Environmental Gradients and Ecological Processes Are Main Drivers of Eukaryotic Diversity in the Eastern Red Sea

ABSTRACT Microeukaryotes, including protists, microalgae, and small fungi, are fundamental components of marine ecosystems, driving energy transfer, nutrient cycling, and primary production. Despite their ecological significance, they remain understudied due to their small size and taxonomic complexity. Here, we present a comprehensive assessment of eukaryotic diversity across the entire water column of the Eastern Red Sea, integrating surface to deep‐sea layers along a latitudinal gradient. Environmental DNA metabarcoding of bottle‐net hauls from 266 samples across 128 stations spanning the eastern Red Sea revealed 4298 MOTUs from 40 phyla, with a substantial fraction lacking reliable taxonomic assignments. While traditional diversity indices showed little variation across regions or depths, multivariate analyses revealed pronounced community turnover along the latitudinal gradient and subtler vertical structuring. Temperature, dissolved oxygen, and turbidity emerged as significant correlates of β‐diversity, with the remainder likely reflecting unmeasured drivers. Despite a large core of MOTUs shared across epipelagic, mesopelagic, and bathypelagic layers, ecological groups displayed depth‐specific abundance patterns, and co‐occurrence networks identified phototrophic and microbial hubs with a southward shift toward stronger benthic–pelagic coupling. Notably, we observed a latitudinal transition from fungal‐ and algal‐dominated communities in the north to more complex microbial–benthic–vertebrate networks in the south. Our results indicate that Red Sea eukaryote communities are shaped by both abiotic gradients and biological interactions, and that water column‐integrated sampling reduces depth bias and captures biodiversity patterns overlooked by single‐depth surveys. This work provides a regional baseline for biodiversity monitoring and conservation in a rapidly changing tropical sea.