Integrative insights into marine protist assemblages between surface and deep chlorophyll maximum

Stratified marine systems are often characterized by a deep chlorophyll maximum (DCM); however, the taxonomic and functional dynamics of protist assemblages within this layer remain poorly understood. We integrated microscopy, pigment-based CHEMTAX analysis, 18S rRNA metabarcoding, and metatranscriptomics to compare protist communities in the surface and DCM layers of the northeastern East China Sea. Microscopy and pigment data revealed higher cell abundances, increased chlorophyll- a levels, and distinct pigment signatures at the DCM, particularly for haptophytes, chlorophytes, and pelagophytes. Amplicon sequencing revealed increased representation of chlorophyte and Syndiniales at depth, whereas metatranscriptomic profiles showed elevated transcriptional activity in diatoms, dinoflagellates, and chlorophytes. Functional gene analyses revealed DCM-specific upregulation of photosystem I subunits, light-harvesting complex proteins, and nitrogen assimilation pathways, indicating photoacclimation and nutrient exploitation under low-light, nutrient-rich conditions. Syndiniales were abundant in DNA-based data but mostly transcriptionally inactive, suggesting dormancy or parasitic stages, while diatoms exhibited high transcriptional activity despite low DNA abundance. These findings indicate a clear decoupling between taxonomic presence and metabolic activity, emphasizing that ecological roles cannot be inferred from abundance alone. Our findings identify the DCM as a biogeochemical hotspot shaped by taxon-specific metabolic strategies and vertical niche partitioning, underscoring the key role of protists in sustaining productivity and carbon cycling in stratified ocean ecosystems.