| Summary: | In response to climate change, biodiversity patterns in the oceans are predicted to shift rapidly, thus increasing the need for efficient monitoring methods. Environmental DNA (eDNA) metabarcoding recently emerged as a potent and cost-effective candidate to answer this challenge. We targeted three molecular markers to determine multicellular metazoan communities from two timepoints across a long-standing transect in the Southern Hemisphere, the Munida Observational Time Series. We detected four community types across the successive water masses—neritic, sub-tropical, frontal, and sub-Antarctic—crossed by the transect, together with important community differences between the two sampling points. From indicator species analysis, we found diversity patterns were mostly driven by planktonic organisms. Mesopelagic communities differed from surface-water communities in the sub-Antarctic water mass, with at-depth communities dominated by single-cellular organisms. We evaluate the ability of eDNA to detect species-compositional changes across surface and depth gradients and lay the foundations for using this technique in multi-trophic environmental monitoring efforts across long time series. We observed community differences across time and space. More intensive sampling will be critical to fully capture diversity across marine gradients, but this multi-trophic method represents an invaluable opportunity to understand shifts in marine biota.
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