Detection of environmental DNA (eDNA) in freshwater systems is a pioneering technique developed to monitor rare or endangered species and combat invasive species. The objective is to mature eDNA as a conservation tool from basic to applied research. The focus is on freshwater ecosystems, particularly streams and rivers, which are highly relevant at Department of Defense (DoD) sites. Aquatic species are difficult to detect with traditional methods; alternatively, traces of eDNA from an organism can remain in suspension and be collected in a water sample, revealing the presence of a target organism. While eDNA documents presence/absence of aquatic species, knowledge of population distributions and abundances is critical for it to be an effective tool. Also, while eDNA can travel long distances in fluvial systems (i.e., streams and rivers), current data come from idealized experiments in standing water, leaving significant knowledge gaps in interpretation of eDNA in streams and rivers. The research will advance the science and knowledge necessary to (i) provide improved confidence in species presence or absence determinations, (ii) more accurately pinpoint the physical location of target species, and (iii) provide more precise links between eDNA concentration and species abundance in flowing aquatic systems.

Technical Approach

The project will determine the potential and limitations of eDNA detection and transport in flowing waters using a unique interdisciplinary approach coupling new molecular techniques that inform eDNA sampling, with integrative hydrologic modeling, informed by targeted experimentation involving the use of unique experimental platforms. The approach will bring together population, community, and ecosystem biologists with specialists in ecohydrology, environmental engineering, molecular ecology, genetics/genomics, and integrative modeling. To clearly understand and quantitatively interpret “positive detection events,” three synergistic approaches will be used: (1) Molecular Ecology (technology development) to improve eDNA quantification and test novel detection platforms to build better spatio-temporal distributions of eDNA in aquatic habitats of DoD interest; (2) Stream Ecology (experiments and field sampling) to accurately quantify environmental factors that influence eDNA detection and its interpretation; and (3) Hydrology (integrative modeling) to incorporate data from (1) and (2) into state-of-the-art predictive models of eDNA fate and transport. These findings will be translated for use by managers and stakeholders through a Management Transition Board linking regional, state, and federal partners to ensure that the research outputs will provide guidelines for managers and regulators that can be applied at existing DoD installations and through eDNA programs across North America.


DoD land managers have many duties, including monitoring biodiversity, understanding the distribution of species, estimating species abundance, determining how plant and animal populations change through time and space, and ultimately upholding federal laws concerning listed species on DoD lands. This work will strengthen their ability to manage and steward their resources by refining how they measure, quantify, and interpret eDNA measurements. By improving eDNA techniques to increase the informational value of each sample, parsing out the many processes that influence eDNA fate and transport in flowing aquatic systems, and building a data-driven physically-based predictive model, this project will empower DoD land managers to effectively use eDNA as an operational research and decision support tool. The results will also support targeted strategic plans that rely on detection and prediction of species abundance and biomass, including the early and accurate detection, and geographic placement, of rare species in flowing waters, so that managers can act.