Fish Diversity and Functional Traits in the Seagrass Based on the Environmental DNA Metabarcoding in the Li’an Bay, China

Environmental DNA metabarcoding has proven to be a powerful tool for monitoring fish diversity, and has been widely used in both freshwater and marine ecosystems. Fish diversity is a critical indicator to assess ecosystem function and its health. In this study, we took 12 samples from four areas (Area 1 (LS1) is the edge of the seagrass field adjacent to oyster reefs; Area 3 (LS3) is the edge of the seagrass field adjacent to coral reefs; Area 2 (LS2) is situated between LS1 and LS3 where there is dense seagrass distribution around the sampling sites; and Area 4 (LS4) is located between LS1 and LS3; we sample in the places at least 4 m by 4 m on the beach where no seaweed is present, each with three replicates) from Li’an Bay to detect fish diversity across multi-habitat seagrass areas based on the environmental DNA metabarcoding. A total of 312 Amplicon Sequence Variants (ASVs) were detected from 12 samples, and 58 fish species were annotated, representing 21 orders, 32 families and 48 generas. In general, the mean of Simpson and Pielou’s evenness indices followed the pattern LS1 > LS4 > LS2 > LS3, while the mean of Shannon–Wiener Diversity Index is LS4 > LS1 > LS2 > LS3. A total of 35 functional entities were observed among the four areas, with functional redundancy (FR) values of 0.800, 0.657, 0.542, and 0.7 for LS1, LS2, LS3, and LS4, respectively. All FR values were below 1.5, suggesting low ecological niche overlap among species within each area. These findings provide fundamental insights into the ecological health and stability of seagrass beds in Li’an Bay and offer a scientific basis for future ecological restoration efforts.