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.

红树林生态系统是至关重要的海岸生境，支撑着对养分循环、有机质分解及生态系统稳定不可或缺的多样微生物群落。尽管其生态价值举足轻重，热带红树林中的微生物多样性仍未得到充分解析，在印度尼西亚地区尤为如此。本研究采用基于18S rRNA标记的环境DNA（eDNA）宏条形码（metabarcoding）技术，以评估印度尼西亚望加锡兰塔邦红树林水域的微生物物种多样性。研究人员从两个采样点位采集水样，通过高通量测序及基于QIIME 2的生物信息学流程进行分析。本次分析共鉴定出5个界的103种微生物物种：原生生物界（Protista，48.5%）、色藻界（Chromista，28.0%）、动物界（Animalia，12.6%）、细菌界（Bacteria，7.8%）及真菌界（Fungi，2.9%）。优势类群包括光合原生生物与色藻，以及功能意义重大的细菌与真菌物种。两个采样点位的物种丰富度与相对丰度存在差异，反映了光照可利用性、盐度及养分流动等环境梯度特征。值得注意的是，暴露程度更高的P1站位物种丰富度更高，而处于红树林冠层内的P2站位则具有更高的个体丰度。本研究结果证实了基于18S rRNA的宏条形码测序技术在捕获微生物多样性方面的有效性，并为热带红树林生态系统的后续生态监测与保护策略提供了宝贵的基线数据。