eDNA Metabarcoding Reveals Microbial Community Composition in Tropical Mangrove Forests in Makassar, Indonesia

Abstract

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 via 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 via 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%). The dominant taxa included photosynthetic protists and chromists, along with functionally important bacterial and fungal species. Species richness and relative abundance differed among the sampling sites, reflecting environmental gradients such as light availability, salinity, and nutrient flow. Notably, Station P1 (more exposed) presented greater species richness, whereas Station P2 (within the mangrove canopy) presented greater 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.

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