Jess - Sometimes We Have To Adjust

To collect samples of zooplankton and phytoplankton from the surf-zone we use a pump that sucks water up from the surf through a hose. The zooplankton (animal plankton) is concentrated in a plankton-catch net and put in samples jars that are to be counted later. The phytoplankton (photosynthetic plankton) samples are collected by filling bottles with the water that we are sucking up with the pump and are then fixed with iodine. So we don't have to hold the hose out in the surf everyday when we are collecting the samples (which could be pretty risky and dangerous) we put a line of poles from the middle of the surf-zone to midway up the beach to secure the hose to with u-bolts and brackets. We did this the week of June 12th, and as you can see from the picture it took a number of people to do it successfully. Because the ocean is very powerful and constantly changing the physical structure of the beach and moving the sand, this last week two of our poles became dislodged.

We needed to get the poles back in as soon as possible and because it is difficult to get the poles in while getting pounded by waves we needed to do it at the lowest tide possible, which just so happened to be at dawn. We arrived on the beach before daylight and got to work. It was early and chilly but we got to see this amazing sunrise. The picture doesn't do it justice. Watching it rise in the company of a bunch of awesome people made me happy to wake up in the dark and start work at dawn.

Poles, pumps and sunrises

Drew - Mapping the Ghost and Mud shrimps

My progress in the stat program R is coming along and early in the week Katelyn and I were able put a few of my newfound skills to use. Admittedly, we were using a sequence of code that Katelyn had developed sometime in the past and we only had to update and modify a little to get the information we needed but I still felt good about what we did. The results we obtained are significant to the method of sampling and the number of samples that need to be taken throughout the shrimp area.

Katelyn is developing a way to sample the entire Idaho mudflat, which is in the Yaquina Bay, by coring the intertidal mudflat and counting the number of shrimp. Without going into too much detail (because I don't know enough) she has determined that 10 large cores throughout Idaho Flats calculated randomly by our cohort Lee, the computing/programing/wizard/technician, will give us a number of shrimp in the bay within 25% of the actual number. We also take other information from the samples like sex, weight, and carapace length but the main project that we are doing is the number of shrimp per core.

So the large core is very heavy (25lbs which is difficult to lug around all over a mudflat that you are constantly sinking into) and it is a fair amount of work to dig out the core and then sieve all of the sand to filter out the shrimp. The small core is more like a clam gun, very portable, no shovel needed and potentially able to collect a representative population of shrimp but this is science right? We can't just say that the small core would probably work and that a bunch of cores will do the trick. We need proof that it would work. So by comparing the core samples (large and small) from last week in R we were able to figure out whether or not they were collecting similar ratios of shrimp per area and determine how many numbers of small cores we need to take. Cool right?

After that I got to go do some more intern-like things. I cleaned out these tanks that Katelyn Bosley is standing next to because too much algae is bad for the shrimp. It turned out to be a breeze cleaning the tanks and now they are beautiful and clean.

So the next step in our efforts begins with having a map that shows the outlines of the shrimp populations. Now there are two species that we are talking about: Upogebia pugettensis (muds) and Neotrypaea californiensis (ghosts). The muds are filter feeders (or at least that is the hypothesis) and ghosts are deposition feeders. Muds live at a lower elevation in the intertidal zone and ghosts live higher with muds sometimes crossing into their territory. A map was created a couple of years ago using GPS to map the boundaries of the populations and this is very similar to what I am doing now. We then use quadrats to measure number of shrimp burrow holes per square meter which has been shown to correlate to number of shrimp per square meter. This gives us a map with population boundaries and density.

That R program I keep talking about, well it takes that map and those densities and calculates a weighted (we know the boundaries and the densities) random small core sampling that will tell us the number of shrimp in the bay! (with some uncertainty)

Another team of interns were out in the mud doing some sampling of their own. They are working with the parasites of the shrimp and boy do they look excited.

While I was on the return leg of some mapping this week I was standing close to a Blue Heron and watched it stalk and then catch a fish! This is the action shot of the bird's head in the water about to show its new fish.

It was a pretty exciting week and next week Lee will be back in town and Katelyn and I can get a random sampling grid to start collecting some shrimp.

