Kaylynne Marquez - Week Two

Hello!

Dr. Alan Shanks has been away since Friday, June 28th and will be gone until Thursday, July 11th. However, I have been photographing nearly every experience this past week and would like to share them with everyone. Enjoy!

Here I am counting the number of cyprids on Plate 1 at Bastendorff beach (Payton and I do this daily).

Plates 2 and 3 (at Bastendorff)

Some of the larger organisms caught in our light trap, collected daily, off of dock F

(Juvenile C.magister, amphipods and isopods).

This is my lab station, where I view the daily light trap catch under a dissecting scope and count everything on the list (a majority of what you see on the plate under the scope are C.magister megalopae).

 The students and interns have gathered for multiple bonfires, hikes and sunsets in our free time. The people here at OIMB are incredible.

  Happy Fourth of July! We had a bonfire on a tucked away cove at Bastendorff and enjoyed the firework show from afar.

The morning after the 4th of July celebration, a group of us jumped into my truck and headed back to Bastendorff to volunteer for the Surfrider Foundation beach cleanup. We filled a whole truck bed in just two hours!

In addition to checking Dr. Shanks field sites, we have been assisting the Shanks Lab graduate students with their field work. Marley Jarvis, a PhD candidate, is researching how nearshore fronts affect larval dispersal, migration and recruitment. Payton (above) and I (below) are counting cyprids at Marley's field sites at Norton's Gulch.

Payton and I (on top of the world!) before our descent to Marley's barnacle sites at Shore Acres.

On Sunday, a group of us drove out to Powers, OR for a hike.

Left to right: Zac, Christy, Will, Hannah and Payton on our hike to Elk Creek Falls & Big Tree Park.

Me & Payton

Today, I helped Marley drill new sites for algae plates.

Here is Marley mixing the epoxy.

After I drilled the sites, she smeared the epoxy onto the rock. Then, a base was pushed into the drilled hole, through the epoxy, for which we can screw in plates once the epoxy has dried.

Its rise and shine, bright and early tomorrow morning! Marley and I will head back out to the site at low tide to attach the algae plates and wait for it to settle! Pictures of the settling algae will be posted next week.

Natasha Christman: Phytoplankton Fun

Around the world, phytoplankton are the foundation of the marine food web. They can be bacteria, single-celled plants, or protists, each a phytoplankton based on its ability to photosynthesize, the capture of sunlight and derived energy production. Few are large enough to be seen by the naked eye and generally they drift freely in the sea, "wandering" as their Greek namesake "planktos" suggests. Altogether, the phytoplankton produce much of the dissolved oxygen present in the ocean waters and sequester a great deal of carbon dioxide as part of their photosynthesis.

Small sketches of some of the plankton observed in our collected samples. 

Natural levels of phytoplankton populations keep the ocean healthy and conducive to biodiversity. However, when pollutants and excess chemicals find their way into the water, the excess of nutrients prompt the phytoplankton populations to explode and to aggrandize primary productivity of the system. This process, known as eutrophication, alters the normal balance of the ecosystem. When the phytoplankton die, their decomposition depletes dissolved oxygen in the water. The surplus of phytoplankton decomposition against normal levels can result in hypoxia, where the lowered dissolved oxygen level negatively affects the aquatic ecosystem.

Earlier in the week we had again gone out for a research cruise in Bellingham Bay, an area experiencing seasonal hypoxia. We sampled nine different stations, getting an early insight to the seasonal hypoxia occurring in the bay,. In addition to water profiling, chlorophyll and nutrient samples, and turbidity measurements, we added several plankton tows to supplement the investigation of the phytoplanktons' relationship to these observed phenomena.

Raising the tow after plankton collection at a depth of 10 meters.

Now we are working on analyzing collected data and processing the samples collected on the cruises. Next week's research will include a larger sampling cruise that includes work on one of the coolest research tech pieces, the CTD.

Payton Hermanson- Week Two

As promised last week, this week's post will be about the life history of the Dungeness crab.

