Unveiling Ross Sea eukaryotic diversity through environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding has emerged as a powerful molecular tool for biodiversity monitoring, particularly in remote and logistically challenging environments such as Antarctic marine ecosystems, where traditional surveys are often limited. Despite the ecological significance of the Ross Sea, comprehensive molecular datasets for this region remain scarce. Here, we present a two-year eDNA metabarcoding survey in the Ross Sea region Marine Protected Area (RSR MPA) during 2024 and 2025. Seawater samples were collected from 20 stations (n = 61) in 2024 and 12 stations (n = 40) in 2025. Eukaryotic communities were characterized across multiple taxonomic levels and assigned to functional groups (autotrophs, heterotrophs, mixotrophs, and other protist-related groups) to assess the associated ecological roles. Annual comparison revealed that 92 species were consistently detected across survey years, indicating ecological stability within core community components. Species-level taxonomic assignments revealed that foundational components, including dinoflagellate and Antarctic diatom species, remained present despite environmental variability. Environmental variables, particularly thermal stratification and water mass properties, emerged as the primary drivers structuring eukaryotic communities in the Ross Sea, generating distinct vertical and horizontal stratification patterns and effectively explaining spatial separations among sample groups. The dataset generated om this study contributes to expanding molecular reference resources for polar marine ecosystems and provides a foundation for future integrative analyses that combine eDNA monitoring with environmental and oceanographic datasets, with broad applicability to the conservation and management of the RSR MPA.