Coty's Reflection

This summer internship opportunity through the COSEE pacific partnerships/PRIME program was an amazing experience. I lived at the Hatfield Marine Science Center in Newport, Oregon. I felt that I was treated with respect and taken care of by the program coordinators Itchung Cheung and Coral Gehrke.

During my time at Hatfield, I worked with the U.S. Fish and Wild Life Service for eight weeks helping wild life and refuge biologists conduct seabird surveys. My mentor Shawn Stephensen was an excellent person to work under. He always made sure that I was well equipt to conduct our surveys and that I was safe. I could also tell that he really cared about me learning proper data collection techniques. During my internship with USFWS I was was fourtunate enough to participate in several different surveys where I learned how to use different fieldwork skill sets.

My stay at the Hatfield student housing was a very plesant one. I felt comfortable in the appartment provided to me. The roomates I had were awesome and fun to live with. As the eight weeks of my internship passed on, I made several close friends that lived there in the housing. I admired how they all were very passionate about marine biology and excited about their internships. I was very sad to leave them when my 8 weeks was up.

Thank you for COSEE Pacific Partnerships, PRIME and USFWS for the amazing experience!

Coty's Final Weeks

Hey Everybody! Sorry that its been such a long time since my last post. In the last few weeks of my internship, I was involved with two more Seabird surveys with the USFWS. First we conducted a Coastline Cormorant Survey and second we did an Island Strom Petrel Survey.

The coastline cormorant survey took two days to conduct. The objective of the survey was to count Comorant nests along a stretch of shorline from Deopoe Bay to Yaquina Bay. The first day was a on-foot patrol of the Yaquina head location.

The second day My metnor and I took a boat form Depoe Bay to Yaquina Bay while slowly surveying the shorline with binochulars for cormorant nests. In past years there have been close to 1000 Comorant nests in this stretch of shoreline, but this year we observed that manyof the spots where there once were hundreds of nests, are now completely vacant :(

The Island Storm Petrel Survey took place off the Southern

Oregon Coast. There were four islands that we were interested in surveying, but we could only get on to one of them due to bad weather and strong tides. There were two objectives of this survey, 1. To obtain data that would later help generate am estimate of the petrels population size and 2. To gather samples of any invertebrates/ vertebrates that exixt on the island. The Petrels on these islands build their nests in burrows, so in order to obtain data about the population we "grubbed". Grubbing is the action of carefully slipping your arm down into the burrows and feeling around with your finger tips for burrow content. To conduct the survey we used a 100 meter transect along the hillside of the island, and took a 1m X 1m quadrat sample at every 10 meter mark along the transect.We found there was an average of 8-12 burrows per quadrat sample and nearly all of the burrows had either eggs or chicks in it! We had to wear snowshoes while we were on the island because we didnt want to step into the burrows with our feet and possilby disturb the petrels nesting within.

Reflection

This experience is one that I would strongly encourage other community college students to participate in. Throughout the summer I have been given the opportunity to work in a diverse environment that has allowed me to learn about a wide variety of topics within the umbrella of marine science. Even if you are unsure if research is something you would be interested in pursuing, this internship is an excellent way to test the waters and learn more about what other opportunities may be out there and may be more suited to your particular interests. This will become just one step of many that will lead to my ultimate education and career goals and it is an excellent starting point to have. I have gained many helpful skills, made contacts with both the advisors in the lab and the other interns from all across the country, and been introduced to the other opportunities that I can pursue after this. Throughout the course of this summer I have faced challenges and obstacles, experienced great successes, learned a lot, and have enjoyed myself while doing it, as well anyone else who also participates in this program.

Thank you everyone at COSEE for this wonderful opportunity!

Final Post- Wrapping It All Up

After having completed all four research cruises in Bellingham Bay, I have been able to create various maps to track the bottom dissolved oxygen concentrations in the bay as well as look at the side view of the transects we performed to identify where the hypoxic layer was located. These maps showed that the hypoxic water layer was much more mobile than we initially thought it to be. Going into this project, I had assumed that the hypoxic area we found would be located at the bottom of the bay and would remain there from week to week. Instead, it traveled up and down the water column and was never in a consistent site. This indicates that tides and currents may be another factor to consider when looking at the hypoxic zone of water in Bellingham Bay.

