Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie and tropical ecosystems

Abstract Background Soil is likely the largest reservoir of antibiotic resistance genes (ARGs), but their distribution across soil resistomes of different ecosystems is unknown. We used a metagenomic approach to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. Results High diversity (242 ARG subtypes) and abundance (0.184–0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance genes and efflux pump the dominant class and mechanism. We identified 55 “background ARGs” which were shared by all 26 soil metagenomes of all three ecosystems, which accounted for more than 81% of resistome abundance. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. Conversion of Amazon rainforest to pasture significantly increased soil ARG diversity, with eight ARGs significantly enriched. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. There was also wide co-occurrence among ARGs in all samples. Conclusions Our results define common background ARGs, quantify resistance classes, provide sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future.