Aquatic Sciences Dissertation Registry

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Use the search boxes provided below to retrieve information from the Registry.  All entries were submitted by the recipient of an advanced degree. ASLO does not check the accuracy of information provided.  All images in the Registry were uploaded by the submitter, and ASLO assumes that the submitter owns the image.  

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Nitrogen Cycling in the Euphotic Zone of the California Current

Brandon Michael Stephens

University of California, San Diego

Defense Date: 26/02/2018

Nitrogen Cycling in the Euphotic Zone of the California Current

dissolved organic matter, nitrate isotopes, nitrificiation, new production

Deep ocean nitrate supply to the surface euphotic zone of the California Current Ecosystem (CCE) increases rates of productivity and leads to an overall increase in the fixed repository of dissolved and particulate organic matter (DOM and POM, respectively). Chapter II demonstrates that DOM production, in carbon units, can represent 12 ± 8% of nitrate-based production during low production periods and up to 28 ± 15% during highly productive periods. DOM can also accumulate in the surface CCE during post-bloom, surface stratified or iron-limited conditions, and therefore can represent a potentially exportable reservoir when subsequently subducted from the surface ocean. DOM production rates are comparable to regional sinking particle export rates, the combination of which matches net oxygen production rates as estimated in previous studies. While Chapters I and II demonstrate that deep ocean nitrate concentrations track patterns of surface productivity in the CCE, Chapter III tests whether all nitrate used in the surface ocean is derived from the dark ocean via upwelling. Stable isotopes of nitrate estimate that 6 - 36% of nitrate uptake is generated by nitrification occurring within the euphotic zone of the CCE. Rates of euphotic zone nitrification spanned 4 - 103 nmol L-1 d-1, rates of which extend to the surface ocean. A strong correlation between euphotic zone nitrification and nitrite concentrations led to the inference that either increased POM substrate or reduced phytoplankton abundance to be determinants of nitrification. Use of nitrate stable isotopes in Chapter IV demonstrates that surface nitrate utilization was enhanced at inshore CCE stations during the 2014 warm anomaly. The effect of utilization was detected as an isotopic enrichment in sinking and suspended POM and Calanus pacificus copepods. Nitrate sourced from the remnant mixed layer depth supports the food web, and was a source that was at times decoupled from deeper (200 - 400 m) nitrate. A relatively low 3.0 ± 0.5‰ nitrate uptake isotope effect corresponded with phytoplankton communities dominated by chlorophytes and flagellates. Data from Chapter IV support hypotheses that isotopes of upper ocean N reservoirs in the CCE will primarily reflect surface ocean nitrate dynamics.

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Characterization of Acantharea-Phaeocystis photosymbioses: distribution, abundance, specificity, maintenance and host-control

