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Experimental to national scale research is building support for using diatom DNA metabarcoding in river and stream biomonitoring efforts
Citation:
Smucker, N., E. Pilgrim, AND C. Nietch. Experimental to national scale research is building support for using diatom DNA metabarcoding in river and stream biomonitoring efforts. EPA Monitoring and Assessment Partnership Group Webinar, Washington D.C., DC, October 20, 2026.
Impact/Purpose:
This work has the potential to (1) reduce the time and costs needed to process, analyze, and interpret algal and microbial samples, (2) improve the consistency and reproducibility of methods, workflows, results, and conclusions, and (3) expand the use of these indicators and monitoring approaches by demonstrating their usefulness to states and how they can inform decisions affecting the water quality and the protection and management of stream ecosystems and their watersheds. This research continues to be driven by state and EPA program office needs and priorities, and the results will be of interest to state and federal monitoring and assessment programs.
Description:
Interest in using DNA metabarcoding as part of monitoring and assessment programs continues to increase since 2020 when EPA first published a study on its use to quantify diatom responses to nutrients in streams at a watershed scale. Since then, EPA has conducted multiple studies focused on developing and testing diatom indicators using DNA metabarcoding from experimental stream mesocosms to state and national scales. This presentation provides a synthesis of results from these studies and identifies key concepts that could support the future use of diatom DNA metabarcoding in monitoring and assessment efforts. Collectively, these studies are building support for using diatom DNA metabarcoding by: ((1) Establishing best practices for collecting, storing, and processing periphyton samples from rivers and streams. ((2) Producing consistent results based on repeated sampling. ((3) Demonstrating that diatoms integrate effects of nutrients over time. ((4) Continuing to find ecologically meaningful results based on multiple studies spanning experiments to national surveys. (5) Finding that DNA-based multimetric index scores were similar to morphology-based ones. (6) Repeatedly finding that results and variables important to diatoms were similar to those reported in morphological-based studies. Results from these research efforts can support EPA Program Office and state-driven needs and be useful for other programs interested in using DNA-based approaches for monitoring and assessment purposes.