Jess - Plankton and the Surf-Zone

Most of my friends call me Jess but my full name is Jessica Noseff. Coming from the small town of Silverton, Oregon and being unsure of the exact career I want to pursue, I decided to take the cheaper route of attending a community college before investing a large amount of money in a University. I got accepted into a Scholars program at Chemeketa Community College in Salem, Oregon where I was introduced to an intriguing variety of people and also where I got to know an inspiring biology teacher that would encourage me to apply for the PRIME internship. When the opportunity for me to apply came up I had just found out that my boss would be moving across the state in May and I would be out of a job, so I didn't hesitate.

I've always been fascinated by the ocean and the beautiful creatures in it, but standing on the sandy beach, sometimes up to my knees in the water, I have always only admired it from a distance with a cautious respect. As far as learning about it, my knowledge extends to what I've seen on Planet Earth and other shows of the sort and not very much further. My human curiosity was a large instigator of my applying for this internship as well as my desire to experience something I have never gotten the chance to experience before.

Funded by the National Science Foundation, I am working under Dr. Alan Shanks from the University of Oregon with collaboration from a team of oceanographers from the Naval Post-graduate school, as well as Dr. Steven Morgan from UC Davis, on a three year grant studying how larval invertebrates are affected by ocean currents. We are spending the first month of my internship doing field work in Carmel Bay, which has a rocky shore and is considered to be a reflective beach. Using a kayak, we collect samples of zooplankton and phytoplankton from offshore waters and we use a hose and pump to collect plankton samples from the surf-zone. After preserving the samples, we count and differentiate the individuals and species in order to compare them to last year's samples collected from a dispersive beach, which has more water exchange within the surf-zone. Once we return to OIMB, we will be spending our time in the lab counting the samples. The third year of the grant (next year) will be dedicated to analyzing the data and publishing the results.

Drew - Ghost Shrimp, Mud Shrimp, and Isopods, Oh my!

My name is Drew Hill and I am an intern with the COSEE PRIME program at Hatfield Marine Science Center. My biology professor at Portland Community College told me of this opportunity to study marine biology and I knew that this would be a great chance to experience the scientific method and be a part of a science oriented community. I have been here just one week and I am glad to say that this going to be a great summer.

I am working with Dr. Brett Dumbauld (associated with U.S. Department of Agriculture and Oregon State University) and Katelyn Bosley Ph.D. student, on their investigation of burrowing shrimp in Yaquina Bay, Newport, Oregon. This first week has been a blur of touring the facilities (which are many), introductions to the dry labs, wet labs, offices, safety features, field locations (watch out muddy conditions in the future!), and I got to meet the shrimp.

A brief explanation of why shrimp are our focus is that they smother oysters with sediment when they burrow and churn up the mud. Oyster farmers have been spraying an insecticide on the mudflats where these shrimp grow during low tide to reduce the their population and protect the oysters. The problems associated with the use of carbaryl in a marine setting have not been fully studied but I bet there are some undesired effects on the ecosystem (more on this later). So what I understand so far is that an isopod parasite of the shrimp species can reduce the fertility of the shrimp. Maybe in conjunction with other pest management techniques, these parasites could reduce the shrimp population enough to bar the need for carbaryl. Either way, my role this summer is to help Katelyn figure out how many shrimp are in the Yaquina Bay area by taking sediment core samples. Using a statistical program called R, we will calculate a random sampling of the mud flats that should represent the larger shrimp population.

Moving on to next week, the tides are going to be perfect for taking core samples of the sediments and defining the edges of the shrimp habitats to be sampled before the 4th of July weekend. I am also focusing on learning the statistical program called R. From what I hear this is a cutting edge program that will serve me in future investigations but it is similar to C-prompt programs and needless to say, I am a bit nervous about developing a functional understanding of R.

I will leave you with one of the specimens that I worked with on Friday and watch out! These shrimp know how to use those claws. Enjoy the week.

