Intern Home Institution Major(s) Project Mentor
Ernestine Ahgeak University of Alaska Fairbanks Fisheries

Title: Juvenile Pacific cod growth rates in response to ocean acidification

Summary: As anthropogenic carbon dioxide emissions increase, more of it will be absorbed by the oceans, lowering its pH. This change in seawater carbonate chemistry may have adverse biological consequences in the future. Ocean acidification may also bring about socio-economic impacts by reducing the harvests of commercially important species of fish, mollusks, and crustaceans. Pacific cod, Gadus macrocephalus, is an important fish species both in an ecological and commercial context in Alaska’s fisheries but there is limited knowledge about its biology. The purpose of this study was to determine how low pH influenced growth rates of juvenile Pacific cod. We reared Pacific cod (99-191 mm TL) for 8 weeks at 8°C in a system designed to maintain seawater pH at levels of 8.05, 7.9, 7.6, and 7.2 and growth rates were calculated from bi-weekly measures of size. Results will help us understand the consequences of human-induced climate change on a commercial fishery in Alaska.

Tom Hurst, Research Fishery Biologist, NOAA - Alaska Fisheries Science Center
Danielle Asson Oregon State University, Corvallis, Oregon Marine Biology

Title: Population structures of the mud shrimp Upogebia pugettensis and its introduced parasitic isopod Orthione griffensis within and among Oregon estuaries.

Summary: Populations of the mud shrimp Upogebia pugettensis, an extremely important geochemical ecosystem engineer of Oregon estuaries, have been declining recently, possibly due to castration effects of the invasive parasitic isopod Orthione griffensis. I am examining the population structure of Upogebia and Orthione within shrimp beds in Oregon estuaries along a low to high intertidal gradient. Three sites, a seaward (closest to the channel), middle, and a landward edge site are selected for each transect. Over 1500 shrimp were collected, sexed, and measured, as were their parasites, from 21 different locations (7 seaward-middle-landward transects) on the Oregon coast, 3 transects from Idaho Point and 2 from Sally's Bend in Yaquina Bay, and one each from Alsea and Tillamook Bays. I am analyzing the measurement data to look for patterns with sex, size, parasitization, and distribution. Hopefully this data will give us more insight into the life histories of Upogebia and Orthione, to forestall the decline of this very important estuarine shrimp.

John Chapman, Department of Fisheries and Wildlife and Brett Dumbauld, USDA-Agriculture Research Service
Megan Cahill Georgetown University Biology

Title: Prevalence of Renibacterium salmoninarum within yearling Chinook salmon (Oncorhynchus tshawytscha) found in the Columbia River Estuary

Summary: Renibacterium salmoninarum, which affects salmon and trout, causes infected fish to develop bacterial kidney disease. This project extracted genetic information from the anterior kidneys of yearling Chinook salmon. A nested PCR (nPCR) was run to amplify any present Renibacterium salmoninarum DNA. Gel electrophoresis was used to determine which samples contained the bacteria’s DNA, and all positive samples were run on a quantitative PCR (qPCR). The data, taken from 2007, 2008, and 2009, was compared with the prevalence of Renibacterium salmoninarum in yearling Chinook salmon from the upriver Bonneville Dam and from the Pacific Ocean.

Kym Jacobson, Biologist; NOAA Ð Northwest Fisheries Science Center
Revanth Chada St. Olaf College Biology

Title: Size-dependent modification of density-dependent habitat selection in juvenile flatfish

Summary: High quality estuarine habitats afford more food and fewer predators than other habitats, enhancing growth and survival of juvenile fish. Intraspecific behaviors that determine how animals occupy nurseries are not well studied, but may have important implications for fisheries management and conservation. Previous experiments indicate that at densities of 6.1 fish m-2, age-0 English sole (Pleuronectes vetulus) preferentially utilize a sandy habitat. As density increases, however, they increasingly utilize a less-preferred gravel habitat. This suggests density dependent habitat selection (DDHS) in juvenile English sole, following ideal free distribution theory. This summer I examined the effect of size on DDHS using equal numbers of small (50-60 mm) and large (70-80 mm) English sole in trials conducted over two different densities of fish.

