Natalie Week 6 Fish Cutting and More

I cannot believe there are only two weeks left of my internship at Hatfield. This week I was given the wonderful opportunity to help with the NOAA's "fish-cutting party".  This is a three-day event where volunteers learn how to dissect juvenile salmon and collect data for many different projects.  All of the salmon from this session were caught in either the Columbia River or in curface ocean trawls in the Pacific near the mouth of the Columbia. There were four different types of salmon species including Coho, Chinook, Sockeye, and Chum.  From each fish the volunteers would collect some or all of the following parts: stomach, intestines with pyloric cecae, tail fin clip, otoliths (fish ear bones), anterior and posterior kidneys, and copper tags that were implanted in the fish noses. We also checked the body cavity and air bladders for nematodes and other worm-like parasites. The hardest part for me was dissecting out the otoliths, which are tiny little bones located on either sides of the spine posterior to the eyes.  The otoliths sit in fluid-filled sacs and help the fish balance and orient itself.  These bones can be used for aging and studying the condition of the water at different stages in the fish's life. Some of the stomachs I dissected had very interesting prey items still inside of them, including other small fish and even squid heads.  The stomachs, intestines, and kidneys will be used by Dr. Kym Jacobson to check for parasites and the stomach contents will also be used to conduct a dietary study for the juvenile salmon. The pieces of fin were taken for genetics studies and each dissected part was labeled with the fish ID number so the results could be correlated with the weight, length, and type of fish it came from, along with where the fish was collected. I was very excited to be a part of this process and it was very impressive seeing how efficiently everyone worked together to accomplish this goal.

This week I also looked at some of the slides I prepared from the lateral teeth of the gastric mills of mud and ghost shrimp (Neotrypaea californiensis shown below).  I was not able to find any ring-like structures or evidence of annual growth patterns so I did some further research and discovered that age rings were found in the ossicles of the gastric mills of larger crustaceans.  Ossicles hard structures (less hard than the lateral teeth) that make up the walls of the gastric mill and hold the lateral and median teeth (pictured above in a petri dish and then embedded in resin) in place.  I dissected some of these ossicles out of my remaining mud shrimp and discovered that there were some ring-like structures in a section of the pyloric ossicle that I polished.  I spent the rest of the week mounting a camera on a compound scope and photographing these images.  I hope to take some measurements and mount more slides with this same part from other shrimp to see how the ring number relates to the size of the shrimp. Overall it was a very promising discovery and I hope to learn more in the next couple of weeks!

Natasha Christman: The Phytoplankton Census

With such a great, fundamental role in the biological structure of the ocean, plankton are always sought to be understood. While they account for less than 1% of the Earth's plant biomass, phytoplankton are responsible for over 50% of the world's plant primary production and 95% of the ocean's primary production. Consequently, when monitoring water quality and investigating hypoxia along the way, knowing the quantity of phytoplankton present is important to get a better understanding of the delicate biological and chemical relationships found underneath the surface. But phytoplankton are microscopic, and unfortunately they are not capable of performing a reliable population census themselves. There can be an enormous number of individuals in one drop of water. So how do we measure the concentrations of plankton present?

Various phytoplankton in a water sample from our research station
near Eliza Island. 

The answer begins with a simple component of all plant life- the photosynthetic pigment chlorophyll a. Chlorophyll a is the primary pigment of photosynthesis, and it absorbs blue wavelengths of light while emitting (fluorescing) red light. Using this property to our advantage, we can filter a sample of water at a fixed volume and isolate the cell particles on a filter pad in the field. The filter is then dropped into a tube of 10ml of 90% acetone, and this solvent extracts the chlorophyll pigment from the cells with minimum alteration of pigment. After a bit more preparation back at the lab, this samples can be put through a device called a fluorometer. The fluorometer measures the chlorophyll pigments by hitting the acetone and extracted pigments with a beam of blue light. By measuring the amount of red light fluoresced back, the concentration of phytoplankton can be measured by its proportional relationship to emitted light.

The fluorometer in the chemistry lab, complete with
cat stickers (and no, they were already there).

When calculated, this data is a valuable contribution to the overall picture of the bay we are constructing. Comparisons of concentrations across transects can be made and crossed with other data collected, like the water column profiles, to further illuminate the research.

A graph of the chlorophyll concentrations at each station
visited on an early summer cruise.

Analyzing chlorophyll pigments on the fluorometer is a valuable tool and major contributor to our research this summer. It makes efficient a task that would be overwhelming, if not impossible on an accurate scale. Additionally, these measurements over time can describe the cycles of the plankton over generations and how these patterns coincide with other aspects of water quality.

