Over the last few decades, Integrated Multi-Trophic Aquaculture (IMTA) in South Africa has developed from early experimental designs to large scale, commercially operating farms. This was in response to uncertainty regarding food availability for stock (primarily kelp in the case of abalone farms) and a desire to recirculate water whilst reducing the environmental footprint of the abalone farms. The growing prevalence of IMTA as a commercially viable activity has brought about a need for an expansion of the knowledge pool regarding the physico-chemical processes at work in such systems. Of particular interest to researchers are mechanisms and dynamics of nutrient transfer between components of the system and how these could be manipulated to increase efficiency and reduce running cost of farms. This work was conducted to try and quantify some of the changes in some physical and chemical characteristics of the water stream on a large-scale IMTA farm cultivating seaweed of the genus Ulva (Ulva rigida) and the locally named perlemoen abalone (Haliotis midae) on the south west coast of South Africa (Viking Abalone Farm at Buffeljagsbaai, Western Cape, South Africa) (34.7550° S, 19.6154° E). Experiment one was a three-day experiment taking place in December of 2018, there was no particular reason for the choice of month, analyses of this nature are potentially useful on any given day of any given month as although the literature contains plenty of gaps, there is no single identifiable data gap sufficient to encourage the use of particular timeframes. The sampling regime involved single sample point testing of three modular clusters each operating a different rate of water recirculation (50%, 75% and 100%) with 50% recirculation being standard farm operation, 75% and 100% tested to gauge effect of increasing recirculation, 75% tested as a potential standard farm operation to reduce load on pumps and reduce volumes of water pumped in, 100% tested in case of emergency situation which requires farm to be isolated from the inbound water stream arriving from the immediate coastal water, ambient conditions were also tested for reference and comparison. Parameters tested were those which the farmers already tested periodically to gauge changes in water quality which may effect the abalone or seaweed, though slightly different methods were used for the testing of ammonia. On the farm the standard method is the Nesler photometric test (Lovibond photometer), whereas this research was conducted using a calibrated indophenol blue spectrophotometric technique (Modified Grasshoff, 1976). Results showed no statistically significant differences (Mood's Median Test, p>0.05) between the 50% and 75% recirculation cluster for temperature, pH, Total Ammonia Nitrogen (TAN) or Free Ammonia Nitrogen NH3 (FAN). At 100% recirculation, statistically significant differences (Mood's Median Test, p0.05) occurred for temperature. At 100% recirculation, TAN and FAN increased rapidly, though the commensurate rapid and considerable decrease in pH meant the FAN increase was not as high in magnitude as it would be at 4 a normal seawater pH of around 8.2. Abalone suffered no mortalities at 100% recirculation for three days and later reports from the farmers suggested no noticeable drop in growth rate that could be attributed to this test in the months following the experiment. From the regulatory perspective, the TAN levels breached WWF guideline maximum effluent concentrations for abalone aquaculture (600µM/l) only in the 100% recirculation cluster, and only then during three of the thirteen sampling runs. The TAN concentrations in 50% and 75% recirculation treatments were far below the WWF guideline maximum effluent concentration with maximum concentrations of 7.15 µM/l in 50% and 13.46 µM/l at 75%, the increase in maximum concentration was large but not egregious and resulted from a more pronounced build-up of ammonia as residence time of water in the cluster increases at 75% recirculation. Experiment two was an intensive 24-hour sampling run; the primary aim was to test the effectiveness of the seaweed biofilter in an Integrated Multi-Trophic Aquaculture (IMTA) farm culturing perlemoen abalone and a green macroalga. Parameters tested were temperature, pH, dissolved oxygen, salinity, TAN, nitrate and nitrite as these are relevant parameters for the farmer and the necessary equipment to test them was available. Samples were stored in a freezer for this experiment due to intensity of sampling regime, and spiked standards were prepared to check shifts in concentration of TAN, nitrate and nitrite that may have resulted from the freezing and thawing processes. Spike recoveries were good in the case of TAN (87%-98%) and nitrite (92%-96%), but random and widely dispersed in the case of nitrate. As such, nitrate and nitrite were removed from the analysis as nitrite values only really held value if taken in conjunction with nitrate values. Minimal and non-useful variation in salinity observations meant that salinity was also discounted from the analysis. Temperatures varied minimally between sampling points during the experiment, though they rose in all sampling points during daytime as would be expected. pH was higher in abalone inbound and Ulva effluent water compared to the abalone effluent water. Total ammonia nitrogen percentage removal across the seaweed biofilters ranged from 65%-85% with the mean and median at 73% and 71% respectively. Free ammonia nitrogen percentage removal across the seaweed biofilters ranged from 41%-80% with the mean and median removals at 63% and 66% respectively. A regression analysis demonstrates a strong positive linear relationship between TAN removal and TAN load to the seaweed biofilter (r2= 0.90). Principal component analysis revealed a strong negative correlation between FAN removal and pH, as pH increased across the seaweed biofilters, the level of FAN removal decreased. This suggests that the perceived benefit of increasing pH in seaweed biofilters during the day-time may have some negative repercussions.