Cliff Ryer, NOAA Alaska Fisheries Science Center
Keith Chavez University of Illinois - Urbana/ Champaign Chemical Engineering

Title: Eddy correlation accuracy in the presence of a seafloor lander framework

Summary: Eddy correlation is a technique that measures the exchange of chemical quantities. In the ocean, dissolved oxygen fluxes across the seafloor can be measured by coupling an oxygen-sensing microelectrode together with an acoustic velocimeter. However, using bulky frameworks to position and support instruments can interfere with the turbulent eddies that contribute to eddy correlation data. The objective of this research is to quantitatively prove whether or not the structure of a novel landing platform alters the resultant eddy correlation fluxes. This work should help affirm the reliability of the eddy correlation method that is used to study rates of seafloor respiration in coastal ecosystems vital for aquaculture, fisheries, ecotourism, and shipping industries.

Clare Reimers, Professor, College of Oceanic and Atmospheric Sciences
Kelsey Dudziak Rhodes College Physics

Title: Applying regional climate models to the western United States

Summary: Climate models are important tools used by researchers to gather information on future climate change; this information is much needed by decision-makers. Employing the technology available on, we at the Oregon Climate Change Research Institute (OCCRI) used regional climate models (RCMs) to improve upon previous methods of climate prediction, especially in areas of heterogeneous terrain, which necessitate a climate model with mesoscale resolution. By recruiting volunteers throughout the country to run climate model simulations on their personal computers, we amassed numerous simulations that would have been impossible to compile without public assistance. This summer marked the launch of the beta test that precedes an official launch in the fall of 2010. We converted the available data from the beta test into visual representations that we then analyzed through comparison with known data so that we could identify any problems with the simulations that must be corrected before the fall launch.

Phil Mote, Director, Oregon Climate Change Research Institute and Oregon Climate Services
Serena Gountanis University of Illinois at Urbana-Champaign Math-Geology

Title: Flow Modeling of the Connecticut River Estuary

Summary: Kelvin-Helmholtz billows, formed from shear flow instability, play a major part in the mixing of adjacent water masses. However, new data collected from the Connecticut River estuary shows that contrary to older models, the main area of mixing in the billow might be in the braid rather than the core. Water covers about seventy percent of planet Earth and its unique properties regulate everything from the nutrients in an estuary to the climate of the Earth, hence, understanding how stratified water mixes is of significance. The Connecticut River estuary will be computer modeled to simulate the growth of the shear instability into a billow and will be analyzed. Since the observations from the Connecticut River estuary have already been taken, the analysis of the numerical flow models will be compared it to these observations to provide a general better understanding of the billows.

Bill Smyth, Professor, College of Oceanic and Atmospheric Sciences
Shannon Hankin North Central College Biology

Title: Diatom and Vascular Plant Responses to Nutrient Addition in Oregon Estuarine Marshes.

Summary: An increase in anthropogenic activity in the Pacific Northwest may lead to increased input of nitrogen into coastal wetlands and other environments. There has been research done on the effects of nutrient addition to wetlands on the East Coast but little work has been done on the West Coast. This study examines the effects of nitrogen addition to tidal wetland plants and microalgae in Yaquina Bay, OR. A liquid nitrogen fertilizer of four different concentrations (0, 2X, 5X, 10X ambient for 2009 and then increased to 0, 200X, 500X, 1000X ambient in 2010) was applied weekly to four different wetlands in Yaquina Bay for two years (2009 and 2010). We could not detect any significant response by macrophytes (including Salicornia viriginica, Distichlis spicata, Jaumea cornosa, and Triglochin maritima) to nutrient enrichment. However, sediment algae analysis suggests that the microalgal community (including the diatom genera Amphora, Navicula, Nitzschia, and Fragilaria) composition changed in the highest nitrogen treatments (1000X ambient) at three of the four sites. This is probably due microalgae being at the bottom of the food web and normally more sensitive to environmental change than macrophytes.

