Summer Research Internships for Undergraduates

Daisy J. Castillo Alteration of rare earth element distribution as a result of microbial activity and empirical methane injection
Daisy J. Castillo, Biochemistry major, University of California-Santa Cruz
CEOAS Mentors: Brian Haley, Andrew Thurber, and Rick Colwell
Presented at 2014 Fall Meeting, American Geophysical Union, San Francisco, CA, December 15-19

As a result of warming, methane is being released in to the marine environment in areas that have not historically experienced methane input. While methane is a potent greenhouse gas, microbial oxidation of methane within the sediment greatly limits the role of marine methane sources on atmospheric forcing. However, in these areas of new methane release, consumption of methane prior to its release into the atmosphere is a result of the response of the microbial community to this new input of methane. Further, rare earth elements (REEs) are not currently thought to be involved with microbial activity, but this assumption has not been rigorously tested. Here we test that: (1) microbial communities will rapidly respond to the onset of methane emission, and (2) the microbial response to this methane input will impact the distribution of REEs within the sediment. Undisturbed cores sampled from a tidal flat at Yaquina Bay, OR, were brought back to a lab and injected with anoxic seawater (as a control) or anoxic sea water saturated with methane gas for a total of 2 weeks. Aerobic methanotrophs proliferated over this short time period, becoming an abundant member of the microbial community as identified using fatty acid biomarkers. Excitingly, the experimental injection of methane also shifted the distribution of REEs within the sediment, a trend that appeared to follow the microbial response and that was different from the control cores. Further, the lightest REEs appeared to be used more than the heavier ones, supporting that the REEs are being actively used by the microbes. While we focused on identifying the response of those microbes responsible in methane-cycling, we also identified how the entire microbial community shifts as a result of methane input, and correlating with shifts in REE distribution. Here we have empirically demonstrated the rapid response of methanotrophs to the onset of methane emission and that REE distribution within the sediment is likely impacted by microbial activity, including that involved with methane cycling. This has broad implications to identifying the role of novel methane seeps in global carbon cycles and our understanding of REE distributions within marine sediments.

Caroline Coccoli Organic matter sequestration in Oregon margin sediments: tectonic, climatic and oceanographic controls
Caroline Coccoli, Environmental Science major, Northwestern University
CEOAS mentor: Miguel Goni
Presented at 2014 Fall Meeting, American Geophysical Union, San Francisco, CA, December 15-19

A combination of box, gravity and piston cores from a site on the upper slope off the Umpqua River in the central Oregon margin were used to create a high-resolution record of organic matter burial over the past ~13,000 years. Our objective is to understand how variations in precipitation intensity and frequency, tectonic uplift rates, and topographic relief affect the magnitude and composition of organic matter deposited along this margin. To examine the possible tectonic and climatic factors influencing the land-ocean relationship of Cascadia during the late Holocene, we measured the organic carbon content, carbon-nitrogen ratio, stable isotopic compositions of organic carbon, yields of lignin-derived and lipid-derived constituents, and mineral surface area of collected sediments from box, kasten and piston cores. Decreases in several organic constituents revealed a potential preferential degradation of marine organic matter over time. Lignin phenol abundances oscillated downcore, pointing towards changes in the provenance of terrigenous organic matter transported to this site. Primary component analysis (PCA) illustrated distinct marine and terrestrial organic matter-dominated segments of the record, which will be correlated to eustatic, tectonic and climatic forcings over the late Holocene.

