In this study, the factors influencing zooplankton community structure in Turkish shallow lakes were elucidated with four main approaches: (i) space-for-time substitution for shallow lakes using snap-shot sampling in 31 lakes along a latitudinal gradient / (ii) in-situ mesocosm experiments in eleven lakes along a latitudinal gradient using three sets of artificial plants systems / (iii)&lsquo / Habitat Choice&rsquo / laboratory experiments mimicking a &lsquo / shallow littoral&rsquo / zone with plants and a &lsquo / deeper pelagic&rsquo / zone with sediments testing the response of Daphnia magna to predation cues / and (iv) long-term monitoring data (1997-2011) from two interconnected lakes. Snap-shot and long-term monitoring showed that eutrophication has a strong influence on the zooplankton community via increased fish predation, nutrient loading and salinization. Here too the zooplankton community shifted towards a smaller sized profile, especially in lakes located at lower latitudes. Moreover, The laboratory and in-situ mesocosm experiments revealed that under predation risk Daphnia preferred to hide near sediment instead of using submerged plants as a refuge. Accordingly, in-situ mesocosm experiments revealed a predation pressure induced size structure shift towards small-medium sized zooplankton and calanoid copepods. The long-term monitored lakes experienced (i) drought-induced water level drop, leading to increased salinity and eutrophication, and consequent anoxic conditions and fish kill / as well as (ii) biomanipulation in the downstream. Both conditions resulted in major reduction in the top-down control of fish and ultimate predomination by large sized Daphnia spp. Nevertheless, the excessive exploitation of lakes and ongoing warming entail Turkish shallow lakes to become more eutrophic, making this study indicative for the Mediterranean region.

Lake Winnipeg has been subject to intense eutrophication and invasive species such as Rainbow Smelt and Eubosmina coregoni for the last 40 years. This study demonstrated significant increases in total phosphorus, total nitrogen, chlorophyll-a, overall zooplankton abundance, and specifically Cladocera, between 1969 and the first decade of the 21st century. There were specific basin differences in the long-term changes of the Cladocera community, with the species Chydorus sphaericus and Ceriodaphnia quadrangula negatively affected by high levels of phosphorus, nitrogen and chlorophyll-a. Moreover, long-term change in the Cladocera community composition and abundance throughout the years (1969-2011) during summer was correlated with intensifying eutrophication. Additionally, weak diel vertical migration in the zooplankton community was observed for the first time in Lake Winnipeg.

Lake Winnipeg has been subject to intense eutrophication and invasive species such as Rainbow Smelt and Eubosmina coregoni for the last 40 years. This study demonstrated significant increases in total phosphorus, total nitrogen, chlorophyll-a, overall zooplankton abundance, and specifically Cladocera, between 1969 and the first decade of the 21st century. There were specific basin differences in the long-term changes of the Cladocera community, with the species Chydorus sphaericus and Ceriodaphnia quadrangula negatively affected by high levels of phosphorus, nitrogen and chlorophyll-a. Moreover, long-term change in the Cladocera community composition and abundance throughout the years (1969-2011) during summer was correlated with intensifying eutrophication. Additionally, weak diel vertical migration in the zooplankton community was observed for the first time in Lake Winnipeg.

