Spatiotemporal succession of sediment microbiomes and nutrients in five large yellow croaker aquaculture areas: Implications for fish quality.

Sediment microbiomes play a central role in regulating benthic nutrient cycling and ecological risk in mariculture systems, yet their succession under contrasting aquaculture modes and links to fish quality remain unclear. Here, surface sediments were seasonally collected from five large yellow croaker (Larimichthys crocea) farming areas along the southeastern coast of China, including one nearshore raft site, ND, and four offshore deep-water cage sites. Sediment nutrients were measured and bacterial and eukaryotic communities were characterized using PacBio full-length 16S and 18S rRNA gene sequencing. Sediments from ND consistently showed higher nutrient loads, particularly TN, TP, PO₄-P and NH₃-N, and stronger seasonal shifts in microbial communities than offshore cage areas. The four offshore cage sites generally maintained higher microbial diversity, more structured co-occurrence networks, and predicted functions associated with aerobic chemoheterotrophy and nitrification, suggesting relatively stable benthic conditions. In contrast, sediments from ND were enriched with Desulfobacterota, and showed higher predicted fermentation- and sulfur-cycling potentials, Dinophyceae, and parasite-related eukaryotic groups, suggesting a shift toward anaerobic degradation and pollution-tolerant community states. Correlation analysis showed that fish quality scores were negatively associated with sediment nutrient enrichment in most seasons. Nitrospirota, Polychaeta and Planctomycetota were positively related to fish quality scores in certain seasons, whereas Desulfobacterota and Dinophyceae showed negative associations. These results indicate that sediment eutrophication and microbiome shifts may be associated with habitat-related quality risks in large yellow croaker aquaculture. Nitrospirota, Polychaeta, Desulfobacterota and Dinophyceae may serve as potential ecological indicators for sediment health assessment and sustainable mariculture management.