Dissertations / Theses: 'Biological oceanography'

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Hinsley, Westley Richard. "Planktonica : a system for doing biological oceanography by computer." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418316.

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Fielding, Sophie. "Biological validation of acoustic backscatter and observations of biological/hydrographic interactions at the mesoscale." Thesis, University of Southampton, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273754.

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Kumar, Vijay. "Modelling the physico-biological processes of eastern Arabian sea." Thesis, IIT Delhi, 2016. http://localhost:8080/xmlui/handle/12345678/7093.

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Syahailatua, Augy BEES UNSW. "Biological oceanography of larval fish diversity and growth off eastern Australia." Awarded by:University of New South Wales. BEES, 2005. http://handle.unsw.edu.au/1959.4/22791.

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Fish larvae in Australian waters have been studied progressively in the last 2-3 decades including the distribution and abundance of taxa, growth and age, their prey and predators. However, the effect of nutrient limitation on ichthyoplankton is unstudied, particularly in the oligotrophic Australian waters. My study was aimed to examine the effect of natural or anthropogenic nutrients on the abundance, distribution, growth and condition of fish larvae along-shore of the NSW coast (latitude 30-34S), where the East Australian Current departs the NSW coast and generates local upwelling of cool nutrient-rich water. This study shows no significant difference in the total abundance or diversity of either larval fishes amongst the 112 taxa (111 families and 1 order), among regions within or upstream of the upwelling. However in both months, there were distinctive ichthyoplankton assemblages at the family level. The Carangidae, Labridae, Lutjanidae, Microcanthidae, Myctophidae and Scombridae were more abundant in the EAC or oceanic water masses, while the Callionymidae, Clupeidae, Platycephalidae, Sillaginidae and Terapontidae were mostly found in the surface or deep upwelled/uplifted water masses. This pattern is observed in other ichthyoplankton studies and may be a general and useful method to determine mixing of water masses. Larvae of silver trevally (Pseudocaranx dentex) and yellowtail scad (Trachurus novaezelandiae) were generally larger and less abundant in the topographically induced upwelling region, than north of the region in pre-upwelled conditions of the East Australian Current. Both species were mostly at the preflexion stage (less than 4.3 mm in body length and less than 10 days old) in the pre-upwelled conditions, particularly during November, and proportionally more larger and older larvae in the upwelled waters (mostly post-flexion, greater than 4.3 mm in body length and greater than 10 days old). Ages from sagittal otoliths ranged from 2-25 increments (~days) and exhibited linear growth for both species and months over the size range (3-15 mm standard length). The otolith radius-length relationship and the growth rates were similar between species and months, despite the 3-4C difference between months. Overall growth rates of the younger larvae were uniform throughout the entire sampling area (0.5-0.6 mm.d-1), while older larvae grew significantly faster in the upwelled water (0.41 mm.d-1) compared to the non-upwelled conditions (0.34 mm.d-1). Both species tended to be depleted in 13C in the upwelling region (from ???18.5 to ???19.0), consistent with expected ratios from deeper water, whereas the 15N composition tended to increase in Pseudocaranx, but decrease in Trachurus indicating different diets and possibly trophic level. The early life history of both species indicates spawning in pre-upwelled waters, but larval transport into upwelled waters is necessary for faster growth in the post-flexion stage. The assemblage of larval fishes did differ between the upwelled region and a region south of Sydney???s deepwater outfalls, but the difference was ascribed to a latitudinal effect and the EAC. Both larval carangids were enriched in 15N, possibly due to the enriched dissolved organic matter of primary treated sewage. In summary, this study found that the larval fish community can provide a biological means to trace water masses, and estimate their degree of mixing. Remarkably there was no significant effect of upwelling or sewage addition to the abundance or diversity of larval fish, in the nutrient poor waters of the East Australian Current. Larval carangids and pilchards were abundant in late spring off northern NSW, and their early life histories were inferred. Both larval carangid species seem to be spawned in the EAC waters, but as post-flexion larvae grew faster in the upwelled zone. Pre-flexion (less than 10 day old) larval carangids of both genera indicated spawning in the EAC, and the rarer post-flexion (greater than 10 days old) carangids grew faster in the upwelled waters. Here, both genera had stable isotope signatures characteristic of upwelled waters for carbon, but had different nitrogen signatures, indicative of different diets and trophic level status. Larval pilchards actually grew more slowly in the upwelling region, as observed in coastal waters off Japan, and their nursery grounds may be further offshore in the Tasman Front, analogous to their early life history in the Kuroshio Extension.

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Kilborn, Joshua Paul. "Investigating Marine Resources in the Gulf of Mexico at Multiple Spatial and Temporal Scales of Inquiry." Thesis, University of South Florida, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10680352.

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The work in this dissertation represents an attempt to investigate multiple temporal and spatial scales of inquiry relating to the variability of marine resources throughout the Gulf of Mexico large marine ecosystem (Gulf LME). This effort was undertaken over two spatial extents within the greater Gulf LME using two different time-series of fisheries monitoring data. Case studies demonstrating simple frameworks and best practices are presented with the aim of aiding researchers seeking to reduce errors and biases in scientific decision making. Two of the studies focused on three years of groundfish survey data collected across the West Florida Shelf (WFS), an ecosystem that occupies the eastern portion of the Gulf LME and which spans the entire latitudinal extent of the state of Florida. A third study was related to the entire area covered by the Gulf LME, and explored a 30-year dataset containing over 100 long-term monitoring time-series of indicators representing (1) fisheries resource status and structure, (2) human use patterns and resource extractions, and (3) large- and small-scale environmental and climatological characteristics. Finally, a fourth project involved testing the reliability of a popular new clustering algorithm in ecology using data simulation techniques. The work in Chapter Two, focused on the WFS, describes a quantitatively defensible technique to define daytime and nighttime groundfish assemblages, based on the nautical twilight starting and ending times at a sampling station. It also describes the differences between these two unique diel communities, the indicator species that comprise them, and environmental drivers that organize them at daily and inter-annual time scales. Finally, the differential responses in the diel, and inter-annual communities were used to provide evidence for a large-scale event that began to show an environmental signal in 2010 and subsided in 2011 and beyond. The event was manifested in the organization of the benthic fishes beginning weakly in 2010, peaking in 2011, and fully dissipating by 2012. The biotic effects of the event appeared to disproportionately affect the nighttime assemblage of fishes sampled on the WFS. Chapter Three explores the same WFS ecosystem, using the same fisheries-independent dataset, but also includes explicit modeling of the spatial variability captured by the sampling program undertaking the annual monitoring effort. The results also provided evidence of a disturbance that largely affected the nighttime fish community, and which was operating at spatial scales of variability that were larger than the extent of the shelf system itself. Like the previous study, the timing of this event is coincident with the 2010 Deepwater Horizon oil spill, the subsequent sub-marine dispersal of pollutants, and the cessation of spillage. Furthermore, the spatial models uncovered the influence of known spatial-abiotic gradients within the Gulf LME related to (1) depth, (2) temperature, and (3) salinity on the organization of daytime groundfish communities. Finally, the models developed also described which non-spatially structured abiotic variables were important to the observed beta-diversity. The ultimate results were the decomposition of the biotic response, within years and divided by diel classification, into the (1) pure-spatial, (2) pure-abiotic, (3) spatial-abiotic, and (4) unexplained fractions of variation. Chapter Five employs a clustering technique to identify regime states that relies on hypothesis testing and the use of resemblance profiles as decision criteria. This clustering method avoids some of the arbitrary nature of common clustering solutions seen in ecology, however, it had never been rigorously subjected to numerical data simulation studies. Therefore, a formal investigation of the functional limits of the clustering method was undertaken prior to its use on real fisheries monitoring data, and is presented in Chapter Four. The results of this study are a set of recommendations for researchers seeking to utilize the new method, and the advice is applied in a case study in Chapter Five. Chapter Five presents the ecosystem-level fisheries indicator selection heuristic (EL-FISH) framework for examining long-term time-series data based on ecological monitoring for resources management. The focus of this study is the Gulf LME, encompassing the period of 1980-2011, and it specifically sought to determine to what extent the natural and anthropogenic induced environmental variability, including fishing extractions, affected the structure, function, and status of marine fisheries resources. The methods encompassed by EL-FISH, and the resulting ecosystem model that accounted for ~73% of the variability in biotic resources, allowed for (1) the identification and description of three fisheries resource regime state phase shifts in time, (2) the determination of the effects of fishing and environmental pressures on resources, and (3) providing context and evidence for trade-offs to be considered by managers and stakeholders when addressing fisheries management concerns. The EL-FISH method is fully transferrable and readily adapts to any set of continuous monitoring data. (Abstract shortened by ProQuest.)

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Wheeler, Sarah Grace. "Biological and oceanographic drivers of larval growth, settlement, and recruitment of rockfishes (Sebastes spp.)." Thesis, University of California, Davis, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3723751.

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Recruitment of marine fishes is largely determined by biological and oceanographic factors acting on early life stages. Coastal upwelling has long been recognized as a critical factor influencing the survival of larvae and recruitment to adult populations. Dynamics in regional upwelling influence the magnitude and timing of primary productivity, affecting the availability of critical food sources for larval fish. In addition, upwelling-relaxation cycles affect the dispersal of marine larvae and their onshore delivery prior to settlement. Challenges with tracking larvae, however, have limited our understanding of how oceanography influences the early life stages of fishes. The objective of this dissertation is to evaluate the biological and oceanographic drivers of larval growth, settlement, and recruitment, using rockfishes ( Sebastes spp.) as model organisms. Overlap of larval production and favorable feeding conditions may drive recruitment for many temperate marine fishes, as small changes in larval growth can result in order-of-magnitude differences in year-class-strength. In Chapter 1, I assess the influence of regional productivity, temperature, and larval condition in explaining growth in rockfishes. I employ a combination of otolith microstructure and satellite imagery to measure initial larval growth and estimate the productivity and temperature experienced by individuals to determine their relative importance in subsequent growth at metamorphosis. I compare model performance using indexed environmental conditions scaled over three different regions. In both years of study, net primary productivity explained the most variation in pre-metamorphic growth relative to temperature and initial growth. This relationship was consistent across spatial regions. Recent settlement, juvenile recruitment, and individual growth were significantly higher in a year when productivity bloomed earlier and individual larvae experienced higher levels of productivity. These results support the hypothesis that large-scale oceanographic processes that stimulate upwelling and secondary production are primary drivers of larval growth and subsequent year-class strength in rockfishes. Characterizing the behavior of larvae prior to settlement is integral to understanding population dynamics because coastal oceanography may facilitate or limit settlement. Otolith microchemistry can be used to determine patterns of fish movement, although there is a limited understanding of how this tool can be applied in coastal marine systems. My goal in Chapter 2 is to evaluate the application of otolith microchemistry to characterize water mass associations of settlement-stage marine fish in a coastal upwelling region using a three-step approach. First, I characterize seawater chemistry of coastal water masses across multiple years, finding significant differences in the chemical signatures of strong upwelling, weak upwelling, and relaxation. Second, I experimentally determine the effect of temperature on the partitioning of trace elements in otoliths for two rockfishes to find that the effect of temperature on otolith partition coefficients was element- and species-specific. Finally, I compare the synchrony in seawater and otolith chemistry of settlement-stage rockfishes that were exposed to naturally variable conditions over an upwelling-relaxation cycle. I subsequently evaluate whether laser ablation inductively coupled plasma mass spectrometry effectively measures otolith chemistry over ecologically relevant time scales. I discovered that elemental concentrations in otoliths respond rapidly to changes in seawater chemistry and reflect equivalent proportional changes. This study provides evidence that elemental signatures are valuable tools for reconstructing larval histories of marine fish. In Chapter 3, I use otolith chemistry to examine water mass associations of two juvenile rockfishes during onshore transport and settlement in an upwelling region. I develop a chemical proxy for upwelling and relaxation by characterizing Sr/Ca and Ba/Ca signatures of otoliths collected during these oceanographic conditions. Otolith chemistry differed between rockfishes collected during upwelling and relaxation, with signatures unique to each year. I subsequently compare otolith signatures of rockfishes collected during high and low settlement periods to determine whether specific water masses affect settlement. I provide evidence that copper rockfish associate with upwelling currents during periods of high settlement, suggesting that upwelling may facilitate settlement for these species. Conversely, I found evidence that the closely related gopher rockfish associate with relaxation events during peak settlement periods. This research takes an important first step at in evaluating the utility of trace element signatures to characterize larval fish movement during onshore delivery and settlement in marine systems. Together, these studies improve our understanding of how coastal upwelling impacts larval growth, settlement, and recruitment, which provides important information for understanding population dynamics in marine ecosystems.