Margaret Mars Brisbin

Okinawa Institute of Science and Technology

Defense Date: 17/04/2020


Acantharea, Phaeocystis, symbiosis, photosymbiosis, plankton, RNA-seq

Microbial eukaryotes (protists) are important contributors to marine biogeochemistry and play essential roles as both producers and consumers in marine ecosystems. Among protists, mixotrophs—those that use both heterotrophy and autotrophy to meet their energy requirements—are especially important to primary production in low-nutrient regions. Acantharian protists (clades E & F) accomplish mixotrophy by hosting ​Phaeocystis spp.​ as algal endosymbionts and are extremely abundant in subtropical low-nutrient regions where they form productivity hotspots. Despite their ecological importance, acantharians remain understudied due to their structural fragility and inability to survive in culture. In order to overcome these challenges and illuminate key aspects of acantharian biology and ecology—including distribution, abundance, and specificity and specialization of symbioses—single-cell RNA sequencing methods were developed for acantharians and used alongside environmental metabarcode sequencing and high-throughput, in-situ imaging. Major findings from this thesis were that i) acantharian cell (> 250 µm) concentrations decrease with depth, which correlates to patterns in relative sequence abundances for acantharian clades with known morphologies but not for those lacking known morphology, and that ii) while individual acantharians simultaneously harbor multiple symbiont species, intra-host symbiont communities do not match environmental communities, providing evidence for multiple uptake events but against continuous symbiont turnover, and that iii) photosynthesis genes are upregulated in symbiotic Phaeocystis​, reflecting enhanced productivity in symbiosis, but DNA replication and cell-cycle genes are downregulated, demonstrating that hosts suppress symbiont cell division. Moreover, storage carbohydrate and lipid biosynthesis and metabolism genes are downregulated in symbiotic ​Phaeocystis​, suggesting fixed carbon is relinquished to acantharian hosts. Gene expression patterns indicate that symbiotic ​Phaeocystis​ is not nutrient limited and likely benefits from host-supplied ammonium and urea, thus providing evidence for nutrient transfer between hosts and symbionts. Interestingly, genes associated with protein kinase signaling pathways that promote cell proliferation are downregulated in symbiotic ​Phaeocystis​. Deactivation of these genes may prevent symbionts from overgrowing hosts and therefore represents a key component of maintaining the symbiosis. This research contributes new insights into the ecologically relevant photosymbioses between Acantharea and ​Phaeocystis​ and illustrates the benefits of combining single-cell sequencing and imaging technologies to illuminate important microbial relationships in marine ecosystems.

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Alpine running water macroinvertebrates as sentinels of global changes

Alberto Scotti

University of Innsbruck (Austria)

Defense Date: 27/04/2020


alpine, streams, climate change, land use change, riverscape, macrozoobenthos, glaciers

Water is present in the mountain environment in many different forms, and it provides a variety of ecosystem services, ranging from sustaining biodiversity, to human consumption, and to recreational uses. However, the climate change and the human footprint on high altitude environments are contributing to disrupting the natural water cycle and to reshaping the mountain landscape and its socio-economic sphere – from mountain-tops down to lowlands. The large-scale phenomenon of land use change that is occurring on the European Alps also takes part in this process: mountain agriculture tends to further intensify in easily accessible and fertile areas and the concurrent abandonment of areas that are economically less viable for agricultural use is causing the expansion of natural forests.
In three different studies, this thesis pursues the overall objective of yielding concrete insights into how these global change processes (i.e. climate and land use change) may affect the running water ecosystems in mountain areas. It aims at providing a framework for measuring the effects of these phenomena on riverine ecosystems, and at establishing new approaches to better assess the effectiveness of potential policy measures that focus on a conscious management of the water resource and of the riverscape. The main methodological approach shared among all the studies involves the sampling and analysis of stream benthic macroinvertebrates, long-established bioindicator organisms.
The presented research makes several empirical contributions: drawing on a dataset of macroinvertebrate records of a unique temporal resolution, it shows how climate change-related issues influence terrestrial and aquatic study sites located in mountain areas where long-term ecological data are continuously collected. Additionally, it focuses on the investigation of the specific habitat of a glacier-fed stream, where the macroinvertebrate communities were studied at a high spatial and temporal resolution, also assessing the independent contribution of space and time to their assemblage. Finally, the influence on the riverine ecosystem of different land cover types typical of the Alpine landscape was quantified, finding out that the effort to preserve the diversity of terrestrial habitats within the landscape is crucial also for aquatic environments.
The results of this thesis can assist researchers in regards to further understanding the ecology and biology of high mountain habitats in the light of global change. Moreover, it encourages policy-makers to broaden their perspective, in order to better tackle the sustainable and equal management of a resource that is increasingly becoming a potential source of conflicts and an eco-social good, rather than just a natural resource.

