The population dynamics and demography of Daphnia galeata was analysed in a five year study in the biomanipulated Bautzen Reservoir. Samples were taken two times a week during the period May-July in the pelagic zone of this highly eutrophic water. Major bottom-up and top-down factors were determined during the study period and analysed with regard to their influence on Daphnia dynamics and life history. Field data on fecundity and population structure of D. galeata were combined with results from life table and growth experiments performed under approximately in situ conditions to gain insight into the mechanisms leading to a midsummer decline of this cladoceran species which dominates the zooplankton community in Bautzen Reservoir. Two main patterns of Daphnia dynamics emerged: In years without a midsummer decline the population increased slowly in spring, starting from low densities. High water transparency was observed already during the build-up of the population of D. galeata. Despite considerable fluctuations, Daphnia abundance remained on a high level throughout summer. In years with a midsummer decline the population started from relatively high densities in early May and more than doubled during one week. Peak densities were reached before the clear-water stage emerged. At the end of this period the population declined to low values which lasted for the rest of the summer. Fecundity of the Population of D. galeata declined, whereas the mean egg volume increased at the beginning of the clear-water stage as a result of declining food levels. The size at maturity (SAM) remained high during this period. Additionally, juvenile growth was reduced and the age at maturity was retarded. Survival probability was low for those daphnids born shortly before or during the clear-water stage compared to those born later. It can be concluded from these results that recruitment to adult stages is strongly reduced during the clear-water stage. The end of this period is marked by an alternation in generations. Only at that time can SAM be reduced because the new generation of adults matures at a smaller size, carrying small eggs. A high impact of non-predatory adult mortality can be expected when the population is dominated by a strong peak-cohort during the clear-water stage according to recruitment patterns during the build-up of the population. The most drastic decline both of Daphnia abundance and SAM was observed in those years when the biomass of juvenile fish exceeded 20 kg ha-1 at the end of the clear-water stage. Due to gape-size limitation juvenile fish mainly feed on juvenile daphnids during this period and thus, they reinforce bottom-up effects on the Daphnia population. When fish change their size selection towards adult daphnids at the time when the new generation takes over, this seems to represent the worst case for the Daphnia population. Consequently, the timing between bottom-up effects and the feeding pressure of juvenile fish determines the extent of the decline. - (This manuscript is also available - in the form of a book - from Shaker Verlag GmbH, Postfach 101818, 52018 Aachen, Germany world-wide web address: http://www.shaker.de, electronic-mail address: info@shaker.de. It has been posted on the web sites of Dresden University of Technology with the permission of the publisher)

