Week Four: Busy As A Bee, Happy As A Clam!

I’m never sure as to what each week will bring here in Coos Bay. Every week has always managed to top the previous and this week was no exception. Tuesday, Scott, Jim, and I boated down to Indian Point to start the ODFW’s annual cockle survey. Using ArcGIS I generated 60 random points and uploaded the locations of these 60 points onto a GPS. These 60 points would serve as our sampling sites. We would lay down one square meter quadrats at the waypoints found on the GPS and rake a four tine rake over the quadrat once and record and collect the cockles found. Then we would turn 90 degrees and rake one more time and record the number of cockles found and collect them as well. This was repeated for each quadrat.

Raking for Pacific Heart Cockles at Indian Point

On Thursday we did this same process, only this time at Valino Island. Valino Island is a protected area and Indian Point is an area known for heavy commercial harvest of cockles. We chose these two sites in order to compare how harvest (or lack thereof) affects cockle size and recruitment over time. While Indian Point was very sandy Valino Island was quite the opposite. Valino Island is essentially a mud flat and it is easy to get stuck and sink. Scott and Jim had to pull me out of the mud several times, but not before musing—i.e., laughing—over how funny they thought my predicament was.


Stuck in the mud at Valino Island

When we returned back to the ODFW I placed the cockles into tanks of circulating water in order to take accurate wet weights. When clams are left out of water they tend to spit water out of their siphons which can give you inaccurate weight data; this is why we placed the clams back into water before recording weight. I also recorded shell length, height, and fatness which will be used in our analysis. Using R we ran some preliminary statistical tests that suggest that Valino Island, the reserve area, has much larger cockles but Indian Point has higher amounts of recruitment.

We also have been continuing our red rock crab surveys and we were lucky enough to have the pleasure of working alongside Sylvia Yamada, a professor and research scientist from OSU. Sylvia has been doing work throughout the years on the invasive green crab and was a delight to work with. Her plethora of knowledge and fascinating anecdotes made for a great week of crab processing. She brought Fukui traps, a Japanese trap that allows all sizes of crabs to walk through. We had been using box traps which bias samples by not letting the larger crabs in. However we did run into some trouble with the Fukui traps: the seals ate all our bait!

Scott, Larry, Sylvia, and I processing red rock crabs

The notorious bait thief!

Thursday was considerably out of the ordinary. Dean, a fish biologist for the ODFW, invited me along to process yellow-eyed rockfish with him. It was truly a treat as yellow-eyed rockfish have a harvest limit of two tons per year—a very small allowance—and are not often encountered. We recorded lengths and weights of the rockfish and also recorded their sex and stage of maturity. Dean also pulled otoliths from the rockfish. Otoliths are ear bones and are used to determine the age of a fish. We even had encountered a few fish that had been eaten by hagfish, which enter through the gills and eat the fish from the inside out. The fish remains whole but the body is completely flaccid as all its musculature and organs have been consumed. It was very surreal to see. And on top of the fun of handling some cool fish, a buyer stopped by to purchase halibut from the boat we were working with and gave us all brownies. Brownies for breakfast: how could I say no to that?

Yellow-eyed rockfish

Later in the week, Jim Carlton, an expert on the subject of Japanese tsunami marine debris (JTMD) and invasive species, came to visit OIMB to give a lecture on the incoming debris and teach a class on the topic of biological invasions. In a previous blog post I mentioned how Scott and I had discovered a Japanese pallet that had washed ashore. We had sent the samples and pictures we had taken to Jim and during his visit he informed us that the pallet had come from the Morinaga-dairy business, a famous dairy business in Yamato which is located in the metropolis of Tokyo. It was determined that the pallet contained various hydroids, Mediterranean mussels (M. galloprovincialis), pelagic barnacles known as Lepas, as well as jingle shells (Anomia cytaeum). Jingles are not commonly found on JTMD which made it an interesting find.

