Tag Archives: Oregon Coast

A big year for small Dungeness crab megalopae

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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.

What’s so big about Dungeness crab?

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Hi, I’m Elizabeth Lee, and I am an Oregon State University master’s student with Dr. Kathleen O’Malley in the State Fisheries Genetics Lab at Hatfield Marine Science Center in Newport, Oregon. My first quarter as Malouf Scholar has been quite busy, but before I dive into my Fall quarter, let me provide a little background on my research.

When you think of the Oregon Coast, what comes to mind? Maybe rocky coastlines? Tides pools? Seals? Beaches? Boats? Seafood? Dungeness crab?

Oregon Coast, Yaquina Head Lighthouse, Newport, Oregon

Oregon Coast Tide Pools
Newport, Oregon

If “Dungeness crab” didn’t come to mind, you need to spend more time along the Oregon Coast! Dungeness crab (Cancer magister) is Oregon’s most valuable single-species commercial fishery. Its cultural, historical, economical, and ecological importance along the Oregon coast is prominent.

Dungeness Crab
(Photo: Delecia Loper)

In 2017, 20.4 million pounds of Dungeness crab were landed by commercial fishing vessels in Oregon, totaling $62.7 million in ex-vessel value. These may seem like large numbers to you, but I will argue, that from the perspective of my discipline, there’s another aspect of Dungeness crab that’s even bigger. The genome of the Dungeness crab.

Dungeness Crab Pots, Newport, Oregon

Let’s take a trip back to Biology 101, remember all the ‘A’s, ‘T’s, ‘G’s, and ‘C’s that make up your DNA? These ‘A’s, ‘T’s, ‘G’s, and ‘C’s (or bases) pair-up to form the double stranded structure that holds the blueprints that makes each of us unique (or DNA). The complete DNA blueprints (or genome) of the Dungeness crab is over 2 billion base pairs long! And, every cell in its shell-encrusted body has a copy of these 2 billion base pairs. So, although we catch tens-of-millions of pounds of Dungeness crab per year in Oregon, the genetic composition that makes a Dungeness crab a Dungeness crab, is even larger!

DNA Diagram
(Figure: Wikimedia Commons)

Considering the importance of Dungeness crab along the West Coast, one would assume we know a lot about the Dungeness crab’s genome and genetics. But in fact, we do not. The O’Malley Fisheries Genetics Lab undertook one of the first large-scale genetics projects on Dungeness crab. They sampled over 7,000 adult Dungeness crab off the coasts of Washington, Oregon, and California to understand the population genetic structure, genetic connectivity, and genetic diversity of Dungeness crab within the California Current System (Jackson et al. 2017)

Dungeness Crab West Coast Range
(Figure: Rasmuson, 2013)

By determining the pattern of ‘A’s, ‘T’s, ‘G’s, and ‘C’s within the crab genome, we can study the genetic structure, genetic connectivity, and the genetic diversity of the population. These findings are informative for managers and conservationists. Defining the population genetic structure of Dungeness crab is important for determining how groups of crab in the ocean are connected and allows managers to define stocks within the fishery. Assessing the genetic diversity within and among populations provides insight into the species ability to respond to environmental changes.

Dungeness Crab
(Photo: Wikimedia Commons)

In their coast-wide population genetics study, Jackson et al. (2017) found that Dungeness crab were highly connected genetically within the California Current System. Interestingly, they found inter-annual variability in the degree of genetic connectivity. This suggests that inter-annual variations in oceanographic conditions are affecting the genetic population structure of Dungeness crab. Specifically, the strength and timing of coastal upwelling, the timing of spring transition, and the phase of the Pacific Decadal Oscillation that effects of the strength of the off-shore current systems.

So, how is it that these large-scale oceanographic conditions might be affecting the bottom-dwelling Dungeness crab? Because of the complex life cycle of Dungeness crab.

