The majority of the ocean contains sufficient oxygen to support aerobic respiration, however some locations are oxygen-stressed. When oxygen concentrations fall to undetectable levels, microorganisms turn to alternative electron acceptors such as nitrogen and sulfur during respiration. Regions of the ocean where this occurs are called Oxygen Deficient Zones (ODZ). ODZs are growing in size due to anthropogenic climate change, and understanding how they operate is important for predicting how the ocean may change in the future. Bacteria play a pivotal role in cycling nutrients through such anaerobic pathways as denitrification, and the sulfur cycle, as well as through the chemoautotrophic process, anammox, which is an important component of the energy web in ODZs. Bacterial enzyme abundances are a good representation for how much of each process may be occurring in low oxygen environments. Specific enzymes are known to be involved in key energy transfer reactions during each of these processes, and peptides within these enzymes can be detected using targeted proteomics. The hypothesis of this research is that there will be vertical zonation between denitrification, anammox, and sulfur cycling within the oxygen deficient waters of the Eastern Tropical North Pacific (ETNP). During this research, bacterial samples from the ETNP, off the coast of Manzanillo, Colima, Mexico, were collected using McLane in situ pumps from December 29th, 2016 to January 15th, 2017 aboard the R/V Sikuliaq. Targeted proteomics were applied to six samples from different depths using a list of predetermined peptides involved in denitrification, anammox, and sulfur cycling in order to assess relative enzyme abundance in each sample. Successful completion of sample analysis resulted in a vertical zonation of denitrification, anammox, and sulfur cycling with relative abundance included across the depth profile.

Sea surface temperatures that far exceeded the average occurred off the western coast of North America in the winters of 2013 and 2014. The uniqueness of this event has caused scientists and journalists to endow it with a name, the “Blob”. While recent research has determined some of the short term effects of the Blob, including extreme weather across the continent, reduction in fisheries, and a net source of CO₂ to the atmosphere, very little has been proposed on the long term effects. Here, we determine the effects on the formation of North Pacific Eastern Subtropical Mode Water (ESTMW), a body of water that acts as long term storage of heat and CO₂. Historical averages of the effective subduction rate, the rate at which water moves into the mode water; potential vorticity, an indication of the volume of water being subducted; and mode water properties, such as salinity and temperature, are determined from global datasets and compared to those properties in the years affected by the Blob. Yearly values are determined through interpolation between Argo floats, the network of autonomous profiling sensors. A decrease in subduction rate and a significant change in potential vorticity, salinity, and temperature, would mean that this anomaly could have reduced the ability of ESTMW to act as a long term storage of both heat and CO₂. The Blob, and similar future anomalies, could act as a positive feedback on climate change at a global scale.

The production of saxitoxin by the dinoflagellate Alexandrium catenella and the bioaccumulation of the neurotoxin in shellfish can result in people contracting paralytic shellfish poisoning (PSP) after consuming contaminated shellfish. While the Washington State Department of Health (WDOH) routinely tests commercially farmed shellfish for saxitoxin concentrations, people who recreationally farm shellfish are at increased risk of contracting PSP because of the long process from water sampling to warning signs or beach closures. Many Alexandrium blooms are initiated by cysts, a dormant form of A. catenella that can remain viable in sediments for long periods of time. The purpose of this research is to develop a low cost and easy to deploy early warning system for Alexandrium blooms that monitors benthic conditions as a proxy for the likelihood of a bloom. The instrument has multiple nodes along the cable containing temperature and light sensors. Temperatures above 7° C and light reaching the cysts on the seafloor can trigger cyst germination making these variables good predictors of Alexandrium blooms. Because of the simple design and spatial coverage of the instrument, citizen scientists can become engaged in this public health issue and have a direct impact by increasing scientific awareness of Alexandrium bloom progression in Puget Sound. 

The Elwha River was dammed between 1911 and 2014 trapping millions of cubic meters of fine and coarse-grained sediment in the two reservoirs created by these dams. Upon dam removal, much of this sediment was re-suspended and transported into the Strait of Juan de Fuca, reducing light availability to photosynthetic organisms. Phytoplankton abundance has not previously been studied near the Elwha Delta, so it is unknown how the dam removal has affected these organisms. Phytoplankton net tows and chlorophyll samples were collected at several stations surrounding the mouth of the Elwha River to determine overall abundance and diversity in and out of the plume. Chlorophyll concentration and phytoplankton abundances were compared to turbidity levels and salinity to determine their location within the plume. Phytoplankton abundance and chlorophyll concentration was reduced in high turbidity, low salinity water, i.e., inside of the plume. The chlorophyll concentrations measured within the plume were less than half the Strait of Juan de Fuca fall and winter average chlorophyll concetrations as documented in Masonn and Peña (2009). The purpose of this study is to provide a foundation for the Elwha dam removals and future dam removals effect on the base of the marine food web.

