Abstract
Subsurface anticyclonic eddies (SAEs) reshape ocean stratification and nutrient–light regimes, yet their microbial and biogeochemical impacts remain poorly resolved. We combined CTD‐ADCP hydrography, nutrient profiles, microscopy and flow‐cytometry, and 18S/16S rRNA transcript sequencing to examine a long‐lived SAE in the northern South China Sea. The lens‐shaped eddy featured a strong velocity core (maximum 0.46 m s −1 at 90 m) and a deepened euphotic zone from exterior reference to edge to center (107.9 → 117.9 → 124.5 m). Depth‐integrated chlorophyll‐ a (25–150 m) was higher inside the eddy (19.7 mg m −2 ) than at reference waters (18.2 mg m −2 ), peaking at the center (20.8 mg m −2 ), indicating subsurface intensification of autotrophic biomass. Alpha‐diversity enhanced within the eddy, especially at its edge, while vertical turnover of protistan and bacterial assemblages exceeded center–edge differences, contrasting with surface‐intensifying anticyclonic eddies that often homogenize communities. Distance‐based redundancy analyses identified water mass, nutrient, viral, bacterial, and nanoflagellate gradients as key correlates of community structure, reflecting light‐nutrient colimitation modulated by top‐down control. Ecotype‐resolved patterns supported this framework that high‐light Ostreococcus tauri declined, whereas low‐light Prochlorococcus MIT9313 was ~ 5‐fold enriched just above the core and toward the center. Protist–bacteria co‐occurrence network formed depth‐ and edge‐specific modules and hub taxa included protist Stramenopiles, free‐living Alphaproteobacteria and particle‐associated Deltaproteobacteria. Collectively, the deepened euphotic zone and elevated subsurface chlorophyll‐ a , together with spatially structured community assembly, demonstrate that the eddy functions as a localized biogeochemical reactor enhancing subsurface productivity and microbial recycling in oligotrophic waters—linking eddy physics to ecosystem function.