Thesis Defenses

Jacquie graduated from St. Edward’s University (SEU) in 2017 with a B.S. in Chemistry. While at SEU, Jacquie participated in a summer undergraduate research program during 2014 as part of a behavioral ecology lab. That summer, she focused on observing the behavior of largespring gambusia (Gamusia geiseri) in the San Marcos River under the guidance of Dr. Raelynn Deaton-Haynes as a TG Grant Summer Research Student. While seining for pipefish in the Gulf of Mexico and snorkeling in the San Marcos River, Jacquie discovered her love for fieldwork-based research.

In effort to expand her chemistry interests, Jacquie switched labs and worked under the guidance of Dr. Tricia Shepherd as a Welch Foundation Undergraduate Researcher from 2015 to 2017. She built computation molecular models of carbon nanotubes (CNTs) to research the pore-filling dynamics of water molecules within CNTs. She presented her CNT findings at the 2016 MERCURY Conference and at the 2017 American Chemical Society Conference. After graduating in 2017, Jacquie began a Ph.D. program at University of California, Santa Cruz (UCSC) in the Chemistry and Biochemistry Department as a Regents Fellowship recipient. There, she worked as a Teaching Assistant for various undergraduate chemistry courses. In order to better pursue her interests in marine chemistry and fieldwork, Jacquie left UCSC and joined the Marine Science M.S. program at Moss Landing Marine Laboratories (MLML) in 2018 as a student in the Nutrient Laboratory and the Physical Oceanography Laboratory. Working under Dr. Kimberly Null and Dr. Thomas Conolly, she studied the influence of nutrient-containing shallow groundwater on local agricultural drainage systems as well as on local estuaries as a California Sea Grant Trainee. As a fieldwork-focused project, Jacquie was ecstatic to play in the mud as part of her research project.

During 2019, she was awarded a Graduate Research Grant from the Geological Society of America, received funding from the California State University Council on Ocean Affairs, Science, and Technology, and served as an Undergraduate Research Opportunities Center mentor. Jacquie presented her research findings at the 2019 Elkhorn Slough Science Symposium, the 2019 American Geophysical Union Conference, and the 2019 Coastal & Estuarine Research Federation Conference. When not in the field, Jacquie brewed beer with the MLML Brew Club, volunteered at Elkhorn Slough National Research Reserve as a Bird-Box Monitor, learned to surf, and worked for various local agricultural start-ups. Following her time at MLML, Jacquie looks forward to catching up on hiking, mountain biking, and volunteering as well as pursuing a career focused on water quality.

Thesis Abstract:

Shallow groundwater and shallow groundwater nitrogen have been suspected to influence agricultural tile drains, agricultural drainage ditches, and estuaries within the Lower Salinas Valley (LSV) of California’s Central Coast. This study used geochemical tracers to evaluate the influence of groundwater to each of these water sources. For agricultural sites, groundwater discharge estimates revealed between 51% ± 16% to 95% ± 30% of tile drain water was sourced from shallow groundwater. Stable isotopes of water (𝛿²H_H2O and 𝛿¹⁸O_H2O) confirmed that sump-influenced ditches are influenced by tile drain discharge, and that tile drains are influenced by shallow groundwater. Further, average nitrate as nitrogen (NO₃-N) concentrations revealed that NO₃-N in sump-influenced ditches were an order of magnitude higher (i.e., 33.78 to 95.21 mg L^-1 NO₃-N) than non-sump-influenced drainage ditches (i.e., 3.38 to 8.50 mg L^-1 NO₃-N). Nitrogen concentrations of shallow groundwater were also significantly lower than those of tile drain and sump water, which suggested that shallow groundwater was not the main source of nitrogen to agricultural drainage water. Stable isotopes of nitrate (𝛿¹⁵N_NO3 and 𝛿¹⁸O_NO3) within sump-influenced ditches were similar to those in tile drain effluent. However, groundwater nutrient discharge estimates revealed that 2.9 ± 0.7 to 5.4 ± 1.2 kg/d NO₃-N of the total 9.4 ± 2.1 kg/d NO₃-N from tile drains comes from shallow groundwater, further suggesting that legacy nutrients in shallow groundwater were not the primary source of nutrients to tile drains. Finally, statistical analyses (ANOVA and PERMANOVA) of nitrogen tracers reveals a lack of seasonality in agricultural drainage system nutrient content that requires further investigation to evaluate correlation with annual NO₃-N variability of local estuaries and waterways (e.g., Moro Cojo Slough). This study is the first assessment of shallow groundwater influence to agricultural drainage systems via tile drains in the LSV and provides essential information for regional growers regarding nutrient water quality monitoring and best management practices, particularly in light of recent regulatory adoption of the Irrigated Lands Regulatory Program (Ag Order 4.0).

