Halotolerant Bacteria are Key Antibiotic Resistant Players in Saline Soils Revealed by Metagenomic Analysis: Exploration of the Underlying Co-Selection Mechanisms

Abstract

Salinity is considered as one of the factors influencing the profiles of antibiotic resistance genes (ARGs) in soils, while its roles in shaping antibiotic resistome are poorly understood. Here, metagenomic analysis was introduced to track the ARGs distributions and disseminations in soils during salt accumulation and desalinization process. 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 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 osmolytes transporter, K+ uptake protein on the same ARC was responsible for the co-selection of ARGs and halotolerant genes. The antibiotic resistome recovered to normal state after desalination and prolonged incubation, through alleviating the salt stress. However, the acquisition of ARGs by opportunistic pathogens after salt treatment were increased, prioritizing further efforts on the health risks correlated with resistance propagation and human exposure in saline soils.

Keywords: Antibiotic resistome, salt tolerant, co-selection, saline soil, opportunistic pathogens