A Comparison of Fish Diversity in Rocky Reef Habitats by Multi-Mesh Gillnets and Environmental DNA Metabarcoding

This study was undertaken in order to explore the practical effectiveness of the environmental DNA (eDNA) metabarcoding approach in evaluating fish composition and diversity in a high heterogeneous rocky reef habitat. We assessed the fish composition and diversity characteristics of the rocky reef habitat at Dachen Islands, Taizhou and the Zhejiang Province in China in November 2020 by comparing two methods: multi-mesh gillnets and eDNA. A comparative analysis was carried out on the fish composition and diversity characteristics gained under the two methods by using taxonomy, ecotypes and diversity indices. The results showed that there were 28 species of fish collected through gillnets, distributed under 24 genera, 19 families, 6 orders and one class. Among them, 4, 18, and 6 species of near-surface, near groundfish and groundfish were found, respectively, with Thryssa mystax, Johnius belangerii , and Sebastiscus marmoratus being the dominant species in each water layer. A total of 81 species of fish detected by eDNA metabarcoding belonging to 67 genera, 46 families, 15 orders and 2 classes. The near-surface, near groundfish and groundfish species were 17, 42, and 22, with Thryssa vitrirostris, Benthosema pterotum, Harpadon nehereus , and Dasyatis akajei being the dominant species in each water layer. Twenty species (71.4%) and 41 species (50.6%) of reef fish were counted by gillnets and eDNA, respectively. The results showed that multi-mesh gillnets can accurately obtain information on fish composition in rocky reef habitats, but with some selectivity. The eDNA technology can detect species not collected by gillnets, but the number of species detected in areas with fast water velocity is significantly less than other eDNA stations where the water velocity is slow. In summary, the combination of traditional nets and eDNA will provide more information on taxonomic diversity and population biomass, transforming natural resource management and ecological studies of fish communities on a larger spatial and temporal scale.