Marine ecosystem-based management requires end to end models, which are models capable of representing the entire ecosystem including physical, chemical and biological processes, anthropogenic activities, and multiple species with different sizes, life histories and from different trophic levels. To adequately represent ecosystem dynamics in shallow coastal regions, end-to-end models may need to include macrobiota species (wild and aquacultured) and may have to allow feedbacks (i.e. two-way coupling) between macrobiota and planktonic ecosystem dynamics. This is because the biomass of macrobiota can locally exceed the biomass of plankton, thus influencing the distribution of planktonic ecosystem tracers and altering the overall food web structure. Here, I describe a hybrid (Eulerian/Individual-Based) ecosystem framework, implemented in the Regional Ocean Modeling System (ROMS), a state-of-the-art 3-D ocean circulation model. The framework was applied to a model of a synthetic embayment containing seagrass, rockweed and kelp beds, a wild oyster reef, a mussel ranch and a fish farm. I found that two-way coupling is essential to reproduce expected spatial patterns of all variables and to conserve mass in the system. I also developed a shellfish ecophysiology model (SHELL E) and compared its results against water samples collected over 5 years in Ship Harbour, a fjord with mussel aquaculture in Nova Scotia, Eastern Canada. Also, from a high-resolution bio-optical survey of the fjord, I found that mussels decrease phytoplankton biomass inside the farm, but also cause a bloom of phytoplankton outside the farm. Using ROMS/SHELL-E, I determined that the increase of phytoplankton around the farm is caused by the waste products of the farmed bivalves, which have a fertilization effect, enhancing phytoplankton production outside the farm during nutrient-limited and light-replete conditions (i.e. late spring to late fall in Ship Harbour). The main conclusion of this thesis is that—in shallow coastal regions—ecosystem models must represent bilateral interactions between macrobiota and physical-planktonic dynamics, in a spatially-explicit setting, to adequately represent mass flows and ecosystem dynamics. The hybrid end-to-end modelling system provides a computationally efficient framework for describing these interactions and, through careful comparisons against observations, can be a powerful tool to test hypotheses and generate insights into coastal ecosystems.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-02-11T16:24:22Z No. of bitstreams: 1 rafaelrodriguesdepaiva.pdf: 1188955 bytes, checksum: b04f0f61a4d3103570287581b800ce0b (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-02-26T12:03:43Z (GMT) No. of bitstreams: 1 rafaelrodriguesdepaiva.pdf: 1188955 bytes, checksum: b04f0f61a4d3103570287581b800ce0b (MD5) / Made available in DSpace on 2016-02-26T12:03:43Z (GMT). No. of bitstreams: 1 rafaelrodriguesdepaiva.pdf: 1188955 bytes, checksum: b04f0f61a4d3103570287581b800ce0b (MD5) Previous issue date: 2014-03-27 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Florações de cianobactérias podem causar efeitos negativos na qualidade da água e em comunidades biológicas. Dentre estas comunidades, copépodos calanóides possuem uma grande importância, sendo o grupo planctônico dominante em muitos ambientes de água doce. Apesar da importância destes copépodos para a dinâmica planctônica nestes sistemas, estudos sobre a interação entre estes animais e cianobactérias são ainda escassos. No presente estudo, os efeitos da cianobactéria invasiva e tóxica Cylindrospermopsis raciborskii (Woloszyńska) Seenayya et Subba Raju (1972) no copépodo calanóide tropical Notodiaptomus iheringi (Wright 1935) foram avaliados. Alimentação (taxas de remoção e seleção alimentar), sobrevivência (curvas de Kaplan-Meier, probabilidades de sobrevivência e Hazard ratio) e reprodução (% fêmeas com ovos e produção de ovos) deste copépodo foram estudadas usando dietas monoespecíficas e mistas de C. raciborskii e algas nutritivas (Chlamydomonas chlorastera ou Cryptomonas obovata). O aumento na proporção de C. raciborskii (> 50%) esteve relacionado a baixas taxas de alimentação, embora nenhuma diferença entre as taxas de remoção na cianobactéria e na alga nutritiva dentro de cada tratamento tenha sido encontrada. Efeitos negativos (25 ou 75% de C. raciborskii) ou neutros (50% de C. raciborskiii) na sobrevivência foram detectados nos tratamentos. Por outro lado, a reprodução em N. iheringi foi afetada pela presença de C. raciborskii, independente da proporção desta cianobactéria. Características da espécie C. raciborskii tais como toxicidade (e.g. saxitoxinas) e baixos valores nutricionais (e.g. ausência de PUFA) juntamente com não aclimatação prévia em N. iheringi à C. raciborskii podem explicar os diferentes resultados encontrados. Em geral, copépodos N. iheringi podem se alimentar e sobreviver em dietas com C. raciborskii. Porém, dietas de C. raciborskii não suportam a reprodução destes animais. Este é o primeiro estudo que avalia o efeito de C. raciborskii na sobrevivência e reprodução de copépodos calanóides. Os resultados deste trabalho podem contribuir para o entendimento do comportamento alimentar assim como a dinâmica populacional de copépodos calanóides na presença da cianobactéria C. raciborskii. / Cyanobacterial blooms can cause negative impacts on water quality and biological communities. Among these biological communities, calanoid copepods have a great importance, being the dominant planktonic group in many freshwater systems. Despite the importance of calanoid copepods to plankton dynamics in freshwater systems, studies on the interaction between these animals and cyanobacteria are still scarce. Here the effects of the invasive and toxic cyanobacterium Cylindrospermopsis raciborskii (Woloszyńska) Seenayya et Subba Raju (1972) on the tropical calanoid copepod Notodiaptomus iheringi (Wright 1935) were evaluated. Feeding (clearance rates and selective feeding), survival (Kaplan-Meier curves, survival probabilities and hazard ratios) and reproduction (% females with eggs and egg production) of this copepod were studied using single and mixed diets of C. raciborskii and nutritious algae (Chlamydomonas chlorastera or Cryptomonas obovata). The increase on C. raciborskii proportion (> 50%) was related to lower feeding rates although no differences between the clearance rates on the cyanobacterium and nutritious algae within each treatment were found. Negative (25 or 75% of C. raciborskii) or neutral (50% of C. raciborskiii) effects on survival were detected throughout the treatments. On the other hand, the reproduction in N. iheringi was strongly affected by the presence of C. raciborskii, independently of the proportion of this cyanobacterium. Features of the species C. raciborskii such as toxicity (e.g. saxitoxins) and low nutritional values (e.g. absence of PUFA) along with non-previous acclimation in N. iheringi to C. raciborskii might explain the different outcomes found in the present study. Overall, N. iheringi copepods can feed and survive in diets with C. raciborskii. However, C. raciborskii diets cannot support reproduction of these animals. This is the first study that evaluates the effects of C. raciborskii on survival and reproduction of calanoid copepods. The outcomes found in this work might contribute to the understanding of the feeding interactions as well as the population dynamics of calanoid copepods in the presence of the cyanobacterium C. raciborskii.