Summer Research Internship

Applications will open on January 2nd, 2023 and close on January 31st, 2023 by the end of the day. Applications will be available on this page. Contact the FHL REU Coordinator with any questions.

1. Biotic and Abiotic Factors Influencing Kelp Bed Communities in the Salish Sea

Dr. Katie Dobkowski, Woodbury University and Friday Harbor Labs, University of Washington

I study marine community ecology and especially focus on foundation species such as bull kelp (Nereocystis luetkeana). Nereocystis is an annual kelp species that provides the bulk of the complex three-dimensional habitat space in rocky subtidal habitats of the San Juan Islands and elsewhere in Washington State. There are a variety of potential summer projects that focus on investigating biotic and abiotic factors influencing bull kelp across their complicated life history using a combination of lab and field work. Topics of interest include investigating:

• green sea urchin (Strongylocentrotus droebachiensis), red sea urchin (Mesocentrotus franciscanus), Northern kelp crab (Pugettia producta), and graceful kelp crab (P. gracilis) feeding preferences (in the lab at ambient and elevated temperatures) and distribution and abundance (in the field; intertidal, snorkel or SCUBA surveys)
• influence of competition from invasive wireweed (Sargassum muticum) on nearshore habitats
• contribution of P. producta feces to detrital food webs (in the lab, using field-collected intertidal copepod Tigriopus californicus
• effects of changing ocean conditions, such as temperature, on invertebrate feeding rates (urchins, kelp crabs).

Subtidal data collection using snorkeling methods, and SCUBA may be possible for a student who is already a trained scientific diver at an AAUS member institution, but diving OR snorkeling is NOT a requirement for any of these projects, very successful field data collection can happen on the shore or from boats as well! A better understanding of the dynamics and interactions of N. luetkeana beds in the Salish Sea is crucial not only because they create valuable habitat for economically and ecologically important species, but also to inform management decisions and restoration efforts in a changing ocean. 

2. How persistent are eelgrass patches? A paleocological pilot study in False Bay, WA

Dr. Sandy Wyllie-Echeverria, Friday Harbor Laboratories, University of Washington
Dr. Bruce Finney, Idaho State University

Zostera marina (eelgrass) is the dominant seagrass species in the Northern Hemisphere. In western North America these marine flowering plants grow in soft-bottom estuarine and coastal environments from Alaska to Baja California, and probably occupied these environments since the Pliocene. The objective of this REU is to determine the persistence of an eelgrass population near the proximal center of this distribution.  Our site, False Bay, San Juan Island, is a shallow water bay that lies within the Salish Sea region of Washington State and is a marine reserve managed by the Friday Harbor Laboratories, University of Washington.

This project will explore the persistence of eelgrass patches using palaeoecological methods.  We will obtain a transect of cores across a gradient of patch persistence and use carbon isotopes (d¹³C) as a proxy for eelgrass abundance.  As the d¹³C of eelgrass is higher than other sources of organic matter to sediments, it will serve as a time series tracer of eelgrass presence. This project will produce data to explore the hypothesis that downcore changes in d¹³C reflect changes in eelgrass presence and abundance in the Anthropocene at this location.

3. Is it worth the risk? Correlations between stickleback armor and behavior

Dr. Stephanie Crofts, College of the Holy Cross

Three-spine sticklebacks (Gasterosteus aculeatus) are a model system for studying eco-evolutionary dynamics, largely due to their repeated invasion of fresh-water systems from marine systems and the myriad of ways populations have diverged and converged over time. A key feature that varies between populations, both marine and freshwater as well as between different fresh-water groups, are the defensive spines and lateral plate armor of these fish. For example, some populations have greater coverage of lateral plate armor than others, likely tied to predator abundance or environmental complexity. This sort of armor represents one aspect of a complex set of traits that have evolved together over time, which also includes other aspects of morphology, behavior, and energy expenditure. The goal of this project is to correlate fish behavior (boldness/exploration/antipredator) with defensive morphology (lateral plate armor/defensive spines) in sticklebacks of the Salish Sea, as a comparison group to the often more studied fresh-water populations.

