Seattle’s Combined Sewer Overflow (CSO) system discharges approximately 100 million gallons of untreated sewage and storm water runoff into its waterways annually. The sewer system includes two combined waste streams: waste from sewer basins, which captures storm water runoff, and wastewater from buildings and industry. Pollutants in the effluent such as human waste, automotive by-products, pesticides, and pharmaceuticals can degrade ecosystems. To determine the impact that CSO outfalls have on Seattle’s waterways, this study tested for pollutant levels in sediment near two discharge areas: Elliott Bay and the western end of Seattle’s Ship Canal. Sediment samples were collected using a Van Veen grab, then handled and stored using sterile, inert materials to avoid contamination. Sediments were tested for heavy metals including mercury, via cold-vapor atomic absorption, and lead, via inductively coupled plasma mass spectrometry. The organic pollutants ammonia, nitrate, and phosphate were quantified via automated calorimetry. Laboratory testing for pollutants was done in accordance with EPA guidelines or standard analytical methods. Results were compared to the Washington Department of Ecology’s Sediment Management Standards. Preliminary results suggest that lead and mercury levels do not exceed the Department of Ecology’s sediment quality standards, while cadmium levels are slightly above or below recommended levels at each site. This data can be used as a baseline to help better understand the contribution of CSOs to pollution levels in these areas. More research will be necessary to determine the extent of damage to ecosystems near the outfalls.

It is accepted that the Amazon rainforest is a significant carbon sink. The Amazon River was only recently discovered to be a supersaturated CO₂ source, outgassing at a rate almost equivalent to that which the forest sequesters (0.5 Pg C yr-1). Since this landmark discovery, one of the principle investigations within the River Systems lab has been developing a refined understanding of the biogeochemical processes that shape the Amazon River into such a prominent CO₂ source. In situ incubations have indicated that lignin and other organic molecules unique to terrestrial flora are in fact decomposed in the water column and are potentially a significant source of CO₂ outgassing. Utilizing Mass Spectrometry we are now analyzing the presence and abundance of various lignin derivatives across spatial and temporal variables to track the fluctuating degradation rate of organic substrates. Linking the forest’s carbon sequestration to the river’s outgassing mechanisms and applying the principles to other river systems around the world is a vital step to better comprehending the complex global carbon cycle.

Amnesic shellfish poisoning is the result of eating seafood contaminated with domoic acid, produced by toxigenic diatom species from the genus Pseudo-nitzschia. In the summer of 2015, abnormally large assemblies, known as super chains, of Pseudo-nitzschia australis appeared in the massive algal bloom that swept up the Pacific Coast. This affected commercial and recreational shellfish harvesting and cost millions of dollars in shellfish sales. Due to their recent appearance, knowledge of P. australis super chains is extremely limited. Here, we investigate the prevalence of super chains in Puget Sound and along the Pacific Coast. The deep chlorophyll maximum, DCM, is a layer in the water column that is often found to contain a high volume of photosynthesizing phytoplankton.  A collection of electronic devices that measure conductivity, temperature, and depth (also called CTD) was deployed to determine DCM, from which plankton samples were collected. Scanning electron and light microscopy were used to identify P. australis species and to examine the morphology of their associated bacteria. Most surveys have been conducted during the late summer when blooms are at their peak. By conducting our survey in the late winter, we have had the opportunity to measure P. australis super chain prevalence during what is typically a less active season. Our results provide novel information of P. australis super chains and their associated bacteria during a season that has been so far neglected. In addition, our diverse sample sites in Puget Sound and along the West Coast present a systematic survey and allow us to make regional comparisons. This study lays a foundation for more comprehensive research of super chains in the future. 

