The composition and abundance of lipids preserved in lake sediments provides information on the past environment, and changes in this geochemical signal through time may be driven by climate. To understand precipitation changes in the Pacific over the last few thousand years, sediment cores have been collected from lakes on multiple islands, including Poza de Los Diablos and Pozas Verdes on Isabela Island in the Galapagos. Lipids from these sediment cores were solvent-extracted, individual compounds were identified by gas chromatography-mass spectrometry (GC-MS), and abundances of these compounds were quantified using a gas chromatograph-flame ionization detector (GC-FID). Poza de Los Diablos data reveal elevated concentrations of both middle and long chain-length n-alkanes from approximately 1450 to 1850 AD, and indicate an enhanced contribution of material from both aquatic and terrestrial plants during this interval, which may be caused by shifting hydrologic patterns. However, these changes might also reflect a local event such as an altered flow path for surface water due to river or wave erosion. To improve our understanding of paleoenvironmental changes indicated by the Poza de los Diablos data, lipids from cores taken from nearby Pozas Verdes were also extracted and analyzed by GC-MS and GC-FID. Due to their close proximity (<1 km), any climate event that affected Posa de Los Diablo would have also affected Pozas Verdes, but with significantly different modern salinity (Diablos = 10, Verdes = 40) and ecology, each lake is likely to have responded quite differently to changing precipitation patters. By analyzing both records together we seek to improve our interpretation of the past environment.

Marine based industries, particularly the shellfish industry, are increasingly concerned about the viability of their product due to changing ocean pH conditions. Many other organisms with calcareous shells or exoskeletons are impacted by this change in sea water acidity due to anthropogenic gases. One such organism is the Artemia salina, or brine shrimp. Acidification causes dissolution of the shells into calcium and carbonate ions that float freely in the water. It was hypothesized that three closed systems could be created to replicate the ocean conditions of the present and future, specifically in 50 years and 100 years. Brine shrimp were chosen to be test subjects due to their ease of propogation. The closed systems provided pH, Ca2+ concentration, and the vitality of the tested brine shrimp community data. The working hypothesis is that Ca2+ ion concentration will increase as the exoskeletons dissolve with the decrease of pH.

Where plankton reside in the water column is affected, among other things, by haloclines. Therefore the salinity stratification of the water can have major effects on the levels of plankton present. Our study focused on Possession Sound zooplanktons’ response to varying levels of salinity in a vertically stratified column. We questioned the preferred salinity level of various zooplankton found in a sample of Possession Sound water. We hypothesized that most zooplankton will prefer waters approximately 24 ppt since that is the average salinity of Possession Sound. We have so far looked at literature surrounding the subject and constructed the necessary apparatuses for the experiment. As part of our spring thesis research, we plan on observing the plankton’s response to the introduction to this environment.

Bioaccumulation of heavy metals due to river runoff is a pressing issue. Through the Ocean Research College Academy (ORCA), I will conduct research during the spring term analyzing the presence of heavy metals in the Puget Sound and the possible bioaccumulation in harbor seals. Sediment is collected using a Van Veen Grab from set sites around the Puget Sound once a month for the span of a year. Sediment samples will also be taken from various sites along the Snohomish River during the month of April. These samples will be sent to the Everett Environmental Laboratory to be tested for levels of mercury, arsenic, lead, zinc, cadmium, and copper. We will then attempt to obtain harbor seal excrement from the Everett Marina and send to the lab to be tested for the heavy metals listed above by the beginning of May. The data will be used to compare the amount of heavy metals found in the sediment of the Puget Sound to the amount of heavy metals found in secondary consumers (in this study harbor seals).

Climate change is arguably the most important issue society faces in the next century. A principle driver of climate change is the emission of “greenhouse” gases to the atmosphere, which enhance warming by trapping heat. Methane in particular has a powerful warming potential relative to other greenhouse gases. One potential source of methane to the atmosphere is gas hydrates, solid crystalline structures of natural gas and water found in marine sediment. Gas hydrates are solid only under certain conditions of temperature and pressure; otherwise, the crystal structure releases gaseous methane in the water column. Gas hydrates pose a threat to the climate in two ways – by dissociation in unstable conditions and by passive “leakages” of methane from deep reservoirs that bypass the gas hydrate stability field. Both processes result in bubble plumes of methane gas in the water column, which may be reaching the atmosphere through gas exchange. Hydrate Ridge, offshore Oregon, represents a good model system to study for understanding gas hydrate dynamics, and it is a known site of passive fluxes of methane. This study uses novel sampling methods, such as ROV sampling for increased accuracy, to collect water samples at Hydrate Ridge which will be analyzed for methane content. Multibeam sonar data were also collected to image the spatial extent of the bubble plumes. The data will indicate the degree to which methane is penetrating into the water column and reaching the atmosphere. Hydrocasts from the research vessel R/V Thompson were taken at Southern Hydrate Ridge over two years, 2010 and 2011, for analysis in the lab with a gas chromatograph. The end goal of the project is to quantify the flux of methane into the mixed layer of the ocean, which exchanges methane with the atmosphere faster than it is consumed by microbial oxidation.

