Deterministic effects of pH in shaping soil resistome revealed by metagenomic analysis

Abstract

Background Research in environmental resistome has been greatly facilitated by the use of the comprehensive database of antibiotic resistance genes (ARGs). Through this approach, the high prevalence of multidrug efflux pump genes was recently found in various ecosystems and has raised concerns. Since most of the efflux pumps were driven by proton-motive-force (PMF), studying whether soil pH, i.e. proton activity, is a determinant in selecting multidrug efflux pump genes and thus shaping soil resistome is of great interest. Results Based on the distribution of soil pH in China, we collected soil samples from forest, cropland and grassland in four typical climatic areas with pH values ranging from 4.37–9.69. ARG profiles of 36 soil metagenomes and 41 metagenome-assembled genomes were obtained by using the SARG database and the ARG-OAPs pipeline. As the result, 264 ARG subtypes associated with 20 classes of antibiotics were identified, while multidrug resistance (69.72% of whole resistome abundances) and efflux pump (82.49%) were the dominant ARG category and resistance mechanism. Independent of sampling location, the abundance of multidrug resistance gene was decreased linearly with increasing pH over the given range, which contributed to almost the entire variation in ARG abundances. In addition, soil pH also determined the diversity, i.e. evenness, of ARGs, and thus explained 75.2% of the resistome variation in the variance partitioning analysis. On this basis, we investigated the relationship between ARGs and bacterial phyla using consistency and correlation analysis, as well as tested their assembly mechanisms using a neutral model, and found ARGs were naturally selected despite the neutral assembly of the bacterial community. Conclusions Our results revealed the deterministic effect of pH on shaping soil resistome, and infer that this is related to the selection of PMF-driven multidrug efflux pumps under high proton activity. Such natural changes in background ARGs deserve further attention.