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George, Caren. "Understanding the physical, chemical and biological processes across the subtropical convergence during austral automn." Master's thesis, University of Cape Town, 2009. http://hdl.handle.net/11427/6475.

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Includes abstract. Includes bibliographical references (leaves 49-58). A research survey was conducted, consisting of six transects between 38°- 46°S and 38 - 41°45'E, during the austral autumn of 2007. The aim of the survey was to investigate the physical, chemical and biological dynamics of the Subtropical Convergence (STC), in the SW Indian sector of the Southern Ocean. Satellite data was obtained and in-situ data were collected. Mixed layer depth (MLD), geostrophic velocities, density and Brunt Vaisala frequencies were calculated. The STC meandered across the survey area between 41 ° - 42°15'S. The total integrated Chl-a ranged from 12.8 to 40.1 mg Chl-a/m2. The most significant correlation between biological and physical data was that of Chl-a and MLD (r=-0.374, n=45, p=0.013) over the entire survey region. Phosphate and nitrate (r=0.8779, n=45, p=0.001) measured over the survey region were strongly correlated, as expected. The surface currents showed cyclonic motion between 38° - 39°E and 38 - 42°S, with the exception of an eddy-like feature between 39.5°and 40.5"S and generally anti-cyclonic motion to the east of 39°E.

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Hirst, Andrew Garwood. "Zooplankton production and energy flow : towards a biological model of Southampton water." Thesis, University of Southampton, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242178.

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MacDonald, Ian. "Burial mechanics of the Pacific sandfish| The role of the ventilatory pump and physical constraints on the behavior." Thesis, Northern Arizona University, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10004157.

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Burial is an important life history strategy employed by benthic fishes that has not been fully explored in its diversity by the biomechanical literature. This thesis explores the mechanism by which the Pacific sandfish buries as well as the physical limitations of the behavior. We first investigate the role of the ventilatory pump in the burial behavior of sandfish by using high-speed videography, dye, and digital particle image velocimetry (DPIV). We determined that sandfish employ a modification of the ventilatory pump, which is used repeatedly to fluidize the substrate ventral to the head. This modification of the ventilatory pump should reduce the energetic costs associated with burial as it decreases the cost of transport typically associated with ‘shoveling’ substrate. Second, we investigate the physical limitations that are caused by the reliance on the ventilatory pump to fluidize substrate. We used sand beds of varying grain sizes, and therefore varied the minimum velocities of fluidization, to determine how sandfish respond variation in substrata. We determined that sandfish can bury in grains smaller than 1.00mm in diameter but were unable to bury in any substrate larger than 1.00mm. We also determined that there was an increase in the time it took sandfish to bury in those substrates smaller than 1.00mm as grain size increased. There was no change in the frequency of the behavior, however, suggesting that sandfish have very little ability to bury in larger substrates. We also determined that it is probably not the absolute velocity produced by the opercular jet that determines burial success, but the ability burying behavior to maintain the sand’s momentum during the expansive phase that occurs between bouts of opercular jetting.

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Wagstaff, Martine C. "Critical forces that structure subtidal ecologial communities in the Gulf of Maine, and the integration of invasive species into these communities." Thesis, University of Massachusetts Boston, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10010593.

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Shallow subtidal epibenthic communities worldwide are under threat from exploitation, pollution, eutrophication, acidification, climate change, and invasive species, with implications for ecosystem diversity, productivity, function, and services. Subtidal ecosystems in the Gulf of Maine are particularly impacted, making it crucial to understand these habitats so that our impacts can be predicted and mitigated. I investigated the basic ecological forces that structure shallow subtidal epibenthic communities in this region, and how invasive species integrate themselves into these communities. I used community phylogenetic and functional trait analyses to investigate if invertebrate communities in the rocky subtidal are assembled via deterministic or random forces, experimental manipulations to quantify how macroalgae might influence sessile invertebrates on subtidal surfaces, and measurements of life history traits of Botrylloides violaceus, an invasive colonial ascidian, to estimate whether growth of this species differs among man-made versus natural habitats. Based on community phylogenetic analyses, rocky subtidal invertebrate communities appear to be structured by deterministic forces, with evidence for both competitive exclusion and environmental filtering operating at different spatial scales. These findings support existing studies that show that competition structures communities at local scales, and also expand our knowledge of the processes that act regionally, i.e. environmental filtering. On shallow sunlit experimental surfaces suspended from floating docks, macroalgae had little effect on invertebrate abundance or diversity, contrary to findings from experiments in the rocky subtidal. Macroalgae did influence composition as well as enhance invertebrate colonization in the early stages of community assembly. Different factors appear to influence the balance between heterotrophs and autotrophs in floating dock and rocky subtidal systems with implications for community structure, function and productivity. In different habitats, colonies of the invasive ascidian B. violaceus exhibited differences in life history traits. It grew faster and attained larger sizes in man-made floating dock versus natural rocky subtidal and eelgrass bed habitats. Again, differences among habitats appear to influence invasion success. In conclusion, competitive exclusion, facilitation, and environmental filtering play key roles in controlling the structure, composition, and function of shallow subtidal communities. Invasive species have the potential to disrupt these forces as they integrate themselves into man-made and subsequently natural habitats.

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Meyer, Kirstin S. "Community assembly of benthic invertebrates on island-like marine hard substrata." Thesis, University of Oregon, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10192050.

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Most of the seafloor is soft sediment, so hard substrata are isolated and island-like. In this dissertation, I explore how species distribution patterns on isolated marine hard substrata resemble terrestrial island communities, drawing on classical island biogeography theory and assembly rules, and describe how benthic invertebrate communities assemble in these island-like habitats. Higher species richness occurred on larger substrata (dropstones and shipwrecks), paralleling terrestrial island communities. However, while larger islands have greater habitat diversity and primary productivity, marine hard substrata are simpler habitats. Greater elevation in the benthic boundary layer may expose fauna to faster current, higher food supply and larval flux. Substrata located closer together had more similar communities, another pattern that resembles terrestrial islands. Dropstone fauna had a clumped distribution, indicating that larvae may disperse among substrata located close together, resulting in similar communities. In Svalbard fjords, benthic megafaunal communities were significantly different between Arctic- and Atlantic-influenced fjords. Depth and temperature had the greatest influence, with the highest diversity occurring in cold Rijpfjorden and on the north Svalbard shelf. Recruitment in Svalbard fjords was spatially and temporally variable, with lower recruitment in Rijpfjorden than in Atlantic-influenced fjords and lower recruitment at greater depth. Most of the recruits in Svalbard fjords were fast-growing, poor-competitive opportunists. On shipwrecks, communities showed two mechanisms of colonization: mobile fauna with long-dispersing planktotrophic larvae, and encrusting fauna with lecithotrophic larvae. Encrusting species reproduce asexually to cover the wreck surface, and philopatry may build up dense populations, leading to uneven communities. On terrestrial islands, non-random co-occurrence is attributed to interspecific competition, but for marine substrata, there may not be a relationship. Fauna were distributed randomly on settlement plates in Svalbard fjords, even when interspecific competition was observed. On dropstones, some morphotypes co-occurred non-randomly in the absence of overgrowth competition. Non-random co-occurrence on isolated marine hard substrata may be a result of restricted larval dispersal (for pairs co-occurring less than by chance) or epibiontism (for pairs co-occurring more often than by chance). While species distribution patterns on island-like marine hard substrata resemble terrestrial islands, the mechanisms are not necessarily the same.

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Tasoff, Alexander J. "Quantifying the Genetic Capacity of California Grunion (Leuresthes Tenuis) to Adapt to Ocean Acidification." Thesis, California State University, Long Beach, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10600671.

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Ocean acidification can reduce survival and growth of marine larvae. However, if populations have the genetic capacity to adapt and increase their tolerance to low pH levels, then such genetic changes may offset the harmful effects of ocean acidification. I used methods in quantitative genetics to measure the genetic variance and project the potential rate of evolution for low pH tolerance in a nearshore forage-fish: the California grunion ( Leuresthes tenuis). I raised grunion larvae across an experimental pH gradient and measured their mortality and growth rates over a 14-day interval during the early larval stage. My results indicated that low pH levels significantly decreased the survival rates of grunion larvae overall. Surprisingly, low pH levels did not significantly affect larval growth rates. However, families varied widely with respect to pH tolerance, and many families had similar mortality and growth rates in high and low pH treatments. Quantitative genetic analyses indicated that low pH tolerance had a substantial genetic basis and is highly heritable within grunion populations. These results suggest that populations of California grunion, and possibly other nearshore fishes, may adapt relatively quickly to long-term changes in ocean pH.

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Mesnick, Sarah Lynne 1960. "Sexual selection and biological diversification: Patterns and processes." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/282239.

