Using eDNA metabarcoding to assess the distribution and ecological drivers of protist communities in subtropical estuaries: insights into environmental filtering and cross-trophic links

Abstract

Estuarine ecosystems are increasingly threatened by intensifying anthropogenic stressors, including nutrient enrichment and heavy metal pollution, which alter biodiversity patterns and ecosystem functioning. Protists, as key drivers of primary production, nutrient cycling, and trophic transfer, exhibit rapid and sensitive responses to environmental change, making them promising bioindicators for estuarine condition assessment. Here, we integrated multi-marker environmental DNA (eDNA) metabarcoding with environmental measurements to characterize protist communities (18S rDNA) and their cross-trophic associations with bacteria (16S rDNA), metazoans (18S rDNA), and fish (12S rDNA) across 30 subtropical estuaries in South China. Protist assemblages were dominated by Gyrista and Ciliophora, with phototrophs forming the major functional group, followed by consumers and parasites. Pronounced spatial variation in α-diversity and community structure reflected strong ecological filtering along gradients of salinity, temperature, and heavy metal concentrations during the dry season. Null model and neutral model analyses consistently indicated that deterministic processes, rather than stochastic dynamics, primarily governed protist assembly. Furthermore, co-occurrence patterns revealed significant cross-trophic associations, particularly with bacterial communities, suggesting potential co-variation under environmental stress. Collectively, our findings identify protists as sensitive indicators of both abiotic filtering and biotic interactions in estuarine ecosystems. The multi-trophic eDNA framework applied here provides an efficient and scalable approach for biodiversity surveillance, offering valuable implications for early environmental warning and sustainable estuarine management under ongoing global change.