The removal of marine species through fishing has impacted marine ecosystems for thousands of years. The pressure of exploitation on marine ecosystems has now reached a point at which there is serious concern over ecosystem well-being on a global scale. There has, therefore, been a global move towards an ecosystem approach to fisheries management. The objective of this study was to develop a decision tree framework to assess the status of exploited marine ecosystems, which could be successfully applied to numerous ecosystems and guide decision support under changing conditions. This work was based on that of the IndiSeas project, which makes use of indicators designed to detect the impacts of fishing on marine ecosystem around the world. A suite of indicators, selected from those utilised in the IndiSeas project, was divided into ecological and fishing pressure indicators. Ecosystem specific suites of environmental indicators were also included, allowing the framework to ascertain the impacts of environmental variability on ecosystem components. This is an important addition as currently many assessments of the impacts of fisheries do not account for the influence of the environment. The framework was developed for the Southern Benguela ecosystem and then applied, with minor adjustments to account for ecosystem-specific characteristics, to the South Catalan Sea and North Sea. Indicator time series were analysed making use of linear regressions, resulting in the assignment of a score between one and five, depending on the direction and significance of trends. Data series were divided into distinct periods based on known environmental changes or shifts within ecosystems. Careful consideration was given as to whether fishing and environmental indicator trends could explain the observed trends in ecological indicators. A method of score adjustment was then developed to account for the impacts of both fishing and environmental variability on ecological indicators. Correlations were conducted to detect potential redundancies of ecological indicators and weightings were applied to decrease the contribution of correlated indicators to overall ecosystem trends. However, as correlations differed between indicators and amongst ecosystems, it was necessary to adjust the applied weightings for individual ecosystems. Results for the Southern Benguela classified the ecosystem as neither improving nor deteriorating during Period 1 (1978-1993) and Period 2 (1994-2003). During Period 3 (2004-2010) the ecosystem was classified as possibly improving. The South Catalan Sea was classified as possibly deteriorating during Period 1 (1978-1990) and neither improving nor deteriorating during Period 2 (1991-2010). The North Sea ecosystem was classified as neither improving nor deteriorating during Period 1 (1983-1992). During the second (1993-2003) and third (2004-2010) periods the ecosystem was categorised as possibly improving. When assessing fisheries impacts at an ecosystem scale there are typically high levels of uncertainty. However, this thesisoncluded that the development of a scoring and weighting system, alongside the addition of environmental drivers and the inclusion of expert knowledge throughout the applications of this framework, has allowed the developed decision tree framework to successfully categorise the three ecosystems. It is anticipated that the knowledge that this framework will add to current methods of generating advice for fisheries management will aid future decision support within these ecosystems.

Consortium for International Earth Science Information Network (CIESIN) initiated a series of nine human dimensions of global change pilot projects in 1991, to better understand how physical, biological, and social scientists must interact in order to address problems of importance to decision -makers. There is also a need to develop methodologies for merging data sets which differ on spatial and temporal scales, and indeed, to ascertain whether or not data are generally available to address specific, highly complex earth and social science. Because there has been virtually no research on the use of remotely sensed data in the social sciences of global change, this is a component of each pilot project. Pilot projects need to show how the results would be transferred to decision makers. All these elements of the pilots are to be used to inform the design of the CIESIN Data and Research Center. One of the CIESIN human dimensions of global change pilot projects is situated on the north coast of the Dominican Republic in Buen Hombre.

