Final Results of the Mesocosms

In my last blog post, I introduced you to the excitement Newport offers outside of Hatfield Marine Science Center, but left you hanging on how the mesocosm project turned out.

We planned on running experiments three days in a row, leaving the mesocosms out in the field for the entire duration. We needed to collect over 360 juvenile Dungeness crab and over 18 Pacific staghorn sculpin, which proved harder than we expected. We quickly saw that we would need to adjust our study due to the natural progression of second instars growing into fourth or fifth instar crabs. The crabs were too large for the Pacific staghorn sculpins to eat, making it difficult to run a predation experiment. However, we realized that the large crab size could be a benefit as it would allow us to study the crabs’ behavior without any predation while also reducing a factor of loss when retrieving the crabs. This increase in crab carapace allowed us to reduce the number of crabs needed to 10 per mesocosm instead of 20, another benefit. We spent three days beach seining at low tide and setting minnow traps overnight to collect the necessary number of organisms.

Brett Dumbauld of USDA-ARS beach seining for juvenile Dungeness crab and Pacific staghorn sculpin in Yaquina Bay, OR.

Water tables in the EPA lab housing over 250 juvenile Dungeness crab and over 40 Pacific staghorn sculpin.

With all of the pieces together, we were able to move forward and set-up the mesocosms in the field to begin running experiments. The mesocosms were set the same as they had been during the first trial, each containing different combinations of two habitat types (on-bottom oyster aquaculture, eelgrass, open mud) in three controls and duplicated in three treatments.

An example of a mesocosm set-up. One side contains eelgrass, the other oysters placed to mimic on-ground oyster aquaculture.

We then prepared the Pacific staghorn sculpins by starving them for 24 hours before they were put in the field. We had previously decided that we would experiment with different lengths of time that the crabs were exposed to the sculpin to see if it had any effect on their behavior. We decided to begin one trial when the water was low enough that it wouldn’t be spilling over the top of the mesocosms (about 2.5′). This trial was run for 2 hours, wherein predators were left in the mesocosms. We then reset the trial by removing and counting predators and prey before adding more organisms for a 24-hour trial which we would come back to the next morning. As we approached the mesocosms that morning with the water just around the tops, we noticed them rocking back and forth.

NOOOO! How were we going to run our 24-hour experiment without the crabs and sculpins escaping? We ran back to Hatfield during our 2-hour wait period and brought back a drill and rebar to reinforce the mesocosms, hoping it would do. Since we already had the organisms prepared, it was best to run the 24-hour experiment and just see what would happen.

Kelly Muething and Anna Bolm clearing out the different habitats after a 24-hour habitat selection experiment involving juvenile Dungeness crab and Pacific staghorn sculpin, in Yaquina Bay, OR.

We had some pretty interesting results. In the 2-hour experiment, we retrieved 95% of the crabs while in the 24-hour experiment we retrieved 106% of the crabs. This was the opposite of what we expected since the mesocosms had been rocking, but apparently some other crabs had run in rather than escape. Given that we only ran two trials, we can’t conclude any real results, but did see some patterns. Crabs preferred oyster shell over both eelgrass and open mud, whether or not there was a predator. The sculpins’ presence didn’t seem to have much impact on crab habitat selection, possibly because they had outgrown the sculpins’ ability to prey. All in all, the mesocosms were a success and Brett plans on using them again next summer, earlier in the crab season to test the second instars.

Last Friday, I presented my work and then participated in a poster session, a really rewarding experience. It felt good to share what I had been working on and I appreciated the exercise of thinking about how to communicate the project to others. It was also informative to see what the other Sea Grant scholars had been working on as well as converse with scientists about our work.

Poster shown on the mesocosms at Oregon Sea Grant poster session.

It’s been a really incredible summer living and working at Hatfield Marine Science Center. I am very grateful to have been given this opportunity and feel lucky to have had such wonderful mentors to work with. To celebrate the end of the summer and completing the final presentation and poster session, my husband guided me out on my first sea kayaking trip, exploring the sea caves beneath Cascade Head. Rising and falling with the swell is an incredible feeling, the water looking like hills around you. We watched a whale play about 100 meters away before heading into a cave. I have to say, it was pretty scary and amazing at the same time. Paddling into darkness with waves booming around you would spook anyone, right? It was cool seeing all of the birds nesting along the rock cliffs, Pacific sea nettles swimming around, and sea stars and anemone exposed at low tide. We also spotted some floating tubes which turned out to be squid eggs. All in all, the perfect end to a perfect summer and a reminder of how much we love the area. We’re hoping to move to Newport so I can continue volunteering and learning at Hatfield while looking for work.