Anthropogenic emissions are projected to double atmospheric concentrations of CO₂ by the end of the century, increasing ocean acidification and fundamentally changing the marine environment. Since diatoms are responsible for ~40% of marine primary production, it is important to understand their response to variations in CO₂ concentration and how they regulate their carbon assimilation. In previous work, we identified gene clusters with differential expression under elevated CO₂ in the model diatom Thalassiosira pseudonana. One cluster of genes that was down-regulated under elevated CO₂ encodes putative carbon concentrating mechanism (CCM) proteins, which participate in control of carbon assimilation. These genes share an upstream cis-regulatory motif involved in the regulation of CCM genes in Phaeodactylum tricornutum, a distantly related diatom that uses cyclic AMP (cAMP) as the second messenger. To test whether cAMP plays a similar role in CO₂-responsive gene regulation in T. pseudonana, we grew T. pseudonana under high and low CO₂ conditions and sampled cultures prior to or following exposure to 3-isobutyl-1-methylxanthine (IBMX), which raises intracellular cAMP concentrations. We have sequenced RNA from these samples and determined differential expression of genes between treatments. Contrary to our predictions, we find that most genes in the CCM sub-cluster are significantly up-regulated following IBMX treatment under high CO₂. We also identify a number of other gene clusters that are highly responsive to the IBMX treatment, suggesting other cellular processes under cAMP control. We are supporting this research with targeted metabolomics to look for changes in the ratio of cAMP:AMP and other key compounds between treatments. This research will facilitate mechanistic insights into diatom responses to changing ocean environments, and improve our understanding of the evolution of carbon concentrating mechanisms in this group of globally significant phytoplankton.

Plastic pollution in the ocean is a global issue that continues to grow as manufacturing and consumption of plastic products increases. Both macro- and micro-plastics are often difficult to discern visually, the latter requiring a microscope, which makes scientific quantification and identification challenging. The full range of plastic’s impacts on/to the marine environment is not completely understood, particularly in New Zealand waters where there is a lack of research on the subject. During the six-week Sea Education Association S-256 research voyage around New Zealand’s North and South Islands, 44 surface water samples were taken to measure microplastic (0.02 – 0.33mm particles) concentrations and 34 neuston net tows were conducted to collect macroplastics (0.33 – 5mm particles). Overall, plastic concentrations in New Zealand waters varied in density and polymer type. However, when compared to major gyre systems such as the North Atlantic and North Pacific, macroplastic and microplastic concentrations in this region were considerably lower. Macroplastics were limited in quantity. 29 total were found along the cruise track, primarily polyethylene and polypropylene polymers; these plastic types come from single-use packaged goods and fishing gear. Microplastic densities were greatest in regions where strong currents converge, suggesting that surface ocean plastic particles are transported by circulation processes. 2,923 microplastic particles were observed, the majority of which were filaments likely indicative of fishing gear. This marine debris may be attributed to relatively high fishing efforts in portions of the New Zealand Exclusive Economic Zone.

Fronts are dynamic regions in the ocean where contrasting water masses meet, characterized by rapid currents, sharp density gradients and high productivity. What drives the phytoplankton community structure in these regions is still not well understood, but it has been hypothesized that fronts could act as either a barrier or a blender. However, few observations exist to test this hypothesis. The Kuroshio Front off the coast of Japan, extending eastward into the North Pacific Ocean, is an important western boundary current front, known to be important for fisheries. During a cruise in October of 2009, fine-scale sampling was conducted, and diatom and dinoflagellate phytoplankton taxa were identified to the species level by microscopy. Concurrent measurements such as salinity, temperature and chlorophyll were also taken to relate the physical and biological characteristics of the sample region. My analysis has revealed that distinct water masses found in the frontal zone have significantly different phytoplankton diversity indices. Conversely, I found that the most frequently observed and most abundant species in these water masses were remarkably similar. Major differences between the water masses were driven by the diversity of rare species. I show the importance of rarity in driving diversity and highlight the disconnect between the physically distinct water masses observed and the structurally similar phytoplankton community. My results reflect the importance of lateral mixing, mingling species from distinct source regions along the front. Rare species most likely represent the least competitive constituents of those original source populations. This research suggests phytoplankton may mix into new water masses diferent than their initial environment even if the water masses themselves remain physically distinct.

