Autonomous Underwater Vehicle Glider Deployment

Hello Everyone!

With summer coming to a close I wanted to share a great experience I had earlier this month tagging along with researchers from OSU for the deployment of an Autonomous Underwater Vehicle Glider (“glider” for short) off the coast of Washington. Not only was it good to get out of the office a bit, but it was also a wonderful opportunity to learn first-hand about some of the advanced oceanographic monitoring and research that is being done off the coast. It was also great to meet Dr. Jack Barth in person, he is the director of the Marine Studies Initiative and professor of Oceanography at Oregon State University, and someone who I’ve been meeting with (virtually) over the last 9 months in the OAH technical workgroup.

Glider Basics

Underwater gliders, which look like small rockets with wings, use pumps to transfer seawater in and out of a holding chamber in the nose, causing the glider’s density to change (either sink or rise). With the help of the attached wings this vertical movement in water is translated to forward motion. What results is a series of dives, where optical, CTD (conductivity, temp, salinity), and oxygen sensors collect data at one second intervals. Numerous dives are strung together into segments and punctuated by trips to the surface to transmit data back to the lab. Gliders can be deployed for weeks at time and can be used for a wide variety of research and monitoring applications. Glider research has evolved dramatically over the last couple of decades and is now considered a foundational piece of modern oceanographic observation systems. More information on the integration of glider monitoring into the national Integrated Ocean Observing Network (IOOS) can be found here.

Loading the glider at the Westport WA bayfront. Photo by Jack Barth

Glider Deployment Trip

Our outing began at the bayfront in Westport Washington, where I met up with Dr. Barth and Dr. Steve Pierce, as well as an OSU student assisting with the deployment. After loading the glider onto the charter boat, we motored offshore for a little over an hour. Once we reached the deployment coordinates Dr. Pierce conducted some tests to make sure the glider was communicating properly with the lab before it was launched. Once in the water the glider performed a test dive to make sure everything was functioning correctly before it was sent it on its 2-week deployment. As a special bonus, two grey whales decided to pay us a surprise visit at the deployment location, it was an excellent sighting and we saw some great fluking before each dive!

Preparing to deploy the glider. Photo by Jack Barth
Fluking Grey Whales. Photo by Kaegan Scully-Engelmeyer

Glider Data and DEQ Water Quality Assessment

As gliders collect continuous data while moving across a large spatial area, they generate datasets that are fundamentally different than most continuous monitoring data currently assessed from Oregon’s water quality monitoring network, which is generally collected at fixed locations. This difference complicates the use of raw glider measurements in the existing data processing/assessment framework at DEQ. There is some guidance on the state and federal levels outlining protocols for using and assimilating this type of data into water quality assessments to identify impaired waters required by Clean Water Act. For example, New Jersey Department of Environmental Protection (DEQ equivalent in that state) implemented a glider monitoring program and developed quality assurance procedures to monitor and assess hypoxia in the state’s marine waters. Going forward it will be interesting to explore ways to integrate glider data into nearshore OAH water quality assessment protocols to help identify impaired waters.

Goodbye Oregon Coast ☹

Hello everyone,

I’ve had an incredible summer working with SEACOR (Shellfish and Estuarine Assessment of Coastal Oregon) at ODFW. I feel so grateful to have gotten the chance to work on such a dedicated and passionate team. 😊 This internship has been so valuable! For example, I knew prior to this summer that I enjoyed fieldwork, but I had never worked in a marine setting. Being able to spend 5+ hours in the water each day was a dream! Even though it can get tiring, it was so fun and cemented what I want to pursue in the future.

This summer has also redefined my career goals. I thought I’d want to work in completely marine settings, with ecosystems such as coral reefs or kelp forests. While I still think these would be amazing to study, I’ve become really interested in estuary work. Estuaries are so important no matter what lens you’re looking through—environmental, economic, and/or cultural. It has felt super rewarding to study and work with them this summer.

