After several months of looking forward to it, I just finished my first week of the Oregon Sea Grant Summer Scholars Program!
The Hatfield Marine Science Center is primarily a research center for Oregon State University, but there are also several other buildings on the campus with various agencies. One of these buildings belongs to the EPA Office of Research and Development, and this is where I’m interning this summer.
Working for the EPA is an interesting mix of science and regulation. Since the EPA is primarily a regulatory agency, this research facility is not the standard EPA workplace. Even so, a lot of federal regulations carry over. All new employees are required to complete an extensive online training, which took two of my days this week. There are also in-person safety trainings, work meetings, and paperwork. After that, I spent my time reading research articles and getting caught up on some of the background knowledge related to my project. It was a slower start than I was expecting, but I enjoyed having time to educate myself about the topic before jumping into research. In addition, the researchers have been extremely friendly and welcoming, and it is exciting to see the many labs, research boats, and scientific equipment.
I was also able to see some of my first sights of the Oregon coast this week, including South Beach, Nye Beach, and Yaquina Head. In Bellingham, WA, where I go to school, the beaches are almost all rocky, so it is a treat to get to enjoy long sandy beaches! I’m so excited to have a whole summer to enjoy here, and my list of places to visit grows every day.
At the end of the day on Friday, my mentor, Cheryl Brown, returned from travelling for a conference and we were able to start planning out research plans for the summer. We have an exciting and complicated project sampling water quality in Tillamook Bay and rivers that enter into this bay. We will be taking samples from the streams and the bay itself to try and get a better idea of how humans and agriculture may be contributing to ocean acidification in the bay. Stay tuned for more updates throughout the summer!
It has only been a week and I am already falling in love with Oregon. I am so grateful to be one of the Oregon Sea Grant Summer Scholars for 2018 and spend my summer in Newport. The project I am working with is in the Oregon Department of Fish and Wildlife (ODFW) Marine Reserves branch helping with ecological monitoring the reserves. So not only do I get to explore Oregon on my free time but also for work! Starting next week I will be conducting field work at three of the marine reserves: Otter Rock, Cascade Head, and Cape Perpetua. When I am not in the field I will be helping analyzing and summarize the data that ODFW’s Marine Reserve Ecological Monitoring Team collected last year. While there is both intertidal and subtidal monitoring that the department conducts, I will be focusing on the intertidal data and collection.
For work, my time will be split between sea star wasting monitoring and intertidal biodiversity monitoring. It is really awesome that the ODFW not only collects their own data for this but also works with other groups of researchers and citizen science projects to be able to collect tons of data and get a very good understanding of the areas that are protected. Occasionally I will be going out with these collaborators during their fieldwork to see first hand how these studies are conducted.
During my free time I have visited the beach,, boardwalk, and farmers market of Newport. Each time I go explore I gain new appreciation for this beautiful place that I get to live in for the summer. The awe-inspiring nature is not the only appeal of Oregon but also the culture of the towns and the people that live here. Everyone I have met is so nice and helpful. The best part is that almost everyone here is a dog person so wherever you go there are always tons of dogs which helps with missing my dog back at home.
Like many of the animals we study, us Oregon Sea Grant Summer Scholars must adapt to our new environment. I am fortunate to be a recipient of the 2018 Oregon Sea Grant Summer Scholar position with NOAA Fisheries. Although working with NOAA Fisheries is a dream come true, this is not the work environment that I am used to. My experience working in fisheries includes wading through Eastern Oregon and Washington desert streams during the hot summer months while collecting population and habitat data. Common hazards during my prior field work included dehydration, rattlesnakes, thorny vegetation, slippery rocks, and getting shocked constantly while electrofishing. During my short time working in a federal office I have found the hazards to be extremely different.
To begin, my training started off learning about the hazard of data breaches and hacking. Recent hacking into large corporations and even during our last presidential election has led federal agencies to take a hard line approach to data security. Secondly, commuting may pose the hazard of getting your semi-formal clothes totally soaked by an unexpected thunderstorm. This will get you to think twice about grabbing your raincoat or umbrella on your way out the door. Lastly, given our current political environment there have been protests outside of our building in recent months seeing as we share floors with other federal agencies facing opposition from the public. This has led to tighter security and awareness of potential physical hazards to federal employees.
