Comparison of Eukaryotic Community Structures Across Different Habitat Types in the Nearshore Waters of Ma’an Archipelago Based on Environmental DNA Technology

Coastal zones are critical areas of marine ecosystems, where biodiversity is a key ecological element for maintaining ecosystem stability and ensuring the sustainability of fishery resources. The Shengsi Ma’an Archipelago Marine Special Reserve features heterogeneous habitats such as rocky reefs, seaweed beds, and artificial aquaculture areas, which are significantly affected by human activities. This study focused on the nearshore waters of Lvhua Island within the reserve. Based on the degree of human disturbance, the study area was divided into five typical habitat types: cage culture area (A), intertidal seaweed bed (B), marine platform area (C), open waters (D), and mussel culture area (E). Environmental DNA (eDNA) technology was employed to analyze the characteristics of eukaryotic community structures across these habitats and their coupling mechanisms with environmental factors. The results showed that a total of 767,360 valid sequences were obtained from 15 seawater samples. Clustering into operational taxonomic units (OTUs) yielded 811 OTUs, taxonomically covering 50 phyla, 104 classes, 220 orders, 334 families, 435 genera, and 530 species. The number of OTUs shared across all habitats was 387. The intertidal seaweed bed (B) had the highest proportion of unique OTUs (4.8%) and showed significant differences (0.01 < p < 0.05) in OTU composition compared to the marine platform area (C) and the mussel culture area (E). Among the major dominant phyla, the abundance of Dinoflagellata across sites was A (74.56%) > E (68.32%) > B (62.15%) > C (58.74%) > D (55.21%). The abundance of Arthropoda across sites was D (27.34%) > C (19.98%) > B (17.89%) > E (9.17%) > A (8.25%). Each of the other sites had 1-2 dominant phyla. Among the major dominant genera, the abundance of an unclassified genus of Dinophyceae was B (41.39%) > C (23.31%) > D (22.03%) > E (19.27%) > A (18.56%). The genus Noctiluca was endemic to Site A, with an abundance of 39.98%. The genus Calanus was dominant in site D (26.17%). The genus Meganyctiphanes was unique to sites C (12.12%) and D (8.76%). The genus Ectopleura was unique to site A. The genus Botrylloides was unique to site E. The remaining genera were evenly distributed across sites without significant habitat specificity. Alpha diversity analysis revealed that the marine platform area (C) had the highest Shannon index (3.32 ± 0.22) and Pielou index (0.54 ± 0.04), while the mussel culture area (E) had the highest Chao1 index (578.96 ± 10.25). All diversity indices were lowest in the cage culture area (A). Principal coordinate analysis (PCoA) and ANOSIM tests indicated significant differences (p < 0.05) in eukaryotic community structures among different habitats. Samples from the seaweed bed clustered separately and were distant from other habitats. Redundancy analysis (RDA) showed that pH was the key environmental factor driving the differentiation of eukaryotic community structure. Temperature was negatively correlated with dissolved oxygen, while salinity was positively correlated with pH. The combined differences in environmental factors were the main drivers of eukaryotic community structure differentiation. In conclusion, this study clarifies the regulatory role of habitat type on the eukaryotic community structure in the nearshore waters of Ma’an Archipelago, confirming a negative correlation between human activity intensity and biodiversity, and a positive correlation between natural habitat complexity and biodiversity. The research findings provide scientific support for assessing the health of the marine ecosystem and formulating ecological conservation and management strategies in this region.