In recent years new ideas for nutrient management to control eutrophication in estuarine environments have been under consideration. One popular approach being considered in the Chesapeake Bay Program is called the “top down” approach based on the premise that restoring algal predators, such as oysters and menhaden, will limit excess phytoplankton production and possibly eliminate costly nutrient control programs. The approach is being considered to replace or use in conjunction with the “bottom up” approach of reducing nutrient loads. The ability to model higher trophic levels such as fish, as well as the eutrophication processes driving production of primary producers in an aquatic ecosystem is needed. CE-QUAL-ICM (ICM) and Ecopath were two models selected for this research. ICM is a time- and spatial-varying eutrophication model that uses nutrient loads to predict primary producers, while Ecopath is a static mass balance model representing an average time period (e.g., season or year) and uses values of primary producers and other groups to predict fish biomass. Linking the two models will provide the means of going up the food chain by trophic levels. The Chesapeake Bay was chosen as the study site since both models are in use there. Before coupling ICM and Ecopath, common links between the two models were found. Ten groups were identified with such variables as production rates, consumption rates, and unassimilated food/consumption. A post-processor/subroutine was developed for ICM to aggregate output data from 3-D to 0-D to be used in Ecopath. Two Ecopath runs were developed with data from ICM and the Chesapeake Bay (CB) Ecopath model to see how network interactions differed with data representing the same system. Four additional runs were made, creating perturbations (i.e., increased phytoplankton production) using the CB Ecopath model and replacing the primary producers with data from ICM. Final runs of ICM were conducted looking at adjusting three parameters to try to restore the Bay back to 1950 conditions. It was demonstrated that ICM data can be coupled with Ecopath to study management strategies in eutrophication. Because of model formulations there was no data exchange from Ecopath back to ICM.

In the northeastern Ionian Sea, two populations of dolphins, the short-beaked common dolphin and the common bottlenose dolphin, have been studied since 1993 by the Tethys Research Institute, Italy. Results show a low density of bottlenose dolphins, and a rapid decline in common dolphin numbers and encounter rates. I constructed an ecosystem model using Ecopath with Ecosim for the northeastern Ionian Sea to explain the two different abundance trends of these species of dolphins, and the trophic interactions with their prey and with the fisheries. The Ecopath model was built for the year 1964, adding data on biomass, P/B, Q/B and diet for each functional group of the ecosystem, fisheries landings and discards. Ecosim was used to generate simulated trajectories to fit with the ‘observed’ trends (e.g., biomass, CPUE and catches) for the most important groups of the ecosystem. The results of the fitting underline a clear decline of common dolphins caused by reduced prey availability. In particular, sardine and anchovy stocks, the main prey of common dolphins, have decreased sharply since the late 1970s due to intensive fishing pressure in the area until the end of 1990s. On the other hand, the population of bottlenose dolphins has increased through time; a positive correlation was observed between this species of dolphin and the development of the fish farm industry in the study area. Ecosim was used to simulate three fishing policy scenarios within the study area. Three different fishing closures were investigated: the closure of purse seiners; the closure of the industrial fisheries (purse seiners, trawlers and beach seiners); and the closure of the entire fishing fleets. According to Ecosim predictions, sardines and anchovies would benefit from all three management strategies. Common dolphins showed a significant increase only when the entire study area was closed to fishing. The creation of MPAs was explored using Ecospace. In particular, two different scenarios were evaluated: a MPA1 that closed the entire area to fisheries, and a MPA2 that allowed the small and big artisanal fisheries to operate. The results obtained using this spatial model agreed with similar scenarios simulated in Ecosim.