Renee Renn: Week 7: Quadurpole Mass Spectrometer

This week I continued working in the lab, and learned how to use a different lab instrument called the quadrupole mass spectrometer.

Image from the internet

  The quadrupole mass spectrometer is one type of mass analyzer used in mass spectrometry.  It consists of four cylindrical rods, set parallel to each other.  In a quadrupole mass spectrometer the quadrupole is the component of the instrument responsible for filtering sample ions, based on their mass to charge ratio.  Ions are separated in a quadrupole based on the stability of their trajectories in the oscillating electric fields that are applied to the rods.

image from the internet

 Two opposite rods have an applied potential of (U+Vcos(wt)) and the other two rods have a potential of -(U+Vcos(wt)), where U is a dc voltage and Vcos(wt) is an ac voltage. The applied voltages affect the trajectory of ions traveling down the flight path centered between the four rods. For given dc and ac voltages, only ions of a certain mass-to-charge ratio pass through the quadrupole filter and all other ions are thrown out of their original path. A mass spectrum is obtained by monitoring the ions passing through the quadrupole filter as the voltages on the rods are varied.

Last week, I leached sediments samples from all four of the collection sites in the Pacific Ocean.  The four sites are at 200 m, 500 m, 1200 m and 3000 m.  I did an acetic acid leach, and a hydroxylamine leach.  All of this work resulted in a total of 72 samples that needed to be analyzed on the quadrupole.   Because of the sensitivity of the instrument, we did a dilution on the samples.  Another important thing that happens is preparing standards to run through the machine along with the samples.   The fundamental purpose of the rods is to translate the number of ions striking the rods into an electrical signal that can be measured and related to the number of atoms of that element in the sample via the use of the calibration standards.  Since this has been an ongoing project, there were standards available to use that also needed to be diluted that would be used to get usable data for Rare Earth Elements (REE).  The REE are the lanthanide row on the periodic table, and the primary focus of interest for testing. 

The machine ran for a little over four hours, and when it was finally done it left a rather large table of numbers.  I then took the data for the quadrupole program, and pasted it into an excel spread sheet.  I am coming up on my last week of my internship, and I will be spending the rest of the time moving the data around, finding out what the numbers mean, and creating graphs using excel. 

I am fascinated by the various lab instruments.  It is quite an amazing thing to spray a bit of sample through this machine, and come out on the other end with a chart of numbers that define exactly what was in each vial.  I feel lucky to have this opportunity to learn how to use this equipment, and also to know what each number represents.   

Ella- week 6- fish cutting parties, beam trawls and more!

The weeks have been going by so quickly, that it is surprising and a little alarming to be looking at presenting our projects in two short weeks. We have started thinking about those presentations by reflecting on the Hawaii interns’s presentations.

A big highlight of this week was helping out with NOAA'S fish cutting party, as mentioned earlier in last week's blog. Never having gutted a fish, I went through a big learning curve with the Chinook, Coho and Steelhead, and now can cleanly and efficiently dissect juvenile salmon.

A juvenile salmon waiting
to be dissected

Mardi Gras beads were given out to those who discovered parasites in the body cavity or swim bladders of the fish as a prize to keep things lively at the party. We took out and labeled separately, the stomachs, intestines, and posterior and anterior kidneys (the latter of which house the trematodes from last week’s blog). A tail clipping was taken for genetics testings. The most exciting and hardest part was extracting the otoliths, or ear bones. The otolith are tiny little bones buried just under the brain of the fish, and a certain amount of technique is needed to locate them. The otoliths are used to roughly age the fish, as a ring is added to the little plate of bone every day that the fish has been in saline water. Scientists then use this information  to determine the exact day that the went out to sea, similar to growth rings on a tree.

The F/V Miss Yvonne

Another big highlight was being able to help out with July’s data collection with Waldo’s beam trawl. We chartered a shrimping vessel, The F/V Miss Yvonne, and headed out to sea, mostly sampling along the Newport hydrographic line which which runs directly perpendicular to Yaquina head. This was such an exciting opportunity, as the sampling that Waldo does currently reflects the methods that were used in collecting the similar data from the 1970’s, which Katlyn and I are now working on entering. In fact one of the main objectives of entering our data set is to be able to make comparisons between the two data sets on juvenile flatfishes. It was wonderful to be able to see how the beam trawls work, and how information was recorded, as both Katlyn and I are now so familiar with the type of information that went along with each cruise.  Our methods were as follows: at each station, we would record the latitude and longitude and the wheel count on our beam trawl. As the beam trawl was drug behind the boat, a counter on the wheel kept track of the meters we covered, an effective way of knowing the exact ground distance covered.