Retrieved from http://californiaoutdoors.files.wordpress.com

The crabs mate in the spring time, the males locating the females by scent prior to the females' molt. During the molt, in which the female sheds their hard outer shell or exoskeleton, the male places his sperm into pouches, called spermathecae, where they remain viable until the female extrudes her eggs, which are then fertilized. This storing process may take many months, with the female retaining the spermatophores until the fall of the same year. (In Oregon, eggs are extruded between October and March.) After extrusion, the female carries the fertilized eggs on the ventral, or underside, of her body for 60 to 120 days as the eggs develop.

Retrieved from http://www.sjsu.edu

The eggs hatch into a stage known as a prezoea, from which it quickly molts into a zoea. The zoea life stage consists of five larval forms and appears little like the adult crab. Zoeae are free swimming, adapted for life in the pelagic (open) ocean, where they spend several months among the plankton (small drifting plants and animals) before being swept inland once more. There, the zoeae molt into megalopae (singular, megalopa or megalops), which are adapted to find a place to settle, then molt into juvenile crabs. It is at the megalopal stage that we are finding the Dungeness crabs snared in the light trap.

Adult crabs reach sexual maturity between two and four years of age, and can live for eight to thirteen years. Adult crab lifespan is heavily determined by the fishing industry, with most males of catchable size (essentially all individuals with a carapace, or top shell, width of greater than 160 mm) being caught within the first two months of the fishing season opening. This presents a very unique opportunity for researchers such as Dr. Shanks to have a highly accurate measure of a specific population size.

Despite the intensive fishing, Dungeness crab populations have not been adversely affected by the fishing industry as other organisms have, with the Washington to California range of Dungeness crab maintaining a "Best Choice" for eating rating courtesy of the Seafood Watch program, which evaluates the sustainability and health of marketable species.

Information and images obtained from the December 1989 National Wildlife Research Center Dungeness crab species profile, the December 2007 Monterey Bay Aquarium Seafood Watch Report, and the published papers of Shanks et al.

Next week: Lab updates and field work!

Leeah: Week 2

This week we focused mostly on molecular work and did some plankton tows on the side. On Monday Terra showed me how to do DNA extractions with some of the larval samples that I had previously frozen the week before. For larval extractions and smaller tissue samples, Instagene is used. This substance is made of tiny beads that hold everything with the exception of the DNA samples. After going through a long process of heating and centrifuging, the beads collect on the bottom of the container and the DNA sample rises to the top where it can easily be removed by means of a pipet. After learning how to do a DNA extraction, Terra taught me how to run a PCR or polymerase chain reaction. This procedure finds a specific segment in the DNA, we use the 16S and CO1 segments, amplifies it and replicates it over and over. Finally I learned to run an agarose gel test. Because DNA is more negatively charged (due to its phosphate backbone I am guessing) it will migrate from a more negative side to a positive side when a current is run through it. After this we are able to put it in a gel imager and with the addition of UV light, we can see how well we extracted the DNA.

 The below image is the results of the Agarose test using the same samples each time. The "After" image was done better as the DNA shows up on all the bars.

Before: July 02--After: July 06

In addition to the intensive molecular work that I have been learning about, Terra and I have also had some time to take two plankton tows. Normally we go when there is a high tide as the waters are able to carry the net out and we just need to hold it. This week we went a little before the tide started coming in and we have gotten much better results. I was very excited on Tuesday to find my very first pilidium larvae in the tow. On Tuesday I had found three pilidia. I kept two of them and froze the third. On Wednesday I found more of them and I was able to freeze two. Terra found about 20 larvae which she categorized into four separate dishes and is now entrusting me to keep alive. Each day thereafter I have been taking pictures of a single more mature larva from these cultures and freezing it as a representative for the entire batch to show how they are growing.

Here are some of the larvae that were caught in our plankton tows this week:

1.  Pilidium larvae close to metamorphosis  2. Captured pilidium larvae (aka "Mr. Squiggles")
3. Pilidium Pyramidum ("Stumpy")  4. Pilidium Recurvatum

I have been very busy this week but I still have had some time to work on drawings. I chose a Red Lineid adult nemertean to draw this week. I did a few short gesture drawings of it coiling and moving. Terra and I then anesthetized it with 50% MgCl2 and 50% filtered sea water. I drew a more detailed ink drawing of the worm and took some close-up photographs of it with the camera attached to the dissecting microscope.