This PhD thesis provides an analysis of how an adaptive governance approach can be applied to address existing and emerging challenges in global governance with a focus on marine, wild-capture fisheries. All the papers share a coupled social-ecological framing while providing diverse but complementary perspectives. Paper I provides a lens through which it is possible understand the types of interactions that link social and ecological components of fisheries systems at the global scale. The key result of this paper was the development of a marine social-ecological framework to guide future modelling and scenario analysis. Paper II describes the process of emergence and spread of new ideas in marine governance using Marine Spatial Planning as an illustrative case study. The study shows how governance innovations may contribute to resolving the mismatches between the scale of ecological processes and the scale of governance of ecosystems. A key finding of the paper is the identification and explanation of the mechanisms by which informal networks of actors are able to influence the emergence and spread of new governance forms from the local to the global scale. Paper III focuses on governance of ocean areas beyond national jurisdiction. The key finding from this paper is the urgent need for existing and emerging governance institutions to build capacity for responding to the challenges facing governance of marine fisheries. These challenges arise from unexpected shifts in markets, technology and society. Paper IV develops a set of four imaginative but plausible ‘radical’ futures for global fisheries drawing on trends compiled from a diverse evidence base. The four resulting narratives aim to act as lenses for engaging debate and deeper reflection on how non-linear changes in technology and society might radically shift the operating context and core assumptions of fisheries governance in the future. These papers make a novel contribution to Sustainability Science through their focus on 1) the conditions for, and mechanisms of emergence of diverse and divergent governance forms, 2) the role of agency in complex actor settings, 3) the need for governance institutions to not only deal with, but also be able to anticipate surprise, and 4) the development of scenarios of marine social-ecological futures using a creative and rigorous narrative approach. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

Bactérias quitinolíticas desenvolvem papel fundamental no ciclo de nutrientes através da degradação da quitina no ecossistema marinho. A hidrólise da quitina é realizada por quitinases, as quais podem ser utilizadas em processos biotecnológicos. O estudo teve como objetivo avaliar as condições ótimas de cultivo de bactérias quitinolíticas selecionadas do gênero Aeromonas e a degradação de quitina durante 96 horas de cultivo. Além disso, caracterizá-las pelo sequenciamento total do gene 16S rRNA e por MLSA. O estudo mostrou que os isolados representam duas espécies do gênero Aeromonas. Os isolados comportaram-se de diferentes maneiras em relação às condições de cultivo pré-determindas. Os halos de hidrólise de quitina não estão relacionados à atividade enzimática ou aos produtos de hidrólise de quitina quantificados. As maiores atividades de quitobiosidases e endoquitinases foram observadas em 24 horas e de N-acetil-glicosaminidases em 96 horas. Os perfis enzimáticos diferem entre os isolados e ao longo das 96 horas de cultivo mostrando diversidade enzimática. / Chitinolytic bacteria have key role in nutrient cycling through the chitin degradation in the marine ecosystem. The hydrolysis of chitin is performed by chitinases, which can be used in biotechnological processes. The study aimed to evaluate the optimal conditions for cultivation of selected chitinolytic bacteria of the Aeromonas genus and the degradation of chitin during 96 hours of culture. Moreover, characterize them by 16S rRNA gene full sequencing and MLSA. The study showed that the isolates represent two species of the Aeromonas genus. The isolates had different behavior in relation under conditions pre-determined. The halos of chitin hydrolysis were not related to enzymatic activity or to their products of chitin hydrolysis quantified. The hightest activities of chitobiosidases and endochitinases were observed in 24 hours and the N-acetyl-glicosaminidases in 96 hours. The enzyme profiles differ between isolates and during 96 hours of cultivation showing diversity enzyme.