The harmful bloom-forming alga, Heterosigma akashiwo, has a dual-stage life cycle, transitioning between a vegetative, motile stage in the water column and a resting, non-motile stage in the sediments. Previous observations have revealed a large shift in neutral lipid content as cells transition between vegetative and resting life stages. The relative neutral lipid content per cell decreases as cells enter the resting stage, followed by a rapid synthesis of neutral lipids once cells emerge from the resting stage. Neutral lipid bodies are thought to be a source of cell energy reserves. The purpose of my research is to study how fatty acid profiles shift in H. akashiwo during these life cycle transitions. Understanding changes in fatty acid profiles is important in understanding how cells respond to changes in environmental conditions and how lipids are used in metabolic processes. In this study, two strains of H. akashiwo (CCMP 452 and UWC 13.03) are signaled to enter the resting stage by putting cell cultures into the dark at 10 °C for 18 days. Resting cells are activated by exposing the cultures to growth supporting conditions of light and increased temperature (12 °C). Cell viability and relative neutral lipid content is determined by staining with the SYTOX-Green DNA stain and the BODIPY505/515 neutral lipid stain, respectively, using flow cytometry. Fatty acid profiles are determined using an established gas chromatography- mass spectrometry method developed in the Cattolico laboratory. I will report on the outcomes of the fatty acid profiling for H. akashiwo over the alga’s dual-stage life cycle. I anticipate distinct change in the fatty acid profiles between these life stages.

Harmful algal blooms (HABs) are an important, but generally not well understood topic in oceanography. The dinoflagellate, Alexandrium catenella, is a common HAB phytoplankton that can lead to a buildup of toxins in commercial shellfish and cause paralytic shellfish poisoning in humans that consume them. When conditions for growth in the water column are unfavorable, Alexandrium forms a protective cyst that sinks and lays dormant in the sediment. The goal of this project is to create a more efficient way to enumerate HAB species cysts in sediments around the Puget Sound to create a record of past HAB events. I propose to use density gradient centrifugation and rapid flow cytometry on sediment cores from Puget Sound to determine how cyst concentration has changed over time, using sediment depth as a proxy for age. Density gradient centrifugation will be used to separate cysts out of sediments by using variations in specific gravity, and provide concentrated cyst samples. Then rapid flow cytometry will be used to determine the cyst concentration in each sediment sample based on the specific fluorescent signature of cysts. Preliminary results indicate that the density centrifugation method is able capture at least 85% of cysts at any given sediment core depth. Using this method I will also estimate the frequency of HABs in the past 50 years using lead 210 isotope dating on sediment cores. These methods will allow HAB researchers to reconstruct past Alexandrium events to fine tune models that predict periodic Alexandrium occurrences. This coupled with performing germination experiments on cysts to understand their biology will help the research community understand the conditions that control Alexandrium blooms as well as their frequency and intensity. None of this can be achieved until a fast, simple, and reliable method for obtaining and enumerating cysts in sediments is created.

In 2011, a 3 week research cruise on board the R/V Atlantis was undertaken to the Endeavor segment of the Juan de Fuca spreading ridge. The main purpose of this expedition was to determine conductive heat flow from lightly sedimented sea floor within the axial valley of the spreading center (in close proximity to an isolated hydrothermal vent system). During a series of Remotely Operated Vehicle (ROV) dives to the seafloor, hundreds of heat flow time series were measured by the deployment of 13 “thermal blanket” heat flow instruments, which will enable researchers to better constrain the spatial extent of the hydrothermal fluid recharge zone. Throughout each dive, continuous video footage was recorded from several cameras on-board the ROV, along with the geographic position, altitude, heading and three dimensional orientation of the vehicle. A geological map of the sea floor across the vent field will be created using geo-referenced and orthorectified frame grabs (“flattened” onto the topography) from ROV video. The primary goal of this project is to provide a means of quantitatively measuring the porosity of spreading ridge seafloor basalt in this area of active hydrothermal venting, through the application of a technique that has never before been attempted at this scale.  A series of trigonometric algorithms were developed to use this reference information as a means of translating a still video image from ROV footage into a series of geo-referenced images.  Geographic Informatics System (GIS) software is being used to create a mosaic-like map of volcanic, biological and geological features from the sea floor near this hydrothermal vent system from these images.  An additional data layer will be produced simultaneously to provide additional information concerning the spatial extent and distribution of geologic features on the seafloor to assist in understanding the results of the heat flow study. 