Geochemical tracers were also employed to evaluate the influence of shallow groundwater on characteristic wet season NO₃-N increases observed within California Central Coast estuaries. During February 2019, the characteristic NO₃-N spike was observed in Moro Cojo Slough, the Moss Landing Harbor, Monterey Bay, Elkhorn Slough, and the Old Salinas River. NO₃-N concentrations decreased in Moro Cojo Slough during the dry season, which highlighted the annual variability of nutrients associated with Central Coast estuaries. Radon-222 (²²²Rn) activities in Moro Cojo Slough surface water did not increase between wet season or dry season downstream monitoring. However, activities were greater along the channel length during the 2019 wet season (2.58 ± 1.39 dpm L^{-1 222}Rn) than during the 2019 dry season (0.81 ± 0.57 dpm L^{-1 222}Rn). Using surface water and groundwater ²²²Rn activities, groundwater discharge estimates revealed that advective groundwater flux remained low during both seasons in Moro Cojo Slough. Shallow groundwater nitrogen flux estimates revealed that groundwater was not a major source of nitrogen to Moro Cojo Slough during the wet season. Elevated dry season shallow groundwater NH₄-N concentrations suggested that groundwater may significantly contribute to dry season surface water nitrogen in Moro Cojo. ²²²Rn activities in Elkhorn Slough (2.38 ± 1.42 dpm L^{-1 222}Rn) were similar in magnitude to Moro Cojo Slough, while ²²²Rn activities in the Old Salinas River were an order of magnitude higher (25.0 ± 4.25 dpm L^{-1 222}Rn ). Paired with our findings from Old Salinas River watershed agricultural drainage ditches and tile drains, we argue that elevated ²²²Rn activities in the Old Salinas River were from ²²²Rn-rich tile drain discharge rather than from advection of shallow groundwater to the channel. These findings highlight that groundwater via advective flux is not a significant source of water or nitrogen to California Central Coast estuaries, but that shallow groundwater discharge via tile drains plays an important role within the watershed.

I am an ocean lover- swimmer, surfer, SCUBA diver, kayaker, sailor, snorkeler, and marine scientist. I’ve spent the last ~10 years doing research on the effects of climate change on marine species and intend to continue on this path!

I majored in Environmental Studies and Philosophy at Santa Clara University (undergraduate) and post graduation returned to Bainbridge Island, WA to get involved with the aquaculture world on the Olympic Peninsula. I began working for Taylor Shellfish as part of the research department and became very engaged with the negative effect ocean acidification is having on local shellfish.  I worked for the UW School of Aquatic and Fisheries Science to look at multi-generational effect of ocean acidification on Pacific oysters. I assisted with a study on a Purple Hinge Rock Scallop growth for commercial development of the scallop industry. I spent my off seasons getting my SCUBA DiveMaster, working as a kayak guide, and interning in Auckland, NZ for a common dolphin population dynamics study.

I am currently in the Ichthyology lab at During graduate school I worked at the Southwest Fisheries Science Center (SWFSC) Ecology Division (NOAA) in Santa Cruz on climate change studies focused on rockfish reproduction.  My thesis research is specifically focused on how changing ocean chemistry (pH and dissolved oxygen) affect larval rockfish survival, deformity and metabolism.  I spent most of my Spring time at the NOAA lab waiting for rockfish to give birth, always on call, a rockfish midwife if you will.  Throughout the rest of the year I have been assisted with another project on the effect of climate change on juvenile rockfish. I helped collect juvenile rockfish at Stillwater Cove and ran behavioral and physiological trials at the NOAA lab in Santa Cruz.

