The Arctic is a region undergoing unprecedented and unequivocal climate change. The seas of this extreme region form a major component of the oceanic thermohaline conveyor and natural carbon cycle. Using a combination of recent and historical datasets this study examines the distribution, diversity, photophysiology and primary productivity of phytoplankton in the Atlantic sector of the Arctic Ocean. CHEMTAX analysis reveals a diverse phytoplankton community structure in the Greenland Sea comprising six main phytoplankton groups. The influence of sea-ice and water column stratification are key factors in the presence or absence of groups such as haptophytes and prasinophytes. Group-specific differences are observed in spectral absorption and photophysiological parameters. However, the influence of environmental factors has a stronger influence than taxonomic composition on photophysiology. A clear division between the photoacclimatory response of algal communities beneath sea-ice and those of open-ocean stations is predominantly due to ‘E_k independent’ photoacclimation beneath sea-ice. This occurs due to the combined effect of sea-ice decreasing irradiance entering the water column and a positive correlation between P_m ^B and temperature. This variation in photophysiology is important for primary production models as a sensitivity analysis shows that errors in these parameters propagate to give the largest final errors in primary production values. The importance of other model parameters varies with the level of biomass in the water column and the presence or absence of sea ice. Accelerated ice-melt and an increase in open water due to climate change are likely to increase primary production in the Atlantic Arctic alongside an altered distribution of phytoplankton groups, with an increase in the importance of prasinophytes or haptophytes.

<p>Effective conservation and management of top predators requires a comprehensive understanding of their distributions and of the underlying biological and physical processes that affect these distributions. The Mid-Atlantic Bight shelf break system is a dynamic and productive region where at least 32 species of cetaceans have been recorded through various systematic and opportunistic marine mammal surveys from the 1970s through 2012. My dissertation characterizes the spatial distribution and habitat of cetaceans in the Mid-Atlantic Bight shelf break system by utilizing marine mammal line-transect survey data, synoptic multi-frequency active acoustic data, and fine-scale hydrographic data collected during the 2011 summer Atlantic Marine Assessment Program for Protected Species (AMAPPS) survey. Although studies describing cetacean habitat and distributions have been previously conducted in the Mid-Atlantic Bight, my research specifically focuses on the shelf break region to elucidate both the physical and biological processes that influence cetacean distribution patterns within this cetacean hotspot. </p><p>In Chapter One I review biologically important areas for cetaceans in the Atlantic waters of the United States. I describe the study area, the shelf break region of the Mid-Atlantic Bight, in terms of the general oceanography, productivity and biodiversity. According to recent habitat-based cetacean density models, the shelf break region is an area of high cetacean abundance and density, yet little research is directed at understanding the mechanisms that establish this region as a cetacean hotspot. </p><p>In Chapter Two I present the basic physical principles of sound in water and describe the methodology used to categorize opportunistically collected multi-frequency active acoustic data using frequency responses techniques. Frequency response classification methods are usually employed in conjunction with net-tow data, but the logistics of the 2011 AMAPPS survey did not allow for appropriate net-tow data to be collected. Biologically meaningful information can be extracted from acoustic scattering regions by comparing the frequency response curves of acoustic regions to theoretical curves of known scattering models. Using the five frequencies on the EK60 system (18, 38, 70, 120, and 200 kHz), three categories of scatterers were defined: fish-like (with swim bladder), nekton-like (e.g., euphausiids), and plankton-like (e.g., copepods). I also employed a multi-frequency acoustic categorization method using three frequencies (18, 38, and 120 kHz) that has been used in the Gulf of Maine and Georges Bank which is based the presence or absence of volume backscatter above a threshold. This method is more objective than the comparison of frequency response curves because it uses an established backscatter value for the threshold. By removing all data below the threshold, only strong scattering information is retained.