Linking sediment porosity to taxon-specific patterns of eDNA preservation in a temperate, semi-enclosed bay

Abstract

Sedimentary environmental DNA provides unique insights into past community dynamics. However, the influence of physical sediment properties, such as porosity, on taxon-specific eDNA preservation remains poorly understood, particularly in temperate inner-bay environments. Therefore, here, we characterized eukaryotic communities in sediment cores from the surface to 6-m depth in the inner and mouth regions of the Uranouchi Bay, a semi-enclosed embayment in temperate Japan. Both 18S rRNA and mitochondrial cytochrome c oxidase subunit I gene metabarcoding revealed marked spatial variation; specifically, inner-bay sediments were enriched in terrestrial plant DNA and dinoflagellates, whereas mouth sediments contained higher proportions of marine diatoms. Vertical profiles further highlighted differences in DNA persistence, with terrestrial and particle-associated taxa retained deeper in the inner-bay sediments. Land-sea connectivity and basin geography strongly shape sedimentary eDNA composition, reflecting both ecological sourcing and preservation bias. We further systematically analyzed the relationship between sediment porosity, a critical physical property governing pore water mobility and solute diffusion, and taxon-specific sedimentary eDNA preservation. To highlight effects of porosity independent of burial depth, we modeled porosity as a function of depth and correlated the residual porosity with the relative abundances of individual phyla. Notably, the phyla exhibited contrasting preservation patterns: Dinoflagellata, Euglenozoa, and Rotifera showed weak to moderate positive correlations with porosity, whereas Chlorophyta and Ochrophyta displayed weak negative correlations. When depth correlations were examined jointly, multiple distinct pattern groups emerged: some taxa (e.g., Dinoflagellata) exhibited negative depth but positive porosity correlations, whereas others showed opposite or neutral patterns. These divergent responses suggest that DNA preservation in marine sediments involves multiple taxon-specific mechanisms rather than a single universal process, with porosity acting as an independent determinant of burial depth. Our results highlight the importance of integrating physical properties of sediments into sedimentary environmental DNA-based paleoenvironmental reconstructions.