Time and energy are finite resources in any environment, and how and when organisms use their available resources to survive and reproduce is the crux of life history theory (Gadgil and Bossert 1970; Balon 1975; Stearns 1976). The different survival strategies used by animals are often shaped by their environment in addition to their biology (Winemiller and Rose 1992), which allows for exploration into biological variability when environmental factors are known. For this reason, the Line Islands in the Central Pacific provide an ideal location to perform observational studies due to their unique productivity gradient and fish assemblage structures across the island chain (Sandin et al. 2008; DeMartini et al. 2008; Fox et al. 2018; Zgliczynski et al. 2019). Many of the world’s coral reefs are in remote regions that lack monitoring programs or even local populations, so conducting ecological surveys on fish communities in these regions can require extensive amounts of time, energy, resources and people. The inherent variability an environment exerts on the many factors that contribute to growth over a lifetime make it difficult to generate a directly proportional formula that calculates age. A novel age estimation method was developed that utilizes in-situ visual census data to estimate the age of fishes, and as a case study, several fish were chosen as representative species to explore its capabilities. Through this process, new ecological information and insight can be gained about the age structures of fish populations both between and throughout the Line Islands.
Aerosol-cloud interactions are one of the largest sources of uncertainty in our understanding of the Earth’s climate system. In order to develop better predictive models and understand how the climate will respond to future changes in atmospheric composition, we must determine the sources and nature of aerosols which serve as cloud condensation nuclei (CCN), thus influencing the properties of clouds. Oceans cover 70% of the Earth’s surface and represent a major source of atmospheric aerosols. Sea spray aerosol (SSA) is formed by the action of breaking waves, whereas secondary marine aerosols (SMA) are formed from the oxidation products of gases emitted from the oceans. Biological activity in seawater (i.e. the life, death, and interactions of marine phytoplankton, bacteria, and viruses) can significantly affect the chemical composition of SSA through processing of dissolved organic matter and SMA through the emission of volatile gases. This dissertation investigates the cloud-relevant properties of SSA and SMA generated using ocean-atmosphere simulators in the laboratory, with a specific emphasis on the influence of biological activity in seawater on the properties of these aerosols. For the first time, SMA was produced from the oxidation of the headspace gases of a phytoplankton bloom grown in natural seawater, enabling measurements of its chemical composition and CCN activity. Overall, these studies show that the formation and properties of SMA are much more sensitive to biological activity in seawater than SSA. In addition, the chemical composition of SMA is highly dependent on the extent of photochemical oxidation, with a distinct shift from organic-rich to sulfate-rich composition in response to increased atmospheric aging. This change in SMA composition leads to a significant change in its hygroscopicity. These results suggest that the properties of SMA evolve temporally in the atmosphere, which has implications for CCN concentrations and cloud properties over the oceans.
Understanding fish diversity patterns is critical for fisheries management amidst overfishing and climate change. Fish egg surveys have been used to characterize pelagic spawning fish communities, estimate biomass, and track population trends in response to perturbations. Environmental DNA (eDNA) metabarcoding has been implemented to rapidly and non-invasively survey marine ecosystems. To understand the efficacy of eDNA metabarcoding for assessing pelagic spawning fish community composition, concurrent eDNA metabarcoding and fish egg DNA barcoding off Scripps Institution of Oceanography’s Pier (La Jolla, CA) were conducted. Both methods revealed seasonal patterns in agreement with previous fish and fish egg surveys. Species richness was highest in late spring and summer. The presence and spawning of commercially important species and species of conservation concern were detected. Both methods showed overlap for pelagic spawning fishes for broadcast spawners, schooling fish, and locally abundant species. Some actively spawning species were not co-detected with eDNA, likely due to different sampling strategies, taxonomic biases, and abiotic/biotic factors influencing eDNA transport, shedding, and degradation. We identified key advantages and disadvantages of each method. Fish egg barcoding provided information on spawning trends but did not detect taxa with alternate reproduction strategies. Metabarcoding eDNA detected species not found in fish egg sampling, including demersal and viviparous bony fishes, non-spawning adults, Chondrichthyan, and Mammalian species, but missed abundant pelagic fish eggs. This study demonstrates that DNA barcoding of fish eggs and eDNA metabarcoding work best in tandem as each method identified unique fish taxa and provided complementary ecological and biological insight.
