Data set for manuscript: eDNA Metabarcoding Reveals Rich Microbial Eukaryote Communities in Tropical Mangrove Forest of Makassar, Indonesia

Mangrove ecosystems are critical coastal habitats that support diverse microbial communities essential for nutrient cycling, organic matter decomposition, and ecosystem stability. Despite their ecological importance, microbial diversity in tropical mangroves remains poorly characterized, particularly in Indonesia. This study employed environmental DNA (eDNA) metabarcoding using 18S rRNA markers to assess microbial species diversity in the waters of the Lantebung Mangrove Forest, Makassar, Indonesia. Water samples were collected from two locations and analyzed through high-throughput sequencing and bioinformatic processing using QIIME 2. A total of 103 microbial species were identified across five kingdoms: Protista (48.5%), Chromista (28.0%), Animalia (12.6%), Bacteria (7.8%), and Fungi (2.9%). Dominant taxa included photosynthetic protists and chromists, along with functionally important bacterial and fungal species. Species richness and relative abundance differed between sampling sites, reflecting environmental gradients such as light availability, salinity, and nutrient flow. Notably, Station P1 (more exposed) exhibited greater species richness, while Station P2 (within mangrove canopy) had higher individual abundance. These findings highlight the effectiveness of 18S rRNA-based metabarcoding in capturing microbial diversity and offer valuable baseline data for future ecological monitoring and conservation strategies in tropical mangrove ecosystems.