Fish diversity in peat swamp waters of East Kalimantan, Indonesia, assessed using environmental DNA metabarcoding

Abstract

Abstract Studies on fish diversity in peat swamp waters using direct capture methods are often hindered by limited accessibility, high water turbidity, and complex habitat structures, frequently resulting in underrepresentative data. To address these challenges, environmental DNA (eDNA) metabarcoding targeting the mitochondrial 12S rRNA region using MiFish universal primers has emerged as a robust alternative, capable of detecting species that are difficult to observe directly, including rare, cryptic, or extremophilic species inhabiting harsh physicochemical conditions such as peat swamp waters. In this study, we employed eDNA metabarcoding (Oxford Nanopore Technologies, UK) to characterize the species composition and community diversity of fish in the peat swamp waters of East Kalimantan. A total of 29 fish species, spanning 7 orders and 16 families, were identified across three sampling areas: Sabintulung, Muara Kaman, and Tuana Tuha. The species exhibiting the highest individual relative read abundance values were Helostoma temminckii (32.62%), Thynnichthys polylepis (27.69%), Trichopodus pectoralis (23.60%), and Channa striata (21.94%), each representing their relative contribution within their respective sampling profiles. Alpha (α) diversity indices indicated that the highest levels of diversity and evenness were located at the Muara Kaman station, whereas the Tuana Tuha station, situated along the Belayan River flow, exhibited the lowest diversity. Furthermore, beta (β) diversity analysis revealed a significant similarity in fish community structure between the Muara Kaman and Tuana Tuha stations. These findings demonstrate that eDNA technology is a highly effective tool for detecting fish species composition and diversity in East Kalimantan’s peat swamp waters, offering significant potential for long-term biodiversity monitoring and conservation efforts.