In summary working at a federal office has been quite the change for me coming from a field-based background. I have been learning a great deal about the organizational structure of NOAA Fisheries, diving into documents explaining the role of NOAA Fisheries under the National Environmental Policy Act, and meeting co-workers in different branches of the office. The people here at NOAA Fisheries are extremely passionate about the work they do and have been very welcoming to us interns. As there is much more to read about NEPA I will conclude my blog here.
We have been collecting the megalopae life stage of Dungeness crab along the Oregon coast and extracting DNA from these individual megalopae. The next step is to sequence the Dungeness crab megalopae DNA so we can conduct statistical analyses that will help us understand how oceanographic conditions impact the Dungeness crab megalopae recruitment and the genomic composition of Dungeness crab along the West Coast of the United States.
Dungeness Crab Larval Recruits in Yaquina Bay, Newport, Oregon (Megalopae)
Before jumping into the details to genomic sequencing, imagine you are given a stack of 100 cover-less books and told that there are several different book series mixed within this stack. You are asked to categorize the books by series.
What if you were given a pile of 100 books and asked to categorize them by book series?
You could read every book, but this might take a very long time… And, it may not be necessary to read every book cover-to-cover if your only goal is to categorize the books by series and not necessarily understand the storyline details of each book. Right?
So, what if instead of reading all 100 books, you systematically read the first paragraph of each chapter. Would you have enough information about each book to group the books into series? Chances are that each series has their own characters, settings, themes, or writing styles. By reading the first paragraph of each chapter in each book, you would be able to pick-up on the characters, settings, themes, or writing styles of each book that differentiate each series. You could then group the books together that had the same characters, settings, themes, or writing styles.
We do something similar with Dungeness crab DNA. Sequencing the Dungeness crab megalopae DNA involves reading the ‘A’s, ‘T’s, ‘G’s, and ‘C’s that make up the DNA and then comparing the patterns of ‘A’s, ‘T’s, ‘G’s, and ‘C’s between individual crab megalopae to look for differences. Considering that the size of the Dungeness crab genome (all of its DNA) is quite large, it would be a costly, time-intensive, and computationally-intensive process to sequence the entire genome of every megalopae we want to analyze.
After collecting Dungeness crab megalopae and extracting DNA from individual megalopae, we use sequencing machines to read the DNA. But instead of reading the entire genome, we read many small sections from across the genome. This type of DNA sequencing is called reduced representation sequencing. Similar to the pile of books example, after this type of sequencing we couldn’t tell you everything about the genome of that particular Dungeness crab, but we would know enough about the individual crabs (or “books”) to tell if they are different from each other and if they were members of different groups (or from different “book series”).
Reduced Representation Sequencing (Truong 2012)
If the groups of crabs (“book series”) differentiate significantly, we can call them different populations. Alas, this is why we call ourselves population geneticists. We know that all Dungeness crab are of the species Dungeness crab (Cancer magister) and that all “books” are of the species “book.” But with population genetics, we are looking within species to to determine if there are sub-populations (or “book series”) within the species. Because of the social, economic, and ecological value of the Dungeness crab species along the West Coast, it is important that we understand the population genetics of the species so that we can continue to sustainability harvest this valuable fishery.
Since I am studying the genomics of Dungeness crab megalopae, I first need to catch some megalopae and extract their DNA! Both last year and this year we have collected Dungeness crab megalopae in Yaquina Bay at the Hatfield Marine Science Center. The Dungeness crab megalopae are about the size of the eraser on a pencil.
We use a light trap to catch Dungeness crab megalopae. A light trap is a device used to collect the larval stages of marine fishes and invertebrates. A light is placed inside a clear container with several funnel entrances on the outside of the container and a mesh collection chamber on the bottom of the container. Below is a picture of the light trap that we use. The light trap is placed in the water and tied to a dock. The trap floats just under the surface of the water and shines bright like a beacon at night.