Dungeness Crab Life Cycle
(Adapted from: Wild and Tasto, 1983)

Before Dungeness crab become 6 ¼-inch-bottom-dwelling (benthic) harvestable organisms in the ocean, they spend 3-4 months as very small, floating (pelagic) larvae within the water column. The pelagic larvae are moved offshore and are dispersed for 3-4 months along the west coast by the ocean currents. The time-period the larvae spend in the ocean current systems and the strength of the ocean currents influence where the larvae finally land on the bottom at the completion of their 3-4 month ocean journey. When the Dungeness crab larvae land along our coasts, we call this process recruitment. After recruitment, the juvenile crabs grow into bottom-dwelling adult crabs.

Dungeness Crab Larval Recruits (Megalopae)
Yaquina Bay, Newport, Oregon

As a graduate student, I am studying the genetic structure and diversity of Dungeness crab larvae that are recruiting to our Oregon Coast. By combining this genetic information with information about the oceanographic conditions and ocean currents along our coast, we can better understand the inter-annual variability that is observed within the adult Dungeness crab genetic population structure. The findings of my research can inform scientists and managers about the population of Dungeness crab off our coasts. Our genetic research is one of the many research projects that can help us tackle the complex questions of ‘how’ and ‘why’ the Dungeness crab fishery and population changes from year-to-year.

I am looking forward to keeping you all updated on my Dungeness crab genomics research this year. And in the meantime, I am enjoying the start of the 2018 Dungeness crab commercial season in Newport, Oregon!

 

References:

Jackson, T. M., Roegner, G. C., & O’Malley, K. G. (2017). Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System. Molecular ecology.

Rasmuson, L. K. (2013). The biology, ecology and fishery of the Dungeness crab, Cancer magister. In Advances in marine biology (Vol. 65, pp. 95-148). Academic Press.

Wild, P. W., & Tasto, R. N. (Eds.). (1983). Life history, environment, and mariculture studies of the Dungeness crab, Cancer magister, with emphasis on the central California fishery resource. State of California. The Resources Agency. Department of Fish and Game.

 

Shellfish Initiative: Oregon’s efforts in a nationwide context

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When I last wrote about the Oregon Shellfish Initiative, the bill to create it was working its way through the 2015 legislative session. House Bill 2209 passed both houses and was signed by the Governor, and a whole new phase of work began. The bill created the Oregon Shellfish Task Force, an 11-member group charged with producing a report to the 2017 Legislature with recommendations related to shellfish in Oregon. The issues to be addressed by the Task Force include creating an efficient permitting process for shellfish growers–eliminating regulatory overlap and gaps where possible and encouraging communication among regulatory agencies, establishing best management practices for cultivated shellfish in Oregon, protection and restoration of wild and native shellfish stocks for conservation as well as recreational harvest, supporting ocean acidification research in collaboration with shellfish growers, and assessing the socioeconomic impacts of commercial and recreational shellfish on Oregon’s coastal communities.

Around this same time, my term as the Oregon Sea Grant Legislative Fellow was coming to an end. Fortunately for me, I was able to move across the street to the Governor’s staff offices and into the position previously occupied by the fabulous Kaity Goldsmith as the Natural Resource Policy Fellow working on ocean and coastal issues. Though the Governor’s office doesn’t have an official role with the Task Force, I’ve been able to support the work in an unofficial capacity, providing an informational presentation at the first meeting, and meeting with committee staff to provide background information and help ensure that interested stakeholders are at the table.