I am moving to Vermont (eek far from the ocean!) for the fall to finish up with thesis edits before moving back to Washington state where I hope to get a job as a fish biologist or marine scientist.

Thesis Abstract:

The California Current ecosystem is experiencing dramatic changes in ocean chemistry resulting in ocean acidification (i.e., decreasing pH) and hypoxia (i.e., lower dissolved oxygen [DO] levels). These changes are exacerbated by increases in upwelling intensity and shoaling of the oxygen minimum zone. Gopher rockfish (Sebastes carnatus) are an ecologically and economically valuable rockfish species, whose habitat is becoming increasingly inundated with low pH and low DO water. To test how ocean acidification and hypoxia may interact to influence the reproductive process in Gopher rockfish, we exposed gravid females of both species to 4 treatments throughout the gestation period: 1) low pH (pH 7.5); 2) low DO (DO 4.0 mg/L); 3) a combined stressor (pH 7.5 x DO 4.0 mg/L); and 4) control (pH 8.0 x DO 8.0). Post-parturition, larvae from each brood were seeded into each of the 4 treatments to evaluate survivorship, metabolism, and hypoxia tolerance as a function of the prior maternal treatment conditions and the subsequent larval treatment. The remainder of the brood was collected and preserved to later quantify the percent deformity of the brood and total fecundity. Our research indicates that Gopher rockfish larvae are resilient to low pH (pH 7.5) and low DO (DO 4.0mg/L) based on both maternal and larval exposures to these stressors. Gopher rockfish may be adapted to gestating in these conditions because their reproductive season overlaps with Spring upwelling on the central California coast. There are some indications of sensitivity to these stressors shown by non-significant trends toward higher percent deformity and lower fecundity in low oxygen stressors. It is unknown how Gopher rockfish will respond as ocean acidification and hypoxia progress due to climate change.

Melissa Naugle graduated from University of Maryland, College Park in 2016 with a B.S. in Environmental Science and Policy. During her time at UMD, she had the opportunity to participate in a coral monitoring internship in Thailand where she learned to SCUBA dive. After that experience, Melissa knew she wanted to pursue marine science research. After graduating, she began a research position at Georgetown University, where she studied how disturbance affects the community ecology and population genetics of salt marsh arthropods. Melissa began her Master’s at California State University, Monterey Bay and Moss Landing Marine Labs in 2018 in the Logan Lab and the Invertebrate Ecology Lab. She studies coral responses to stress and is interested in using genomics to learn more about coral conservation. During her time at MLML, Melissa has taken part in multiple outreach activities including a mentorship program she led called Future Leaders in Marine Science, which aims to teach marine science to high schoolers at North Monterey County High School. She served on MLML student body as CSUMB representative. She also served as a MLML liaison, and later as co-chair of the Monterey Area Research Institution’s Network for Education (MARINE). Melissa has also worked at the Monterey County Public Health Laboratory, processing PCR tests for COVID-19 and later sequencing SARS-CoV-2 viral RNA to monitor variants across Monterey County. After graduating from MLML, Melissa will begin a PhD with the Reef Restoration and Adaptation Program and Southern Cross University to study genetic markers of coral bleaching on the Great Barrier Reef.

Thesis Abstract:

Phenotypic plasticity is one way that species may cope with stressful environmental changes associated with climate change. Reef building corals present a good model for studying phenotypic plasticity because they have experienced rapid climate-driven declines in the past twenty years, often with differential survival among individuals during heat stress. One potential reason for underlying differences in thermotolerance may be due to differences in baseline stress levels. Stress associated with pollution has been shown to produce synergistic effects with heat stress, exacerbating the physiological damage of heat stress. Conversely, it is possible that mild pollution stress could prepare corals to better cope with heat stress via cross tolerance mechanisms. Cross tolerance occurs when a mild stressor prepares an organism for more extreme, subsequent stress, reducing the impact of that stressor on the organism. To examine these two possibilities, acute heat stress experiments were conducted on Acropora hyacinthus from five sites around Tutuila, American Samoa with differing pollution impact. Bleaching responses were measured visually, using photographic assessment to estimate chlorophyll content, and using pulse amplitude fluorometry to measure photosynthetic efficiency. Endosymbiont community composition was assessed at each site using quantitative PCR. RNA sequencing was used to compare differences in genes expression patterns prior to and during heat stress. Symbiont communities differed among sites, with heat tolerant Durusdinium dominating in areas with higher pollution impact and heat sensitive Cladocopium more common in pristine areas. Pollution stress may induce a shift towards Durusdinium thereby enhancing resistance to subsequent heat stress in the near term. Gene expression patterns showed few differences correlating to site or pollution level. Thermotolerance, however, did affect gene expression patterns, both during heat stress and in control conditions. In this thesis, I present potential mechanisms underlying coral thermal tolerance in pollution-impacted areas. My results highlight the importance of measuring pollution impacts on thermotolerance and identifying heat tolerant corals in “non-pristine” areas and their potential to seed nearby reefs following bleaching events.

