Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics

Abstract

Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58%) and Acidobacteria (6.04%) were identified as the dominant phyla and Thiobacillus (1.84%) and Lysobacter (0.99%) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r>0.7, p<0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p<0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.