Ecopath with Ecosim is a modeling software that allows the creation of mass-balanced models of the trophic flows of an ecosystem to explore the past and present impacts of fishing and environmental change on the trophic flows of a given food web. Currently, Algoa Bay supports the world’s largest breeding colony of endangered African penguins (Spheniscus demersus). The breeding success of African penguins is largely dependent on the availability of their food, mainly anchovy (Engraulis encrasicolus) and sardine (Sardinops sagax). African penguins breed year-round however, peak breeding season begins during the summer months (January to March) in Algoa Bay, when penguins begin building up fat reserves and laying eggs. In order to investigate the interaction between the small pelagic fish and penguin population, mass-balanced trophic models of the Algoa Bay ecosystem were constructed using the software Ecopath with Ecosim. Input parameters were derived from data compiled from published literature and survey data collected by DAFF (Department of Agriculture, Forestry, and Fisheries; formerly Marine and Coastal Management, MCM) and SAEON (the South African Environmental Observation Network). Two seasonal models were created to depict the summer (January to March) and winter (June to August) seasons from 2010-2014. Additionally, two seasonal models were created to represent a marine protected area where all fishery catch was set to zero. These static marine protected area models were created to investigate how the removal of fishery predation impacts the trophic structure of the Algoa Bay ecosystem by comparing ecotrophic efficiency values to those of the fished system. Two Ecosim simulations were used in fishery sensitivity analyses. The first, by setting all fishery catches to zero over a period of 30 years for each season to investigate the sensitivity of trophic groups to the removal of fishing pressure. The second, by setting fishery mortalities of anchovy and sardine to levels reported in the west coast (also over a period of 30 years) to investigate the sensitivity of trophic groups to an increase in small pelagic fishing pressure. Seasonal differences were observed with an increase in primary production and zooplankton biomass in the summer season compared to the winter season. The increase in plankton biomass resulted in an approximately 3x greater summer total system throughput, and total net primary production. Transfer efficiencies were higher than the average of 10% for aquatic ecosystems at trophic levels II and III with the seasonal averages being 17% and 19% respectively. The greatest seasonal change in modeled biomass occurred at trophic level III with summer biomass being 72% larger, indicating that small pelagic fishes benefit the most from the increase in summer plankton biomass. Linefish ecotrophic efficiency values were smaller in the marine protected area models in the summer and winter respectively, reflecting the reduced mortality on linefish under MPA conditions. Although the removal of fisheries resulted in an overall drop in predation pressure of 27% in the static MPA models, predation by other predatory trophic groups in the bay increased by 13% as a result of their subsequent biomass increases after the removal of fishery predation. Ecosim results showed the greatest change in biomass occurred in linefish which increased in both seasons when fishery catch was set to zero. The increase in linefish biomass can be attributed to the removal of fishery pressure on themselves and their prey, and may be an indication that linefish are overexploited in the bay. As a result of the biomass increase of some predator groups, some lower trophic level fish groups decreased despite the removal of fishery pressure. The results of the marine protected area analyses indicate that fisheries do not necessarily only have direct impacts on a target species as food-webs can have moderating effects. When fishing mortalities for sardine and anchovy were increased to west coast values, African penguins had the largest decrease in modeled biomass followed by other seabirds. Although, the observed decrease in modeled biomass of African penguins over the 30-year period does not fall within IUCN criteria for major concern, African penguins are already listed as endangered. An added decline of 10% on the largest breeding colony could have major implications on the future of the species. This study was a preliminary attempt at constructing mass-balanced trophic models of the Algoa Bay ecosystem, highlighting seasonal differences while investigating the possible impact of implementing a marine protected area in the bay and the sensitivity of trophic groups to fishing. Future research is needed to improve the more uncertain model parameters; however, these models are a good base for future work and the application of spatialized modeling of the bay using EcoSpace