Diatoms are unicellular photosynthetic algae, or phytoplankton, and account for approximately 20% of global primary production. The diatom Pseudo-nitzschia can produce a neurotoxin called domoic acid (DA) that builds up in the tissues of shellfish when this diatom blooms. DA poisoning causes life-threatening conditions in mammals and humans when these shellfish are ingested. Parameters such as shellfish exposure length and bloom toxicity can be found by understanding what regulates diatom communities. One mechanism of bloom regulation that we know little about is that of viral infection, despite viruses being the most abundant predator in the ocean. My lab is isolating and characterizing viruses to develop a model system. After a toxic Pseudo-nitzschia bloom at Sunset Beach, Oregon was sampled in 2009, the first Pseudo-nitzschia infecting virus was isolated by infecting the host P. multiseries Clnn-16. This virus was named PmDNAV and was characterized by its burst size, latent period, host range, morphology, and nucleic acid content. I hypothesize that there are many different viruses that can infect diatoms of the genus Pseudo-nitzschia in addition to the PmDNAV. My project focuses on isolating and characterizing more viruses, in order to compare them to the PmDNAV. I have samples from 4 different blooms and 43 different hosts in culture to test these lysates on. I found that the host Clnn-16 dies when inoculated with lysates from the Sunset Beach sampling. I repeated this experiment to prove that my lysates could infect a new healthy host. I am working to prove that this death is due to a virus by looking for small pinpricks of light on a slide after staining the nucleic acids of the putative viruses. After that, I will make the virus clonal and work to characterize this virus, later repeating this process with as many viruses as possible.

Synechococcus is a unicellular cyanobacterium about 1µm in diameter. It is an abundant photosynthetic microorganism and a great contributor to the primary productivity of the Earth’s oceans. Synechococcus communities are composed of different phylogenetic clades that are believed to represent physiologically and genetically diverse populations. Previous data has shown two phylogenetically distinct populations of Synechococcus, clade I and clade IV, to be dominant in Puget Sound, with fluctuations in these populations during different seasons and regions. For my research, I will attempt to identify a clade IV strain. In an attempt to enhance conditions where clade IV will be most competitive, I have varied the culturing parameters such as using multiple media types. Filtered whole water samples containing mixed assemblages of Synechococcus were collected from Puget Sound and were initially cultured in natural Puget Sound seawater. These cultures were poured onto agar plates with sterilized natural Puget Sound water as well as plates with artificial seawater with different concentrations of AMP1 nutrients. The 16S rDNA of the isolates identified as clade IV will be sequenced by the use of PCR using primer sets that target specifically Synechococcus clade I or clade IV. The success, or failure, of amplification will indicate whether the Synechococcus DNA template was Synechococcus clade I or Synechococcus clade IV. Any Synechococcus DNA that results in a successful amplification using the Synechococcus clade IV primer set, I will send off to be sequenced. We have nutrient and physical measurements for these samples to help explain the environmental parameters that control distribution of these populations. With this information and ITS sequences I can compare Synechococcus clade IV populations within Puget Sound, and compare these with coastal populations that have been previously isolated. We seek to understand how these populations fluctuate seasonally and throughout different regions of the Sound.