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Coral Symbioses Under Stress: Spatial and Temporal Dynamics of Coral-Symbiodinium Interactions

Danielle C Claar

University of Victoria

Defense Date: 26/11/2018

Title slide of Ph.D. defense, with an image of a Kiritimati coral reef in the background

coral, Symbiodinium, symbiosis, resilience, El Niño, warming, multiple stressors

Coral reefs, the planet’s most diverse marine ecosystems, are threatened globally by climate change and locally by overfishing and pollution. The dynamic partnership between coral and their endosymbiotic algae (Symbiodinium) is the foundation of all tropical reef ecosystems. Symbiodinium provide coral with nutrients for growth, but stress can break down this symbiosis, causing coral bleaching. There are also life-history trade-offs amongst Symbiodinium types - some provide coral with more nutrition, while others are better able to cope with environmental stressors. Although these symbioses are believed to be a critical element of reef resilience, little is known about how local and global stressors alter these partnerships. In this thesis, I combine synthetic literature reviews and a meta-analysis, with field research, molecular analyses, bioinformatics, and statistical analyses to investigate environmentally-driven mechanisms of change in coral-symbiont interactions with the aim of advancing understanding of how corals will adapt to the stressors they now face.

First, I conducted a review of coral-Symbiodinium interactions, from molecules to ecosystems and summarized the current state of the field and knowledge gaps. Next, I conducted a meta-analysis of coral bleaching and mortality during El Niño events and created an open-source coral heat stress data product. I found that the 2015-2016 El Niño instigated unprecedented thermal stress on reefs globally, and that, across all El Niño events, coral bleaching and mortality were greater at locations with higher long-term mean temperatures. I provided recommendations for future bleaching surveys, and in a related perspectives piece, highlighted the importance of survey timing during prolonged coral bleaching events.

The latter three empirical chapters are based on my six field expeditions to Kiritimati (Christmas Island). Taking advantage of the atoll’s natural ecosystem-scale experiment, I tagged, sampled and tracked over 1,000 corals across its chronic human disturbance gradient. Since corals can uptake Symbiodinium from the surrounding environment, I first investigated the effect of local disturbance and winter storm waves on Symbiodinium communities in coral, sediment, and seawater. Greater variability in Symbiodinium communities at highly disturbed sites suggests that local disturbance destabilizes symbiont community structure. Since local disturbance influences Symbiodinium community structure and coral-associated microbial communities, I next examined the covariance of coral-associated Symbiodinium and microbial communities for six coral species across Kiritimati’s disturbance gradient.

Most strikingly, I found corals on Kiritimati that recovered from globally unprecedented thermal stress, experienced during the 2015-2016 El Niño, while they were still at elevated temperatures. This is notable, because no coral has previously been documented to recover from bleaching while still under heat stress. Only corals protected from local stressors exhibited this capacity. Protected corals had distinct pre-bleaching algal symbiont communities and recovered with different algal symbionts, suggesting that Symbiodinium are the mechanism of resilience and that protection governs their communities.

Together, this research provides novel evidence that local protection may be more important for coral resilience than previously thought, and that variability in symbiotic and microbial communities provides a potentially flexible mechanism for corals to respond to both local and global stressors.

Available online at:

Algal blooms in the alpine: investigating the coupled effects of warming and nutrient deposition on mountain lakes

Isabella A Oleksy

Colorado State University

Defense Date: 06/10/2019

Sky Pond, Loch Vale Watershed in Rocky Mountain National Park, Colorado.

limnology, nitrogen deposition, lakes, global change, algae, chlorophytes, pigment analysis, machine learning

