Dave - Three tank system

Busy busy busy. I have finally gotten the chance to sit down and write another post. I have a lot of new info and exciting experiments that I have done. I devised the bio filter and have gotten a lot of data form it. I took three 200 liter tanks and created a flow through system where the water goes in from the top and out from the bottom. I built an aeration system and plumbed a seawater line, an air line and a freshwater line for cleanup. I've never done any plumbing before so this was a great new experience.

After the initial set up I ran the tanks without the Ulva for five days to get baseline water quality measurements to determine how much was being done by the heavy aeration and how much was being done by the presence of the Ulva. I decided to use PH measurements as my indicator for the amount of dissolved CO2 being removed(this will be tested later to determine whether this is an accurate indicator) . As it turns out the heavy aeration itself seemed to stabilize and slightly raise the PH. The incoming water was fluctuating between 7.50 and 7.85 while the water coming out of the system was only fluctuating between 7.90 and 8.00. I also tested other parameters such as; flow rate of water, flow rate of air, alkalinity, temperature, salinity, time of day, date, and dissolved O2. I focused mainly on PH, time of day, date, and temperature.

I then settled on a way to standardize the amount of Ulva that was placed into each tank. I took an ordinary salad spinner and decided on ten spins as my mode of getting consistent dryness so I could get an accurate weight of the algae and not the variation in wetness. I stocked each tank with 0.200 kilograms of the Ulva that had been dried in this way. The picture of the system shows the tanks at this stocking density. I took water samples from the water going into the system and from the water going out of it. I will write about those results in a future post.
~ Dave

Mark - Week 2

Week 2, Monday July 12, 2010 thru Friday July 16, 2010

We met at the SSNERR shop at 5am Monday. Steve Rumrill, Hans Klausner, myself, two students from OIMB Laura and Lora, and Max, a volunteer from the S. Slough. We went by boat to the S.Slough Olympia oyster site by Younkers Point where there are thirty pallets arranged in three rows of ten pallets each.



At the site, there are also about eight PVC pipe racks, three ft. by four ft. by almost three ft. high. These also have Olympia oysters growing on top of them. We selected one of the pallets and carefully tagged each bag, then put each one into a plastic tub to contain any organisms that are living in the bag and we then we took them back to OIMB. We can only work the low tide at the oyster grow out site so in the afternoon we took the oyster shells that the juveniles are growing on out of their bags and separated the ones that have juveniles on them for count and measurement.

My first initial observation of the fish and crab that are living in the bags are various types of Gunnel fish (Family: Pholidae), probably Rockweed Gunnel and Saddleback Gunnel. There are many crabs in the bags too, probably Dungeness, (Cancer magister) two or more species of Redrock Crab, (Cancer productus, Cancer antennarius) and many tiny crab less than 5mm that look like mud crabs (Rhithropanopeus harrisii). Besides the fish and crab, there are various types of Polychaetes, Annelid worms and small shrimp but I’ll just be concentrating on the fish and crab. Tuesday and Wednesday we had other volunteers from the S. Slough, Mike, Laura, Max, with Christine, another student from OIMB. Thursday July 15th, I did the water quality-monitoring route again, and came back and entered the data.

Mark - Week 1

Week 1, Tuesday, July 6, 2010 thru Friday July 9, 2010

Tuesday I met with Coral Gehrke at the Oregon Institute of Marine Biology (OIMB) in Charleston. She is the Coordinator for COSEE Pacific Partnerships. We went over the PRIME (Promoting Research Investigations in the Marine Environment) program outline notebook and she got me started. I then met my mentor for my internship with the South Slough National Estuarine Research Reserve (SSNERR), Dr. Steve Rumrill. The project we will be working on is the restoration of native Olympia oysters to the S. Slough and Coos Bay estuaries.

Next Monday is the lowest minus tide of the summer so we will be working out in the field. We will select one pallet pyramid of fourteen sacks of juvenile Olympia oysters set out in the South Slough by Younker Point (picture on right), and bring them back to the lab to study the growth and survival rate of the juvenile oysters in relation to the bags position in the pyramid, and we will collect any sea life that are using the pyramid for a habitat or are preying on the juvenile oysters. It will also be interesting to see what effects the silt and the epifouling algae, seaweed, and marine organisms and growing on the outside of the bags will have on the juvenile oysters.

