Salt Tolerance Evolution Facilitates Antibiotic Resistome in Soil Microbiota: Evidences from Dissemination Evaluation, Hosts Identification and Co-Occurrence Exploration

Abstract

Salinity is considered one of the factors influencing the profiles of antibiotic resistance genes (ARGs) in soils, while its roles in shaping the antibiotic resistome are poorly understood. Here, metagenomic analysis was introduced to track the ARGs distributions and dissemination in soils during salt accumulation and desalinization processes. Neutral-salt accumulation for 45 and 90 days significantly increased the relative abundances of ARGs and mobile genetic elements (MGEs) carrying antibiotic resistance contigs (ARCs). The ARGs within antibiotic efflux and target protection families primarily carried by Streptomyces , Nocardioides , Rhodanobacter and Monashia were measurably enriched. The high degree of synteny between ARGs subtypes of the resistance-nodulation-division (RND) family, ATP-binding cassette (ABC) family, other efflux, rRNA methyltransferase and MGEs contributed to ARGs enrichment. Furthermore, the genetically linked ARGs subtypes and transposons with the salt-tolerance mechanisms of organic osmolyte transporters and K + uptake proteins on the same ARC were responsible for the coselection of ARGs and halotolerant genes. The antibiotic resistome recovered to a normal state after desalination and prolonged incubation by alleviating salt stress. However, the acquisition of ARGs by opportunistic pathogens after salt treatment was increased, serving to prioritize further efforts on the health risks correlated with resistance propagation and human exposure in saline soils.

Keywords: antibiotic resistome, salt tolerance, coselection, saline soil, opportunistic pathogens