The potential for life to control its environment was first suggested by Lovelock (1972). Charlson et al (1987) proposed a role for marine planktonic ecosystems in global climate regulation via the production and ventilation to the atmosphere of dimethylsulphide (DMS), a by-product of phytoplankton metabolism. Once in the atmosphere DMS contributes to the formation of cloud condensation nuclei, and increases the amount and brightness of cloud. This affects the albedo of the planet, reflecting more incident sunlight back into space, and cooling the earth. In common with many other 'hypotheses' regarding complex adaptive systems, the hypothesis proposed by Charlson et al (1987) is not experimentally testable. The production and ventilation to the atmosphere of DMS is the result of complex interactions between biological, chemical and physical processes. Consequently, increasing use is being made of mathematical models that simulate these processes to advance understanding of it (Archer et al. 2002). This study examines one of the fundamental mechanisms proposed by the Charlson et al (1987) hypothesis, that increasing global temperatures will lead to increased ventilation of DMS from the ocean to the atmosphere. The study develops one-dimensional biogeochemical models of DMS production by upper ocean ecosystems, based on the model proposed by Gabric et al. (1993b). The models are examined to elucidate their fundamental mathematical properties, and are subjected to sensitivity analysis to identify important processes and parameters. These investigations identify a simpler model that can reproduce the predictions of the Gabric et al. (1993b) model. Predictions derived from model simulations forced by climatologies of measured physical data are compared to a global database of measurements of sea surface DMS concentrations, and to observed depth profiles of DMS in the upper ocean. These comparisons confirm that all models are in good qualitative agreement with measured data. The fifteen global climate prediction models currently in use around the globe all predict substantial warming effects from the ventilation of anthropogenic carbon dioxide to the atmosphere. A simplified DMS model is calibrated to climatologies of Antarctic chlorophyll and DMS data and reproduces the data with great precision. The calibrated model is applied in global warming scenarios to 'test' the efficacy of the mechanism proposed by the Charlson et al (1987) hypothesis. This simulation provides evidence that the response predicted by the hypothesis is indeed feasible, and that substantial increases (up to 45%) in the ventilation of DMS to the atmosphere could be possible in some circumstances. The results of the modelling study provide impetus for further examination of field data. If couplings between marine biota and atmosphere are feasible, then they may be operating contemporarily, and may be detectable. Atmospheric DMS is oxidised to form aerosols (Miller et al. 2002) that influence the aerosol optical depth of the atmosphere. Archives of remote sensed ocean chlorophyll a concentration and aerosol optical depth are examined for evidence of the biologically mediated couplings. A clear coupling between aeolian dust and marine phytoplankton is evident from this analysis, suggesting that the deposition of dust from the atmosphere is a major factor controlling phytoplankton growth in many parts of the ocean. A second coupling between marine phytoplankton and atmospheric aerosols is also detected. This coupling is apparently not related to dust and is symmetrical about the equator, despite the substantial differences in the atmospheres and oceans of each hemisphere. It is speculated that this coupling may reflect the influence of the ventilation of DMS produced by marine phytoplankton on the atmosphere. This thesis provides new evidence supporting the important role of marine ecosystems in global climate regulation by the production of DMS. This evidence is principally obtained from a biogeochemical modelling approach, but is supported by analyses of empirical data. The concordance of results obtained from different approaches suggests that the contribution of marine ecosystems to global climate regulation is real, important and currently active.

As human activity along coastlines increase, degradation and destruction of coastal marine ecosystems around the globe will increase at an alarming rate. In an effort to mitigate degradation and destruction of coastal marine ecosystems, artificial reefs have been used in restoration and enhancement projects. As artificial reefs are the main method of restoring diversity to a degraded area, it is important to know the mechanisms that drive marine community assembly and diversity on those reefs. Understanding community assembly patterns of foundational species, in particular, may provide insight to community assembly patterns at higher trophic levels. Subtidal macroalgae are commonly seen as foundational species in marine environments and both deterministic and stochastic processes play a role in their assembly. Environmental gradients, which are deterministic processes, play a significant role in structuring subtidal macroalgae communities. Depth, which is negatively correlated with light, is the main driver structuring subtidal macroalgal communities, however, other gradients such as water flow, and distance to a propagule source also impact their assembly. This study sought to determine which environmental gradients play a prominent role in subtidal macroalgal community assembly. To study subtidal macroalgal community assembly, 92 artificial reef units called Reef Balls were deployed east of the Ogden Point Breakwater in Victoria, BC in June 2009. Two years passed to allow for macroalgal growth and early successional processes to occur prior to sampling the communities on thirty Reef Balls via underwater collection in July 2011. Algae were sorted by genus and dry weight was measured. To determine effects of environmental gradients on community assembly light, depth, water flow, distance to the nearest Reef Ball and distance to the breakwater were measured at each Reef Ball. A redundancy analysis revealed that depth was the most significant environmental gradient shaping algae communities and had the greatest effect on upper canopy algae. Spatial plots reveal a depth and coastline zonation of algae genera comprising the canopy. While depth was found to significantly structure algae genera found in the canopy, there was a high degree of unexplained variation in the model. This suggests that unmeasured variables such as colonization and priority effects may be driving algal community structure in the lower canopy. Differences in community structure between upper and lower canopy reveal that multiple mechanisms are responsible for shaping subtidal algal communities. Further study is required to determine the importance of stochastic colonization events and priority effects. / Graduate / 0329 / vmucciar@uvic.ca