</p><p>In Chapter Three I analyze the distribution of the categorized acoustic regions of interest during the daytime cross shelf transects. Over all transects, plankton-like acoustic regions of interest were detected most frequently, followed by fish-like acoustic regions and then nekton-like acoustic regions. Plankton-like detections were the only significantly different acoustic detections per kilometer, although nekton-like detections were only slightly not significant. Using the threshold categorization method by Jech and Michaels (2006) provides a more conservative and discrete detection of acoustic scatterers and allows me to retrieve backscatter values along transects in areas that have been categorized. This provides continuous data values that can be integrated at discrete spatial increments for wavelet analysis. Wavelet analysis indicates significant spatial scales of interest for fish-like and nekton-like acoustic backscatter range from one to four kilometers and vary among transects. </p><p>In Chapter Four I analyze the fine scale distribution of cetaceans in the shelf break system of the Mid-Atlantic Bight using corrected sightings per trackline region, classification trees, multidimensional scaling, and random forest analysis. I describe habitat for common dolphins, Risso’s dolphins and sperm whales. From the distribution of cetacean sightings, patterns of habitat start to emerge: within the shelf break region of the Mid-Atlantic Bight, common dolphins were sighted more prevalently over the shelf while sperm whales were more frequently found in the deep waters offshore and Risso’s dolphins were most prevalent at the shelf break. Multidimensional scaling presents clear environmental separation among common dolphins and Risso’s dolphins and sperm whales. The sperm whale random forest habitat model had the lowest misclassification error (0.30) and the Risso’s dolphin random forest habitat model had the greatest misclassification error (0.37). Shallow water depth (less than 148 meters) was the primary variable selected in the classification model for common dolphin habitat. Distance to surface density fronts and surface temperature fronts were the primary variables selected in the classification models to describe Risso’s dolphin habitat and sperm whale habitat respectively. When mapped back into geographic space, these three cetacean species occupy different fine-scale habitats within the dynamic Mid-Atlantic Bight shelf break system. </p><p>In Chapter Five I present a summary of the previous chapters and present potential analytical steps to address ecological questions pertaining the dynamic shelf break region. Taken together, the results of my dissertation demonstrate the use of opportunistically collected data in ecosystem studies; emphasize the need to incorporate middle trophic level data and oceanographic features into cetacean habitat models; and emphasize the importance of developing more mechanistic understanding of dynamic ecosystems.</p> / Dissertation

<p>Although there are many examples of microbial biogeography, few microbes have been studied at high taxonomic resolution over large spatial scales. As a result, the environmental and ecological processes that drive niche partitioning, diversity, composition, and activity of microbial taxa are often poorly understood. To address this gap, I examine the most abundant phytoplankton in the global ocean, Prochlorococcus sp., a marine cyanobacterium. Using amplicon libraries of the Prochlorococcus internal transcribed spacer (ITS) region and 23S rRNA gene as markers, I demonstrate several key differences between the two major high light (HL) clades of Prochlorococcus. First, by examining ITS amplicon libraries at high taxonomic resolution it is revealed that “sub-ecotype” clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Whereas unique combinations of environmental traits drive the distribution of the HL-I sub-ecotype clades, the HL-II sub-ecotype clades appear ecologically coherent. Second, using 23S rRNA and rDNA libraries I show that activity (rRNA) and abundance (rDNA) are highly correlated for Prochlorococcus across all sites and operational taxonomic units (OTUs) in the surface ocean, demonstrating a tight coupling between activity and abundance. Finally, I investigate the associations between Prochlorococcus and the rest of the microbial community in the North Pacific and find region-specific trends in both strength and sign. Associations with other microbes are strongest for HL-I in the temperate region and strongest for HL-II in the sub-tropical gyre. This dissertation clarifies the relative importance of the environment, geography, community, and taxonomy in terms of their role in creating complex assemblages of Prochlorococcus and helps improve our understanding of how marine microbial communities are assembled in situ.</p> / Dissertation

xx, 198 p. A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / "Bathymodiolus" childressi is a mixotrophic mussel from Gulf of Mexico cold seeps. There is no genetic differentiation of mussels among the seeps, suggesting wide dispersal of their larvae. This dissertation describes larval biology, ecology, and recruitment dynamics for "B." childressi. Cleavage is spiral at a rate of one per 3-9 hours, with blastula larvae hatching by 40 hours at 7-8 à à °C. At 12-14 à à °C, D-shell veligers developed by day 8 without being fed. Egg size and shell morphology indicate planktotrophy, but feeding was not observed. Embryos developed normally from 7-15 à à °C and 35-45 ppt. Although survival of larvae declined with temperature, some survived at 25 à à °C. Larval survivorship was similar at 35 and 45 ppt. Oxygen consumption increased from blastulae to trochophores and was higher