I’m very excited to share that I’ll be working at the Smithsonian Marine Station in the Benthic Ecology Lab in Florida starting in September! The research project’s focus is on characterizing the little invertebrates that live at the bottom of an estuary called Indian River Lagoon. The estuary has suffered biodiversity loss caused by many different threats, including harmful algal blooms, development, and excess freshwater input. For 15+ years, the Benthic Ecology Lab has used invertebrate biodiversity as a measure of ecosystem health! I’m incredibly excited to continue my scientific career focused on estuary work and am interested to see how I can apply what I’ve learned in Oregon down there!

Photo 1. Emma Chesley holding a cockle clam on a mudflat in Tillamook Bay. Photo taken by Summer Henricksen on 8/13/2022.

Perspectives on coastal climate work

The first half of my fellowship has been such an incredible experience of working with experts in conservation science and policy and learning how science can support policy and vice-versa. My fellowship project is a general exploration of how blue carbon pathways operate in Oregon’s coastal ecosystems, how they may contribute to the state’s greenhouse gas reduction goals, and who is currently doing the work. Blue carbon as a climate mitigation strategy is a fairly recent development, and the research is still in its early stages in the Pacific Northwest. My fellowship work will hopefully help inform how blue carbon can fit into Oregon’s natural and working lands.

To be honest, it’s hard to think about climate change daily without having to manage some amount of climate anxiety. The crisis we face is at a scale bigger than comprehension, and at times it’s hard to imagine blue carbon alone having a large enough impact to offset—let alone reduce—carbon emissions to have a positive climate effect. At the same time, defeatism is less than helpful, and it’s simply incorrect to believe that nothing we do can mitigate climate change and its effects. There will not be one solution. It will take a lot of people working in lots of ways to tackle the challenge, to change systems and turn the tide. Natural climate solutions (NCS), including blue carbon, is one tool we have to approach climate and biodiversity issues. NCS use conservation and restoration strategies to enhance climate benefits but does not elevate carbon reduction above ecosystem function. This is one aspect that I appreciate about NCS—it does not look at nature as a technology to maximize carbon sequestration but instead values ecosystem health and function for multifaceted benefits.

I had struggled initially because carbon crediting seems to focus simply on the most ‘productive’ estuarine systems that build carbon-rich soils However, many of the people working on blue carbon do not think of carbon projects as simply carbon farms that are separated from ecosystem function. There is deliberate consideration of the inherent value of coastal and nearshore ecosystems alongside the many ecosystem services, of which carbon is one. This attitude shared by my new colleagues is really a heartening one, and I’ve been supported in considering the role of complex oceanic ecosystems (like kelp forests) that are critical Oregon coastal habitat and sequester carbon.

Aequorea among bull kelp

A Summer of Growth

Hello everyone!

I have only a few weeks left working as a member of the SEACOR (Shellfish and Estuarine Assessment of Coastal Oregon) team! ☹ This summer has been instrumental in my personal and professional growth. Before this internship, I thought I would want to pursue a career in academia. However, this summer has shown me there are so many other paths I can take while still doing exciting scientific work. I can totally see myself pursuing a career with a state or federal agency now. Being able to communicate our data so readily with the public is what sparked my interest in pursuing this different path.

A professional development opportunity arose to work on an independent data project. So, I’ve also taken time this summer to learn how to code in R, which is a programming language for statistics that is often used in ecology. We’re looking at habitat associations between the different clam species in Tillamook Bay. I’m still working on the project, but I’m excited to present my findings at the symposium next week! Coding is completely out of my comfort zone, but it’s such a valuable skill to have in this field. I’m hoping to continue my R learning after this internship.

The biggest thing that surprised me this summer is I don’t mind getting up at 4:00 AM to go sampling. Who would’ve thought?!

Photo 1. Emma Chesley cooling off in a dry suit in Tillamook Bay. Photo taken by Mo Bancroft on 8/4/22.