This graph of the bottom water dissolved oxygen concentrations in Bellingham Bay is from the first week of testing. This was the week when the hypoxia was the most severe and extensive. After creating this map, I used it to calculate the volume of the hypoxic zone so I could find a comparable value. I calculated that the hypoxic zone had a total volume of 3.6 billion cubic meters, which is roughly equivalent to the volume of 35 Metrodomes (the Minnesota Viking football stadium). This value will be useful to have in the future to compare the sizes of hypoxic zones to examine trends as to whether the hypoxia is becoming more extensive.

I also worked on comparing Hood Canal to Bellingham Bay from July 2007 to February 2011 to see if there were any correlations between the two hypoxic systems. There were not any
significant correlations between the two bodies of water; however, they did follow some of the same annual trends and patterns. One of the most interesting similarities that was noted between the two bodies of water was a salt water wedge that came over a sill, which is a feature that both of the systems have. As deep marine water that has a high salinity, low temperature, and high density is pushed over the sill, it forces the hypoxic water at the bottom to move upwards in the water column. As the water is pushed up, it can move into more shallow areas, where fish may become trapped in the hypoxia and cause a fish kill. This process is shown in the figure.

Overall, the research that I have worked on this summer has helped identify some of the patterns that hypoxia in Bellingham Bay follows. However, it also raised many more questions about causes and influences, duration, location, and behaviors of hypoxia in the bay that require additional research.

I would like to thank my advisor Dr. Apple for taking me in this summer for this research project. I have enjoyed my time here and appreciate all of the help and guidance you have provided throughout the summer. Hopefully I will get the opportunity to continue this research with you in the future!

Akiko- Final Post

My goodness, I can't believe that the weeks passed by so quickly.

Before I came here, I knew that I wanted to work in the ocean, but I wasn't sure whether research was my thing. The only exposure that I'd had to research was in my science classes. I didn't think that I would enjoy microscopy very much, since I had generally found microscopy in my science labs to be rather boring. My viewpoint definitely changed as soon as I started my project. Looking at a prepared slide of dead organisms is not nearly as cool as looking at living organisms. I was constantly impressed with the abundance and the variety of life to be found on my little petri dishes. I was more dedicated and invested in my project than I expected to be, because it was *my* project-- no one was telling me what to do or what to look at.

I have had such a wonderful time here at the Oregon Institute of Marine Biology. I'm sad that the summer is over, but honestly thankful and happy to have had such a great opportunity to do research in marine science. I would highly recommend the COSEE PRIME program to any budding marine scientist.

Akiko- Week 8: Almost done

Hey all, Akiko here.

In the eighth week, my adviser asked me to stay at OIMB for one extra week, in order to polish up the website. I happily agreed, so I'll be here for a total of nine weeks. The website definitely needs a good deal of work so I am happy to put in more hours on it. Though to be honest, photo processing is exhausting work!

Most of this week was spent preparing for final presentations, which took place on Friday. I spent most of Tuesday reviewing notes on good ways to structure presentations. I gave a few practice presentations to my friends and felt ready to present on Friday. The presentations took place in a classroom at the Oregon Institute of Marine Biology. Unfortunately the Hatfield Marine Science Center interns did not come down to Charleston for the day, but we did get the chance to see their presentations via Skype.

During my presentation, I spoke briefly about my future plans for the website (akiko-invertebrates.weebly.com), which I made to house the identification key which is my summer project. With my extra time at OIMB, I hope to label the basic anatomy of the juvenile settlers, and post a few photos of what each settler looks like as an adult colony. The website needs a lot of editing, and I have received many helpful comments about how to improve it. I hope that I have enough time to apply them all!