for "B." childressi than for shallow-water mussel trochophores. Estimated energy content of "B." childressi eggs was greater than the energy content of shallow-water mussel eggs. An energetic model predicts that the eggs provide sufficient energy for "B." childressi trochophores to migrate into the euphotic zone. In fact, "B." childressi veligers were found in plankton tows of surface waters. The influence of recruitment on fine-scale distributions of adults at the Brine Pool cold seep was examined through manipulative field experiments. The "Bathymodiolus" childressi population at this site has a distinct bimodal size structure that shifts across an environmental gradient. New recruits of "B." childressi are abundant in the inner zone, where methane and oxygen are high and sulfide is low, leading to the inference that larvae settle preferentially there. Experiments were placed in the inner and outer zones and 2-m away from the bed. The number of larvae collected in traps did not differ among the three zones, nor did settlement density. Juveniles survived and grew in all zones, but more caged than uncaged juveniles survived. Mortality of uncaged juveniles was similar in all zones, suggesting that predation does not cause the bimodal distribution. These results suggest that the bi-modal distribution cannot be attributed to settlement preferences or juvenile mortality, but instead to migration or early post-settlement mortality. This dissertation includes my co-authored materials. / Adviser: Craig M. Young

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 159-168). / Thecosome pteropods are planktonic mollusks that form aragonite shells and that may experience increased dissolution and other adverse effects due to ocean acidification. This thesis focuses on assessing the possible biological effects of ocean acidification on the shells and locomotion of pteropods and examining the response of a local pteropod population to environmental change over time. I analyzed shell condition after exposing pteropods to elevated CO₂ as well as in natural populations to investigate the sensitivity of the shells of different species to aragonite saturation state ([omega][subscript A]). The pteropods (Limacina retroversa) from laboratory experiments showed the clearest pattern of shell dissolution in response to decreased [omega][subscript A], while wild populations either had non-significant regional trends in shell condition (Clio pyramidata) or variability in shell condition that did not match expectations due to regional variability in [omega][subscript A] (Limacina helicina). At locations with intermediate [omega][subscript A] (1.5-2.5) the variability seen in L. helicina shell condition might be affected by food availability more than tA. I examined sinking and swimming behaviors in the laboratory in order to investigate a possible fitness effect of ocean acidification on pteropods. The sinking rates of L. retroversa from elevated CO₂ treatments were slower in conjunction with worsened shell condition. These changes could increase their vulnerability to predators in the wild. Swimming ability was mostly unchanged by elevated CO₂ after experiments that were up to three weeks in duration. I used a long-term dataset of pteropods in the Gulf of Maine to directly test whether there has been a population effect of environmental change over the past several decades. I did not observe a population decline between 1977 and 2015, and L. retroversa abundance in the fall actually increased over the time series. Analysis of the habitat use of L. retroversa revealed seasonal associations with temperature, salinity, and bottom depths. The combination of laboratory experiments and field surveys helped to address gaps in knowledge about pteropod ecology and improve our understanding of the effects of ocean acidification on pteropods. / by Alexander Bergan. / Ph. D.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / "February 2008." / Includes bibliographical references (p. 133). / I build on the deterministic phytoplankton growth model of Sosik et al. by introducing process error, which simulates real variation in population growth and inaccuracies in the structure of the matrix model. Adding a stochastic component allows me to use maximum likelihood methods of parameter estimation. I lay out the method used to calculate parameter estimates, confidence intervals, and estimated population growth rates, then use a simplified three-stage model to test the efficacy of this method with simulated observations. I repeat similar tests with the full model based on Sosik et al., then test this model with a set of data from a laboratory culture whose population growth rate was independently determined. In general, the parameter estimates I obtain for simulated data are better the lower the levels of stochasticity. Despite large confidence intervals around some model parameter estimates, the estimated population growth rates have relatively small confidence intervals. The parameter estimates I obtained for the laboratory data fell in a region of the parameter space that in general contains parameter sets that are difficult to estimate, although the estimated population growth rate was close to the independently determined value. / by Lorraine Thomas. / S.M.