The Task Force convened in November and has been meeting approximately every other month. The fourth meeting is coming up next week, and this halfway point in their process seems like a good time to weigh in on their work to date. After an initial organizational and informational first meeting in November to bring up to speed those TF members who were new to the conversation, the January meeting was held at Hatfield Marine Science Center in Newport and focused on shellfish research in Oregon, particularly related to the effects of ocean acidification and changing ocean conditions on oysters and other bivalves. The meeting also included a tour of the research facilities at HMSC where Oregon State researchers Chris Langdon and Burke Hales research the effects of changing ocean chemistry, including Dr. Langdon’s Molluscan Broodstock Program which aims to select oyster broodstock that is resistant to increased CO2, temperature, and other fluctuations. The third meeting, held in Salem at the Capitol, focused on the role of federal and state agencies in the shellfish industry, as well as conservation concerns related to wildstock and native oysters. Representatives from several federal and state agencies discussed their role in permitting and regulating the shellfish industry in Oregon. It was a very productive meeting, with some agencies presenting efforts they are already making to simplify the permitting process, and several others bringing recommendations for opportunities to increase inter-agency collaboration and communication in order to make the process more efficient. Dr. Bill Hanshumaker, Oregon Sea Grant Chief Scientist, also presented to the Task Force on work Sea Grant will be doing to support development of a coordinated statewide program to support Oregon aquaculture, expansion of new and existing shellfish operations through reduced regulatory barriers, and supporting shellfish aquaculture operations in being more diversified and sustainable in the nearshore, offshore, and estuary environments.

On a related note, I was invited to represent Oregon in a Shellfish Initiatives session at the World Aquaculture Society triennial conference in Las Vegas in February. The session was kicked off by Michael Rubino, director of NOAA Fisheries Office of Aquaculture in Silver Spring, Maryland, who gave an update on the National Shellfish Initiative, introduced in 2011. The presentations then started with Alaska and proceeded south with Washington, Oregon, and California, and then to the Gulf states and up the East Coast including Maryland, Rhode Island, and Connecticut. It was fascinating to hear where other states are in their Shellfish Initiative process and how they’re approaching supporting their shellfish industries. It was also the first time I had a clear sense of where Oregon falls in this larger context, and I was pleased to note that we are right in step with the other states–not as far along as Washington, Maryland, and Rhode Island, all of whom started before we did, but further along than other states who haven’t had the support of legislators like our Coastal Caucus who have really helped drive this process.

I do work on other issues besides shellfish, but it’s been great to have the continuity with this effort for the last sixteen months or so, and to see the  results taking shape.

In my next post I’ll try to encapsulate the other things I’ve gotten to work on:  ocean acidification, marine debris, and the launch of the Oregon Ocean Science Trust.

 

From Cornfields to Coastal Mudflats

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It has been roughly 12 days since I departed on my 4 day cross-country road trip from Indiana to the coast of Oregon. Many sites were seen like Medicine Bow, Winnemucca Mountain, and Crater Lake. Taking the time to see such colossal structures really made me realize how small we are in the vastness of our own country, let alone the planet.
It took 35+ hours to get to Oregon, and I’ve only been here for roughly a week, but I already feel a sense of home here. For the next 9 weeks, to my understanding, I will be working with integrating different pit trap methods for the capture of juvenile Dungeness crabs (Cancer magister) as well as the utility of using underwater video to get quality quantitative data on fish and invertebrate use of US West Coast intertidal estuarine habitats. Working this week with the USDA under my mentors, I have been very fortunate to already be getting out into the field.

 

Dungeness Crab (Cancer magister) caught from pit trap

This week we drove 60 miles north to Netarts, OR and checked shell bags for colonization by shellfish. We also took water quality in areas that were bare (lacked vegetation) and areas with seagrass present. Closer by (Yaquina Bay), pit traps were set up for the capture of Dungeness crabs to quantify their morphometrics to create more accurate size selection in the future. To our delight, we managed to catch several crabs, along with a few mud shrimp.

Mud shrimp that was dug up with the traps

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

There is no doubt that the next 9 weeks will pass by quickly, a lot will be learned and a lot of great memories are to be made. With that I hope you continue to enjoy my blogging as the weeks go by. I’m lucky to call this beautiful city and state my home for the summer. Follow me on here or via twitter @Prechtelguy93

Prozac project changes

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When I last checked in, I had just begun a pilot study that would assess how shell thickness in mussels may be affected by exposure to Prozac. Unfortunately, the experiment was a bust, mostly owing to the impractical housing conditions which stressed the animals and led to high mortality. I quickly scrapped this project, with the intention of returning to it as a side project sometime later next year. My new focus will still assess the affects of prozac on marine life, but from a completely different angle: animal behavior.

