Collaborating with NOAA Laboratories to Advance Marine Environmental DNA (eDNA) Science

Overview

Vessel: Not Applicable; Expedition Dates: August 1, 2021 to July 31, 2022; Ports: Not Applicable to Not Applicable

Project Principals: Jesse Ausubel¹

Co-Project Principals: Mark Stoeckle¹, David Thaler²

PI Institution(s): ¹The Rockefeller University, ² University of Basel

Partnerships: NOAA, Office of Naval Research, Office of Science and Technology Policy/Subcommittee on Ocean Science and Technology, Monmouth University, New Jersey Bureau of Marine Fisheries, Ocean Biodiversity Information System/Intergovernmental Oceanographic Commission, Southern California Coastal Water Research Project Authority

Grant #: NA21OAR0110145; Award Period: August 01, 2021 - July 31, 2022

Collaborating with NOAA Laboratories to Advance Marine Environmental DNA (eDNA) Science Overview Map

Metabarcoding, a method of organism identification based on DNA, is often used to analyze marine environmental DNA (eDNA); however, questions remain with regard to optimal methods for extracting and assessing eDNA with minimal bias. The project team intended to improve existing eDNA methods and explore new frontiers in eDNA research in collaboration with NOAA. Their goals included comparing DNA primers, optimizing input DNA for metabarcoding, assessing cross-contamination risk during field collection, developing candidate metabarcoding primers for understudied taxa, and improving bioinformatic software pipelines for use by a broad range of users. The team conducted experimental work related to improving core methods by optimizing primer concentration, evaluating increased sequencing depth, measuring absolute eDNA concentration, and assessing nontarget eDNA effects. In experimental testing, the team found that including an internal standard in metabarcoding polymerase chain reactions can quantify absolute fish eDNA copies; this creates the potential to assess absolute fish abundance with metabarcoding. This project was funded by NOAA Ocean Exploration in fiscal year 2021 through a Broad Agency Announcement.

Processed Project Datasets

Raw Sequence Reads	Open
Smithsonian's Global Genome Initiative eDNA Library contributions	Open

Products

Software for Matching Sequences with Species	Open
Software for Matching Sequences with Species Supporting Information	Open
Oral Presentation: Stoeckle MY, Ausubel JH. NOAA 'Omics Seminar, October 29, 2021, "Fishing for eDNA: how much water to catch and other questions." Talk posted open access at https://noaabroadcast.adobeconnect.com/pnnos0mcsh3z/	Open
Oral Presentation: Stoeckle MY. Plenary presentation at 2nd National Workshop on Marine eDNA, September 13, 2022. "What can eDNA say about the abundance of fish?", Talk posted open access at https://www.sccwrp.org/about/research-areas/bioassessment/dna-barcoding/second-national- workshop-on-marine-environmental-dna/	Open
Additional materials from 2nd National Workshop on Marine eDNA, including Agenda, eDNA primer, link to recording and slides for Training Day and Plenary Day, and virtual posters	Open
Online eDNA Educational Materials	Open

Publications

Stoeckle, Mark Y, Jason Adolf, Jesse H Ausubel, Zach Charlop-Powers, Keith J Dunton, and Greg Hinks. 2022. "Current Laboratory Protocols for Detecting Fish Species with Environmental DNA Optimize Sensitivity and Reproducibility, Especially for More Abundant Populations." Edited by William Grant. ICES Journal of Marine Science 79 (2): 403-12. https://doi.org/10.1093/icesjms/fsab273.	Open
Stoeckle, Mark Y., Jesse H. Ausubel, and Michael Coogan. 2022. "12S Gene Metabarcoding with DNA Standard Quantifies Marine Bony Fish Environmental DNA, Identifies Threshold for Reproducible Detection, and Overcomes Distortion due to Amplification of Non-Fish DNA." Environmental DNA 00:1-11, https://doi.org/10.1002/edn3.376	Open

Data Citation

Ausubel, Jesse; Stoeckle, Mark; Thaler, David (2023). Environmental data and products from NOAA Ocean Exploration Grant Award NA21OAR0110145 Project: Collaborating with NOAA Laboratories to Advance Marine Environmental DNA (eDNA) Science. [indicate subset used]. NOAA National Centers for Environmental Information. Project Datasets. https://www.ncei.noaa.gov/waf/ocean-exploration-nofo/21ednanoaacollab/21ednanoaacollab_cruise_landing_page.html. Accessed [date].