Coty Spies on Costal Birdies Week #1

Hey yall! My name is Coty Krebs. I am an intern through the COSEE/PRIME program for the summer of 2011 here at the Hatfield Marine Science Center. I am a student at Linn-Benton Community College and Oregon State University majoring in Biology and minoring in Chemistry with an option in Pharmacy Science. My long term goal as a student is to become a well rounded scientist and a professional in the growing future of global healthcare. More specifically, I hope to work in the research field looking for new medicinal compounds from many marine and terrestrial lifeforms that will serve as alternative cures/treatments for diseases.

I chose this internship because I wanted to gain more experience working as a field biologist and to expand my knowledge of marine science. I am interning at the U.S. Fish and Wildlife office at Hatfield. Over the duration of this summer I will be involved in several different studies, which I will report about on a weekly/biweekly basis.
The study that I am currently working on is researching how the fireworks during the Fourth of July festivies disturb/effect a colony of birds residing on a rock in Depoe Bay, OR. For a period of one week prior to one week after July 3rd and 4th a masters student and I will be surveying the colony from two different vantage points while collecting data. We will be observing the birds behavior and nesting habits on a daily basis. Some of the data that we are collecting includes nest conditions, nest contents, total number of the nests, total number of birds and the bird's reaction to distrubances. To assist our obsevations we have taken pictures of the colony from the two different ground vantage points and from above in an aircraft. We then analyze the photos and give each visible nest an ID #. From these photos we can then orient ourselves with the colony and make more accurate observations. Next week there will be more techinques of data collection used, but until then this is all that I am doing.

So far I have really enjoyed my experience, both working as an intern with the U.S. Fish and wildlife office and amongst the other interns living in the housing here. Everybody here seems to be very friendly and determined to positivley influnece the progression of research here in the facilities.

Karyn - Week 1 at OIMB, Fantastic!

Hey everybody! I've been reading your posts and I think that we all have awesome research projects we get to be a part of this summer! My name is Karyn and I am a COSEE PRIME intern at the Oregon Institute of Marine Biology (OIMB) campus in Charleston, OR. I have been a student at Portland Community College for the past couple of years and hopefully I will be co-admitting with Portland State University in the Fall. I plan on becoming a medical doctor and eventually I want to be a part of research and development and help improve modern medicine. This internship really appealed to my desire to experience research. Also, I have always been intrigued by the vast diversity of marine life and so I'm excited to learn more about marine science this summer.

My project this summer will be investigating wound healing in invertebrate larvae. I'm working with George von Dassow (Senior Research Associate for OIMB, University of Oregon). My project will basically involve me shooting at some cells on sand dollar larvae (called echinopluteus) with a laser creating a wound, and then following the larvae over a couple of weeks to investigate how the cells around the wound react to heal the wound. I'm really excited about this project and find the regenerative abilities of echinoderms quite fascinating!

In the beginning of the week we went out on the boat and dredged for sand dollars. This was my first time ever on a boat like this out on the ocean, so I was excited but a little nervous. I was asked if I get sea sick, but since I had never gone out on a boat I didn't know. Well the day we went out it was particularly rough, and I learned in the worst possible way that yes I do get sea sick. So rest assured the next time we go out on a boat I will take something for sea sickness before I step on the boat! However, I did have a good time on the boat before I got sick, and hopefully I'll get to experience the trip again when it's less rough out.

The rest of the week was spent simply getting acquainted with the equipment and also watching the development of the sand dollar (Dendraster excentricus) from fertilized egg to larva stage. I actually got to watch cell division right before my eyes as I watched through the microscope. It was really fun to watch. Nature is awesome! I have also learned to take pictures of the specimens under the microscope using a special microscope camera. This will be very helpful when following the wounded larvae over time and is a good way to document the activity of the cells around the wound.

Here is one of our sand dollars. George actually described this one as one of the largest sand dollar he's ever seen. I had never seen a live sand dollar before so this was a trip! I still get mesmerized by all the tiny little spines all across the the sand dollar's body. They can really move those spines fast! Now that we got a ton of sand dollars from the ocean, we can use these sand dollars to spawn eggs and sperm so we can fertilize the eggs and use the larvae that grow from them. Each morning we inject a sand dollar with potassium chloride which causes its gonads to spit out all its eggs if it's a female or sperm if it's a male. We collect the sperm or eggs in a beaker and work with them from there. We have to do this every morning because the eggs are only good for about 12 hours. What I think is really interesting is that we can't tell the difference between a male or a female by just looking at the sand dollar. We have to inject it with the potassium chloride and then find out if it spits out eggs or sperm to find out the sex of the sand dollar!

