Distribution patterns of microbial communities along the environmental gradients in the Yangtze River estuary

Microorganisms are vital to trophic dynamics and biogeochemical cycling in estuarine-offshore ecosystems, yet integrated analyses of prokaryotic and microeukaryotic communities across water and sediment habitats remain limited for the Yangtze River Estuary (YRE). We combined 16S and 18S rDNA amplicon sequencing to characterize prokaryotic and microeukaryotic communities in surface water, bottom water, and sediment samples collected along an estuary-offshore transect in the YRE. Microeukaryotes showed higher alpha diversity in the water column than in sediments, whereas prokaryotes were more diverse in sediments. These contrasting diversity patterns were accompanied by clear shifts in dominant taxa, from benthic and anaerobic lineages in sediments and hypoxic bottom waters to phototrophic and copiotrophic groups in nutrient-rich estuarine surface waters. Along the estuary-offshore continuum, salinity, nutrients, and dissolved oxygen were the main drivers of community turnover, with a transition from eutrophic, low-salinity assemblages to saline, oligotrophic, and low-oxygen offshore communities, including potentially harmful dinoflagellates. Co-occurrence networks revealed widespread associations between microeukaryotes and prokaryotes, with microeukaryotes exhibiting a relatively sparse and modular interaction structure and prokaryotes showing a dense, highly clustered, and less compartmentalized network. These findings underscore the combined influence of habitat heterogeneity and environmental gradients on microbial diversity and community structure in the YRE.