Seasonal phytoplankton blooms in the Benguela Upwelling System (BUS) play a crucial role in ecosystem services and driving climate change through air-sea gas exchanges. Upwelling systems are particularly are sensitive to effects of climate change including the transport of nutrients, which influence the composition of phytoplankton communities. This is important because species composition affects a number of key processes that have significant climate feedbacks. This study uses historical long-term in situ data (at 10 and 70 NM stations) as well as OC-CCI satellite ocean colour data to investigate seasonal phytoplankton bloom phenology and community structure of diatoms, dinoflagellates and coccolithophores in the northern BUS. The seasonal cycle of satellite chlorophyll was used to determine the timing of bloom initiation at inshore and offshore boxes that overlapped the in situ stations. An ocean colour algorithm to detect coccolithophore presence and absence was used to determine the inshore-offshore seasonal cycle of coccolithophores. Results indicate a gradual decrease in chlorophyll concentration further offshore as well as high intra-seasonal, inter-annual and spatial variability. Offshore blooms initiate later and last longer than inshore blooms which have a higher magnitude. Diatoms are dominant over dinoflagellates and coccolithophores throughout the northern BUS, with higher concentrations observed at the inshore station (10 NM) for all three phytoplankton groups. However, satellite results show a higher presence of coccolithophores in the offshore region during spring and summer that is associated with periods of strong stratification. This study provides a better understanding of the characteristics of the phytoplankton seasonal cycle in the northern BUS which is useful for detecting trends and possible change associated with climate change forcing in response to global warming.

This dissertation is about the long-distance navigators who constructed a global marine world as agents of the sixteenth-century Spanish maritime empire. The hard-won pragmatic and empirical expertise on which they relied developed in an uneasy tension with the priorities of the bureaucracy centered at the Casa de la Contratación in Seville. In the Atlantic, bureaucratic standardization driven by the Casa made commercial ocean travel increasingly routine, while exploratory sailors, particularly in the Pacific, continued to apply their expertise in unknown and unpredictable waters. The quotidian and the pragmatic defined these long-distance mariners’ relationship to their environment. They organized space into networks of knowable pathways that connected places identified by names and markers that communicated the sailors’ experience to future navigators; they interpreted local conditions based on inferences from distant stimuli and ocean-scale systems; and they introduced their natural and human surroundings to metropolitan and colonial scholars and administrators. The resources and instruments developed by the Casa informed these practices, but voyages of discovery always remained outside of direct institutional control from Seville. This relationship—between the local, individual, and contingent on the one hand and the universal, bureaucratic, and synthetic on the other—not only defined the dynamics of intellectual authority governing scientific endeavors under the Spanish monarchy, but also shaped strategies for projecting imperial claims across areas of uneven and limited physical control, whether marine or terrestrial. Reevaluating the balance between marine and terrestrial territorial claims recasts the Americas as a waypoint into the Pacific and beyond for the globally-aware westward gaze of Spanish imperial ambition. More fundamentally, it highlights the multicentric and networked arrangement of power in the early modern period by refocusing our attention on those islands, whether literal or figurative, of physical Spanish presence surrounded by spaces of hypothetical control. The Spanish empire’s maritime orientation during the sixteenth century developed the intellectual, political, and institutional strategies to balance and resolve these tensions between embodied and archival knowledges, local contingencies and universal frameworks that defined the distribution of power under the Spanish monarchy. / text

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 1996. / Includes bibliographical references (leaves 69-71). / by Erik Alfred Burian. / S.M.