Marine microbes drive virtually every major biogeochemical cycle in the ocean. These microbial communities consist of two major groups: primary producers, called phytoplankton, that use energy from sunlight to transform carbon dioxide into organic matter, and consumers, like heterotrophic bacteria, that degrade about half of phytoplankton-derived organic carbon. Recently, it has been recognized that certain phytoplankton and heterotrophic bacteria form intimate relationships with one another and exchange specialized metabolites. This project has focused on characterizing such relationships between phytoplankton and bacteria, particularly between diatoms (a type of phytoplankton) and bacteria that enhance or deter diatom growth. These bacterial-diatom interactions impact rates of carbon fixation and nutrient flux in the ocean, and this project aims to better characterize the types and specificity of these interactions using laboratory cultures. To observe the effects of bacteria on diatoms, laboratory studies were conducted in which diatoms were exposed to individual bacterial strains in order to examine the specific effects of each strain on each diatom. In subsequent experiments, diatoms were exposed to multiple bacterial strains simultaneously in order to examine the impacts of multi-bacteria consortia and to create a more realistic model of the environment in which diatoms are exposed to many different types of bacteria.

Growing human population in coastal areas within the last century has intensified the level of underwater sound pollution globally and consequently its impact on marine habitats. The increased complexity in the ambient underwater soundscape of the urbanized shoreline is due to the convoluted use of nearshore and coastal waters for marine related activities such as recreational and commercial boating, shoreline roads, and industrial and residential development. These uses impose stress on the ecological quality of nearshore habitats for Pacific Northwest fish during transit through urbanized waters. This study examined the characteristics of ambient sound sourced from traffic on the I-5 Bridge in Seattle, Washington near Portage Bay on February 12th, 2015. The soundscape was investigated through passive acoustic measurements of ambient underwater sound at varying distances from the bridge using two built hydrophones utilizing piezo elements and three professional grade hydrophones, in effort to prototype the built hydrophones and ensure quality data collection. The propagation and attenuation of sound from the I-5 Bridge characterized the potential for this point source of sound pollution to impact fish during transit. The variation in the acoustic spectrum at multiple distances from the bridge identified the spatial extent of preferential attenuation of frequencies and intensity of sound as a contributor to noise pollution. Fish utilize the canals connecting the Puget Sound to Lake Union and Lake Washington, where bridge noise pollution could be affecting their behavior during migration.

The South Pacific Convergence Zone (SPCZ) is the most prominent rain feature of the Southern Hemisphere, but is a very understudied region. Changes in the SPCZ can affect freshwater availability to people living on the islands in the South Pacific. The satellite record shows precipitation patterns from the past 37 years; in the tropics the best way to investigate rainfall before 1979 is to examine lake sediment. We used sediment cores with age models from Barora Lake, a shallow freshwater lake in the Solomon Islands, to obtain a detailed view of past rainfall patterns. This lake’s lack of oxygen one meter below the water’s surface has left its sediment in a uniquely undisturbed state. Because of this, and a high accumulation rate, the sediment provides a record of the rainfall in the Solomon Islands over the last millennium. Lipids are well-preserved in sediment over geologic time, making them an ideal proxy for reconstructing tropical paleoclimate. The lipid dinosterol is produced primarily by a limited group of dinoflagellate microalgae and acts as a “molecular fossil”. The isotopic ratio of deuterium to hydrogen (2H/1H) found in dinosterol reflects the 2H/1H ratio in the lake water, which is dictated by changes in precipitation and evaporation. In the tropics, more rain results in 2H-depleted rain and lake water. After purifying dinosterol from the sediment with column chromatography and high-performance liquid chromatography, we found minor fluctuations in the dinosterol 2H/1H ratios, which implies a fairly stable rainfall pattern at this location during the past millennium.
 

