Soil eDNA as Hydrological Tracer

Tracer-based approaches have advanced our understanding of subsurface hydrology, yet conventional tracers often lack sensitivity to the fine-scale physical and ecological structures that influence water movement through soils. Environmental DNA (eDNA) has recently emerged as a promising natural tracer, capturing biological signals that may reflect hydrological connectivity while simultaneously enabling biodiversity assessment. We investigate the three-dimensional structuring of soil biodiversity and evaluate its potential for hydrological flow path tracking across contrasting catchments. Using tree-of-life (ToL) metabarcoding, we characterised eDNA-based community composition of bacteria, protists, fungi, plants, and invertebrates from 10 soil drilling cores (0.7–3.2 m depth) across twelve hillslopes in four catchments in Germany and Austria, differing in parent material, land cover, and geomorphological and geochemical properties. We identified 5493 eDNA sequences consistently associated with specific soil depths and habitat types. Despite differences in geology, parts of this vertical and horizontal biodiversity structuring were conserved across catchments, suggesting the presence of broad-scale, potentially catchment-independent sequences that may serve as natural tracers of subsurface hydrological processes. Overall, our findings demonstrate the potential of eDNA as a naturally occurring tracer to identify subsurface flow pathways and enhance process understanding in the unsaturated zone. While the application of eDNA in hydrological tracing is still in its early stages, integrating biodiversity information into tracer frameworks offers a promising avenue for advancing the study of hidden subsurface flow processes.