 Here are my sketches from this week:

Katlyn - Week 2 at Hatfield

This week at Hatfield, Ella and I continued to help Matt Yergey and Waldo Wakefield with their historical data cataloging. This data contains information on what was caught on the research vessel from 1977 to 1979. It includes the fish caught, what they were, and how long they were in millimeters. By entering this long-term data set into an online database we are able to preserve this historical data that at the moment is solely composed of handwritten notes. Also, once the data is properly stored in the database it can be compared statistically with current population data that Matt and Dr. Waldo have been collecting for the past couple years.

This week we were also able to get some time out of the office. We went to the lab with Matt to help identify, measure, and preserve some fish from part of last year's catch. The picture above shows one of the sample bags after it has been thawed. Below, a fish identified as a Slender Sole (Lyopsetta exilis) is being measured. After it is measured it will be patted dry, weighed, and preserved in formalin, which is a chemical derived from formaldehyde, that is used to preserve flesh.



The photo at the very top is of me helping a graduate student, Morgan Bancroft, with his project. He is studying live juvenile Dungeness crab and English Sole in artificially-made hypoxic environments in the lab. Ella and I were able to help Mo by feeding the juvenile crabs. It was so much fun because the hungry ones will take the food right off of the forceps. They are very cute, and it was nice to deal with some live animals after being in the lab with dead fish. Over all this week I learned a lot and was able to get some real research experience!

Anna Russell - Herbivores and Eelgrass

When we collected the isopods and snails to use as our herbivores in this study, I wasn't actually sure if they would eat the eelgrass. Diatoms (a type of phytoplankton) grow on eelgrass and both the isopods and the snails eat the diatoms off the eelgrass.If the micrograzers were just eating the diatoms, the phenolic acid levels would not change.  Last week, after the herbivores had been collected, I put the snails and isopods in separate containers holding only eelgrass that had been cleaned of all the diatoms. This way they would be forced to eat the eelgrass. However, I wasn't sure if they would eat the eelgrass or wait until they found their preferential food.
After the weekend had passed, I checked the containers to see if they had eaten any eelgrass. In the isopod container, the isopods had bitten the edges.

Isopod and damaged eelgrass

In the snail container, the snails had mowed the center of the eelgrass, turning it into lace.

Snails and damaged eelgrass 

These results were surprising to me because I did not think the snails would actually eat the eelgrass and that the isopods would cause more damage. Judging by these pictures and the other eelgrass strands, the snails were actually more effective in causing mechanical damage to the eelgrass than the isopods.
While these results were good, the snails and isopods have not been causing the same kinds of damage in the actual experiment. They were put in to the trial tanks on Wednesday. On Friday, the eelgrass was inspected for damage. While I could see a couple of snails and isopods on the plants, I couldn't observe any damage. I did not take the plants out of the tank and do a thorough examination so there could have been unseen damage. However, the trial tanks do have diatoms in them, so it is possible that the snails have gone back to eating diatoms. The tanks will be checked over the weekend and next week to see if damage has occurred.

Natalie Week 2 Down in the Mud at Hatfield

My second week at Hatfield Marine Science Center was extremely educational and exciting.  This week I went with Dr. Dumbauld to do field work in the upper intertidal zone across the estuary from Hatfield campus.  Our goal was to collect a different species of burrowing shrimp known as Neotrypaea gigas or “ghost shrimp” to use for genetic research and the study of how to tell this species from their relatives Neotrypaea californiensis. These samples were harder to get than the mud shrimp Upogebia puttegensis because these N. gigas shrimp are less densely populated. Because of this difference, we used a “slurp gun” (shown below)  instead of a big core device with sieve. This gun is placed over the mouths of burrows and then the center rod is pulled to create suction and suck the water (and hopefully shrimp) out of the burrow.  The burrows of this species are very convoluted which means there are a lot more places to hide.  This explains why after three hours we only ended up with eleven shrimp!

During the rest of this week  I also helped deconstruct a wet lab experiment that Katelyn Bosley had set up to monitor the effects of water temperature on shrimp metabolism and growth.  The many biotic—living—and abiotic—non-living—factors that affect the growth of burrowing shrimp make the sizes of same-aged shrimp extremely variable, which makes the alternate aging methods so important.  I also spent time in the lab measuring the carapace length for “recruits” of the other species of ghost shrimp Neotrypaea californiensis.  This data could be used to observe changes in the size of young populations over several years. A view of the Upogebia puttegensis burrows can be seen below.

