Abstract
Microbial communities that are present in aquaculture production systems play significant roles in degrading organic matter, controlling diseases, and formation of antibiotic resistance. It is important to understand the diversity and abundance of microbial communities and their genetic adaptations associated with environmental physical and chemical changes. Here we collected water and sediment samples from a high-intensity catfish production system and its original water reservoir. The metagenomic analysis showed that Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes were the top five phyla identified from all samples. The aquaculture production system significantly changed the structure of aquatic microbial populations. Substantial changes were also observed in SNP patterns among four sample types. The gene-specific sweep was found to be more common than genome-wide sweep. The selective sweep analysis revealed that 21 antibiotic resistant (AR) genes were under selection, with most belonging to antibiotic efflux pathways. Over 200 AR gene gains and losses were determined by changes in gene frequencies. Most of the AR genes were characterized as ABC efflux pumps, RND efflux pumps, and tetracycline MFS efflux pumps. Results of this study suggested that aquaculture waste, especially waste containing therapeutic antibiotics, has a significant impact on microbial population structures and their genetic structures.
Highlights
Aquaculture has been a fast-growing industry in recent years because of dramatic increases in fish and seafood demand worldwide
Most of these studies were limited to one or a few bacterial species cultured in the laboratory environment and did not reflect the dynamic evolutionary processes that occur in a real production system
Growing concerns are expressed about the potential effects of ever-increasing aquaculture waste on the microbial ecosystenms in these systems
Summary
Aquaculture has been a fast-growing industry in recent years because of dramatic increases in fish and seafood demand worldwide. The development of antibiotic resistance is outpacing the discovery and development of new antibiotics, and the fact that certain bacterial infections are becoming untreatable has made evaluation of the therapeutic usage of antibiotics an urgent need Such evaluation should include analysis of the diversity and abundance of microbial populations as well as changes and adaptations in their genetic structures. Because of the differences seen between previous findings and theories, adaptive laboratory evolution experiments have been conducted in order to better determine the potential selection regime of microbial resistance[26,27] Most of these studies were limited to one or a few bacterial species cultured in the laboratory environment and did not reflect the dynamic evolutionary processes that occur in a real production system. Given that antibiotics are used in aquaculture only for disease treatment and require a veterinary prescription, an evaluation focusing on the therapeutic usage of antibiotics in a real aquaculture production system is needed
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