Exploring the relationship between planktonic and benthic eukaryotes in coastal zones is of great significance for us to further understand the influence of environmental conditions on microbial ecosystems and the integrated management of biological resources and ecological landscape in coastal areas. In this study, environmental DNA (eDNA), co-occurrence network analysis and the SourceTracker analysis were used to analyze seawater and sediment samples from Dinghai Bay, Fujian Province. Community structure, diversity, and co-occurrence patterns of eukaryotes, especially microeukaryotes in different habitats were compared. The results showed that: (1) There are differences between planktonic and benthic eukaryote communities to some extent. The diversity of benthic eukaryotes is significantly higher than that of planktonic eukaryotes. Environmental factors such as transparency, TDS (total dissolved solids) and salinity are significantly correlated with planktonic eukaryotes, while benthic eukaryotes are only correlated with conductivity. In addition, the planktonic community shows a strong distance-decay pattern while the benthic community did not. (2) There is strong connectivity between planktonic and benthic eukaryotes. The proportion of shared zero-radius operational taxonomic units (ZOTUs) in planktonic and benthic eukaryotes was 96.70% and 77.65%, respectively, and more than 92% of shared ZOTUs were not significantly different between two habitats. In addition, SourceTracker analysis showed that 59.70% of the benthos came from the planktonic community and 91.22% of the plankton from the benthic community. Plankton such as copepod, diatoms, dinoflagellata and ciliates live in sediments at some life stages,and there is often a planktonic larval stage in the life cycle of benthos. On the other hand, our study area is located in the intertidal zone and subtidal zone with special environmental conditions, which is influenced by tides, winds and river freshwater, and the constant mixing of surface and bottom water is also a possible reason. (3) The co-occurrence network analysis shows that the co-occurrence patterns of eukaryotes in the two habitats are similar to a considerable degree. Positive correlations are dominant in both planktonic and benthic communities, and the ratio of positive and negative correlations has no significant difference between two communities.
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