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This dissertation investigates the evolutionary consequences of three very different behavioral mechanisms by which males may bias female mating decisions in their favor, elaborate male displays (Chapters I and II) and sexual coercion and resource brokering (Chapter III). The results presented here suggest that sexual selection is an important force in evolution. In Chapters I and II, I investigate the relationship between male courtship displays and speciation. Chapter I utilizes the multiple sister-taxa comparison method to test the hypothesis that sexual dimorphism is correlated with increased species diversity in teleost fishes. In 21 of 27 sister-group comparisons, the lineage with the greater degree of sexual dimorphism was more species-rich than its hypothesized sister taxa. The pattern holds across taxonomic levels and sensory modalities, and whether the male, or the female, is the displaying sex. Additional data supporting the sexual selection-diversity hypothesis in other taxa are also discussed. Chapter II investigates how variation in the signals displayed during social and sexual interactions affect reproductive isolation and may facilitate subsequent speciation, utilizing both field and laboratory experiments with the marine fish, Acanthemblemaria crockeri, a chaenopsid blenny endemic to the Gulf of California, Mexico. The anterior portion of the body, the "signal organ", displayed during social interactions, was found not only to be the most variable but was also the most geographically informative. The behavioral responses of the fish themselves, in both male courtship discrimination trials and in female spawning trials, reinforce these geographical differences and results suggest that variation in socially selected traits may accelerate reproductive isolation. In Chapter III, I examine how, if some males in a population use force to bias female mating decisions, protection can become a valuable resource that other males can use to attract females. I term this the bodyguard hypothesis of female mate choice. I present data illustrating the effectiveness of protective males in reducing the probability of aggression from other males and suggest the importance of protective mating alliances in the evolution of a diversity of animal mating systems including mate guarding, leks, "harems", monogamy, polygyny, and pair-bonding in humans.

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Dumousseaud, Cynthia. "Physical and biological forcings on the carbonate chemistry in the North Atlantic Ocean." Thesis, University of Southampton, 2010. https://eprints.soton.ac.uk/168949/.

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The atmospheric concentration of CO2 has risen considerably since the industrial revolution, and the subsequent uptake of atmospheric CO2 by the oceans has affected the carbonate system and caused a reduction in the pH of the oceans. Model estimates involving future CO2 emission scenarios have predicted a significant increase of oceanic Dissolved Inorganic Carbon concentrations by the end of the century, corresponding to a decrease in oceanic pH by up to 0.4. In order to observe and predict changes in primary productivity and community structure in the oceans associated with future climate change, precise measurements of all the carbonate system parameters are important. The natural processes affecting the seasonal and regional variations of the carbonate chemistry are still poorly understood and sustained monitoring programs are required in order to determine the importance of hydrographical and biogeochemical forcings. The relationships between physical and biological parameters and carbonate system parameters were investigated in several regions of the North Atlantic Ocean, allowing a better understanding of the natural processes affecting the carbonate system in this ocean basin. For this purpose, the seasonal and inter-annual variability of the carbonate system in the Northeast Atlantic Ocean was studied through a ship of opportunity program, allowing observations of the short-term processes affecting the carbonate system and air-sea CO2 fluxes. The results showed contrasting effects of winter mixing and sea surface temperature on the carbonate system and the air-sea CO2 fluxes. In addition, the distributions of the carbonate system parameters were determined in the Iceland Basin and in the sub-tropical Northeast Atlantic Ocean. The carbonate system in the Iceland Basin was characterized by mesoscale variability associated to the presence and development of an eddy dipole in the study region; while the sub-tropical Northeast Atlantic Ocean showed spatial variability in all the chemical parameters, associated with coastal upwelling and remineralization in an oxygen minimum zone. Although the physics appeared to be the main forcing on the carbonate system in this study, the role of biology in the seasonality of the carbonate system is highly important. However, physical forcings tend to set the level for biological drawdown and therefore highly contribute to the variability of the carbonate system and CO2 fluxes.

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Krayesky-Self, Sherry L. "New Insights into the Rhodolith Microenvironment, With a Focus on the Gulf of Mexico." Thesis, University of Louisiana at Lafayette, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10002405.

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SEM observations have revealed unknown and previously undetected stages of the bloom-forming dinoflagellate Prorocentrum growing inside calcium carbonate-encrusted perithallial cells of the rhodolith-forming Lithothamnion sp. (Hapalidiaceae, Hapalidiales, Rhodophyta) in the NW Gulf of Mexico. Roundish structures inside the coralline cells were clustered together, surrounded by a thin membrane. Organized blebs, projections of the cytoplasm into the plasma membrane, as well as a suite of varying extracellular ornamentation patterns, were observed. Openings on the surface of some of the structures looked like characteristic thecal pores found in thecal plates of some dinoflagellates. DNA was extracted from inside the rhodolith and sequenced using dinoflagellate-specific cob1-primers. When blasting the resulting DNA sequences, it proved to be an exact match for Prorocentrum lima. Cells were isolated from inside the rhodoliths and cultured, revealing the presence of another set of endolithic life stages identified as Haptophyta (Prymnesiophyta), confirmed by single cell 18S rDNA sequencing. This research illustrates and illuminates newly found benthic life history stages of two ecologically important taxa of primary producers that also cause harmful algal blooms, such as the formation of red tides, fish kills, or shellfish poisoning events in the Gulf of Mexico.

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Kniskern, Tara A. "Spatial and Temporal Variability of Physical and Biological Mixing in the York River Subestuary." W&M ScholarWorks, 2001. https://scholarworks.wm.edu/etd/1539617975.

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Wheeler, Jeanette Danielle. "Behavioral responses of invertebrate larvae to water column cues." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/103337.

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Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2016. Cataloged from PDF version of thesis. Includes bibliographical references (pages 139-150). Many benthic marine invertebrates have two-phase life histories, relying on planktonic larval stages for dispersal and exchange of individuals between adult populations. Historically, larvae were considered passive drifters in prevailing ocean currents. More recently, however, the paradigm has shifted toward active larval behavior mediating transport in the water column. Larvae in the plankton encounter a variety of physical, chemical, and biological cues, and their behavioral responses to these cues may directly impact transport, survival, settlement, and successful recruitment. In this thesis, I investigated the effects of turbulence, light, and conspecific adult exudates on larval swimming behavior. I focused on two invertebrate species of distinct morphologies: the purple urchin Arbacia punctulata, which was studied in pre-settlement planktonic stages, and the Eastern oyster Crassostrea virginica, which was studied in the competent-to-settle larval stage. From this work, I developed a conceptual framework within which larval behavior is understood as being driven simultaneously by external environmental cues and by larval age. As no a priori theory for larval behavior is derivable from first principles, it is only through experimental work that we are able to access behaviors and tie them back to specific environmental triggers. In this work, I studied the behavioral responses of larvae at the individual level, but those dynamics are likely playing out at larger scales in the ocean, impacting population connectivity, community structure, and resilience. In this way, my work represents progress in understanding how the ocean environment and larval behavior couple to influence marine ecological processes. by Jeanette Danielle Wheeler. Ph. D.

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Sullivan, Matthew Brian 1975. "Ecology, diversity and comparative genomics of oceanic cyanobacterial viruses." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/39163.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2004. Also issued in pages. Includes bibliographical references. The marine cyanobacteria Prochlorococcus and Synechococcus are numerically dominant primary producers in the oceans. Each genera consists of multiple physiologically and genetically distinct groups (termed "ecotypes" in Prochlorococcus). Cyanobacterial viruses (cyanophages) that infect Synechococcus are abundant (to 104-106 phage ml-1) in the oceans and calculations suggest that they play a small but significant role in host mortality. Cyanophages are also thought to shape their host populations through regulation of sub-populations and through transfer of genes. Here we describe the isolation of Prochlorococcus cyanophages and the assembly of a culture collection established using a broadly diverse suite of Prochlorococcus and Synechococcus hosts. The collection contains three morphological families, Myoviridae, Podoviridae and Siphoviridae, known to infect marine bacteria and cyanobacteria. Host strains of similar ecotypes often yielded cyanophages of the same family. Host-range analyses of these isolates demonstrated varying levels of specificity among the different morphological types, ranging from infection of a single strain to infection across ecotypes and even across both cyanobacterial genera. Strain-specific cyanophage titers were low in open ocean waters where total cyanobacterial abundances were high, suggesting low phage titers might be a feature of open oceans. Investigations of the underlying cause(s) of this trend require culture-independent assays for quantifying phage that infect particular hosts. (cont.) We used the phage g20 gene, which encodes the portal protein, to examine the diversity of Myoviridae isolates and found that g20 sequences from our isolates had high similarity to those from other cultured isolates, but not to six phylogenetic clusters of environmental g20 sequences that lacked cultured representatives. Three Prochlorococcus cyanophage genomes were sequenced and analysis of these genomes show striking similarity to the well-studied T7- and T4-like phages, but additionally suggest that these Prochlorococcus cyanophages are modified for infection of photosynthetic hosts, that live in nutrient-limited environments. All three cyanophage genomes contain, among other novel genes of interest, photosynthetic genes that are full-length, conserved, and clustered in the genome suggesting they are functional during infection. Phylogenetic inference suggests that some of these genes were horizontally transferred between host and phage influencing the evolution and ecology of both host and phage. by Matthew Brian Sullivan. Ph.D.

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Oleksiak, Marjorie Frances. "Diversity and characterization of novel Cytochrome P450 2 genes in the marine teleost Fundulus Heteroclitus." Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/55319.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. Includes bibliographical references (leaves 179-199). by Marjorie Frances Oleksiak. Ph.D.

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Fripp, Deborah 1970. "Techniques for studying vocal learning in bottlenose dolphins, Tursiops truncatus." Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/85610.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1999. Vita. Includes bibliographical references. by Deborah Redish Fripp. Ph.D.

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Ruzicka, James Joseph 1966. "Integrating bioenergetics and foraging behavior : the physiological ecology of larval cod (Gadus morhua)." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/39164.

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Thesis (Ph. D.)--Joint Program in Oceanography/Biology (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2004. Includes bibliographical references. How do larval cod, Gadus morhua, balance foraging effort against the high cost of swimming in a viscous hydrodynamic regime? A respirometry system was developed to measure the activity metabolism of individual larvae. The cost of swimming was modeled as a power-performance relationship (energy expenditure as a function of swimming speed) and as the cost of transport (the cost to travel a given distance). The cost of transport was high relative to juvenile and adult fish, but larvae swam more efficiently as they grew and became better able to overcome viscous drag. A large-volume observation system was developed to record foraging behavior in three dimensions. There are two phases of the saltatory search cycle used by larval cod: the burst which serves to position larvae within a new search volume and the pause when larvae search for prey. Burst characteristics did not change under different prey treatments, but pause duration increased while foraging capacity and swimming activity decreased when prey were absent. Longer pause durations could reflect greater effort to visually process each search volume when prey were difficult to find. Reduced swimming activity could also be an energy conservation strategy under unfavorable foraging conditions. By applying the cost of swimming model to the observed swimming intensity of freely foraging larvae, foraging activity was estimated to account for up to 80% of routine metabolism. A trophodynamic model was developed incorporating observed foraging behavior and swimming costs to estimate the prey density required to cover all metabolic demands. (cont.) Small larvae (5mm) can survive on typical mean Georges Bank prey densities in mildly turbulent conditions. Larger larvae (>6mm) can survive even at high turbulence levels. Simulated alternative foraging strategies predict that when predator-prey contact rates are high, the greatest net energy gain is realized with short pause durations. When predator-prey contact rates are low, larvae should achieve greater net energy gains by remaining at rest for extended periods. Larvae observed foraging in the absence of prey do not change behavior as much as the simulation model predicts, suggesting that they use a prey encounter maximization strategy rather than an energy conservation strategy. by James Joseph Ruzicka. Ph.D.