Aquatische Gemeinschaften sind stark körpergrößenstrukturiert mit einer exponentiellen Abnahme der Häufigkeit der Individuen mit zunehmender Körpergröße, die als Größenspektrum (SS) bezeichnet wird. Körpergrößenbasierte Ansätze bieten eine einfache und kostengünstige Methode zur Beantwortung komplexer ökologischer Fragestellungen in aquatischer Forschung. Widersprüchliche Ergebnisse zu den wichtigsten Faktoren, die Größenspektren beeinflussen unterstreichen jedoch die Notwendigkeit weiterer Studien. Um einige dieser widersprüchlichen Schlussfolgerungen anzugehen, habe ich eine Reihe von Fragen in den Bereichen Limnologie und Korallenriffökologie untersucht. In dieser Dissertation wurden größenbasierte Ansätze wie SS verwendet, um zu untersuchen, (i) was die Größenverteilung von Zooplankton beeinflusst und ob Zooplankton-fressende Fische (topdown) oder Ressourcenverfügbarkeit und Umweltbedingungen (bottom-up) die SS der Zooplanktongemeinschaft bestimmen, (ii) ob traditionelle Schleppnetze oder moderne hydroakustische Methoden Fisch-SS zuverlässiger darstellen, und (iii) ob SS von Korallenriff- Fischgemeinschaften und die strukturelle Komplexität der Korallen bzw. deren Beziehung zueinander sich unter verschiedenen anthropogenen Stressoren verändert. Zuallererst konnte ich zeigen, dass weder Top-down- noch Bottom-up-Kräfte stark die Größenverteilung der Zooplanktongemeinschaft beeinflussten. Zooplankton SS scheinen robust gegenüber Prädationseffekten zu sein, aber ein empfindlicher Indikator für die Energieverfügbarkeit und Transfereffizienz im Nahrungsnetz des untersuchten Sees. Des Weiteren konnten meine Studien bestätigen, dass hydroakustische Methoden die SS von pelagischen Fischgemeinschaften zuverlässig darstellen, was sie zu einer kostengünstigen und minimalinvasiven Alternative zu traditionellen Fischentnahmemethoden macht. Ich konnte jedoch kein allgemeingültiges Muster hinsichtlich der Größenverteilung von Korallenrifffischen und der strukturellen Komplexität der Korallen in Beziehung zu unterschiedlichen anthropogenen Stressoren finden. Insgesamt zeigt die Dissertation das weite Anwendungsspektrum von SS, um Strukturen und Prozesse in aquatischen Gemeinschaften und Fischfangmethoden zu untersuchen. Die hohe Variabilität von Größenspektren und der Einfluss von Umweltbedingungen unterstreicht weiter die Wichtigkeit, Daten über einen langen Zeitraum einzubeziehen. Darüber hinaus unterstreichen die Ergebnisse dieser Arbeit auch die Grenzen der Anwendung von SS, da für die Beantwortung mancher ökologischer Fragestellungen artenspezifische Informationen, wie Lebensraum- und Nahrungspräferenzen benötigt werden. / Aquatic communities are highly body-size structured with an exponential decline of abundance with increasing body size, which is referred to as the size spectrum (SS). The importance of body size as a principal and simplifying framework within aquatic communities, has led to a high number of theoretical and empirical studies on energy fluxes in food webs and predatorprey interactions using Size Spectra. These size-based approaches offer a rather simple and inexpensive method to answer complex ecological questions. However, conflicting findings on the key drivers of SS highlight the need for further studies. To address some of these conflicting conclusions, I investigated a range of questions within the fields of limnology and coral reef ecology. In this thesis size-based approaches such as SS were employed to explore (i) what drives zooplankton size distribution and whether zooplanktivorous fish (top-down) or resource availability and environmental condition (bottom-up) determine zooplankton community SS, (ii) whether traditional midwater trawling or modern hydroacoustic methods more reliably represent fish SS, and (iii) coral reef fish community SS and habitat structural complexity and their relationship across site-specific anthropogenic stressors. By analysing long term data, I first found that neither top-down or bottom-up forces drove the zooplankton community size distribution. Zooplankton SS seem robust against predation effects but a sensitive indicator for lake-wide energy availability and transfer efficiency in the food web. Then I found that hydroacoustic methods reliably represent pelagic fish community SS, making it a great alternative to traditional and more invasive fish removal sampling methods. Finally, I discovered that coral reef fish SS slope and structural complexity of the reef exhibited a significant negative relationship on two of the examined reef sites which are least exposed to anthropogenic disturbances. A consistent pattern of fish SS and reef complexity was missing, indicating that other environmental factors may also impact the assessed parameters. Overall, my studies show the range of applications of SS to effectively answer universal questions from trophic interactions and the importance of habitat characteristics in a community to a methodological comparison of fish sampling methods. The high variability of SS behaviour and the influence of environmental conditions further underlines the importance to include data on a large temporal scale. Community information, such as taxonomic identity and consideration of species-specific feeding and habitats preferences, for example, are still beneficial in some cases to answer ecologically questions extensively.