There is no such thing as a dull weekend at OIMB. Friday night the director, Jan, announced that a dying dolphin had washed up on Bullard’s Beach in Bandon and was hoping to have help in retrieving it. And so, Saturday morning I had the opportunity to drive to Bandon with a group of friends to help Jan retrieve the dolphin so that it could be dissected in the Birds and Mammals course. After about fifteen minutes of combing Bullard’s Beach we found the dolphin, loaded it onto a stretcher and carried it up and over the dunes to the truck to be hauled back to OIMB. The dolphin weighed over 200 lbs. but with one person on each corner of the stretcher it wasn’t as difficult as I thought it would be to carry. Though, I’d be lying if I said I didn’t feel a little sore!

Recovering a striped dolphin for dissection

As you can see, the birds had gotten to the specimen before we did

This coming week I’ll be heading to Corvallis to talk to the public about my summer work and Oregon Sea Grant. Each week always unfolds a new and exciting surprise and I’m ready to see what that will be this week! Until next time!

Week 4: Self-Directed Accomplishment

This week I was supposed to be on a trip with my lab in Willapa Bay, Washington, doing field work. My foot is not healed enough that I was comfortable to go, so I had to sit this one out. I was able to go to the doctor and get an x-ray and my pinky toe is definitely fractured. This means another month of healing, which is basically my whole summer. The silver lining of the situation is that my injury lined up nicely with my move to a new house, allowing me to take it easy while still getting things done, like unpacking and getting settled. My injury means that I had to miss out on the fun and the other people in the lab have to do a lot more work to do, but we’re trying to make the best of it. I should be able to go on the next one though, which leaves this upcoming Friday!

Although I can’t go in the field, I have still been useful doing computer and lab work, which I had a lot of this week. My mentor wanted to give me something hands-on to do, so instead of processing some samples in the field like they normally would do, they brought them back in Ziploc bags so I could process them in the lab. These samples were from the mud and eelgrass areas near some bags of oyster shells that were put out a couple months ago, when Dungeness crabs were recruiting (metamorphosing from larvae into juveniles). The oyster shells create three-dimensional habitat at low tide, attracting crabs seeking shelter and providing suitable habitat for . We periodically sample the bags and some of the sediment underneath, as well as areas nearby with no bags, to look at the number and size of any crabs we find, which are mainly Dungeness (Metacarcinus magister) and shore crabs (Hemigrapsus spp.). This data helps my mentor look at the recruitment and growth of juvenile Dungeness, as well as their preferred habitats. In the lab, I sorted bags of eelgrass, measuring crabs I found and weighing the eelgrass both wet and after drying in an oven.

Because everyone was gone this week, I was responsible for my own success in getting things done, but I think I did a very good job. It helps that I am so used to being in school, where you set your own schedule. I’ve learned a lot of time management, and it’s good to know that this helps in the real world too!

I’m not sure what this next week has in store for me, but I’m definitely looking forward to going to Washington on Friday!

Week 3: Happy Fourth of July

This week of my internship turned out to be quite short. Because of an unfortunate accident over the previous weekend, my foot might be broken, (a week later, it is feeling much better and I can almost walk normally but I am still not able to do field work), so I missed Monday to go to the doctor and rest up. The Fourth of July and the following EPA furlough day gave me a four-day weekend. I guess it was great timing, because I was able to rest up plenty and relax but still have fun. My friends hosted a BBQ at their house, and we all biked down to the Willamette River in Corvallis where there was a fireworks show, as well as hundreds of people lighting off their own in the street. The Fourth is one of my favorite holidays, and although I was not in tip-top shape, it was still a wonderful time.
Before I hurt my foot, I was able to go tidepooling in Boiler Bay, just north of Newport. I spent three hours there (and consequently got a little sunburned, it was a beautiful day), and had a great time taking pictures, touching things, and trying to catch fish. The Oregon Coast has an amazing diversity of marine life, and I’m so glad I get to experience it!


