Investigating the distribution of antibiotic resistance genes in relation to bacterial, fungal, and functional diversity in a hay field

The spread of antibiotic resistance in pathogenic bacteria is one of the most pressing public health threats of the 21 ^st century, with at least 5 million deaths currently associated with it. While recent work has shown the importance of environmental reservoirs in the emergence of antibiotic resistance genes (ARGs), it is unclear which features of microbial diversity relate to ARGs of clinical relevance. Here, we investigate the role of bacterial, fungal, and functional diversity on the distribution of clinical and environmental ARGs along a single transect located in an aging hay field on an otherwise active farm. This transect spans a length of several hundred meters, increasing in distance from an agricultural access road and stream. We use 16S rRNA and ITS amplicon sequencing to measure bacterial and fungal diversity respectively, in combination with whole-genome sequencing (WGS) to characterize functional and ARG diversity. We find increasing bacterial and functional diversity along the transect, as well as distinct community structures for both bacteria and fungi. While we find that the diversity of environmental ARGs is significantly correlated with both bacterial and fungal diversity, clinical ARG diversity only significantly decreased as fungal diversity increased. Our results suggest that while microbial diversity increases with distance from the road and stream; and this diversity tends to determine the diversity of the majority of ARGs; this trend is not observed for ARGs of clinical relevance, which appear to be largely driven by the variety of fungal groups in the environment.