Predicting the impacts of non-native species remains one of the greatest challenges to invasion ecologists. Because of their insularity, freshwater systems are particularly vulnerable to invasions, especially from non-native predators. The research in this thesis explores the role of abiotic and biotic factors in mediating the distribution and impact of Bythotrephes longimanus, a predatory cladoceran that has been introduced to freshwater systems in North America. Although the general impacts of this invasion have been documented, little is known about the factors that modulate them. Using a combination of field surveys and experiments, I tested several hypotheses concerning the influence of interactions with native species, as well as the role of heterogeneity in the light environment, in mediating the impact of Bythotrephes. Results demonstrated that biotic resistance by native macroinvertebrate predators does not play a limiting role in the establishment success of Bythotrephes. However, the within-lake distribution of Bythotrephes was influenced by these macroinvertebrates, suggesting that the native predator context matters when trying to understand the impacts of non-native predators. This was demonstrated with a mesocosm experiment in which the impact of Bythotrephes was constrained by the native Chaoborus larvae. In terms of the abiotic environment, in situ feeding experiments demonstrated that refuges from impact could exist for some prey taxa, as the outcome of predation by Bythotrephes was dependent on light availability and some prey taxa were more successful at evading predation under low light conditions. Finally, results show that adaptive behaviour by prey is also an important determinant of impact, as migrating Daphnia can escape predation effects by Bythotrephes. The combination of light-limited predation and a shallow distribution by Bythotrephes selects for prey that occupy relatively deeper positions during the day. As a whole, this research highlights the importance of complex interactions in mediating the impact of Bythotrephes and may help to explain some of the variation that has been documented among invaded lakes. A better understanding of these complex interactions can improve our ability to anticipate impacts as Bythotrephes continues to spread, as well as provide insight on some of the long-term effects following invasion. / Thesis (Ph.D, Biology) -- Queen's University, 2013-06-17 09:26:35.221

A comprehensive investigation into the relationship between physical forcing and sus- pended particles in the shallow shelf region of the Western English Channel has been conducted, in order to evaluate the temporal dynamics of suspended particle populations. Measurements were taken across tidal cycles and seasons at station L4, part of the Western Channel Observatory (WCO), using the combination of a free-fall microstructure profiler and holographic imaging. Confirmation that L4 is weakly stratified is given, and that the formation of the seasonal thermocline is substantially altered by the spring-neap cy- cle. Stratification is variable and prone to periodic and partial erosion from atmospheric forcing during any point in any season. L4 undergoes moderate turbulent dissipation, principally as a result of tidal forcing. Typically, values of ε do not exceed 10−4 W kg−1 . L4 also exhibits tidal asymmetry, chiefly in response to stratification which, albeit weak, is frequently able to suppress turbulence when generated from the sea bed. The potential energy anomaly is small at L4, as expected for a weakly-stratified environment. Maxi- mum values in summer were shown to not exceed 50 J m−3 . Values of bed stress, τ0 , are rarely greater than around 0.18 N m−2 . Nonetheless, the critical erosion threshold falls below this, and is therefore smaller than that observed in similar locations around the UK. Seasonality in the amount of material resuspended from the seabed is important at L4. The presence of certain biological particles strongly influence particle size and may also determine if a given particle is lifted from the bed. Particles ≥ 200 μm are relatively rare, the site is dominated by particles smaller than this value in line with many other UK sites. Under certain conditions the theoretical maximum limit of particle size, the Kolmogorov length scale, does not hold and many examples of occasions when this threshold is exceeded are shown. This may generate important consequences in subsequent work undertaken at this site and other temperate shelf locations globally, particularly as these results indicate that maximum particle size appears to be governed less by the size of the local turbulent eddies and more by the presence of biological particles. This is another key seasonal component to particle dynamics in the Western English Channel. Phytoplankton populations are readily advected into and out of the L4 site, calling into question the current sampling strategy of the WCO to rely exclusively upon point measurements. Small increases in atmospheric forcing have the ability to rapidly disperse patches of phytoplankton, possibly to the point of cell mortality. Traditional sampling techniques for assessing zooplankton density have been shown to radically underestimate the number of animals present at L4, which will increase error estimates on current ecosystem models.