The microscopic cyanobacteria Prochlorococcus is the smallest and most abundant photosynthetic organism in the ocean, playing a large role in the global cycling of nutrients. Prochlorococcus form ecotypes, which are genetically variable lineages with differing physiological traits adapted to various environmental niches that enable them to be so widespread. They reside in oligotrophic (nutrient depleted) waters where certain required nutrients like phosphate can be scarce, and use a high affinity phosphate uptake pathway to take in phosphate. However, this pathway cannot completely differentiate a phosphate molecule from the physiochemically similar arsenate molecule, leading to the uptake of arsenic into cells, especially when the phosphate to arsenic ratio is low. Recent work performed by my mentors has studied the two pathways Prochlorococcus uses to detoxify arsenic, the efflux detoxification pathway, which was previously known, and the recently discovered putative methylation pathway, and they have found that strains of Prochlorococcus have different genomic capacities for arsenic detoxification. We are currently testing that genomic capacity for arsenic detoxification correlates to relative arsenic tolerance among lab strains of Prochlorococcus by batch culturing and comparing growth inhibition rates of four Prochlorococcus strains that differ in the pathway genes they contain, MED4, NATL2A, AS9601 and SS120. By inoculating the cultures in three different conditions with variable arsenate concentrations and calculating the inhibition rates, we will answer if Prochlorococcus genomic capacity correlates to relative arsenic tolerance. This would have impacts on how we look at the global circulation of arsenic because the two arsenic pathways have varying outputs that affect the circulation of arsenic and can influence the bioaccumulation of arsenic in upper trophic levels.

Pseudo-nitzschia is a diverse and cosmopolitan genus of diatoms composed of 37 species and known for its production of the neurotoxin domoic acid (DA). The phylogeny of the Pseudo-nitzschia genus is complex due to the presence of cryptic species complexes and the frequent discovery of new species. In previous phylogenetic studies, large subunits of ribosomal RNA (LSU) were used as a genetic marker to estimate how Pseudo-nitzschia species were related to one another. We sought to reevaluate the phylogeny of Pseudo-nitzschia both through recreating a LSU tree that accounts for recent discoveries made about the genus, as well as using the rbcL gene, which encodes the large subunit of the carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO), in order to better understand the evolutionary relationships within the genus. Both trees provided better resolution in the branching pattern of Pseudo-nitzschia species and identified the presence of a third clade within the genus. Each clade had distinct morphological and physiological characteristics, such as cell size, frustule morphology, pigment content and DA production, which further supported the branching order. Metatranscriptomic reads obtained from four stations along a transect ranging from the Washington coast to the open ocean were placed on the rbcL tree and reflected a biogeographical distinction between the clades. The resolution provided in these phylogenies reflects the importance of continued identification and sequencing of new species. Furthermore, the phylogeny of the rbcL shows that it is an excellent marker for both phylogenic comparison as well as community profiling in the environment.

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 best-studied 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 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.

Anthropogenic carbon dioxide (CO₂) has been identified as a primary driver of climate change, the oceans have been shown to be a large sink of this CO₂. Fjord systems have been identified as potential sinks for the CO₂ in summer due to high primary production, but also in winter due to cool surface waters. Our study focuses on the temperate fjord system of Nootka Sound, BC, Canada, during December 2015. Investigation of this precipitation driven fjord system during a strong El Niño may help us to understand the impacts that warming oceans have on the ability of fjords to act as sinks for atmospheric CO₂. Depth profiles at 12 stations began outside of Nootka Sound and went into the head of Muchalat Inlet. Vertical profiles and water samples at 5 depths were collected using the CTD rosette system onboard the R/V Thomas G. Thompson. Additional samples from the surface 10cm of the water column were collected within 2 of the inner fjords, Muchalat and Tahsis. Analysis of these samples for dissolved inorganic carbon (DIC) and alkalinity allowed for the calculation of pCO₂, a measure of the partial pressure of CO₂ in water. From this and atmospheric pCO₂ data provided by Environment Canada, the flux of CO₂ across the air-sea interface was calculated. Preliminary results of surface samples show effluxes of CO₂ near riverine inputs, while surface waters within the inlets appear to be in near equilibrium with the atmosphere. Preliminary transect results show deep waters have higher pCO₂, further analysis will reveal if a relationship between air-surface fluxes and deep water exists.

