Evaluating Climate Warming Effects on Soil Resistome and Pathogenome: Future Risks for Agriculture and Human Health

Abstract

How climate change affects the collection of antibiotic resistance genes (ARGs), called resistome, is a critical question for environmental and human health. By scrutinizing the dynamics of soil resisomes in a six-year (2014-2019) climate change experiment, this study provides explicit insights into the risk of antibiotic resistance in cropland and grassland microbiomes under future climate scenarios. Extreme summers (+2.2° and -35.4% soil moisture during 2018-2019) significantly shifted the resistomic composition of soil bacteria, resulting in a prominent increase in abundance of ARGs (copy/cell) conferring resistance to novobiocin (52.7%-72.8%), tetracycline (32.5%-53.0%) and vancomycin (31.5%-62.9%. Importantly, simulated warming (+0.6° and -9.1% soil moisture) significantly increased the proportion of mobilizable ARGs, possibly resulting from the warming-induced SOS response of soil microbes. In contrast, extreme summers decreased the mobility potential by dramatically filtering the hosts (e.g., γ-Proteobacteria) of mobilizable ARGs. Besides resistome conditioning, climate warming and extreme summers also disrupt the ecological balance of soil microbiome, offering a worrisome competitive advantage for specific soil-dwelling antibiotic-resistant phytopathogens (Clavibacter michiganensis and Rhodococcus fascians) and human pathogens (e.g., Staphylococcus aureus, Mycobacterium tuberculosis, Streptococcus pneumoniae and Listeria monocytogenes). This worrisome advantage will increase the likelihood of outbreaks of particular plant and human infectious diseases, resulting in significant economic losses and severe threats to human health worldwide. Overall, our findings emphasize the importance of surveilling soil resistomes and pathogens under future climate scenarios.