Akiko: Invertebrate settlers project

My name is Akiko Onuma, and I am lucky enough to be one of the COSEE Pacific Partnership PRIME interns. About a week ago, I wrapped up my finals and projects at Portland Community College and moved out here to the Oregon Institute of Marine Biology in Charleston, Oregon. It’s my fourth day here and so far I’ve had a pretty awesome time!

On my first day of the program, I met with my mentor, Dr. Richard Emlet, to get an idea of the purpose of my project. He told me about the many different invertebrates living in the two boat basins in Charleston. A few of them include colonial invertebrates, where hundreds of tiny individual organisms make up a larger colony. The organisms that I will be studying are called fouling species, meaning that they attach themselves to hard surfaces underwater. Most of them look like slime growing on rocks or boat hulls, which is how they got their name "fouling organisms". My project will be to make a photographic timeline/identification key that will look at a variety of these marine invertebrates from when they are very small to when they are much bigger. Most of these organisms go through a larval period, meaning that they start off as a microscopic swimmer floating through the water. Soon, they find a hard surface and settle down on it, undergoing metamorphoses in order to attach themselves to the substrate. Then, they start to “grow” by asexual reproduction, which basically means making more of yourself in order to start a colony. It is the colony that is visible to the naked eye, and identifiable. So my job is to take pictures of these species from the time when they first settle (attach themselves to the surface of my petri dishes) until they are big enough to be identified.





This is the harbor where I will be deploying my petri dishes to collect settling invertebrates.




Harbors and marinas are often hotbeds for introduced and invasive species because boats will pick up and distribute these hitch-hiking species wherever they dock, much like the marks left by a child playing with a jar of glitter. One particularly important introduced species is called Didemnum vexillum. This colonial organism, which looks like pale orange slime growing on the rocks, is an invasive species. Scientists believe that this organism originally came from Japan, but it is showing up in docks all over the world. Didemnum has documented presence in Japan, New Zealand, France, Ireland, California, New Hampshire, and now recently has started settling in Oregon. Furthermore, once introduced, Diademnum grows rapidly and can cover large areas in a short period of time, out competing other native species for space and resources.



Diademnum is an introduced species to the Charleston inner boat basin, and has only been here for a couple of years.

Sam - Reflection on my experience

The flats teem with living organisms that interact with one another and collectively serve our ecosystem. In a somewhat different way, scientists such as the ones at Hatfield are pooling their expertise from an extensive range of fields to examine the what and the how of things aquatic. I enjoyed living, working and playing with members of such a vibrant, dynamic community.

It was great to get a behind the scenes tour of the Oregon Coast Aquarium. After the tour, I had the chance to watch the sea otters (Enhydra lutris) during feeding time.

Though I still tend to feel a bit anxious when I'm up to my shins in mud, I believe the worry will lessen over time with practice. I'm glad I've had this opportunity to work on the Oregon Coast, meet lots of interesting people, and hone skills I hope to use in the future. While at Oregon State, I want to learn more about estuarine habitats.

Laury - My final post

This summer has been an incredible experience and one I will remember later on in life. I am still in awe with how much I have accomplished in the last 8 weeks! The first few weeks seemed long as I was becoming adjusted to lab and field work, but the last 6 weeks have flown by. I started out primarily doing field work so we could collect the samples I would later process in lab. The last two weeks I spent all of my time in lab calculating out the energetic content of the individual species so it would be ready to present at our presentation at the end. I would highly recommend this internship to anyone who is interested in marine sciences. Not only will you be surrounded by people who are just as passionate about marine science as you are, but they will guide you and help you grow as a future scientist.

Sam - Gaper Clam Burrowing Rates and Reburial Capabilities

I measured the changes in each clam's burrow depth for 1-2 weeks. The data suggests that there is a moderately negative association between shell length and average burrowing rate. In other words, the larger clams tended to dig slower than the smaller clams, but there was no evidence of a cause-effect relationship.