The inland waters of the Puget Sound, Washington, USA, and Georgia Basin, British Columba, Canada, is a complex system of high energy river inputs to lower energy large basins with direct connection to the open ocean through the Straits of Juan de Fuca. High energy systems acting as transport mechanisms for coarse sediment interact with low energy regions with transport deposition of finer sediments to create the vertical stratigraphy of the seafloor. In regions of high energy the seafloor expression is dominated by a rougher seafloor with more geomorphic features of coarser material, while low energy regions are expressed in a seafloor of uniform lamination. This research investigates the link between the surface expression of seafloor roughness and the underlying vertical structure of sediment deposition. Using a high resolution bathymetric surface derived from multibeam sonar synchronized with low frequency sub-bottom acoustic profiles, the depth of acoustic penetration is correlated with a focal calculation of seafloor roughness. Areas of lower acoustic impedance have a larger range in penetration, with lower ranges of penetration persisting in areas of high acoustic impedance. High acoustic impedance is indicative of harder sediments, such as sand, and low acoustic impedance indicates softer sediments, such as mud. The research is a comparative study between a high energy system adjacent to the mouth of the Elwha River and the low energy protected region of South Possession Sound. The research illustrates the strong link between seafloor geomorphology and the terrestrial sources of sediment input and mitigation of sediment transport energy.

Sediment cores were collected from White Lake (15°2.46' S 167°5.35' E) and Red Lake (15°1.97' S 167°5.40' E), located on Thion Island, Vanuatu, to analyze precipitation patterns in the South Pacific Convergence Zone (SPCZ) during the last millennium. The SPCZ is a poorly understood and understudied region of the Tropical Pacific, with a very short instrumental record of rainfall. Extending the record of natural variability in precipitation is important for assessing future risks of freshwater availability to islands in the tropical pacific. Known for high precipitation rates and spanning 3000 km in a NW to SE orientation, the South Pacific Convergence Zone is the most prominent rainfall feature in the Southern Hemisphere. These freshwater lakes contain the dinoflagellate sterol, dinosterol, which acts as a “molecular fossil” or lipid biomarker and is used to infer variations of the deuterium/protium (²H/¹H) isotopic ratio of the lake water over time since algal lipids track changes in environmental water. The fluctuations in the ²H/¹H ratio in both the lake water and dinosterol are linked to changes in SPCZ precipitation since in the tropics, the rainfall rate is correlated with the isotopic composition of rain. Dinosterol was purified using column chromatography and High Performance Liquid Chromatography, identified and then quantified using Gas Chromatography-Mass Spectrometry and Gas Chromatography-Flame Ionization Detection. The ²H/¹H ratio of the purified dinosterol was determined using Gas Chromatography-Isotope Ratio Mass Spectrometry.

Marine ammonia-oxidizing archaea (AOA) are abundant marine microorganisms that compose their cell membranes with glycerol dialkyl glycerol tetraethers (GDGTs). These lipids are useful biomarkers for developing a record of sea surface temperature. Through the TEX86 temperature proxy, GDGTs have been able to provide insight into historic patterns of sea surface temperature through the relationship between annual average sea surface temperature and the composition of GDGTs. Existing data suggest that in addition to temperature, other environmental factors might influence TEX86. We postulate that varying light, salinity and peroxide concentrations would have an effect on the GDGT composition of AOA in culture. We conducted experiments with varying light, salinity and peroxide levels to test their effect on TEX86 on strains of AOA. We observed that light levels influenced the GDGT composition. The calculated TEX86 values were higher when the cells were exposed to light. Salinity concentrations above and below the optimal salinity of 25 resulted in lower calculated TEX86 (below 17°C). Peroxide levels did not affect calculated TEX86 temperatures, which suggest the presence of different adaptations that allow for archaea to acclimate to relatively extreme conditions. Our work demonstrates that different environmental stressors have an effect on lipid composition.

