Seabirds are often used as markers of ecosystem health due to their heavy dependence on the base of the food chain. The Alcidae family consists of small, diving birds who feed exclusively within the water column and rely on the sea year-round. Because of this, many view alcids as the only “true” seabirds. A research apprenticeship at UW’s Friday Harbor Laboratories on the pelagic ecosystem, Pelagic Ecosystem Function, has observed all seabirds since 2004, with consistent data since 2013. Alcids have been largely ignored in previous Pelagic Ecosystem Function studies, as the Common Murre (Uria aalge) artificially inflates the alcid family data due to their high abundance within the San Juan Channel. Upon removal of this species, it is found that non-Common Murre alcids are declining at a higher rate than any other seabird family within the channel, with a near-linear decline since 2013. In order to investigate the leading drivers of population decline, variables regarding food availability and habitat were collected in the form of chlorophyll, photosynthetically active radiation, and sea surface temperature. Compelling correlations were found between non-Common Murre alcid density and photosynthetically active radiation, as well as between chlorophyll and sea surface temperature. The data presented here is important not only for the mitigation of local ecosystem degradation, but also due to the consistency with global trends of seabird populations.

In Spring of 2018, I helped collect a 45 cm sediment core from San Blas Basin on the continental shelf of pacific México, 50 km off the coast and north-west of Puerto Vallarta. After noticing that there were large sticks and seeds in the sediment, our Méxican collaborators gifted me the core to analyze lignin, a biomarker for terrestrial organic matter (TOM). Sticks in oceanic mud 50 km off the coast is unusual so we were excited to find out this geological story. I found that the total amount of lignin phenols ranges between 1.5 to 4.5 mg lignin phenol/10 g sediment except for an order of magnitude increase between 18 cm and 26 cm which was 20 to 40 mg lignin phenol/10g sediment. Acid to aldehyde ratios of vanillin-type lignin (Ad/Al (v)), a proxy for degradation, had a range of 0.36 to 0.58 while the section between 18cm to 26cm was fresher with a range of 0.26 to 0.28. S/V to C/V analysis indicated that the lignin is sourced from angiosperms. The section between 18 cm to 26 cm had statistically similar values ranging between S/V of 0.85 to 0.95 and C/V of 0.19 to 0.21. S/V to Ad/Al (v) analysis had a negative slope indicating S-type lignin is preferentially degraded and the background lignin signal could look more like the fresher 18-26 cm section if degradation had not occurred. My lab partners, Méxican collaborators, and I conclude that a large flooding event brought fresh TOM off of the land and the sediment deposition and deposited 8 cm of sediment in one event due to the S/V and C/V values overlapping. The flooding was likely a tsunami, large hurricane, or flash flood from the nearby Santiago river.

Oceanic biogeochemical pathways, and particularly nitrogen, play a large role in global carbon cycling. Oxygen Deficient Zones (ODZs) such as the Eastern Tropical North Pacific (ETNP) have microbes that use distinct metabolic pathways for energy and nutrients in the absence of oxygen. These ODZ pathways shape the global inventory of nutrients and are thought to be responsible for around half of marine bioavailable nitrogen losses. While some of these pathways such as canonical denitrification and the more recently discovered anaerobic ammonia oxidation have been studied, there are also other potentially significant pathways. Trimethylamine N-oxide (TMAO), a small nitrogen-containing organic molecule with pathways that connect into other nitrogen cycle pathways, was seen to be diminished to nonexistence in ODZs which suggested it was being utilized. While studied in other environments, microbial utilization of TMAO in ODZs has not been significantly studied. We mapped metagenome reads collected from the ETNP ODZ onto a phylogenetic tree annotated with genes for TMAO degradation found outside the ODZ. We were able to confirm the presence of genes for TMAO degradation pathways and identified a range of organisms involved. We also examined the distribution of these genes and organisms across the different depths we sampled from to create a more complete picture of nitrogen cycling in ODZs.

