Assessment of microbial community changes in seawater of marine cage- culture large yellow croaker (Larimichthys crocea) farms.

Microbial communities in aquaculture seawater are fundamental to ecosystem stability and health, serving as critical indicators of environmental change. However, the specific impacts of large-scale marine cage culture on these planktonic communities remain poorly understood. Using 16S and 18S rRNA sequencing, we assessed prokaryotic and eukaryotic communities in seawater from nearshore and offshore large yellow croaker farms, as well as a non-farmed site on Nanji Island, China. Our analysis revealed ecologically notable taxonomic and functional trends, despite overall community composition showing only modest changes. Cage-culture operations were associated with an apparent reduction in eukaryotic diversity alongside enrichment of heterotrophic (Cryothecomonas aestivalis) and parasitic taxa (Syndiniales). In contrast, prokaryotic communities exhibited increased phylogenetic diversity at the offshore farm, suggesting organic enrichment may drive niche diversification. Functionally, core metabolic pathways were largely conserved, though nitrogen and sulfur cycling processes appeared more prominent in the farmed sites. Co-occurrence networks revealed a modular structure, with key associations surviving False Discovery Rate (FDR) correction, characterized by a negative association between oligotrophic and copiotrophic niches. Crucially, the absence of significant biomarkers for classic pathogens, combined with microbial patterns indicative of system stability, suggests that the microbial community in this region may remain balanced despite the presence of aquaculture activity. These findings provide preliminary insights that could inform the management of ecological sustainability in offshore mariculture.