Monthly Archives: June 2018

Stream ecosystems and a changing climate

Examining the effect of climate change on stream ecosystems

Oak Creek near McDonald Dunn research lab. The salamander and trout in the experiments were collected along this stretch of creek.

As a first year Master’s student in the lab of Ivan Arismendi, Francisco Pickens studies how the changing, warming climate impacts animals inhabiting stream ecosystems. A major component of stream ecosystem health is rainfall. In examining and predicting the effects of climate change on rainfall, it is important to consider not only the amount of rainfall, but also the timing of rainfall. Although a stream may receive a consistent amount of rain, the duration of the rainy season is projected to shrink, leading to higher flows earlier in the year and a shift in the timing of the lowest water depth. Currently, low flow and peak summer temperature are separated by time. With the shortening and early arrival of the rainy season, it is more likely that low flow and peak summer temperature will coincide.

A curious trout in one of the experimental tanks.

Francisco is trying to determine how the convergence of these two events will impact the animals inhabiting streams. This is an important question because the animals found in streams are ectothermic, meaning that they rely on their surrounding environment to regulate their body temperature. Synchronization of the peak summer temperature with the lowest level of water flow could raise the temperature of the water, profoundly impacting the physiology of the animals living in these streams.



How to study animals in stream ecosystems?

Salamander in its terrestrial stage.

Using a simulated stream environment in a controlled lab setting, Francisco studies how temperature and low water depth impact the physiology and behavior of two abundant stream species – cutthroat trout and the pacific giant salamander. Francisco controls the water temperature and depth, with depth serving as a proxy for stream water level.

Blood glucose level serves as the experimental readout for assessing physiological stress because elevated blood glucose is an indicator of stress. Francisco also studies the animals’ behavior in response to changing conditions. Increased speed, distance traveled, and aggressiveness are all indicators of stress. Francisco analyzes their behavior by tracking their movement through video. Manual frame-by-frame video analysis is time consuming for a single researcher, but lends itself well to automation by computer. Francisco is in the process of implementing a computer vision-based tool to track the animals’ movement automatically.

The crew that assisted in helping collect the animals: From left to right: Chris Flora (undergraduate), Lauren Zatkos (Master’s student), Ivan Arismendi (PI).

Why OSU?

Originally from a small town in Washington state, Francisco grew up in a logging community near the woods. He knew he wanted to pursue a career involving wild animals and fishing, with the opportunity to work outside. Francisco came to OSU’s Department of Fisheries and Wildlife for his undergraduate studies. As an undergrad, Francisco had the opportunity to explore research through the NSF REU program while working on a project related to algae in the lab of Brooke Penaluna. After he finishes his Master’s degree at OSU, Francisco would like to continue working as a data scientist in a federal or state agency.

Tune in on Sunday, June 24th at 7pm PST on KBVR Corvallis 88.7 FM, or listen live at  Also, check us out on Apple Podcasts!

Crabby and Stressed Out: Ocean Acidification and the Dungeness Crab

One of the many consequences associated with climate change is ocean acidification. This process occurs when high atmospheric carbon dioxide dissolves into the ocean lowering ocean pH. Concern about ocean acidification has increased recently with the majority of scientific publications about ocean acidification being released in the last 5 years. Despite this uptick in attention, much is still unknown about the effects of ocean acidification on marine organisms.

Close-up of a Dungeness crab megalopae

Our guest this week, Hannah Gossner, a second year Master’s student in the Marine Resource Management Program, is investigating the physiological effects of ocean acidification on Dungeness crab (Metacarcinus magister) with the help of advisor Francis Chan. Most folks in Oregon recognize the Dungeness crab as a critter than ends up on their plate. Dungeness crab harvest is a multimillion dollar industry because of its culinary use, but Dungeness crab also play an important role in the ocean ecosystem. Due to their prevalence and life cycle, they are important both as scavengers and as a food source to other animals.

