Dynamic Bacterial Communities, Resistome–Virulome Coupling, and Biomonitoring Paradigms at Direct Sea Discharge Outlets: An Integrated Microbiome Perspective for Coastal Pollution Control

Direct sea discharge outlets served as critical conduits for urban sewage and industrial wastewater disposal, playing dual roles as pollutant dilution channels and hotspots for pathogens and antibiotic resistance genes. Traditional monitoring approaches relying on physicochemical parameters and fecal indicator bacteria failed to capture the latent and cumulative risks posed by complex microbial communities. In this review, a holistic microbiome perspective was adopted to systematically synthesize current knowledge on the bacterial community dynamics, assembly mechanisms, resistome–virulome coupling patterns, mobilome-associated risk characteristics, and emerging biomonitoring strategies in direct sea discharge outlets. By integrating high-throughput multi-omics technologies with ecological network analysis and machine learning, we delineated a paradigm shift from cataloging microbial presence to deciphering functional interactions, risk propagation dynamics, and proactive surveillance strategies. Furthermore, under the “One Health” framework, we discussed emerging research frontiers and future challenges in managing pollution at discharge outlets, aiming to provide a scientific basis for environmental risk management in coastal zones.