Soaking in all things Newport

After realizing the summer was quickly slipping away, I spent the last three weeks exploring Newport and soaking in what it has to offer. There was a free screening of the documentary, Reluctant Radical, at the Newport Performing Arts Center followed by a Q&A with the director, Lindsey Grayzel, and the subject of the film, Ken Ward. The film offers the perspective of father and eco-activist Ken Ward by following him through: blocking the Shell icebreaker from leaving Portland Oregon, shutting down the U.S. tar sands oil pipeline, and the trial following his arrest. When framed by the fear of his son’s future given current oil consumption, Ward’s actions make sense. To view the film you can find or host a screening at .

I also participated in the NOAA fish cutting party which was a huge success!! Three days were scheduled for fish processing but a great early turnout of volunteers cut the processing time in half. Over 1900 fish were processed, which included removing the stomachs and otoliths, as well tags and fin clips in some. While I have gutted and filleted fish before, searching for otoliths was a whole new challenge. Otoliths, tiny little ear bones the size of a sesame seed, slip from your tweezers in the blink of an eye escaping to a mess of brain and tissue. It was easy to become immersed in the search and all the more satisfying when the little piece was found, especially knowing the otoliths were being used to age the fish by counting growth layers like rings on a tree.

Up at a nearby café, Café Bosque, my roommate and I spent an evening with Ranger Ryan talking about marine debris along Oregon’s coast. He presented a slide show on the subject and then screened Chris Jordan’s Albatross the Film while providing commentary along the way. I am currently working on research outside of my Sea Grant project which investigates the presence of microplastics in seawater and zooplankton and it was nice to see the combination of art and science to help communicate such a hidden yet ubiquitous issue.

A photograph, inspired by Chris Jordan’s Albatross the Film, of a bird I spotted while walking along Nye Beach. The film documents the dying albatross population on Midway Atoll. Jordan dissects multiple birds to find their stomachs filled with plastics.

I went and checked out the historic Nye Beach neighborhood which was filled with live music. There was a band playing outside the Newport Visual Arts Center, another at the Taphouse at Nye Creek, and more at Nana’s Irish Pub! Nye Beach is a cute little area with a lot of shops and restaurants near the beach. I ended up taking my visiting family there for breakfast at Cafe Stephanie where we all had delicious breakfast burritos and complimentary scones.

I also finally made it to the Saturday farmers market with my roommate, where I stocked up on berries, salad, and tomatoes. There were so many good smelling food stands serving prepared food that next time I’ll have to remember to go hungry. Later that day, my roommate and I went crabbing on the public dock. We sat out in the sun, reading our books, and chatting with fellow crabbers for about four hours. We had some exciting catches of a couple Dungies that were just a little too small to keep. We ended up with 3 Red Rock crabs but realized we wouldn’t be around for dinner, so passed them along to our neighbors.

The crab that was JUST too small. My roommate Meg is to my left and a little helper who offered to throw it back for us.

While my brother and sister-in-law were visiting we checked out the Aquarium Village, then went for a hike in Wilder, followed by a beer at the nearby Wolf Tree Brewery, and topped it off with dinner in Nye Beach. It was a lot of fun showing them around and exploring new places at the same time.

Family fun at Aquarium Village, diving into the deep unknown.

I am currently soaking in a little more Newport by eating some clam chowder I made from cockles gathered in Yaquina Bay. I have to say, it was a lot of work shucking and cleaning the cockles, but it is the best clam chowder I have ever had and am already planning when I can get back out and harvest more.

In other news, my summer project is complete! We ran the last experiment on Friday, but you’ll have to wait until the next blog post for all of the details.

Me in my happy place, at Nye Beach.


Mesocosms and Mud shrimp

These past three weeks have been filled with getting to know my new coworkers, fieldwork, and our first run with the mesocosms mentioned in my first blog post.

Kelly Muething (left) and Ylva Durland (right) enjoying the joy ride while pulling into port at Nahcotta, WA

I began working with Ylva Durland and Kelly Muething, two of Dr. Brett Dumbauld’s technicians. Kelly just finished her masters degree at OSU and had Brett as an adviser so has worked on many projects with him. She is also continuing her work comparing the growth of two oyster types in and out of eelgrass beds. Ylva Durland had been working with ODFW’s SEA-COR program before beginning with Brett and is bringing knowledge on both eelgrass and shellfish. Ylva earned her masters in her home country, Sweden, studying predation patterns of green crab on native oysters. I feel lucky to be working with such talented women and Brett, and appreciate their support and guidance.

We spent a hectic week finishing up preparations to have the mesocosms ready to deploy during the neap tides at the beginning of July. Being ready required collecting Pacific staghorn sculpin and housing them long enough to starve them for 24 hours, collecting over 130 second instar Dungeness crab and marking them with nail polish so we knew which crabs we placed at the end of the experiment, and acquiring oysters to place as our oyster habitat. We also had to find an appropriate edge of an eelgrass bed to work on. Most importantly, we had to determine how much time we would have during the tidal exchange to work within our two-foot tall mesocosms.