The Salish Sea is a ecologically important coastal region located on the southwest part of British Columbia. Optical measurements were taken using a set of hyperspectral radiometers, the SAS Solar Tracker developed by Satlantic. This sensor is installed on the Queen of Oak Bay ferry, that runs between Nanaimo and Vancouver, as part of the Ferry Ocean Colour Observation Systems (FOCOS) project. We developed a computer program to process the raw sensor data and generate remote sensing reflectance (Rrs) values. This performs similar functions to Prosoft, Satlantic’s own software to process the data. However, we added new features such as an additional preprocessing step to filter the data based on longitude, and new meteorological flag testing and wind speed calculations. The system was tested using Pearson correlation to compare our output with the output from Satlantic Prosoft. Testing helped us identify a few issues, such as adding longitude flags to remove data at the start and end of the trip where the sensor could produce inaccurate results if aiming at land instead of water. Another issue was where the SAS Solar Tracker does not update its pointing angle fast enough when the ferry makes sharp turns and could result in inaccurate data. / Graduate

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Coastal and estuarine environments experience large variability and rapid shifts in pCO₂ levels. Elevated pCO², or ocean acidification, often negatively affects early life stages of calcifying marine invertebrates, including bivalves, but it is unclear which developmental stage is most sensitive. I hypothesized that initial calcification is a critical stage during which high pCO₂ exposure has severe effects on larval growth and development of bay scallop (Argopecten irradians). Using five experiments varying the timing of exposure of embryonic and larval bay scallops to high CO₂, this thesis identifies two distinct stages of development during which exposure to high CO₂/low pH causes different effects on bay scallop larvae. I show that any exposure to high CO₂ consistently reduces survival of bay scallop larvae. I also show that high CO₂ exposure during initial calcification (12-24 h post-fertilization) results in significantly smaller shells, relative to ambient conditions, and this size decrease persists through the first week of development. High CO₂ exposure at 2-12 h post-fertilization (pre-calcification), does not impact shell size, suggesting that the CO₂ impact on size is a consequence of water chemistry during calcification. However, high CO₂ exposure prior to shell formation (2-12 h post-fertilization) causes a high incidence of larval shell deformity, regardless of CO₂ conditions during initial calcification. This impact does not occur in response to high CO₂ exposure after the 2-12 h period. The observations of two critical stages in early development has implications for both field and hatchery populations. If field populations were able to time their spawning to occur during the night, larvae would undergo initial calcification during the daytime, when CO₂ conditions are more favorable, resulting in larger veliger larvae. Hatcheries could invest minimal resources to monitor and modify water chemistry only during the first day of development to ensure larva are exposed to favorable conditions during that critical period. / by Meredith Megan White. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / 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 (pages 169-182). / Protists play important roles in grazing and nutrient recycling, but quantifying these roles has been hindered by difficulties in collecting, culturing, and observing these often-delicate cells. During long-term deployments at the Martha's Vineyard Coastal Observatory (MVCO) (Massachusetts, USA), Imaging FlowCytobot (IFCB) made it possible to study live cells in situ without the need to culture or preserve. IFCB records images of cells with chlorophyll fluorescence above a trigger threshold, so taxonomically resolved analysis of protists is limited to mixotrophs and herbivores, which have eaten recently. To overcome this limitation, I coupled a broad-application 'live cell' fluorescent stain with a modified IFCB so that protists which do not contain chlorophyll (such as consumers of unpigmented bacteria and other heterotrophs) can also be recorded. Staining IFCB (IFCB-S) revealed higher abundances of grazers than the original IFCB, as well as some cell types not previously detected. To analyze a 10-year time series of herbivorous ciliates at MVCO and address broad patterns of seasonality of major ciliate classes and their components, I employed a statistical model that estimates a seasonal density pattern and