Thesis Abstract:

Marine fishes that persist across broad geographic ranges experience gradients in environmental and oceanographic conditions, anthropogenic stressors, and ecological factors that influence their population dynamics. Understanding the spatial- and temporal-scales at which life history characteristics and demographic patterns vary, are essential for successful management and long-term sustainability of marine fisheries. From 2017 through 2019, 1,567 Canary Rockfish were collected from 13 port locations along the U.S. West Coast, to investigate latitudinal patterns in size- and age-structure, growth, maturity, condition, and mortality, as wells as to identify biologically relevant population breakpoints along the coast. Sex-specific differences in life history parameters were also investigated coastwide. Canary Rockfish exhibited strong latitudinal patterns in life history parameters; Canary Rockfish from colder, northern port locations exhibited larger sizes-at-age, lived longer, matured at larger sizes, and had lower mortality rates than Canary Rockfish from warmer, southern port locations. Male Canary Rockfish exhibited smaller sizes-at-age, lived longer, and matured at similar sizes in comparison to female conspecifics. Trends in life history parameters were correlated with coastwide environmental patterns in sea surface temperature and primary productivity (chlorophyll a). Cluster analysis using life history traits indicated central Oregon as a biologically relevant break point for Canary Rockfish populations along the U.S. West Coast and should be considered in future stock assessment models. Further research should explore stock structure through genetic analysis and compare hook-and-line data from untrawlable habitats with fishery-independent bottom trawl surveys to assess habitat-based differences in Canary Rockfish life history and demography.

Thesis Abstract:

In fission-fusion societies, individuals do not need to conform to a social structure in which their demographic or relatedness dictates their behavioral state or associations. Therefore, studies of fission-fusion societies provide a framework in which to compare the feeding dynamics across demographics unrestrained by stable associations. This study used bio-logger data and surface observations combined with long-term population data from the Gulf of Maine humpback whale, Megaptera novaeangliae, population to better understand the influence of demographics on feeding methods, time spent feeding and determine if a coordinated feeding method, kick-feeding, was a cooperative behavior. The results suggest that demographics did influence the feeding method used and highlighted the need to determine how energetic needs change across the feeding season. The results suggest that kick-feeding was not a form of cooperation. In contrast, demographics and the broader population structure did influence the roles that individuals filled in kick-feeding dyads.  Additionally, females’ extensive use of bottom-feeding, compared to males, suggests that different energetic requirements influence the feeding methods used. Preferential use of the lower water column by mother-calf pairs and pregnant females should be considered in future studies about anthropogenic threats.

Images taken under NOAA permit #981-1707, 775-1875, 605-1607, 605-1904, and 18059

Thesis Abstract:

Changes in the Earth’s climate are closely associated with the changes in the concentration of CO₂ in the atmosphere. One process that may play a major role in modulating CO₂ availability is the chemical weathering of silicate rocks into clays. Chemical weathering and the associated CO₂ drawdown are especially efficient in the islands of the Indonesian Archipelago, including New Guinea, due to the combination of warm, wet conditions and tectonic uplift.  Despite New Guinea’s potential global significance as a major contributor to Earth’s carbon cycle, few studies have addressed its rapid geological evolution and the weathering conditions associated with it during the Pleistocene.