Megan Gomez Assessing LiDAR data accuracy with vegetation data: efforts to improve visualization of climate change scenarios
Megan Gomez, Marine Science major, Evergreen State College
CEOAS mentor: Mary Santlemann

Estuarine environments are critically important habitats for anadromous salmonids, both for juveniles in the transition from fresh to salt water and for adult salmon as they return to their natal streams to spawn. These dynamic systems are currently compromised as a result of extensive alterations from development, installation of tide gates and berms, and agricultural conversion. They face further threats from changing climate and projected sea-level rise. Current scenarios of sea-level rise predict up to a 2-m increase. Alterations in the availability of salmon habitat are expected to occur. Mapping of habitat has become a crucial step in the process of coastal planning to guide efforts toward mitigation of sea-level rise. In this study, vegetation surveys were performed to complement and enhance light detection and ranging (LiDAR) data for mapping the ground surface of the Coos River Estuary, estimating the relative accuracy of the LiDAR data, and quantifying the relationships between vegetation and salt marsh zonation along the gradient from the coastal margin to the upland. These data have the potential to assist in development of future sea-level rise scenarios and provide detailed information on vegetation boundaries to be considered in investigation of the potential effects of sea-level rise on salmon habitat.

Sam Greydanus Exploration of salt wedge dynamics in the Columbia River Estuary using optical measurements of internal ship wakes
Sam Greydanus, Computer Science major, Dartmouth College
CEOAS mentor: Rob Holman
Presented at 2014 Fall Meeting, American Geophysical Union, San Francisco, CA, December 15-19

In May of 2013 and beyond, Argus optical measurements of the mouth of the Columbia River (MCR) estuary and plume were collected as part of the RIVET II multi-investigator _eld experiment. One surprise was the strength of eddy and internal wave signatures observed in movies computed from one- minute averages of high-frequency snapshots (such that gravity waves were averaged out but slicks and variable surface roughness remained). In particular, passing ships left wakes that propagated away at speeds on the order of 0.5 m/s, much slower than gravity waves. They are presumably surface manifestations of internal waves associated with the time-varying salt-wedge. Thus, these internal ship wakes appear to act as probes of internal strati_cation dynamics. This paper will explore the time variations of these internal waves and relate them to corresponding variations in the estuary salt wedge.

Elizabeth Patterson An investigation of the affect of particle size on the bulk magnetic record of sediments from continental shelf and slope of the Gulf of Alaska
Elizabeth Patterson, Geology major, Bates College
CEOAS Mentors: Rob Hatfield and Joe Stoner

Magnetic properties of four particle size fractions from the sediment core EW0408-85JC located on the continental slope in the Gulf of Alaska were used to interpret the bulk magnetic record from the core. Compared to North Atlantic sediments not much is known about the magnetic properties of North Pacific sediments, despite this region experiencing many of the same large-scale processes. Interpretation of the data showed that magnetic susceptibility (MS) varied between different particle size fractions indicating that particle size abundance was a driving factor in the bulk magnetic susceptibility signal. This theory held true for explaining higher levels of MS in the last deglacial, but could not explain the whole core. Hcr data and Day plots for the fine silt fraction of the core showed a coarsening and hardening of the magnetic minerals in one region of the core, which helped identify a diagenetic interval in the core that was located in between the last deglacial and the Holocene time periods. The data and results collected will hopefully be useful for analysis of future cores and drill records from the Gulf of Alaska and elsewhere.

Nicole Rocco Trace gas anomalies in the 2012 Greenland melt layer
Nicole Rocco, Earth Science major, Oregon State University
CEOAS mentor: Ed Brook

