Metagenomic Insights Into Red Sea Biodiversity Across the Web of Life

Earth's biodiversity is central to ecosystem health and resilience, providing essential functions and services. The Red Sea is a recognised marine biodiversity hotspot with high endemism and unique environmental conditions that support extensive but poorly resolved biodiversity. Here, we applied metagenomic analyses to sediment samples collected from coastal to deep-sea environments during the Red Sea Decade Expedition 2022 to characterise biodiversity across the web of life. From a single shotgun assay per sample, this approach simultaneously characterised the sediment microbiome, which amplicon-based surveys recover only through parallel, targeted assays, and extended detection to higher eukaryotes. Using high-throughput sequencing, we generated 12.8 billion sequences, revealing taxa covering all domains of life. Although eukaryotic sequences represented only 0.7% of the taxonomically annotated dataset, we managed to identify 679 eukaryotic families. Prokaryotic diversity was high, as expected in a basin-scale sampling coupled with high sequencing depth, with groups covering a wide functional array. Community structure analyses revealed depth-driven stratification of open-ocean benthic microbial communities and latitudinal structuring of coastal benthic eukaryotes. Overall, this dataset provides an empirical reliability-coverage trade-off with direct consequences for the design of eDNA monitoring programmes targeting conservation-priority taxa, and clear priorities for taxa specific reference-database expansion.