As dam removals become more frequent across the United States and globally, understanding kelp forest response to coastal dam removals, in particular, is critical for managing nearshore habitat. Dam removals impact flow and sediment regimes of rivers, both of which can influence coastal kelp forests. The removal of the Elwha River, WA dams released ~19 Mt of sediment into marine ecosystems. This sediment flux dramatically influenced the turbidity of the nearshore water column and permanently increased the amount of sediment released from the river. The objectives of this study were two-fold. First, I developed methods to remotely sense and quantify the abundance of canopy forming kelps from aerial images. Next, I determined how changes in suspended sediment concentration and light attenuation during and following a major dam removal event in the Elwha River impacted the growth of nearshore bull kelp, Nereocystis luetkeana. By incorporating remote sensing to quantify the relative abundance of bull kelp in the area, my study observed that following dam removal, bull kelp abundance declined in the study area. This was an unexpected finding because I calculated that suspended sediment concentration decreased following dam removal, thus improving conditions for kelp growth. Although suspended sediment concentration decreased after the dam removals, other factors, such as an increase in herbivorous predation, could have played a large role in suppressing bull kelp abundance. The supervised classification scheme that I developed for remotely monitoring kelp abundance will make analyzing larger areas feasible in future studies, which may help to better identify regional trends in kelp abundance. Marine aerial monitoring remains an important avenue to better predict and manage future kelp forest response to dramatic changes in the ecosystem.

Wave energy converters (WECs) are devices that convert the motion of waves into useful energy. An interdisciplinary team of University of Washington students have designed and prototyped a WEC to power ocean sensors. One of the primary advantages of a sensing system powered by a WEC rather than relying on external charging of batteries is the potential for an increase in power output, which means that the system can support higher sensing loads at finer temporal resolutions. The characteristics of the environment in which such a device would be deployed place constraints on the device’s design because they impact durability and performance. To determine these characteristics and inform design decisions, analysis of wave model data was performed at potential locations of device deployment for parameters including significant wave height, mean period, and dominant period. Analysis revealed typical wave conditions as well as statistically extreme conditions that are associated with storms and lulls in wave energy. Then, in situ measurements from ocean sensing buoys were used to determine model bias and provide potential error/offset values for the model-based analysis of wave parameters. This evaluation of model-based analysis was done by comparing model data at locations of National Data Buoy Center buoys to the in situ measurements from those buoys using regression and distribution based statistical methods. The computed error/offset values were then extrapolated to the potential device deployment locations and used as a confidence metric for the accuracy of the model-based analysis. These results ensure that the WEC design team has an accurate understanding of the constraints of the environment that they are designing for. This analysis is also essential for market research because it can establish if an area, and thus potential users, provides a viable opportunity for the deployment of the WEC-powered sensing system.

In this study, I aimed to determine whether the genetic signature of Nitrate Reductase (NR) from phytoplankton in the environment is correlated with the in-situ nitrate concentration. To accomplish this, I first generated a phylogeny of phytoplankton NR amino acids sequences to determine if the sequences separate into monophyletic groups that match their taxonomic identification. Secondly, I placed RNA transcripts for NR derived from samples collected off the coast of Hawaii onto the tree to determine which clades expressed NR. Finally, I constructed heat maps to show the abundance of RNA transcripts for each phytoplankton clade by latitude and nitrate concentration to establish trends in phytoplankton phyla distribution. Results indicated that all phytoplankton, no matter phyla or cell size, were more abundant in higher nitrate concentrations. If instead RNA transcript abundance was normalized by chlorophyll concentrations, there was little separation in distribution based on plankton size, and different trends based on phyla emerged. Alveolata, Archaeplastida, and Stramenopiles were found in similar low to moderate nitrate concentrations (0.0023µM-0.8052µM). In contrast, Cryptista did not display a consistent trend across the phylum, as all clades displayed different abundance patterns. Haptophyta, both large and small, made up a significantly higher proportion of phytoplankton found in low nitrate environments (0.0009µM). These results indicate that there is separation of phytoplankton phyla by nitrate concentration, supporting the hypothesis that these phyla have evolved to utilize different ecological niches, however further research is needed with higher taxonomic resolution to fully quantify the factors controlling the distribution of different phytoplankton clades.

