Seagrass meadows support diverse fish assemblages but monitoring marine fauna in complex habitats remains challenging, particularly in highly turbid environments. Traditional monitoring methods can be inconsistent due to variability with environmental factors and methodological biases. Environmental DNA (eDNA) metabarcoding has emerged as a non-invasive alternative for assessing taxonomic richness and community structure, though its application in tropical seagrass meadows is still emerging. Implementing novel monitoring methods are essential for understanding fish community dynamics and how seagrass meadows respond to environmental change.
Trinity Inlet, a highly turbid seagrass meadow, has experienced fluctuations in cover and biomass due to disturbance events, where it has been in an observed recovery since 2016. Selecting appropriate fish survey methods is crucial in such environments, where turbidity and habitat complexity can impact species detection.
Our study evaluates fish and prawn communities in Trinity Inlet using traditional capture methods and eDNA metabarcoding. We assessed the practicality of eDNA metabarcoding at this turbid site by evaluating different filtration pore sizes (5, 10, and 20μm) and two teleost fish primers targeting the 16S and CO1 mitochondrial genes, to optimise species detection. We discuss how this research advances our ability to monitor fish populations and their responses to environmental change.