The marine leeches of California are found on many host species, but the biology, distribution, and ecology of these leeches is not well understood. In this thesis I describe two previously unknown species: the leeches Mysidobdella californiensis, found on mysid shrimp hosts in Bodega Bay, CA, and Heptacyclus cabrilloi, found on giant kelpfish in San Pedro, CA. I also describe a method that addresses the problem of measuring the size of leeches, which is considered to be difficult because of the inconsistencies in the body proportions of soft-bodied invertebrate organisms. I utilize digital photography to measure leech size and use maximum- likelihood estimation to fit a model of size/age cohort distributions to a sample of leeches.
The western North Atlantic is a dynamic region characterized by the Gulf Stream western boundary current and inhabited by a diverse host of odontocete, or toothed whale, top predators. Their habitats are highly exploited by commercial fisheries, shipping, marine energy extraction, and naval exercises, subjecting them to a variety of potentially harmful interactions. Many of these species remain poorly understood due to the difficulties of observing them in the pelagic environment. Their habitat utilization and the impacts of anthropogenic activities are not well known. Over the past decade, passive acoustic data has become increasingly utilized for the study of a wide variety of marine animals, and offers several advantages over traditional line-transect visual survey methods. Passive acoustic devices can be deployed at offshore monitoring sites for long periods of time, enabling detection of even rare and cryptic species across seasons and sea states, and without altering animal behaviors. Here we utilized a large passive acoustic data set collected across a latitudinal habitat gradient in the western North Atlantic to address fundamental knowledge gaps in odontocete ecology. I approached the problem of discriminating between species based on spectral and temporal features of echolocation clicks by using machine learning to identify novel click types, and then matching these click types to species using spatiotemporal correlates. I was able to identify novel click types associated with short-beaked common dolphins, Risso’s dolphins, and short-finned pilot whales in this way. Next I characterized temporal patterns in presence and activity for ten different species across our monitoring sites at three different temporal scales: seasonal, lunar, and diel. I observed spatiotemporal separation of apparent competitors, and complex behavioral patterns modulated by interactions between the seasonal, lunar, and diel cycles. Finally I investigated the relationships between species presence and oceanographic covariates to predict habitat suitability across the region, and explored niche partitioning between potentially competitive species. The insights gained here significantly advance our understanding of toothed whale ecology in this region, and can be used for more effective population assessments and management in the face of anthropogenic threats and climate change.
Spatial management is a popular tool for resource managers to protect and conserve natural resources. However, a number of emerging threats are testing the ability of these tools to address management needs. Marine protected areas and slow speed zones are popular tools employed by resource managers to mitigate anthropogenic threats; however climate change and whale ship strikes represent new threats that may complicate the benefits of these tools. This dissertation examines the efficacy of incentivizing slow vessel transits to reduce cetacean mortality risk and the application of MPAs to mitigate climate change. A trial program to monetarily incentivize slow transits through the Santa Barbara Channel showed high compliance compared to a similar voluntary program. During incentivized transits, the large majority of ships maintained a 12 knot transit speed as determined by the program guidelines. An incentivized program may be key in reducing risk to whale mortality and reducing ships speeds; however scaling up this program may face financial difficulty.Marine Protected Areas have been claimed to offer additional protection to areas affected by climate change. However, a recent warm water marine heatwave changed the fish community’s abundance, biodiversity, and recruitment around the Channel Islands. While the ecological community changes across strong longitudinal biogeographic patterns, forecasts built from GLMs with environmental conditions predict shifts in species abundance. Upwelling and cool waters coming to the surface may mitigate warming ocean conditions in the region but marine protected areas showed no increased resilience to acute climate affects like marine heatwaves.