Dr. Brett Dumbauld USDA-ARS, searching for megalope in Yaquina Bay, OR.

Tagging 130 juvenile Dungeness crabs with red and orange nail polish.

On July 4th, we set out the mesocosms to acclimate to the environment for the following day’s experiment. The next day, we placed the crabs in all mesocosms and gave them one hour to acclimate before introducing the predator into the three treatments. After another hour, we placed dividers along the edge of the habitat and scooped out the sculpin and as many crabs as we could. We recorded the number and color of crabs on each side of the mesocosms to compare against what was originally deployed.

Ylva Durland showing off the installation of the mesocosms in Yaquina Bay, OR.

An example of a mesocosm in action. One side contains eelgrass, the other oysters placed to mimic on-ground aquaculture. There were two with this configuration to have a treatment (predator) and control. We also had a treatment and control for mesocosms with oyster aquaculture on one side and bare ground on the other, as well as eelgrass on one side and bare ground on the other. 

Ylva Durland placing the two sculpins into a treatment tank with Kelly Muething on standby.

Our preliminary results show a trend of higher crab presence within eelgrass and less movement of crabs in the treatment mesocosms. However, we only retrieved 76% of the crabs deployed and are unsure if they were eaten or simply weren’t retrieved. We plan on rerunning the project in early August and are still fine-tuning the details beforehand.

I’m happy to say that I’m writing this blog while sitting in my hotel room, looking out on the Pacific Ocean. We are currently on a field-trip to Willapa Bay and staying in Long Beach, WA. We’ve been out in the field collecting data on burrowing shrimp size and frequency, checking on Kelly’s oyster growth study, and sampling native eelgrass to measure biomass later. Between the boat rides, working outside with great people, and stopping at the Cranberry Museum, it’s hard to choose a favorite part of the trip!

Brett Dumbauld and Kelly Muething heading back to the boat over the tide flats in Willapa Bay, WA.

Me and the trusty toothbrush I used to remove periphyton from the oyster-growing tiles for Kelly’s project in Willapa Bay, WA.

The boat waiting for us while we collect and monitor burrowing shrimp in an oyster aquaculture site in Willapa Bay, WA.

Brett Dumbauld measuring ghost shrimp carapaces collected from one of the monitoring sites in Willapa Bay, WA.

Kelly Muething (the frog), Ylva Durland (left), and I (right) taking advantage of the photo-op at the Cranberry Museum in Long Beach, WA.

The Summer of Sea Grant Begins!

I have just concluded my first week at Newport’s Hatfield Marine Science Center (HMSC) as an Oregon Sea Grant summer scholar. I have been looking forward to this experience and am so grateful to call Newport and Hatfield home for the next nine weeks! I feel fortunate to have already been introduced to multiple research projects, though know I am only skimming the surface. There is such an array of research happening, I hope to learn as much as I can to help narrow my interests for graduate school.

My first day on campus, my mentor, Dr. Brett Dumbauld, took me out on the nearby Idaho Flats with Dr. John Chapman, a professor at Oregon State University. John and Brett have collaborated on burrowing shrimp and were taking a group of REU students out to pull sediment cores to look at the mud shrimp burrows (Upogebia pugettensis).

A sediment core pulled from Idaho flats, showing the burrows from mud shrimp.

A cross section of a mud shrimp burrow. Dr. John Chapman from OSU is investigating whether or not the burrows are used by the mud shrimp to grow and harvest food.

Brett is an aquaculture ecologist with the United States Department of Agriculture-Agricultural Research Service (USDA-ARS), focused on the West coast shellfish culture industry. This summer we’ll be investigating habitat selection of Dungeness crab in response to threat from predation by Pacific staghorn sculpin. The habitats we will be testing are structured: oyster aquaculture and native eelgrass, and unstructured: open mudflat/sand. We spent time brainstorming until constructing the mesocosms we’ll use.

Cutting out holes for side windows and the camera setup.

A nearly finished mesocosm.


This week was also the graduate student poster session and Ignite Talks, five minute presentations showcasing selected work. From investigating native oysters as a viable market to understanding how anthropogenic sounds affect whale communication, I learned a lot about the diversity of research happening at Hatfield.

Other highlights of the week included: exploring the south jetty with my roommates, checking out the local brewery, camping in Drift Creek Wilderness, a NOAA wetting down party, new running trails, and walks on the estuary nature trail- just outside my door. I’m looking forward to what the rest of the summer brings!

Agate Beach from Yaquina Head in Newport, OR.