Multi-class metazoan diversity and community composition in tropical estuaries assessed by eDNA metabarcoding: a baseline dataset from South Sumatra, Indonesia

Abstract

The present study employed environmental DNA (eDNA) metabarcoding of the metazoan community composition and diversity in relation to water quality parameters from four major river estuaries of South Sumatra, Indonesia (Sembilang, Banyuasin, Musi, and Air Salek). Surface water samples (1 L each) were collected in triplicate from each of the four estuaries, yielding a total of 12 samples. The study was conducted in September 2025, and the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was amplified using mlCOIintF/jgHCO2198 and sequenced with Oxford Nanopore. In total, 26,300 quality-filtered sequence reads were obtained across eight taxonomic classes: Malacostraca (54.4%), Teleostei (27.2%), Bivalvia (10.9%), and Thecostraca (7.2%), with contributions from Scyphozoa, Elasmobranchii, Merostomata, and Hydrozoa, all of which either contributed < 1% or failed to be identified as a class-level hit. Banyuasin had the highest read abundance, extreme dominance by the mantis shrimp Odontodactylus cultrifer, and very low diversity (Shannon H′ = 1.35). Conversely, the community of Air Salek was the most balanced (H′ = 3.18) and had the highest species richness (S = 58). Permutational multivariate analysis of variance (PERMANOVA) revealed significant differences between stations (pseudo-F = 3.24, p = 0.002), and principal coordinates analysis (PCoA) based on Bray–Curtis distances explained 48.3% and 32.5% of variance, respectively. Simpson dominance showed strong negative correlations with dissolved oxygen (r = −0.99) and salinity (r = −0.88), as demonstrated by Pearson correlations. This dataset serves as a reproducible baseline for local biomonitoring and conservation planning in tropical estuarine ecosystems, identifying priority areas (e.g., Air Salek as a high-diversity refuge and Banyuasin as a stressed site requiring restoration interventions) through eDNA’s capacity to capture a wide range of biodiversity, extending well beyond fish.