Environmental DNA (eDNA)
Marine environments and organisms continue to be impacted by a myriad of factors. While marine organisms can be challenging to access and assess, all organisms shed their DNA, referred to as environmental DNA (eDNA), which can assist in detection of organisms without having to capture them. Our eDNA projects have developed faster, cheaper, and more sensitive approaches for collecting biological baselines and measuring how shifts in biodiversity composition occur over time.
Developing eDNA techniques allows for streamlined sampling of species and ecosystems worldwide, putting the evidence on the table for the relevant agencies, parties, and the public to consider for more informed and transparent decision-making. In partnership with management agencies, multiple institutions, engineers and scientists, COS is developing novel genetic techniques to more efficiently track biodiversity and species abundance in the ocean.
Across multiple eDNA projects, COS has contributed to the science and optimization of technologies to collect eDNA samples and ground truth DNA identification with biodiversity assessments to inform ecosystem monitoring and management needs.
In collaboration with the Monterey Bay Aquarium, COS tested the potential to detect eDNA from multiple species simultaneously in the Open Sea Exhibit, a 1.2 million gallon seawater tank at the Monterey Bay Aquarium (Kelly et al., 2014).
Additional collaborations between COS, the Monterey Bay Aquarium, Hopkins Marine Station, and Stanford enabled COS staff to break new ground in using eDNA for biodiversity detections in marine environments. eDNA detections in the wild kelp forest of Monterey Bay were comparable to those observed via SCUBA visual surveys done by SCUBA divers (Port et al. 2016).
Experiments conducted at Hopkins Marine Station distinguished differences in the shedding and persistence rates of the eDNA of anchovies, sardines and mackerel, three commercially and ecologically important fish species. Anchovy, sardine and mackerel DNA persisted on the order of days, suggesting eDNA is a promising tool for efficiently and effectively tracking fish in marine waters (Sassoubre et al., 2016).
COS collaborated with the National Oceanic and Atmospheric Administration as well as partners at multiple institutions to implement eDNA monitoring in both the Florida Keys and Monterey Bay National Marine Sanctuaries. As part of the five-year Marine Biodiversity and Observation Network (MBON) Sanctuaries Project, we collected eDNA baselines (Andruszkiewicz et al., 2017; Kelly et al., 2017; Sawaya et al., 2019; Closek et al., 2019; Djurhuus et al., 2020) and determined standardized eDNA methods (Djuhuus et al., 2017).
Additionally, we identified that eDNA data can add organismal detections to standard monitoring methods (Kelly et al., 2017). We used standard survey and eDNA methods to observe different distribution patterns of marine vertebrates in the central California Current Ecosystem during a warmer el Niño year versus when typical ocean conditions returned (Closek et al., 2019). We identified seasonal patterns of organisms in Monterey Bay and networks of organisms (from bacteria to vertebrates), which highlighted potential key organisms that could serve as indicators of the ecosystem’s state (Djurhuus et al., 2020).
COS News Stories, Publications and Related Webpages
- NOAA Ocean Expedition Takes eDNA to the Deep Sea || May 2015
- Environmental DNA used to track biodiversity || February 2016
- DNA left by ocean animals provides rare glimpse of marine ecosystems, Stanford researchers say || June 2017
- Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding || June 2017
- New Video Release: Second of a Series of Solutions || June 2017
- New study uses eDNA to monitor biodiversity || January 2019
- COS eDNA Project, BBC World Service Podcast || December 2016
- Testing the water: identifying marine communities through eDNA || February 2017
- A world in a bottle of water || August 2019
- eDNA Expands Species Surveys to Capture a More Complete Picture || December 2019
- eDNA Used to Track Marine Biodiversity Over Time in a Research First || January 2020
- How can we track life in the ocean? || June 2020
- Andruszkiewicz EA, Starks HA, Chavez FP, Sassoubre LM, Block BA, Boehm AB (2017). Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding. PLoS ONE, 12(4): e0176343. doi: 10.1371/journal.pone.0176343
- Closek CJ, Santora JA, Starks HA, Schroeder ID, Andruszkiewicz EA, Sakuma KM, Bograd SJ, Hazen EL, Field JC and Boehm AB (2019) Marine Vertebrate Biodiversity and Distribution Within the Central California Current Using Environmental DNA (eDNA) Metabarcoding and Ecosystem Surveys. Front. Mar. Sci. 6:732.doi: 10.3389/fmars.2019.00732
- Djurhuus, A., Closek, C.J., Kelly, R.P. et al. Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nat Commun 11, 254 (2020). https://doi.org/10.1038/s41467-019-14105-1
- Djurhuus A, Port J, Closek CJ, Yamahara KM, Romero-Maraccini O, Walz KR, Goldsmith DB, Michisaki R, Breitbart M, Boehm AB and Chavez FP (2017) Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels. Front. Mar. Sci. 4:314. doi: 10.3389/fmars.2017.00314
- Kelly RP, Closek CJ, O’Donnell JL, Kralj JE, Shelton AO and Samhouri JF (2017) Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem. Front. Mar. Sci. 3:283. doi: 10.3389/fmars.2016.00283
- Kelly, R. P., Port, J. A., Yamahara, K. M., Martone, R. G., Lowell, N., Thomsen, P. F., … Crowder, L. B. (2014). Harnessing DNA to improve environmental management. Science, 344(6191), 1455 LP – 1456. https://doi.org/10.1126/science.1251156
- Kelly RP, Port JA, Yamahara KM, Crowder LB (2014) Using Environmental DNA to Census Marine Fishes in a Large Mesocosm. PLoS ONE 9(1): e86175.
- Port, J.A., O'Donnell, J.L., Romero‐Maraccini, O.C., Leary, P.R., Litvin, S.Y., Nickols, K.J., Yamahara, K.M. and Kelly, R.P. (2016), Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Mol Ecol, 25: 527-541. https://doi-org.stanford.idm.oclc.org/10.1111/mec.13481
- Sassoubre LM, Yamahara KM, Gardner LD, Block BA, Boehm AB (2016). Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish. Environmental Science Technology, 50: 10456–10464. doi: 10.1021/acs.est.6b03114
- Sawaya, NA, Djurhuus, A, Closek, CJ, et al. Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding. Ecol Evol. 2019; 9: 1029– 1040. https://doi-org.stanford.idm.oclc.org/10.1002/ece3.4742