Ted Dewitt, Ecologist, US EPA-Pacific Coastal Ecology
David Janssen Humboldt State University Chemistry

Title: Determination of dissolved cadmium concentrations in Baffin Bay

Summary: Samples from the July-August 2003 Baffin Bay and Nares Strait research cruise (HLY031) on board the USCGC Healy were analyzed for dissolved cadmium (Cd) using isotope-dilution inductively coupled plasma mass spectrometry (ID-ICP-MS) after a concentration step with the chelating resin NTA Superflow. Cadmium concentrations in surface waters were higher than reported for the Pacific and Atlantic oceans but in agreement with Arctic Ocean data and previous Baffin Bay data. Depth profiles for Cd likely reflect the different water masses found in Baffin Bay, and illustrate the value of multiple tracers for identifying and tracking different bodies of water. A deviation was seen from the typical oceanic cadmium to phosphate ratios (Cd:P), with Cd:P values higher values than reported elsewhere in the oceans for all but the deepest samples. Analytical limitations were encountered that could be overcome through higher analyte yield in the preconcentration step and greater precision in isotopic spike delivery.

Kelly Falkner, Professor, College of Oceanic and Atmospheric Sciences
Amy Johnson Ball State University Biology

Title: In-situ video analysis of  escape behavior of juvenile flatfish exposed to hypoxic conditions

Summary: Globally hypoxic conditions are becoming larger in size and more frequent resulting in “dead zones” and shifts in the biological communities of affected areas. While historically the majority of hypoxic waters have been caused by anthropogenic factors in enclosed and semi-enclosed areas, non-anthropogenic upwelling driven coastal hypoxia has also been documented on central Oregon’s continental shelf where important nursery grounds for juvenile flatfish are located. Strong relationships were observed between average escape percentage and depth (r2=0.9981) and average total length and depth. The percentage of fish that escape and the average total length increased with increased depth while average abundance and dissolved oxygen decreased with increased depth. In situ video analysis provided evidence that juvenile flatfish reaction duration decreased with decreased dissolved oxygen. The largest range in oxygen levels was observed in 30 meters of water where the largest percentage of juveniles (89.9%) and the lowest escape frequency (11.3%) was documented. While juvenile flatfish were observed at all sampling stations the community composition shifted with an increase in depth. The most abundant species shifted from English sole (Pleuronectes vetulus) in waters from 30.0-47.0 meters deep to Pacific sanddad (Citharichtys sordidus) in waters 60.0 to 81.6 meters deep. Behavioral running and hopping were the two dominant behaviors at all stations while burying was only observed in waters 30-47 meters deep. The evidence suggests that decreased dissolved oxygen has the potential to cause sublethal effects on juvenile flatfish and fish located in areas of abundant communities largely composed of juveniles are particularly vulnerable.

Lorenzo Ciannelli, Assistant Professor, College of Oceanic and Atmospheric Sciences
Elizabeth Lopez California State University, Monterey Bay Environmental Science Technology and Policy (ESTP) with a concentration in Marine and Coastal Ecology

Title: Baseline survey of macroinfaunal invertebrate community at potential wave energy site off the Oregon coast

Summary: The Northwest National Marine Renewable Energy Center (NNMREC) plans to deploy a wave energy device testing facility called the Mobile Ocean Test Berth (MOTB) in an area off Yaquina Head, near Newport, Oregon. Wave energy capture devices can potentially alter the physical conditions and in turn impact the macroinfaunal invertebrate community, which act as a food source for major commercial species. The samples that were taken are meant to act as an image of the Mobile Ocean Test Berth Site before deployment of wave energy devices, to later be compared to results of a follow-up study after the devices have been installed. The sampling stations were located in and around the MOTB area. Samples were sorted, and densities of polychaetes, crustaceans, molluscs, echinoderms will be reported and compared to historical surveys in a similar area. Additionally, several major taxa were identified to species, and densities of these will be reported. Relationships between physical conditions and species abundances will be explored.