In the northeastern Ionian Sea, two populations of dolphins, the short-beaked common dolphin and the common bottlenose dolphin, have been studied since 1993 by the Tethys Research Institute, Italy. Results show a low density of bottlenose dolphins, and a rapid decline in common dolphin numbers and encounter rates. I constructed an ecosystem model using Ecopath with Ecosim for the northeastern Ionian Sea to explain the two different abundance trends of these species of dolphins, and the trophic interactions with their prey and with the fisheries. The Ecopath model was built for the year 1964, adding data on biomass, P/B, Q/B and diet for each functional group of the ecosystem, fisheries landings and discards. Ecosim was used to generate simulated trajectories to fit with the ‘observed’ trends (e.g., biomass, CPUE and catches) for the most important groups of the ecosystem. The results of the fitting underline a clear decline of common dolphins caused by reduced prey availability. In particular, sardine and anchovy stocks, the main prey of common dolphins, have decreased sharply since the late 1970s due to intensive fishing pressure in the area until the end of 1990s. On the other hand, the population of bottlenose dolphins has increased through time; a positive correlation was observed between this species of dolphin and the development of the fish farm industry in the study area. Ecosim was used to simulate three fishing policy scenarios within the study area. Three different fishing closures were investigated: the closure of purse seiners; the closure of the industrial fisheries (purse seiners, trawlers and beach seiners); and the closure of the entire fishing fleets. According to Ecosim predictions, sardines and anchovies would benefit from all three management strategies. Common dolphins showed a significant increase only when the entire study area was closed to fishing. The creation of MPAs was explored using Ecospace. In particular, two different scenarios were evaluated: a MPA1 that closed the entire area to fisheries, and a MPA2 that allowed the small and big artisanal fisheries to operate. The results obtained using this spatial model agreed with similar scenarios simulated in Ecosim.

In the northeastern Ionian Sea, two populations of dolphins, the short-beaked common dolphin and the common bottlenose dolphin, have been studied since 1993 by the Tethys Research Institute, Italy. Results show a low density of bottlenose dolphins, and a rapid decline in common dolphin numbers and encounter rates. I constructed an ecosystem model using Ecopath with Ecosim for the northeastern Ionian Sea to explain the two different abundance trends of these species of dolphins, and the trophic interactions with their prey and with the fisheries. The Ecopath model was built for the year 1964, adding data on biomass, P/B, Q/B and diet for each functional group of the ecosystem, fisheries landings and discards. Ecosim was used to generate simulated trajectories to fit with the ‘observed’ trends (e.g., biomass, CPUE and catches) for the most important groups of the ecosystem. The results of the fitting underline a clear decline of common dolphins caused by reduced prey availability. In particular, sardine and anchovy stocks, the main prey of common dolphins, have decreased sharply since the late 1970s due to intensive fishing pressure in the area until the end of 1990s. On the other hand, the population of bottlenose dolphins has increased through time; a positive correlation was observed between this species of dolphin and the development of the fish farm industry in the study area. Ecosim was used to simulate three fishing policy scenarios within the study area. Three different fishing closures were investigated: the closure of purse seiners; the closure of the industrial fisheries (purse seiners, trawlers and beach seiners); and the closure of the entire fishing fleets. According to Ecosim predictions, sardines and anchovies would benefit from all three management strategies. Common dolphins showed a significant increase only when the entire study area was closed to fishing. The creation of MPAs was explored using Ecospace. In particular, two different scenarios were evaluated: a MPA1 that closed the entire area to fisheries, and a MPA2 that allowed the small and big artisanal fisheries to operate. The results obtained using this spatial model agreed with similar scenarios simulated in Ecosim. / Science, Faculty of / Zoology, Department of / Graduate

Este trabalho teve como objetivos analisar a estrutura e funcionamento do ecossistema de Cabo Frio, levando-se em consideração a variação sazonal do fenômeno de ressurgência, através do modelo trófico Ecopath. Foram elaborados dois modelos sazonais (primavera-verão e outono-inverno) e um modelo médio anual. Os modelos sazonais apresentaram pouca diferença entre si, com exceção da biomassa dos produtores que é muito mais elevada no período de primavera-verão, quando a ressurgência é mais intensa. Essa pequena diferença pode ser explicada pela pouca variação sazonal nas dietas dos grupos do modelo e, possivelmente, pela indisponibilidade de dados de desembarque pesqueiro. O modelo anual foi considerado como representativo do sistema de Cabo Frio, cujos descritores ecológicos permitiram classificá-lo como um sistema em desenvolvimento com grau elevado de desorganização, característica comum para regiões de ressurgência. Caracterizou-se também por apresentar alta conectância e onivoria, caracterizando-o como um sistema de alta resiliência. O Nível trófico calculado pelo modelo foi semelhante ao nível trófico isotópico disponível na literatura de grupos tróficos similares confirmando a confiabilidade ao modelo gerado. / The structure and trophic functioning of the ecosystem of Cabo Frio were analyzed considering the seasonal variation of the upwelling events. Two different seasonal models (Ecopath) and an annual model were constructed. The seasonal models did not show great differences, except for a higher biomass of producers during the spring-summer period, when the upwelling is more intense. Possibly, this difference was due to the small seasonal variation in the diet among trophic groups and lack of information on fishery catch data. The annual model could be considered as representative of the system of Cabo Frio, and according to the ecological descriptors it is a developing system with a high degree of disorganization, common characteristic in upwelling regions. The trophic levels calculated by the model were similar to the isotope trophic levels available in the literature for similar trophic groups, showing the confidence of the obtained results.