Widespread in tropical and subtropical oceans, the marine Cyanobacteria Prochlorococcus are the smallest and most abundant photosynthetic organisms on Earth, playing an important role in global primary production. As a collective group, Prochlorococcus have a very large pangenome, consisting of a conserved core genome and variant accessory genes. Prochlorococcus forms two ecotypes, the low-light (LL) adapted lineages—which possess large amounts of accessory genes—and the more streamlined high-light (HL) adapted lineages. The gain and loss of accessory genes in Prochlorococcus reflects their genomic and physiological differences and allows ocean niche differentiation. Recently, uncultivated lineages of LL-adapted Prochlorococcus have been identified in oxygen deficient zones (ODZs) that dominate under high-nutrient, low-light, and low-oxygen conditions. In my research, I explored the possibility that LL-adapted ODZ Prochlorococcus possess accessory genes related to low-oxygen stress (e.g. redox-sensitive enzymes and redox-dependent metabolic processes such as photosynthetic electron transport and photorespiration) that are likely lost in HL-adapted Prochlorococcus. To understand the effects of low-oxygen stress on the LL-adapted Cyanobacteria Prochlorococcus, I assessed the genomic potential for low-oxygen genes through computational analysis of a metagenomics dataset capturing native ODZ Prochlorococcus as well as the annotated genomes of the LL-adapted cultured isolates MIT9303 and MIT9313. I am currently measuring the physiological response of LL-adapted culture isolate MIT9313 under low oxygen conditions through growth experiments, during which the presence and scope of metabolites showing changes in redox chemistry due to low-oxygen stress will be analyzed using liquid chromatography mass spectrometry. My results will show if LL-IV strains contain low-oxygen accessory genes, and if they combat the negative physiological effects of low O2 concentrations. As ODZs grow the global rising temperatures, knowing how LL-adapted Prochlorococcus responds to low-oxygen stress could give insight on how primary production will be affected by a changing ocean.

El Niño and La Niña are large-scale ocean-atmosphere phenomena that originate in the equatorial Pacific Ocean and last on scales of months to years. In addition to driving the global climate, the El Niño-Southern Oscillation (ENSO) also influences local-scale activities such as oceanic nutrient concentrations and microbial processes. The location where ENSO temperature oscillations originates is upstream of the world's largest, naturally occurring oxygen deficient zone (ODZ), implying that ENSO temporal variations could impact ODZ dynamics. With very little to no oxygen in these waters, microbes use nitrogen species for anaerobic processes, denitrification and anaerobic ammonium oxidation (anammox), in lieu of oxygen. These microbial processes identify by their chemical markers: nitrate, nitrite, and ammonium. This project was to examine ENSO-driven changes in both the vertical extent of oxygen deficient waters and nutrient concentrations in the Eastern Tropical North Pacific (ETNP) off the coast of Manzanillo, Colima, Mexico. In addition to data from 1965, 1969, 1972, 1994, 2007 and 2012 to the ETNP, I collected seawater samples from December 2016 to January 2017 aboard the R/V Sikuliaq to compare oxygen and nutrient profiles over the past 50 years. I hypothesized that ENSO influences fluctuations in oxygen, nutrient, and microbial process regimes. Nutrient data was compared to the global ENSO and oceanographic state during the preceding and following years of each cruise to examine possible relationships between the variables. Rates of denitrification and annamox were also calculated to see if anaerobic processes also correspond with the ENSO cycle. This project provides insight on the microbial and oceanographic response to ENSO dynamics in an economically and ecologically critical part of the ocean. El Niño and La Niña are modules of the global climate, which are becoming stronger and more frequent in response to anthropogenic climate forcing.