The objective of this project is to investigate the gas chemistry of the 2012 Greenland Ice Sheet melt layer. The melt layer samples were collected at Summit Station in the dry snow zone of Greenland during the 2013 field season from two distinct pits. There were two different depths collected – the 2012 surface layer (when collected, ~65cm below the surface), and a deeper layer (~110cm). While there is some information about melt layers in the literature, there is little understanding about their impact on the ice core record. Anomalous gas levels have been observed in melt layers within firn and ice cores; this has caused deliberation on why the levels are elevated. The current consensus is the solubility/dissolution of gases in the melt water and, if concentrations are higher than those given by Henry's Law, microbial activity. We are investigating this further with gas chromatography and stable isotope analysis of the melt layer itself. Along with physical observations of the ice, we analyzed twelve samples for methane concentrations and seven samples for carbon dioxide concentrations. Through gas chromatography, we found elevated levels of both gases – both within and above the range calculated through Henry's Law. The methane concentrations ranged from near current atmospheric levels (~1800 ppb) to over 5000 ppb. The carbon dioxide levels ranged from 6000 ppm to as high as 24000 ppm. One of the burning questions left looming is what process or processes produced gas concentrations beyond the scope of solubility/dissolution. While microbial activity is a viable answer, this process tends to occur only in anoxic environments – it has been considered and discussed regarding deep ice cores that lie below the firn layer (about 80m). We intend to complete noble gas/nitrogen ratios also to further constrain the effects of solubility and dissolution. Ultimately, the goal is to learn about what processes are taking place in melt water, how they differ from normal glacial processes, and how they affect the continuous ice core record. With more melt modeled for the Greenland Ice Sheet in the future, this study means to give more insight into the long term effects of climate change (both past and future) and long scale glacial melting, as well as paving the way for future research on ice sheet melt layers.

Tuesday Simmons A community analysis of benthic microbes across the deep ocean floor
Tuesday Simmons, Ecology and Microbiology major, Marshall University
CEOAS mentor: Andrew Thurber

Despite covering two-thirds of the Earth's surface, the deep oceans are largely unexplored. With recent advances in technology, however, the deep sea is becoming more accessible to exploration and exploitation. Here we aimed to identify the variation in ecosystem function in a variety of deep sea habitats through analysis of the microbial communities of surface sediment. DNA was extracted from surface sediment samples from 37 different sites from depths of 200m to 5300m and the microbial community sequenced. The resulting 7.9 million 350 bp sequences are currently being processed using bioinformatics approaches, however here we present preliminary results from a subset of our data from four locations. These results were compared using a Bray-Curtis similarity matrix and presented as a non-metric multi-dimensional scaling plot. As our data processing continues, we will test the hypotheses that the biodiversity of these benthic communities will positively correlate with primary productivity at the surface, along with other physical factors such as temperature. Although these microbes may seem insignificant in size compared to Earth's vast oceans, they are incredibly numerous, and it is important to know about the factors that structure the marine ecosystem.

Michael Spagnolo Classification and Analysis of Clouds around Marys Peak
Michael Spagnolo, Meteorology major, Pennsylvania State University
CEOAS mentors: Simon de Szoeke, Eric Skyllingstad, and Chris Thomas

In late April of 2010, the Marys Peak Observatory mounted a camera on Burt Hall on the Oregon State University campus in Corvallis, OR. Every twenty seconds, this camera saved an image looking west towards Marys Peak, the highest point on the Oregon Coastal Range. At the end of each day, a time-lapse was made from the resulting images. Marys Peak is the highest in the coast range and is popular for hiking trips, camping trips, and other outdoor activities year round. Weather, especially temperatures and cloud cover, can change rapidly due to varying air masses in close proximity. A classification scheme was created with seven categories of clouds most commonly seen along the peak: marine stratus and orographic stratus, convective cumulus, altocumulus and altostratus, stratocumulus, lenticularis, ground fog, or clear skies and cirrus. 780 videos were watched over the four years and cloud types were recorded and digitized. Climatology was then constructed from the data and placed on the newly updated, publicly accessible Marys Peak Observatory website. Marine stratus and orographic stratus were the most common, occurring on 448 separate days, with lenticular clouds only developing 45 separate times. Ground fog and clear skies were the most seasonable cloud types, with nearly 80% of the days in August being clear and 50% of the mornings in November starting out with ground fog. An in depth case study on an exceptional day was also completed.

