Integrating eDNA and eRNA for Stream Health Assessment Using Benthic Diatoms

Environmental DNA (eDNA) and environmental RNA (eRNA) are increasingly used in aquatic biomonitoring, but they serve different ecological purposes. eDNA can persist in biofilms, reflecting accumulated environmental signals, while eRNA is short-lived and indicates metabolically active communities. To assess their suitability for evaluating stream health, we compared benthic diatom assemblages derived from both eDNA and eRNA. Alpha diversity indices revealed negligible differences between the two nucleic acid types, although total read abundance showed a small effect size (Cliff’s δ = 0.207). Taxonomic overlap was significant, with 70% of species shared between the two sources, though several genera displayed source-specific patterns. Community analyses indicated that eRNA-based assemblages had greater internal consistency and clearer differentiation between groups. The Trophic Diatom Index application revealed that eDNA captured cumulative water quality conditions, while eRNA provided a more sensitive reflection of current ecological states. These findings highlight that eDNA offers broad taxonomic coverage, whereas eRNA delivers a higher resolution of active ecological responses. By integrating both markers, we can achieve a more comprehensive assessment of long-term environmental history and current stream health, enhancing the accuracy of diatom-based bioassessment frameworks.