Carbendazim shapes microbiome and enhances resistome in the earthworm gut

Abstract

Background It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental risk assessment, earthworm is still a neglected focus that the effects of the fungicide carbendazim (CBD) residues on the gut microbiome and resistome are largely unknown. In this study, Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods. Results CBD could significantly perturb bacterial community and enrich specific bacteria mainly belonging to the phylum Actinobacteria. More importantly, CBD could serve as a co-selective agent to elevate the abundance and diversity of ARGs, particularly for some specific types (e.g., multidrug, glycopeptide, tetracycline, and rifamycin resistance genes) in the earthworm gut. Additionally, host tracking analysis suggested that ARGs were mainly carried in some genera of the phyla Actinobacteria and Proteobacteria. Meanwhile, the level of ARGs was positively relevant to the abundance of mobile genetic elements (MGEs) and some representative co-occurrence patterns of ARGs and MGEs (e.g., cmx-transposase and sul1-integrase) were further found on the metagenome-assembled contigs in the CBD treatments. Conclusions It can be concluded that the enhancement effect of CBD on the resistome in the earthworm gut may be attributed to its stress on the gut microbiome and facilitation on the ARGs dissemination mediated by MGEs, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil. Graphical Abstract

Effects of Zinc Thiazole and Oxytetracycline on the Microbial Metabolism, Antibiotic Resistance, and Virulence Factor Genes of Soil, Earthworm Gut, and Phyllosphere

“…A key resistance mechanism for the inactivation of β-lactam antibiotics depends on the action of β-lactamases, which can directly degrade or replace active groups by destroying their structure, causing them to lose their original functions. Several previous studies have also demonstrated that both the carbendazim and cypermethrin mainly increased the abundance of β-lactam and multidrug resistance genes in the soil fauna gut. , In addition, in this study, the enriched VFGs were mainly related to immune modulation and nutritional/metabolic factors in the gut. As observed for ARGs, the alteration of VFGs could also be due to shifts in the microbial community, especially changes in the functions of bacteria and potential pathogens.…”

“…Several previous studies have also demonstrated that both the carbendazim and cypermethrin mainly increased the abundance of β-lactam and multidrug resistance genes in the soil fauna gut. 13,52 In addition, in this study, the enriched VFGs were mainly related to immune modulation and nutritional/ metabolic factors in the gut. As observed for ARGs, the alteration of VFGs could also be due to shifts in the microbial community, especially changes in the functions of bacteria and potential pathogens.…”

“…Previous studies have also confirmed that several pollutants could facilitate the horizontal transfer of genes via MGEs. 52,56 In addition, exposure to ZT was shown to increase the abundance of these MGEs, which can, in turn, enhance the corresponding ARGs and VFGs. In the present study, the analysis of the metagenome-assembled contigs identified the patterns of co-occurrence of ARGs and MGEs.…”

“…In the present study, the results of host-tracking analysis revealed that ARGs and VFGs were both mainly harbored by a number of genera belonging to the Actinobacteria and Proteobacteria phyla, which was in line with effects of the fungicide carbendazim on the earthworm gut resistome. 52 The most prominent characteristic of Actinobacteria is the ability to produce a wide variety of antibiotics, such as streptomycin, tetracycline, and oxytetracycline, which are used in clinical practice and agriculture. 55 Even some biochemical drugs, including enzyme inhibitors and agricultural insecticides, are major secondary metabolites of these microbes that carry multiple ARGs.…”

Mechanisms Underlying the Overlooked Chiral Fungicide-Driven Enantioselective Proliferation of Antibiotic Resistance in Earthworm Intestinal Microbiome

“…13,14 Meanwhile, ARG dissemination via horizontal gene transfer (HGT) associated with mobile genetic elements (MGEs) occurred frequently among gut microbiome. 15,16 Therefore, the abnormal proliferation and dissemination of ARGs in the earthworm gut need more attention.…”