Marine fisheries resources are under increasing threat, necessitating the development of new effective monitoring and management strategies. Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has emerged as a non-invasive and sensitive alternative method for monitoring fish biodiversity and fisheries resources and assessing the fisheries impact of anthropogenic activities. Here, we summarize crucial technical details about eDNA metabarcoding for marine fish monitoring and provide meta-analytical trends in primer selection and sample size, assessment standards, fish and fisheries databases, reference fish genomic databases, and other relevant metrics. The pressing need for better reference databases and standardization methods is discussed. We further highlight the potency of emerging eDNA metabarcoding studies for monitoring global fish diversity and revealed regional study hotspots in South China, Atlantic and Mediterranean Seas. The innovative advances in using eDNA/eRNA metabarcoding for fish diversity monitoring and assessment from the detection of rare or invasive species to branching applications in biomass estimation, population genetics, food web analysis, fish migration and feeding studies were reviewed. We also explore the potential of eRNA metabarcoding as an upcoming extension of eDNA metabarcoding in marine fish monitoring and assessment with improved functional relevance. We envision the integration of eDNA/eRNA metabarcoding-based fish monitoring methods with traditional monitoring approaches to significantly improve marine fish surveillance, ecological research, and conservation efforts.
Keywords: DNA metabarcoding; Environmental monitoring; Impact assessment; Marine fish and fisheries; Next-generation sequencing.
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