Crab detectives: Quantifying dungeness crab populations with environmental DNA

My name is Dwan Jackson, and I am a MSc student from Jackson State University interning in the PMEL Ocean Molecular Ecology (OME) group for the summer. My program, Center for Coastal and Marine Ecosystems-II (CCME-II), funds a NERTO (NOAA Experiential Research and Training Opportunities) internship for students to further their research abilities and gain experiences highly sought after within NOAA. In collaboration with OME, my MSc thesis focuses on the validation and application of a quantitative PCR (qPCR) assay to detect Dungeness crab in hopes of bolstering current crab monitoring efforts. Dungeness crabs are an important component of the coastal food web and the most valuable single-species fishery along the US West Coast. Understanding their future population size through larval counts helps to promote data-driven management efforts. Similar to a COVID-19 qPCR test, our assay targets Dungeness crab DNA sequences specifically, providing a sensitive, accurate, and quantitative method to detect Dungeness crab in the environment. The quantitative aspect of this assay allows for the exploration of our data to determine if there is a relationship between DNA concentration and the number of Dungeness crabs in the samples. The relationship allows for the potential to estimate larval numbers and expand population assessments in scope and scale without the time and labor of individual counting.

This project has granted me a variety of hands-on NOAA research opportunities this summer. Before collecting samples, we had to validate the assay performance, which involved both computer design of the assay and laboratory work using synthetic Dungeness crab DNA to test the assay sensitivity. This hands-on testing was invaluable, allowing me to master techniques like using a multi-channel pipette and a 384-well plate. Once we got to a good place in our assay validation testing, we coordinated with the PMEL Carbon group and the Pacific Northwest Crab Research Group (PNWCRG) to pair manual counts of crab larvae with the quantifiable DNA we can detect in the overlying water. These kinds of tests allow us to understand the relationship between the number of crab larvae and the amount of DNA they shed into the environment.

We began with previously collected Dungeness crab larvae collected by the PMEL Carbon Group from net tows along the US West Coast in 2016. Though these provided a few data points for comparison, we wished to broaden and strengthen our correlation between organism count and released DNA by adding additional range and replication. Thus, we partnered with the PNWCRG to incorporate those additional crab larvae samples.

Schematic of a light trap made of standard materials. Credit: PNWCRG

Our work with PNWCRG allowed us to sample water and larval crab specimens in Anacortes, WA. We joined Sarah Grossman, an environmental specialist with the Swinomish Indian Tribal Community, as she collected and counted the crabs from light traps. A light trap is an active sampler that depends on the larvae’s attraction toward the light source and traps them through funnel constriction points to prevent escape. During our collection, we were able to collect some of the Dungeness crabs and preserve them in buffered ethanol to add data for quantification purposes from controlled experiments with precise crab counts in jars. Additionally, while the light trap was pulled from the water, we collected the water that poured from the traps, providing a paired environmental sample to understand the overall impact on DNA quantification with the potential for crab signal from the surrounding environment. We also collected water from the dock and down shore for eDNA analysis. I enjoyed our sampling time a lot, from seeing light trap recovery first hand, observing the other species that also enjoy the light traps, and collecting water during the very low tide.

My time here has been valuable to me in developing my skills as a scientist and becoming better at communicating my science.

Dwan Jackson and Han Weinrich filtering water samples collected from the light traps in Anacortes, WA. Credit: Mugdha Chiplunkar