Adaptation and Resistance of Microbial Communities to Antibiotic Contamination in the Surrounding Environment of a Sustainable Pig Farm

Abstract

An investigation was conducted in the vicinity of a sustainable pig farm to assess the presence of antibiotics through SPE-HPLC/MS/MS, microbial communities via Illumina high-throughput sequencing, and antibiotic resistance genes using SmartChip technology. The study revealed that tetracyclines were the predominant antibiotics detected in the soil and sediment surrounding the pig farm, with residual concentrations ranging from 33.3 to 1244.2 μg∙kg⁻¹. The most prevalent phyla identified at various sampling sites were Firmicutes, Chloroflexi, Proteobacteria, Actinobacteria, and Acidobacteria. A total of 188 antibiotic resistance genes (ARGs) and 9 mobile genetic elements were found in the sediment, with aminoglycoside (particularly aadA2-03), sulfonamide (specifically sul2), and tetracycline (particularly tetX) resistance genes being the most frequently observed. The presence of tetracycline residue was observed to influence the composition of the microbial community, whereas no significant association was found between antibiotics and ARGs. Examination of the correlation between ARGs and bacteria at the phylum level demonstrated that Cyanobacteria, Acidobacteria, Planctomycetota, and Gemmatimonadota were the predominant phyla associated with ARG presence near an intensive pig farm. Notably, Cyanobacteria may function as a continual reservoir and/or shelter for ARGs, thereby potentially contributing to the dissemination of ARGs in the sediment environment in close proximity to a pig farm. This study presents evidence of the ecological risks posed by antibiotics in a pig farm-cropland system, highlighting the connection between microbial community structure and ARGs. Therefore, the issue of antibiotic residues must be factored into the sustainability of animal husbandry practices.