This is me looking through the dissecting microscope, which I used for the bulk of my work. Every day, for four weeks or so, I looked through this microscope to take pictures of the settling organisms.








A friend of mine took this photo of me and some ascidians. The large orange blobs are Distaplia occidentalis colonies, growing on a piece of netting that has been submerged for several months.

Winkler Method vs YSI meter

Week 4 Blog
Lance Brockie

My agenda for this week was focused solely on my research pertaining to Smugglers Slough. One of my main concerns was that I was getting out of the ordinary results or findings when comparing the two testing methods (YSI vs. Winkler Method). When expressing my concerns to Dr. Apple he advised me to set up an experiment to compare the two methods using 100 percent saturated water to see if they come up with the same dissolved oxygen reading. After completing the experiment I found that there was no significant difference between the two testing methods.
Upon finding that there were no flaws in my testing methods, Dr. Apple suggested that I standardize the sodium thiosulfate I’ve been using to get as approximate N-value (Normality). After completing the standardization of the sodium thiosulfate I discovered that I had been working with the wrong N-value this whole time. This was a big relief to me as now I knew why my results have been so out of the ordinary.
This week I learned that there are a lot of factors you need to take into consideration when using the Winkler Method. One being that you should insure that the reagents that you’re using are not too old. I discovered that during my study old reagents are capable of affecting your results during the titration process. Another thing that I discovered was that when calculating the milliliters of titration (ml of titration) that was used to get the milligrams per liter (mg/L D.O.) dissolved oxygen, you need to insure that you’re using the proper N-value. I discovered that if you use the wrong N-value your results will be inaccurate. Now that I have obtained this information, I now feel a lot more comfortable and confident about utilizing the Winkler Method.

Week 3 Blog
Lance Brockie


This week was a little different from the activities that I’ve been involved with so far involving this internship. On Tuesday, we participated on a working cruise aboard the R/V Centennial, which is a research vessel based out of Friday Harbor Labs. The purpose of this cruise was to conduct depth profiles utilizing the Conductivity, Temperature, Depth Sensor (CTD), as well as to collect water samples at various depths which would be used to measure the chlorophyll and dissolved oxygen levels back at the Shannon Point Marine Center Lab.

Each intern who participated was assigned a specific task to perform aboard the vessel. Another student (Mike Murphy) and I were assigned with lowering the CTD into the water as well as bringing the CTD back aboard once it made its descent to the bottom and back to the surface (see picture). Once the CTD was back aboard, I was then tasked with collecting water samples from designated niskin bottles which are located on the CTD. Once the BOD bottles were filled I then added the Winkler reagents (Manganous chloride, and Alkaline iodide) to each sample and stored them to be analyzed later at the Shannon Point lab using the Winkler Method.

This was a great learning experience not only for me but I would have to say all the other interns as well. Once learning about the CTD and visually seeing what this instrument measures in the water column (see figure below), I now have a greater understanding of what is going on at various depths of the ocean. I consider myself very lucky that I got the opportunity to learn how this piece of equipment operates and was able to work with it firsthand. I would have to say that this week has been the highpoint of this internship thus far, and I’m certainly looking forward to the next time we get to participate on another cruise.

Blog 3- Bellingham Bay Research

The cruises in Bellingham Bay have been the main focus for my research on hypoxia. So far we have gone on three research trips in the bay in order to collect a large amount of data with the CTD. For these cruises, we perform a transect of ten stations from north to south and eight stations from east to west, as well as CTD casts at eight historic sites in the bay. Water samples are also collected at the surface of each site for chlorophyll a analysis and from deep water at selected sites for dissolved oxygen and nutrient analysis.

Our first cruise was rather long because we had to figure out where exactly to send down the CTD, then create a rhythm in our data collection to make everything go as smoothly as possible. At the fifth station we sent the CTD down at, we found hypoxic conditions in the deep water. From there, we found many other sites also showed evidence of hypoxia in the deep water. All of this was in support of what we believed we would see due to the trends that had been found in the past. First I drew graphs of the data by hand to allow myself to visualize the hypoxic area. Then I made contour plots using a computer program called Surfer, which I will be using to make graphs for the data I collected at later dates as well. Graphing the data in Surfer will allow me to look more accurately at the hypoxic areas in Bellingham Bay and potentially find the volume of the hypoxic water mass.