Nitrogen, a limiting nutrient, controls oceanic primary production which directly affects the global carbon cycle. Consequently the nitrogen cycle has great implications for how the oceans will react to climate change. Oxygen Minimum Zones (OMZs) are areas of the ocean characterized by low oxygen levels and as areas of nitrogen removal. OMZs are expected to grow in the future, possibly increasing nitrogen removal from the ocean. Because nitrogen is requirement for primary productivity, the growth of OMZs has potential to slow the biological pump. The Eastern Tropical Pacific (ETNP) OMZ is the largest OMZ in the world, running from 0-25 ° N with a core reaching depths from 280m to 850m.  Anammox (anaerobic ammonium oxidizing) bacteria are of particular interest in the ETNP because their ability to convert fixed nitrogen (ammonium and nitrite) into the form of N₂ gas, which is biologically unavailable. Anammox bacteria produce N₂ autotrophically by oxidizing ammonium in low oxygen environments using nitrite as an electron acceptor. Understanding the presence of anammox bacteria through the water column is crucial to gaining a clear understanding of the nitrogen cycle. Presence/ absence data of anammox bacteria has been constructed using PCR with primers that target the anammox specific Hzo gene. Samples from 5 vertical profiles were collected while aboard the RV Thomas G. Thompson during the oceanography senior thesis cruise from March 16^th to 27^th. Samples were taken at every layer in the water column, including the oxycline, the OMZ core and bottom of the OMZ. During the cruise denitrification rates and oxygen concentrations were determined. Comparing denitrification rates to presence absence data of anammox bacteria will help uncover the role of anammox bacteria as denitrifyers in the ETNP.

Previous studies have found that certain lipids in mangrove leaves can be useful indicators for the presence and abundance of mangroves in the geologic past. Certain lipids found in mangroves have the potential to be excellent biomarkers (i.e. molecular fossils) for paleoclimate reconstructions. These reconstructions based on sediment cores are important in determining past sea level changes and local climactic conditions. Although certain sterols and triterpenols can be good biomarkers of mangroves, it is often unclear what function they serve. In this study, I investigated how salinity of surrounding water influences lipid distributions in different species of mangroves. To achieve these goals, I created an artificial tidal cycle in four tubs of differing salinities. Within each tub I cultivated four species of mangrove propagules (Rhizophora apiculata, Rhizophora mangle, Laguncularia racemosa, and Avicennia germinans). The mangroves were grown to a harvest size of ten leaves and then processed to analyze lipid distributions within leaves and stems of each plant via gas chromatography techniques. These mangroves cope with living in saline conditions with different mechanisms (i.e. secreting, excluding). By comparing the differences of lipid distributions of mangroves with different salt management strategies, I will determine if there is a correlation between these two factors.

Marine bacteria carry out nutrient transformations that maintain the chemistry of seawater. Most marine bacteria are uncultured and little is known about their specific roles in marine biogeochemical cycles. We identified several cultures from the beta-proteobacterial OM43 and gamma proteobacterial sulfur oxidizer (GSO) clades in a culturing experiment from the North Pacific. Members of the OM43 clade use single carbon compounds produced by phytoplankton, suggesting that they contribute to carbon cycling in surface waters. Members of the GSO clade use energy from sulfur oxidation to assimilate organic and inorganic carbon, suggesting that they contribute to carbon and sulfur cycling throughout the water column. We selected four OM43 and three GSO cultures to establish a culture collection. Several OM43 and GSO cultures were revived from freezer stocks and purified. Their identity was confirmed by 16S rRNA gene analyses and they were added to the UW marine bacterial culture collection. OM43 and GSO isolates obtained in this study will be used to further characterize the roles of these important groups of bacteria in marine carbon and sulfur cycles.

The fact that hydrogen isotope deuterium/protium (D/H) ratios in algal lipids co-vary with their surrounding water D/H ratios is well established. Paleoclimatologists have taken advantage of this relationship in their compound-specific D/H analyses, but little is known about the individual environmental parameters, such as temperature, salinity, light levels, and nutrient concentrations that influence D/H fractionation. Laboratory experiments conducted with batch cultured green algae, Eudorina unicocca and Volvox aureus, grown at temperatures of 15°C and 25°C suggest that there is increased fractionation with increased temperature. The work presented here aims to elucidate the magnitude of D/H fractionation in a natural population of algae where temperature is the primary environmental variable. We hypothesize that D/H fractionation will also increase with rising temperatures under natural conditions and that D/H fractionation will be greatest during the summer months. To test this relationship, surface water is sampled from Lake Washington Ship Canal once a month for one year, with a surface temperature range from ~8°C in February to ~24°C in August. Phytoplankton are filtered from the water, and lipids are extracted and analyzed by gas-chromatography isotope ratio mass spectrometry (GC-IRMS) to determine the extent of D/H fractionation. To date, samples have been collected and analyzed for three out of twelve months. The results from this research, as well as the results of similar experiments with other environmental parameters, will give paleoclimatologists accurate modern-day calibrations to apply to the analysis of lipids extracted from sediment cores in order to reveal climatic variations for the past.