While 20th-century atmospheric nitrogen (N) deposition has been strongly linked to changes in diatom assemblages in high-elevation lakes, contemporaneous changes in other algae suggest additional causes. Using proxies preserved in lake sediments, we explored the origin and magnitude of changes in an alpine and subalpine lake from the end of the Little Ice Age in the 19th century to ca. 2010. We found dramatic changes in algal community structure. Diatom analyses revealed a pronounced shift from majority benthic to planktonic diatoms ca. 1950, coincident with the rise of atmospheric N deposition. Pigments representing benthic green algae have increased 200-300% since ca. 1950; diatom pigments suggest stable or slightly declining populations. Cyanophytes and cryptophytes are not abundant in the sediment record, but there has been a slight increase in some taxa since ca. 1950. While some changes began ca. 1900, the shifts in nearly all indicators of change accelerate ca. 1950 commensurate with many human-caused changes to the Earth system. In addition to N deposition, there have been marked recent increases in aeolian deposition to western mountains that contributes phosphorus. Strong increases in summer air (0.7 °C per decade) and surface water (0.2-0.5°C per decade) temperatures since 1983 have direct and indirect consequences for high elevation ecosystems. While our links between the causes of changes and the responses of mountain lake primary producers are inferred, the drivers and their responses are indicators of changes in the Earth system that have been used to define the Anthropocene.
Algal communities (or assemblages) in historically unproductive mountain lakes are shifting, and these changes are taking place commensurate with increasing water temperatures and nutrient availability. However, the mechanisms promoting chlorophytes over bacillariophytes and the implications for ecosystem function are not well understood. We tested the effect of nutrient enrichment on the relative abundance of algal taxonomic groups in a field experiment. We also tested the interactive effects of nutrients and temperature on ecological function of chlorophyte-dominated benthic communities in a laboratory experiment. Nutrient enrichment of both nitrogen and phosphorus favored chlorophytes and led to the highest overall algal biomass. In the absence of nutrient enrichment, the relative abundance of bacillariophytes was significantly greater than chlorophytes and cyanobacteria. Nitrogen assimilation increased significantly, but net ecosystem production decreased, with warming temperatures. Collectively, our results show how chronic N deposition, permafrost thaw, P deposition, and a warming climate interact to alter both the structure and function of mountain lake algal communities. Climate change is altering biogeochemical, metabolic, and ecological functions in lakes across the globe.
Historically, high-elevation lakes in temperate regions have been unproductive due to brief ice-free seasons, a snowmelt-driven hydrograph, cold temperatures, and steep topography with low vegetation and soil cover. Observed increases in high elevation lake productivity in the Southern Rocky Mountains over the past decade led us to ask: what are the drivers behind increasing primary productivity? We tested the relative importance of winter and summer weather, watershed characteristics, and water chemistry as drivers of phytoplankton dynamics. Boosted regression tree models were applied using data from 28 high-elevation lakes in Colorado to examine spatial, intra-seasonal, and inter-annual drivers of variability in lake phytoplankton, using chlorophyll a as a proxy. Similar to previous studies, we found that phytoplankton biomass was inversely related to the maximum snow water equivalent (SWE) of the previous winter. However, even in years with average SWE, summer precipitation extremes and warming enhanced phytoplankton biomass. Peak phytoplankton biomass consistently coincided with the warmest water temperatures and lowest nitrogen to phosphorus ratios. While links between declining snowpack, lake temperature, nutrients, and organic matter dynamics are increasingly recognized as critical drivers of change in high elevation lakes, this study identifies additional processes that will influence lake productivity as the climate continues to change. Continued changes in the timing, type, and magnitude of precipitation in combination with other global change drivers (e.g., nutrient deposition) may have consequences for production in high elevation lakes, potentially shifting these historically oligotrophic lakes toward new ecosystem states.

Available online at:

Copepods, ecological stoichiometry, and behavioral responses to food quality

Emily M. Herstoff

Stony Brook University

Defense Date: 15/05/2019


ecological stoichiometry, copepod, Acartia tonsa, marine, ontogeny, selectivity, behavior, carbon, nitrogen, phosphorus