Next week I hope to begin surveying the population of Upogebia puttegensis at several locations in the Yaquina Bay estuary to assess how the population may be fluctuating.  I also hope to begin collecting samples of both species of shrimp to see if the aging of the eye stalks is a viable technique.

Luc P. Frauens - Week One

This first week at the Hatfield Marine Science Center has been incredible. Being a surfer and a wildlife management student residing in Portland, OR, I’ve of course always dreamed of living on the coast so arrival day at HMSC was a truly surreal moment. Last month I graduated from Mt. Hood Community College with an Associates of Applied Science Degree in their Natural Resources Technologies Program as a Wildlife Technician. The next step in my educational career is to continue on and do the Fisheries & Wildlife program at Oregon State. Conveniently enough this internship will be my first official class at OSU! This summer I will be working as a student intern for Oregon Department of Fish & Wildlife on their shellfish project. My supervisors on the shellfish project are Dr. Steve Rumrill, Mitch Vance, and Justin Ainsworth. I will be aiding in the creative process of generating an extended survey questionnaire for shellfishers, as well as implementing the survey in the field. The extended survey’s purpose is to seek information and input from sport clammers and crabbers about their current harvesting practices and reasons why they first became interested in collecting clams and crabs in Oregon’s bays and estuaries. The information collected from the survey will be valuable for improving outreach activities, i.e shellfish clinics, youtube videos, and interpretive signage.

This first week has been a lot to digest. Already they have me conducting catch and effort surveys with shellfishers all over Yaquina Bay, Waldport, and Lincoln City. For being a relatively shy person I initially was nervous about approaching a complete stranger and interviewing them, but with a little motivation and encouragement I’ve realized conducting the interviews are nothing to lose sleep over. I am very much excited to continue learning new things everyday, which I think will be the case, and to observe the progress of the ODFW shellfish project over the next seven weeks!

Cris Rangel - Week 1 in the Emlet Lab at OIMB

Hello, my name is Cris Rangel and I go to school at Santa Barbara City College in California. I will transfer to UCSB in the Fall of 2014 and major in biochemistry. I have lived by the coast my entire life and have always been fascinated by sea life. I decided to apply to the PRIME internship program so that I could have a chance to do some field work and research to decide if that was the path I wanted to take. My interest in marine biology began when I was still in elementary school and did my very first tide pooling. I was in awe at all the life I saw and was able to interact with and my interest only grew when I moved to Hawaii in 2005, which was when I discovered that I would major in biology.

 

Didemnum vexillum

My internship is sponsored by the Centers for Ocean Sciences Education Excellence Pacific Partnerships (COSEE - PP) through Promoting Research Investigations in the Marine Environment (PRIME). This summer I will work with Dr. Richard Emlet on determining the settlement patterns and rates of various fouling species - organisms that attach themselves to a hard substrate underwater - in the inner and outer boat basins in Charleston, OR. While working in the Emlet Lab at the Oregon Institute of Marine Biology (OIMB) I will focus specifically on the invasive colonial tunicate Didemnum vexillum (D. vexillum). One of its common names is marine vomit, and as illustrated by its appearance it is easy to see why.

It is currently only found in two locations in Oregon, here in Charleston and at the mouth of the Umpqua river in an area known as The Triangle. It is important to study D. vexillum because it outcompetes other organisms in aquaculture farms and is rapid to spread in already settled locations. It is also a threat to native species where it settles and can smother other organisms in competition for suitable substrate. One proposition made by a group of scientists was to simply scrape the tunicate off of its substrate to remove it, but D. vexillum has the ability to resettle after fragmentation and scraping it would simply help to increase its spread. 

I have had a lot of time to work in the machine shop and create my own settlement plate frames, made from PVC, and have already been very involved with this project. To the right are the settlement plate frames complete with the plates themselves, which have been placed on the docks of the inner and outer basin 1m below the surface of the water. I have really enjoyed my time in the lab, shop, and being able to construct the very apparatuses that I will be working with for the next 7 weeks.

