance, we can gain insight into how antibiotic resistance genes (ARGs) from the environment have contributed to the evolution and emergence of resistance in pathogens. These studies are particularly important in soils where polar amplification and human expansion has already impacted the frequency and intensity of soil disturbance events (e.g., wildfires, deglaciation, land-use). In Alaska these disturbances augment permafrost thaw shifting the biogeochemical properties of active layer soils that structure microbial community composition and hypothetically the resistome (i.e., summation of ARGs). Thus, the goal of this thesis was to assess how soil disturbance, and the subsequent shift in community composition, will affect the types, abundance, and mobility of ARGs that comprise the subarctic soil resistome. In the first chapter I cultured bacteria from a permafrost thaw gradient in Interior Alaska, tested the isolates for susceptibility to antibiotics, annotated their genomes for ARGs, and compared their resistance profiles to a global database of soil bacteria genomes. I found that phylogenic and ecological factors structured the resistome. Additionally, antibiotic resistance phenotypes and genotypes were widespread in the soil isolates suggesting resistance is an intrinsic component of bacterial evolution. In the second chapter, I used long read metagenomics to identify predominant ARGs, ARG host taxa, and the relationship between community composition and ARG abundance. From the long read data, I unearthed major trends in the types of ARGs at our study site and determined ARG abundance had a quadratic relationship with disturbance and negative relationship temporally by year highlighting the complex interplay soil conditions have in structuring the taxa that enrich ARGs in the community. To analyze how individual bacteria contribute to ARGs in the community, I generated metagenome assembled genomes (MAGs) using Hi-C proximity ligation. From the MAGs, I found a significant difference in ARGs per genome between phyla that emphasized how an enrichment of specific bacteria can affect the abundance of ARGs in subarctic soils. I also identified several plasmid-borne ARGs highlighting the potential for horizontal gene transfer. Overall, this thesis provides evidence that ARGs in permafrost-associated soil are structured by disturbance-induced community shifts. Thus, as climate change increases t the frequency of disturbance events that shift the microbial communities in active layer soils, One Health can be impacted by alterations to ARGs comprising the resistome.