Light Trap Used to Collect Dungeness Crab Megalopae
Some larval stages, such as Dungeness crab megalopae, are attracted to light and move towards light sources. This behavior is called positive phototaxis. You have probably seen this phenomenon when you turn on an outdoor-light at night and then within the hour moths are surrounding the light. For this reason, marine light trapping is an effective way to collect live larval fishes, or live Dungeness crab megalopae.
Dungeness Crab Megalopae
At night, Dungeness crab megalopae are attracted to the light in the light trap. They swim towards the trap and through the funnel entrances where they are then entrapped within the container. In the morning, the trap is pulled out of the water and the collection chamber is emptied. We count how many Dungeness crab megalopae are collected each night and preserve a subsample of the megalopae for genomic analyses.
Light Trap Floating Below the Surface in Yaquina Bay
Our light trapping for Dungeness crab megalopae in Yaquina Bay follows methods from Dr. Alan Shanks’ Lab at the University of Oregon’s Oregon Institute of Marine Biology (OIMB) on Coos Bay in Charleston, Oregon. At OIMB, the Shanks Lab has been light trapping and documenting the daily abundances of Dungeness crab megalopae for over a decade. They are studying how oceanographic conditions impact Dungeness crab megalopae recruitment patterns. Dr. Leif Rasmuson, a 2011-2012 Malouf Scholar, worked on this long-term project.
You may remember from my first post, that I am specifically looking at how coastal upwelling, the timing of spring transition, and the Pacific Decadal Oscillation influence annual Dungeness crab genetic composition. The reason I am studying these three specific ocean conditions is because Shanks and colleagues have found relationships between these three ocean conditions and the annual abundance of recruiting megalopae collected by light trap in Coos Bay, Oregon.
Megalopae Light Trapping Locations in Oregon (Photo Adapted from Rasmuson 2013)
The Dungeness crab megalopae recruitment season is April through September each year. In 2017, we caught a total of 12,000 megalopae in Yaquina Bay throughout the season. Currently, we are only two and a half months into the 2018 Dungeness crab megalopae recruitment season, but it is already turning out to be a big year for megalopae recruitment catches. This year we have caught over a half-million Dungeness crab megalopae in our Yaquina trap! And the Shanks Lab at OIMB has also been seeing record numbers of megalopae recruits this year. It is a very exciting time to be studying Dungeness crab megalopae!
A Big Daily Catch of Dungeness Crab Megalopae in the Yaquina Bay Light Trap (May 2018)
So, I mentioned that we preserve some megalopae from the light trap for later genomic analysis. To study the genomic composition of Dungeness crab megalopae, we need to extract the DNA from the megalopae. In fisheries genetics, we immediately preserve fish or crab tissue while in the field by placing a fish fin, a crab leg, or a full megalopae into a plastic tube of ethanol. This ensures that the DNA does not degrade before we can extract the DNA from the fish or crab tissue.
Preserved Megalopae Collected from Yaquina Bay, Newport, Oregon (Photo by Ketchum 2017)
DNA extraction sounds like it might be a complicated process, but it is relatively a simple protocol. You can actually extract your own DNA quite easily with ingredients from under your sink! Take a look at the below video if you want to try and extract your own DNA!
When we extract fish or crab DNA in the laboratory, we use slightly different chemicals than in the above video, small plastic tubes instead of plastic cups, a heating step to break the double stranded DNA into single strands, and a centrifuge machine and filters to separate the DNA from the rest of the solution. Think of the centrifuge machine like the spin cycle on your washing machine. The wet clothes spin at high speed and the water is removed from the clothes by being forced out of the small holes in the sides of washing machine like a filter. You are left with only dry clothes and no water, just like you are left with only DNA and not the liquids you used to extract the DNA.
Laboratory DNA Extraction (Photo from http://2017.igem.org/)
We extract the DNA from many Dungeness crab megalopae collected throughout the 2017 and the 2018 recruitment season. The next step is to determine the sequence of ‘A’s, ‘T’s, ‘G’s, and ‘C’s in the extracted DNA so we can conduct genomic analyses and better understand how ocean conditions are impacting the genomics of Dungeness crab.
