Hyporheic eDNA Removal Outweighs Water Column Degradation in a Natural River

Abstract Advances in the measurement of environmental DNA (eDNA) have transformed biodiversity monitoring in aquatic ecosystems. However, linking eDNA concentrations in streams and rivers to species abundance remains challenging as flowing water, streambed retention, and degradation combine to transport eDNA away from its origin point and dilute it. Here, we apply a continuous time random walk model to jointly analyze conservative (Rhodamine WT) and eDNA tracer profiles collected across a morphologically complex reach of a natural river (Missouri, USA), in order to quantify the role of water column and hyporheic residence times in driving eDNA losses. Modeled hyporheic removal rates (degradation and physical retention) are one to five orders of magnitude greater than water column degradation rates, indicating that the subsurface dominates reach-scale eDNA losses in the study river. These results demonstrate that eDNA removal is strongly shaped by spatially varying hydrologic processes, particularly hyporheic exchange, and that relying solely on laboratory degradation rates may substantially underestimate in-stream eDNA loss.