As human activity along coastlines increase, degradation and destruction of coastal marine ecosystems around the globe will increase at an alarming rate. In an effort to mitigate degradation and destruction of coastal marine ecosystems, artificial reefs have been used in restoration and enhancement projects. As artificial reefs are the main method of restoring diversity to a degraded area, it is important to know the mechanisms that drive marine community assembly and diversity on those reefs. Understanding community assembly patterns of foundational species, in particular, may provide insight to community assembly patterns at higher trophic levels. Subtidal macroalgae are commonly seen as foundational species in marine environments and both deterministic and stochastic processes play a role in their assembly. Environmental gradients, which are deterministic processes, play a significant role in structuring subtidal macroalgae communities. Depth, which is negatively correlated with light, is the main driver structuring subtidal macroalgal communities, however, other gradients such as water flow, and distance to a propagule source also impact their assembly. This study sought to determine which environmental gradients play a prominent role in subtidal macroalgal community assembly. To study subtidal macroalgal community assembly, 92 artificial reef units called Reef Balls were deployed east of the Ogden Point Breakwater in Victoria, BC in June 2009. Two years passed to allow for macroalgal growth and early successional processes to occur prior to sampling the communities on thirty Reef Balls via underwater collection in July 2011. Algae were sorted by genus and dry weight was measured. To determine effects of environmental gradients on community assembly light, depth, water flow, distance to the nearest Reef Ball and distance to the breakwater were measured at each Reef Ball. A redundancy analysis revealed that depth was the most significant environmental gradient shaping algae communities and had the greatest effect on upper canopy algae. Spatial plots reveal a depth and coastline zonation of algae genera comprising the canopy. While depth was found to significantly structure algae genera found in the canopy, there was a high degree of unexplained variation in the model. This suggests that unmeasured variables such as colonization and priority effects may be driving algal community structure in the lower canopy. Differences in community structure between upper and lower canopy reveal that multiple mechanisms are responsible for shaping subtidal algal communities. Further study is required to determine the importance of stochastic colonization events and priority effects. / Graduate / 0329 / vmucciar@uvic.ca

Bactérias quitinolíticas desenvolvem papel fundamental no ciclo de nutrientes através da degradação da quitina no ecossistema marinho. A hidrólise da quitina é realizada por quitinases, as quais podem ser utilizadas em processos biotecnológicos. O estudo teve como objetivo avaliar as condições ótimas de cultivo de bactérias quitinolíticas selecionadas do gênero Aeromonas e a degradação de quitina durante 96 horas de cultivo. Além disso, caracterizá-las pelo sequenciamento total do gene 16S rRNA e por MLSA. O estudo mostrou que os isolados representam duas espécies do gênero Aeromonas. Os isolados comportaram-se de diferentes maneiras em relação às condições de cultivo pré-determindas. Os halos de hidrólise de quitina não estão relacionados à atividade enzimática ou aos produtos de hidrólise de quitina quantificados. As maiores atividades de quitobiosidases e endoquitinases foram observadas em 24 horas e de N-acetil-glicosaminidases em 96 horas. Os perfis enzimáticos diferem entre os isolados e ao longo das 96 horas de cultivo mostrando diversidade enzimática. / Chitinolytic bacteria have key role in nutrient cycling through the chitin degradation in the marine ecosystem. The hydrolysis of chitin is performed by chitinases, which can be used in biotechnological processes. The study aimed to evaluate the optimal conditions for cultivation of selected chitinolytic bacteria of the Aeromonas genus and the degradation of chitin during 96 hours of culture. Moreover, characterize them by 16S rRNA gene full sequencing and MLSA. The study showed that the isolates represent two species of the Aeromonas genus. The isolates had different behavior in relation under conditions pre-determined. The halos of chitin hydrolysis were not related to enzymatic activity or to their products of chitin hydrolysis quantified. The hightest activities of chitobiosidases and endochitinases were observed in 24 hours and the N-acetyl-glicosaminidases in 96 hours. The enzyme profiles differ between isolates and during 96 hours of cultivation showing diversity enzyme.

