Manman Li

Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China
Author    Correspondence author
International Journal of Marine Science, 2026, Vol. 16, No. 4   
Received: 10 Jul., 2026    Accepted: 15 Aug., 2026    Published: 28 Aug., 2026

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Marine aquaculture is moving toward greater production intensity while facing persistent challenges from infectious disease, environmental instability, and antimicrobial resistance. In this setting, microbial communities should no longer be treated only as a background component of the culture environment. They participate in nutrient cycling, organic matter transformation, host nutrition, mucosal defense, pathogen exclusion, and disease development. This review examines how microbial monitoring can be translated from a descriptive research tool into a practical component of marine aquaculture health management. Conventional culture, PCR-based assays, 16S rRNA gene sequencing, metagenomics, multi-omics approaches, flow cytometry, biosensors, and field-deployable molecular methods provide complementary information at different levels of taxonomic, functional, quantitative, and temporal resolution. Particular attention is given to potential pathogens, health-associated microorganisms, community stability, dysbiosis, and functional genes as candidate indicators. Current evidence indicates, however, that no single microbial taxon or diversity metric can serve as a universal marker of health. Monitoring is most informative when microbial signals are interpreted against farm-specific baselines and integrated with water quality, production stage, and host-health observations. On this basis, the review proposes a tiered framework linking routine surveillance, early warning, risk classification, proportionate intervention, and post-intervention feedback. The framework intentionally avoids fixed universal thresholds because microbial communities vary substantially among species, farms, seasons, and production systems. Future progress will depend on standardized sampling, absolute microbial quantification, longitudinal and multi-farm validation, functional confirmation of biomarkers, and integration of rapid microbial monitoring with environmental sensors and data-driven decision support. Microbial monitoring can therefore support a gradual shift from reactive treatment of disease toward preventive, adaptive, and precision health management in sustainable marine aquaculture.

Marine aquaculture; Microbial monitoring; Microbiome; Microbial dysbiosis; Health management; Disease early warning; Microbial indicators; Sustainable aquaculture