Recent increases in atmospheric carbon dioxide levels have led to a decrease in the pH of the world’s oceans. These changes in seawater chemistry could have severe consequences for calcifying organisms such as corals. Ocean acidification (OA) poses an imminent threat to the world’s coral reef ecosystems, which could lead to massive reductions in global marine biodiversity. Much of the response of corals to OA is still poorly understood from a detailed physiological perspective, particularly the impact of OA on a fundamental process of skeletal growth called nucleation. Nucleation is the process by which calcium and carbonate ions combine in solution to form a new piece of solid calcium carbonate, which corals use to build their skeleton. While calcification has been measured in corals, the specific step of nucleation has not been quantified and has the potential to be more sensitive to ocean acidification. Coral fragments of Stylophera pistillata and Acropora microphthalma were grown on microscope slides secured in petri dishes in normal ocean conditions suitable for growth. Half of the fragments will be placed into another tank that has constant alkalinity and a set pH of about 7.8 controlled with bubbling air at 800ppm carbon dioxide into the water, the predicted level of atmospheric carbon dioxide in 2100 with the current rate of emissions. This will allow for a big enough change in pH to clearly determine if nucleation is affected by lower pH. With an inverted microscope, the calcifying space was visible through the glass slides, and time-lapses were taken to quantify nucleation rates of corals in the normal ocean conditions. Reefs play a huge role in supporting biodiversity, economies, and population health. Understanding how nucleation rates are changing in variable ocean conditions is a key step in developing new ways to conserve reefs.

Members of the genus Psychrobacter, within the class Gamma-proteobacteria, generally live in very cold marine habitats. These bacteria can be found in Arctic and Antarctic sea ice and sediments, in deep-sea environments, and in permafrost containing relic marine sediments (cryopeg). Each of these environments provides a different combination of temperature and salinity, with different strains of Psychrobacter spp. potentially adapted to grow at different rates depending on environmental source and in situ conditions. I am exploring the growth characteristics of two Psychrobacter spp., each isolated from a different extreme environment. Psychrobacter sp. nov. strain CB7C was isolated from cryopeg brine (originally at –6°C and 140 ppt), and Psychrobacter sp. nov. strain 7E was isolated from winter sea ice brine (originally at –12°C and 128 ppt). We incubated strain CB7C in duplicate at 57 different sets of temperature and salinity conditions, including 19 temperatures, ranging from –7 to 12°C, and salinities of 35, 75, and 120 ppt. The strain was grown in a complex medium, Marine Broth 2216 (at 50% organic strength), adjusted to desired salinity. At regular intervals during the incubations optical density was measured, with cell counts made at start and end. Calculated growth rates and cell yields for CB7C varied across the different temperatures for each salinity. At higher salinity, the temperature at which the bacteria showed maximal growth shifted downwards, a result consistent with in situ conditions (lower temperatures at higher salinities) but novel in microbiology. By conducting similar incubations with strain 7E I will be able to compare growth patterns of the two isolates across a wide set of temperatures and salinities and determine if results with CB7C are singular or represent a more common trait amongst Psychrobacter strains, helping to explain their prevalence under such extreme conditions.

Nearly half of Americans live in earthquake prone areas. Many primary fault zones that host large earthquakes, such as the Cascadia, Alaska, and San Andreas fault zones, extend into the offshore regime. These offshore fault systems have been historically difficult to study due to challenges in observational techniques. Through the creation of an algorithm that uses geospatial analytical tools, this study seeks to identify seafloor faulting structures from data collected by high frequency multichannel acoustic methods. In doing so, we improve our capabilities of characterizing offshore fault zones. In addition, we examine these geospatial analytical methods for accuracy and explore the impact of data collection and post-processing procedures on associated errors. Data utilized subsists of bathymetric data collected in the Cascadia and South African regions, which are active and passive margins respectively. Methods for surface fault identification include visual inspection, as well as geospatial analytical methods consisting of the Bathymetric Position Index, slope, and aspect of surface morphology. Faults identified from surface morphology are compared to those identified using a coherence-based detection method from seismic reflection data. Surface expressed faults indicate high-amplitude and/or recent geologic deformation and can give insight into tectonic stress regimes and associated faulting hazards. An improved understanding of faulting hazards through efficient surface fault identification would aid in preparation and planning for earthquakes. Through the creation of this algorithm, our capabilities to accurately identify surface expressed faults in bathymetric datasets will be enhanced and thus our understanding of global tectonic processes and earthquake risks to population centers like those in the Pacific Northwest will be improved.