The 2021 West Coast Ocean Acidification (WCOA) cruise aimed to better understand how changing ocean chemistry affects marine communities along the U.S. West Coast, from Mexico to Canada. As part of this effort, researchers used plankton tows to capture detailed snapshots of phytoplankton and zooplankton species and their diversity. The Ocean Molecular Ecology (OME) group, in partnership with the Carbon Group, is working to compare these traditional plankton collections with environmental DNA (eDNA) sampling. This comparison is helping validate the use of eDNA for future ocean monitoring efforts.
To start this process, UW undergraduates Mugdha Chiplunkar and Karina Lai spent several weeks inventorying the extensive collection of preserved plankton samples from the cruise. They cataloged each sample in a spreadsheet, recording collection details (like date and location) and taking photos of each container from multiple angles. This organized inventory made the samples more easily accessible, as it was faster to locate and reference individual samples without having to dig through the entire storage cabinet.
The next phase involved carefully removing a small volume of ethanol, the preservative in the jars, from each sample. This ethanol contains traces of DNA from the organisms in the sample, so filtering and analyzing it can reveal information about community composition. The process wasn’t always easy; some jars were packed with plankton, which made drawing out the ethanol a slow and tricky task.
To estimate the volume of plankton in each jar, Mugdha and Karina, alongside OME researcher Shannon Brown, used weight displacement. First, they estimated the total volume of the ethanol and plankton together using a graduated cylinder. Then, the contents were poured through a sieve to collect the liquid separately from the plankton. Subtracting the liquid volume from the total volume helped them estimate the volume of the plankton only. This process was time-consuming and required a lot of stirring, especially when larger plankton slowed the draining process. Transferring samples was also messy which required extensive sterilization and definitely left the lab smelling distinctly of preserved plankton for days.
Karina Lai & Mugdha Chiplunkar busy at work during the weight displacement step
After volume estimation, the team took the previous aliquoted ethanol and filtered over 150 ethanol samples onto disc filters over the course of three days. These filters were then processed for DNA extraction, PCR-amplified for target genetic markers, and sent out for sequencing. In parallel, OME also extracted DNA directly from the plankton subsamples taken from the jars themselves. This provided an additional comparison point in the study.
Though labor-intensive, this work provided Mugdha and Karina with valuable hands-on experience in marine sampling, molecular techniques, and ecological research. Along the way, they encountered a fascinating array of plankton, and even discovered a few tiny squid hiding among the samples. Their efforts are helping NOAA and the OME team advance the use of eDNA to monitor the ocean’s changing ecosystems.