Este trabalho teve como objetivos analisar a estrutura e funcionamento do ecossistema de Cabo Frio, levando-se em consideração a variação sazonal do fenômeno de ressurgência, através do modelo trófico Ecopath. Foram elaborados dois modelos sazonais (primavera-verão e outono-inverno) e um modelo médio anual. Os modelos sazonais apresentaram pouca diferença entre si, com exceção da biomassa dos produtores que é muito mais elevada no período de primavera-verão, quando a ressurgência é mais intensa. Essa pequena diferença pode ser explicada pela pouca variação sazonal nas dietas dos grupos do modelo e, possivelmente, pela indisponibilidade de dados de desembarque pesqueiro. O modelo anual foi considerado como representativo do sistema de Cabo Frio, cujos descritores ecológicos permitiram classificá-lo como um sistema em desenvolvimento com grau elevado de desorganização, característica comum para regiões de ressurgência. Caracterizou-se também por apresentar alta conectância e onivoria, caracterizando-o como um sistema de alta resiliência. O Nível trófico calculado pelo modelo foi semelhante ao nível trófico isotópico disponível na literatura de grupos tróficos similares confirmando a confiabilidade ao modelo gerado. / The structure and trophic functioning of the ecosystem of Cabo Frio were analyzed considering the seasonal variation of the upwelling events. Two different seasonal models (Ecopath) and an annual model were constructed. The seasonal models did not show great differences, except for a higher biomass of producers during the spring-summer period, when the upwelling is more intense. Possibly, this difference was due to the small seasonal variation in the diet among trophic groups and lack of information on fishery catch data. The annual model could be considered as representative of the system of Cabo Frio, and according to the ecological descriptors it is a developing system with a high degree of disorganization, common characteristic in upwelling regions. The trophic levels calculated by the model were similar to the isotope trophic levels available in the literature for similar trophic groups, showing the confidence of the obtained results.