I also have another project to work on when I can. I am to make two underwater camera mounts. One camera mount will be on the end of a handheld extension pole, and the other a sled to be towed behind a kayak at a range of depth down to about forty feet. I have several good ideas for this and hope to start on it soon. I believe the ideas I have will work, and that assembly, then trial and correction of error to work out the bugs.

Once a week I will also run a water quality monitoring route to nine sites extending from the OIMB Boathouse, which is by the entrance of Coos Bay, as far up the Coos River as Sause Brothers’ Shipyard, and south out Hwy. 101 to the boat launch at Shinglehouse Slough.

Sam - Lather, Rinse, Repeat

On Friday, 7/9/10, I set up an informal juvenile Tresus capax reburial trial. Most of the specimens used during this test were confiscated from an overenthusiastic clam-digger by an Oregon Department of Fish and Wildlife employee . To view 2010 Oregon shellfish regulations, visit http://www.dfw.state.or.us/MRP/shellfish/regulations.asp.


















All the specimens sat still after I placed them in the tank for varying amounts of time. A specimen usually began reburial by extending its neck (left photo, see the leathery plates?) and perhaps waving it from side to side. The specimen pictured on the left changed its orientation and location by using its neck and foot in tandem. The first specimen to attempt reburial extended its foot and inserted it into the sand using undulating motions (right photo). Whether a specimen dug straight down or at an angle to the surface, it facilitated the process by pushing jets of seawater down below its foot to liquify the sand (see video).

A clam changes the shape of its foot using a hydrostatic (fluid) skeleton to change the foot's internal pressure, longitudinal muscles to change foot's length, and circular muscles to change foot's diameter. As I was preparing to film this video, I observed how tightly gapers can cling when I pulled one clam's foot free of another clam's shell. It reminded me of pulling a snail off a rock! If I find time next week, I want to test for mucus by placing one of the gaper clams on glass.

sam - The Data Is in The Burrow

Literature tends to claim that gaper clams (Tresus capax) are virtually incapable of making new burrows when they are removed from their original homes. That might be valid for the large adult gapers, whose shells can reach over 20cm (about 8 inches) in length, but given enough time and some protection from predation, my juvenile specimens seem quite capable of reburying themselves. Compare the photo of the surface treatment group taken on the first day of the experiment (upper left) with one taken less than 6 days later (upper right). The object in the upper right photo that resembles an earthworm is part of a gaper's neck. The necks of Tresus capax have fused incurrent and excurrent siphons that allow food and water exchange with the clam's environment.


I measure how far my molluscan minions delve by using a thin wooden dowel marked with 1cm increments (left). If a gaper hasn't hidden its shell below the surface, I note how far the surface is from the clam's highest elevation and record it as a negative distance. If it has, I measure its depth by gently probing the opening of the burrow with the dowel until I feel the tip of the gaper's shell, pinch the dowel at the level of the surface with the thumb and index finger of my other hand, and pull the dowel out to get a reading.

Mark Burnap, South Slough National Estuarine Research Reserve, OIMB

Hi, I am Mark Burnap. I am a COSEE/PRIME Intern this summer working for the South Slough National Estuarine Research Reserve (SSNERR) with mentor Dr. Steve Rumrill. The project I am working on with Steve and others at South Slough is to restore native Olympia oysters (Ostrea lurida) to the South Slough and Coos Bay Estuaries. I am a student at Southwestern Oregon Community College (SOCC) here in Coos Bay, and have been granted additional transfer credits to work toward my Bachelors Degree in either Natural Resources or Marine Biology in the fall. My main interests are in Marine Biology, the Marine Sciences, and Geology. In short, I've always loved learning and science. Having worked as a commercial fisherman, I would like to put my knowledge and experience of the sea and vessels to work in the study of the ocean. The reasons I applied for the PRIME Internship Program are my interest in the ocean and the encouragement of my Biology teacher at SOCC Robert Fields.