Ellen Svadlenak Trace Element Variations and Age of Colombian Emeralds
Ellen Svadlenak, Earth Science major, Oregon State University
CEOAS mentor: John Dilles
Presented at 2014 Annual Meeting, Geological Society of America, Vancouver, BC, October 19-22

The Colombian emerald deposits are recognized as the most economically significant emerald deposits in the world, and are hosted in hydrothermally altered black shales on either side of the Cordillera Oriental — a setting unique compared to other known emerald deposits. As such, uncertainty persists in the path or source of the trace metals (namely chromium and vanadium) which are responsible for the brilliant green color in these emeralds. We have used electron microprobe analysis to study variations in trace element concentrations in transects across Colombian emeralds, and used the 40Ar/39Ar method to determine the age of the Muzo emerald deposits, located on the western side of the Cordillera Oriental. EMP analysis of lightly colored emerald crystals from the Puerto Arturo, Matefique, Taquendama, and Catedral mines indicate that higher concentrations of trace metals (Cr, V, Sc, Mn, Mg, and Fe) coincide with lower concentrations of aluminum, and suggest that these metals substitute for aluminum in the beryl crystal structure. In addition, deeper green color in the samples (in particular from Matefique) is correlated with higher concentrations of vanadium and chromium, while other trace metal concentrations show very little variation with color, suggesting V and Cr are the main chromophores. More strongly colored samples contain an average of 7910.5 ± 2442.45 (1σ) ppm V and 4062.83 ± 853.59 (1σ) ppm Cr, while weakly colored samples show only 1044.89 ± 782.55 (1σ) ppm V and 574.43 ± 686.68 (1σ) ppm Cr. In future, we plan to further investigate the source of these trace metals. We obtained 40Ar/39Ar weighted mean ages on hydrothermal mica (muscovite) found in wall rock at the margins of emerald-bearing veins. The ages of two mica samples from the Muzo mine are 62.05 ± 0.40 Ma (2σ) and 60.54 ± 0.63 Ma (2σ). Previous 40Ar/39Ar ages from the western Cordillera Oriental include 35-38 Ma at Coscuez and 32 Ma at Muzo (Cheillitz et al., 1994). However, ages from the eastern Cordillera Oriental reported by Cheillitz et al. (1994) are 65 Ma, and Ordonez et al. (2001) have obtained 61 to 67 Ma Rb/Sr ages for emeralds from both the eastern and western Cordillera Oriental. Our ages indicate that hydrothermal activity affected the Muzo area around 61 to 62 Ma as well, and establish the need for additional isotopic dating of the Muzo emerald deposit.

Irina Tolkova Effects of Stratified and Random Sampling on Determining the Size-at-Age of Pacific Cod in the Eastern Bering Sea
Irina Tolkova, Applied Mathematics major, University of Washington
CEOAS mentor: Lorenzo Ciannelli
Presented at 2015 ICES Annual Science Conference, Copenhagen, Denmark, September 21-25

Stock assessments of Pacific cod – an economically and ecologically important groundfish – draw on the size-at-age relationship of the population. The size-at-age function may differ among individuals within a population due to the effects of environmental variables (such as temperature and depth-related factors) on fish growth and due to local adaptations in genetically structured stocks. Therefore, spatially uneven sampling methods may cause bias in the size-at-age function if this spatial variability is not taken into account. For the past two decades, the Alaska Fisheries Science Center has conducted groundfish trawl surveys on Pacific cod in the Bering Sea and collected records of both environmental variables and catch lengths and ages. We used these records to characterize the temporal and spatial patterns in the distribution of cod size-at age with respect to environmental variables. In addition, we simulated the two sampling methods currently in use – random sampling and length-stratified sampling – to compare the resulting size and age structures and the population size-at-age relationships. We found that there is a consistent significant spatial variation in size-at-age, where individuals between the ages of 1 to 3 were on average about 5 cm larger offshore than inshore. Random sampling resulted in a better representation of the size and age distributions of the cod population, though both random and stratified sampling created very similar overall size-at-age relationships. A simple size-at-age key from either sampling method curve did not capture the spatial variation in growth, but this problem can be overcome by including spatial and environmental factors when computing an age length key. These results are instrumental to inform assessment strategies and improve current methods to sample and characterize cod demographic parameters in the Eastern Bering Sea.