The Delta Smelt (Hypomesus transpacificus) is a small Osmerid native to the San Francisco Bay Delta (Bay-Delta) in California. Delta Smelt population has declined dramatically since the species was declared as endangered in 1993, and now has been listed as critically endangered by the International Union for Conservation of Nature (IUCN). The Bay Delta is a highly modified ecosystem, and the Delta Smelt has been used as an indicator species to assess the overall health of this ecosystem. Recently, a wealth of evidence exists showing that anthropogenic intervention and change in ecosystems leads to alteration in the sensory perception of the environment by aquatic animals compromising survival in highly modified environments. One of the main modalities used by aquatic organisms to assess and survive in the wild is the olfactory system. The olfactory system is involved in pivotal functions such as recognition of predators, kin recognition, mating, foraging and migration. The olfactory system is highly susceptible to contaminants including copper, which is a common contaminant and a well-studied and measurable olfactory toxicant of fish. A link between the olfactory biology and the effects of common contaminants (i.e., copper) found in the Bay Delta on Delta Smelt is lacking. I studied the basic morphological characteristics of the olfactory organ (olfactory rosette) of Delta Smelt using histological, immunohistochemical and ultrastructural techniques; the olfactory mediated behavioral responses to predation related odorants using a behavioral standardized assay and tracking software; and finally, I evaluated morphological changes of the olfactory epithelium and behavioral responses to alarm cues after copper exposures using concentrations of 2, 8 and 32 µg/L and two exposure times (24 and 96 hours). The Delta Smelt can be classified as a macrosmatic fish, based on the morphological features of the olfactory rosette. This fish has multilamellar, paired olfactory rosettes containing a highly specialized olfactory epithelium. The olfactory epithelium was composed by several populations of cells including sensory neurons with distinct morphology and immunocytochemical features. Delta Smelt have a highly sophisticated and sensitive response to predation related odorants. They detect alarm cues in a concentration dependent fashion using olfaction and display specific behaviors (escape responses and freezing) upon detection that all together are considered as olfactory mediated antipredator behaviors. Finally, I demonstrated using histopathological and immunohistochemical techniques that Delta Smelt olfactory epithelium is highly susceptible to copper exposure at concentrations commonly found in the Bay Delta and considered as sublethal. Moreover, there were differential effects on antipredator behaviors after exposure to copper for 24 and 96 hours. Fish exposed to 8 µg/L of copper for 24 hours showed severe damage to the olfactory epithelium and hyperexcitability when presented to alarm cues. At higher concentrations, the epithelium was severely damaged, the antipredator response was absent and there were signs of histological and behavioral toxicity. The results of these experiments demonstrate that Delta Smelt is a highly olfactory species and establishes that copper contamination can impair olfactory responses at environmentally relevant concentrations in this endangered fish.
Profiling multiomic biomarkers in bulk and in situ provides critical information which enables basic research and clinical applications. Unfortunately, most existing profiling methods are limited due to either low multiplexing, sensitivity, costs, or assay complexity. This thesis aims to develop two core technologies that address 1) bulk profiling issues with sensitivity and low throughput as well as 2) in situ profiling issues with low multiplexing capabilities, costs, and limited throughput. To address the first issue, this work introduces a novel liquid biopsy approach that utilizes a platform technology called Integrated Comprehensive Droplet Digital Detection (IC3D). This integrated approach combines microfluidic droplet partitioning technology, fluorescent multiplexed PCR chemistry, and our own unique and rapid particle counting technology to deliver ultrasensitive and ultrafast detection of colorectal cancer-specific genomic biomarkers from minimally processed blood samples. To address the second issue, this work introduces a new spatial multi-omics technology termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA) that integrates a) in situ labeling of molecular markers (e.g. mRNA, proteins) in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, and b) spectra and time-resolved fluorescence imaging and analysis to enable rapid, high-throughput, and cost-effective spatial profiling of multi-omics biomarkers. By utilizing both time and intensity domains for labeling and imaging, this technology seeks to discriminate a vast repertoire of lifetime and spectral components simultaneously within the same pixel or image of a sample to enable highly increased multiplexing capabilities with standard optical systems. Overall, these two technologies represent simple, versatile, and scalable tools which enable more rapid, sensitive, and/or multiplexed protein/transcriptomic analysis.