As direct products of weathered silicate rocks, clay minerals are a useful and widespread tool for reconstructing past weathering environments and source rocks. Clay mineral data from New Guinea are limited, with no clay records from the Sepik-Ramu Rivers, the island’s largest river system and one of the largest contributors of sediments to the world’s ocean. Deep-sea sediment cores collected by the International Ocean Discovery Program (IODP) Expedition 363 just offshore of the Sepik River mouth provide an unprecedented opportunity to evaluate the history of chemical weathering in a critical, rapidly-evolving region during the middle to late Pleistocene (the past ~550 kyr). This thesis identified and quantified the relative abundance over time of the clay mineral species in the core record in order to establish the regional weathering conditions, test a recent model of the Sepik’s development from an epicontinental sea to an enclosed river valley, and examine the relationship of tropical weathering rates with sea level change during glacial-interglacial cycles. Additionally, this thesis evaluated weathering microtextures on silt-sized feldspar particles to provide a secondary supporting dataset.

This project processed and analyzed the clay compositions of 124 samples from two IODP Expedition 363 sites: Sites U1484 and U1485, along with 16 samples from Site U1486, a site located further offshore from the Sepik River mouth. Isolated clay fractions from each sample were measured with x-ray diffractometry and quantified as clay percentages using simulation software (NewMod). For the corollary study, fine sand-sized feldspar particles were evaluated for weathering microtextures using a scanning electron microscope.

Overall, the clay assemblage is dominated by illite (~25-62%) and chlorite (~20-62%) with secondary amounts of smectite (~2-26%) and kaolinite (~3-32%), suggesting that mechanical rather than chemical weathering is the dominant mechanism responsible for clay generation in this region, possibly due to the active tectonic setting. The record also shows an increase in chlorite over time, attributed to ongoing tectonic uplift and the associated expansion of high-altitude glaciers and mechanical weathering. In addition, a sharp decrease in illite after the oldest samples is interpreted as the cessation of the diagenetic transformation of smectite to illite.

The clay mineral record also shows short-term compositional shifts—the most notable of which include two shifts in clay abundance from 400-430 ka and 125-140 ka characterized by an increase in smectite and kaolinite and a decrease in illite and chlorite. These shifts coincide with glacial terminations, suggesting that rapid sea level rise during deglaciations may have resulted in the reworking of older and more chemically weathered soils. The 400-430 ka shift also coincides with a unit of coccolith ooze indicative of a pelagic environment. This suggests that in the oldest part of the record, marine deposition and sea level transgression may have both contributed to the short-term enrichment of smectite, whereas later clay mineral shifts were driven mainly by sea level rise. The apparent increase in influence from marine transgressions may reflect increasing areas of lowland created by the filling of the Sepik Basin.  These results highlight the numerous processes controlling tropical weathering and document their changing relative significance throughout the evolution of the region.

Thesis Abstract:

Demon catsharks (Carcharhiniformes: Pentanchidae: Apristurus Garman) are one of the most diverse genera of sharks, with 39 described species. The genus is further divided formally into three subgroups based on morphological characters and molecular phylogenies, and referred to as the brunneus-, longicephalus-, and spongiceps subgroups. Six Apristurus species are considered valid in the Southwestern Indian Ocean (SWIO) where the spongiceps subgroup makes up a third of the species in the area. This study identifies and formally describes two additional Apristurus species in the spongiceps subgroup from the SWIO Ridge based on morphometric and meristic data, and includes re-examination of type specimens of Apristurus species from the North Atlantic and Southwestern Pacific oceans due to their close morphological relationship to one of the species found in the area. In this study, morphological characteristics and meristics, along with multivariate statistical tests, were used to determine that significant differences existed between the putative species, confirming species designations. Overall, two species were identified with the first record of A. ampliceps in the area and one new species, referred here to as A. cf. albisoma. An improved Apristurus identification key for the Western Indian Ocean (WIO) will assist fisheries managers in developing conservation policies for fisheries operating in this area.

Matthew Jew grew up in Southern California and attributes his passion for Marine Science to Mr. Tom Clarke, his science teacher during his senior year of high school.  He attended California State University, Monterey Bay, and graduated Magna Cum Laude with degrees in Marine Science and Mathematics.  As an undergraduate, he worked with Dr. James Lindholm and Paul Clerkin as a research assistant.  He credits Dr. Lindholm for fostering his love for research and SCUBA which led him on his career path to MLML.

