Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

Soils are reservoirs of antibiotic resistance genes, but dynamics of antibiotic resistance genes in the environment are largely unknown. Long-term disturbances offer extended opportunities to examine microbiome responses at scales relevant for both ecological and evolutionary processes, and therefore can be insightful for studying the dynamics of antibiotic resistance genes in the environment. We examined antibiotic resistance genes in soils overlying the underground coal seam fire in Centralia, PA, which has been burning since 1962. As the fire progresses, previously hot soils can recover to ambient temperatures, which creates a gradient of contemporary and historical fire impact. We examined metagenomes from fire-affected, recovered, and reference surface soils to examine gene-resolved dynamics of antibiotic resistance using a gene-targeted assembler. We targeted 35 distinct types of clinically-relevant antibiotic resistance genes and two horizontal gene transfer-related genes ( intI and repA ). We detected 17 antibiotic resistance genes in Centralia, including AAC6-Ia, adeB , bla_A , bla_B , bla_C , cmlA , dfra12 , intI , sul2 , tetA , tetW , tetX , tolC , vanA , vanH , vanX , and vanZ . The diversity and abundance of several antibiotic resistance genes ( bla_A , bla_B , dfra12 , tolC ) decreased with soil temperature, and changes in ARGs could largely be explained by associated changes in community structure. We also observed sequence-specific dynamics along the temperature gradient and observed compositional shifts in bla_A , dfra12 , and intI . These results suggest that increased temperatures can reduce soil antibiotic resistance genes but that this is largely due to a concomitant reduction in community-level diversity.