Abstract
Abstract The Ross Sea, Antarctica, while largely pristine, is experiencing increased anthropogenic pressures, necessitating enhanced biomonitoring efforts for conservation purposes. Environmental DNA (eDNA) extracted from marine sponges provides a promising approach for biodiversity monitoring in remote areas by circumventing the need for time‐consuming water filtration. Investigations into the efficacy of eDNA signal detection across the tree of life from marine sponges have yet to be fully explored. Here, we conducted a seawater and sponge eDNA metabarcoding survey at seven coastal locations in the Ross Sea to assess spatial eukaryote biodiversity patterns and investigate eDNA signal differences between both substrates. In total, we detected 1450 operational taxonomic units (OTUs) across 30 phyla. Significant differences in water and sponge eDNA signal richness and composition were observed, with a partial overlap in OTU detection between both substrates and, thereby, underscoring the crucial role of substrate selection in eDNA metabarcoding surveys. Furthermore, alpha and beta diversity analyses revealed distinct eDNA signals among sampling locations, which were corroborated by known species distributions. However, only 135 OTUs (9%) could be successfully assigned to species level, and 574 OTUs (40%) were unable to be taxonomically classified, due to limitations in the reference database. Our results provide evidence for the potential of eDNA monitoring in remote areas, demonstrate the need to consider more sophisticated sampling strategies whereby multiple eDNA substrates are incorporated, and highlight the importance of complete reference databases for robust taxonomy assignment of eDNA signals.