eDNA uncovers hidden fish diversity in the coral reef ecosystems of Karimunjawa National Park, Indonesia

Abstract

Environmental DNA (eDNA) has emerged as a powerful tool for swiftly assessing coral reef ecosystems, particularly for detecting fish diversity. This study focused on employing eDNA to investigate fish biodiversity and its functional traits in the Karimunjawa National Park (KNP), Indonesia. The use of eDNA and then validating with visual census results to reveal fish diversity was implemented across four management zones within the park (i.e., the core zone at Taka Malang, the protection zone at Menjangan Kecil Island, the tourism zone at Cilik Island, and an open access location at Genting Island). Sampling involved collecting one liter of seawater per site, filtering, and processing to target the 12S locus, and then sequencing using the MinION machine (Oxford nanopore). The eDNA results show higher species diversity in the tourism zone compared to the core, protection, and open access zones. However, beta diversity analysis revealed no significant differences in community composition between the zones. Moreover, this research revealed 147 species belonging to 31 families, with 60 % species and 30 % families identified solely through eDNA, that were not covered by the visual census. This research also reveals that eDNA is an excellent approach to detecting functional trait diversity, including environment preference and migratory and nocturnal behavior. This research underscores the potential of eDNA for evaluating fish diversity in KNP, proposing a combined eDNA and visual census approach to fill existing gaps in biodiversity assessment. Such integration promises to bolster conservation efforts within Marine Protection Areas like KNP.