In Saanich Inlet, a fjord located in southern Vancouver Island, British Columbia, dense aggregations of euphausiids exhibit diel vertical migration behavior and their capability of generating turbulence has been suggested. Despite decades of research on diel vertical migration of zooplankton, its variability has not been well studied. In addition, the physical oceanographic environment in Saanich Inlet has not been thoroughly quantified, which raises the possibility of previously observed turbulent bursts of O(10^-5 – 10^-4 W kg^-1) having physical (rather than biological) origin. This work characterizes variability of diel vertical migration behavior using a moored 200-kHz echosounder, complemented by plankton sampling. Physical properties such as barotropic, baroclinic and turbulent signals are described, and the relationship between turbulence and internal waves/scattering layer examined. A two-year high-resolution biacoustic time-series provided by the Victoria Experimental Network Under the Sea (VENUS) cabled observatory allowed quantification of the seasonal variability in migration timing of euphausiids. During spring – fall, early dusk ascent and late dawn descent relative to civil twilight occur. During winter, late dusk ascent and early dawn descent occur. Factors regulating the seasonal changes in migration timing are light availability at the daytime depth of the scattering layers, and size-dependent visual predation risk of euphausiids. Instead of the traditional view of diel vertical migration timing correlated solely with civil twilight, euphausiids also adapt their migration timing to accommodate changes in environmental cues as well as their growth. The pre-spawning period (February – April) is an exception to this seasonal pattern, likely due to the higher energy demands for reproduction. Turbulence and internal waves in Saanich Inlet are characterized based on a one-month mooring deployment. Average dissipation rates are nearly an order of magnitude larger than previously reported values and higher dissipation rates of O(10^-7 – 10^-6 W kg^-1) are occasionally observed. A weak correlation is observed between turbulent dissipation rates and baroclinic velocity/shear. To examine the possibility of biological generation of turbulence, an echosounder at the VENUS cabled observatory is used to simultaneously measure the intensity of the euphausiid scattering layer and its vertical position. Turbulent bursts of the sort previously reported are not observed, and no relation between diel vertical migration and turbulent dissipation rates is found. Physical forcing at the main channel remains as a possible cause of the turbulent bursts. / Graduate / 0416 / 0415

Small- and fine-scale biological and oceanographic processes may have a measurable electromagnetic signature. These types of processes inherently involve turbulence and three-dimensional dynamics. Traditional models of the electromagnetic signature of oceanographic processes are of an analytical nature, do not account for three-dimensional boundary layer dynamics or turbulence, self-inductance, and may not describe the variety of the environmental conditions occurring in the ocean. In order to address this problem, I have implemented magnetohydrodynamic (MHD) computational fluid dynamics (CFD) tools, which has allowed for the evaluation of the electromagnetic signature of a number of small- and fine-scale biological and oceanographic processes in the ocean. The suite of computational tools has included the commercial models ANSYS Fluent, coupled with the MHD module, and ANSYS Maxwell. These computational tools have been well-established in fluid and electromagnetic engineering. The application of CFD and MHD tools in oceanography is new but is undergoing rapid development. In this work, substantial effort was made toward the CFD, MHD, and magnetostatic model verification and identification of model limitations. Verifications of the CFD, MHD, and magnetostatic models were conducted by successfully comparing their results with the field measurements and laboratory experiments. Comparison with the traditional (analytical) models for surface and internal waves, has revealed their limitations related to bottom boundary layer physics, effect of self-inductance, and, to a lesser extent, the magnetic permeability difference at the air-sea interface. These limitations become important for shallow water internal waves. As a result, the traditional models significantly overestimate the magnetic signature of internal waves observed at the Electromagnetic Observatory. After model verification with the field and laboratory data, the computational models were then applied to evaluate the magnetic signature of diel vertical migration (DVM) of zooplankton, surface waves, internal wave solitons, freshwater lens spreading, and Langmuir circulation. The quantitative estimates have been made for typical environmental conditions. In other environmental conditions, their magnetic signature may be somewhat different. The suite of computational models developed in this dissertation work allows for the estimation of the magnetic signature of fine- and small-scale oceanographic processes in virtually any environmental conditions (e.g., in oil emulsions). I anticipate the result of this study will have Naval, environmental, and oil exploration applications.