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Bayer, Skylar (Skylar Rae). "Reproductive traits of pioneer gastropod species colonizing deep-see hydrothermal vents after an eruption." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/65300.

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Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2011. Cataloged from PDF version of thesis. Includes bibliographical references (p. 27-33). The colonization dynamics and life histories of pioneer species are vital components in understanding the early succession of nascent hydrothermal vents. The reproductive ecology of pioneer species at deep-sea hydrothermal vents may provide insight into their dispersal, population connectivity, and ability to colonize after disturbance. An opportunity to study the reproductive traits of two pioneer gastropod species, Ctenopelta porfera and Lepetodrilus tevnianus, presented itself in 2006 after an eruption on the East Pacific Rise (EPR) eliminated vent communities near 9°50'N. Standard histological techniques were used to determine whether reproductive characteristics, such as timing of gamete release, fecundity, or time to maturation, differed from other vent gastropods in ways that might explain arrival of these two species as early colonizers. Both species exhibited two-component oocyte size frequency distributions that indicated they were quasi-continuous reproducers with high fecundity. In C. porifera, the oocyte size distributions differed slightly between two collection dates, suggesting that environmental cues may introduce some variability in gamete release. In samples collected within one year of the estimated eruption date, individuals in populations of both C. porfera and L. tevnianus were reproductively mature. The smallest reproducing C. porifera were 4.2 mm (males) and 5.4 mm (females) in shell length, whereas reproductive L. tevnianus were smaller (2.3 and 2.4 mm in males and females respectively). Most Cporifera in the population were large (> 6.0 mm) compared to their settlement size and reproductively mature. In contrast, most L tevnianus were small (< 1.0 mm) and immature. Reproductive traits of the two species are consistent with opportunistic colonization, but are also similar to those of other Lepetodrilus species and peltospirids at vents, and do not explain why these particular two species were the dominant pioneers. It is likely that their larvae were in high supply immediately after the eruption due to oceanographic transport processes from remote source populations. by Skylar Bayer. S.M.

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Moeller, Holly Villacorta. "On the economic optimality of marine reserves when fishing damages habitat." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/57574.

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Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2010. This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. Cataloged from student submitted PDF version of thesis. Includes bibliographical references (p. 125-127). In this thesis, I expand a spatially-explicit bioeconomic fishery model to include the negative effects of fishing effort on habitat quality. I consider two forms of effort driven habitat damage: First, fishing effort may directly increase individual mortality rates. Second, fishing effort may increase competition between individuals, thereby increasing density-dependent mortality rates. I then optimize effort distribution and fish stock density according to three management cases: (1) a sole owner, with jurisdiction over the entire fishery, who seeks to maximize profit by optimizing effort distribution; (2) a manager with limited control of effort and stock distributions, who seeks to maximize tax revenue by setting the length of a single, central reserve and a uniform tax per unit effort outside it; and (3) a manager with even more limited enforcement power, who can only set a tax per unit effort everywhere in the habitat space. I demonstrate that the economic efficiency of reserves depends upon model parameterization. In particular, reserves are most likely to increase profit (or tax revenue) when density-dependent fish mortality rates are affected. Interestingly, for large habitats that are sufficiently sensitive to density-dependent fish mortality effects, reserve networks (alternating fished and unshed areas of fixed periodicity) emerge. These results suggest that spatial forms of management which include marine reserves may enable signicant economic gains over nonspatial management strategies, in addition to the well-established conservation benefits provided by closed areas. by Holly Villacorta Moeller. S.M.

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Schlezinger, Jennifer Joy. "Involvement of cytochrome P450 1A in the toxicity of aryl hydrocarbon receptor agonists : alteration of arachidonic and acid metabolism and production of reactive oxygen species." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/55323.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. "August, 1998." Includes bibliographical references (p. 219-254). Two cytochrome P4501A-dependent mechanisms of aryl hydrocarbon receptor (AhR) agonist toxicity were examined in the marine teleost scup (Stenotomus chrysops), alteration of arachidonic acid (AA) metabolism and production of reactive oxygen species (ROS). In scup hepatic microsomes, cytochrome P450s including CYP1A and CYP2B-like proteins catalyzed regioselective metabolism of AA to eicosatrienoic and hydroxyeicosatetraenoic acids. Benzo[a]pyrene (BP) treatment induced liver microsomal AA metabolism, but that effect varied with season. Endogenous AA epoxides were recovered from scup liver, heart, and kidney, and their composition in the liver was altered by treatment with BP or 2,3,7,8-tetrachlorodibenzo-p-dioxin. In scup and mammals, the formation of ROS was stimulated by binding of 3,3',4,4-tetrachlorobiphenyl (TCB) to CYP1A, apparently CYP1A1. Attack of that ROS inactivated scup CYP1A. ROS release and inactivation of CYPlA were stimulated only by substrates of CYP1A that are slowly metabolized. In vivo, 3,3',4,4',5- pentachlorobiphenyl (PeCB) potently induced CYPlA mRNA, protein and catalytic activity at low doses (0.01-0.1 mg/kg), suppressed induction of CYPlA protein and catalytic activity at a high dose (1 mg/kg) and transiently induced oxidative stress in scup liver. The suppression of CYP1A induction was organ-dependent, with hepatic CYP1A being most susceptible to inactivation. The results suggest that ROS could be involved in the in vivo suppression of scup liver CYP1A by planar halogenated aromatic hydrocarbons. The reactive oxygen sensitive transcription factor, nuclear factor-KB (NF-KB), was characterized in scup. An NF-KB consensus binding sequence bound specifically to 3 proteins in scup liver, heart and kidney. One protein was recognized by an antibody to mammalian p50. Injection alone appeared to activate NF-KB. BP did not increase the activation of NF-KB, and PeCB activated NF-KB in only 1 of 2 experiments. Last, CYP1A induction in endothelial cells of the American eel (Anguilla rostrata), a site which may be particularly susceptible to alterations in AA metabolism and ROS production, was described. Eel liver CYPlA responded to BP, 13-naphthoflavone and TCB in a dose-dependent fashion, and induction was correlated with hepatic inducer concentration. Endothelial CYP1A was inducible in a number of organs and was metabolically active. In the rete mirabile, penetration of endothelial CYP1A induction increased with increasing dose of AhR agonists, corresponding with an increase in inducer concentration. A transition from endothelial to epithelial staining occurred in the gill, heart and kidney at high inducer doses. by Jennifer Joy Schlezinger. Ph.D.

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Richberg, Kevin Patrick. "Identification of chemoautotrophic microorganisms from a diffuse flow hydrothermal vent at EPR 9° north using ¹³C DNA stable isotope probing and catalyzed activated reporter deposition-fluorescence in situ hybridization." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/61888.

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Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2010. Cataloged from PDF version of thesis. Includes bibliographical references (p. 47-54). At deep-sea hydrothermal vents chemolithoautotrophic microbes mediate the transfer of geothermal chemical energy to higher trophic levels. To better understand these underlying processes and the organisms catalyzing them, this research used DNA Stable Isotope Probing (SIP) combined with Catalyzed Activated Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to identify the microorganisms chemoautotrophically supporting the food web at a diffuse flow hydrothermal vent. Both anaerobic and aerobic shipboard incubations containing various augmented electron donor and acceptor species showed that Epsilonproteobacteria were the dominant chemoautotrophs with greater than 70% of the cells counted within the first 24 hours. 13C DNA SIP identified unique organisms not previously characterized from low temperature diffuse flow venting: green sulfur bacteria (Chlorobi-like organisms) possibly utilizing photoautotrophy, aerobic Lutibacter litoralis-like organisms growing under anaerobic conditions, and Epsilonproteobacterial Thioreductor sp. at temperatures above maximum known tolerances. This research illustrates both the promise and pitfalls of the SIP technique applied to hydrothermal systems, concluding that timing of the incubation experiments is the critical step in eliminating undesired 13C labeling. These results set the stage for a more thorough future examination of diffuse flow microorganisms by presenting interesting questions that second generation experiments could be designed to answer. by Kevin Patrick Richberg. S.M.

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Green, Rebecca E. (Rebecca Erin) 1972. "Scale closure in upper ocean optical properties : from single particles to ocean color." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/29058.

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Thesis (Ph.D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology, and the Woods Hole Oceanographic Institution), 2002. Includes bibliographical references. Predictions of chlorophyll concentration from satellite ocean color are an indicator of phytoplankton primary productivity, with implications for foodweb structure, fisheries, and the global carbon cycle. Current models describing the relationship between optical properties and chlorophyll do not account for much of the optical variability observed in natural waters, because of the presence of seawater constituents that do not covary with phytoplankton pigment concentration. In an attempt to better understand variability in these models, the contributions of seawater constituents to ocean optical properties were investigated. A combination of Mie theory and flow cytometry was used to determine the diameter, complex refractive index (n+n'i), and optical cross-sections of individual particles, based on a method developed in the laboratory using phytoplankton cultures. Individual particle measurements were used to interpret variability in concurrently measured bulk optical properties in New England continental shelf waters in two seasons. The summed contribution to scattering of individual particles in the size range of 0.1-50 Cpm accounted for approximately the entire scattering coefficient measured independently using bulk methods. In surface waters in both seasons, the large diameters and n' of eukaryotic phytoplankton caused them to be the main particle contributors to both absorption and scattering. Minerals were the main contributor to backscattering, bb, in the spring, whereas in the summer both minerals and detritus contributed to bb. Synechococcus and heterotrophic bacteria were less important optically, contributing <11% each to attenuation in either season. (cont.) The role of seawater constituents in determining remote sensing reflectance, Rrs, was determined using radiative transfer theory. Seasonal differences in the spectral shape of Rrs were contributed to approximately equally by eukaryotic phytoplankton absorption, dissolved absorption, and non-phytoplankton bb. A higher inverse wavelength dependence of non-phytoplankton bb in the summer was caused by the contribution of small detritus, in contrast to larger minerals in the spring. Measurements of bb and Rrs were compared to values from bio-optical models based on chlorophyll concentration. Differences in measured and modeled bb and Rrs were caused by higher dissolved absorption and higher backscattering efficiencies and scattering by non-phytoplankton than were assumed by the model. by Rebecca E. Green. Ph.D.

