Philpott, Darcy E., Dibattista, Joseph D., Rasheed, Michael a., Missen, Laura A., Coles, Robert G., Villacorta Rath, Cecilia, and York, Paul H. (2026) Comparing Beam Trawl Sampling and eDNA Metabarcoding for Assessing Fish Diversity in Turbid Tropical Seagrass Habitats. Estuarine, Coastal and Shelf Science, 340. 109968.

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Abstract

Tropical seagrass habitats support diverse fish assemblages and provide critical nursery habitat for many ecologically and economically important species. However, biodiversity assessments in these systems are challenging due to turbidity, suspended sediments, and dense vegetation, which can restrict both traditional capture- and visual-based surveys, as well as emerging molecular approaches. In this study, we compared fish assemblages detected using beam trawl sampling and multi-assay environmental DNA (eDNA) metabarcoding, including two fish-targeted assays, 16S-Fish/D and MiFish-U, and the broader metazoan COI-Leray assay in a turbid tropical seagrass meadow in Trinity Inlet, north Queensland, Australia.

Environmental DNA metabarcoding detected greater genus-level richness than beam trawling, recovering 112 genera compared with 27 genera detected by beam trawl surveys. Beam trawls detected a smaller subset of taxa associated with local, trawl-accessible fishes, including four taxa not recovered by eDNA metabarcoding. Among the metabarcoding assays, MiFish-U and 16S-Fish/D recovered substantially more fish taxa than COI-Leray, which produced limited fish detections. Univariate analyses indicated that site-level richness patterns varied among sampling approaches, with MiFish-U detecting higher richness at Ellie Point, and beam trawl sampling detecting higher richness at the Esplanade. Multivariate analyses revealed a significant Method x Site interaction, suggesting fish assemblages detected by the two sampling techniques respond to local conditions in different ways. Incomplete overlap in taxonomic detections between MiFish-U and 16S-Fish/D further highlighted the strong influence of marker choice on fish detection.

These findings demonstrate that eDNA metabarcoding and beam trawl surveys capture complementary components of seagrass-associated fish assemblages within the same habitat. Integrating molecular and capture-based methods therefore provides a more comprehensive and reliable assessment of biodiversity in turbid tropical seagrass ecosystems.

Item ID:	92041
Item Type:	Article (Research - C1)
ISSN:	1096-0015
Keywords:	Biodiversity; Environmental DNA; Seagrass; Nursery Function; Turbidity; Estuarine; Species richness
Related URLs:	Publisher
Copyright Information:	© 2026 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Funders:	Australian Research Council (ARC), BHP Billiton, North Queensland Bulk Ports Corporation (NQBP), Holsworth Wildlife Research Endowment
Projects and Grants:	ARC LP210300851
Date Deposited:	30 Jun 2026 22:14
FoR Codes:	41 ENVIRONMENTAL SCIENCES > 4104 Environmental management > 410401 Conservation and biodiversity @ 30% 31 BIOLOGICAL SCIENCES > 3103 Ecology > 310305 Marine and estuarine ecology (incl. marine ichthyology) @ 30% 41 ENVIRONMENTAL SCIENCES > 4104 Environmental management > 410402 Environmental assessment and monitoring @ 40%
SEO Codes:	18 ENVIRONMENTAL MANAGEMENT > 1802 Coastal and estuarine systems and management > 180203 Coastal or estuarine biodiversity @ 50% 18 ENVIRONMENTAL MANAGEMENT > 1802 Coastal and estuarine systems and management > 180201 Assessment and management of coastal and estuarine ecosystems @ 50%
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