Hannah pulling seawater samples from a CTD Carrousel on the R/V Oceanus off the coast of Oregon

To study the effect of ocean acidification on Dungeness crab, Hannah simulates a variety of ocean conditions in sealed chamber where she can control oxygen and carbon dioxide levels. Then by measuring the respiration of an individual crab she can better understand the organism’s stress response to a range of oxygen and carbon dioxide ratios. Hannah hopes that her work will provide a template for measuring the tolerance of other animals to changes in ocean chemistry. She is also interested in the interplay between science, management, and policy, and plans to share her results with local managers and decision makers.

Hannah working the night shift on the R/V Oceanus

Growing up in Connecticut, Hannah spent a lot of time on the water in her dad’s boat, and developed an interest in marine science. Hannah majored in Marine Science at Boston University where she participated in a research project which used stable isotope analysis to monitor changes in food webs involving ctenophores and forage fish. Hannah also did a SEA Semester (not to be confused with a Semester at Sea) where she worked on a boat and studied sustainability in Polynesian island cultures and ecosystems.  Hannah knew early on that she wanted to go to graduate school, and after a brief adventure monitoring coral reefs off the coast of Africa, she secured her current position at Oregon State.

Tune in Sunday June, 17 at 7 pm PST to learn more about Hannah’s research and journey to graduate school. Not a local listener? Stream the show live or catch the episode on our podcast.

Hannah enjoying her favorite past time, diving!

Ocean sediment cores provide a glimpse into deep time

Theresa on a recent cruise on the Oceanus.
Photo credit: Natasha Christman.

First year CEOAS PhD student Theresa Fritz-Endres investigates how the productivity of the ocean in the equatorial Pacific has changed in the last 20,000 years since the time of the last glacial maximum. This was the last time large ice sheets blanketed much of North America, northern Europe, and Asia. She investigates this change by examining the elemental composition of foraminifera (or ‘forams’ for short) shells obtained from sediment cores extracted from the ocean floor. Forams are single-celled protists with shells, and they serve as a proxy for ocean productivity, or organic matter, because they incorporate the elements that are present in the ocean water into their shells. Foram shell composition provides information about what the composition of the ocean was like at the point in time when the foram was alive. This is an important area of study for learning about the climate of the past, but also for understanding how the changing climate of today might transform ocean productivity. Because live forams can be found in ocean water today, it is possible to assess how the chemistry of seawater is currently being incorporated into their shells. This provides a useful comparison for how ocean chemistry has changed over time. Theresa is trying to answer the question, “was ocean productivity different than it is now?”

Examples of forams. For more pictures and information, visit the blog of Theresa’s PI, Dr. Jennifer Fehrenbacher:

Why study foram shells?

Foram shells are particularly useful for scientists because they preserve well and are found ubiquitously in ocean sediment, offering a consistent glimpse into the dynamic state of ocean chemistry. While living, forams float in or near the surface of the sea, and after they die, they sink to the bottom of the sea floor. The accumulating foram shells serve as an archive of how ocean conditions have changed, like how tree rings reflect the environmental conditions of the past.

Obtaining and analyzing sediment cores

Obtaining these records requires drilling cores (up to 1000 m!) into deep sea sediments, work that is carried out by an international consortium of scientists aboard large ocean research vessels. These cores span a time frame of 800 million years, which is the oldest continuous record of ocean chemistry. Each slice of the core represents a snapshot of time, with each centimeter spanning 1,000 years of sediment accumulation. Theresa is using cores that reach a depth of a few meters below the surface of the ocean floor. These cores were drilled in the 1980s by a now-retired OSU ship and are housed at OSU.

Theresa on a recent cruise on the Oceanus, deploying a net to collect live forams. Photo credit: Natasha Christman.

The process of core analysis involves sampling a slice of the core, then washing the sediment (kind of like a pour over coffee) and looking at the remainder of larger-sized sediment under a powerful microscope to select foram species. The selected shells undergo elemental analysis using mass spectrometry. Vastly diverse shell shapes and patterns result in different elements and chemistries being incorporated into the shells. Coupled to the mass spectrometer is a laser that ablates through the foram shell, providing a more detailed view of the layers within the shell. This provides a snapshot of ocean conditions for the 4 weeks-or-so that the foram was alive. It also indicates how the foram responded to light changes from day to night.