To respond to a question from my last post, “testing” the GoPro cameras involved taking pictures and videos, trying to figure out the battery life, size of the SD card, and the size of the field of view at various heights off the ground. I put testing in quotes because it felt more like playing with the cameras. We came up with a design for the mount of the camera and built and deployed it last week to get some test video. It worked surprisingly well the first time, and I learned how to use a drill press. We just bought materials for the rest of the camera mounts, and will be building them soon.
In the meantime, I am continuing my video analysis from previous years so we will have historic data to compare to. I am also sorting through samples of seagrass, measuring any crabs I find and weighing the plant matter, as part of another ongoing project looking at the crabs that live in Yaquina Bay. We are trying to determine where they are most abundant (in the native seagrass, the invasive seagrass, or bare mud), and if the ages of the crabs is different between them.
Hopefully my foot will be better soon so I can get back to field work!

Field Work Frenzy!

Hello all!
I’m so excited to update you on my week! This past week was all about field work, which is my favorite part of any job. Monday we kicked off the week heading down to Indian Point where Jim, my officemate and colleague, and Scott, my mentor, had previously placed two crab pots filled with pit tagged cockles. Our goal was to dig up the crab pots (no easy feat in such coarse sand!) and retrieve the cockles to measure their growth over the previous two weeks. Unfortunately, many of the cockles had died but we could still collect all the growth data we needed from them, such as shell length, height, fatness, and clam weight.

A typical day at the ODFW in Charleston, OR

Wednesday I had the opportunity to venture outside of shellfish biology and got to ride along and seine with the marine fish department. Our target species was Chinook salmon but we also found many other species of fish such as greenlings, sand lances, English soles, staghorn sculpins, and smelts. We also found hundreds of small Dungeness crabs and comb jellies.  A few people held one end of the seine on the beach and the boat was driven around in an arch until the boat reached the other end of the beach. We then pulled the seine up to the shore and then sifted through the bag for fish.
We sampled 4 sites along a seven mile stretch of water, from Charleston to North Bend. We measured lengths and weights of our target species in order to later be able to calculate a condition factor (K) which is used to estimate the condition (health) of fish. We also identified which salmon were hatchery salmon by checking to see if the adipose fin was clipped. Clipped fins indicated hatchery spawned salmon.

Port Orford

Thursday’s field site in Port Orford

Thursday was by far my favorite field work day of the week. Jim and I drove out to Woodruff Creek near Port Orford. After scaling down a sharp cliff-face in waders to get to our sampling site my adrenaline was definitely pumping. We sampled eight, random, 1m^2 quadrats. Our target species was littleneck clams. Digging through all the tide pools was amazing and we found some cool intertidal species; my favorite find was a clown nudibranch (sea slug). The tide pools were teaming with diverse fauna: several species of crabs, gunnels, peanut worms, sea stars, sculpins, the list goes on and on! Though we were out sampling in the warm sun for three or so hours I enjoyed every minute of lifting cobble and boulders and digging through sand to find littleneck clams. When you love what you do, it never seems like work!


A clown nudibranch (sea slug) I found in one of our quadrats in Port Orford

And what’s work without a little play? I have made some good friends at the Oregon Institute of Marine Biology (OIMB) where I am being housed. All the students are friendly and always ready for adventures. After dinner, rain or shine, we’ll get together to play volleyball or Frisbee or go hang out on the beach. Thursday was particularly fun, as I swam in the Pacific Ocean for the first time. It took a few minutes to get used to the cold water but soon we were having the time of our lives swimming through the breakers.


A typical night at OIMB

This weekend, a few friends and I drove over to Sunset Bay where we spent our day climbing through the cliff sides where we found some pretty stellar tide pools. As the tide began to roll in, so did the fog. The fog is a unique part of the Oregon coast that I have come to love.  In Indiana, fog is something you wake up to and it appears as a boring, thick sheet. Here in Oregon, fog comes in at random times throughout the day and it rolls in looking like thick cumulus clouds gliding across the ground and pouring like falls over cliff sides. It’s a beautiful event that I’ve fallen in love with and there is something very relaxing about the whole occurrence. On our way back to OIMB we stopped at an overlook of the cove and ended up sighting some sea lions and even a whale, which was the cherry on top of a good day. I can’t wait to see what adventures this week holds!

Week 2: First Day in the Field!