A Day in the Life of a Shellfish Biologist

Hello everyone,

Four weeks down like that! Working on the SEACOR (Shellfish and Estuarine Assessment of Coastal Oregon) team has been incredible. We are collecting data on the four major bay clam species in Tillamook Bay to inform shellfish catch limits. This project involves lots of fieldwork on the tide flats of the bay, digging up clams, crab, and shrimp!

There’s no typical day for the SEACOR team. We work on the ocean’s schedule and try to go out during low tide so we can sample the most sites. This means some days start at 4:00 AM while others not until 9:00 AM! We have a variety of sampling methods, RAM (Rapid Assessment Method), DAM (Detailed Assessment Method), and Megacoring. Each site is RAM sampled which involves recording habitat data and collecting eelgrass, then raking about 15 centimeters (six inches) looking for clams (Photo 1). Some of our sample sites are further examined using the DAM method. This involves digging approximately 30 centimeters (12 inches) down. Some sampling sites are covered by too much water for us to DAM sample, so we use a giant pump to “megacore”. The megacoring pump basically acts as a vacuum that traps all the shellfish in a mesh bag and spits out the sediment (Photo 2). Species such as cockle clams are found at the surface whereas others such as butter clams and gaper clams are found at deeper depths, which is why we like to use a variety of sampling methods. The last few hours of our day are spent measuring all the shellfish we collect.

Photo 1. SEACOR biologists (Emma Chesley, Armand Martinez, Maddie Farmer) RAM sampling on an eelgrass bed in Tillamook Bay. Photo taken by Morgan Bancroft on 6/28/22.
Photo 2. Maddie Farmer (left) and Emma Chesley (right) megacoring in Tillamook Bay. Photo taken by Summer Henricksen on 6/24/22.
Photo 3. Burrito from La Providencia in Tillamook. Photo taken by Emma Chesley on 6/29/22.

Since we are living in a hotel in Tillamook during the week, we all get tired of microwave meals pretty quickly. That’s why we go out for a team dinner at least once a week! We’ve become loyal customers of “La Providencia,” a Mexican food truck in Tillamook (Photo 3). During downtime, I love to facetime my friends and family back home.  

While I really enjoy the work, my least favorite part is stripping eelgrass of epiphytes (Photo 4). Epiphytes are organisms that grow on plants. Algae and eggs are usually the epiphytes found on eelgrass. It’s a real time-consuming process that can feel tedious. However, it’s a job that must be done for accurate data on eelgrass biomass!

Photo 4. Blade of eelgrass stripped of epiphytes (left) vs. blade of eelgrass covered in epiphytes (right). Photo taken by Emma Chesley on 7/7/22.

My favorite part of the job is simply working in the ocean. It’s been a dream to work in this ecosystem that’s been inaccessible to me growing up in the Midwest. While I spent so much time reading and learning about marine ecosystems back home, it’s remarkable to learn first-hand with so many intelligent biologists on the SEACOR team! (Photo 5).

Photo 5. Emma Chesley (front) and Armand Martinez (back) recording habitat data. Photo taken by Morgan Bancroft on 6/28/22.

Day In the Life of a Phytoplankton Researcher 🔬🛥

Hello everyone! My name is Alex Ang, and this is the first of many blog posts detailing my experience as a 2022 Oregon Sea Grant Summer Scholar. After graduating from Macalester College in May, I packed my bags and flew out to the west coast for the first time in my entire life. For the next ten weeks in Newport, Oregon, I’ll be working with the Newport Hydrographic Line Team at NOAA Fisheries and Oregon State University. I will be examining harmful algal blooms on the Oregon coast, specifically looking at the diatom, Pseudo-nitzschia. Though I’ve worked with harmful algal blooms (HABs) many times before, this is my first time working with this species and bloom dynamics on this side of the world. My experience with HABs was limited to laboratory growth experiments, never looking at the organisms in their natural environment. I will also be dipping my toes into studying the toxin they produce, domoic acid. I will use both field surveys and processing water samples to inform my research about patterns in toxin production when different environmental drivers are present. 

