The marine pelagic zone extends from the open ocean basins to the continental shelves. It is a habitat for commercially important wild fish stocks and lesser known deep sea species. Both are crucial to oceanic ecosystems but poorly understood on an ecological level. Current fishery models are specific to harvested species and fail to capture the historical population collapses that occur periodically. The California sardine fishery collapse in 1949 instigated the formation of the California Cooperative Fisheries Investigations (CalCOFI), a coalition of organizations that conducts oceanographic cruises in the Southern California Current. The resulting 65 year time series of hydrographic and fish larva data represents an opportunity to observe and analyze the interactions between different fish species and their environment. This study uses first principles and the CalCOFI data to construct spatially averaged time-dependent population models parametrized for the environmental variables of temperature and dissolved oxygen. These models show bifurcations where variations in environmental parameters lead to extreme fluctuations in larval populations. In the current climate these critical parameter values are only reached under the influence of periodic events such as the Pacific Decadal Oscillation. Future climate projections indicate that environmental parameters will reach critical values over seasonal cycles. This may lead to long term changes in fish species distributions and the structure of globally important ecosystems. These considerations underscore the importance of continued observations and modeling research in the world’s oceans. Both are necessary to understand historical fishery collapses and to prepare for changes in the future climate.

Half of all carbon fixation on the planet is performed by phytoplankton, making these photosynthetic marine microbes essential to the global carbon cycle. It is therefore critical that we understand the factors affecting phytoplankton dynamics to predict the responses of the communities to future climate changes. While we have learned a great deal about phytoplankton growth, little is known about the factors that influence phytoplankton mortality. Studies that have focused on phytoplankton mortality rates have relied on incubations in a bottle, a labor-intensive approach that is limited in its broad-scale applicability. Our approach utilizes SeaFlow, a novel flow cytometer that can continuously measure the abundance and size distribution of phytoplankton in situ, from which cell division rates and net population loss rates are estimated using a size-structured population model. This approach essentially eliminates the bottle effects and allows for greater spatial and temporal resolution. Our goal is to monitor cell growth and loss processes of cryptophyte Rhodomonas prey populations during a bloom of a dinoflagellate predator in the Columbia River estuary, using SeaFlow. We first estimated cell growth of the cryptophyte during a time course experiment in the lab to validate our model. We then monitored the dynamics of cryptophyte populations in the Columbia River estuary, and have found that cell growth and loss processes varied widely during tidal cycles. Our findings shed new light into the biological and physical interactions that drive the dynamics of cryptophyte populations in the Columbia River estuary, and our approach will be able to be applied to previously gathered field data.

Through their use of fertilizer, humans have critically impacted the nitrogen cycle, which must be understood in terms of addition and loss. This research focused on one aspect of the nitrogen cycle; the loss of nitrogen from the ocean that occurs in suboxic waters. Nitrogen is added to the ocean reservoir through river inputs, nitrogen fixation, and deposition from the air. Nitrogen losses ultimately strip nitrogen out of the ocean through annamox and denitrification. Oxygen minimum zones (OMZs) are responsible for 50% of oceanic nitrogen loss. One of the 3 largest OMZs where anammox (ANerobic AMMonium Oxidation), and denitrification occurs is in the Eastern Tropic South Pacific (ETSP) where I utilized a new method of targeted proteomics. I quantified the abundance of four enzymes key in the loss of nitrogen from the oceans. N2O reductase catalyzes the critical step of denitrification. Hydrazine hydrolase & hydroxylamine oxidoreductase are two enzymes necessary for the anammox reaction and cytochrome c nitrite reductase (nrfA), an enzyme specific to the DNRA pathway (where DNRA stands for Dissimilatory Nitrate Reduction to Ammonium). My overarching question was “Are there trends in the abundances of the enzymes over space within the ETSP?” I collected samples during the summer of 2013 on the R/V Nathaniel Palmer. Tryptic (a proteoenzyme that cleaves peptide chains after specific amino acids) digest of the samples were injected on a Liquid Chromatography Mass spectrometry and quantified. The data are being analyzed for spatial trends, focusing on a near shore to distant from shore transect. Of the 26 samples analyzed, 15 had detectable anammox proteins, and 6 had detectable denitrification proteins. None of the proteins for DNRA gave usable data. I will discuss quantities and correlations of enzymes over space within the ETSP and connect it to the local and global nitrogen budget.