A distribuição da biomassa do plâncton é a chave para o entendimento de vários processos inclusive a compreensão da migração vertical diurna. Entender a fototaxia positiva, como responsável por esta distribuição, com enfoque na qualidade espectral da luz é uma campo vasto a ser explorado. Investigamos a percepção espectral luminosa do mesozooplâncton marinho através da quantificação de capturas em uma nova arte de coleta com armadilha de luz. Estas armadilhas foram testadas com tratamentos luminosos na cor vermelha, verde, azul e branco. Elas foram fundeadas na enseada do Flamengo e de Ubatuba (Ubatuba-SP) no fim do verão e outono de 2015 durante a lua cheia e lua nova em três noites consecutivas. Foram avaliadas as associações de exposição (fase lunar, local de coleta e esquema de randomização dos tratamentos) baseada nos dados de captura através de gráficos NMDS, teste PERMANOVA e tabelas de contingência de Chi-quadrado. Os táxons mais abundantes nas capturas foram dois gêneros de copépodes Calanoida (Acartia sp e Temora sp) seguidos pela família Podonidae e Brachyura. Demonstramos que os organismos capturados do zooplâncton marinho expressaram seleção espectral induzidos pela fototaxia positiva. O tratamento luminoso verde exerceu maior atração nos organismos em detrimento ao tratamento luminoso vermelho. A influência das fases lunares ou dos esquemas de randomização dos tratamentos luminosos dependem da sensibilidade espectral de cada táxon. Porém local não implicou em diferenças entre as coletas. Estas particularidades da fototaxia positiva seletiva podem explicar a variação vertical da biomassa do zooplâncton marinho na coluna d\'água inclusive no entendimento da MVD. / The distribution of plankton biomass is the key for understanding many processes including diel vertical migration (DVM). Understand the positive phototaxis, as responsible for this distribution, with a focus on spectral quality of light is a vast field to be explored. We investigate the spectral light perception of the marine mesozooplankton through quantification of catches in a new art with light trap. These traps were tested with light treatments in red, green, blue and white. They were anchored in the Flamengo and Ubatuba bay (Ubatuba-SP) in late summer and autumn of 2015 during the full moon and new moon on three consecutive nights. Exposure associations were evaluated (lunar phase, site and treatment randomization scheme) based on the data capture through NMDS graphics, PERMANOVA test and Chi-square contingency tables. Most abundant taxa catched were two kinds of copepods Calanoida (Acartia sp and Temora sp) followed by Podonidae and Brachyura. We have demonstrated that the captured marine zooplankton showed spectral selection induced by positive phototaxis. The green light treatment exerted biggest attraction in organisms over the red light treatment. The influence of lunar phases or randomization schemes of bright treatments depend on the spectral sensitivity of each taxon. But location did not result in differences between collections. These specifics of selective phototaxis may explain the vertical variation of marine zooplankton biomass in water column including the understanding of DVM.

A distribuição da biomassa do plâncton é a chave para o entendimento de vários processos inclusive a compreensão da migração vertical diurna. Entender a fototaxia positiva, como responsável por esta distribuição, com enfoque na qualidade espectral da luz é uma campo vasto a ser explorado. Investigamos a percepção espectral luminosa do mesozooplâncton marinho através da quantificação de capturas em uma nova arte de coleta com armadilha de luz. Estas armadilhas foram testadas com tratamentos luminosos na cor vermelha, verde, azul e branco. Elas foram fundeadas na enseada do Flamengo e de Ubatuba (Ubatuba-SP) no fim do verão e outono de 2015 durante a lua cheia e lua nova em três noites consecutivas. Foram avaliadas as associações de exposição (fase lunar, local de coleta e esquema de randomização dos tratamentos) baseada nos dados de captura através de gráficos NMDS, teste PERMANOVA e tabelas de contingência de Chi-quadrado. Os táxons mais abundantes nas capturas foram dois gêneros de copépodes Calanoida (Acartia sp e Temora sp) seguidos pela família Podonidae e Brachyura. Demonstramos que os organismos capturados do zooplâncton marinho expressaram seleção espectral induzidos pela fototaxia positiva. O tratamento luminoso verde exerceu maior atração nos organismos em detrimento ao tratamento luminoso vermelho. A influência das fases lunares ou dos esquemas de randomização dos tratamentos luminosos dependem da sensibilidade espectral de cada táxon. Porém local não implicou em diferenças entre as coletas. Estas particularidades da fototaxia positiva seletiva podem explicar a variação vertical da biomassa do zooplâncton marinho na coluna d\'água inclusive no entendimento da MVD. / The distribution of plankton biomass is the key for understanding many processes including diel vertical migration (DVM). Understand the positive phototaxis, as responsible for this distribution, with a focus on spectral quality of light is a vast field to be explored. We investigate the spectral light perception of the marine mesozooplankton through quantification of catches in a new art with light trap. These traps were tested with light treatments in red, green, blue and white. They were anchored in the Flamengo and Ubatuba bay (Ubatuba-SP) in late summer and autumn of 2015 during the full moon and new moon on three consecutive nights. Exposure associations were evaluated (lunar phase, site and treatment randomization scheme) based on the data capture through NMDS graphics, PERMANOVA test and Chi-square contingency tables. Most abundant taxa catched were two kinds of copepods Calanoida (Acartia sp and Temora sp) followed by Podonidae and Brachyura. We have demonstrated that the captured marine zooplankton showed spectral selection induced by positive phototaxis. The green light treatment exerted biggest attraction in organisms over the red light treatment. The influence of lunar phases or randomization schemes of bright treatments depend on the spectral sensitivity of each taxon. But location did not result in differences between collections. These specifics of selective phototaxis may explain the vertical variation of marine zooplankton biomass in water column including the understanding of DVM.

