Food Microbiology and Safety Lab, Department of Animal Sciences, Auburn University, Auburn, Alabama, USA.
The Key Laboratory of Mariculture, Ocean University of China, Qingdao, China.
Sci Rep. 2017 Dec 13;7(1):17491. doi: 10.1038/s41598-017-17640-3.
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.
水产养殖生产系统中存在的微生物群落在降解有机物、控制疾病和形成抗生素耐药性方面发挥着重要作用。了解与环境物理化学变化相关的微生物群落的多样性和丰度及其遗传适应性非常重要。在这里，我们从一个高强度鲶鱼养殖生产系统及其原始水库中采集了水样和底泥样。宏基因组分析表明，从所有样本中鉴定出的前 5 个门是变形菌门、放线菌门、拟杆菌门、蓝细菌门和厚壁菌门。水产养殖生产系统显著改变了水生微生物种群的结构。在四种样本类型之间，SNP 模式也发生了显著变化。发现基因特异性的选择比全基因组的选择更常见。选择分析表明，有 21 个抗生素耐药（AR）基因受到选择，其中大多数属于抗生素外排途径。通过基因频率的变化，确定了 200 多个 AR 基因的获得和丢失。大多数 AR 基因被鉴定为 ABC 外排泵、RND 外排泵和四环素 MFS 外排泵。本研究结果表明，水产养殖废物，尤其是含有治疗性抗生素的废物，对微生物种群结构及其遗传结构有重大影响。