 The ocean is the largest and arguably the most important ecosystem on the planet. Within the ocean a successful and widespread group of algae, the diatoms, are major contributors to the global carbon cycle with primary production rates rivaling the terrestrial rainforests. Yet in many areas of the open ocean, low concentrations of bioavailable iron limit the growth and photosynthesis of diatoms and other phytoplankton. Marine phytoplankton have evolved several adaptive strategies to compensate for the scarcity of this metal. Here we present a comparative analysis of the molecular repertoire utilized by diatoms to respond to variable iron concentrations. Utilizing sequence data from over 75 diatom transcriptomes, we have identified homologues for key iron metabolism genes. We are using this data in conjunction with environmental metatranscriptomes to map the distribution of these genes in the environment. Here we will demonstrate a selection of our findings. We show that the gene coding for ferritin, the iron storage protein, is expressed in ancient and derived diatom groups and forms a monophyletic clade, sharing a common ancestor with marine cyanobacteria. Several species of diatoms co-express two unique ferritin paralogs, and these show differential transcription in the environment. We also show widespread constitutive expression of the electron transfer protein flavodoxin, which substitutes iron-using ferredoxin under iron limitation. Iron responsive Clade II flavodoxin is expressed by members of coastal and off-shore diatom assemblies. We are now able to examine these and other iron-related genes with a higher taxonomic resolution and utilize them as environmental biomarkers.

In the marine environment, hypoxia is defined as: a level of dissolved oxygen (DO) that has fallen below 2.0 mg O₂/L. This level is approximately 20% of a system that is at oxygen saturation. Should the DO reach 0% it is described as “anoxic”. Due to anthropogenic influences, incidences of hypoxia and anoxia in coastal marine environments are increasing globally. In Hood Canal, a sub-estuary of Puget Sound, Washington, research is underway to define and quantify the effects of hypoxia on zooplankton distribution and community structure. One copepod, Calanus pacificus, is considered to be a keystone species in this community due to its prominence in the food chain. My research has been to determine the physiological tolerances of Calanus to dissolved oxygen then compare with data from samples taken in Hood Canal to determine whether there is evidence that Calanus avoids areas with low DO. To identify oxygen tolerances, DO in seawater was manipulated in the laboratory by bubbling with N₂ gas, then 24-hr survival of copepods was tested at several DO levels. In the field, Calanus abundance was estimated from depth-stratified plankton samples taken during day and night, in regions and at depths, of high and low DO. Laboratory experiments showed that Calanus were adversely affected by low DO with a sharp decrease in survival from 87% survival at 1.44 mg O₂/L to 13% at 0.96 mg O₂/L. My research relates these findings to distributions observed in the field data. Substantial decreases in Calanus populations due to increased hypoxia in Hood Canal could cause large changes in the food web. Further research into Calanus’ behavioral reactions to these conditions could help understand, and even predict these changes.

The cosmopolitan pennate diatom Pseudo-nitzschia is notable for production of the neurotoxin domoic acid. Recently, a virus was isolated on Pseudo-nitzschia multiseries that has a broad host range, infecting many genera of diatoms. This is contrary to previous reports of very specific host ranges amongst diatom viruses, and suggests a nested infection network whereby specialist viruses infect only the most permissive hosts, while generalist viruses can also infect hosts that are well-defended. To explore the infection patterns of Pseudo-nitzschia and its viruses, new Pseudo-nitzschia strains were isolated monthly at a coastal and estuarine location in the Pacific Northwest for one year. Over 100 new strains of Pseudo-nitzschia were identified by sequencing the ITS region. These new strains are then challenged with environmental viral communities that were sampled at each location concurrently. To date, 28 of 47 strains tested are susceptible to infection by at least one viral community. Three strains are lysed by the majority of viral communities, suggesting we have identified permissive hosts. This analysis will continue until all currently isolated strains are challenged. Seasonally, May and July contained viruses that infected the widest range of strains, suggesting either high concentration of generalist viruses in those months, or high concentration of both specialist and generalists together. Understanding the seasonal structure of these infection networks will inform future virus isolation attempts and provide insight into a key component of these diatom-virus interactions.