Erick White Phytoplankton cell growth under fluctuating light regimes
Erick White, Biology major, Swarthmore College
CEOAS mentor: Ricardo Letelier

Light functions as an essential resource for photosynthetic organisms to grow and perform physiological functions. The goal of this research project is to determine how the perturbations in light sources (intensity/frequency) can alter the photosynthetic production and growth rates of phytoplankton. Any understanding of phytoplankton ecology and predictions about how environmental changes will affect marine ecosystems comes down to what factors control growth and photosynthesis, and how variations in those factors affect the community. In vivo fluorescence, primarily through chlorophyll a light emission, will be used to determine growth rates of phytoplankton cultures incubated in batch culture mode under constant temperature and varying light levels with conditions. Samples will be run through Tau-Turner and PAM Fluorometers to determine fluorescence as a measure of chlorophyll concentration. Data on how phytoplankton respond to light fluctuations will provide a better understanding of how species respond to fluctuations of light in the ocean, and how that will affect communities.

Catherine Wielgasz Distribution of carbon isotopes (δ13C) in the Pacific Ocean during the past 23,000 years
Catherine Wielgasz, Environmental Chemistry major, Castleton State College
CEOAS mentors: Andreas Schmittner and Alan Mix

Stable carbon isotope ratios (δ13C) measured on shells of fossil foraminerfera found in ocean sediments can be used to reconstruct ocean circulation and carbon cycling. By compiling and reporting published and unpublished data measured on two species of foraminifera (C. wuellerstorfi and U. peregrina) in Mix's lab over the past decades, changes in Pacific ocean δ13C over time are reconstructed. The core-top sediment data, which represent the late Holocene (past 0-3,000 years) show a similar distribution as modern water column measurements such as a lower values in the North Pacifc than in the South Pacific, a minimum in the North Pacific at shallow waters (400-1,500m) and in the South Pacific at mid depth (1,500 - 3,000 m). This agreement confirms that the sediment data reflect the water column distribution and indicate that they can be used for past reconstructions. For the past 23,000 years (which corresponds to the last glacial maximum, the deglaciation, and the Holocene), the δ13C in the Pacific Ocean has been increasing by about 0.4 permil indicating a loss of respired carbon. However, the general pattern of the distributions remained unchanged indicating that the circulation pattern of the modern deep Pacific prevailed over the past 23,000 years.

Elizabeth Yankovsky Response of the Length and Stratification of the North River Estuary to Changes in Forcing
Elizabeth Yankovsky, Physics major, University of South Carolina
CEOAS mentor: Jim Lerczak
Presented at 2014 Fall Meeting, American Geophysical Union, San Francisco, CA, December 15-19

The response of the length and stratification of the North River estuary (MA) to variations in river discharge Qf and tidal amplitude UT is analyzed using time series from four along-channel locations in conjunction with cross- and along-channel boat board surveys collected from April 4 to June 22, 2006. The North River is a periodically stratified to well-mixed estuary with a channel depth of 5 m and width of 60 m. Its length is defined as distance between the mouth and the location where bottom salinity reaches a value of 5 psu, determined by approximating a linear along-channel salinity gradient. During the period of low discharge (5 m3/s) spanning April, the average length of the estuary is relatively high and varies based on tidal amplitude. Lengths are typically 7-9 km for neap, 8-11 km for intermediate, and 10-14 km for spring tides. During two storm events marked by high discharge (Qf >15, reaching 85 m3/s) mean length remains shorter, at 6-9 km. Length of the estuary has a weak dependence on discharge and a positive relationship to tidal amplitude. Stratification exhibits an increase with increasing discharge and a decrease with increasing tidal amplitude at mid-estuarine locations. Within tidal cycles, peak stratification is typically observed at flood-ebb transitions. Using a one-dimensional salt balance, the along-channel diffusivity has a strong dependence on river discharge, and less so on tidal amplitude. It ranges from 100-200 m2/s during low discharge periods and peaks at 1200 m2/s during storm events. Although a simplified linear model of the salinity gradient was assumed, insight was gained as to how the estuary responds to river discharge and tidal variability.