I arrived on campus at the perfect time, just as my team was getting ready to test drive an autonomous sailing vehicle, known as the Triton, capable of collecting offshore water samples for HABs. In a huge collaborative effort between the University of Washington, Oregon State University, the Northwest Association of Networked Ocean Observing SystemsNOAA Northwest Fisheries Science Center, and the Olympic Region Harmful Algal Bloom Partnership they hope to significantly enhance HAB forecast accuracy and sampling capability. Being on the water was a lot of fun, as I rarely got to do any type of field work in my previous research experiences. I learned that when out in the field, I have to be prepared for anything, since the weather can be unpredictable and research plans often change. Though not every week will look like this (testing out an autonomous vehicle!), it was amazing to have an opportunity to see a sampling vehicle in action. 

When I’m not on a boat, my days will consist of processing a backlog of water samples from 2021 with enzyme-linked immunoassays (ELISAs) to detect particulate domoic acid (pDA) as well as extracting chlorophyll from preserved samples. I will look at these data in tandem with conductivity, temperature, and depth profiles to examine patterns in toxin production and Pseudo-nitzschia abundance. Through helping the Newport Hydrographic Line Team process this backlog of data, I am contributing to a broader understanding of PN toxin production that could help inform recreational/commercial shellfish management. 

While the research is a huge part of my project this summer, I am also invested in working on adding a science communication aspect to it. At the end of the summer, I will produce an exhibit in the Hatfield Marine Science Visitor Center about the Newport Hydrographic Line and its research efforts. With my display, I hope to increase awareness of the Line and get the public interested in the various research that is being completed. Leveraging my experience with community outreach, I will also contact local boat tours about incorporating wording about the NHL. My project’s interdisciplinary approach aligns with Oregon Sea Grant’s mission of promoting discovery, understanding and resilience to Oregon’s communities and ecosystems. As a STEM and Humanities major myself, it has been quite the journey to bridge the gap between my two disciplines. 

Next week, I’ll be jumping into more lab and field work related to my project. I will begin to uncover the patterns of pDA production and drivers of Pseudo-nitzschia blooms on the Oregon coast. Stay tuned and follow me through my summer journey! 

Fieldwork Galore

Hello everyone!

I have officially finished my first two weeks as a Summer Scholar working for the Oregon Department of Fish and Wildlife on their SEACOR (Shellfish and Estuarine Assessment of Coastal Oregon) team! These first few weeks consisted of some intense fieldwork on the tide flats of Tillamook Bay (Figure 1). We are focused on two main projects this summer. The first, and most extensive, is shellfish and habitat data collection. The goal of this project is to figure out where recreationally significant clam species are in Tillamook Bay, as well as the abundance, biomass, and preferred habitat for each species. The four major target species are cockle clams (Figure 2), butter clams (Figure 3), gaper clams, and native littleneck clams. Data collected from this field season will later influence management decisions regarding the commercial harvest of bay clams in Tillamook. To get these data, we dig a bunch of holes in the tide flat and collect any critters we find! We’ve already dug up loads of clam, crab, and shrimp. Since we rely on low tides to get a lot of our work done, we’ve had many early mornings!

  • A map of Tillamook Bay in Garibaldi, Oregon, with the main tide flats and channels labeled.
  • A hand holding a small cockle clam with water in the background.
  • A woman kneeling in shallow water, holding a butter clam and smiling at the camera.

The second smaller project involves using drones to map eelgrass beds. Since eelgrass acts as important nursery habitat for a variety of fish and invertebrates, the goal of this project is to see exactly where eelgrass is growing in the bay. This is a collaborative project with the Coastal Drone Academy which is based out of the Career Tech High School in Lincoln City. While the students operate the drones, the SEACOR team helps set up the GCPs (Ground Control Points) at known locations (Figure 4). GCPs allow us to overlay all our imagery data later on!