After finding hypoxic levels on the first cruise, I fully anticipated seeing either the same results or intensified hypoxia on the following two cruises. However, this was not the case at all. The two figures below are the graphs for the concentrations of oxygen for the second research cruise. There was a small hypoxic area higher in the water column, but the concentrations for this cruise fell higher in the 2-4 mg/L range than the hypoxic areas the week prior. Based on all of the wind and mixing that had taken place, we hypothesized that the hypoxic area we had found at the bottom dispersed as a result of the mixing. The most recent cruise we went on, I expected the hypoxic area to return as a result of layers becoming stratified once more. Instead, the water column had the same general trend as the week before and did not have a significant hypoxic area.

These results are quite surprising and it will be interesting to see what we find on our final research trip later this week. I will soon begin analyzing and visualizing my data to calculate the volume of the initial hypoxic area that was found in the first week.

Akiko- Week 6 & 7: Crunch time!

Hey Everyone, Akiko here.

The weeks have flown by! I have been hard at work. During the sixth week, I finally stopped taking daily photos of the settlers. It's fun to do work under the microscope, but hard when you're doing it every day! I compiled all of the photos I took (over 2,000!) and began sorting through them in order to find the highest quality ones for each species. Once I had chosen the nicest photographs, I began the long process of modifying them with Adobe Photoshop. Since I am new to both microscopy and photography, most of the pictures that I took were blurry, too dark, too bright or off-colored. Additionally, many of the organisms that I photographed are translucent, making them even harder to see on a picture. With Adobe Photoshop, I can adjust the photo to make the image clearer and more representative of the actual organism.

In addition to image quality modifications, I can also use Photoshop to create composites of multiple images. This is a very useful way to deal with the limitations of microscopy. With microscopes, the focal plane-- that is, how much of the object is in focus-- is very thin. This means that at any one time, only some parts of the 3D organism will be in focus. In any one picture, only a portion of the organism will be in focus and the rest of the organism will be blurry, as shown below. However, with Photoshop, I can slice out the parts from each picture that are in focus, and combine them together to make a composite image in which most of the organism appears to be in focus.

Here, the base of the organism is in focus.










Here, the top part of the organism is in focus.








This picture is a composite that I have made using Photoshop, by combining the two above images.






Photo processing takes a good deal of time to do, and I spent many hours going through the photos in order to get them cleaned up and presentable. In addition to that, I also began to learn how to make a website on using the "Weebly" website creation page. Thankfully, the interface on the Weebly page is very user-friendly. I am still ironing out the finer points of the web page but so far it is looking good! It is still under construction, but is viewable at: akiko-invertebrates.weebly.com .

Outreach Work

It has been a while since I last updated all of you, and I have quite a bit to catch up on. I have been working hard on collecting my data, both during cruises in Bellingham Bay and the San Juan Channel, as well as spending time on the weekends doing outreach with SPMC. In order to cover as much as possible, I will focus each of my upcoming blogs on a separate aspect of my work these past few weeks. This outreach has been a way for everyone here to help raise awareness in the community about what it is we are working on at SPMC and about the environment that is right in their own backyard.

The last two Saturdays I have helped bring a touch tank from Shannon Point to the Kids Are Best Fest and Bivalve Bash. I worked with some of the other interns and graduate students to share some of the local intertidal organisms with the people of the area. This was a chance for me to work on allowing people to work on answering their own questions and inquiring further about the animals in the area when interacting with them at the tanks. It was hard at first not to immediately answer the question and end the interaction, but after a bit of practice I was able to have a dialogue with the people who were visiting the touch tanks.