While their autotrophic prey can contain variable amounts of carbon (C), nitrogen (N), and phosphorus (P), primary consumers often display a more limited range of stoichiometric ratios. Elemental requirements of consumers also change throughout ontogeny. By modulating their responses to prey stoichiometry, consumers may reduce the risk of limitation by the elemental quality of their food. I examined four gaps in our knowledge of ecological stoichiometry and consumer behavior using copepods as a model system.
First, I performed a systematic review to determine whether there are overarching patterns in copepod C:N:P across ontogeny, and within different environments and phylogenetic groups. I found differences in C:N:P in copepods from freshwater and marine habitats, and between tropical and high-latitude copepods. These differences may simply reflect deep evolutionary divisions among copepods from different environments, or the stoichiometric requirements imposed by different ecological strategies.
Next, I performed a series of grazing choice experiments to examine whether consumers can exploit nutritional differences in their prey by using the prey’s physical traits. The marine calanoid copepod, Acartia tonsa, displayed compensatory grazing when fed poor quality food, and preferentially grazed on larger prey when those prey were similar in nutritional value to small prey. When offered prey that differed in both size and stoichiometry, copepods appeared to use dietary complementarity to obtain the same overall daily C:N ingestion.
I determined how different copepod life-history stages alter their behavior in response to prey C:N:P, using high-speed videos. Adult displacement and behavior was more sensitive than younger stages to the quality of food offered during a preconditioning phase. Copepodite displacement was affected by food quality during both preconditioning and trials. Nauplii were generally insensitive to food quality. Only adults significantly increased feeding behaviors when feeding on high-quality food, which could allow the selective use of high-quality prey patches.
I built a model to examine how behavioral responses to food quality might affect use of patches containing high quality prey. Variability in behavior improved the copepod’s ability to remain in such patches and maintain more optimal dietary C:N, especially if the patches accounted for a large fraction of the environment and were fragmented. My results suggest that in the field, copepods can rapidly locate and utilize small patches of high-quality food.

Assessing the competitive advantage of carbonic anhydrase in estuarine microalgae through removed enzymatic activity

Eilea R Knotts

University of South Carolina

Defense Date: 22/10/2019


carbonic anhydrase, carbon, CCM, diatoms, estuary, phytoplankton

Carbon concentrating mechanisms (CCMs) are used by photoautotrophs to overcome possible limitations in carbon acquisition but the competitive strategies and efficiencies of these mechanisms among photosynthesizers can be variable. The diversity in carbon acquisition abilities establishes the potential for alterations in community structure with shifting carbon concentrations. Given the role of phytoplankton and benthic microalgae (BMA) in the trophodynamics of estuaries, understanding the mechanisms of carbon acquisition in these systems is important in predicting how primary productivity and nutrient cycling might change in response to increasing concentrations of atmospheric CO2. Our approach to investigate whether induced carbon limitation would show predictable shifts in microalgal community structure and production was conducted through the inhibition of an enzyme used in CCMs, carbonic anhydrase (CA). CA catalyzes the rates of interconversion between CO2 and HCO3- to facilitate transport of inorganic carbon into the cell and trap that carbon there. Although CA has the potential to help mitigate increasing CO2 levels in the atmosphere, evaluations on how different species use CA and the physiological roles it may perform in microalgae are needed. We show phytoplankton communities from different environments are altered when a CA inhibitor (i.e. ethoxyzolamide, EZ) is present and CA activity is suppressed. Diatoms remained the dominant taxonomic group in all samples following a 3-day inhibition of CA but there were lower-level community shifts. These shifts in community structure suggest that phytoplankton composition is affected by carbon acquisition using CA, and some diatom genera may depend on the competitive advantage of this enzyme for their CCMs to maintain high abundances in estuarine environments. Most of the diatom genera had strong growth limitation and cell mortality without active CA, however, some pennate diatoms like Cylindrotheca persisted with positive growth rates. All four of our cultured diatoms experienced a decrease in gross primary production (GPP) and relative electron transport rate at high irradiance levels indicating that some other physiological traits were giving Cylindrotheca the competitive benefit. Decreased GPP was similarly observed in the BMA communities as well with CA inhibition. However, this limitation in carbon acquisition drove motile benthic microalgae to make use of a smaller vertical profile closer to the sediment surface rather than exhibit the mortality seen in most of our cultured diatom genera. Predicting marine microalgal responses to changes in CO2 availability requires further characterization of other physiological traits across a higher diversity of growth conditions and taxa. Our research demonstrates that there can be wide variability in carbon acquisition strategies within the diatom genera and that the competitive advantage provided by CA and efficiency of their CCMs may be dependent on the environment’s carbon availability. Continued mechanistic approaches are needed to recognize the impacts of CA activity on microalgal communities with respect to their assemblage, cell-size fractions, primary production rates, and physiological performance.

Available online at:

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