Putting the beam trawl in the water.

Measuring larger fish so that they can be
released if they are greater than 150 mm. 

We caught many other exciting things besides our juvenile flatfish that we were after. We only kept fish that were under 150 mm in length, and tossed the rest of it back. Most hauls saw many shrimp, while Dungeness crab, sea nettles and sea stars frequently came up as well. Following are pictures of some of the neat organisms we encountered:

The contents of our last beam trawl of the day:
many flatfish and one beautiful sunflower star.  

A juvenile squid

Sea Nettle

Egg cases of some sort

Warty poacher displaying mating colors,
along with many juvenile Dungeness crab

Sea brittle

Big skate egg case. We could feel life inside!
They usually hold 4-5 embryos. 

Although this is not the best
quality photo, this was a really cool
 looking nudibranch, otherwise known as
a sea slug. To the right and barely
 visible is a clear ctenophore . 

Scallop

Staghorn sculpin. The horns hold poison!

We sorted the very small flattish from the krill using forceps, a task that could have made us very sea sick, but that was actually very easy to do, thanks to the flawlessly calm water that day. 

Katlyn, on left, sorting fish. 

Making friends. This one was big enough to be
tossed back after being measured

Counting Eelgrass

Although I did not get the chance to blog about it in my post last week, I was able to volunteer for a NOAA mitigation project, counting eelgrass beds in a newly created mudflat in Yaquina bay. The project came about because of a new dock that NOAA has built in the bay which has disturbed vital eelgrass habitat. In order to mitigate this impact, part of the bank was dug out to create a level surface, and eelgrass was transplanted from where the edge of the bay used to be in this new area which now floods with the high tide and harbors many different species of marine life.The objective of the morning was to investigate how well the compensatory eelgrass was growing.We used small square made of pvc to measure the number of eelgrass plants in our squares at regular intervals. It was great to be a part if the counting effort, as it offered an excellent opportunity to reflect on how science is done. There were obviously obstacles that we encountered such as a rising tide, which interfered with our methods when it came earlier than expected.

Cris - Weeks 5 and 6: Surprise Settlement, Sabotage, and a (single) Gooseneck

  

Unidentified mass covering mooring 7

On week 4 I set out a seventh mooring with 4 settlement plates between sites 4 and 5 (seen here), which I then collected on week 5. There was a significant difference in the settling of species across sites 4 and 5, the latter having a large number of barnacles. This additional site is also where the basin is split into the inner and outer portions, and collecting data would give a better idea of the distribution of fouling species across the basin. When I brought my plates up for inspection under the microscope, the seventh site had very different settlement. I was unable to identify what covered most of the plates (shown above), a white globular mass with no visible structures. They were very delicate and would burst when I rinsed the plate using a wash bottle to remove the detritus. The next time I set out mooring 7 I will leave it out for two weeks so that I may see the unknown mass at a later point in development. 

Gooseneck barnacle

Unfortunately, during week 4 my mooring at site 3 was taken out of the water and left on the dock for at least 6 hours. I found it on the dock wrapped up in its support rope after being notified by a fellow intern. Although the settlement remained relatively close to the observed pattern of previous weeks for that site, the ascidian Botryllous schlosseri was phenotypically different than what I had seen before. It was in a more immature state than what I have been seeing every week. This may be due to stress the animal incurred while being face down on the cement and out of the water. On the plus side, I found the only gooseneck barnacle (above) that I have seen on any of my plates throughout the basin. It was very active and had a peduncle (the "gooseneck") that was about half the length of its body. 

Distaplia occidentalis

By far the most abundant organism I have seen these past two weeks has been the colonial ascidian Distaplia occidentalis (right). It is also very abundant as an adult on the sides of the docks throughout all sites, but it has had especially high settlement at my second mooring in the inner basin. On a single plate I found over 90 individual zooids, and some with their tails still attached from their larval stage. It is very easy to see the pharyngeal basket and the cilia within it using just a dissecting scope and fiber optic lighting. 

The coast north of Blacklock Point

On the weekend I had some free time and was able to go to Shore Acres State Park with two other interns while they did some field work with their settlement plates.  It was a very nice day and I was able to explore the park and see the botanical gardens. I also spent some time at Blacklock Point, a few miles south of Bandon. The views were spectacular and there were many trails to choose from, leading down to the beach, through the forest, or along the cliff. Until next week, cheers!

