Environmental DNA reveals coastal fish biodiversity response across the Atlantic-Indian Ocean environmental transition gradient

The South African coast exhibits high spatial and environmental variability, which supports a diverse biodiversity of fish, and other marine species, providing valuable ecosystem services, including fisheries, nutrient cycling, habitat stabilization and tourism. However, ongoing anthropogenic pressure, including climate change and land-use alterations, are contributing to coastal biodiversity loss, necessitating the need for effective conservation strategies and a deeper understanding of the environmental factors driving marine biodiversity dynamics. Environmental DNA (eDNA) offers a non-invasive means to assess marine biodiversity and is becoming widely adopted as effective means to conduct ecological and biodiversity assessments . Here we looked to determine the spatial and environmental effects on coastal fish biodiversity across the entire extent of South Africa’s coast using environmental DNA (eDNA). From 31 sites we detected 310 unique amplicon sequence variants (ASVs), representing 157 genera and 89 families. Genus, family and ASV richness all significantly increased with increasing temperature (p < 0.01), aligning with the west-to-east temperature gradient. Beta-diversity also significantly increased with difference in temperature (p < 0.01) and distance (p = 0.01), with turnover having a stronger influence compared to richness difference. We identified 22 key genera as indicators of spatial biodiversity change, and with hierarchical modeling provide insights into spatial and environmental influences on specific genera distributions along the coast This study underscores the utility of eDNA as a powerful, cost-effective, and non-invasive tool for capturing biodiversity dynamics across extensive spatial scales, offering a comprehensive understanding of the factors shaping coastal biodiversity and supporting global marine biodiversity monitoring and conservation efforts.