Structure, assembly, and biological assessment of microbial communities based on eDNA metabarcoding in the continuous...

Environmental DNA (eDNA) metabarcoding offers a promising tool for ecological monitoring. This study employed eDNA metabarcoding to examine microbial communities along the continuous river-estuary-sea gradient in the Yellow River Delta (YRD). We aimed to elucidate how habitats shape microbial biogeography across these complex environmental transitions. Results revealed clear spatial heterogeneity in microbial diversity and community structure among habitats. The Beta Nearest Taxon Index analyses showed that the assembly of microbial communities in the river and estuary were influenced by stochastic processes, while deterministic processes in the estuary and sea, which showed an increase from stochastic processes to deterministic processes in winter. Furthermore, spatial factors were identified as more influential drivers than environmental variables. IBI was applied to quantitatively assess the ecological status of YRD, and the assessment outcomes exhibited satisfactory health status. This study demonstrates the potential of eDNA metabarcoding for assessing ecological impacts across river-estuary-sea continua, providing a new perspective for the management of the Yellow River Estuary.