This project will explore how spine and armor morphology vary with behavior and environmental cues in two parts. For part 1 we will observe and record fish behavior to quantify exploration, risk-taking, and anti-predator behavior. For part 2, we will CT scan each individual to reconstruct their skeleton and measure dorsal and pelvic spine morphology, as well as lateral plate armor density and coverage. Behavior data will be correlated to morphology, and the results of this study can be further compared to on-going work with fresh-water populations to illustrate if and how these complex trait interactions have evolved in different populations.

4. Animal Behavior in Marine Terrestrial Environments

Dr. Amy Cook, The Evergreen State College

One of the greatest challenges animal behaviorists face is observing their subjects in the wild. However, San Juan Island offers opportunities to make detailed observations of the behavior of a variety of animals in the field with relative ease. My mentees will learn the techniques of studying behavior in the field including how to describe behaviors, sampling and recording methodologies, and data collection and analysis. Once they are comfortable with the methodology, my mentees can apply the field behavior techniques they learned to one of the following projects –breeding and social behavior in Pigeon Guillemots or the behavior of juvenile tidepool sculpins (Oligocottus maculotus) in intertidal pools. Animal behavior intersects with conservation biology, ecology, and evolutionary biology and we will discuss these connections in regular research seminars. On San Juan Island, the interaction between human behavior and the behavior of other animals is an important factor in many of our study systems. This project will benefit mentees interested in pursuing a careers or advanced study in animal behavior, field ecology, or conservation biology.

5. Intertidal Ecological Monitoring on Yellow Island

Chris Mantegna, University of Washington Graduate Student & Black in Marine Science (BIMS) Scientist

The impacts of anthropogenic activities on natural environments are growing ever more complex and far-reaching. Moreover, the impacts can be more pervasive and yet go unnoticed in aquatic habitats like marine intertidal environments. Long-term monitoring programs provide an opportunity to examine the (changing) relationship between organisms and their habitats to better inform our understanding of the interplay between biotic and abiotic conditions. This is the second year of the Yellow Island Monitoring project and the first full season of data collection.

The Yellow Island project focus is on (1) understanding the island’s ecology using observation, molecular techniques, and the synthesis of multi-source data, and (2) understanding the interconnectedness of the Salish Sea ecosystem and the foundational changes induced by human activities and climate change. Students will work both onsite at Yellow Island and in the lab collecting qualitative and quantitative data that can help us answer questions of intertidal community composition, food web dynamics, predator prey interactions, and physiological trade-offs in the face of a changing climate.

This project will support skill building and growth in community science project development and management, data collection in the field, analysis using BASH and R programming languages, and public facing science communication and teaching.

6. Thermal Stress and Physiological Performance in Intertidal Mussels

Dr. Mike Nishizaki, Carleton College

In this age of climate change, the biological impacts of rising temperatures have been documented in marine ecosystems worldwide. Such effects are especially evident on rocky intertidal shores, where organisms commonly live near their thermal limits. Understanding how benthic organisms like mussels cope physiologically to the harsh conditions present in intertidal habitats is important in predicting their ecological distribution both today and in the future. For sessile mussels, water temperature and velocity are two key environmental factors when considering processes like respiration that depend on the uptake of oxygen. Moreover, mussels are found across a range of temperature and flow conditions, so the effects of multiple environmental factors on their physiology remains unclear. This REU project will assess the potentially interactive effects of water temperature, pH, and/or flow on the physiological performance (e.g., respiration rates) of mussels. The REU researcher will work closely with a team of other undergraduate researchers studying the responses of endemic and invasive mussels to environmental change.

7. Coastal Fog and Climate Refugia: Combining Photos, Temperature Sensors, and Tide Tables with Satellite Remote Sensing

Dr. Jessica Lundquist, University of Washington

Marine stratus and coastal fog are common along the western U.S. coast, but studies disagree about whether fog frequency is increasing or decreasing.  This marine boundary layer is fast-moving, hard to forecast, a hazard for air and sea navigation, and provides huge contrasts in air temperatures during summer heat waves. While most prior studies have focused on California, fog and humidity are more critical to Washington area intertidal organisms due to the timing of the tides For example, Friday Harbor and Seattle, Washington have over twice as many hours of midday low tide exposure as most California locations (Helmuth et al., 2002). For this project, undergraduate interns will deploy and collect timelapse cameras along with air temperature and relative humidity sensors at coastal and interior sites across San Juan Island, adding data to measurements taken since summer 2021.  Interns will analyze this data in the context of regional winds, tides, and heat waves to understand when and where small-scale temperature variations matter the most to local ecology.  Interns will work with python programming tutorials to process GOES and ECOSTRESS satellite data to put the local observations in a regional context and better understand what controls the extent and duration of summer temperature peaks and marine cloud cover (see example imagery below, highlighting 15°C (27°F) variation in peak temperatures across San Juan Island on 12 August 2021).  Prior programming experience is a plus but not required; anyone with an interest to learn is encouraged to apply.

