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Exploring Aquatic Biodiversity Using eDNA

Brooke Penaluna wades in to collect streamwater samples for eDNA testing for the presence of aquatic species.

Brooke Penaluna wades in to take a water sample for eDNA testing to detect aquatic species.

Biodiversity is disappearing faster than at any time in recorded
history, and freshwater species are among the most vulnerable
to extinction, making it imperative to understand aquatic
biodiversity. Logistical challenges and financial costs combine to
make aquatic biodiversity monitoring an increasingly overwhelming
task, especially as demand for biodiversity information outpaces
funding resources and available taxonomic expertise.

Collaborators:
Brooke Penaluna
Rich Cronn, USDA FS PNW Research Station
Tiffany Garcia, Oregon State University

Research Description:


Environmental DNA (eDNA) metabarcoding is increasingly used as an alternate method for measuring biodiversity, as DNA left behind by individuals in the water can be used to identify their taxonomic identity (e.g., family, genus, and even species). Typically, eDNA metabarcoding uses the polymerase chain reaction (PCR) to amplify short, taxonomically informative genomic regions (“DNA barcodes”) from samples. Amplified DNA is then sequenced, and the sequences are classified to reveal a breadth of taxonomic and genetic diversity in the DNA present in each water sample.

Key Findings:


We are applying eDNA metabarcoding to waterways throughout the Pacific Northwest of the continental United States to identify aquatic biodiversity and population genetic diversity, which will help managers meet multiple management objectives. For example, we identified 878 taxa at Fall Creek in the Alsea River basin in the Oregon Coast Range (Hauck et al. 2019). DNA sequences were obtained for multiple targeted groups, including sequences from fish (Actinopteri, Petromyzontidae; 50.1% of sequences), pathogenic oomycetes (21.3%), arthropods (classes Insecta, Decapoda; 16.5%), and apicomplexan parasites (3.8%), and even amphibians and beaver (less than 1% each). The resulting genomic databases can be used to track the magnitude and distribution of genetic diversity in managed species (Weitemier et al. 2021), as well as the presence and diversity of forest pathogens that play a key role in forest health. These approaches provide science-based, region specific biodiversity information that empower managers to make science informed-decisions.

Filters at the bottom of these two clear plastic cups capture environmental DNA (eDNA) when water samples are pushed through them.

eDNA filters from water sampling in Fall Creek in the Alsea River basin, Oregon. Photo: Brooke Penaluna


Management Implications:


• Our work broadens the scope of eDNA information by allowing for data-driven prioritization of multiple aquatic species, including common, endangered, rare, and cryptic species, to inform conservation actions and forest health objectives.

• Being able to better detect freshwater biodiversity allows managers the opportunity to recognize the diversity of and within species across riverscapes to ensure their persistence into the future.

• As human activities continue to impact aquatic habitats and their populations, continued genetic monitoring of multiple aquatic species is necessary to assess the direction and extent of those impacts and provide critical information to managers tasked with maintaining healthy ecosystems.

This work was featured in an article and radio broadcast by Oregon Public Broadcasting in March 2013, "Tiny scoops of water are unlocking worlds of information about Oregon watersheds": https://www.opb.org/article/2021/03/13/salmon-trout-health-oregon-watersheds-dna-research/

Map of results from eDNA sampling of mitochondrial haplotypes in Coastal Cutthroat Trout in western Oregon and northern California.

Mitochondrial haplotypes of Coastal Cutthroat Trout using the ND2 locus (gene). Coloured pie charts represent reads, with pie size proportional to the number of reads observed (summed across replicates), given by the scale in the lower right. Coloured slices represent unique haplotypes, with white slices representing a combination of low-frequency haplotypes. White squares mark sampling locations where trout were not captured. Figure 3a from Weitemier et al. 2021.

Selected Publications:


Note: Most PDF files linked in the publications section of this page were not created by the USDA Forest Service, and may not be accessible to screen-reader software. Many publications are open access, and links to the html versions on the journal websites are also provided, where applicable.

Coble, A.A., C.A. Flinders, J.A. Homyack, B.E. Penaluna, R.C. Cronn, and K. Weitemier. 2019. eDNA as a tool for identifying freshwater species in sustainable forestry: a critical review and potential future applications. Science of the Total Environment 649: 1157–1170. https://doi.org/10.1016/j.scitotenv.2018.08.370

Hauck, L.L., K.A. Weitemier, B.E. Penaluna, T.S. Garcia, and R. Cronn. 2019. Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets. Environmental DNA 1(3):251–267. https://doi.org/10.1002/edn3.26

Weitemier, K.A., B.E. Penaluna, L.L. Hauck, L.J. Longway, T.S. Garcia, and R. Cronn. 2021. Estimating the genetic diversity of Pacific salmon and trout using multi-gene eDNA metabarcoding. Molecular Ecology. https://doi.org/10.1111/mec.15811 [open access]