My work this week has been defined by many miscellaneous tasks I have done for various members of my mentor’s lab, almost none of which are related to my project, but I had a lot of fun with them. I have done analysis of videos taken in an estuary in Washington, measured tiny mud shrimp recruits (juveniles) after sorting through mud to find them, and measured, sexed, and examined adult mud shrimp to look for parasites and infection. I also “tested” the GoPro cameras we will be deploying in July to record the fish and crabs found in the invasive species of eelgrass.

A picture of the video I’m analyzing. You can see a full-sized Dungeness crab.

Mud samples on a tray that I sorted through looking for small mud shrimp recruits (juveniles)

Today was the first day I went out in the field to do sampling, on the mudflats near Hatfield Marine Science Center. Thank goodness it was a beautiful day today, so we didn’t have to wear heavy rain gear. We got very muddy, and I wish I had pictures but I don’t have a camera I wouldn’t mind getting dirty. We were looking for mud shrimp to measure and look for parasites. We used what is called a bucket core, which looks like a giant stainless steel bucket without a bottom and is about three feet tall. We pushed it all the way down into the mud, and shoveled the mud out into sieves, sorting through them and pulling out the shrimp as we found them. It was hard work, but the most fun I’ve had so far, and a great excuse to get outside and play in the mud!

Overall, it was a great week. I also bought a new camera, so hopefully I’ll have some higher quality pictures from now on. Next week I’m looking forward to building the mounts for our cameras and testing them in the field, and the Fourth of July, of course!

Week 1: Getting Oriented


My name is Sarah Heidmann, and I am one of the Summer Scholars this year for Oregon Sea Grant. I attend Oregon State University, and will be graduating in June 2014. I’m majoring in biology with the marine option, and minoring in statistics. I am originally from California, but am loving my experiences so far in Corvallis and Newport studying marine biology. This past spring term at OSU I lived in Newport taking an intensive marine biology course, and am excited to put all my new knowledge to the test.

Although I am working in Newport, I am living in Corvallis. Since OSU’s main campus is there, it was easier for me to live in the house I will have throughout the next year, in addition to being able to be with my friends who are here this summer. It’s about an hour driving distance, and I’ve been riding in a vanpool that allows me to sleep both ways, but I still have to get up pretty early.

Part of the beautiful bike ride I have every morning and afternoon in Corvallis on my way to and from the vanpool pickup location

This summer I am working in Newport with the US Department of Agriculture (USDA-ARS) studying fish and invertebrate use of coastal estuarine habitats. We are focusing on the habitat provided by a non-native species of seagrass, Zostera japonica, using GoPro cameras to record video in different areas and analyzing the numbers of fish and crabs that appear in the field of view. I’ll be in the field a lot this summer, getting very muddy.

The outside of the EPA building, where I work

So far I’ve been mostly practicing analysis of video from past years, trying to find some ways of improving the sampling technique. Although I’ve had some previous research experience, I still have so much to learn! I have been getting some training in Microsoft Access databases as well as statistics using R, which has a very steep learning curve when you have never programmed before. It seems like I’ll gain a some skill sets this summer that will be very useful farther down the road in my career.

Thanks for taking the time to read about my adventures! I am greatly looking forward to the rest of the summer.

Bandon or Bust!

Hello readers!

My name is Catherine Courtier and I have recently graduated from the University of California Santa Cruz with a B.S. in Marine Biology. During my time as an undergraduate I was not only fortunate enough to work in the labs of some truly inspiring professors, but  got the chance to take part in field study classes that enabled me to get a taste of what exactly it was that I was spending my undergraduate career working towards. Now I am one of six lucky Summer Scholars chosen by Oregon Sea Grant to work with Wild Rivers Coast Alliance. My main focus has always been on marine organisms, (specifically invertebrates) however I have recently become interested in the issues that surround coastal conservation, something I hope to learn more about through WRCA.

I was born and raised in Southern California, so you could definitely classify me as a sun, sand, and sandals type of girl. So naturally when I found out that the town of Bandon Oregon (where I will be spending the next ten weeks of my life) typically reaches a summer high of 68° I was a bit concerned. However, when I arrived in this cozy coastal town my worries seemed to disappear as I caught glimpses of the landscape on my way down the 101.