The majority of vertebrate species diversity are within fish. Marine fish occupy a diverse array of ecological niches including a wide range of salinity tolerance, oxygen tolerance, temperature, depth, desiccation, and light. Fish also have adapted a range of biological traits including varying trophic level, morphology, swimming performance, and reproduction. The microbiome, the total aggregation of microscopic organisms including fungi, bacteria, archaea, and viruses in a specified environment, has largely been studied in mammals, particularly humans from which many associations to disease and health have been demonstrated. Fish microbiome research has largely focused on the gut environment from freshwater captive populations including farmed carp, tilapia, and catfish with marine studies primarily limited to food fish such as salmon. The goal of this dissertation was to develop and apply microbiome tools including sampling methods, DNA extraction, and library preparation (16S and WGSS, whole genome shotgun sequencing) which could be deployed to study a wide range of questions surrounding the parameters which influence the fish mucosal microbiome. With these set of tools, I have asked 1) how do intentional anthropogenic impacts to the water column (organic fertilizer) influence fish gastrointestinal communities, 2) how body sites differ in mucosal communities and changes across environmental gradients, 3) feasibility of developing a model marine fish to use in microbiome experiments to mimic tuna, 4) how the hatchery built environment influences fish mucosal microbiota. My dissertation can be summarized by several key findings. First, the mucosal environments of fish are highly differentiated in that the gill, skin, and digesta communities from the same species of fish are colonized by a large range of phylogenetically diverse microbes. In a freshwater system, organic inputs do influence the fish gut communities but indirectly through nutrient changes. In a wild marine fish, body sites are impacted by different environmental gradients with external body sites like the gill and skin most influenced by temporally variable environmental conditions including sea water temperature. In both freshwater and marine indoor hatchery systems, the built environment plays a critical role in influencing or being influenced by the fish mucosal microbiome.
Parasites and pathogens exert strong selection on their hosts and alter the structure, diversity, and productivity of communities of ecosystems. This paper presents results of a survey of parasite composition and prevalence observed on and within the freshwater hybrids Owens (Siphateles bicolor snyderi) and Lahontan (Siphateles bicolor obesa) Tui Chubs, a native minnow species, in the Eastern Sierra Nevada mountains of California. The Owen and Lahontan Tui Chub is present in many lakes and rivers in Northern California and its parasite community has yet to be characterized. My thesis asks what kinds of parasites are found in the freshwater Tui Chub, which lakes or streams held the highest parasitic loads, and which features of individual fish and the habitat influence parasite density and/or types of parasites. Fish samples were collected in Summer 2019 by PhD student Henry Baker at 10 different sampling sites including freshwater lakes and streams that vary in size, temperature, water chemistry and species present across Owens Valley, California. I dissected 134 individual fish to characterize the ecto- and endo-parasite communities. My results show that two of the locations had significantly higher parasite infection rates than the others, where few macroscopic parasites were observed. These two locations were both geothermal with warmer waters and distinct water chemistry with high salinity and alkalinity. This pattern suggests that some aspects of geothermal habitat favor the parasite life cycle and makes fish in these sites more easily accessible as a host, though the mechanism behind the pattern is unknown. Four main types of visually distinct parasites were found: one adult life-stage tapeworm, one adult life- stage nematode and two metacercaria trematodes, though none were identified taxonomically. The greater parasite infection rates in geothermal habitats may be related to the greater abundance of snails in these sites, which may serve as intermediate hosts to fish parasites. No differences in parasite infection rates or composition were observed between lake and stream habitats. My thesis suggests that the atypical thermal and chemical environment of geothermal springs promotes parasitism in Tui Chub, but that lakes and streams are similar in containing low rates of infection by any parasites among fish.