Pseudo-nitzschia is a cosmopolitan genus of marine diatoms known for its production of the neurotoxin domoic acid (DA) and resultant harmful algal blooms. The production of DA varies across species; of approximately 37 defined Pseudo-nitzschia species, at least 14 have produced DA in laboratory studies. Previous work based on ribosomal RNA sequences suggested the genus Pseudo-nitzschia could be divided into two major clades, or groups made up of an ancestor and its descendants. With the discovery of new species and identification of cryptic species complexes, the structure of these clades has eroded. We sought to integrate phylogeny, morphology and physiology of Pseudo-nitzschia, by re-examining their phylogeny, using both ribosomal LSU sequences and the rbcL gene, which encodes the large subunit of the carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO). Trees based on rbcL sequences provided higher resolution to resolve the branching orders of Pseudo-nitzschia species. By mapping physiological characteristics such as cell size, frustule morphology, pigment content and DA production onto the tree we can interpret the evolutionary history of these features and species distributions in the context of our presumed clades.

One of the main areas of focus in computational geology is how to quantitatively assess the nature of geomorphic features, in particular those that cannot be directly observed, such as the seafloor. An expert may know what a feature is simply by looking at it, and will be able to expound on why the feature is what it is, but there are relatively few features for which a rigid, quantitative criteria exists, one that will define, without subjectivity, why a feature is this and not that. This project aims to develop such a criteria for the submarine features known as debris slumps, where large amounts of the seafloor along a ridge detach from the surrounding area and slowly move downwards, creating a large block of loose material. Using sonar data of a debris slump off of Samoa, several techniques are used to determine precisely where the slump begins and ends. These techniques include analysis of sediment distribution, geostatiscal models of changing depths, and analysis of slope, hill aspect, and other models of geologic change. Combining all of these results produces a distinct profile of what that debris slump quantitatively looks like. This profile can then be validated by comparing it to the profile the same suite of metrics produces for an area that is not part of a debris slump. The difference between the two profiles shows that a different set of processes are shaping each area of the seafloor, and the slump was created in a different way than the surrounding seafloor. Profiles of this nature allow marine geomorphologists, geologists, and remote sensing experts to quickly determine the identity of objects on the seafloor, and be able to assess the impact they will have on the surrounding region.

Thrust faults are a type of fault where the hanging wall is thrust on top of the foot wall. In some situations, such faults cause another thrust fault to occur in the same area, but facing the opposite direction. These are called back-thrust faults. In the Seattle Fault Zone, an area which spans from the Kitsap Peninsula through Lake Sammamish and is about 8km wide, there are three main thrust faults and five back-thrust faults. However, the expression of these faulting features on the seafloor may be masked by on-going sedimentation processes. This study focuses on an area off the East coast of Bainbridge Island in Elliot Bay near Seattle, Washington. The use of ship-based SONAR (SOund Navigation and Ranging), which produces an acoustic signal and determines depth based upon the two-way travel time of sound, was used to create bathymetric surfaces. The survey was conducted by following navigational track lines which span the survey the area in parallel lines. During the survey, acoustic signal was received by multiple beams at various angles from the center of the ship. A high-resolution multi-beam sonar survey was conducted over this area of uncertainty in fault locations. Post-processing of these data generated a three-dimensional seafloor map, or surface. The excursion was used to amplify changes in bathymetry in hopes of discovering evidence of faulting. While the locations of the back-thrust faults were not indicated on the created surface, some abnormal surface features were located along a proposed main thrust fault. These features could solidify the location of the main thrust as well as indicate recent movement along the fault.

 The population of surfers has grown rapidly over the past 50 years and the surfing industry has expanded with it. The surfing industry was calculated in 2005 to be worth $7 billion annually and has grown since then. With this increase in popularity the ‘perfect’ surf spots around the world have become overcrowed (Scarfe, 2009). Hence there is a desire for Artificial Surf reefs (ASR) that take into account coastal, ecological and surf enhancement. In order to build successful Artificial Surf Reefs (ASR) there are many parameters that need to be taken into consideration. Three important ones are breaking wave height, wave peel angle and underlying bathymetry. Combining these three parameters produces a simple ranking system for the Surfablilty of both the wave and the location. I collected data at 3 different locations in the southern hemisphere each with a different ranking to allow a good range in data (New Zealand; Te Arai & Shipwreck bay, Tahiti; Vairao). Data was collected on underlying bathymetry, wave height and wave peel angle. I hypothesized that there was a relationship between bathymetry and the surfability of waves specifically; a sharper change in bathymetry into shallower water depth regions would produce a higher ranked wave.  Wave height mesurements were collected using pressure sensors located at the seabed, for peel angle video recordings were analyzed. For bathymetry I surved each location using a depth sounder and single beam transducer.

