Taxonomy‐Independent eDNA Approaches in Groundwaters: A Prospective Tool for Improved Ecological Assessments

Abstract

Groundwater continues to be managed predominantly as an abiotic resource for human use, a paradigm that overlooks the biological communities responsible for many indispensable ecosystem services and ultimately the integrity of the global water cycle. A shift towards a holistic ecological perspective is therefore essential but requires innovative techniques to monitor a challenging environment. Environmental DNA (eDNA) approaches are being rapidly applied to groundwater ecosystems, but comprehensive community assessment is hampered by taxonomic challenges leading to the exclusion of informative, high‐value biological information. In surface waters, such impediments are being bypassed with taxonomy‐independent approaches to ecosystem assessment using eDNA, maximising data usage and giving rise to a new generation of novel, data‐driven biotic indices powered by machine learning. Here we identify the potential for taxonomy‐independent eDNA methods to address longstanding taxonomic challenges hindering the development of biotic indices in groundwater ecosystems. Although these approaches have not yet been widely applied to groundwater ecosystems, they offer the potential for robust, integrative tools for advancing biomonitoring and enhancing ecological assessment frameworks. Given the need for improved biomonitoring tools in groundwaters, we advocate for the development of taxonomy‐independent eDNA biotic indices to safeguard groundwater resources and conserve the communities that maintain their integrity.