Each festival had an entirely different target group who was visiting. At Kids Are Best Fest, we were mainly sharing the animals with, you guessed it, kids. Parents were often interested in the organisms as well, and helped their children work up the courage to touch some of the more unusual looking animals. One of the favorite animals of all the kids was the leather star we had (pictured below), mainly because of its size and color. It was great to see all the kids get the wide-eyed look of astonishment as I would pull the huge star out of the water and let them all feel it. One of the most common questions asked was whether or not the sea stars were alive or dead or if they were fake. Without the typical head with the eyes and mouth that most children expect to see on an animal, the sea stars and many of the other organisms we had in the tanks helped them learn more about the variation in the animals on this planet.

At Bivalve Bash, we had a much wider audience of people who came to check out the animals. Most commonly, it was adults who were visiting, but they often just wanted to look at and discuss the animals rather than touch them. The kids who came by, though, were more than eager to get a chance to feel some of the organisms. Working with more adults was a chance for me to really work at helping challenge them to puzzle their way through figuring out what the animal was by using what prior knowledge they had. Although it was often tempting to simply rattle of the common name and a few random facts about the animals, having them answer their own questions allowed them to learn more and helped create a conversation about the organisms in our coastal waters.

It was wonderful to be able to help the people who have lived here most of their lives learn more about the animals that live in the environment around them. Some of them had no idea about what sort of animals live in the tide pools around them and were pleasantly surprised to learn about the interesting creatures living right in their own backyard.

Akiko- Week 5: Visitors

Hey all, Akiko here again.

In the fifth week of the internship, all of the OIMB interns in Charleston and the Hatfield Marine Science Center interns from Newport got the chance to come together and show off our projects. The COSEE PRIME program makes a huge effort to support communication and collaboration among scientists, which is such a great initiative. Having spent many hours in the lab, I can see how a researcher could become so involved in their work that they don't get the chance to see what other scientists are doing in similar fields. However, collaboration is so important, because the results that you get under a microscope could heavily influence the work of another researcher doing a similar project.

On Wednesday, Coty and Drew came down to Charleston with their adviser Itchung. I showed them all my project and let them watch the little ascidians pump water into themselves. Every once in a while, the organisms will contract their branchial baskets and close their siphons as if they are coughing or exhaling. From what I've read, this is to keep large particles from entering their incurrent siphons. This reaction is touch-sensitive, so sometimes I will tickle the ascidian with a single hair (that's how small and sensitive they are) and watch them contract. Later on that afternoon, we all went out with Professor Jan Hodder to see some marine mammal action at Cape Arago. Seals and sea lions sunbathed on the rocks, and a few gray whales broke the surface every few minutes.

On Thursday, Karyn, Jess, and I with our adviser, Coral, went up to Newport to visit with the interns there and see their projects. This was the first day in over 3 weeks that I took a full day off and didn't look at my petri dishes! It was nice to have a little break and it gave me time to reflect on my project progression and to write in my research notebook. We got to stomp around in the mud with Drew, and visit Coty's bird-watching location. It was a nice trip, but good to come back home!

Playing around in the mud was fun. I got to use a huge siphon to suck shrimp out of the mud. We saw ghost shrimp and mud shrimp.












We had a blast at Cape Arago looking out at the marine mammals.

Drew - The Tide is in...

Monday of this past week allowed for just enough low tide to finish the GPS work needed to generate a population density map of both species of shrimp in Yaquina Bay. However, the data has to be differentially corrected using the NAD 83 UTM 10 North GPS information system and that requires waiting at least 24 hours. By Tuesday I was knee deep in ARCGis and related computer software trying to generate an inverse distance weighted interpolation of our data. That was my last chance to work on the map because on Wednesday, all the COSEE interns took off at 8am to visit Charelston, OR.

We went to visit the Oregon Institute of Marine Biology (OIMB) and to meet the other COSEE PRIME interns (who were all awesome). In the photo to the right is Akiko showing an experiment in progress in the boat harbor. We toured their facilities, asked lots of questions (about the interns research and graduate school), and enjoyed all-you-can-eat dining hall meals. Thank you OIMB for a great visit!

