Depth-dependent eDNA abundances across ecosystems inform deep-sea sampling strategies

Environmental DNA (eDNA) surveys are increasingly used to assess marine biodiversity and inform deep-sea environmental decision-making, including mineral resource management and fisheries oversight. Yet standard low-volume protocols inherited from coastal work may be inadequate at depth, and no quantitative framework links depth and ecosystem context to defensible filtration volume targets. We compiled 841 eDNA samples from eight expeditions across the North Atlantic, Wider Caribbean, and Pacific (surface to 4000 m) to quantify how recoverable eDNA scales with depth and surface productivity, and to derive depth- and productivity-aware sampling targets. Total eDNA concentration declined with depth as a power law, with attenuation exponents ( b ) modulated by surface productivity: most gradual in eutrophic waters ( b = 0.67), intermediate in mesotrophic ( b = 0.90), and steepest in oligotrophic systems ( b = 1.25); volume-weighted models explained 66–88% of the variance. At a fixed extract-concentration target, required filtration volumes diverged ∼7-fold between oligotrophic and eutrophic systems at 200 m and ∼38-fold at 4000 m. Conventional Niskin sampling, therefore, undersamples deep-sea biodiversity, particularly in mid-to low-productivity systems. Among laboratory parameters, the assay-specific extract-concentration target exerted greater leverage on required volume than extraction efficiency or elution volume. Volume-aware sampling paired with optimized recovery should be routine in deep-sea eDNA surveys.