I’d like to introduce this new project by telling you how I came up with the idea. While visiting Netarts, Nehalem, and Yaquina Bay, I noticed the abundance of shore crabs living in the estuary and that they reside primarily in soft sediments, mud, and beneath rocks, never too far from the water margin. This struck me as another creature that may be at risk from contaminants as they are transported from waters upstream and adsorb onto the sediments. I wondered if these crabs were in contaminated estuaries, how would their behavior change and how would this influence food web dynamics. To my knowledge, this is a somewhat unexplored connection linking contaminants as an agent to potentially influence shifts in food webs. We often hear about bioaccumulation of contaminants up the food web, but what if contaminants also affect the behavior of animals and cause them to be more or less susceptible to predation because of abnormal behavior?

The shore crab Hemigrapsus oregonensis, has been extensively studied and their behaviors have been well documented. My aim was to assess whether crabs exposed to Prozac at  3 and 30ng/L (i.e. documented concentrations in estuaries) would be more at risk of predation when compared to unexposed crabs. Because Prozac is a psychoactive drug, it is likely that their behavior will be altered at even low levels with persistent exposure. I am conducting this experiment by creating simulated estuary habitats in 30 tanks (10 replicates for each treatment) with rocky substrate and hideouts to allow for normal predator escape/evasion behavior. We will be dosing the shore crabs every 10 days with Prozac to simulate pulse events (e.g. increased rainfall) into the estuary. The meat of the study will be the addition of the predator, the Red rock crab, to the shore crab tanks and assessing the response to the predator during the behavioral trials, which will last ~1hr. We will run these behavioral trials during the day and at night to see observe their reactions. This project will run from June 1-August 15.

We have already had the animals living in our estuary mesocosms since June 1 and we will be conducting the first set of  behavioral trials next week. More developments to follow. I’m very excited about this study and I believe it is important to explore how contaminants might affect wildlife in Oregon’s estuaries should we

Silent Seas and Shifting Winds

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Hello Oregon Sea Grant Community!

Before I even get started with my whirlwind update of field work, conferences and dramatic life changes I first want to apologize.  It has been far longer than I ever expected since my last post.  While I certainly can’t fix my prolonged absence… I can at least begin to explain what’s kept me so far away from my computer since my last post this spring.

First- Conference update!

Thanks in large part to the Malouf Fellowship I was able to attend a marine mammal conference this May in Bellingham, WA.  I’m a member of the Society for Marine Mammalogy — but wasn’t able to go to the “big girl” international conference in Dundin New Zealand this past year (as a lowly grad student with teaching responsibilities and a tight budget, well the South Pacific just wasn’t in the cards).  What I love about the marine mammal community though, is our ability and desire to collaborate.  International conferences are biennial (every two years) but as students we hold an annual chapter meeting.  The Northwest Student Chapter for the Society of Marine Mammalogy (NSCSMM- check us out on facebook and get involved!) hosts a one day conference every year at one of the Pacific Northwest Universities.  This year Western Washington University had the lucky draw, and the conference organizer was none other than my dear friend and former intern Kat Nikolich.  The marine mammal world is quite small.

The conference, which is organized entirely by students, was spectacular.  It was a priceless opportunity to hear the latest and greatest in marine mammal research, and entirely from the Pacific Northwest.  Further, we had a chance to take a boat ride out of the Western Washington Marine Lab, where we saw heaps of marine life and generally kicked back and got our feet wet.  It was also a great place to make some collaborators.  At the conference I chatted with a number of  students with similar interests in acoustics who I now have plans to work with in the future.  (Phew… people say science is competitive, that must be why they created conferences.  Working together is always easier than racing to the top).  I’m also proud to report that I was elected the new Chapter Representative, and will be working with Pacific Northwest Students for the next few years keeping everyone informed about conferences and opportunities to participate in marine mammal science.

