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Progress toward developing DNA-based diatom indicators for stream monitoring in the United States: watershed to national scale efforts
Citation:
Smucker, N., E. Pilgrim, C. Nietch, L. Yuan, R. Mitchell, C. Carpenter, L. Gains-Germain, J. Darling, AND A. Pollard. Progress toward developing DNA-based diatom indicators for stream monitoring in the United States: watershed to national scale efforts. 2024 Society for Freshwater Science Annual Meeting, Philadelphia, PA, June 02 - 06, 2024.
Impact/Purpose:
Diatoms have a long history of being used to characterize changes in environmental conditions and to identify effects of pollution in freshwater ecosystems. Recent advancements in DNA techniques and bioinformatics could help expand their use in monitoring and assessment programs by providing increasingly effective ways to quantify diatom diversity in environmental samples. This research provides and overview of multiple studies and summarizes nationwide DNA metabarcoding (rbcL) results for diatoms collected from 1788 streams and rivers during the summers of 2018 and 2019. Results can inform indicator development and applications of molecular tools to help manage environmental problems.
Description:
Benthic diatoms are highly responsive to changes in environmental conditions associated with human activities. Their changes in assemblage structure can be used to develop stressor-response relationships, metrics, and indices that can help identify effects of pollution and inform management targets in streams. Recent advancements in DNA techniques, metabarcoding, and bioinformatics could help expand the use of diatoms in monitoring and assessment programs by providing relatively quick, consistent, and increasingly cost-effective ways to quantify diatom diversity in environmental samples. However, these DNA-based approaches are relatively new and only a few studies have been conducted in the United States. Here, we provide an overview of multiple projects exploring how diatom DNA metabarcoding can be used for stream monitoring and assessment. Results from the first nationwide study to use diatom DNA metabarcoding (EPA’s National Rivers and Streams Assessment) showed that it is a robust approach that could be useful to monitoring and assessment programs throughout the conterminous United States, despite the great heterogeneity in conditions among ecoregions. Analyses also are contributing to understanding national patterns and drivers of diatom diversity. To help remove barriers and increase the usability for new users, we also are developing an R workflow and database to improve reproducibility and to simplify the integration and analysis of new DNA metabarcoding data. We will discuss possible applications of these approaches and how these developments have led to new collaborations and state partnerships with a variety of goals.