Shore Acres State Park

Anna Russell- Trial and Error

I mentioned last week that we were going to inoculate the eelgrass with Labyrinthula spp. on Monday. This was to test the resistance of herbivore-damaged eelgrass to eelgrass wasting disease, caused by Labyrinthula spp. On Monday, I pipetted Labyrinthula cells onto autoclaved 2-cm pieces of eelgrass. I also pipetted sterile sea water onto autoclaved 2-cm pieces of eelgrass as negative controls. After letting them rest for three hours (to give the Labyrinthula time to infect), I used a plastic clip to attach the autoclaved, infected eelgrass to one of the healthy blades of eelgrass. This was a little tricky because I had to use sterile technique, which means I had to attach the clip with tweezers. After awhile, I got the hang of it and it went pretty fast. Then, we just had to wait for the eelgrass to get infected. I had expected to see signs of infection by the next day but when I checked the eelgrass on Tuesday, it showed no signs of infection. On Wednesday, one looked infected. On Thursday, a couple more showed black spots. By Friday, twelve plates looked infected so I took the plastic clips and autoclaved eelgrass off.

However, twelve out of seventy-two is a very low percentage. The lack of infection could be for many different reasons. When a disease like Labyrinthula is cultured in a lab, it becomes less pathogenic over time. The two strains I used have been cultured for many years so it is possible they are not very infective anymore. Another possible reason is that the Labyrinthula didn't stick to the autoclaved eelgrass so when I attached the autoclaved eelgrass to the healthy piece, there wasn't any Labyrinthula to infect the plant. The last reason is that perhaps the eelgrass is extremely healthy. It isn't stressed by dessication or tidal fluctuation. Labyrinthula is an opportunistic infection so if the eelgrass hasn't been weakened, perhaps the Labyrinthula can't infect.

An eelgrass piece that shows no sign of infection

The black spots could be Labyrinthula but it is not large enough to tell for sure

An eelgrass blade clipped to the autoclaved piece of eelgrass

Luc - Week Six

This being the final week to collect my social/demographic shellfisher information marks a significant landmark in my time here at Hatfield Marine Science Center. Due to having a relatively small number of boat interviews I have recently been targeting boaters at locations like Sawyers Landing and the Marina docks in Yaquina Bay, along with the Port of Alsea Bay down in Waldport. Luckily, my high demand for boat interviews comes at an excellent time as peak crab season is just getting into full swing around here. But unfortunately it is a little disappointing how my window of time to gather shellfisher data ends right as the crabbing is picking up. This makes me feel like I’m only getting a small taste for how large the crabbing population around here truly is. During my stay here I have become rather accustomed to low amounts of crabbers, but this last week has blown all previous assumptions. For instance, yesterday was an all depth halibut day which brought hoards of offshore fishermen to the coast. Yet almost every boat was also pursuing crab as a secondary catch by basically throwing pots while they weren’t hooking fish. There were honestly so many boaters here in town that someone actually used the Hatfield housing parking lot to park their trailer over night. Goodness gracious! This next leg of my research will primarily consist of using Microsoft Access to analyze the data. Some initial summary questions I’d like to have answered: are what percentage of crabbers and clammers harvest from Alsea Bay, Yaquina Bay, and Siletz Bay? and what is the average group size? ect. Once I’ve answered those questions and other similar ones I imagine more in depth questions will become apparent. Spending time indoors versus talking with fishermen of course is not as thrilling but I can already tell I am going to learn a lot about Microsoft Access from simply spending the time sitting down with it and working out whatever problems arise.

-Lazy Sunday in Pacific City.

Leeah: Week 5

 Quest for the Giant Ma

This week was a low tide series and we focused on collecting adult worms to put in the ever-shrinking area of our sea tables. Terra came back on Tuesday and the first place we visited was the mudflat next to the High Tide Café restaurant.

Panoramic view of the High Tide mudflat

 I was hoping that we would be able to find a Micura sp. “giant ma” worm (part of the species complex that we are studying). So far in the sea tables we have a fragment of one but not the entire worm itself. Despite our efforts we were unable to find this kind of nemertean, however; we did bring back a very rare find. I managed to dig up a Carinoma sp. "yellowback", a Paleonemertean. It is very different than the ones I am used to finding as it is not as fragile and is fairly large.

Here is a  photograph of the Carinoma. Dr. Maslakova told me that they do not last long in captivity so we provided it with sand for comfort.

Carinoma sp. "yellowback"

 During this week we also visited our usual collecting location, Portside mudflat, where we collected more Micura alaskensis and some fragments of Carinoma.