Cryopreservation is a technique that uses very low temperatures in order to store and preserve biological material for an extended period of time without deterioration. With the use of cryoprotectants, a substance that prevents the damage of freezing, cells are protected from the normally lethal effects of freezing. In order to understand the effects of cryopreservation in marine microorganisms, we are developing this technique with Phaeodactylum tricornutum, a marine pennate diatom with a sturdy body type. Diatoms are important drivers for biogeochemical cycles and the versatility of Phaeodactylum tricornutum in different environments allow it to be used as a model organism in studies about global phytoplankton primary production. By using a cryoprotectant such as DMSO, and a two-step freezing protocol, we allow the cells to experience freezing at a gradual rate giving it as stress-free of an environment as possible. Once frozen, the Phaeodactylum will be preserved until the thawing process begins, using a protocol that allows the rate of thawing to be gradual as well. This technique could allow for successful preservation and could be applied to many aspects of biology, in our case a laboratory model for ecological work.

Cold seeps, like Southern Hydrate Ridge (SHR) on the Cascadia margin, are ubiquitous features along continental margins where fluids discharge from the seafloor into the water column. The chemical composition of fluid expelled at seep sites is distinct from the surrounding seawater due to sub-seafloor fluid-rock reactions and biological activity. This altered fluid is important in driving biogeochemical processes that allow diverse biological communities to thrive in these environments. Previous short-term fluid flow studies at SHR and other seep systems have observed upward flow of altered fluids concentrated in regions of bacterial mats and downward flow of seawater-like fluids in regions of vesicomyid clams. To investigate longer-term variability in the magnitude and direction of fluid flow at SHR, three continuous-measurement flowmeter/chemical samplers (MOSQUITOs) were deployed in bacterial mats to measure fluid flow rates and solute fluxes. The MOSQUITO continuously monitors three-dimensional fluid flow rates within the upper 50 cm of the sediments by injecting a point source of non-reactive tracer dye and measuring its concentration at various distances away from the point-source injection. The fluid time-series record at each depth was sampled at 4-day resolution, and from these samples, tracer concentrations were analyzed using fluorescence spectrophotometry. This two-year continuous record of fluid flow shows that the flow rate at SHR is temporally and spatially variable, however there is an annual trend of ~20-40 cm/yr of downward fluid flow in regions of bacterial mats. Chloride and sulfate concentration profiles will also be determined from MOSQUITO subsamples in order to examine their fluxes across the sediment-water interface, potential methane hydrate dynamics, and other sources of fluid. This net downward transport of seawater circulation is more constant than previously recognized, it likely plays an important role in controlling the distribution of benthic biological communities, and could be important in marine biogeochemical cycles. 

Zooplankton serve as vital components to the marine food web, and their distributions implement limits on population growth for organisms of both higher and lower trophic levels. Many zooplankton species, such as Calanoid and Cyclopoid copepods, are the primary food source for the juvenile fishes that are part of the fisheries within the temperate coastal Northeast Pacific, including Chinook, Chum, Pink, and Coho salmon. A better understanding of the environmental parameters that influence zooplankton abundance and distribution is essential for the proper management of these economic and culturally valuable fisheries. This study investigates the correlation between the abundance and distribution of Oithona, other small copepods (<2mm), large copepods (>2mm), euphausiids, hyperiids, gammarids, ostracods, chaetognaths, and larvaceans to dissolved oxygen, salinity, and chlorophyll conditions to determine which parameters have the greatest impact on zooplankton distribution. The ultimate goal of this study is to generate a model to predict the distribution of zooplankton populations under different environmental conditions. It was expected that distribution would favor higher dissolved oxygen, more saline, and high chlorophyll conditions. Samples were collected in Nootka Sound, British Columbia, onboard the R/V Thomas G. Thompson during the Oceanography Senior Thesis Cruise at 4 stations using 211-micron closing net. Four samples were collected at each station from 100-75m, 75-50m, 50-25m, 25-0m depth ranges to observe vertical distribution within the upper 100m of the water column. Results identified significant correlation between dissolved oxygen and salinity and zooplankton abundance and distribution. However, abundance appeared to be greater at stations and depths with lower dissolved oxygen and salinity concentrations. We also tested an alternative method of measuring zooplankton abundance and distribution by constructing an underwater video profiler (UVP), designed to capture imaging data of zooplankton at 15m depths, and used video analysis software to quantify this data.