Mysid shrimps (Mysidacea, Crustacea) are efficient zooplanktivores in both marine and freshwater systems as well as lipid rich prey for many species of fish.  Although some efforts have been made to study the role of mysids in the Baltic Sea, very few studies have been carried out in recent time and there are still knowledge gaps regarding various aspects of mysid ecology. This thesis aims to explore some of these gaps by covering a mixture of topics. Using multifrequency hydroacoustics we explored the possibility to separate mysids from fish echoes and successfully established a promising and effective method for obtaining mysid abundance/biomass estimates (paper I). An investigation of the current mysid community in a coastal area of the northern Baltic proper (paper II) demonstrated that the formerly dominant, pelagic mysid Mysis mixta had decreased substantially (~50%) in favor for phytoplanktivorous, juvenile Neomysis integer and Mysis relicta sp. By examining different aspects of mysid behavior, we studied the vertical size distribution of mysids in the field and found that size increased with depth/declining light, irrespective of temperature; indicating that their vertical size distribution primarily is a response to predation (paper II). In paper III, a combination of ecological and genetic markers was used to investigate intraspecific differences in migratory tendency. Both marker types indicated that some part of the Mysis salemaai population is sedentary on the bottom and that this strategy is a phenotypically plastic but persistent trait, analogous to the partial migrations seen in many birds and fishes. In paper IV a temperature and weight specific respiration model was developed for the littoral Praunus flexuosus. Routine respiration was moreover elevated by post-prandial effects (specific dynamic action) for longer times than previously suggested. Consequently, ignoring such effects could significantly bias respiration measurements. / At the time of doctoral defence the following papers were unpublished and had a status as follows: Paper  2: Accepted; Paper 3: Submitted; Paper  4: Accepted

This thesis was written within the framework of a biomanipulation project where young-of-the-year (YOY) pikeperch (Sander lucioperca) were stocked to a Baltic Sea bay to improve water quality through a top-down trophic cascade. The aim of my doctorial studies was however focused on a broader ecological question, namely predation (the main driving force in a biomanipulation). Hence, this thesis consists of four papers where we study the interactions between predator and prey using fish and zooplankton and how these interactions can be measured. In paper I we evaluated the performance of different diet analysis methods by individual based modelling and found that when having a nutritional gain perspective, mass based methods described diets best. Paper II investigated how the explorative, foraging and anti-predator behaviour of the YOY pikeperch used for stocking were affected by their rearing environment (pond vs. tank rearing). The more complex and varied environment in the semi-natural ponds seemed to promote a more flexible and active behaviour, better equipping young fish for survival in the wild. For paper III we studied the diel vertical migration in the six copepodite stages of the zooplankton Acartia spp. and Eurytemora affinis in relation to fish biomass, phytoplankton abundance and temperature. Both species migrated and in addition showed increased migration range with size within species, indicating evasion from visual predators. Paper IV addressed the movement of littoral Eurasian perch (Perca fluviatilis) via stable isotope signatures (13C and 15N) and body condition. We found clear indications of sedentarity and intra-habitat dietary differences. Interactions between predators and prey are complex and affected by both physiological and environmental characteristics as well as behavioural traits. The results in this thesis suggest that different species and even different life stages pursue different strategies to survive. / At the time of doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Submitted.  Paper 2: In press.  Paper 4: Submitted.