Effects of copper and cadmium stress on resistance genes in farmland soil
Description
Current farmland soils are increasingly affected by contamination from antibiotic resistance genes (ARGs) and heavy metals, with the evolution of microbial antibiotic resistance potentially influenced by metal stress. The distribution effects of antibiotic resistance genes (ARGs) in farmland soils under cadmium (Cd) and copper (Cu) combined pollution remain unclear. Results This study aims to: Results show that Cu and Cd exhibit significant dominant effects on Bacitracin, fosfomycin, sulfonamide, trimethoprim-beta-lactam, polymyxin, tetracycline, trimethoprim, and vancomycin. Interactions between Cd/Cu and fosmidomycin, MLS, multidrug resistance, sulfonamide, and vancomycin abundance are significant. Co-occurrence network analysis identifies Pseudomonadota, Actinobacteria, and Acidobacteria as primary potential host groups for ARGs. Structural equation modeling analysis further demonstrates that Cd exhibits more pronounced effects on ARGs abundance compared to Cu. Contrary to previous studies, this research reveals that bacterial community αdiversity and mobile genetic elements (MGEs) contribute relatively minimally to ARGs abundance, while mobile genetic regions (MRGs) demonstrate a highly significant positive correlation with ARGs.These findings hold substantial implications for assessing potential ecological risks in soil metal pollution and provide new insights into the co-selection mechanisms between Cd and Cu in shaping ARGs dynamics.
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Steps to reproduce
Microbial DNA was extracted from soil samples using the E.Z.N.A. stool DNA Kit (Omega Bio-tek, Norcross, GA, U.S.) according to manufacturers protocols. Metagenomic shotgun sequencing libraries were constructed and sequenced at Shanghai Biozeron Biological Technology Co. Ltd. In briefly, for each sample, 1g of genomic DNA was sheared by Covaris S220 Focused-ultrasonicator (Woburn, MA USA) and sequencing libraries were prepared with a fragment length of approximately 450 bp. All samples were sequenced using next generation sequencing platform (MGI-T7 or Illumina) (Shanghai BIOZERON Biotech. Co., Ltd ) with PE150 mode according to the standard protocols. Raw sequence reads underwent quality trimming using Trimmomatic [[[] Bolger, A. M., M. Lohse, et al. (2014). "Trimmomatic: a flexible trimmer for Illumina sequence data." Bioinformatics 30(15): 2114-2120.]](http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic) to remove adaptor contaminants and low quality reads. Reads through quality control were then mapping against human[[[] Lin L, Ma H, Zhang J, Yang H, Zhang J, et al. 2024. Lignocellulolytic microbiomes orchestrating degradation cascades in the rumen of dairy cattle and their diet-influenced key degradation phases.Animal Advances 1: e002 https://doi.org/10.48130/animadv-0024-0002.]] genome (version: hg19) by BWA mem algorithm (parameters: -M -k 32 -t 16, http://bio-bwa.sourceforge.net/bwa.shtml). The reads removing host-genome contaminations and low-quality data were called as clean reads and used for the furthur analysis.
Institutions
- Guizhou UniversityGuizhou, Guiyang