 Another exciting part of this week occurred in the plankton tows. Due to the fact that I lost the cod end to one of our nets last week, I had to use the finer mesh net in our lab. While this net does the job, it collects far more diatoms than needed which turns the task of sorting plankton into a visual nightmare. Still I managed to find two pilidium recurvatum, our sock-like friends, One of which had not fully developed as Dr. Maslakova pointed out to me.


On our final day of collection week, Terra, Dr. Maslakova and I went to a mudflat in Glasgow; this is a little community right outside of North Bend, Oregon, to look for two particular species of hoplonemerteans. Pantinonemertes californiensis is a species of nemertean that is semi-terrestrial and that lives in rocky intertidal zones under rocks. Immature adults will appear a grey color but as they reach sexual maturity, their gametes will show through their body walls. Females will be a rich pink color and the males are a very pale white. Dr. Maslakova had us searching for several “ripe” worms of this type. We were also looking for a red and green species called Ramphogordius sanguineus. This kind of nemertean has amazing regenerative properties and is one of the few ribbon worms that can grow its head back.

I also managed to find a worm that we could not identify in Glasgow. At first we thought it was an odd color morph of one of the worms that we were looking for. Upon inspection under the dissecting microscope we found that its head was a different shape than that of a Pantinonemertes. Next week we will be removing its head to look at its stylets. A stylet is a hard pointed structure that arms the proboscis of hoplonemerteans. It is used to stab prey and inject toxins into the prey. We will also be fixing a tissue sample in order to send it for DNA sequencing which will tell us if we have found a new species of nemertean.

Here is a picture of the hoplonemertean we will be dissecting next week:

And here are my sketches for this week:

Katlyn: Week 6- Crazy Adventures with Fish and Boats!

A Sea Nettle jelly at the Oregon Coast Aquarium

Mammal food preparation station

This last weekend I had to opportunity to go on a backstage tour of the Oregon Coast Aquarium with Natalie, Luc, Waldo, and Waldo's wife, Clare. It was so exciting to see what happens behind the scenes at the aquarium and what goes into making the exhibits possible. We were able to see where they raise

Top view of the "Deep Sea" exhibit

Strawberry anemones and barnacles on exhibit 

some of the jellys that they have on exhibit including Moon jellys and Sea Nettles. We also got to see the huge walk-in freezer where they store all the food for the animals (except filter feeders) on exhibit. After that we saw where the food is prepared for the mammals at the aquarium. It was interesting to see how complicated the feeding regimen for these animals is. We continued our tour by seeing the top view of the "Deep Sea" exhibit. This area was where the divers go into the tanks to do any necessary cleaning or feeding. Being able to see what the tanks looked like from above was a neat experience because before this tour I had only seen the exhibit by walking through the tunnel that visitors use. The final stop on our tour was the area where the mammals are taken when they are not on exhibit. The facility had many toys in this area so the animals are challenged daily and do not get bored, and it seemed like a nice place where they could get away from the visitors. When our tour was over, we were able to stay in the aquarium and look around at the exhibits. This was also a lot of fun because I always like going through the aquarium.

A sea otter on exhibit

This aquarium visit was only the beginning of a very exciting week. Another experience that made this last week so great was the "fish cutting party". This is where people from Hatfield get together to dissect juvenile salmon and save specific pieces of the body for different research projects. Each fish had a specific list of body parts that needed to be kept for research. Some needed the stomach, fin clip, intestines, kidney, and otoliths (bones in the inner ear), while others only needed two or three of these. The fish cutting lasted for three days, and I participated in two of those days. I am glad I got this opportunity because it allowed me to see the different parts of the fish and learn what goes into some of the research projects at Hatfield.

Fish being dissected at the "fish cutting party"

The final adventure this week was going out on a boat with Waldo, Ella, and Mo. We went out on the Miss

The beam trawl in the water

Yvonne, which is a commercial fishing boat. The weather was very calm and the boat had a much smoother ride than the Elakha, so I had a much better trip than the last time. This trip was also a lot of fun because we were collecting bottom-dwelling fish with a beam trawl. This made for a great trip because we were able to see numerous amounts of different marine life. We saw some sea stars including the sunflower star and brittle star. We also saw crabs, nudibranchs, juvenile squid, shrimp, krill, and many different types of fish. We through back everything except juvenile flatfish and other fish that were under 150 mm SL (standard length, from the tip of the nose to the base of the tail). This was an excellent experience because Ella and I were able to see what went into retrieving all the data

One of the catches complete with sunflower star and
numerous flatfish

that is in the binders that we are entering into the database. The data is no longer just names and numbers on a page; it is now connected to a real animal that we have seen with our own eyes. 

 

Bobtail squid

Me holding a large dungeness crab