   

Anthopleura elegantissima

  

Sunset Bay State Park

Apart from my work as an intern, I have also had time to explore and see some beaches. The photo to the right was taken at Sunset Bay State Park, and the colonial   anemone to the left (found at Lighthouse beach) is the most abundant species found on the Pacific coast of America. I was able to see the fog rolling in as well as some really good tide pooling. My stay so far has been great and I cannot wait to see what the rest of my time here has to reveal and to read about the progress of all of the interns. Until next week, cheers!

Renee Renn - Week #1

Hello, my name is Renee and I have been attending Portland Community College (PCC).  In the fall, I am planning on transferring to Portland State University (PSU)  to purse a bachelor's degree in environmental engineering.  I decided to apply for the PRIME internship because I thought it would be a great opportunity to explore an aspect of marine science and to get a chance to research what direction I want to go with my education.  I know that I want to obtain a degree in environmental engineering, and I am interested in linking it to marine science but am still looking for my niche.  I have always been fascinated by the processes of the ocean, and I would love to pave a career were I focused on some facet of the marine sciences. 


This summer I am working at Oregon State University (OSU)  with Jim McManus and Brian Haley.  I will be studying the chemistry of marine sediments.  I have already been introduced to the lab that  I will be spending most of the summer in.  It is a clean room lab which means that we work very hard to not introduce germs from the outside into this lab.  It also means that I must change my shoes, wear a lab coat and a hat.

   
For the summer I will mainly be working in the lab.  Later on this summer I will have the opportunity to go to sea for ten days to collect core samples off the coast of Oregon.  (More to come on this later!)  After we return from sea, I will get the chance to process samples from the start to finish of the process.  Currently I am working on samples that have already been through some on the testing, and I am sort of jumping into a middle step.  Also, in the lab I will get to learn how to use a Multicollector Inductively Coupled Plasma Mass Spectrometer (MC-ICPMS), which is an instrument that measures isotopic ratios that are used in geochemistry, geochronology, and cosmochemistry.

This is a photo of the back side of the machine.  (More to come on this as well!)

So far this has been a great and enlightening experience.  There is a lot of amazing research and research teams here at OSU, and I certainly feel honored to be apart of this summer experience working along side some highly educated and passionate individuals. 

Ella Deck - WEEK ONE at Hatfield!

Hello, my name is Ella Deck and I have been working towards my associate of science degree at both Portland Community and Lane Community colleges. I plan to transfer to the University of Oregon’s general biology degree program in the fall. I applied for the COSEE internships because I believe that the study of marine sciences is critical to understanding the implications of a changing environment. I hope that the work I do this summer will further understanding of the intricate marine systems in place. 

I am working with fellow COSEE intern Katlyn Haven on Dr. Waldo Wakefield's characterization of soft sediment fish project. We are entering historical data from 1977-1979 on juvenile flatfish species of the central Oregon coast. The data has been used in multiple papers because it is so comprehensive, including information on multiple fish species. The two most common species collected in this data set were sole and sanddab species and were collected using a beam trawl. Current data being collected by Dr. Wakefield and others also includes flatfish species collected by beam trawl in a similar fashion. Because of this similarity of collection methods we will be able to compare the historical data to the recently collected data on the flatfish. Our job is to enter and decipher the notes from the historical data, learning a lot about the scientific names of the flatfish along the way.

One paper based off of this data collection examined the effects of hypoxia on the flatfish, a concerning event especially for these fish as they may have a slower reaction to hypoxic and therefore harmful waters. The recent data sets use a video camera to measure the reactivity of the flatfish. A chain is passed over the sand in which the fish hide and the fish are seen as they swim out of the way. These recordings of their responses are analyzed later back in the lab. Just as video cameras were not used in the '70s, there was not an easy way to measure the D.O. (dissolved oxygen level) so the data that we are entering does not include this level of detail. Instead, size and number of fish were recorded as well as location of collection, reflecting characterizations of the various populations at the time. 

I got  to spend the sunniest day so far this week outside collecting mud shrimp in Yaquina Bay mudflats for a different COSEE project “cross-training” (or honing my science skills in a new  way). There has been a lot of opportunity to network with the professors and graduate students here, and it is very exciting to be a part of the work being done at Hatfield!

Pictured: our new and very own office space and the famous Newport bridge.