 After softening the mud, we collected and tagged more clams to use in our final experiment I divided the clams into 3 size classes based on their shell length and let them acclimate overnight. The next morning, I placed 29 clams in the buckets and let them go at it for 24 hours before photoing them and giving them a score from 1 (no evidence of burrowing) to 5 (shell completely below surface). The results show that the largest class had a wide range of scores, and nearly all of the smallest class rated 5, but a cracked one only got a 2. It was clearly unable to stand up and squirt water below its foot, and died a few days later. The fragility of the young clams' shells may be one reason ODFW wants us to keep them if we catch them.

Laury - Smooth Bay Shrimp (Lissocrangon stylirostris)

After a month of sampling and “bombing” my samples I learned how to input all of the data collected into excel so we could calculate out the energetic content in joules. A joule is a measurement of heat, as are calories. Because smooth bay shrimp (Lissocrangon stylirostris) were so easy to catch in our samplings we had a lot of data collected on them. We were finding three categories of smooth bay shrimp, we would find ones that were brooding (had eggs), some that had been parasitized, and what I inaccurately called “regular” meaning they were neither brooding nor parasitized. From the beginning we separated out all the shrimp we caught from seining into the three categories and I bombed them accordingly. I started to notice some trends once I had calculated out their energetic content. The brooding shrimp had a higher caloric value than the other two shrimp categories. This was not a surprise because eggs naturally have more energy, and supply more nutrition. However what I found interesting was that the shrimp with parasites seemed to have the same caloric content (aka energetic content) as the shrimp that were deemed regular. Why this was so surprising to me was because the shrimp that had parasites were around the same large size as the shrimp that were brooding. The regular shrimp were small in size so that might have had an effect of their caloric content as well. So I started to research the relationship between the parasite (Argeia pugettensis) and it’s host the smooth bay shrimp. What I had discovered by reading some science journals that Jose (my mentor) had recommended to me was that there wasn’t a lot known about the shrimp and the relationship between the parasites.

Jose had asked me earlier if there was anything I wanted to research independently, well I had found my topic. How are the parasites effecting the shrimp? Because I have been working so much with the Bomb Calorimeter I formed my question to ask: “Are the shrimp effecting the caloric content of the shrimp?” I hypothesized that if I were to remove the parasites from the shrimp I would find that the shrimp would have a lower caloric content.

Dr. Jessica Miller, Jose and I came up with an experiment design on how I would go about asking this question. We decided to have a total of 30 shrimp that I would bomb, and collect 15 from each of our two sampling locations. So 15 shrimp from Alsea Bay and 15 Shrimp from Coos Bay. Within the 15 I would collect from each site I would have 5 brooding shrimp, 5 parasitized shrimp, and 5 “regular” shrimp. So that’s what we did! I removed all of the eggs and parasites off the shrimp so I would put them back to their “regular” state.

(This is what the shrimp infected with parasites look like, the one on the very right had a parasite missing, I think it may have fallen off when we caught the shrimp). The parasite live on the gills under the shrimp just under the exoskeletons.

(This is what the parasite looks like after being removed from the shrimp).

(this shrimp is around 5.5cm long, the point of this picture is to show just how big the parasites are compared to the size of the shimp).

After entering and graphing the data, I found that parasites do not seem to effect the caloric content of the shrimp. This isn’t the result I expected, but it was still a surprising discovery!

Laury - Surf Zone Sampling!

Hello fellow bloggers! As promised I am going to talk to you a little bit about how we collect all of our samples. The primary focus of these outdoor adventures is to catch salmon out in the surf, but we also want to collect the prey that salmon eat. How do I know what salmon eat? Well Jose (my mentor) has been doing this study for 5 years now, and part of what he does when he catches salmon is conduct a stomach analysis. Basically he looks at all of the stomachs of the salmon that’s been caught and identifies what they’ve been eating. So far the main prey species seem to be mysids, amphipods, megalopae and other juvenile fish, or their fish larvae.

How do we sample? Well there are a couple different ways that we collect our samples. First is the “seining method” which is a 15 meter long mesh net. Three people carry the net from the shore to the surf and then once we reach a deep enough spot the middle person stakes the middle pole into the ground and the other two people with poles stretch out the net to form a “V” shape. Once we know the net is not tangled up we drag the net across the sea floor and back to shore. We are literally scooping up all of the inhabitants of the surf in the net and bringing them back to shore.

