The interaction between incoming salt water from the ocean, which is driven by tides, and exiting freshwater from rivers drives circulation through estuarine environments. As a result of the interaction between the incoming water and the exiting water, nutrients and sediment are moved around the estuary. This study focuses on the interaction between tides and the Snohomish River as it enters the Possession Sound estuary, located in Everett, Washington. To acquire data, I deployed a boat-mounted acoustic Doppler current profiler (ADCP), which uses sound to measure water current direction and velocity. I collected these data at varying tide stages at three different sites between the Snohomish River’s southern output to nearby Mount Baker Terminal, located 3.6 miles southwest of the river output. I have collected 8 samples over the course of 7 months at both ebb and flood tide stages. Each transect survey lasted 3-6 minutes and collected data from the first 20 meters of the water column. To get accurate analysis of current velocity and direction I split the data into categories based on depth. Preliminary analysis shows a southward current at many sites during all tide stages and depths. This raises questions about the scope of the river influence and the potential for southward currents regardless of tidal stage. However, further analysis of current velocity and river discharge are needed. Due to the complexity of the currents in the area, understanding how the river and the tides are interacting can provide a greater understanding of how these currents are impacting the dispersal of sediment and nutrients throughout the estuary.

Metabolites are small organic compounds that are the products of cellular metabolism and the building blocks of macromolecules. The analysis of a multitude of metabolites in a sample simultaneously is known as metabolomics and is a powerful tool for understanding microbial interactions in the ocean. In particular, metabolomics provides a way to investigate how marine communities vary in composition during shifts in environmental conditions. The North Pacific Subtropical Gyre (NPSG) is a region where inorganic nitrogen availability limits phytoplankton productivity and microorganisms rely partially on diazotrophs for fixed nitrogen in the surface ocean. Because N2 fixation is often iron-limited, bioavailable iron should control fixed nitrogen levels in the gyre. Here, we tested this hypothesis by collecting metabolomic samples during a large-volume incubation in which tanks were amended with various nutrient combinations of iron, nitrogen, and phosphate during a month-long incubation. It was expected to stimulate a diazotroph bloom by limiting the incubation for nitrogen. In these nitrogen-limited tanks, we expect to see a strong metabolic response to the absence of fixed nitrogen, followed by the ingrowth of nitrogen fixers with their own metabolite fingerprints as the experiment progresses. I will compare metabolomes of incubations to those of phytoplankton cultures, including the nitrogen-fixing cyanobacteria UCYN-A and Trichodesmium. I will also use the incubation's nutrient concentration and microbial community metabolomics to test the hypothesis that altering nutrient supply ratios (Fe: N: P) in the NPSG microbial population will result in metabolite shifts. As the critical link between inorganic matter and the formation of the organic material that powers the ocean’s food chains and biological carbon pump, metabolomics provides a way to better understand the critical role that nitrogen fixation plays in regulating the taxonomy and biochemistry of the world’s largest biomes.

About one-quarter of photosynthetically fixed carbon is cycled through the marine microbial community in the form of metabolites, the intermediate compounds or products of metabolic processes. Marine heterotrophic bacteria are largely responsible for consuming these metabolites as a source of carbon, energy, and nutrients, yet little is known about transporter affinity and uptake kinetics of bacteria for abundant substrates. Homarine is a small, nitrogen-containing, zwitterionic metabolite that is produced by the cyanobacterium Synechococcus as well as some diatoms and haptophytes, where it is thought to function as an osmolyte. Dissolved homarine is present in the ocean at very low concentrations (~1.1 nM in Puget Sound). I hypothesize that these low concentrations are the result of high affinity bacterial transporters for homarine. Homarine can be used as a sole carbon and nitrogen source for OBi1, a marine bacterium isolated from Puget Sound. In this study, I investigate the uptake kinetics of homarine by OBi1 in the lab using the Michaelis-Menten model. I compare the uptake kinetics of OBi1 to similar homarine uptake experiments in the Salish Sea in June 2019. I expect that OBi1 will have a high affinity for homarine uptake and will take up homarine at nanomolar concentrations. I also anticipate that the marine microbial community in Puget Sound will have similar uptake kinetics to those observed with OBi1. Understanding the uptake kinetics of homarine by marine bacteria sheds light on the cycling of homarine in marine environments like Puget Sound and can help us understand the processes that keep the dissolved homarine concentration so low.

Anthropogenic change has increased the frequency and severity of harmful algal blooms (HABs). Along the US west coast, blooms of the phytoplankton species Pseudo-nitzschia australis are proliferating, aided by anthropogenic and climatic increases in temperature and nutrient availability. P. australis produces domoic acid (DA), a neurotoxin that induces sickness and mortality in marine organisms and humans, inhibits fishery and shellfish industries, and threatens entire ecosystems. Consequently, it is vital to understand the specific conditions promoting P. australis growth and DA production. In this experiment, we determined P. australis exponential and stationary phase growth rates and DA production across a nitrogen (N) concentration gradient from 0 – 100 μM at 13 °C and 21 °C. These temperatures reflect those of upwelled water and marine heat waves respectively, processes predicted to increase with climate change. During the exponential phase, P. australis growth rates increased with N concentration, reaching maximums at 10 μM for 13 °C and 30 μM for 21 °C. Growth rates were significantly higher at 13 °C than at 21 °C during the exponential phase, except at N concentrations of 30 μM or more, where we observed similar growth rates. Although we also found positive relationships between growth rate and N concentration during the stationary phase, growth rates were lower and were not significantly different between temperature treatments. Therefore, we expect cool temperatures associated with upwelling conditions to generate faster HAB growth. We collected DA data for analysis and presentation. Based on prior research, we expect stress from nutrient limitation during the stationary phase to induce higher DA production. Thorough understanding of how anthropogenic and climatic changes impact P. australis growth and toxicity allows for accurate prediction of future HAB development and severity, thus ensuring the aquatic ecosystems sustaining not only marine life, but human industries, cultures, and societies, are preserved.

Cyanobacteria are tiny photosynthetic microbial organisms responsible for producing roughly an eighth of the oxygen we breathe. Synechococcus is a model cyanobacteria, meaning the species has characteristics making it easy to study and modify. As a scientific community, we don’t know the function or purpose of many genes expressed by Synechococcus. The goal of this project is to determine the function of particular genes hypothesized to be important to the adaptive survival of Synechococcus in different environments. We are approaching this by building a start-to-finish gene characterization method, starting with computational analysis to identify genes of interest, followed by knocking out, or disabling these genes and observing the effect on the growth of the culture. On the computational side, I’m now analyzing residual gene expression, using that information to characterize gene clusters, and analyzing external data to infer genetic context. On the laboratory side, I’ve characterized the growth of the un-modified base strains and developed procedures for genetic modification. Identifying the function of Synechococcus genes allows scientists to better study the response of Synechococcus to varying environments, which is especially important in a changing climate. Increasing understanding of the molecular mechanisms of Synechococcus also opens the door to genome engineering for the production of biofuels, plastics, and other commodities, or for using Synechococcus as a tool for bioremedial carbon sequestration. Additionally, the genes of Synechococcus are similar to those in other related oceanic microbes such as Prochlorococcus, the most ubiquitous photosynthetic organism in the world. For all these reasons, Synechococcus is an important model organism, and a deeper understanding of its biology will bolster our sparse understanding of marine genomics.