 Deposits of methane sequestered along continental margins and their associated seeps are found worldwide. These seeps are of increasing interest and importance because of their potential as an energy source, their contribution to greenhouse gases, and the unique community of chemosynthetic microorganisms and fauna that they host. One of the bestudied methane seep sites is Southern Hydrate Ridge, which is at a water depth of ~800 m. It is located ~90 km west of Newport, Oregon. Despite extensive geophysical and biological research completed here, no studies have quantified the relationship of seep sites and seafloor geology to the spatial distribution and abundances of microbial and macrofaunal communities. High resolution, georeferenced photomosaics of the individual seeps and the associated biological communities at this site were collected in 2011, using the remotely operated vehicle ROPOS. Detailed visual and spatial analyses of these images has allowed for the quantification and characterization of the diversity and structure of the faunal community. Results show that both the distribution and abundances of seep organisms are highly variable. Further examination of these photomosaics may improve understanding of the relationships between faunal distributions and seep locations, with implications for the impacts that chemical gradients have on these ecosystems

Diatoms are responsible for roughly 45% of all oceanic primary production and play a unique role in carbon cycling. This crucial role makes understanding their behavior and interactions vital. In the environment, diatom samples are typically xenic (marine bacteria present around and on the diatoms). These diatom-bacterial interactions have been shown to have striking effects on diatom growth rates due to bacterial release phytohormones. These plant-based signaling molecules are well characterized in terrestrial organisms but their marine impact is not fully understood. One such phytohormone, indole-3-actetic acid (IAA), is responsible for bacteria-plant mutualistic behavior on land. Previous work in our lab has shown that addition of IAA to axenic diatoms has no effect at moderate levels and is lethal at high levels. However, when diatoms are co-cultured with IAA-producing bacteria, their growth rate increased. Thus, IAA alone is not sufficient to induce increased growth. We used this information, and the known bacterial IAA biosynthetic pathway to select IAA derivatives and precursors (methyl-IAA, Tryptophol, Tryptamine, Indole-3-acetamide, indole-3-carboxylic acid, and Tryptophan) to test their endogenous expression in marine bacteria found on diatoms in the environment. Of the bacterial species tested, none expressed every compound and most expressed novel combinations. This project tests the effects of various IAA derivatives as well as a cytokinin (phytohormone),6-(γ,γ-Dimethylallylamino)purine (2ip), on diatom growth. We investigate suites of compounds, based on bacterial expression data, as well as individual compounds. We also seek to use phylogenetic tree building to identify the bacterial producers of these compounds using IAA-producing, terrestrial bacteria as a reference. Impacts of bacteria on diatom growth, blooms, behavior and the metabolites left behind from these interactions would aid in analyzing environmental transcriptomic data and ultimately result in a fuller understanding of diatoms and their response to chemical stimuli.

Numerical tidal models are used to investigate the relationships between tides and arctic sea ice development, polynya dynamics, and turbulent mixing. Therefore, in order to evaluate numerical tidal models, we present observations of M2 tidal amplitude and propagation collected by pressure sensors attached to moorings off the west coast of Spitsbergen, in Hornsund, Isfjorden, and the Yermak Plateau. Through harmonic analysis, M2 tidal amplitude is calculated to be 0.50m in Hornsund and Isfjorden, and between 0.34m and 0.42m on the Yermak Plateau. M2 amplitude maximums occur simultaneously at Hornsund and Isfjorden, and 1.3 hours later on the Yermak Plateau. M2 tidal amplitude is shown to decay away from the coast on the Yermak Plateau with maximum amplitude of 0.42m at the mooring nearest to the coast, 0.41m 8km farther away from the coast, 0.37m 48km farther away from the coast, and 0.34m 66km farther out to sea than the nearest shore mooring. These observations agree reasonably well with numerical tidal models and Kelvin wave propagation and amplitude decay theory. However, AOTIM-5 modeled M2 amplitudes are shown to be biased low, 0.04m on the west coast of Spitsbergen. 

In recent years, local organizations have moved to restore the anthropogenically-altered shorelines of the Salish Sea. Changes to the beach and intertidal have been observed, however little research has recorded effects on the subtidal. This region is home to several species including eelgrass (Zostera marina), an important species in the Salish Sea often used to indicate ecosystem health. This research utilizes multibeam sonar bathymetric data to analyze changes to subtidal seafloor structure in response to shoreline modification and investigates potential subsequent ecosystem consequences. Two Washington state study sites were analyzed, Seahurst Park in Burien, and the Snohomish County Nearshore Restoration Project in Everett. Multibeam data was acquired using a Kongsberg EM 2040 system and post-processed in Caris HIPS to generate a base surface of sub-meter resolution. The data detected eelgrass beds in addition to revealing bathymetric changes. ArcGIS was used to generate descriptive and pattern metrics such as total elevation change, percent area changed, surface roughness, and Bathymetric Position Index. Data revealed small but noticeable changes in bathymetry and the presence of eelgrass following shoreline alteration. The changes observed could indicate that restoration may have negative consequences for Zostera populations and may potentially affect other organisms using the sublittoral habitat.