Once the net is dragged up on shore, we extend out the net and collect everything that we’ve caught. We count everything we found and record that in a little handy dandy notebook, and everything is returned back to the water with the exception of salmon or shrimp, or other species of prey that the salmon eat for “bombing” later. Some of the cool things we have found by doing this are: starry flounders, staghorn sculpins (grumpy little guys), English sole, pike fish (look similar to a seahorses), gooseberries, jellyfish, and lots of smooth bay shrimp! Of course when we find salmon they are the real trophy prizes.

In this picture above are some of the CSC crew members (highschool kids working their summer jobs at The Natural Resource Crew of Community Service Consortium located in Newport, Oregon), and Jose who is at the very right of the photo. In this picture they are dragging back a tow to shore, we do about 6 tows per sampling day.

This picture above shows Jose preparing the sledge or commonly known as a “sled”. The sled works by having two very fine mesh nets that catches all of the smaller invertebrates that salmon eat. We carry out the sled into the surf, and lower it to wear it’s just surface deep, and drag it around a total of 400 meters, and all of the prey get scooped up into the net and end up in the codends at the end of the net. A couple of times we’ve accidently caught an English sculpin in the net, and an anchovy. We released the sculpin and kept the anchovy to bomb since they are also prey for the salmon.

This is a picture of a juvenile Chinook salmon that we caught while we were seining out in Alsea Bay. So far we have around 90 salmon that we’ve caught in the last 8 weeks.

Dave - Ulva bioassay using oyster larvae

Having determined that the Ulva was capable of affecting the pH, I moved on to using the three sources of water to do a bioassay with oyster larvae.  I took four 10 liter samples each from the three tank system, the large tank system and from the incoming filtered HMSC water. I stocked each 10 liter sample with 50,000 larvae. I did periodic water changes, using water from the corresponding sources, and feed each sample with a calculated amount of micro algae. After 6 days I sieved the larvae out and restocked the samples with 10,000 larvae each to remove any excess dead to avoid fouling the water. After 10 days I again sieved the larvae out of the samples. I used a 60 micrometre sieve and put each sample into 800 ml of water, from that I took three 20 ml from each 800 ml sample.  I then took photos, did counts and took measurements form each 20 ml sample.






In the samples taken from the filtered HMSC water, 48% of those found survived, and of those alive the average length was 116 micrometers across.











In the Three Tank System, 57% of those found survived, and of those alive the average length was 120 micrometres across.


There doesn't appear to be a significant difference between the filtered HMSC water and the Three tank system treatments. But...





In the Large Tank System, 83% of those found survived, and of those alive the average length was 150 micrometres across. This is a significant difference between the filtered HMSC water and the large tank system.

This bioassay is the conclusion to my research. it shows that there is a potential for Ulva to be used as a biofilter to improve the health and survival of oyster larvae.
~David L. Hubert

Dave - Large tank system

This is the large tank system.

This tank was storing the Ulva but was not getting a desirable growth rate. The basic setup is a round tank that is 4 feet tall and 10 feet across, with an inverted lawn sprinkler suspended above the tank to keep the Ulva from drying out. The drain is on the bottom of the tank and enables the water level to be adjusted by raising or lowering the exit point. This is where I would take my samples to test.

When I took over this tank the water depth was about 7 inches, the single sprinkler was reaching about half of the surface of the water, there was a ring with light aeration around the edge of the tank, and the bottom was filled with various types of debris intended to be an anchor for the Ulva to grow on.

 






The first thing I did was raise the water level to about 16 inches, I removed all of the debris and I increased the amount of aeration. This resulted in an increase in the growth but still not what we were looking for.




The next set of adjustments I made was to raise the water level to about 23 inches. I tripled the water flow, added a second sprinkler resulting in full coverage of the surface of the water. I removed all of the aeration from the tank, creating a calmer surface allowing the Ulva to spread, and I placed a small submersible pump into the tank to create some movement under the water. This combination seemed to do the trick and resulted in approximately 95% coverage within a few days.

~David L. Hubert