simultaneously accounts for and separates any annual-scale effects. I describe the seasonality of three functional groups: a phototrophic ciliate, a mixotroph, and a group of strict heterotrophs, and comment on potential drivers of these patterns. DNA sequencing has also contributed to the study of protist communities, providing new insight into diversity, predator-prey interactions, and discrepancies between morphologically defined species and genotype. To explore how well IFCB images can be used to detect seasonal community change of the class Spirotrichea, an important and numerous group, I used high-throughput sequencing (HTS), which does not discriminate between chlorophyll-containing cells and the rest of the community. I report on species and genera of ciliates for which morphotype and genotype displayed high congruency. In comparing how well temporal aspects of genotypes and morphotypes correspond, I found that HTS was critical to detect and identify certain ciliates occupying a niche associated with warmer temperatures. I further showed that when these types of analyses are combined with IFCB results, they can provide hypotheses about food preferences. / by Emily Fay Brownlee. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 131-143). / Coral reefs are biodiverse ecosystems that are at risk of degradation as a result of environmental changes. Reefs are constantly in a state of flux: the resident species assemblages vary considerably in space and time. However, the drivers of this variability are poorly understood. Tracking these changes and studying how coral reefs respond to natural and anthropogenic disturbance can be challenging and costly, particularly for reefs that are located in remote areas. Because many reef animals produce and use sound, recording the ambient soundscape of a reef might be one way to efficiently study these habitats from afar. In this thesis, I develop and apply a suite of acoustics-based tools to characterize the biological and anthropogenic acoustic activity that largely comprises marine soundscapes. First, I investigate links between reef fauna and reef-specific acoustic signatures on coral reefs located in the U.S. Virgin Islands. Second, I compare those findings to a more expansive study that I conducted in Maui, Hawaii, in which the drivers of bioacoustic differences among reefs are explored. Third, I investigate the distances over which sounds of biological origin may travel away from the reef and consider the range within which these acoustic cues might be usable by pelagic larvae in search of a suitable adult habitat. Fourth, I assess the extent to which the presence of vessel noise in shallow-water habitats changes the ambient soundscape. Finally, I present the results of a modeling exercise that questions how ocean noise levels might change over the next two decades as a result of major projected increases in the number and size of and distance traveled by commercial ships. The acoustics-based tools presented here help provide insight into ecosystem function and the extent of human activity in a given habitat. Additionally, these tools can be used to inform an effective regulatory regime to improve coral reef ecosystem management. / by Maxwell Bernard Kaplan. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 113-127). / White sharks (Carcharodon carcharias) are highly migratory, ecologically important, vulnerable, and understudied marine predators. Ecogeochemistry, which takes advantage of natural variations in chemical signatures recorded in body tissues, can help determine lifetime movement, age, and ontogenetic diet history in difficult to study species. Shark vertebrae are constructed of distinct layers of tissue laid down sequentially over an individual's lifetime and may preserve a chemical record of environmental exposure. In this thesis, I investigate the ecology of the understudied northwest Atlantic (NWA) white shark population by applying several ecogeochemistry techniques to their vertebrae. I generate the first radiocarbon ([delta]¹⁴C) age estimates for adult white sharks, dramatically extending the maximum age and longevity compared to earlier age studies. [delta]¹⁴C results also verify a lack of reworking of vertebral material and hint at possible sexual dimorphism in growth rates. Using amino acid and bulk stable isotope analyses, I show that individual sharks have marked variation in feeding and movement, and that pinnipeds do not constitute a large portion of their diet. Finally, I explore the utility of elemental chemistry to retrospectively infer movement. This work provides an important informational baseline for future NWA white shark ecological studies and conservation and management efforts. / by Li Ling Hamady. / Ph. D.