Marine phytoplankton are vital for global primary production and carbon fixation in marine ecosystems. Understanding the distribution patterns and assembly mechanisms of phytoplankton in varying nutrient conditions is crucial for phytoplankton ecology, yet research in this field is limited. This study employed environmental DNA technology targeting the phytoplankton 23S rRNA gene to investigate the community structure and assembly processes of phytoplankton (algae and cyanobacteria) in the East China Sea. We identified 224 phytoplankton species: 72 Bacillariophyta, 44 Cyanobacteria, and 34 Chlorophyta. Bacillariophyta and Dinoflagellata were predominant in the nutrient-rich Changjiang Diluted Water (CDW), while cyanobacteria dominated in the low-nutrient Kuroshio Branch Current (KBC). Phytoplankton distribution was significantly influenced by salinity and nutrient levels. Deterministic processes mainly governed phytoplankton community assembly in both CDW and KBC. Co-occurrence network analysis revealed that interactions among phytoplankton in the KBC were significantly higher than in the CDW, indicating greater cooperation or competition in the KBC. Conversely, the modularity of the CDW network was notably higher, likely due to greater environmental heterogeneity. This study highlights the effectiveness of environmental DNA technology in exploring phytoplankton community structure and assembly mechanisms in different nutrient environments. These findings emphasize the significance of understanding phytoplankton dynamics, as enhanced carbon fixation could greatly impact carbon cycling and climate regulation in marine ecosystems.

Community composition is determined largely by drift, selection, dispersal, and speciation. The crucial issue is disentangling the relative importance of different processes in community assembly. However, this issue has not been adequately discussed in benthic foraminiferal communities. Here, we studied the community composition, co-occurrence network, and community assembly of benthic foraminifera (protozoa) on the Xisha carbonate platform and their coupled relationships. The community composition was determined via the environmental DNA (eDNA) technique. Heavy metals, grain sizes, loss on ignition (LOI), organic carbon, and pH were measured for environmental assessment. The results showed that spatial variations in foraminiferal community composition were mainly controlled by organic carbon, whereas the effects of other variables were minimal. Similarly, spatial variations in the co-occurrence network were determined by organic carbon and pH. Despite the impacts of environmental variables on community composition, null and neutral models demonstrated that foraminiferal community assembly is driven by ecological drift instead of selection. This study is the first to couple community composition and co-occurrence networks with community assembly processes. A hypothesis was proposed that selection increases community heterogeneity and network heterogeneity, whereas stochastic processes eliminate such heterogeneities. This mechanism would bridge the gap between processes and community patterns. A comparison with our previous study revealed that foraminiferal community assembly may depend on specific systems (habitats). This insight could inform new strategies for the conservation of marine biodiversity.