The ocean is extremely important in the biogeochemical cycling of carbon, nitrogen and other elements. Half of all photosynthesis occurs within the ocean, mostly from marine algae, phytoplankton. Additionally, half of all nitrogen, a key nutrient for both terrestrial and marine plants, is lost through the conversion to N2 from microbial processes called denitrification. Another product of denitrification is N2O, a greenhouse gas 310 times more potent than CO2 that also has the potential to damage the ozone layer. Denitrification occurs in anoxic environments, such as special areas called Oxygen Deficient Zones (ODZs), which in certain areas start at about 100 meters deep in the water column. Prochlorococcus, a marine phytoplankton, is the most abundant photosynthesizer on the planet and the low-light ecotype of Prochlorococcus can inhabit the edge of the euphotic zone and continue to photosynthesize. It has been found in an unlikely environment: The top of ODZ in the Eastern Tropical North Pacific (ENTP) located off the Western coast of Mexico. This is interesting because photosynthesizers traditionally don’t reside in low oxygen content areas. The Prochlorococcus found in the ODZ has been observed with a Hybrid Cluster Protein (HCP), which in other organisms, such as E. coli, is responsible for the reduction of NO to N2O for intracellular purposes. There are three identified classes of the hybrid cluster protein represented in multiple bacteria. We explored which of these classes were present in Prochlorococus' HCP. We started by investigating the metagenome generated from a 2012 ENTP ODZ cruise for genes containing the HCP, using various Python programs, we were able to obtain full length sequences, 8 of which were a match to previously identified Prochlorococcus. These sequences were then aligned against organisms with known HCP classes to compare different amino acids at key differentiating positions. From the alignment we were able to find that ENTP ODZ Prochlorococcus have a class 1 HCP.

 Euphausia superba, commonly known as Antarctic krill, are the dominant krill species in the Southern Ocean, and one of the most abundant species on Earth. This project focused on the swimming patterns of Antarctic krill in increasing chlorophyll concentrations to help understand the relationship between food availability and krill response by using 3-D data points from synchronized videos. Samples were collected aboard the RV Gould throughout Autumn of 2019 at both the South Shetland Islands and Gerlaches Straight at depths of 100-150m using 750 micrometer mesh square 2 x 2m nets. Samples were stored in a 500L tank and kept at 6 degrees Celsius. For the trials, 5 krill were placed in a 50L tanks in varying chlorophyll-a concentrations and recoded for 10 minutes using synchronized cameras. Afterwards, krill movement was analyzed using MATLAB’s DLTdv8 software. R Studio was used to assign ‘bins’ to various tank depths and count the number of individuals in each bin at a given time. Currently, I am still working on the results, however, it is hypothesized that the time spent in multiple bins will decrease as the chlorophyll concentration increases, since the krill will develop a more horizontal swimming pattern. It is important to understand this mechanism because in future climates, phytoplankton abundance is uncertain, which could have negative consequences for krill and the surrounding environment because of their keystone species status.

Mid ocean ridges are large interruptions in the expansive abyssal plains that dominate ocean basins. Volcanically active ridges release heat and chemicals into the surrounding ocean through hydrothermal plumes. Benthic organisms are dependent on these plumes for nutrients and distribution of their larvae. Quantifiable changes in hydrothermal plumes have been documented in response to volcanic eruptions. These plumes experience increases in fluid temperature and rise height after eruptions and become event plumes. This study investigates the effects on circulation from the 2015 eruption at Axial Seamount: a submarine volcano located along the Juan de Fuca Ridge, 300 miles off the coast of Oregon. After the eruption, an unusual temperature increase was measured within the summit caldera. This increase is unique compared to other eruptions in that it is widespread, uniform, and has a large amplitude of 0.6 to 0.7 °C. Two hypotheses exist for the temperature anomaly: a large brine layer was expelled from the subsurface after the eruption, and a neutrally buoyant event plume formed above a lava flow and was advected above the summit. Since no salinity data is available, I evaluate the two hypotheses using the mean flow direction, magnitude, and variation of currents measured at a site within the caldera. There was an abnormal sustained flow to the southeast lasting 12 days with high speed coinciding with the rising temperature. This observation is consistent with the movement of a large volume of warm fluid. The increase in standard deviation and by proxy, turbulence, are not significant enough in the presence of increased flow speed to imply either a brine layer or event plume as the cause. Understanding fluid motion after eruptions will help give insight into how microorganisms are distributed amongst and establish new communities in hydrothermal vent fields.