The ability to conduct and communicate climate related environmental changes relies heavily on the tool used for documentation. A key benefit of video as a scientific tool can allow scientists to obtain uninterrupted documentation over all temporal scales that provide physical and structural evidence of change. We present a video system to be used for the acquisition of duel field of view angles and 360 degree mosaics that is easily deployed and compatible for use with both stationary and mobile data collection. The visual acquisition system focuses on providing physical change information for use in comparison of GIS-based change models. Along with the video system, we present the protocol for its use and results from preliminary tests focused on measuring the accuracy and precision of the system. Additionally, a case study of a nearshore habitat, a system that experiences a significant amount of change from different climate and environmental forcings, was conducted. Completion of such a system allows scientists to use video to monitor and collect visual data regarding ecosystem change over temporal and spatial scales, and provides a communication tool for education and outreach purposes.

The world’s reliance on plastic is a contemporary dependence as its malleable function, low production cost, and increasing abundance has been universally favored over all other products. Created with the intention of short-term and one-time use, the global production of plastic reached 299 million tonnes in 2013, with 10-20 million tonnes ending up in the oceans annually. This study explores the contribution of microplastics to the marine environment from river systems, and quantifies the microplastic load within the stream as it passes from rural to urban environments. Microplastics are separated into two categories based on how they are formed; primary and secondary. Primary microplastics are manufactured, generally as resin pellets, which are melted down to form anything from shampoo bottles to water bottles. Secondary microplastics form from the breakdown of macroplastics after extended exposure to UV radiation and/or weathering. The sampled river is fed by a remote, glacially fed lake in the Cascadia Mountain Range, flowing into the upper Skykomish River, the Snohomish River, and eventually to the Puget Sound. Samples were collected by towing a 335 µ mesh manta trawl and analyzed, after a wet peroxide oxidation and density separation, to quantify the concentration of microplastics present in the stream. From the samples processed thus far, and the data from another study conducted on the same river system, a correlation has been found between the amount of plastics in the stream and the populations of the towns the stream passes through. This correlation implies that the growing quantity of microplastics within the stream, as it flows from rural to urban environments, is supplied through anthropogenic influences. Following this study, microplastic pollution can no longer be thought of as a coastal and marine issue, but rather a problem that starts much further inland. 

Plastic pollution in the marine environment is an increasing concern leading to the need for more studies. Microplastics (0.3-5 mm in size) are the most concerning because they cannot be easily spotted, last the longest, and are easily ingested by marine organisms and make their way through the food chain. These microplastics are generated by many industries from cosmetics to laundry, to traffic erosion of tires. This study examines the distribution of microplastics found on Seattle beaches and on beaches to the north and south of the city. I collected sediment from three 1 m² quadrants on each beach of my 10 sample sites using the Beach Sampling Protocol from the Port Townsend Marine Science Center to ensure comparison of data with other studies. Samples were taken directly below the wrack line left by the previous high tide. In the lab, after a subsample was weighed out, density separation and wet peroxide oxidation were performed, in addition to other standardized analyzes. My results show the levels of microplastics and changes in concentration of microplastics found in sediments close to Seattle and at greater distance on the beaches. As the beaches erode, these microplastics are transported into Puget Sound and the larger Pacific Ocean. It is important that marine plastics are studied so that preventative measures can be put in place to limit microplastic pollution, in addition to having a baseline study for future research. 

Chlorophyll concentration is an indicator of plant health, but is challenging to quantify. As a result, normalized difference vegetation index (NDVI) imaging was developed to help solve this problem by making use of of chlorophyll’s varying reflectance of light waves. This is a proven and powerful tool for observing terrestrial vegetation, allowing for efficient monitoring of living plant populations worldwide. However, no research had been published regarding the use of NDVI for submerged aquatic vegetation, thus our team sought to apply the technique to an aquatic environment, specifically seagrass beds in Queensland, Australia. Seagrass provides both nutrition and habitat for marine life, as well as carbon dioxide storage. The ability to monitor seagrass ecosystems is essential to understand and, in turn, preserve them. We saw NDVI imaging as a potential improvement to current seagrass monitoring methods and conducted experiments to find what issues this technique has in the underwater environment. After testing many aspects of NDVI imaging on in-situ seagrass beds and other test environments, we ultimately found it was not a viable option. This is largely due to basic optical transmission characteristics of water.