Sarah Henkel, Assistant Professor (Sr Res), OSU/Hatfield Marine Science Center
Derick Monroy New Mexico State University Mechanical Engineering

Title:Slocum Electric Glider control for improved adaptive sampling relative to a drifting buoy

Summary: The Oregon State University College of Ocean and Atmospheric Sciences(COAS) will participate in a study of lateral mixing in the Atlantic Ocean next summer. In addition to a number of other instruments being used in the study, a small fleet of Slocum Electric Gliders will adaptively sample the water while maintaining a desired positional relationship with a drifter. In order to simplify the process of piloting the fleet, a program will has been developed to use the most recent GPS coordinate of the drifter to generate “goto” files containing newly updated waypoints to be used in the glider navigation. A simulation of the gliders roll in the lateral mixing study has been created to utilize previously recorded drifter GPS data to observe the predicted operation of the gliders in the study. Testing of a one glider mission was conducted to evaluate the effectiveness of the program for use in the four gliders fleet study next summer and has provided positive results in maintaining the relationship.

Kipp Shearman, Associate Professor, College of Oceanic and Atmospheric Sciences
Alissa Morson Carleton College Geology

Title: Thermal evolution of the Aucanquilcha Volcanic Complex based on Fe-Ti oxide temperature models

Summary: The Fe-Ti oxide geothermometer of Andersen and Lindsley (1985) is used to quantify the thermal evolution of the last 8 Ma of the Aucanquilcha Volcanic Complex, northern Chile, to understand processes in continental crust building. The calculated temperatures are also compared to recently published titanium-in-zircon temperatures on the same rocks to verify the accuracy of the new geothermometer. The compositions of touching magnetite and ilmenite pairs were measured via electron microprobe, and the data were reduced using the ILMAT reduction spreadsheet to determine FeO/Fe2O3 ratios based on charge balance. Calculated Fe-Ti oxide temperatures range from 697±30º in older rocks associated with the initiation of volcanism to 1079±30º C at the thermal maximum at ~4 Ma to 825±30º C in younger rocks associated with tapering volcanism of the last ~1 Ma. The temperatures found through the Fe-Ti oxide geothermometer parallel those of the titanium-in-zircon geothermometer with some variation, although a poor determination of activity of Ti in these lavas may have a strong effect on the accuracy of the calculated temperatures. The geothermometer data support the hypothesis of lower temperatures at the initiation of volcanism, higher temperatures as mantle-derived basalt acquisition increase with volcanic activity and lower temperatures as mantle-derived basalt acquisition slows and crustal interaction potentially increases. This model of thermal evolution is consistent with other similar volcanic systems, such as Yanacocha, Peru, and San Juan Volcanic System, Colorado.

Frank Tepley, Assistant Professor, Geosciences
Alison O'Connor Oberlin College


Environmental Studies

Title: Characterizing organic matter in Arctic shelf sediments: a biomarker analysis

Summary: Studying organic matter (OM) in arctice marine shelf sediments can provide insight into global functioning of biogeochemical cycles, and how it may change in response to climatic variations. OM from marine shelves sediments from the Bering Sea, Chukchi Sea, Beaufort Sea, the Canadian Archipelago, and the Baffin Bay/Davis Strait area was characterized using analysis of the bulk composition, particularly stable carbon and nitrogen isotopes; and of CuO oxidation product biomarkers, particularly lignin, cutin acids, amino acids, fatty acids, and dicarboxylic acids. This analysis revealed that there is comparatively little terrigenous OM in the Canadian Archipelago sediments; however, an unusually large proportion of the terrestrial material comes from angiosperm plants. Although the western Alaskan and Mackenzie shelves both have high inputs of terrigenous OM, the chemical signature of this OM is distinct in the western Alaskan shelf as compared to the eastern Alaskan and Mackenzie shelves. Due to similarities between peat signature and the signature for the western Alaskan shelf samples, it is possible that increased coastal erosion leads to greater input of terrigenous OM on the western Alaskan shelf.