My first stop in Bandon was at the Bandon Dunes Golf Resort, and home of the Wild Rivers Coast Alliance, where I had lunch with my mentors Marie Simonds and Jim Seeley while overlooking the Bandon Reserve Course. Aside from its spectacular beauty, this course is of particular interest because all its proceeds go to funding Wild Rivers Coast Alliance.


Now that I am all settled in, I’ve had some time to begin exploring Oregon’s South Coast. Despite the questionable weekend weather and encroaching storm, I ventured out to the beach and was rewarded with mild temperatures and amazing tide pooling! In addition to the vibrant anemones and adorable sea stars, I caught a glimpse of some sunning sea lions and quite a bit of what I believe to be an orange sea sponge washed up on the beach.



Sadly the storm eventually caught up with me, so my plans to explore the various hiking and biking trails Bandon has to offer will have to wait till next weekend! While I’m not by any means an expert cyclist, I hope to improve my riding over the course of this summer so I can help with the final stages of a new coastal scenic bike pathway.  Tomorrow marks week two of this amazing experience and I can’t wait to see what adventures are in store for me!

Coos Bay: My New Frontier

Hello, all!

Thanks for joining me on my adventures in the Pacific Northwest this summer! Allow me to introduce myself, I’m Sam Thiede. I’m an undergraduate student at Purdue University majoring in Fisheries and Aquatic Science and minoring in Wildlife Science. I’m a senior and will be graduating May 2014 and plan on pursuing my masters and Ph.D. in either fisheries sciences or aquatic resource management. Currently, I am working at the Oregon Department of Fish and Wildlife (ODFW) as a technical research assistant to Scott Groth through the Oregon Sea Grant Summer Scholars program, but you will all hear much more about that topic throughout the summer.

I’m a Midwesterner, specifically from Indiana. Before my arrival in Oregon I had never been farther west than St. Louis, Missouri and the trip here was quite a shock. My plane had a short layover in Salt Lake City, Utah. I have never seen desert before and I was in true awe of the scenery throughout my short hour there. Seeing the Great Salt Lake and all the desert salt flats in between the mountain tops looked like something out of a painting! As I flew out of the desert and into the mountains of Oregon, again I was in for a total shock. Mountain tops covered with snow, gigantic confiners leaning over open ocean, I was in love before I even stepped off the plane.

OIMB Beach

Upon my arrival into Coos Bay, my mentor, Scott Groth, gave me a tour around the area. As we drove up Cape Arago highway we stopped off at an overlook of the bay to check for tsunami debris. Sure enough, all the way down at the bottom of the cliff face was a washed up Japanese plastic pallet. Much of the debris from the tsunami that struck Japan several years ago has been floating up on the coast of Oregon and biologists have been avidly collecting samples and trying to remove live specimens to avoid the spread of Japanese invasive species.

Within hours upon my arrival I was already scaling down the side of a cliff, sample bags and scraper in hand, to retrieve samples off of Japanese tsunami debris and at that moment I was assured I was in for an interesting and informative summer. We scraped off many kinds of unknown shellfish and algae (we are still processing the sample) and I was given a tour of the surrounding tide pools at the base of the cliff—full of shellfish, anemones, sculpins, etc.—to the soundtrack of sea lions (which I had never seen outside of a zoo!) barking on a nearby island. It was truly an exciting first day on the job.

OIMB Beach Anemones

As the week went on I had begun to learn the ropes of the ODFW’s shellfish program. This week was all about collecting data on pink shrimp, cockles, and spot prawn. Local fishing boats and clammers offer samples to the ODFW in order for us to keep track of size structure and monitor age class trends over the years in order to ensure sustainable fisheries. Not only did I learn how to measure carapaces and sex shrimp but I also had the pleasure of meeting with the local fishermen and hearing their tales of their times out at sea, which is always very colorful! This coming week’s project will be littleneck clam surveys and will bring even more excitement as good stories always seem to come from field work.

I hope you will all continue to tune in as I delve more into the science of marine life here on the Oregon coast with the ODFW! I will post weekly about my experiences here in Coos Bay and am excited for the coming weeks as well as having you all following me along in my journey!

Tide Pool Sea Star