The primary producers of the ocean are responsible for nearly 50% of the carbon fixation on Earth. Many eukaryotic primary producers such as globally important diatoms require Vitamin B₁₂, also known as cobalamin, as they lack the biosynthetic pathway for the metabolically expensive molecule. A symbiosis between eukaryotic autotrophs and some marine bacteria has been proposed as the source of cobalamin to these B₁₂-requiring phytoplankton, but the quantitative nature of this relationship is not fully understood. With advancements in analytical techniques in liquid chromatography-mass spectrometry, we can learn more about microbial symbiosis, including vitamin interchange in pelagic microbial communities. This research will investigate the null hypothesis that the mean production of cobalamin of two species of pelagic proteobacteria (Ruegeria pomeroyi DSS-3 and Sulfitobacter sp. SA11) is equal under three different treatments: growth in a limited-carbon environment, growth in an environment enriched with stress molecules from a well-studied model diatom (Thalassiosira pseudonana), and growth in media with stressed T. pseudonana filtrate added. The alternate hypotheses state that cobalamin output will be affected by these different treatments. Data resulting from the experiments will undergo one-way ANOVA tests to determine statistical differences between means. With a more complete understanding of how bacteria and eukaryotic autotrophs interact, the possibilities for this field are significantly expanded. Quantifying cobalamin production in marine bacteria on a per-cell basis under varying conditions is a possible benefit of this research, as well as understanding more about the level of control bacteria exert on their symbiosis with eukaryotic autotrophs.

The Amazon tidal river consists of the lowermost 800 km of the Amazon River that is affected by tides.  The effect of tides on surface suspended sediment concentration (SSC) in the Amazon has not yet been characterized, and may impact estimates of surface SSC as monitored through remote sensing.  To assess potential tidal influence on surface SSC, water samples were collected and filtered in field; published remote sensing maps were also collected and compared to field measurements.  Thus far, this project has identified discrepancies between in situ and remotely-sensed estimates of surface SSC, and constrained the influence of tides on the observed signals.  In situ surface SSCs more accurately matched with remote sensing maps on sites located directly in the Amazon mainstem, while tributaries showed exaggerated differences in surface SSC.  Field surface SSCs in the Amazon mainstem also did not vary significantly with tidal  seasons, suggesting that ocean tides play a smaller role in surface sediment transport than originally hypothesized.  Further conclusions will look into the roll that tides play on total bedload, especially at sites close to the river mouth where tidal influence is strongest.  Explanations for surface SSC discrepancies will also be included in the paper's conclusions; since many of the discrepancies occur in freshwater tribuataries, the seasonality of phytoplankton blooms will be cross-linked to satellite SSCs.  Finally, suggestions for future usage of remote sensing in strong tidal areas of the Amazon River will be given and the success rate/percentage of correlation of satellite surface SSC with field SSCs will be assessed.  With a better understanding of the effects of tides on surface SSC and how well remote sensing captures variability, we can better monitor sediment discharge into the tropical Atlantic Ocean as well as sediment delivery to the floodplain of the Amazon River during seasonal floods.

Dead reckoning is the process of calculating one's current position by using a previously determined position, or fix, and advancing that position based upon known or estimated speeds over elapsed time.  It is typically used when external systems, such as GPS satellites or acoustic tracking, are unavailable to track a vehicle relative to earth-fixed coordinates. When used on an autonomous underwater vehicle (AUV) it cannot account for the influence of tidal currents changing the vehicle’s displacement without influencing internal speed and heading data. My research experiments with an Ecomapper AUV in Australia in September 2016 illustrate the influence of such tidal currents on dead-reckoning AUV tracks. The experiment was completed at the Morton Bay Research Center of Queensland University and the research data were collected by Ecomapper AUV from designed runs. As a result, the comparison of actual AUV track with the predicted one that was calculated by Matlab with the application of Dead reckoning method showed how much the tidal current influenced the predicted track, and how to reduce this difference by setting the AUV's heading with the tidal current in particular angles. The results are useful for planning new AUV missions in similar tidal currents for reducing position errors generated by this technique.

Rivers are conduits for transporting sediments and organic material through the watershed and to the ocean. The Elwha River recently was involved in the largest dam removal in history within the USA. Studies of the dam removal impacts have never been done as extensively as they have for the Elwha River Restoration project. Now, the river is no longer blocked, and 21 million m³ of sediments have been made available for erosion, and it is not fully known where the sediments are depositing and how they are affecting the ecosystem. In order to quantify where organics are being stored in the river system, sediment samples were collected along the river and shoreline, and grain size and loss on ignition (LOI) analysis performed on them. Most of the samples with more than 2% organic content were at sites in the reservoir and side channels, and organics less than 1% were retained on the beach and riverbank. Therefore, finding organic matter in the river and shoreline systems can inform us how the ecosystem is recovering, and whether overtime organics are fully transported to the ocean, or whether organics will be consumed, transformed, or altered along the way.