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.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and, the Woods Hole Oceanographic Institution), 2005. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / Despite the importance of microorganisms for global and engineering processes, currently lacking is a theoretical framework to describe how the structure of a microbial assemblage translates an environmental condition into a system-level response. Prerequisite to developing such a framework is an understanding of how microbial diversity is partitioned into functional groups of organisms. This thesis has explored the organization and dynamics of microbial diversity within coastal bacterioplankton using the genus Vibrio as a model system. Vibrios are ubiquitous marine bacteria, and include a variety of pathogens. Quantification of Vibrio environmental dynamics by cultivation- independent quantitative PCR and constant denaturant capillary electrophoresis (CDCE), suggests that sea surface temperature is a driving factor in the distribution and abundance of Vibrio populations and that groups of organisms with >98-99% 16S rRNA sequence similarity maintain similar responses to temperature-mediated environmental change. Fine-scale analysis of the genetic structure within one Vibrio population (>99% rRNA similarity to V. splendidus) reveals vast co-occurring genomic diversity. The average concentration of unique genome-types is observed to be 1000-fold lower than the total population size and individual genomes vary in gene content by as much as 1.1 Mb (the equivalent of -1,000 genes). It is proposed that competition between individual genome variants is a weak driver of population genetic structure while stochastic interactions in the water column promote genetic heterogeneity rendering much of the observed diversity in natural populations neutral or effectively neutral. / (cont.) Quantification of Vibrio diversity and dynamics is critical to understanding the global factors that determine the prevalence and proliferation of disease-causing strains and their potential contribution to ecosystem-level processes such as organic matter degradation and macronutrient cycling. In addition, an understanding of how diversity is organized in natural assemblages is an important step in the effort to predict the characteristics of microbial systems based upon their component populations. / by Janelle Renée Thompson. / Ph.D.

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. / The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity of available markers have allowed more complex and fine-scale questions to be asked at a variety of taxonomic levels. At the phylogenetic level, whole mitochondrial genome sequencing of two polychaetes (the deep-sea tubeworm Riftia pachyptila and the intertidal bamboo worm Clymenella torquata) supports the placement of leeches and oligochaetes within the polychaete radiation, in keeping with molecular evidence and morphological reinvestigations. This re-interpretation, first proposed by others, synonomizes "Annelida" and "Polychaeta", and lends further support to the inclusion of echiurids, siboglinids (previously called vestimentiferans) within annelids, and sipunculans as close allies. The complete mt-genome of C. torquata was then rapidly screened to obtain markers useful in short timescale population genetics. / (cont.) Two quickly evolving mitochondrial markers were sequenced from ten populations of C. torquata from the Bay of Fundy to New Jersey to investigate previous hypotheses that the Cape Cod, MA peninsula is a barrier to gene flow in the northwest Atlantic. A barrier to gene flow was found, but displaced south of Cape Cod, between Rhode Island and Long Island, NY. Imposed upon this pattern was a gradient in genetic diversity presumably due to previous glaciation, with northern populations exhibiting greatly reduced diversity relative to southern sites. These trends in C. torquata, combined with other recent short time scale population genetic research, highlight the lack of population genetics models relevant to marine benthic invertebrates. To this end, I constructed a model including a typical benthic invertebrate life cycle, and described the patterns of genetic differentiation at the juvenile and adult stages. Model analysis indicates that selection operating at the post- settlement stage may be extremely important in structuring genetic differentiation between populations and life stages. Further, it demonstrates how combined genetic analysis of sub-adult and adult samples can provide more information about population dynamics than either could alone. / by Robert M. Jennings. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 155-181). / This thesis describes the development and application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the "genome proxy" microarray, which targeted marine microbial genomes and genome fragments using sets of 70-mer oligonucleotide probes. In a natural community background, array signal was highly linearly correlated to target cell abundance (R² of 1.0), with a dynamic range from 10²-10⁶ cells/ml. Genotypes with >/=~80% average nucleotide identity to those targeted crosshybridized to target probesets but produced distinct, diagnostic patterns of hybridization. Chapter 3 describes the development an expanded array, targeting 268 microbial genotypes, and its use in profiling 57 samples from Monterey Bay. Comparison of array and pyrosequence data for three samples showed a strong linear correlation between target abundance using the two methods (R²=0.85- 0.91). Array profiles clustered into shallow versus deep, and the majority of targets showed depth-specific distributions consistent with previous observations. Although no correlation was observed to oceanographic season, bloom signatures were evident. Array-based insights into population structure suggested the existence of ecotypes among uncultured clades. Chapter 4 summarizes the work and discusses future directions. / by Virginia Rich. / Ph.D.