Figure 4. Emma Chesley (left) and Mitchell Gellhaus (right) setting up a GCP during low tide on an eelgrass bed. Photo taken by Morgan Bancroft on 6/16/2022.

A large portion of Oregon Sea Grant’s vision and mission involves studying the human dimensions of coastal and marine fisheries. Currently, there is a lot of controversy regarding the recreational and commercial harvest limits in Tillamook Bay. Data collected from this project influences harvest limits which can cause conflict between different fishing communities. This bay has not been surveyed by the SEACOR team since 2012, so there is a lot of interest (and some pressure) to get all the tide flats surveyed.

I am super excited to be a helping hand on this project in hopes we can collect lots of good data this field season! I’ve already learned so much about Oregon’s marine ecology as well as research in general. I can’t wait to see where the season takes us. Here’s to more gorgeous 4 A.M. mornings! ;)

More information regarding Oregon clamming can be found on SEACOR’s website: or/index.asp

Ocean Acidification Science-Policy Translation

Hello again! Hard for me to believe, but I recently passed the six month-mark in my Ocean Acidification and Hypoxia fellowship with Oregon Department of Environmental Quality (DEQ). As I talked about in my last post, I’ve been working with the water quality assessment team at DEQ, and assisting in the development of procedures to assess biological impacts of Ocean Acidification (OA) and Hypoxia in Oregon’s near shore waters for the purposes of Clean Water Act 303(d) assessment. DEQ has convened a technical workgroup of scientists, researchers, and partner agency staff to help answer critical technical questions as we develop assessment procedures to understand impacts of these stressors. So far, my main task in this fellowship has been to help coordinate this workgroup towards this end. Since my last post we’ve been continuing to work with a subgroup of workgroup members versed in both scientific and policy perspectives to draft OA assessment procedures and an accompanying set of technical questions to bring to the full workgroup for refinement. We’ve had three meetings with the subgroup and are making progress on the set of questions and draft procedures. As we proceed with this workgroup made up of individuals with such a wide array of expertise and specialization across this topic area I thought I would share a couple of underlying elements of this process we’ve been considering and discussing as we formulate the set of questions for the technical group.

One challenging aspect of this process comes down to the inherent differences between scientists and policymakers in terms of approaches and methods of communicating knowledge and information. Translation between scientific research and information needs for policy development hinges on considering both styles of communication and making sure a shared understanding exists around terminology. The same terms can mean very different things depending on usage and context, so defining some key terms has been critical in this process.

Another key element of this translation involves the synthesis of information and ensuring the appropriate type and level of detail is included in conversations and questions, it’s easy to get “in the weeds” when talking about a complex topic such as OAH. One way we are currently addressing this is to divide our questions into a sequence of information needs, which has helped organize the dizzying amount of technical information we will be gathering into a structured framework. Finding the right level of detail to include along this sequence, especially in terms of how each question fits into DEQ’s overall assessment picture, has been an interesting iterative process, and I’m sure it will continue to be.

Overall, I’ve found that working in the subgroup has created opportunities for excellent discussions around these and other process-based factors that underly this work, and I’m looking forward to continuing to incorporate these elements into the remainder of my fellowship.

Oregon Seaweed Learning Tour

It has officially been two months since I started my position as a Restorative Aquaculture Fellow with Oregon Sea Grant and The Nature Conservancy! So far, the fellowship has been a great experience and I’m grateful for this amazing opportunity to network within the restorative aquaculture space and learn more about seaweed farming.

