Utilizing eDNA methods in biodiversity studies of a river affected by anthropogenic pollution: a case study on the Batanghari River in Indonesia

Aquatic biodiversity is rapidly declining owing to global climate change, increasing anthropogenic activities, and species invasions. The Batanghari River, one of the Indonesia’s longest rivers, faces severe pressure from illegal gold mining, industrial pollution, and domestic waste. Despite evidence of biodiversity loss, a comprehensive assessment has yet to be undertaken. This study used eDNA metabarcoding, targeting the mitochondrial cytochrome c oxidase I (co1) gene fragment, to analyze the diversity of aquatic biota in Batanghari River. Environmental DNA (eDNA) metabarcoding, as used in this study, offers broader insights compared with traditional methods by enabling the detection of a wider range of species, including those that are rare, cryptic, or difficult to capture. A total of 22,180,436 reads were generated from five river watersheds. Approximately 80% of reads were classified to the species level (72.5–100% of identical matches), with the remainder identified as unidentified taxa. Significant differences in species richness and community composition were observed between upstream and downstream areas. Taxonomic richness was highest at Batanghari Hulu, the most upstream site, with 9161 amplicon sequence variants (ASVs), including 5773 Chordata, 1755 Arthropoda, and 433 Mollusca. In contrast, downstream locations such as Batanghari Hilir exhibited lower richness, with 3888 ASVs, including 2681 Chordata, 651 Arthropoda, and 224 Mollusca. These differences are likely influenced by increasing anthropogenic stressors downstream. Furthermore, beta diversity analysis showed significant variation in taxonomic composition among sampling locations (permutational multivariate analysis of variance, PERMANOVA, p < 0.05). Additionally, several extinct or endangered species were detected at multiple sites, as confirmed by our previous work. This study highlights the critical role of eDNA metabarcoding in assessing biodiversity, providing valuable insights for conservation and management efforts aimed at protecting the Batanghari River ecosystem.