Theresa is early in her PhD program, and in the next few years plans to do field work on the Oregon coast and on Catalina island off the coast of California. She also plans to undertake culturing experiments to further study the composition of the tiny foram specimens.

Why grad school at OSU?

Theresa completed her undergraduate degree at Queen’s University in Ontario, followed by completion of a Master’s degree at San Francisco State University. She was interested in pursuing paleo and climate studies after transformative classes in her undergrad. In between her undergraduate and Master’s studies she spent a year working at Mt. Evans in Colorado as part of the National Park Service and Student Conservation Association.

Theresa had already met her advisor, Dr. Jennifer Fehrenbacher, while completing her Master’s degree at SF State. Theresa knew she was interested in attending OSU for grad school for several reasons: to work with her advisor, and to have access to the core repository, research ships, and technical equipment available at OSU.

To hear more about Theresa’s research and her experience as a PhD student at OSU, tune in on Sunday, June 10th at 7pm on KBVR Corvallis 88.7 FM, or listen live at  Also, check us out on Apple Podcasts!

How high’s the water, flood model? Five feet high and risin’

Climate change and the resulting effects on communities and their infrastructure are notoriously difficult to model, yet the importance is not difficult to grasp. Infrastructure is designed to last for a certain amount of time, called its design life. The design life of a bridge is about 50 years; a building can be designed for 70 years. For coastal communities that have infrastructure designed to survive severe coastal flooding at the time of construction, what happens if the sea rises during its design life? That severe flooding can become more severe, and the bridge or building might fail.

Most designers and engineers don’t consider the effects of climate change in their designs because they are hard to model and involve much uncertainty.

Kai at Wolf Rock in Oregon.

In comes Kai Parker, a 5th year PhD student in the Coastal Engineering program. Kai is including climate change and a host of other factors into his flood models: Waves, Tides, Storms, Atmospheric Forcing, Streamflow, and many others. He specifically models estuaries (including Coos and Tillamook Bay, Oregon and Grays Harbor, Washington), which extend inland and can have complex geometries. Not only is Kai working to incorporate those natural factors into his flood model, he has also worked with communities to incorporate their response to coastal hazards and the factors that are most important to them into his model.

Modeling climate change requires an immense amount of computing power. Kai uses super computers at the Texas Advanced Computing Center (TACC) to run a flood model and determine the fate of an estuary and its surroundings. But this is for one possible new climate, with one result (this is referred to as a deterministic model). Presenting these results can be misleading, especially if the uncertainty is not properly communicated.

Kai with his hydrodynamic model grid for Coos Bay, Oregon.

In an effort to model more responsibly, Kai has expanded into using what is called a probabilistic flood model, which results in a distribution of probabilities that an event of a certain severity will occur. Instead of just one new climate, Kai would model 10,000 climates and determine which event is most likely to occur. This technique is frequently used by earthquake engineers and often done using Monte Carlo simulations. Unfortunately, flooding models take time and it takes more than supercomputing to make probabilistic flooding a reality.

To increase efficiency, Kai has developed an “emulator”, which uses techniques similar to machine learning to “train” a faster flooding model that can make Monte Carlo simulation a possibility. Kai uses the emulator to solve flood models much like we use our brains to play catch: we are not using equations of physics, factoring in wind speed or the temperature of the air, to calculate where the ball will land. Instead we draw on a bank of experiences to predict where the ball will land, hopefully in our hands.

Kai doing field work at Bodega Bay in California.

Kai grew up in Gerlach, Nevada: Population 206. He moved to San Luis Obispo to study civil engineering at Cal Poly SLO and while studying, he worked as an intern at the Bodega Bay Marine Lab and has been working with the coast ever since. When Kai is not working on his research, he is brewing, climbing rocks, surfing waves, or cooking the meanest soup you’ve ever tasted. Next year, he will move to Chile with a Fulbright grant to apply his emulator techniques to a new hazard: tsunamis.

To hear more about Kai’s research, be sure to tune in to KBVR Corvallis 88.7 FM this Sunday May, 27 at 7 pm, stream the live interview at, or find it in podcast form next week on Apple Podcasts.