Dans le cadre de la transition énergétique, le gouvernement Français prévoit la constructionde huit parcs éoliens en mer (offshore) le long des côtes Manche-Atlantique parmi lesquels le futurparc éolien au large de Courseulles-sur-mer. A ce jour, il n’existe pas d’étude globale et intégrée deseffets de la construction et de l’exploitation de ces parcs sur l’écosystème. L’innovation principale decette thèse a donc été de poser les bases d’une approche écosystémique des Energies MarinesRenouvelables (EMR) à travers l’exemple du futur parc éolien de Courseulles-sur-mer. Pour ce faire,une combinaison d’outils de modélisation a été utilisée afin de : 1) caractériser le fonctionnement etla structure de l’écosystème du site d’implantation du parc ; 2) tester des scénarios d’évolutionpossible du fonctionnement trophique du système. Ainsi, un modèle de réseau trophique et troisscénarios ont été construits afin d’analyser les conséquences de l’effet récif et réserve générées par leparc sur l’écosystème. Les indices de l’analyse des réseaux écologiques ainsi que d’autres indices telsque le niveau trophique moyen ont été analysés afin de caractériser le fonctionnement du système.Toutefois, conscient que cet écosystème est menacé par de multiples pressions, il estnécessaire de comprendre comment ces activités humaines vont interagir entre elles et quelles sontleurs conséquences sur l’écosystème dans un contexte de changements globaux. Ainsi, une visionglobale des impacts cumulés a également été développée grâce à un autre type de modélisation appelé'modélisation qualitative’ ou en ‘digraphe orienté’. Les résultats ont mis en évidence des changementsdans la structure et le fonctionnement de l’écosystème après la mise en place du parc éolien. Lesrésultats de ces modèles pourraient être utilisés dans la définition de mesures de suivi aprèsl’installation du parc et dans l’évaluation de la nécessité de mettre en place des mesures decompensation. Enfin, les modèles qualitatifs pourraient également servir d’outils de communicationavec le public et ainsi permettre une meilleure appropriation des projets EMR. / As part of the energy transition, the French government is planning the construction of eightOffshore Wind Farms (OWF) along the English Channel and Atlantic coasts including the Courseulles-sur-mer OWF. Until now, there is no holistic study on the OWF construction and operation effects onan ecosystem taken as a whole. This thesis is the first study to lay the foundations for an ecosystemapproach of Marine Renewable Energy (MRE) through the Courseulles-sur-mer OWF example. For thata combination of innovative modelling tools was applied to 1) characterise the ecosystem structureand functioning before the OWF construction; 2) simulate the impacts of this future OWF on theecosystem structure and functioning. A food-web model and three scenarios were constructed toinvestigate the “reef” and “reserve” effects induced by the OWF on the ecosystem. Ecological NetworkAnalysis indices, other ecosystem attributes and Mean Trophic Level were derived to investigate theecosystem health and state.However, being aware that this ecosystem is threatened by multiple perturbations, there is aneed to understand how human activities interact to influence ecosystem functioning in a long termclimate change context. Thus, a holistic view of cumulated impacts on the Courseulles-sur-mer’ecosystem through the use of an oriented signed digraph was also developed. Results highlighted acombination of significant changes in the food-web structure and ecosystem functioning. These resultscan play a vital role in both decision making by improving long term planning for the marineenvironment but also as tool for communication with the public and so contribute to a betteracceptability of MRE project.

L'objectif de la thèse est d'évaluer l'impact de l'immersion des sédiments de dragage du Grand Port Maritime du Havre (GPMH) sur l'environnement faunistique et sédimentaire à proximité du site de clapage d'Octeville (baie de Seine Orientale), en proposant une démarche scientifique originale, apportant une vision intégrée par (1) l'utilisation de marqueurs géochimiques couplés à une étude sédimentaire (2) l'étude de la dynamique spatiale et temporelle de la macrofaune benthique en lien avec une expérimentation in situ (3) la mise en place d'un nouvel indicateur multicritères spécifique de la pression de clapage (4) l'étude de l'ensemble du réseau trophique via le développement d'un modèleECOPATH. D'une part, les résultats ont mis en évidence l'existence d'une zone à l'équilibre sédimentaire au nord-ouest, avec deux gradients opposés de COT, contrôlés par les courants de marée et de houle. De plus, il est possible d'identifier les sédiments portuaires grâce à leur composition chimique différente. La zone impactée par les clapages est relativement restreinte. D'autre part, la macrofaune benthique apparaît peu impactée par les clapages. La communauté est particulièrement bien inféodée à l'environnement bio-hydro-sédimentaire de la zone d'étude. Des variations d'abondances et de dominances ont été observées depuis 2003. De plus, le nouvel indicateur proposé permet de classer l'impact engendré par les dépôts de sédiments en mer. Le réseau trophique est actuellement stable sur la zone impactée comme sur celle non-impactée par le clapage. / The aim of this thesis is to assess the impact of dumping by Le Havre harbour on the faunistic and sedimentary environment near the Octeville dumping site (Eastern part of the bay of Seine). This thesis propose an original scientific approach, including an integrated view (1) by the use of geochemical markers coupled with a sedimentary study (2) a study of the spatial and temporal benthic macrofauna dynamics with an experimentation in situ (3) the creation of a new multicriteria specific indicator of the dumping pressure and (4) a study of the food web with the development of an ECOPATH model. On the one hand, the results showed the existence of a sedimentary equilibrium area in the north-west, with two opposite TOC gradients, controlled by tidal and swell. Harbour sediments can be identified by their different chemical compositions. The area impacted by the dumping is limited. On the other hand, the benthic macrofauna appears less impacted by the dumping. The community is adapted in the bio-hydro-sedimentary environment of the study area. Variations in abundance and dominance have been observed since 2003.In addition, a new indicator allows the classification of dumping impact. The food web is currently stable in both impacted and not impacted areas.

