Deterministic Effect of pH on Shaping Soil Resistome Revealed by Metagenomic Analysis

Abstract

Soil is recognized as the major reservoir of antibiotic resistance genes (ARGs), harboring the most diverse naturally evolved ARGs on the planet. Multidrug resistance genes are a class of ARGs, and their high prevalence in natural soil ecosystems has recently raised concerns. Since most of these genes express proton motive force (PMF) driven efflux pumps, studying whether soil pH is a determinant for the selection of multidrug efflux pump genes and thus shaping the soil resistome are of great interest. In this study, we collected 108 soils with pH values ranging from 4.37 to 9.69 from multiple ecosystems and profiled the composition of ARGs for metagenomes and metagenome-assembled genomes. We observed the multidrug efflux pump genes enriched in the acidic soil resistome, and their abundances have significant soil pH dependence. This reflects the benefits of high soil proton activity on the multidrug efflux pump genes, especially for the PMF-driven inner membrane transferase. In addition, we preliminary indicate the putative microbial participants in pH shaping the soil resistome by applying ecological analyzing tools such as stepwise regression and random forest model fitting. The decisive influence of proton activity on shaping the resistome is more impactful than any other examined factors, and as the consequence, we revisited the influence of edaphic factors on the soil resistome; i.e., the deterministic selection of resistance mechanisms by edaphic factors could lead to the bottom-up shaping of the ARG composition. Such natural developing mechanisms of the resistome are herein suggested to be considered in assessing human-driven ARG transmissions.

Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly

“…bacA is responsible for the biosynthesis of peptidoglycan and cell wall components, which protects bacteria from the destruction of chlorination . Multidrug ARG could be used to resist the environmental pressure for microbiota such as disinfectants and antibiotics by efflux pump mechanism. , In particular, the mex genes from multidrug ARGs can confer resistance to almost all known antibiotics and also pump out many toxic matters, facilitating the microbial survival in chlorinated DWDS. ,, In addition, the big variations of microbial community diversity as well as antibiotic resistome within the same seasons are attributed to the biofilm age and spatial heterogeneity (Figures S6, S7, S14 and S18). We suggested routinely monitoring biofilms about ARGs and pathogens, temporally and spatially, which could help us prevent the disease-causing agents.…”

“…The assembly mechanism regarding microbiome or antibiotic resistome could be explained using the NCM . The distribution pattern of the antibiotic resistome, the microbial community, and the MGE composition were analyzed using the vegan package (procrustes analyses) . Variation partitioning analysis (VPA) was used to explain the contributions of the microbial community and MGEs to antibiotic resistance variation using the ecodist and vegan R packages .…”

“…16 The distribution pattern of the antibiotic resistome, the microbial community, and the MGE composition were analyzed using the vegan package (procrustes analyses). 44 Variation partitioning analysis (VPA) was used to explain the contributions of the microbial community and MGEs to antibiotic resistance variation using the ecodist and vegan R packages. 45 Furthermore, redundancy analysis (RDA) was performed using the vegan package to screen the key microbial genera driving the antibiotic resistome shift.…”

“…65 Multidrug ARG could be used to resist the environmental pressure for microbiota such as disinfectants and antibiotics by efflux pump mechanism. 21,44 In particular, the mex genes from multidrug ARGs can confer resistance to almost all known antibiotics and also pump out many toxic matters, facilitating the microbial survival in chlorinated DWDS. 44,45,66 In addition, the big variations of microbial community diversity as well as antibiotic resistome within the same seasons are attributed to the biofilm age and spatial heterogeneity (Figures S6, S7, S14 and S18).…”

“…21,44 In particular, the mex genes from multidrug ARGs can confer resistance to almost all known antibiotics and also pump out many toxic matters, facilitating the microbial survival in chlorinated DWDS. 44,45,66 In addition, the big variations of microbial community diversity as well as antibiotic resistome within the same seasons are attributed to the biofilm age and spatial heterogeneity (Figures S6, S7, S14 and S18). We suggested routinely monitoring biofilms about ARGs and pathogens, temporally and spatially, which could help us prevent the disease-causing agents.…”