8. Seagrass Wasting Disease Ecology

Dr. Drew Harvell and Dr. Olivia Graham, Cornell University

Our work focuses on seagrass wasting disease, caused by the protist Labyrinthula zosterae (Lz). This pathogen contributes to significant seagrass declines in the San Juan Islands, WA. We will conduct field and lab experiments exploring pathogen transmission dynamics, including: seasonal infection development and disease monitoring in the field and experiments exploring the role of herbivores in transmitting Lz. There will also be an opportunity to collaborate with colleagues at the Washington State Department of Natural Resources and Friends of the San Juans to monitor disease along the deep edge of local seagrass meadows to provide insight on resiliency of these valuable habitats. There may be an opportunity to collect and process eDNA water samples. These projects are part of a multi-year effort to better understand how Lz spreads in natural eelgrass meadows and broadly has conservation implications for the sustainability of regional seagrass meadows.

As this internship will involve substantial fieldwork, the intern will be immersed in the intertidal environment. The ideal applicant will be detail-oriented, enjoy working on team, and, most importantly, be enthusiastic about marine ecology! Experience working in aquatic/intertidal environments is a plus but not required.

9. Mussel Poop and Climate Change

Dr. Aaron Ninokawa, Friday Harbor Laboratories, University of Washington

This project investigates the drivers and consequences of seawater chemistry modification by foundation species. Many marine habitats, such as mussel beds, are created by habitat-forming species and are homes for many other organisms. A natural consequence of these dense aggregations is that metabolic processes modify seawater chemistry within the interstices of the habitat. The extent of this modification depends on the balance between physical factors, like water current speed and habitat flushing, and biological processes, like respiration and/or photosynthesis rates. This is especially important to understand in places like mussel beds and oyster reefs where respiration increases carbon dioxide, exacerbating stress due to ocean acidification, a component of global climate change. My goals for this summer are to better understand the drivers of this chemical modification and its ecological consequences. Projects will include determining the extent to which accumulating sediment and mussel excrements contribute to chemical alterations within mussel beds and testing the role of physical factors, like tidal height and currents, in controlling this accumulation. We will also conduct experiments with the mussel bed community to examine whether there are tradeoffs between the stressful chemistry caused by this sedimentation and the potential utilization of the particles as food. These results will help us understand the role of mussels in shaping marine community responses to climate change. Prior experience with these topics is not required but students should be excited to learn new chemical analyses and conduct experiments in either the lab or the field (or both!).

10. Shape and Consequence; Puncture Resistance of Biological Armor, or; Bending Stiffness of Bayleen

Dr. Cassandra Donatelli, Chapman University and Dr. Shirel R. Kahane-Rapport, California State University, Fullerton

(Three project options to choose from)

Shape and Consequence: Fishes come in an enormous variety of shapes and sizes, but a lot of them swim in a similar way, by beating their tails back and forth. We are curious about the hydrodynamic consequences of different body shapes, fin shapes, and body ornamentation (like spines and armor) during forward swimming. For this project, the student(s) will work with us to build a “flapper” that will actuate passive robotic models of fishes in a flow tunnel (essentially a treadmill for fish). The flapper will move the models the same way a fish swims (by making them beat their tails back and forth). We will also attach force sensors to the motor to measure lift and drag generated by the models. The specifics of the models will be decided by the student! We are interested in all sorts of different aspects of morphology, so the exact question is TBD. Some examples include but are not limited to the following: “How do different caudal fin shapes affect thrust production in elongate fishes?”, “How does different body ornamentation like spines on the head or armor on the body affect the drag profile of the animal?”, “What are the hydrodynamics of fishes with different aspect ratios (i.e. long and round vs short and flat)?”