Which leads me to the next exciting conference news. In May, 2015 Oregon State University will be hosting the NWSCSMM Meeting in Newport, OR. We’ll be inviting students from throughout the region (Northern California to Alaska) to present their research (completed or in progress) to friends and colleagues.  You don’t need to present to be involved; undergraduates, high schoolers, or graduate students are encouraged to attend.  This is an excellent chance for students (or anyone) who wants to learn more about the marine mammal field, or perhaps wants some advice on how to break into marine mammal science, to hobnob with some early career researchers.  Feel free to contact me personally if you have questions about attending or presenting, and keep an eye out on this blog and others.  I’ll be sure to circulate the details as they unfold.

But I’m not done yet… I know this post is already growing long… hang in there.

Due again in large part to the Malouf Fellowship that I’m so honored to have received, I was able to travel to Washington D.C. (o.k. Leesburg Virginia) this summer for a weeklong Marine BioAcoustics Summer School (SeaBASS).  I know not everyone gets excited about spending a week learning about marine physics and underwater sound production, but I do!  It was spectacular!  I won’t bore you with all of the details here, except to say that fish do vocalize and it’s amazing, and that physics tells us a lot about ocean ecology.  You can read a more detailed account of the trip on my lab blog here.

In the interest of brevity just a few more points.   I was invited to speak to the American Cetacean Society’s Oregon Chapter this past spring in Newport, OR.  I gave a talk on acoustic communication in cetaceans, with an emphasis on critters we have here on the Oregon Coast- which if you didn’t know includes white sided dolphins, Pacific dolphins, harbor porpoise, sperm whales, humpback whales, and gray whales… among others.  I’ve also since given two other lectures (one on a small cruise ship and one as a master class at the university) on similar topics.  This fall I’ll be teaching two master classes, both of them for universities on the east coast, with a little help from the internet :)

Lastly, I want to pass along some exciting, but bittersweet news.  My PhD project has changed.  I know.  It’s a little strange for me.  When I started my PhD I began working on what I believed (and continue to believe) is an extremely valuable marine mammal monitoring project here on the Oregon Coast.  Over the part year I’ve been able to recruit a series of talented and committed students and volunteers to act as marine mammal observers looking for whales, dolphin, and porpoise from the R/V Elakha.  In my previous posts I told you a little about what we’d been seeing on the water, and this spring we deployed our first round of hydrophones and started listening as well- very exciting.

But, somewhere along the lines something happened.  My phone rang. Funding had come available studying the impact of noise on humpback whales in Glacier Bay National Park, and the Park biologist wanted to know if I was able to shift my dissertation focus to Alaska.  Prior to working on cetaceans here in Oregon I lived and studied humpback whales in Southeast Alaska.  After completing my M.S.at OSU my focus shifted locally to the Oregon Coast, but as you may know funding in science is incredibly tight.  When the opportunity for a fully funded PhD position arose, I wasn’t really in a position to say no.  Given my background in humpback whale acoustics I was a good fit for the project, and although the decision was a tough one (tougher than you might imagine) I opted to accept the offer.

The flip side of the coin? The good news is that I’ve still been working on the Oregon Coast project, and it’s flourishing.  We have a new graduate student in our lab named Courtney Holdman who started as one of our volunteers on the project.  She has since taken over the project for her master’s thesis.  Our volunteers are still going strong, and the program has expanded somewhat.  Two students initially slated to collect data for our marine mammal project are headed out on a 4 day research cruise this September.  Three other students from here in Oregon will be headed into the field with me in Glacier Bay next summer.  So while I’ll be looking at noise impacts up north, I’ll be bringing a little bit of Oregon with me.

I know this has been quite the earful (eyeful?).  Thanks for hanging in there with me on my PhD adventure. It’s been exciting, and I never would have managed it without Oregon Sea Grant (I mean that).  I’ll be sure to stay in touch as things unfold! ~Michelle