Different structuring factors and distribution patterns of marine prokaryotic and eukaryotic communities in the subtropical Kuroshio region

To clarify the differences in the effect of environments on community structures and in distribution patterns between marine prokaryotes and microbial eukaryotes, microbial communities were investigated spatially and seasonally in the surface layer of the subtropical Kuroshio region using environmental DNA (eDNA) metabarcoding analysis. Prokaryotic communities were primarily different between seasons and dominated by Flavobacteriales (33.4 ± 11.6%) and Synechococcales (25.0 ± 21.2%) during spring and autumn, respectively. For eukaryotes, diverse dinoflagellates including Syndiniales were frequently dominant (46.7 ± 8.2%) regardless of seasons, and the horizontally and vertically collected eDNA samples successfully captured the spatially heterogeneous dominance of Copelata (34.3–36.4%) and Doliolida (60.3–67.3%) at shallower depths (10–50 m) and Spumellaria (39.4–94.9%) at deeper depths (100–150 m). A large proportion (64.6%) of the variance in the community structure of prokaryotes was explained by physical conditions and chlorophyll (chl.) a concentration, which indicates that the physical environments of water masses and resource supply by phytoplankton mainly shape prokaryotic communities. On the other hand, the effect of physical conditions on community structure was much smaller for eukaryotes (10.7%) compared to prokaryotes (29.6%), and the variance was most (24.7%) explained by chl. a concentration but largely (64.6%) unexplained. This result suggests that food environments and other factors including parasitic interactions determine eukaryotic communities rather than physical conditions. The communities of prokaryotes and some eukaryotes such as Dinophyceae and Spirotrichea showed relatively similar spatio-temporal distributions probably due to their symbiotic and trophic interactions and were detected commonly. In contrast, the distinct and unique distributions of other heterotrophic eukaryotes such as Doliolida were observed, indicating their sporadic and massive blooms in favorable environments for each community. The comparison of these distribution patterns across taxonomic and trophic levels implicates the ecological roles of microbial communities in maintaining the stable structure and functions of marine ecosystems and changing the structure of the microbial food web locally.