My project involves working with TNC’s Global Aquaculture Strategy Lead, Global Aquaculture Manager, and TNC staff from Oregon, Washington, British Columbia, and Alaska to explore the potential to invest in and create restorative seaweed aquaculture farms in the Pacific Northwest. A major deliverable of my fellowship will be a situation analysis to better understand challenges and opportunities for Oregon’s seaweed aquaculture industry. Much of my work to date has involved meeting with folks from academia, private industry, NGOs, and state agencies to map out current research, projects, and seaweed farming. I’ve also gotten to do some wild seaweed harvesting in my spare time!

Recently we completed an Oregon learning tour with potential partners to build a shared understanding of farming methods, environmental conditions, and the community context of seaweed aquaculture in the state. We started in Newport, OR with some in-person and virtual presentations focused on a general background for mariculture in Oregon and the restoration of wild kelp. The next day we learned about urchin ranching efforts on the south coast, toured two innovation labs in Newport and headed north to visit Oregon Seaweed’s land-based farm in Garibaldi. We also got lunch at Local Ocean Seafood – my favorite restaurant in Newport.

In the past two months I’ve already gained a deeper understanding of this industry thanks to the help of all the folks I’ve had the opportunity to meet with. I’m very much looking forward to the learning tours we’re planning for Washington and British Columbia in the fall.

We’re gonna need a bigger boat…and a better understanding!

It’s June and we’re in the depths of field season! 

Myself and a WDFW colleague tagging a younger sevengill shark in Washington

My project focuses on incorporating broadnose sevengill sharks into ecosystem modeling in the northern California current ecosystem, which encompasses the coasts from San Francisco up to British Colombia. Historically, predators, in general, have not been included in our understanding of the Pacific Northwest coastal ecosystems (the few studies done have focused on orcas or pinnepeds such as sea lions). So, very little is known about sharks in this region. The broadnose sevengill is a large (up to 10 ft/3 meters and 230+ lbs/107 kgs), apex predator in other locations around the world. I suspect they play a similar role here in Oregon and Washington…especially when it comes to our very important local fisheries, like salmon, halibut, and crab! To find out, I am tagging sevengills with acoustic tags (to track movement) and taking tissue samples (to determine what they’re eating over different periods of time, using stable isotope and stomach content analysis). 

Since April, I’ve been going out once a month to look for sevengill sharks in Willapa Bay, WA. Sevengills – which live in temperate waters – show up seasonally in certain bays around the world. Willapa Bay, the second largest BAY on the west coast of the United States, is one of those specific bays. We’re not sure why sevengills show up there, but we do know that Willapa is also an important estuary for many species, including salmon, Dungeness crab, harbor seals, as well as Endangered Species Act-listed green sturgeon. Originally we thought that the sevengills showed up in June or July. But after doing some reading of some previous studies, I suspected that they might be showing up as early as April. And if they were, I wanted to sample them.
So out we went in April. Three days on the water and…..nothing! I was confused. I thought they’d be here! Maybe I’m just wrong? After talking with some local fishermen, though, we discovered…the local Chinook salmon run was running late. Maybe related? Unknown. We went home empty-handed.

In May, we returned. Before we got on the water, a local fisherman revealed…the salmon are here! Okay, but where are the sharks? Unknown. We got out on the water and spent most of the day fishing for sharks. Waiting waiting waiting. Right as I was about to give up — tug tug tug. “Did I catch a stick?” I pulled up my line and…..SHARK! It’s a sevengill! They’re here! I almost cried (a moment captured perfectly on camera by my advisor). How exciting!!! We caught two more sharks that day. AND we detected previously tagged sharks…from 2021! They are here! Which begs the question. What are they doing though? Unknown!

The exact moment that I saw the first sevengill shark in April, confirming they had officially arrived! I almost cried. (Shoutout to my advisor for snapping this picture).

Is it related to the salmon, or is it something else? Still unknown. But that’s what I’m trying to find out. Stay tuned (links below to keep up with me and my lab on social media)!

A broadnose sevengill shark, ready to be released after tagging!