---still working on results

The Elwha is a small mountainous river that discharges into the Strait of Juan de Fuca, and is the location of largest dam removal project in U.S. history. Millions of cubic meters of fine-grained sediment that have been trapped for a century are expected to be delivered to the nearshore in the two to five years following the complete removal of the dams. Strong influxes of suspended sediment into the Strait associated with large discharge events provide a unique opportunity to gain a better understanding of the surface plume and how it transports sediment. This study used filtration, optical backscatter data, and grain size analysis to find concentration and grain size distribution of suspended sediment in the subaerial delta channels and surface plume. Since the project began, suspended sediment in the river and its surface plume has increased by two orders of magnitude. Sediment concentration increased seaward in the western distributary channel, and the highest concentrations of suspended sediment in the surface plume occurred immediately outside of the delta and decreased rapidly away from the river’s mouth. Large amounts of sand found suspended in the western channel suggest further seaward expansion of the sandy delta.

Ocean circulation is a complex and important component of the marine environment. By understanding the dynamics of ocean circulation, including upwelling, one may be able to accurately predict future ocean conditions. Using hindcast output from a Pacific Northwest (PNW) circulation model developed by Parker MacCready and Neil Banas, relationships between wind stress and coastal upwelling in the PNW were examined. Wind stress was analyzed using several different indices, and then these indices were correlated with biogeochemical water properties throughout the coastal domain of the model. Examinations were focused on which indices were most correlated with which water properties and how these correlation patterns varied spatially. Differences in correlation were found for coastal Oregon, the mouth of the Columbia River, and coastal Washington/Canada near the Juan de Fuca Canyon. These findings indicate that different wind patterns are needed to provide biologically favorable conditions in different areas of the PNW, and they help increase the accuracy of upwelling predictions throughout the PNW. The variability in optimal wind conditions point to differences in biogeochemical properties in the coastal PNW that have important implications for U.S. west coast fisheries.

The Elwha River dam removal project is the largest such project carried out in the U.S., and offers a unique opportunity to study the effects of a sudden sediment flux from the river to the coastal environment. A huge amount of new littoral sediment has accumulated at the river mouth since the start of dam removal in 2011; however, it is unknown whether it will migrate eastward and accrete on the chronically eroding beaches, and on what timescales this will occur. In this study, grain-size data and beach elevation profiles were collected along three shore-perpendicular transects east of the river mouth in early March, and again for three consecutive days in mid-April, with the goal of observing short-term changes. Physical sediment samples were collected for grain-size analysis and CobbleCam autocorrelation was used to obtain mean grain size from digital photographs. Beach profiles were constructed for these periods of spring tides and large waves. Results indicate that the upper foreshore of the transect farthest from the river mouth (Line 198) lost 0.38 m of elevation between the two study periods, and the lower foreshore gained 0.41 m elevation. In addition, slope breaks on all transects migrated in the off-shore direction, and foreshore sediments coarsened, both temporally (during the three-day April sampling period) and spatially (down the foreshore). These results demonstrate that daily changes can occur on the Elwha beaches. This study adds to our understanding of how new sediments will influence this region, and possibly of mixed grain-size beach dynamics in general.

Seasonal hypoxia in Hood Canal, initiated by eutrophication, is a persistent condition that can overtax marine organisms and potentially affect the marine food web. While many organisms cannot survive in hypoxic areas for an extended time and may display stress or avoidance, low metabolic jellyfish could exploit such conditions to their advantage and proliferate. The health of Hood Canal and surrounding Puget Sound fisheries require detailed quantitative analyses to determine if jellyfish populations pose a threat to the balance of these unique ecosystems. During 2012 and 2013, zooplankton samples were collected monthly through June to October using 200 micron nets from four stations representing the greatest range of dissolved oxygen levels in Hood Canal: Union, Hoodsport, Duckabush, and Dabob. After preservation, samples were cataloged by identification, counts, and measurements using a dissecting microscope. Currently, nineteen genus/species have been identified in the classes Scyphozoa and Hydrozoa and in the phylum Ctenophora. Dominant species include the ambush predator hydromedusa Aglantha digitale and the siphonophore Muggiaea atlantica. Seasonal changes showed significant increases in densities of M. atlantica from 2012-2013 during July through August. Seasonal and interannual distributions of community structures will be further explored alongside environmental conditions to identify patterns and changes in the functional diversity of Hood Canal’s jellyfish and to infer their ecological impacts.

