Networks and genome-resolved analyses reveal persistent particle-mediated coupling between prokaryotes and eukaryotic plankton

Interactions between bacterioplankton and eukaryotic plankton are often inferred from short-lived algal blooms, leaving it unclear whether coupling persists under natural seasonal variability and which traits sustain it. We conducted seasonal sampling of coastal seawater over an annual cycle in South China Sea, separating particle-attached (PA > 3 μm) and free-living (FL 0.2 to 3 μm) prokaryotes, and integrating 18S/16S rRNA gene-based community profiling, prokaryote-eukaryote association networks, and genome-resolved metagenomics. PA diversity tightly tracked eukaryotic diversity (Pearson’s r = 0.459, p < 0.05), whereas FL diversity was comparatively stable and weakly coupled ( r = 0.194, p = 0.4). Network analysis revealed many more positive PA-eukaryote links (2,521,013) and fewer negative links (15,126) than in FL networks (1,451,947 positive; 18,434 negative), indicating recurrent particle-mediated facilitation across seasons. Functional contrasts showed that PA communities were enriched in seven KEGG pathways, suggesting broader carbon and nitrogen metabolic potential, enhanced energy conservation, and increased biosynthesis of antibiotic- and toxin-like secondary metabolites. From 120 high-quality MAGs, PA genomes were significantly larger than FL genomes, and phylogenetically matched PA-FL pairs exhibited PA-linked expansions in chemotaxis, biofilm formation and secretion systems, polymer-processing capacity, respiratory flexibility, and detoxification functions. From an evolutionary perspective, these near-neighbor contrasts indicate habitat-driven genomic divergence: persistent selection in the patchy, competitive particle microhabitat favors the gain or retention of costly interaction and metabolic-breadth traits. Together, these network- and genome-resolved results support a niche-based interpretation in which eukaryote-derived particles act as persistent microhabitat interfaces that increase habitat heterogeneity and filter for a particle-adapted interaction toolkit, strengthening PA-eukaryote coupling across seasonal succession. Video Abstract