eDNA Metabarcoding as a Promising Conservation Tool to Monitor Fish Diversity in Indonesia Marine Protected Areas

ABSTRACT Marine Protected Areas (MPAs) play a crucial role in conserving marine biodiversity while providing ecological, social, and economic benefits. Effective monitoring is essential for assessing changes in biodiversity and ensuring the sustainability of MPAs. In this context, biodiversity monitoring in Karimunjawa National Park (KNP) provides an excellent opportunity to examine effective monitoring practices. Traditionally, biodiversity assessments have been conducted through visual census methods, which have limitations such as challenges in species identification, time constraints, and high survey costs. To complement visual surveys, this study employed environmental DNA (eDNA) metabarcoding with the 12S rRNA gene, utilizing Oxford Nanopore sequencing to assess fish diversity across different zonation systems within KNP. eDNA analysis detected a total of 183 fish species, with 87 species (38% of the 229 species recorded by visual census) and 25 families (71%) shared between the two methods. Alpha diversity (ANOVA, p > 0.05) showed no significant differences between sites and zonation, whereas community structure (PERMANOVA, p < 0.05) revealed significant differences between sites and zonation. Additionally, eDNA offered complementary insights by detecting broader functional traits than the visual census, such as nocturnal behavior, habitat preferences, and migratory variations of fish species, whereas the visual census predominantly only recorded reef‐associated and nonmigratory taxa. These findings demonstrate that eDNA, particularly when integrated with Oxford Nanopore sequencing, is a powerful tool for marine biodiversity monitoring. Standardizing bioinformatics workflows is crucial for ensuring data comparability and maximizing the effectiveness of eDNA‐based conservation strategies in Indonesia's MPAs.