The flux of oxygen between the ocean and atmosphere is a measure of net biological oxygen and carbon production in the euphotic zone of the ocean, which are key fluxes in the global carbon cycle. Seasonal measurements of O2 in the surface ocean are necessary to determine the flux. To date these measurements have been made in only a few time-series sites in the world’s oceans, but it may soon be possible to determine the global flux by deploying oxygen sensors on the world-wide Argo profiling float program. Before this can be achieved the accuracy of oxygen sensors deployed on these floats must be improved. My project will evaluate a series of calibration methods for increasing oxygen sensor accuracy to better than ±0.5% and establish a standard calibration protocol. Ten Aanderaa oxygen sensors will be submerged in a constant-temperature water bath under different oxygen concentrations. The sensor response will be determined along with the oxygen concentration measured by Winkler titration at each temperature and pOOxy value. The sensors will then be cycled in a separate housing between water and air at 100% humidity, constant temperature, and known atmospheric pressure to determine the oxygen sensor response in air. Laboratory-calibrated oxygen sensors will be deployed on the University of Washington vessel, R. V. Thompson in Northwest Pacific Kuroshio current in winter of 2012/13 to demonstrate increased accuracy and test in-situ calibration capabilities. The establishment of a standard calibration protocol will expand the spatial and temporal scale of dissolved oxygen oceanographic research.

This project is an interpretation of high-resolution bathymetric data from the Norwegian Mapping Authority (Statens Kartverk), acquired between 2004 and 2008 at Engelskbukta, a bay located in West Spitsbergen in the Norwegian high arctic archipelago of Svalbard. Engelskbukta is bordered on the southeast by Comfortlessbreen, a large, surge-type tidewater glacier, and on the northeast by Uversøyra, a delta formed by the melting and outwash of the land-anchored Uversbreen glacier. The dataset was imported using CARIS processing software and was analyzed with ESRI ArcGIS. Initial interpretations of the seafloor morphology indicate a retreat moraine series, representative of long-term warming and recession of the glacier terminus, and larger thrust moraines indicative of active surging phases. Fluvial features, such as glacier-proximal grounding line fans and channels, indicate zones of past and present subglacial sediment flux from Comfortlessbreen and deltaic flux from the Uversøyra delta. These features can offer significant negative feedbacks against terminus melting by marine heat flux. Satellite and aerial imagery, descriptive models of surge-type glacier processes, and in-situ sediment dating from the adjacent Kongsfjorden offer further opportunities to constrain both retreat rate and surge frequency and predict future glaciodynamic responses to climate forcing.

Nitrous oxide (N₂O, dinitrogen monoxide, commonly called laughing gas) is an important greenhouse gas with a global warming potential, over a 100 year time scale, about 298 times higher than that of CO₂. N₂O is also the major source of NO in the atmosphere, which is a natural agent of stratospheric ozone destruction. The ocean is an important natural source of N₂O providing up to 25% of emissions to the atmosphere. However, although it is known the ocean is a net source for atmospheric N₂O, our understanding of the distribution and magnitude of the oceanic source is limited. Eastern-boundary upwelling zones which contain large oxygen-depleted intermediate waters, like the Eastern tropical North Pacific (ETNP), act as large sources of N₂O to the atmosphere but have not been adequately studied. I investigated the concentration of N₂O in the ETNP aboard the R/V Thompson between March 16th and 27th 2012. Water samples were collected at 6 locations between 20°N and 32.5°N along the west coast of Mexico on board the R/V Thompson and N2O concentrations measured on board the ship using gas chromatography. Using these results I plotted depth profiles of N₂O and O₂ from each station in order to characterize the vertical distribution of N₂O and compare the stations to see how N₂O concentration varies on a North-South axis. I consistently found a large peak in N₂O concentrations at around 200 m depth at the oxic-suboxic boundary. I used surface N₂O concentrations and known atmospheric N₂O concentrations to calculate the flux of N₂O across the air-sea boundary to determine the magnitude of the source of atmospheric N₂O in the ETNP and to explore the spatial and temporal variability of N₂O production in the region.

Nearly half the world’s population lives in a coastal watershed where all anthropogenic input to the hydrologic network are transported downstream and onto the continental shelf. This connectivity then extends to the movement of terrestrial matter by submarine canyon channels. The morphology and evolution of these two essential coastal transport systems have been shown by previous literature to be strongly linked. I investigate the changes in channel morphology across a coastal zone on the Baja peninsula, and quantifying the link between river and submarine channel complexity through measurements of channel sinuosity, network slope gradient, and order length. Quantifying the changes in channel complexity across the coastal zone provides the means to monitor anthropogenic impacts upon terrestrial riverine system on submarine canyons.