Miguel Goni, Professor, College of Oceanic and Atmospheric Sciences
Evan Portier University of California Berkeley Environmental Science

Title: Sources and composition of terrigeneous organic matter from the Fly River floodplains

Summary: The Fly River fluvial system in Papua New Guinea contributes a significant portion of the global organic matter (OM) flux into the marine environment. However, the interaction between the river channels and floodplains with respect to OM cycling is less clear. In order to understand these interactions and their associated biogeochemical roles, it is necessary to identify the sources and composition of OM deposited in the floodplains. Sediments collected along the Fly River floodplains were analyzed using a biomarker approach. Alkaline cupric oxide oxidation was performed and characteristic phenolic products were then quantified using gas chromatography and mass spectrometry. Quantification of lignin-derived phenolic products is particularly interesting as these compounds represent terrestrial biomarkers exclusively synthesized by vascular plants. Together with elemental and isotopic data (i.e. C/N ratios, δ13C, and %OC), the biomarker data provides the first comprehensive examination of OM in this system. The results suggest that floodplain OM is a heterogeneous combination of soil organic material and angiosperm plant debris. In particular, the input of woody and non-woody angiosperm tissue demonstrates the incorporation of surrounding grassland and forest vegetation. Lastly, preliminary analysis of downcore sediments indicates the active sequestration of OM in regions of the floodplain.

Miguel Goni, Professor, College of Oceanic and Atmospheric Sciences
Melissa Prechtl Oregon State University Biology

Title: Impacts of ocean acidification on hatching and development of marine copepod species, Calanus pacificus and Calanus marshallae, and euphausid species, Euphausia pacifica

Summary: Ocean acidification is a growing concern that is a direct result of rising atmospheric CO2 concentrations. With an expected drop in the pH of the world’s oceans, it is important to explore the effects of ocean acidification will have on the foundation of the marine food web. The objective of this study is to analyze how a lower pH impacts hatching and development of 2 marine copepod species and 1 species of krill. I will be participating in biweekly oceanic cruises to collect zooplankton samples. Eggs from female copepods and krill will be put into tanks of varying pH and hatching success and development will be monitored for up to 8 days. Results from this study will give us a better understanding of how climate change could impact oceanic food webs. All three species under investigation are important for local fisheries such as salmon, hake, and halibut.

Bill Peterson, Professor, Oceanography (Courtesy); NOAA - Northwest Fisheries Science Center 
Rick Rusotto Yale University

Geology & Geophysics

Applied Mathematics

Title: Determination of nearshore surface slope field and wave heights using optical polarimetry

Summary: In order to gain a predictive understanding of nearshore dynamics, it is necessary to be able to measure the heights of waves. We are developing a technique to do this remotely, by exploiting the polarization properties of light reflected from the ocean surface. A camera that measures polarization properties has been installed in the field at Duck, NC, but it could not be used to measure wave height before the technique was demonstrated by laboratory testing under known conditions. A second polarization camera was built for the purposes of laboratory testing, and was calibrated to determine filter orientations and correct for gain differences between pixels, lens distortion, and slightly varying fields of view of the four component cameras before being used in laboratory tests. The camera’s ability to determine degree and azimuth of linear polarization (DOLP and AOLP) was then tested by comparing calculated polarization parameters to known conditions created by an external polarizer; while error in DOLP could not be precisely quantified without further tests, we found that we could determine AOLP to within one degree. Following this, the camera was used to make measurements of known wave conditions at the Hinsdale Wave Research Laboratory at OSU. Analysis of the wave tank data, involving signal processing to filter out noise and high-frequency chop, is still in progress as of the time of this writing.