Karenia brevis dinoflagellate blooms off the west coast of Florida can create devastating effects on marine communities when they release a neurotoxin known as a brevetoxin. These blooms, informally referred to as red tides, can cause massive fish kills, necessitate closures of shellfish fisheries, and can even leave lingering toxins that impact shelf communities long after the bloom has dissipated. As a result, much effort has been put into studying K. brevis bloom initiation and dynamics. However, how K. brevis blooms impact Florida's fisheries is not fully understood because the relationship between K. brevis cell counts and fish mortality is poorly described. To study this relationship and the ecosystem response to K. brevis blooms, Ecopath with Ecosim (EwE) modeling is used to force K. brevis bloom mortality on the shelf ecosystems by using a recently developed time series that indexes K. brevis bloom severity. This index dynamically drives K. brevis bloom mortality in EwE in a historical reconstruction scenario from 1980 to 2009. Three hypotheses on ecosystem response are explored using Gag grouper as a case study. We postulate a) that K. brevis blooms impose bottom-up and top-down effects on the food web, b) that episodic perturbations by these blooms shape the community structure and c) that fishing pressure exacerbates those effects. Results support the hypothesis that K. brevis blooms pose top-down food web pressures, which is seen by evidence of trophic cascading. Changes in community structure with bloom mortality are also evidenced by changes seen in biodiversity and richness. An exacerbation of those effects as a result of heavy fishing pressure is evident, however, is only seen during severe bloom events. Little to no changes were found in the mortality from K.brevis blooms during blooms of average severity, and less mortality was imposed on the system during blooms of particularly low severity. However, this may be an artefact of the mode of action of K. brevis in EwE. Investigation of bloom effects on Gag showed that natural mortality rates of Gag appear to be largely influenced by mortality incurred during K. brevis blooms relative to the low rate of predation on Gag. Moreover, consumption rates of Gag on its prey were found to increase under a realistic schedule of these blooms. This may be due to a combination of effects, including increased mortality on competitors (making more prey available for Gag) and a lowering of the mean age of the Gag stock, which increases population productivity.

Understanding the interaction of multiple drivers and their compounded effects on ecosystem dynamics is a key challenge for marine resource management. The Baltic Sea is one of the world’s seas most strongly impacted by effects from both human activities and climate. In the late 1980’s changes in climate in combination with intensive fishing initiated a reorganization of the Central Baltic Sea (CBS) food web resulting in the current sprat-dominated state. In the future, climate change is projected to cause drastic changes in hydrodynamic conditions of the world oceans in general, and the Baltic Sea in particular.   In this thesis, CBS food web responses to the combined effects of fishing, nutrient loads and climate were tested for the past (1974-2006) and projected into the future (2010-2098). A new food web model for the CBS (BaltProWeb) was developed using extensive monitoring data across trophic levels. This model described the past food web dynamics well, and was hence also used for future (2010-2098) projections. Different ensemble modeling approaches were employed when testing the food web response to future scenarios. The results show that regardless the climate change, the management of nutrient loads and cod fishing are likely to determine the food web dynamics and trophic control mechanisms in the future Baltic Sea. Consequently, the variation in the food web projections was large, ranging from a strongly eutrophied and sprat-dominated to a cod-dominated CBS with eutrophication levels close to today’s values. The results also suggest a potential risk of abrupt ecosystem changes in the future CBS, particularly if the nutrient loads are not reduced. Finally, the studies illustrate the usefulness of the ensemble modeling approach, both from the perspective of ecosystem-based management as well as for studying the importance of different mechanisms in the ecosystem response. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: In press. Paper 5: Submitted.</p>