Puncture Resistance and Biological Armor: Poachers are a diverse group of armored fishes native to the Pacific Ocean. They are characterized by tough armored plates that cover their entire bodies which vary greatly by species. Most people assume that their extensive armor is good for protection, but how good is it really? When poachers bend their bodies to swim away from predators, the amount of overlap in their armor changes, potentially exposing them to the sharp teeth of the creature trying to eat them. Is it better to sit still and hope your armor does the trick? Or should you risk bending your body to swim away? Our goal is to understand how different armor shapes function during an attack from a predator. Using both fresh specimens and physical models, the student will test puncture resistance using the Universal Testing Machine (UTM). This is a machine used by engineers to measure the mechanics of materials. In our case, we will use it to measure the force needed to puncture armor with a tooth. The student will test their specimens both straight and bent so that we can see how puncture resistance changes as the fish bends its tail to swim away from predators.

Bending Stiffness of Baleen: Mysticete whales are gigantic filter feeders, commonly known as baleen whales due to their unique oral filter, baleen. The upper jaw of a baleen whale is lined with baleen plates that vary in size and width throughout the mouth. The proximal edge of the baleen forms a dense mat of keratin tubules that emerge from the plates. This mat of fringes traps the prey that is engulfed during lunge filter feeding. We are curious about the material properties of baleen, as it likely has a direct impact on performance. We are also interested in how to best create 3D models of baleen for flow experiments. For this project, the student will measure the material properties of the baleen across the plate using the Universal Testing Machine (UTM). We will do this using gray whale, minke whale, and humpback whale plates collected by Fish and Wildlife. The student will also experiment with different manufacturing techniques (3D modeling, 3D printing, casting, etc.) to create realistic and idealized models of baleen for modeling and flow projects in the flume.

11. What Drives Free-Living vs. Motile Life Strategies Among Microorganisms in Intertidal Sediments?

Dr. Mark Lever, University of Texas, Austin

Despite major advances in the field of microbial ecology in recent years, basic aspects concerning the life history strategies of microbial populations in the environment remain unknown. One of these concerns whether microorganisms live free, planktonic lifestyles, or grow attached to particles. While this question has been studied in water columns, little is known about sediments. This may be surprising given that growth modes give key insights into microbial niches in the environment.

This project will investigate the prevalence of free-living vs. particle-attached lifestyles in intertidal sediments of False Bay. Using quantitative PCR and fluorescence microscopy-based methods, the student(s) will investigate environmental patterns in the percentages of free-living microorganisms in intertidal sediments and determine which growth mode is most common among Bacteria and Archaea. Furthermore, relationships between planktonic vs. attached lifestyle and metabolism, e.g. potential links to solubility of energy substrates, or syntrophic life styles, will be investigated by quantifying marker genes indicative of particular metabolisms. Additional project components may include DNA sequencing and bioinformatic analyses, to reveal how free-living and particle-attached taxa differ in their phylogenetic affiliations. Alternatively, based on the student’s interests, motility experiments might be added to test whether free-living vs. particle-attached lifestyles depend on motility, and/or  tests may be added to verify organismal rather than detrital origin of free vs. particle-attached DNA pools.

12. Understanding Substrate Mobility as a Disturbance in Hard Rock Marine Communities

Dr. Alli N. Cramer, Friday Harbor, University of Washington

Disturbance, including fluid forces via waves on rocky shores, is well understood as a community organizing and structuring force. Foundational concepts within ecology, such as Connell’s Intermediate Disturbance Hypothesis and Menge and Sutherland’s Competition/Predation/Disturbance model, recognize that communities exist within a complex mosaic of physical and biological disturbance. This mosaic presents challenges when measuring disturbance regimes since the scales, causes, and consequences of disturbance vary between systems. However, in the marine environment, substrate mobility represents an explicit measure of disturbance impact present across marine ecosystems. This research will investigate a mechanism for disturbance via substrate mobility on benthic organisms through lab experiments and field surveys to compare patterns of substrate mobility with the distribution of benthic communities and species functional groups. Lab experiments will test the performance of benthic organisms, such as mussels and urchins, in adhering to substrates of various strengths against varying fluid forces. If substrate mobility (the combination of experienced fluid forcing and substrate strength) impacts benthic organisms, attachment strength should vary with substrate mobility. Field surveys will examine functional community composition against substrate mobility patterns.