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Manning, Cara Charlotte Marie. "Insight into chemical, biological, and physical processes in coastal waters from dissolved oxygen and inert gas tracers." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/108917.

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Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017. Cataloged from PDF version of thesis. Includes bibliographical references (pages 185-213). In this thesis, I use coastal measurements of dissolved O₂ and inert gases to provide insight into the chemical, biological, and physical processes that impact the oceanic cycles of carbon and dissolved gases. Dissolved O₂ concentration and triple isotopic composition trace net and gross biological productivity. The saturation states of inert gases trace physical processes, such as air-water gas exchange, temperature change, and mixing, that affect all gases. First, I developed a field-deployable system that measures Ne, Ar, Kr, and Xe gas ratios in water. It has precision and accuracy of 1 % or better, enables near-continuous measurements, and has much lower cost compared to existing laboratory-based methods. The system will increase the scientific community's access to use dissolved noble gases as environmental tracers. Second, I measured O₂ and five noble gases during a cruise in Monterey Bay, California. I developed a vertical model and found that accurately parameterizing bubble-mediated gas exchange was necessary to accurately simulate the He and Ne measurements. I present the first comparison of multiple gas tracer, incubation, and sediment trap-based productivity estimates in the coastal ocean. Net community production estimated from ¹⁵NO₃⁻ uptake and 02 /Ar gave equivalent results at steady state. Underway O₂/Ar measurements revealed submesoscale variability that was not apparent from daily incubations. Third, I quantified productivity by O₂ mass balance and air-water gas exchange by dual tracer (³He/SF₆ ) release during ice melt in the Bras d'Or Lakes, a Canadian estuary. The gas transfer velocity at >90 % ice cover was 6 % of the rate for nearly ice-free conditions. Rates of volumetric gross primary production were similar when the estuary was completely ice-covered and ice-free, and the ecosystem was on average net autotrophic during ice melt and net heterotrophic following ice melt. I present a method for incorporating the isotopic composition of H₂O into the O₂ isotope-based productivity calculations, which increases the estimated gross primary production in this study by 46-97 %. In summary, I describe a new noble gas analysis system and apply O₂ and inert gas observations in new ways to study chemical, biological, and physical processes in coastal waters. by Cara Charlotte Marie Manning. Ph. D.

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Richardson, David Earl. "Physical and Biological Characteristics of Billfish Spawning Habitat in the Straits of Florida." Scholarly Repository, 2008. http://scholarlyrepository.miami.edu/oa_dissertations/26.

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The objective of this dissertation was to examine sailfish (Istiophorus platypterus) and blue marlin (Makaira nigricans) spawning in the Straits of Florida, with a specific focus on 1) the physical and biological characteristics of the spawning environment, and 2) the role of the region within the broader spawning patterns of these two species. In order to accomplish these objectives, two years of monthly ichthyoplankton collections and physical measurements across the Straits of Florida were combined with a finer-scale Lagrangian study. Additionally, a molecular species-identification methodology was developed that was both high-throughput and suitable for use with a broad taxonomic range of species. An initial analysis considered the diversity, assemblages and associated habitat of the larvae of large and medium size pelagic species. In total 36 species and 14,295 individuals were collected during this study, with the highest diversity occurring during the summer, and in the western frontal region of the Florida Current. Sailfish were included in an assemblage with Auxis rochei, A. thazard and Euthynnus alleterattus, all species found in highest abundance during the summer along the western edge of the Straits of Florida. Blue marlin grouped most closely with Thunnus atlanticus, Ruvettus pretiosus and Lampris guttatus, all summer spawners, whose larvae tended to occur further offshore. The primary environmental factors associated with these assemblages were SST (highest summer-early fall), day-length (highest early summer), thermocline depth (shallowest on the Florida side) and fluorescence (highest on the Florida side). A Lagrangian sampling effort was then used to more specifically evaluate the role of frontal zones in sailfish spawning. The results of this sampling indicated that the highest levels of sailfish spawning occurred in a frontal zone associated with the formation of a submesoscale frontal eddy. This spawning resulted in the first-feeding larvae occupying an area rich in prey items. Given the small spatial-scale of the front, and the distribution of the eggs of adult prey items, the results of this work would suggest that sailfish are actively targeting features for spawning that are favorable to the growth and survival of their larvae. Finally the relative importance of the Straits of Florida as a spawning ground was evaluated by calculating the annual egg production of both sailfish and blue marlin within this region. In total it was estimated that 2.1% of western Atlantic sailfish spawning and 1.6% of Atlantic wide blue marlin spawning occurs in the SF. Pop-up satellite tags deployed on sailfish at the start of the spawning season revealed their short residency times in the SF, suggesting that a large (≈10%) transient portion of the sailfish population is responsible for the SF egg production. These results indicate that the SF is a migratory bottleneck for sailfish. In conclusion the results of this study indicate that a hierarchy of physical and biological processes influence the distribution of billfish spawning in space and time. The results provide insights into the movement patterns and life history strategies of these species, and ultimately may aid in the development of the spatially explicit ecosystem based management approaches that are currently being advocated.

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Smith, Edward G. "Exploring the biological function of green fluorescent protein (GFP)-like pigments in corals." Thesis, University of Southampton, 2012. https://eprints.soton.ac.uk/359120/.

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Ruby, Caitlin A. "Application of Coastal and Marine Ecological Classification Standard (CMECS) to Remotely Operated Vehicle (Rov) Video Data for Enhanced Geospatial Analysis of Deep Sea Environments." Thesis, Mississippi State University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10268275.

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The Coastal and Marine Ecological Classification Standard (CMECS) provides a comprehensive framework of common terminology for organizing physical, chemical, biological, and geological information about marine ecosystems. Federally endorsed as a dynamic content standard, all federally funded data must be compliant by 2018; however, applying CMECS to deep sea datasets and underwater video have not been extensively examined. The presented research demonstrates the extent to which CMECS can be applied to deep sea benthic habitats, assesses the feasibility of applying CMECS to remotely operated vehicle (ROV) video data in near-real-time, and establishes best practices for mapping environmental aspects and observed deep sea habitats as viewed by the ROV’s forward-facing camera. All data were collected during 2014 in the Northern Gulf of Mexico by the National Oceanic and Atmospheric Administration’s (NOAA) ROV Deep Discoverer and ship Okeanos Explorer.

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Jones, Randolph M. "The Influence of Short-Term Events on the Hydrographic and Biological Structure of the Southwestern Ross Sea." W&M ScholarWorks, 2015. https://scholarworks.wm.edu/etd/1539617963.

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Relative to the rest of the Southern Ocean, the Ross Sea continental shelf experiences very high productivity and phytoplankton biomass, which supports an extensive food web including high concentrations of upper trophic level biomass. Conventional observational methods, including ship-based sampling, instrumented moorings, satellite imagery, and computer-based modelling, have illustrated the seasonal progression of the phytoplankton bloom over the past four decades. While we have been sampling phytoplankton variability in the Ross Sea on a variety of relatively large scales, with observations at specific locations or times, over spans of time, or at specific depths, our understanding of smaller scales of variability (on the order of a few hours or several kilometers) is still poor. Utilizing two seasons (2010-2011 and 2012-2013) of high-resolution autonomous glider deployments in the southwestern Ross Sea, I examined the mechanisms driving both the transitions between stages of the phytoplankton bloom and the short-term perturbations in average 0-50 m chlorophyll. By including the available raw fluorescence data from both glider seasons and three mooring seasons, I determined that the 2012-2013 season had greater than average variability, with greater levels of variability observed in only two other seasons. Differences in the timing of bloom transitions were relatively constrained; the transition from bloom to post-bloom levels occurred within a temporal span of 6 d. These findings were likely the result of the location of the 2012-2013 glider adjacent to Ross Island and the Ross Ice Shelf, where complex bathymetry, turbulent flows, and the presence of an ice field contributed to the greater observed variability. To investigate the mechanisms driving the short-term perturbations in chlorophyll, I examined the relationships between average chlorophyll, average temperature, and mixed layer depth measured by the gliders and wind speed measured by two automatic weather stations atop the Ross Ice Shelf. Over the course of the 2012-2013 season, perturbations or responses in chlorophyll were heavily influenced by the degree of temporal coupling between wind events and the depth of mixing. Longer delays of 12-24 h observed prior to the biomass maximum shortened following the transition to biomass dissipation to 2-12 h. Furthermore, by causing aggregate formation and rapid vertical flux, physical forcing factors contributed to the observed short-term perturbations through reductions in biomass in surface layers and the appearance of chlorophyll in deeper layers. These results suggest that the small-scale observing capabilities of autonomous gliders allow for an improved understanding of the mechanisms that drive variability and short-term perturbations in shallow chlorophyll in the southwestern Ross Sea.

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Champieux, Terrance M. "Impacts of a constructed oyster bed on infaunal invertebrate communities in Jack Dunster Marine Reserve." Thesis, California State University, Long Beach, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=1598629.

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Oysters are important to estuarine ecosystems because of the functions they provide. Thus, oyster restoration projects are undertaken in areas where natural populations have declined. However, restoration techniques can impact sediment organic matter and benthic invertebrates that provide trophic support for important species. This study assesses the impacts of a constructed shell bed on associated sediment and invertebrate communities in a southern California bay. Within the bed site, organic matter, invertebrate abundance, and invertebrate species richness are lower only under the oyster bed. The alteration in the community under the shell is driven by a reduction in species. Tubificidae were the only remaining species under the shell. These results may be explained by the shells’ action as a barrier to the mud-water interface. While significant, impacts of oyster bed construction are spatially restricted to just under the bed. Longer-term studies should be conducted to address effects of the oysters themselves.

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Baumann, Justin H. "The effects of elevated temperature stress on the acquisition and allocation of carbon to lipids in Hawaiian corals." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1374229960.

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Collins, James R. (James Robert). "The remineralization of marine organic matter by diverse biological and abiotic processes." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/109053.