Sam - Gapers and Pea Crabs

In the field, Mitch has introduced me to a number of species that inhabit Idaho Flat. Once or twice during our diggings, I've been surprised to find a little crab escaping from the gaper's shell as I pulled the clam from its burrow. The pea crab (Pinnixa sp., photo obtained via google search from beachwatchers.wsu.edu) establishes a commensal (one species benefits with little or no harm to the other) relationship with gapers by using their shells for shelter. Adult females become too large to leave the shell, and feed by scraping plankton from a fringe of tissue attached to the clam's visceral mass. This fringe is called a visceral skirt. Adult male pea crabs are much smaller, have a tougher upper portion of their exoskeletons (carapace) and can move from clam to clam. Though several pea crabs may inhabit a gaper clam's shell simultaneously, no more than a heterosexual pair of adults will reside in one gaper at the same time. The common name "pea crab" is used to describe members of Family Pinnotheridae that have commensal or parasitic relationships with bivalves and other marine species. The three species of pea crab that favor gaper clams are Pinnixa faba, P. littoralis and Fabia subquadrata.

Laury Perry, Coastal Oregon Marine Experiment Station, HMSC

Hi, my name is Laury Perry and I just finished my third and last year at Portland Community College. I will be transferring to Portland State University this fall, and I’m super excited about it. I am currently a biology major, but I’m interested in looking into majoring in either Marine Biology, or Environmental Science/Studies. I just turned 23 this week and got to spend my birthday out in the surf zone trying to catch some Chinook salmon; it was a pretty cool way to spend my birthday. I have been interested in marine biology since I was very young and had my first memorable experience at the Oregon Coast Aquarium. It was during the time when Keiko made a temporary home at the Aquarium. I was mesmerized by the harbor seals, and tried to teach them tricks through the glass. Well to my surprise they completely interacted with me, and followed my finger as I traced it around the window. I felt connected to them, and that’s when my love for the ocean and its inhabitants began.


I was extremely excited to have this opportunity to intern at the Hatfield Marine Science Center! Especially to be asked to intern for the project of my first choice! I am working with Dr. Jessica Miller and Jose Marin Jarrin (PhD Candidate), and their study on Chinook salmon (Oncorhynchus tshawtshca) and the role of the sandy beach surf zone as a habitat for Chinook salmon. Jose is my mentor and I’m so lucky to have him. He is awesome, fun, and super patient! He also really knows a lot about the ocean, and it’s a cool opportunity to have him teach me about the different invertebrates and vertebrates that live in the surf zone. Basically Jose is investigating why Chinook salmon leave estuaries at the time they do. Is it because of food? Are they finding valuable nutrition in the surf zone before they migrate out in the ocean? That’s where my job comes into play. I am helping Jose study the invertebrates and some small vertebrates that Chinook salmon eat. I am finding their energy values using a Bomb Calorimeter. I know the word “bomb” makes this process sound pretty intense, but it’s not exactly what you think.


It’s time to freshen up your chemistry knowledge just a little bit. A Bomb Calorimeter is a device using Calorimetry which is the science of measuring heat capacity, chemical reactions, or physical changes. The reason we want to know the heat capacity is that we can determine the energy given off of from the combustion (in joules) of the organisms the Chinook eat. We can then determine how much energy Chinook salmon are getting from eating certain invertebrates. This valuable knowledge tells us if they are getting valuable food sources in the surf zone rather than estuaries.


Chemistry lesson over! So below I want to show you some cool pictures of the Bomb Calorimeter itself. Let me just add, it is a very long and delicate process, that I have only recently started to master!

This is my work bench. To the very left just above my bomb manual is the lid to what I call "the science crock pot" which is just above the oxygen tank. On that lid is a thermometer and a rotator that circulates the water in the science crock pot. To the right of the lid is the actual bomb, and in this picture I am filling it with around 26-30 atmospheres of pressure (that’s a lot of pressure!). Next to my science crock pot is the ignition pad that I will ignite later, which makes the sample combust! And to the right of the ignition pad is an OHAUS Scale, which is super sensitive and really annoying to use. Not pictured is the water reservoir which is inside the science crock pot.

If you’re curious how the whole process works I will make a separate entry including the process step by step. This blog entry is just an introduction!

In the picture to the right are some smooth bay shrimp we caught out in the surf zone. You see that yucky grey stuff on their bellies?  Yeah, you guessed it; those are eggs. All the more energy for our little Chinook salmon! This picture was taken before I put the shrimp into a dehydrator, where I would then macerate the dried shrimp into a very fine powder, and blow them up in the bomb calorimeter!

This next picture shows the leftovers of the shrimp after being combusted at an intense heat. Pretty intense stuff! And those small pellets are not eggs, they are the charcoaled remains of the smooth bay shrimp.

That’s all I have for you today! Next time I’ll talk more about the field work we do to collect these samples so I can bomb them!!