Thesis Abstract:

In marine communities, there are often multiple species that occupy the same or similar niches. When resources are in short supply, competitive interactions can negatively affect the survival of one or both of the species involved. Understanding the trophic habits and interactions of species helps explain their role in a given ecosystem. Additionally, knowing the trophic habits of targeted or bycaught species captured in fisheries can help to influence management decisions on an ecosystem level. Apristurus brunneus and Parmaturus xaniurus (Family: Scyliorhinidae) are abundant deep-sea predators native to the Northeastern Pacific Ocean. Central California offers a unique opportunity to study these sympatric species in a location where they have large populations and the potential to compete for dietary resources. This study identifies: (1) the dietary composition each predator; (2) what biological and environmental factors are associated with variation in their trophic habits; (3) the trophic level of each species; and (4) the level of trophic overlap and potential for interspecific competition between the two species. To investigate the trophic habits of these two predators, this study used two complimentary techniques: stomach content analysis (SCA) and stable isotope analysis (SIA). Specimen from both species were collected during fishery-independent trawl surveys along the central California coast. Stomachs (for SCA) and dorsal white muscle tissue (for SIA) were removed from sharks after biological and catch data were recorded for each individual, including potential explanatory variables (e.g., depth, latitude, longitude, maturity, season, sex, trawl composition, and total length). Trophic habits and trophic position were calculated for each species independently and the level of trophic overlap between each species were calculated for SCA and SIA. Both shark species consumed the same three major prey groups (shrimp, squid, and fishes), however A. brunneus exhibited a similar preference for all three prey categories, while P. xaniurus placed a disproportional preference for shrimp. Apristurus brunneus diet composition varied with sampling season, latitude, sex, and total length. In contrast, the diet of P. xaniurus only varied with sampling season and total length. The results of the SIA indicated similar results. In A. brunneus, δ 15 N varied with latitude, sex, and total length while δ 13 C varied with latitude and total length. Parmaturus xaniurus’ SIA variation was as a function of total length, latitude, and season for δ 15 N and δ 13 C varied with latitude and season. SCA and SIA metrics indicated that the size of dietary niche was consistently smaller for P. xaniurus. Species with a smaller niche size are considered to implement specialist feeding strategy, whereas a much larger niche (like A. brunneus) would indicate generalist diet. Despite the differences in the size of the dietary niche, both SCA and SIA found significant trophic overlap between the two species, such that P. xaniurus samples are nearly completely contained within the isotopic space of A. brunneus. While there is significant dietary overlap, in order for there to be competition between species resources must be limiting. In central California, resources are likely not limiting and these two species have implemented feeding strategies that maximize their net energy gain even when a strong co-competitor is present. Ultimately, the knowledge gained on the dietary and competitive habits of these two species improves our understanding of their role in the deep-sea ecosystem of central California and this new knowledge will aid managers in the implementation of ecosystem-based fisheries management.

Thesis Abstract:

Dietary studies of fishes provide an understanding of predator-prey interactions and may be used to inform resource managers about food web dynamics. Along the West Coast of North America, Lingcod (Ophiodon elongatus) are top marine predators in rocky-reef habitats and an economically important fishery. In this study, gut content and stable isotope analyses were used to evaluate differences in the diets of Lingcod collected along the U.S. West Coast (Alaska to Southern California) in 2016 and 2017.  Overall, Lingcod consumed a wide variety of prey and exhibited both generalist and opportunist feeding strategies. Significant variability in Lingcod diets were driven by factors such as depth, region, sex, and total length. Small, shallow water, male Lingcod consumed more lower trophic level prey items (e.g. cephalopods) and had less diverse diets. Large, deep water, female Lingcod consumed more higher trophic level prey items (e.g. gadids) and had more diverse diets. Geographic variation in trophic level was associated with environmental conditions of primary productivity (i.e., chlorophyll a), and sea surface temperature. Southern Lingcod fed more on cephalopods while northern Lingcod fed more on various fish groups. This study fills in data gaps in the trophic ecology of a top marine predator and can be used to inform food web models and fisheries management.