In this thesis I explore the effect of parameter uncertainty in ocean biogeochemical models on the calculation of carbon uptake by the ocean. The ocean currently absorbs around a quarter of the annual anthropogenic CO2 emissions to the atmosphere [Scholes et al., 2009], slowing the increase in radiative forcing associated with the increasing atmospheric CO2 concentration. Ocean biogeochemical models have been developed to study the role of the ocean ecosystem in this process. Such models consist of a greatly simplified representation of the hugely complex ocean ecosystem. This simplification requires extensive parameterisation of the biological processes that convert inorganic carbon to and from organic carbon in the ocean. The HadOCC ocean biogeochemical model is a Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD) model that is used to represent the role of the ocean ecosystem in the global carbon cycle in the HadCM3 and FAMOUS GCMs. HadOCC uses twenty parameters to control the processes of biological growth, mortality, grazing and detrital sinking that control the uptake and cycling of carbon in the ocean ecosystem. These parameters represent highly complex and in some cases incompletely understood biological processes, and as a result are uncertain in value. A sensitivity analysis is performed to identify the HadOCC parameters that due to uncertainty in value have the greatest possible effect on the exchange of CO2 between the atmosphere and the ocean—the air-sea CO2 flux. These are found to be the parameters that control phytoplankton growth in the well lit surface ocean, the formation of carbonate by marine organisms and the sinking of biological detritus. The uncertainty in these parameters is found to cause changes to the air-sea CO2 flux calculated by the FAMOUS GCM. The initial effect of these changes is equivalent to the order of the error of current estimates of the net annual carbon uptake by the ocean (2.2 ± 0.3 Pg C y−1 [Gruber et al., 2009], 2.2 ± 0.5 Pg C y−1 [Denman et al., 2007]). This indicates that while the effect of ocean biogeochemical parameter uncertainty is non-negligible, it is within the bounds of the uncertainty of the total (inorganic and organic) ocean carbon system, and is considerably less than the uncertainty in the carbon uptake of the terrestrial biosphere [Houghton, 2007]. However, as the ocean plays a crucial role in the global carbon cycle and the regulation of the Earth’s climate, further understanding and better modelling of the role of the ocean ecosystem in the global carbon cycle and its reaction to anthropogenic climate forcing remains important.

Zooplankton assemblages were examined from waters off the west coast of Scotland encompassing the Firths of Lorn and Clyde, the North Channel, and the Malin Shelf. Size fractionated samples (coarse, >1000μm; medium, 1000μm-330μm; fine, 330μm-180μm) were collected with a submersible pump from 10m and 30m depth in March (1987) and May (1986) providing a composite picture of the fauna in early and late spring conditions, respectively. The feasibility of using image analysis as a method for processing zooplankton samples was examined. Although a programme was successfully operated to obtain individual measurement data, much work is still required before a fully automated programme for routine use by planktologists is available. Total zooplankton numbers and biomass, and species distributions and relative abundances were examined. Species assemblages were identified using multivariate analyses. Biomass and abundance spectra by size were examined for the major station groupings. In general, meroplankton dominated the fauna in the Firth of Lorn while large numbers of Calanus spp. occurred in the Firth of Clyde. Small copepods such as Oithona spp. were characteristic of the assemblage on the Malin Shelf. Salinity, followed by temperature, showed the strongest association with the observed station clusters. Chlorophyll a and depth did not generally appear to influence station groupings. The potential for the mixing and exchange of zooplankton between the regions of the study area was evaluated. The results suggest that zooplankton may be entrained from the Firth of Clyde by the Scottish Coastal Current during the spring period. The Malin Shelf may also be an important source of zooplankton for the Firth of Lorn during winter months when an onshore flow of Atlantic water occurs.

Acidic atmospheric deposition and acidification of soil and water on the Earth's surface, due to emissions of sulfur and nitrogen into the atmosphere, have led to drastic changes in the composition of surface waters and their biota in many regions of the world over the last century. The number of species and biomass of phytoplankton, zooplankton and benthos were reduced, or some components (zooplankton, zoobenthos, fish) became extinct. In the Jizera Mountains (Northern Bohemia, Czech Republic), the man-made acidification has always been combined with a natural acidity (dystrophy) of waters, caused by a high amount of organic acids. Despite a strong recovery of water chemistry from acidification, that has started in the 1990s, biological recovery is delayed and much more complex. This master thesis is a study of the succession of zooplankton (crustaceans) in mountain reservoirs Souš, Bedřichov and Josefův Důl after decades of strong acidification. Biological recovery from acidification has been in progress differently in the drinking water reservoir Souš, which has long been limed, in the Bedřichov reservoir with naturally high content of organic material, and in the drinking water reservoir Josefův Důl, which is the largest and deepest one and which was most affected by acidification. Recovery of...

