Hydrographic Restructuring Drives Lineage Turnover of Small Diazotrophs in Regions of the Southern East China Sea Influenced by the Kuroshio Current

Marine diazotroph communities are highly sensitive to hydrographic gradients. However, shifts in water-column structure interact with vertical habitat partitioning, and short-term temporal variability remains poorly understood in marginal seas influenced by the Kuroshio Current. Here, we investigated small diazotrophs (0.2–5 μm) in the southern East China Sea during spring and summer using nifH amplicon sequencing and qPCR, targeting UCYN-A1, UCYN-B, UCYN-C, and Trichodesmium . Water samples were collected every 6 h from the surface, deep chlorophyll maximum layer, 1% light intensity layer, and bottom waters at five shelf-to-slope stations. Diazotroph community composition showed depth-associated variation in both seasons, but the dominant cyanobacterial lineages changed markedly between cruises. Upper-water assemblages were dominated by UCYN-A1 in spring, whereas summer communities showed increased representation of Trichodesmium- associated nifH genes in the 0.2–5 μm fraction under warmer, more strongly stratified conditions. Phylogenetic analysis further identified multiple ASVs associated with taxonomically unresolved UCYN-B-related environmental nifH sequences. qPCR showed that UCYN-A1 displayed short-term variability, whereas other targeted groups showed less coherent temporal variation. This study indicated that hydrographic restructuring drives lineage turnover and vertical niche partitioning of small diazotrophs in the southern East China Sea.