Bottom water hypoxia is a feature of many coastal embayments and fjords in the Salish Sea. Ongoing research in Bellingham Bay (Bellingham, WA USA) by Northwest Indian College and Western Washington University has identified a seasonally recurring area of low dissolved oxygen near the center of the bay. Similar to other regions of the Salish Sea, hypoxia in Bellingham Bay may be a naturally occurring phenomenon, yet the extent of eutrophication and anthropogenic nutrient loading’s influence on patterns of hypoxia is poorly understood. The present study has continued an established monitoring program documenting the range, duration and severity of hypoxia in Bellingham Bay, while adding an experimental component investigating factors that regulate respiration of heterotrophic bacterioplankton. Profiles of water column parameters and sample collection were performed on six regularly scheduled cruises. Dissolved oxygen concentrations below the hypoxic threshold were observed in bottom waters in the center of Bellingham Bay for most of the summer, although the layer of hypoxic water appeared to migrate upwards into the water column in late July. Manipulative experiments were conducted on collected water samples to investigate effects of temperature and organic carbon on water column respiration. These experiments revealed that temperature had a negligible effect on water column respiration, while organic carbon stimulated oxygen consumption and was thus identified as a possible limiting factor. The study’s findings broaden our knowledge of factors regulating oxygen dynamics in coastal embayments of the Salish Sea and provide further insight into the potential effects of anthropogenic stressors and climate change on Salish Sea water quality.

Calcium carbonate deposits precipitate in ocean sediments when biochemically-produced bicarbonate ions react with calcium ions in seawater. Bicarbonate is the product of a reaction that consumes methane derived from thermal and biological degradation of organic matter. In areas of the Washington margin where tectonic activity squeezes water and entrained methane up through the subseafloor sediments, methane flux is very high. During a research cruise on the Washington margin in August 2013, we discovered a field of unusually large carbonate deposits at a depth of approximately 1000 meters in close association with active methane seeps. As previous studies of carbonates in this area have been limited to dredge sampling, our study will be the first to utilize sonar mapping and in-situ photos acquired with remotely operated vehicle (ROV) Jason. In order to address questions regarding the spatial extent and formation of these carbonates, we will 1) assemble photomosaics from the ROV photos, 2) process multichannel seismic data to assess whether the methane driving the formation of our carbonates was transported though the sediments via linear faults, single vents, or diffuse venting, and 3) create a large-scale sonar map using both bathymetric and acoustic backscatter data of the area. Multichannel seismic data reveals faults and other subseafloor structures through interpretation of reflected seismic waves that travel through the sediment. Acoustic backscatter data provides us with an image of the seafloor through interpretations of reflected sonar waves. We are also attempting to date the growth of the carbonates by testing embedded mineral grains for the presence of volcanic ash from the Mazama volcanic eruption that occurred 6000+ years ago. With these four datasets, we anticipate gaining an understanding of how these carbonates formed and over what time scale, ultimately contributing to the growing geological knowledge of the Washington margin.

An estimated 500-2500 gigatons of methane carbon is sequestered in the seafloor along continental margins and these deposits are associated with overlying methane seeps. The growing interest in these dynamic systems stems from 1) their importance to future energy reserves, 2) their novel microbial communities and 3) the importance of methane as a greenhouse gas. In order to constrain the impact that seeps have on methane concentrations in overlying ocean waters and to characterize the bubble plumes that transport methane vertically into the water column, water samples were collected above Southern Hydrate Ridge, a well-studied methane hydrate seep site ~90km west of Newport, Oregon. These samples were co-registered with acoustic imaging of the plumes and with robotic vehicle observations, informing more accurately on the origin of the seeps, on the rise height of the plumes above the seafloor and on the temporal variability that characterizes plume propagation. Dissolved methane concentrations exceeding background levels were observed in the upper water column, indicating that methane is transported much further vertically than previously recorded. These data provide the first detailed investigation of the short-term variance in plume dynamics and methane release into the overlying ocean, and will improve understanding of the role that sub-seafloor methane deposits play in oceanic carbon cycles.