Better understanding the circulation of the ocean's deepest waters is critical to predicting how the world ocean will respond to a rapidly heating atmosphere. The deep and abyssal circulation across 30°S in the Brazil Basin is inferred from multiple decades of full-depth CTD data by an angular momentum and salt conserving inverse model which parameterizes mixing across ocean layers as a function of the roughness of the seafloor. This inverse model was originally designed by my advisor for use in the North East Pacific basin. My work was writing an extensible software library in Python to apply the same inverse technique to other ocean basins like the Brazil basin. From this inverse we learned the Brazil basin exhibits strong diapycnal mixing especially towards its boundaries, and weak lateral mixing. The largest transport outside of boundary currents across 30°S is the southward flow of Antarctic Bottom Water (AABW) at a rate of ~10^10 kg s-1. AABW flows northward through the Vema Channel and southward in the interior of the basin creating a cyclonic circulation around the Rio Grande Rise. Flow along -30°S is westward in the Antarctic Intermediate Water (AAIW) and Upper Circumpolar Deep Water (UCDW), and eastward in the North Atlantic Deep Water (NADW). Southward east of the Rio Grande Rise would have large impacts on the mixing and heat budgets of the Brazil basin.

ARGO floats are a fleet of autonomous robots that measure various oceanographic data while drifting with ocean currents and moving through the water column using a buoyancy engine. This buoyancy engine utilizes oil and air which is pumped in and out of a bladder at the base of the float. A typical function of an ARGO float is to sink to depth in the water column and then float back up to the surface, this is called a “profile”. When the float reaches the surface again, it communicates to satellites across the globe using an antenna which must emerge from the water completely to transmit its collected data. Recently, there have been suspicions of bladder problems in floats being produced as well as in deployed floats due to communication issues with the telemetry system which may be caused by the antenna not getting fully out of the water. I have refined a method of identifying bladder problems in ARGO floats using the data the float transmits. Preliminary analyses I have done shows that a decrease in vacuum with an increase in air pump runtime overtime has identified floats with bladder problems with high confidence. I then found all the floats that have been deployed since 2012 that have bladder problems and compiled data visualizations showing the relation between these floats and other data variables. Finally, I will analyze the data to decide whether this problem affects the overall lifespan and/or functionality of the floats. From this analysis I will then possibly find a solution for future floats to resolve the bladder problems detected and additionally to set up a system to automatically monitor for more problems.

Dam removals are becoming more common as many dams reach the end of their lifespans. As a consequence, it is important to understand the characteristics of the sediment accumulated behind them for sometimes over 100 years when it is released. These sediments can contain organic matter that is deposited in river deltas and reservoirs and can have an impact on the ecosystem. The Elwha River dams were removed starting in 2011, releasing 19Mt of sediment, and also a fraction of organic material that is unknown, some of which made its way to nearshore subtidal deposits. To characterize the relationship specifically between organic content and sediment size in sub-tidal deposits, box cores were collected and examined using x-radiography, wet sieving, and loss on ignition procedures. In subsamples with a lower percent of mud, the percent of organic matter is less than in subsamples that contained more mud. There is also a relationship between both percent mud and organic matter with the distance that the samples were collected from the river, with more mud and organic matter being found farther from the river mouth. These relationships can be explained by the settling velocity of flocculated sediment because organic matter better combines with mud particles and flocs sink slower than sediment of a larger size. This study is useful for future dam removals to determine what range of impacts it might have downstream.