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Thesis: Ph. D., Joint Program in Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017. Cataloged from PDF version of thesis. Includes bibliographical references. While aerobic respiration is typically invoked as the dominant mass-balance sink for organic matter in the upper ocean, many other biological and abiotic processes can degrade particulate and dissolved substrates on globally significant scales. The relative strengths of these other remineralization processes - including mechanical mechanisms such as dissolution and disaggregation of sinking particles, and abiotic processes such as photooxidation - remain poorly constrained. In this thesis, I examine the biogeochemical significance of various alternative pathways of organic matter remineralization using a combination of field experiments, modeling approaches, geochemical analyses, and a new, high-throughput lipidomics method for identification of lipid biomarkers. I first assess the relative importance of particle-attached microbial respiration compared to other processes that can degrade sinking marine particles. A hybrid methodological approach - comparison of substrate-specific respiration rates from across the North Atlantic basin with Monte Carlo-style sensitivity analyses of a simple mechanistic model - suggested sinking particle material was transferred to the water column by various biological and mechanical processes nearly 3.5 times as fast as it was directly respired, questioning the conventional assumption that direct respiration dominates remineralization. I next present and demonstrate a new lipidomics method and open-source software package for discovery and identification of molecular biomarkers for organic matter degradation in large, high-mass-accuracy HPLC-ESI-MS datasets. I use the software to unambiguously identify more than 1,100 unique lipids, oxidized lipids, and oxylipins in data from cultures of the marine diatom Phaeodactylum tricornutum that were subjected to oxidative stress. Finally, I present the results of photooxidation experiments conducted with liposomes - nonliving aggregations of lipids - in natural waters of the Southern Ocean. A broadband polychromatic apparent quantum yield (AQY) is applied to estimate rates of lipid photooxidation in surface waters of the West Antarctic Peninsula, which receive seasonally elevated doses of ultraviolet radiation as a consequence of anthropogenic ozone depletion in the stratosphere. The mean daily rate of lipid photooxidation (50 ± 11 pmol IP-DAG L⁻¹ d⁻¹, equivalent to 31 ± 7 [mu]g C m⁻³ d⁻¹) represented between 2 and 8 % of the total bacterial production observed in surface waters immediately following the retreat of the sea ice. by James R. Collins. Ph. D.

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Forrer, Heather. "Toward an improved understanding of the Southern Ocean's biological pump: phytoplankton group-specific contributions to nitrogen and carbon cycling across the Subantarctic Indian Ocean." Master's thesis, Faculty of Science, 2021. http://hdl.handle.net/11427/33675.

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Iron (and silicate) (co-)limitation of phytoplankton is considered a primary cause of the Southern Ocean's inefficient biological pump. However, the role of phytoplankton community structure and response to nutrient cycling remains poorly understood. In a mass balance sense, phytoplankton consumption of new nitrogen (N; e.g., allochthonous nitrate) is proportional to net carbon (C) export, while growth fueled by recycled N (e.g., ammonium) yields no net C flux. The N isotope ratio (δ15N) of surface biomass has long been used as an integrative tracer of new versus regenerated uptake. This approach is rendered more accurate by coupling either fluorescence-activated cell sorting (FACS; of nano- and picophytoplankton; 0.4-20 μm) or microscopy (for microphytoplankton; >20 um) with groupspecific δ15N measurements. Samples were collected for the analysis of nutrients and nitrate-, FACS-, and microscopy-δ15N on a mid-summer transect of the Subantarctic Indian basin during the 2016/17 Antarctic Circumnavigation Expedition (ACE) cruise. The data show that all phytoplankton populations preferentially utilize nitrate (≥55%) across the Indian Sector of the Subantarctic, potentially driving higher C export potential than previously estimated. Indeed, near the Subantarctic islands, 72% of microand >80% of nano- and picophytoplankton growth is supported by nitrate. This is likely due to the partial alleviation of phytoplankton iron and silicate stress, largely as a result of bathymetric upwelling, which constitutes a manifestation of the island mass effect. C export potential is lower in the open ocean region away from the islands where iron stress has been shown to be higher; here, nitrate supports >55% of micro- and picophytoplankton and 7 to 79% of nanophytoplankton growth. In terms of relative abundance (RA), the open Subantarctic is dominated by picoeukaryotes (64%), although there exists a large disconnect between relative abundance and potential contribution to C export. The three largest surface-ocean phytoplankton populations included in this study – microphytoplankton, cryptophytes, and nanoeukaryotes – each contribute ~30% to the total C export potential across the Subantarctic Indian sector while picophytoplankton contribute ~5%. Thus, as has been concluded previously, the larger phytoplankton size classes are disproportionately important drivers of the Subantarctic biological pump. Other interesting ecological findings include diatom-dominated microphytoplankton populations apparently fueled by a significant fraction of regenerated N, even in areas of iron supply, and Synechococcus relying near-exclusively on new N, in contrast to subtropical observations. Additionally, the abundance of Synechococcus appears to be controlled by the availability of iron across the Subantarctic, with silicate and temperature playing a supporting role.

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Poulton, Nicole Jane 1970. "Physiological and behavioral diagnostics of nitrogen limitation for the toxic dinoflagellate Alexandrium fundyense." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/91509.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), February 2001. Includes bibliographical references. by Nicole Jane Poulton. Ph.D.

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Boissonneault, Katie Rose 1973. "Gene discovery and expression profiling in the toxin-producing marine diatom, Pseudo-nitzschia multiseries (Hasle) Hasle." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/39415.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and, the Woods Hole Oceanographic Institution), 2004. Includes bibliographical references (leaves 169-180). Toxic algae are a growing concern in the marine environment. One unique marine diatom, Pseudo-nitzschia multiseries (Hasle) Hasle, produces the neurotoxin domoic acid, which is the cause of amnesic shellfish poisoning. The molecular characterization of this organism has been limited to date. Therefore, the focus of this thesis was to identify and initiate characterization of actively expressed genes that control cell growth and physiology in P. multiseries, with the specific goal of identifying genes that may play a significant role in toxin production. The first step in gene discovery was to establish a complementary DNA (cDNA) library and a database of expressed sequence tags (ESTs) for P. multiseries. 2552 cDNAs were sequenced, generating a set of 1955 unique contigs, of which 21% demonstrated significant similarity with known protein coding sequences. Among the genes identified by sequence similarity were several involved in photosynthetic pathways, including fucoxanthin-chlorophyll a/c light harvesting protein and a C4-specific pyruvate, orthophosphate dikinase. Several genes that may be involved in domoic acid synthesis were also revealed through sequence similarity, for example, glutamate dehydrogenase and 5-oxo-L-prolinase. In addition, the identification of sequences that appear novel to Pseudo-nitzschia may provide insight into unique aspects of Pseudo-nitzschia biology, such as toxin production. Genes whose expression patterns were correlated with toxin production were identified by hybridization to a microarray manufactured from 5376 cDNAs. 121 cDNAs, representing 12 unique cDNA contigs or non-redundant cDNAs, showed significantly increased expression levels in P. multiseries cell populations that were actively producing toxin. (cont.) The up-regulated transcripts included cDNAs with sequence similarity to 3-carboxymuconate cyclase, phosphoenolpyruvate carboxykinase, an amino acid transporter, a small heat shock protein, a long- chain fatty acid Co-A ligase, and an aldo/keto reductase. These results provide a framework for investigating the control of toxin production in P. multiseries. These transcripts may also be useful in ecological field studies in which they may serve as signatures of toxin production. Prospects for further application of molecular genetic technology to the understanding of the physiology and ecology of P. multiseries is discussed. by Katie Rose Boissonneault. Ph.D.

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Sancho, Gorka (Gorka Antonio Sancho-Bizcarrondo) 1968. "Behavioral ecology of coral reef fishes at spawning aggregation sites." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/55320.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. Includes bibliographical references. by Gorka Sancho. Ph.D.

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Bochenek, Eleanor A. "Virginia's pelagic recreational fishery: Biological, socioeconomic and fishery components." W&M ScholarWorks, 1989. https://scholarworks.wm.edu/etd/1539616572.

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Catch, effort, fleet size and boat owner expenditure data were collected on Virginia's recreational marlin/tuna fishery for the 1983-1985 seasons. Logbooks, dockside interviews and a telephone survey were evaluated to determine which method was the most efficient and effective for collecting and estimating catch and effort for Virginia's pelagic recreational fishery. In 1984, logbooks were used to collect catch and effort data and fishing effort was estimated using Bochenek's method. Very few fishermen returned their logbooks and as a result this data is probably less reliable than the data collected in other years. Due to the poor return of logbooks, this method should not be used to assess Virginia's marlin/tuna fishery. For the 1985 season, Figley's telephone survey (1984) was compared to the NMFS dockside interview technique for large pelagics. Both the telephone survey using Figley's technique (1984) and dockside interviews using Bochenek's method for calculating effort appear to provide similar estimates of projected total catch. However, the dockside method is very labor intensive, costly and fraught with problems in estimating fishing effort. Therefore, the telephone survey technique using Figley's method for estimating effort appears to be a better method for analyzing this fishery. If telephone interviewing will not work in an area and dockside sampling methods must be relied upon to study the pelagic fishery, Bochenek's method appears to produce a better estimate of fishing effort. Using Figley's (1984) mark-recapture technique, Virginia's pelagic recreational fleet was estimated at 455 and 774 vessels in 1983 and 1985, respectively. Boat owner expenditures for this fleet were estimated at &3,863,045 in 1983, \&4,057,020 in 1984 and &5,538,191 in 1985. Bluefin tuna were caught at SST ranging from 58-83 F but seem to prefer SST of 70 to 75 F. Yellowfin tuna were caught at SST ranging from 68-86 F with the majority landed at SST of 76-80 F. White marlin appear to prefer SST of 74 to 81 F.

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Smallwood, Barbara. "The influence of physical and biological processes on organic matter distribution and preservation in recent marine sediments from the Oman Margin, Arabian Sea." Thesis, University of Liverpool, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366242.

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Bates, Nicholas Robert. "Investigation of the physical and biological controls of the oceanic CO2 system in the Sargasso Sea." Thesis, University of Southampton, 1995. https://eprints.soton.ac.uk/358400/.

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Smith, Helen E. K. "The contribution of mineralising phytoplankton to the biological carbon pump in high latitudes." Thesis, University of Southampton, 2014. https://eprints.soton.ac.uk/376448/.

