Seasonal succession and niche differentiation in Skeletonema species driven by temperature and salinity in inner Tokyo Bay

The genus Skeletonema is a dominant diatom in coastal waters worldwide, frequently causing blooms, and it includes several cryptic species. To elucidate the occurrence patterns and niche differentiation among Skeletonema species in Tokyo Bay, Japan, sampling was conducted between June 2021 and February 2023. Species composition and abundance were determined using species-specific quantitative polymerase chain reaction (qPCR) and were analyzed using an environmental framework in temperature, salinity, and nutrient concentrations. Niche characteristics were determined using outlying mean index (OMI) analysis, focusing on five frequently detected species: S. ardens, S. marinoi-dohrnii complex, S. menzelii, S. potamos, and S. japonicum. Seasonal succession was evident, wherein S. japonicum predominated in winter, followed by the S. marinoi-dohrnii complex in spring and S. menzelii, S. ardens, and S. potamos in summer. Principal component analysis indicated that S. japonicum was associated with low temperature and high salinity, whereas other frequently detected species were positively correlated with temperature. The OMI analysis revealed that niche breadth differed among species, with S. potamos, S. marinoi-dohrnii complex, and S. menzelii showing a wide niche breadth and S. ardens and S. japonicum being specialists. Marginality was highest for S. potamos, indicating an association with low salinity, but it was lowest for S. japonicum due to a high frequency of high-salinity conditions. This study demonstrated that (1) seasonal succession in the bay is primarily structured by associations with temperature and salinity but (2) niche partitioning is not always clear. When the environment was highly disturbed in the summer rainy season, more than two Skeletonema species frequently co-occurred, suggesting potential competition for nutrients.