We report a 40 year record of eutrophication and hypoxia on an estuarine ecosystem and its recovery from hypereutrophication. After decades of high inorganic nutrient concentrations and recurring anoxia and hypoxia, we observe a paradoxical increase in chlorophyll-a concentrations with decreasing nutrient inputs. We hypothesise that algal growth was inhibited due to hypereutrophication, either by elevated ammonium concentrations, severe hypoxia or the production of harmful substances in such a reduced environment. We study the dynamics of a simple but realistic mathematical model, incorporating the assumption of algal growth inhibition. It shows a high algal biomass, net oxygen production equilibrium with low ammonia inputs, and a low algal biomass, net oxygen consumption equilibrium with high ammonia inputs. At intermediate ammonia inputs it displays two alternative stable states. Although not intentional, the numerical output of this model corresponds to observations, giving extra support for assumption of algal growth inhibition. Due to potential algal growth inhibition, the recovery of hypereutrophied systems towards a classical eutrophied state, will need reduction of waste loads below certain thresholds and will be accompanied by large fluctuations in oxygen concentrations. We conclude that also flow-through systems, heavily influenced by external forcings which partly mask internal system dynamics, can display multiple stable states.

<p>The timing of the spring phytoplankton bloom in the subpolar North Atlantic Ocean has important consequences for the marine carbon cycle and ecosystems. There are currently several proposed mechanisms to explain the timing of this bloom. The conventional theory holds that the bloom begins when the ocean warms and the seasonal mixed layer shoals in the spring, decreasing the depth to which phytoplankton are mixed and increasing the light available to the population. Recent work has attributed the beginning of the bloom to decreases in turbulence within the upper ocean, driven by the onset of positive heat fluxes or decreases in the strength of local winds. Other studies have focused on the increase in the seasonal mixed layer in the winter as a driver of changes in ecosystem interactions and a control on the spring bloom. Finally, submesoscale eddies, occurring as a result of lateral density gradients, have been proposed as a stratification mechanism that can create phytoplankton blooms prior to the onset of ocean surface warming.</p><p>This dissertation critically examines and compares the proposed theories for the initiation of the spring bloom and draws on these theories to propose a new framework: that blooms begin when the active mixing depth shoals, a process generally driven by a weakening of surface heat fluxes and consequent shift from convective mixing to wind-driven mixing. Using surface forcing data, we develop a parameterization for the active mixing depth from estimates of the largest energy-containing eddies in the upper ocean. </p><p>Using in situ records of turbulent mixing and biomass, we find that the spring phytoplankton bloom occurs after mixing shifts from being driven by convection to being driven by wind, and that biomass increases as the active mixing depth shoals. Using remote sensing data, we examine patterns of bloom initiation in the North Atlantic at the basin scale, compare current theories of bloom initiation, and find that the shoaling of the active mixing depth better predicts the onset of the bloom across the North Atlantic subpolar basin and over multiple years than do other current theories. Additionally, using a process study model, we evaluate the importance of submesoscale eddy-driven stratification as a control on the initiation of the spring bloom, determining that this mechanism has a relatively minor effect on alleviation of phytoplankton light limitation. Finally, we describe potential techniques and tools to examine whether interannual variability in the active mixing depth acts as a control on variability in the timing of the spring bloom.</p> / Dissertation