David Hubert, Molluscan Broodstock Program

My name is David Hubert. I am currently enrolled at Linn-Benton Community College working toward an associates of science with an emphasis in biology. This past school year (2009-2010) I finished my first year of college. I currently have an accumulative GPA of 4.0 and I plan to attend Oregon State University when I complete my transfer degree from Linn-Benton. I have not been able to pin point the exact major I plan to pursue at OSU but definitely in the field of biology. I have had a strong fascination with fish and aquatic organisms since I was a child, getting my first of many (a very great many) fish tanks at the age of 4. In the last two years or so I have become very fond of cuttlefish and would love an opportunity to work with them; this interest brought me to the field of marine biology and to the COSEE PRIME internship program.

The program I was selected to work with is the Molluscan Broodstock Program. This program focuses on the selective breeding of oysters for the purpose of aquaculture. They are selecting for flavor, size, shape, and a little for color. I am working under the guidance of Dr. Chris Langdon and Kiril Chang-Gilhooly. I will be helping them with their daily duties and I will also have a project of my own.

My project will be working with a green macroalgae called Ulva. I will be devising an experiment to test the viability of Ulva as a bio filter to reduce the effects of too much dissolved CO2 caused by upwelling. Excess dissolved CO2 lowers the pH of the water causing the water to become more acidic. This can be detrimental to the developing larvae making it difficult to fully form their shells. If this experiment is successful, the system I develop may be used to help maintain stability for larvae tanks. Also I will be working with their existing Ulva and other macroalgae storage tanks and trying to make them more productive. There are several smaller tanks and one very large one.

Samuel Moore, Oregon Department of Fish and Wildlife - Home on the Mud Flats

My name is Samuel Moore. I graduated from Portland Community College in June 2010 and plan to enroll at Oregon State University in August. I rediscovered a latent interest in marine biology when I attended the 2010 meeting of the Oregon Academy of Sciences. Before then, I had admired John Steinbeck and Joseph Campbell for their literary works, but had no clue that they had played a role in the inception of a new ecological perspective of the Pacific Northwest Coast. One of the reasons I applied to participate in Centers for Ocean Sciences Education Excellence Promoting Research Investigations in the Marine Environment (COSEE-PRIME) was to learn whether I'd prefer working as a botanist, a marine biologist, an environmental scientist, or some combination of each.

Thanks to my former botany/biology instructor April Fong, the National Science Foundation, and COSEE-PRIME, I am currently working with the Oregon Department of Fish and Wildlife (ODFW) at Hatfield Marine Science Center (HMSC) in Newport, Oregon with shellfish guru Mitch Vance in a study of the phenomenon of fat gaper clam (Tresus capex) reburial. Gaper clams are prized by recreational clam-diggers because they can grow up to 8 inches in shell length. Current ODFW regulations state that a harvester has catch limit of 12 gaper clams per day and they must be retained regardless of size or condition. The purpose of my research was to examine their burrowing behavior above and below the sediment after they are harvested.

Above (upper left) is a picture of me at Idaho Flat (a mud flat directly adjacent to HMSC), during high tide with some freshly-hauled experimental units (photo by Mitch Vance). This method of sediment collection was easier and more efficient than the one used the previous morning. I don't recommend dragging two 5 gallon buckets of mud across the flat with a sled- the units are very heavy and traversing the mud in this fashion takes a significant amount of physical strength.

T. capax has several common names, including empire, horse and blue clam. In Yaquina Bay the common name is gaper clam or simply gaper. Note the opening in the shell that accommodates its prodigious neck (center, photo obtained via google search from wallawalla.edu). Its close relative, the Pacific gaper clam (Tresus nutttallii), is virtually absent in Yaquina Bay but more abundant in California estuaries. One of the easiest ways to tell the difference between a gaper and geoduck (Panope generosa) is by the presence of two leathery plates at the end of the gaper's neck.

We collected 6 gapers during low tide at Idaho Flat on June 24th, recorded their weights and shell lengths, tagged them with ID numbers, and relocated them to an outdoor open system seawater tank. We placed three specimens on the surface of the sediment of one bucket and and planted the rest in a second bucket so that the tops of their shells were somewhat level with the sediment surface. Planting the second group made the water turbid, but I have a photo of the surface group taken about 40 minutes after the beginning of the experiment (right).