Rob Holman, Professor, College of Oceanic and Atmospheric Sciences
Jillian Schleicher University of Saint Thomas



Title: Effects of small-scale, high-frequency ocean variability on shelf and adjacent interior ocean transport of passive tracers

Summary: Wind-driven coastal currents and summer upwelling of cold waters are the dominant patterns of variability along the Oregon coast, occurring on the temporal scales of several days to months.  This variability is modulated by high-frequency processes associated with three-dimensional, baroclinic tidal flows (known as internal tides). Through the study of the coastal ocean system using model simulations and observations, it is possible to obtain a better understanding of how these different types of flow influence each other.  Gaining this insight is necessary to learning more about surface ocean transports, e.g. of pollutants and nutrients.    Simulated Lagrangian passive tracers released into current flow fields generated from the Regional Ocean Modeling System (ROMS) with cases driven by heat flux and wind (WO), wind with the M2 semidiurnal tide (M2), and wind with 8 tidal constituents (TW) give insight to the effects internal tides have on transports in the ocean.  The addition of tides into the model creates new dynamical system structures in the current flow fields, altering the trajectories of passive tracers and in many regions, causing an increase in the relative dispersion of these particles.

Alex Kurapov, Assistant Professor, College of Oceanic and Atmospheric Sciences
Leah Segui San Diego State University Biology, emphasis in marine biology

Title: Species composition and energy density of black rockfish (Sebastes melanops) diets off Newport, Oregon

 Summary: Variable oceanographic conditions may affect the diversity and abundance of mid-trophic level species which are subsequently reflected in the diets of higher trophic level predators. We collaborated with sport fishermen to obtain stomachs from black rockfish (Sebastes melanops) caught in nearshore reefs off the coast of Newport, Oregon to determine if their diets can indicate fluctuations in local prey availability. I quantified prey items to calculate the relative importance of each prey species and utilized a bomb calorimetry to energy density which may indicate intra-seasonal changes in the energetic needs of black rockfish. It is unknown, however, whether changes in diet reflect prey availability or predator selection. My research is part of Amanda Gladics’ (Marine Resource Management) master’s thesis which aims to use halibut, Chinook and Coho salmon, common murre, and black rockfish diets to assess changes in forage fish availability in the northern California Current.

Ric Brodeur, NOAA/NW/NMFS and Rob Suryan, Assistant Professor (Sr Res), OSU/Hatfield Marine Science Center
Sonia Trevino-Dopatka University of Wisconsin-Madison Biochemistry

Title: Detecting microbial activity by RNA extraction from marine sediments

Summary: Subsea sediments contain large accumulations of methane, a key component of the carbon cycle and a potential source of commercial energy. A microbial consortium removes most of the methane produced in subsea sediments by anaerobic oxidation of methane (AOM). The type and amount of microbial messenger RNA (mRNA) in a sample provides information about the levels of activity of a particular microbial community. Our goal was to estimate microbial activities in the AOM biofilm consortium and surrounding sediments by quantifying mRNA. We used a protocol that enables extraction, quantification, and reverse transcription of mRNA from model marine sediments (Newport Bay: NB) then from subsea sediments (north Cascadia Margin: NCM) were AOM is thought to occur. We detected RNA levels from NB sediments that are consistent with previous findings, but we have not detected RNA from NCM sediments. Future studies with larger sediment quantities may increase our ability to detect RNA in low-activity communities. This approach is an important first step to bridge the current gap between geochemical and biological studies attempting to explain the role of microbes in carbon cycling in a location key to climate and energy concerns.

Rick Colwell, Professor, College of Oceanic and Atmospheric Sciences