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The biological carbon pump (BCP) exports 5 - 12 Gt C yr−1 to the deep sea and is important for the distribution of carbon within the ocean. Previous studies proposed that the phytoplankton community structure and availability of dense biominerals are key in defining regional export. This thesis examines these factors and their influence on export in the Southern Ocean and the Arctic through the examination of upper ocean species composition, distribution and marine snow particles. In the Southern Ocean, the samples were collected from the high reflectance feature known as the Great Calcite Belt (GCB). The marine snow catcher was used to capture sinking particles and allowed the examination of both the large, fast sinking particles and the slow sinking fraction of particulate organic carbon (POC). The GCB was dominated by nanophytoplankton (<20μm), where the coccolithophore Emiliania huxleyi and diatoms Fragilariopsis nana, Fragilariopsis pseudonana and Pseudonitzschia sp. were the dominant species driving the variation in biogeography. The variation in biogeography was best described by a combination of temperature, nutrients and pCO2. E. huxleyi forms distinct features in the GCB on the Patagonian Shelf, near South Georgia and the Crozet Islands. A southwards progression of E. huxleyi occurs within High Nutrient Low Silica Low Chlorophyll waters in post-bloom conditions after silicic acid and iron drawdown by diatoms. When examined in terms of biomass, the diatoms dominate the GCB, although E. huxleyi was the single biggest contributor as a species. A statistical comparison of surface species and slow sinking material indicated that there was a degree of similarity between the surface and exported community but was regionally variable. Coccolithophores and diatoms contributed minimally (<10%) to upper ocean biomass and total carbon export. The results of this thesis indicate that even though the coccolithophores and diatoms are important phytoplankton for primary production, their direct contribution as cells to carbon export is low. POC flux correlated with opal flux but not calcite flux indicating that the opal was more important in driving POC flux in the GCB. Two types of sinking particles were examined, marine snow aggregates and faecal pellets and there was no significant difference between the sinking velocities. Marine snow sinking velocity was not dependent on size of the aggregate. The concentrations of biominerals and POC in the surface waters and the biominerals in the sinking particles did not influence the sinking velocity. This indicates that porosity and POC content could be more important in determining the sinking velocity and the carbon flux. The synthesis includes the species composition and biomass of the Arctic, which displayed similar trends to the GCB. The results from this thesis suggest that the slow sinking carbon export may not be significantly affected by potential changes in upper ocean biomineralising phytoplankton community structure and upper ocean chemistry. The effects of porosity and POC contents of the particles are here considered to be just as important for determining the export flux than upper ocean community structure and biomineral ballast availability. This implies that the impacts of ocean acidification will become more important deeper in the water column as biominerals become more important within sinking particles as POC is removed.

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Gazda, Stefanie K. "Examining sociological differences and the influence of prey distribution and environmental variability in the distribution of a top marine predator, the bottlenose dolphin (Tursiops truncatus)." Thesis, University of Massachusetts Boston, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10010739.

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The purpose of this dissertation was to examine the influence of environmental variability on the distribution of prey, and the influence of prey spatial structure and habitat variability may have on the distributions of bottlenose dolphins (Tursiops truncatus). Additionally I examined how sociological differences (behavior type and the changes in a foraging behavior specific to Cedar Key Florida) influences the relative roles of bottlenose dolphins within the population. The Gowans et al. scheme assumes that small groups form small communities and that foraging groups are small and rare as there are few foraging benefits to promote grouping. Using network analysis, I found that foraging occurs in small groups or alone, but there were preferential associations between individuals in Overall, Socialize, and Travel networks. I examined driver-barrier foraging behavior over several field seasons to assess the prediction that there are few foraging benefits to promote grouping. The driver dolphin does have greater catch success than the barrier dolphins regardless of group size. There is also evidence that barrier dolphins may have a role in increasing foraging efficiency by decreasing the number of incomplete bouts. Both the driver and barrier dolphins do better in larger groups when incomplete bouts are factored in. Therefore there are some foraging benefits that can promote grouping. In bottlenose dolphin foraging research, it is often assumed that habitat use is related to prey availability, though this is rarely directly tested. From my collaborative work using a database collected by the Florida Fish and Wildlife Commission’s Fisheries-Independent Monitoring (FIM) program, I evaluated the abundance of potential prey and their relationship to habitat and other biological and physical variables. I used MULTISPATI, which uses principal components analysis to partition and display patterns of spatial variation. The results show that there are correlations between fish-site scores and environmental variables. Spatial analysis of fish produced clear results, however neither PCA nor MULTISPATI could explain dolphin distribution. This is likely because the spatial scales are not the same grain for the comparisons; dolphins are highly mobile large marine predators (the scale is fine grained), and their prey are significantly smaller and habitat-specific (the scale is coarser).

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Schoepf, Verena. "Physiology and Biogeochemistry of Corals Subjected to Repeat Bleaching and Combined Ocean Acidification and Warming." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1376923711.

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Schroeder, Stephanie Lynn 1978. "The behavioral ecology and territoriality of the owl limpet, Lottia gigantea." Thesis, University of Oregon, 2011. http://hdl.handle.net/1794/11263.

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xvii, 141 p. : ill. Territoriality, defined as an animal or group of animals defending an area, is thought to have evolved as a means to acquire limited resources such as food, nest sites, or mates. Most studies of territoriality have focused on vertebrates, which have large territories and even larger home ranges. While there are many models used to examine territories and territorial interactions, testing the models is limited by the logistics of working with the typical model organisms, vertebrates, and their large territories. An ideal organism for the experimental examination of territoriality would exhibit clear territorial behavior in the field and laboratory, would be easy to maintain in the laboratory, defend a small territory, and have movements and social interactions that were easily followed. Lottia gigantea , the owl limpet, is just such a model animal. With a small territory (< 900 cm 2 ) and slow movements (3 mm/min), the interactions of several L. gigantea can be continuously and simultaneously monitored. Using time-lapse photography, experiments were conducted to observe behaviors of L. gigantea , ranging from how L. gigantea form home ranges to how territorial L. gigantea interact. Lottia gigantea formed home ranges within four weeks, returning to a home scar after each foraging cycle. To determine whether L. gigantea returned to areas with greater food resources, three different algal density treatments were used, and individuals were monitored to see which tiles they frequented the most. Lottia gigantea actually avoided areas with a thick algal covering, potentially due to the loss of suction they experienced while moving across algae. When L. gigantea established territories, home ranges overlapped considerably. Two individuals were placed in one arena, under the assumption that a dominance hierarchy would be established. Dominant status was predetermined, and in four of the seven dyads both individuals were evasive. When subjected to territorial encounters for two weeks, L. gigantea avoided areas where they experienced agonistic losses. Mucus may serve as an olfactory cue to define territorial boundaries. Individuals avoided tiles with conspecific's mucus more often than tiles with self-mucus or no mucus. Committee in charge: Barbara (“Bitty”) Roy, Chairperson; Alan Shanks, Advisor; Craig Young, Member; Mark Hixon, Member; Frances White, Outside Member

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Gribble, Kristin Elizabeth. "The ecology, life history, and phylogeny of the marine thecate heterotrophic dinoflagellates Protoperidinium and Diplopsalidaceae (Dinophyceae)." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/39221.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. Page 296 blank. Includes bibliographical references. Marine thecate heterotrophic dinoflagellates likely play an important role in the consumption of primary productivity and in the trophic structure of the plankton, yet we know little about these species. This thesis expanded our understanding of the autecology and evolutionary history of the Protoperidinium and diplopsalids. The distributions of Protoperidinium species off the southwestern coast of Ireland were influenced by physical oceanographic conditions coupled with the availability of preferred prey. The distributions of individual Protoperidinium species varied widely from the distribution of total Protoperidinium, indicating differences in ecologies among species. Certain species of Protoperidinium co-occurred with known preferred phytoplankton prey species. Concentrations of other Protoperidinium species were not related to those of any particular phytoplankton species, indicating that these Protoperidinium may rely on phytoplankton or other food sources beyond those already known, may not be species specific selective feeders, or may have become uncoupled from their preferred prey. The description of the sexual and asexual life history of Protoperidinium steidingerae provided the first account of the life history of any Protoperidinium species. (cont.) Asexual division occurred by eleutheroschisis within a temporary, immotile cyst, yielding two daughter cells. Daughter cells were initially round and half to two-thirds the size of parent cells, then rapidly increased in size, forming horns before separating. Sexual reproduction was constitutive in clonal cultures, indicating that the species may be homothallic. Fusing gametes were isogamous, and resulted in a planozygote with two longitudinal flagella. Hypnozygotes had a mandatory dormancy period of ca. 70 days. Germination resulted in planomeiocytes with two longitudinal flagella. Nuclear cyclosis may occur in the planomeiocyte stage. A high level of morphological diversity among life history stages of P. steidingerae has led to mis-classification and taxonomic inaccuracy of Protoperidinium species identified from field samples. The large subunit ribosomal DNA (LSU rDNA) molecular phylogeny of the heterotrophic dinoflagellates revealed that the genus Protoperidinium appeared to be recently diverged within the dinoflagellates. In maximum parsimony and neighbor joining analysis, Protoperidinium formed a monophyletic group, evolving from diplopsalid dinoflagellates. (cont.) In maximum likelihood and Bayesian analyses, however, Protoperidinium was polyphyletic, as the lenticular, diplopsalid heterotroph, Diplopsalis lenticula Bergh, was inserted within the Protoperidinium clade basal to Protoperidinium excentricum (Paulsen) Balech, and Preperidinium meunieri (Pavillard) Elbrichter fell within a separate clade as a sister to the Oceanica section and Protoperidinium steidingerae Balech. In all analyses, the Protoperidinium were divided into two major clades, with members in the Oceanica group and subgenus Testeria in one clade, and the Excentrica, Conica, Pellucida, Pyriforme, and Divergens sections in another clade. The LSU rDNA molecular phylogeny supported the historical morphologically determined sections, but not a simple morphology-based model of evolution based on thecal plate shape. LSU rDNA gene sequences are frequently used to infer the phylogeny of organisms. The many copies of the LSU rDNA found in the genome are thought to be kept homogenous by concerted evolution. In Protoperidinium species, however, there was high intragenomic diversity in the D1-D6 region of the LSU rDNA. For each species, the clone library was usually comprised of one highly represented copy and many unique sequences. (cont.) Sequence differences were primarily characterized by single base pair substitutions, single base pair insertion/deletions (indels), and/or large indels. Phylogenetic analysis of all clones gave strong support for monophyly of the polymorphic copies of each species, and recovered the same species tree as an analysis using just one sequence per species. Analysis of LSU rDNA gene expression in three species by RT-PCR indicated that copies with fewer substitutions and fewer and smaller indels are expressed, and that 50% or more of the copies are pseudogenes. High intraspecific and intraindividual LSU rDNA sequence variability could lead to inaccurate species phylogenies and over-estimation of species diversity in environmental sequencing studies. This thesis has explored the ecology, life history, molecular phylogeny, and intraspecific DNA sequence variability of marine thecate heterotrohic dinoflagellates using a wide range of methodologies, including field sampling, culturing, microscopy, morphological analyses, histological staining, and molecular biology. The work here has broadened our understanding of the Protoperidinium and diplopsalids, providing new insights into the ecological and evolutionary relationships of these heterotrophs with other plankton species. by Kristin Elizabeth Gribble. Ph.D.