The following day the COSEE interns came to Hatfield. Here we all are listening to Brett

introduce our project. No one got stuck in the mud...but it was a close call :)

This next week my focus will be on writing up a draft paper, completing that population density map that I keep talking about, and towards the end of the week the tide will finally be low enough to warrant a day of field work, collecting some of our last samples for this project.

Introduction to Bellingham Bay and Smugglers Slough Study

Lance Brockie
Blog #2
7/16/2011

This week of this internship I participated on a couple of projects, the first project being the Bellingham Bay Hypoxia Study with Dr. Apple where we measured dissolved oxygen levels in the bay as well as levels of chlorophyll and nutrient levels. Being that this is my second summer participating in this study I’m excited to see what’s going on in Bellingham Bay this summer compared to last summer. This year we are implementing depth profiles where we could measure the quality of the water from the bottom of the water all the way to the surface. As the summer progresses I’m excited to find out and see what’s going on with the water throughout the bay.
I also began collecting water samples at various locations along Smugglers Slough, which is a body of water that is located on the Lummi Indian Reservation. With these samples I will be measuring the levels of dissolved oxygen at various locations throughout the slough. My main focus throughout this study will be to try to determine if the oxygen levels in this particular slough are healthy or high enough to sustain juvenile salmon populations. This past year the Lummi Tribe reconnected the Smugglers Slough with the Nooksack River in hopes that by doing so juvenile salmon will utilize this particular body of water on the Lummi Reservation.
For the Smugglers Slough study I will be utilizing the YSI-556 meter to collect dissolved oxygen levels as well as temperature, conductivity, and pH levels. Also I will be measuring the dissolved oxygen levels utilizing the Winkler Testing Method to try to determine which is more accurate when testing for levels of dissolved oxygen. I must say that I am very excited and am looking forward to continuing with these studies in the weeks to come as I am learning more and more about water quality every day.

Akiko- Week 4: Photos of settlers

Hey All, Akiko here.


My goodness the weeks are passing by so quickly! During the fourth week, I watched my six new plates get colonized by a variety of settlers. The plates are fouling quickly, which is good because it means that a lot of organisms are settling down on it, but is also difficult because algae and particles have clouded the petri dish and make it hard to clearly see the organism in photos.
I decided to make a little side-experiment out of the redeployment. I actually deployed 12 plates with velcro on the sides instead of underneath. Of the 12 plates, six of them have abrasion on the top side (I scrubbed them with sandpaper to make the surface rough) while six of them are simply smooth plastic. I did this because supposedly settlers prefer to settle on roughened surfaces, and I figured that I could keep track of the rate of settlement on the clear plates versus the smooth plates. I'll count the number of settlers on each plates at some future time during the experiment and see whether the settlers really prefer rough over smooth.


For my main experiment, every day is the same procedure: get the petri dishes out of the water, look at each of them under the dissecting microscope, take photos of specific organisms, and keep track of new species that arrive on my plate. It sounds easy, but the entire process takes about 3-4 hours, and I do it every day (even the weekends). I am trying hard to be a good scientist, even if it means sacrificing my days off. On the bright side, once I start looking at the plates I'm often so absorbed in observing the changes that go on from day to day that the time goes by faster than it would otherwise.


Here are some of the new organisms that have collected on my plates. I haven't had time to adjust the images or put in scale bars, but suffice to say that they are really tiny!


This is probably Schizoporella japonica, a bryozoan. Bryozoans are little animals that settle onto surfaces and reproduce asexually to form larger colonies. This kind of bryozoan is an encrusting bryozoan, meaning that it will continue to spread over the surface in a hard thin layer, like dried paint. When this bryozoan gets bigger, it will begin to reproduce assexually to form a colony.







The spiral shell in this photo belongs to what I believe is a serpulid polychaete worm. You can see little feeding structures sticking out of the mouth of the shell. That is the worm. With these guys, I have to wait for them to peek out of their shells before photographing them.