Spatiotemporal variations in the response mechanism between ARGs removal and the microbial community in estuary sediments under the bio-ecological restoration

Estuarine sediments are reservoirs of antibiotic resistance genes (ARGs). However, spatiotemporal variations in the response mechanism between ARGs removal and the microbial community under the bio-ecological restoration of estuaries remain unclear. In this study, spatiotemporal hydrological and water quality data were collected from a 14,000 m² estuary located in the downstream of the Yangtze River to construct a MIKE 21 hydrodynamic model. Based on this, a bio-ecological combined restoration technology of estuaries was constructed and has been running steadily for more than two years. Water and sediment samples in different sections of the bio-ecological restoration and in different seasons were collected to reveal the spatiotemporal variations and response mechanism of ARGs and the microbial community. In total, nine typical ARGs, intI1, and the microbial community were investigated by quantitative polymerase chain reaction and evaluation of the 16S rRNA. The results revealed that the ecological restoration improved the hydrodynamic conditions of the estuary, mitigated the accumulation of pollutants, and considerably removed macrolide (ermC: 63.17–99.06%, ermB: 30.32–96.29%), sulfonamide (sul2: 31.25–98.91%), and tetracycline (tetA: 26.93–98.68%, tetW: 64.86–94.99%) resistance genes. Meanwhile, the ARGs exhibited significant spatiotemporal variation, and that the dominant genes in the estuarine sediments were sulfonamide, macrolide, and tetracycline resistance genes. The absolute abundances of the ARGs followed the order winter > summer > autumn > spring. Proteobacteria (45.33%), Chloroflexi (11.24%), and Acidobacteria (9.99%) were the dominant phyla in the estuary sediment. Massilia and Pseudarthrobacter were the dominant genera in spring, whereas the genera belonging to Proteobacteria were dominant in the other three seasons. Proteobacteria, which was positively correlated with sul1, sul2, tetA, tetM, tetW, ermB, ermC, qnrS, and floR, was recognized as typical antibiotic resistant bacteria, while Thiobacillus, Massilia, and Dechloromonas were found to be potential host genera. Network analysis also revealed the possibility that sul1, tetA, and ermC can act as multi-antibiotic resistance genes. Furthermore, environmental factors including total phosphorus, total nitrogen, and heavy metal concentration also affected ARG dissemination by affecting microbes (p ≤ 0.05). Overall, our findings provided practical evidence for the role that bio-ecological restoration plays in controlling the propagation of ARGs by regulating the microbial community in the estuary sediment.