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Tolonen, Andrew Carl. "Prochlorococcus genetic transformation and genomics of nitrogen metabolism." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/43721.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. Includes bibliographical references. Prochlorococcus, a unicellular cyanobacterium, is the most abundant phytoplankton in the oligotrophic, oceanic gyres where major plant nutrients such as nitrogen (N) and phosphorus (P) are at nanomolar concentrations. Nitrogen availability controls primary productivity in many of these regions. The cellular mechanisms that Prochlorococcus uses to acquire and metabolize nitrogen are thus central to its ecology. One of the goals of this thesis was to investigate how two Prochlorococcus strains responded on a physiological and genetic level to changes in ambient nitrogen. We characterized the N-starvation response of Prochlorococcus MED4 and MIT9313 by quantifying changes in global mRNA expression, chlorophyll fluorescence, and Fv/Fm along a time-series of increasing N starvation. In addition to efficiently scavenging ambient nitrogen, Prochlorococcus strains are hypothesized to niche-partition the water column by utilizing different N sources. We thus studied the global mRNA expression profiles of these two Prochlorococcus strains on different N sources. The recent sequencing of a number of Prochlorococcus genomes has revealed that nearly half of Prochlorococcus genes are of unknown function. (cont.) Genetic methods such as reporter gene assays and tagged mutagenesis are critical tools for unveiling the function of these genes. As the basis for such approaches, another goal of this thesis was to find conditions by which interspecific conjugation with Escherichia coli could be used to transfer plasmid DNA into Prochlorococcus MIT9313. Following conjugation, E. coli were removed from the Prochlorococcus cultures by infection with E. coli phage T7. We applied these methods to show that an RSF1010-derived plasmid will replicate in Prochlorococcus MIT9313. When this plasmid was modified to contain green fluorescent protein (GFP) we detected its expression in Prochlorococcus by Western blot and cellular fluorescence. Further, we applied these conjugation methods to show that Tn5 will transpose in vivo in Prochlorococcus. Collectively, these methods provide a means to experimentally alter the expression of genes in the Prochlorococcus cell. by Andrew Carl Tolonen. Ph.D.

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Pope, Welkin Hazel. "Genes and structural proteins of the phage SYN5 of the marine cyanobacteria, Synechococcus." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/39190.

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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. Includes bibliographical references (p. 157-171). Bacteriophage have been proposed to be the most abundant organisms on the planet, at an estimated 10³¹ particles globally (Hendrix et al., 1999). The majority of bacteriophage isolates (96%) are double-stranded DNA tailed phages (Caudovirales). These phages possess a distinctive icosehedral head, with a protein tail structure protruding from a single vertex. This organelle determines host specificity and provides the mechanism of passage of the phage genome into the host cell. Phages infecting differing microbial hosts may have access to a global pool of genes, albeit at different levels. Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are numerically dominant photosynthetic cells in the large oligotrophic gyres of the open oceans, and contribute an estimated 30% to the oceanic photosynthetic budget. Cyanophages have been isolated which propagate on many strains of Synechococcus and Prochlorococcus. Cyanophages can effect community structure and succession through lytic infection of their hosts, and have implications in lateral gene transfer, mediated through lysogeny, mixed infections, pseudolysogeny, and transduction. (cont.) The broad host ranges (between genera) observed in some phages indicates that lateral gene transfer is not confined to cells of the same strain. These phage/host interactions begin by host recognition by the tail of the infecting phage. Few studies have examined the structural proteins of cyanophage, partially due to the lack of a robust protocol for the growth and purification of phage particles. Cyanophage Syn5 is a short-tailed phage isolated from the Sargasso Sea by Waterbury and Valois (1993) which infects Synechococcus strain WH8109. Methods of growing the host cells and the phage, and concentrating the phage by PEG precipitation were developed. These methods led to highly concentrated purified phage stocks, to titers of 1012 particles/ml. Preliminary characterization of the growth of Syn5 gave a burst size of approximately 30 phage/cell and a lytic period of approximately 10 hours when inoculated into exponentially growing host cells acclimated to a temperature of 26⁰C and a light intensity of 50[mu]E m⁻² s⁻¹. Isolation of the phage nucleic acid yielded dsDNA molecules of approximately 40kb. The Syn5 particles were comprised of twelve structural proteins, as determined by SDS-PAGE. (cont.) The most intense band on the gel was assigned to the capsid protein of Syn5 ([approx.] 35kDa). However, it was not possible to distinguish putative tail proteins via this method. Purified Syn5 particles were sent to the Pittsburgh Bacteriophage Institute for genome sequencing. The completed Syn5 genome was 46,214 bp long with a 237bp terminal repeat. Annotation of the completed Syn5 genome identified 61 putative ORFs, and revealed that Syn5 appeared closely related to the enteric phage T7 and cyanophages P-SSP7 and P60, as determined by gene similarity and synteny, although the genome was [approx.] 10kb longer than T7. Syn5 appeared to possess a more extensive DNA replisome that T7, containing copies of genes that encoded proteins of known T7 host co-factors, such as thioredoxin, utilized by the T7 DNAP. Several large ORFs were identified between the gene encoding the putative tail fiber and the gene encoding the putative terminase. These ORFs encoded proteins similar to some fibrous sequences within the NCBI non- redundant (nr) gene sequence database as of March, 2005; but had unknown functions within the phage. Unlike other recently sequenced cyanophages, SynS did not contain any photosynthetic genes. (cont.) The structural proteins of SynS, as visualized by SDS-PAGE, were characterized by mass-spectroscopy and N-terminal sequencing. This allowed the assignment of sequences to putative ORFs within the Syn5 genome. The Syn5 particle was comprised of eleven discreet protein chains of molecular weight 152kDa, 139kDa, 99kDa, 90kDa, 66kDa, 60kDa, 47kDa, 35kDa, 22kDa, 21kDa, and 16kDa. The identified proteins included the portal, capsid, two tail tube proteins, and three internal virion proteins. Each of the genes encoding these proteins were found in the same gene order in the Syn5 genome as the corresponding genes were ordered in the T7 genome. There were three unidentifiable proteins within the particle (66kDa, 47kDa, and 16kDa). These mapped to the area of the SynS genome between the gene encoding the putative tail fiber and the gene encoding the putative terminase. No minor capsid or decorative capsid proteins were detected. The copy numbers of the corresponding protein chains were similar to those known for T7, with the exception of the tail fiber, which was present at a number of three chains per particle in comparison to T7's eighteen per particle. (cont.) Polyclonal antibodies were raised against Syn5 particles. A Western blot with these antibodies showed that the tail fiber and the two unknown fibrous sequences were highly antigenic. This evidence implies that the unknown structures may act as host recognition proteins in addition to the tail fiber. Characterization of these novel proteins may provide insight to the host recognition abilities of cyanophages. An additional study was also carried out, investigating the high temperature limit of the growth of phage P22. The results revealed that the production of infectious particles was limited by the temperature sensitivity of the folding and assembly of the P22 tailspike protein. This work has been published and is included in the Appendix. by Welkin Hazel Pope. Ph.D.

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Stanley, Rachel H. R. "A determination of air-sea gas exchange and upper ocean biological production from five noble gasses and tritiugenic helium-3." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42282.

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Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007. Includes bibliographical references (p. 215-225). The five noble gases (helium, neon, argon, krypton, and xenon) are biologically and chemically inert, making them ideal oceanographic tracers. Additionally, the noble gases have a wide range of solubilities and molecular diffusivities, and thus respond differently to physical forcing. Tritium, an isotope of hydrogen, is useful in tandem with its daughter helium-3 as a tracer for water mass ages. In this thesis, a fourteen month time-series of the five noble gases, helium-3 and tritium was measured at the Bermuda Atlantic Time-series Study (BATS) site. The time-series of five noble gases was used to develop a parameterization of air-sea gas exchange for oligotrophic waters and wind speeds between 0 and 13 m s-1 that explicitly includes bubble processes and that constrains diffusive gas exchange to ± 6% and complete and partial air injection processes to ± 15%. Additionally, the parameterization is based on weeks to seasonal time scales, matching the time scales of many relevant biogeochemical cycles. The time-series of helium isotopes, tritium, argon, and oxygen was used to constrain upper ocean biological production. Specifically, the helium flux gauge technique was used to estimate new production, apparent oxygen utilization rates were used to quantify export production, and euphotic zone seasonal cycles of oxygen and argon were used to determine net community production. The concurrent use of these three methods allows examination of the relationship between the types of production and begins to address a number of apparent inconsistencies in the elemental budgets of carbon, oxygen, and nitrogen. by Rachel H.R. Stanley. Ph.D.

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Wilcox, Freeburg Eric D. "Exploring the link between otolith growth and function along the biological continuum in the context of ocean acidification." Thesis, University of Massachusetts Boston, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3622214.

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Oceans are acidifying as atmospheric CO2 is drawn down. This process, known as ocean acidification (OA), is well known and documented. Over the next 100 years, pH of the surface ocean is projected to decrease by up to 0.35 units. This CO2 draw down has a direct effect on dissolved inorganic carbon (DIC) balance in the ocean. OA is expected to impact calcifying organisms that rely on constituencies of the DIC system, specifically carbonate ion [CO32-]. It is clear that externally calcified structures, such as coral skeletons, bivalve shells, etc., will be significantly affected as pH, and consequently [CO32− ], of the oceans decline. What is unclear, however, is how these changes will impact internally calcified structures, such as earstones (otoliths) of teleost fish. This dissertation examines the impacts of OA on otolith mineralization in larval reef fish (Amphiprion clarkiiand A. frenatus ). This research included the development of a laboratory controller system for control of experimental aquaria pH through pCO2 dosing, exposure of larvae from hatch to settlement under various pCO2 treatments and evaluation of otolith structure and morphology across treatments within a single genus. No standard method for pH-stat CO2 dosing controllers existed prior to this study. Incorporating low-cost, flexible hardware allowed high precision and accuracy pH controllers to be designed and implemented. Following system stability studies, we found that our system performed at or beyond the level of control exhibited in the literature. Two species of clownfish, Amphiprion clarkii and A. frenatus, were exposed to different pCO2 conditions, reared to settlement and otoliths extracted and studied. I found that the sagittae (largest of the 3 otolith types) of both species exhibited circularity changes towards more oblong otoliths under increased pCO2. For A. clarkii, I found a significant negative relation between pCO 2 and lapilli otolith circularity, indicating a shift toward more circular lapilli under increased pCO2. Since lapilli are critical to gravisensing in teleosts these results explain my anecdotal observations that, at high pCO2, larvae exhibited lethargic, uncoordinated swim patterns. The core development of otoliths (sagittae, lapilli, and asterisci) from both species was analyzed using SEM imagery. Otolith images were scored by 6 independent readers for core development (poorly developed to well-developed). Otolith scores were regressed against aragonite saturation state (&ohm;Ar). Results showed significant and strong relations between &ohm;Ar and development score, indicating a shift toward protruding, unorganized crystal clusters within the core under high pH/low &ohm;Ar. This research is the first to comprehensively examine the impact of OA on the otolith system in larval fish. The research revealed direct impacts on otolith structure and morphology as well as mineralogy. These changes will directly impact survival of the larvae. It remains unknown whether the otolith system recovers post-settlement or whether the anecdotal observations on swimming behavior are directly related to otolith deformation. Future research will include exploration of these relations across genera as well as more deeply examine the recovery of the system and behavioral impacts of otolith deformation across life stages.

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Dissertations / Theses on the topic 'Biological oceanography'

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