Assessing Accuracy and Costs of Ecological Assessments Based on Environmental DNA

Biological assessments of waterbody condition rely on estimates of what species occur in a specific waterbody. Ideally, we would detect all species present in a waterbody, but practical constraints require that we sample (rather than census) the species that are present. Sampling seldom captures all species present, especially for small, diverse taxa such as algae and invertebrates of which we collect a very small fraction of the total individuals present. Moreover, some taxonomic groups (e.g., microbes, protozoans, microcrustaceans) are not typically used in bioassessments because of the expense and time it would take to quantify these microscopic organisms to determine what taxa occur at a site. Even for those taxa frequently used in bioassessments, imperfect detection associated with the use of small sample counts can lead to distorted estimates of taxa richness and other metrics and endpoints. Fortunately, the use of either DNA extracted from benthic samples or environmental DNA (DNA shed by species and suspended in the water column) samples holds great promise in improving the detection of species in all taxonomic groups while simultaneously reducing the time and expense to produce usable data (species counts) from raw samples and the costs of sample processing. We are actively involved in research designed to evaluate the effectiveness of (and ultimately the transition to) DNA based bioassessments in collaboration with the USGS, the BLM, and different state agencies. We plan to continue that collaboration in the context of ultimately improving the effectiveness of the indices we are currently using.