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

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 sampling was conducted in September 2025; the mitochondrial COI gene was amplified using mlCOIintF/jgHCO2198 and sequenced with Oxford Nanopore. In total, 26,300 sequence reads were obtained across eight taxonomic classes: Malacostraca (54.4%), Actinopteri (27.2%), Bivalvia (10.9%), and Thecostraca (7.2%), with contributions from Scyphozoa, Chondrichthyes, Merostomata, and Hydrozoa, all of which either contributed < 1% or failed to be identified as a class-level hit. Banyuasin exhibited 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). PERMANOVA revealed significant differences among 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 was significantly negatively correlated with dissolved oxygen (r = -0.99) and salinity (r = -0.88), as demonstrated by Pearson correlations. This species-level read abundance matrix is available as Supplementary Table S1. This dataset, which we are revealing for the first time, serves as a reproducible baseline that will facilitate biomonitoring and conservation planning in tropical estuarine ecosystems by leveraging eDNA's unprecedented ability to capture a wide range of biodiversity, extending well beyond fish.