COMPARATIVE STUDY OF FLUVIAL LAKES IN FLOODPLAINS OF THE ELBE, LUŽNICE AND SVRATKA RIVERS Petra Havlíková ABSTRACT The aim of the thesis was to specify key differences in chemistry and biota (zooplankton communities) among fluvial lakes in three regions of Czech Republic: "střední Polabí" (central part of the Elbe River on the territory of Bohemia), "Horní Lužnice" (the upper part of the Lužnice River on the territory of Bohemia), and the Svratka River near Milovy (upper part of the Svratka River). The 10 studied lakes of the three regions differ in size, geology, shading, the influence of the river, and the level of anthropogenic impact. The following hypotheses were tested: 1) The chemical composition of the water in fluvial lakes is significantly different in different areas (floodplains). In the central Elbe River floodplain, there are the highest values of conductivity and concentrations of organic matter and nutrients. Fluvial lakes of the Svratka River floodplain near Milovy show the lowest level of these parameters, and fluvial lakes of the upper Lužnice River occur between the two previous regions. 2) The chemistry of fluvial lakes that have contact with the river through surface connection is significantly influenced by the river, and differs from the chemistry in fluvial lakes without any direct...

Cyclopoids are together with Calanoids and Harpacticoids a part of the largest, very diverse group of crustaceans and the most numerous aquatic metazoans of the world. The history of their research goes as far back as to the beginning of 19th century when the first cyclopoid copepods were described. The taxonomy of cyclopoids started to develop gradually since that time, adding new and more detailed methods and morphological characters, as well as a certain degree of taxonomical confusion. In last decades, the molecular-genetic techniques of DNA sequencing have become available offering a new independent tool for taxonomists. This work contains different studies concerning the morphology, taxonomy, ecology, distribution and colonisation of cyclopoid copepods, with the use of molecular tools as a uniting element. Chapter 1 of this thesis summarizes basic knowledge about the taxonomy, morphology and biology of cyclopoid copepods and introduces the following chapters containing four studies presented as single publications. The taxonomy of copepods of the genus Cyclops is based mainly on the morphology which is sometimes ambivalent and some of the most problematic species groups are presented here. Chapter 2 presents our unique results, the first reconstruction of phylogenetic relationships among 15...

Desenvolveu-se, pela Universidade de São Paulo, o protótipo de um equipamento submersível de captura para estudo de plâncton. Baseado na técnica shadowgraph, é formado por um feixe de LED infravermelho colimado e uma câmera de alta resolução, executados por um sistema de controle automatizado. Foram utilizados softwares de visão computacional desenvolvidos pelo Laboratório de Sistemas Planctônicos (LAPS) que executam várias tarefas, incluindo a captura e segmentação de imagens e a extração de informações com o intuito de classificar automaticamente novos conjuntos de regiões de interesse (ROIs). O teste de aprendizado de máquina contou com 57 mil quadros e 230 mil ROIs e teve, como base, dois algoritmos de classificação: o Support Vector Machine (SVM) e o Random Forest (RF). O conjunto escolhido para o treinamento inicial continha 15 classes de fito e zooplâncton, às quais foi atribuído um subconjunto de 5 mil ROIs. Os ROIs foram separados em grandes classes de, pelo menos, 100 ROIs cada. O resultado, calculado por meio do algoritmo de aprendizagem RF e SVM e fundamentado no método de validação cruzada, teve uma precisão de 0,78 e 0,79, respectivamente. O conjunto de imagens é proveniente de Ubatuba, no estado de São Paulo. Os perfis verticais elaborados apresentaram diferentes padrões de distribuição de partículas. O instrumento tem sido útil para a geração de dados espacialmente refinados em ecossistemas costeiros e oceânicos. / The University of São Paulo developed an underwater image capture system prototype to study plankton. Based on the shadowgraphic image technique, the system consists of a collimated infrared LED beam and a high-resolution camera, both executed by an automated control system. Computer vision software developed by the research laboratory was used to perform various tasks, including image capturing; image segmentation; and extract information to automatic classify news regions of interest (ROIs). The machine learning test had 57,000 frames and 230,000 ROIs, based on two classification algorithms: Support Vector Machine (SVM) and Random Forest (RF). The chosen set of the initial training had 15 classes of phytoplankton and zooplankton, which was assigned a subset of 5,000 ROIs. Big classes of, at least, 100 ROIs each were organized. The result, calculated by the RF and SVM learning algorithm and based on the cross-validation method, had a 0.78 and 0.79 precision score, respectively. The image package comes from Ubatuba, in the state of São Paulo. The vertical profiles elaborated presented different particles distribution patterns. The instrument has been useful for spatially refined data generation in coastal and oceanic ecosystems.