Some of the major problems we face today are human induced changes to the nitrogen (N), phosphorus (P) and carbon (C) cycles. Predicted increases in rainfall and temperature due to climate change, may also increase dissolved organic matter (DOM) inflows to freshwater ecosystems in the boreal zone. N, P, C and light, are essential resources that most often limit phytoplankton (PPr) and bacterial production (BP) in the pelagic zone of lakes. PPr and BP not only constitute the total basal C resource for the pelagic aquatic food web, but also influence ecosystem function and biogeochemical cycles. In this thesis I studied how N, P, C and light affect the relative and absolute rates of PPr and BP, along a wide latitudinal and trophic gradient using published data, and in two in situ mesocosm experiments in a clear water oligotrophic lake. In the experiments I manipulated bottom-up drivers of production and top-down predation to examine how these factors interact to affect pelagic food web structure and function. The most important predictors of PPr globally (Paper I) were latitude, TN, and lake shape. Latitude alone explained the most variation in areal (50%) and volumetric (40%) PPr. In terms of nutrients PPr was primarily N-limited and BP was P-limited. Therefore bacteria and phytoplankton were not directly competing for nutrients. BP:PPr was mostly driven by PPr, therefore light, N, temperature and other factors affecting PPr controlled this ratio. PPr was positively correlated with temperature, but not BP, consequently, higher temperatures may reduce BP:PPr and hence the amount of energy mobilised through the microbial food web on a global scale. In papers II and III interaction effects were found between C-additions and top-down predation by young-of-the-year (YOY) perch. Selective predation by fish on copepods influenced the fate of labile C-addition, as rotifer biomass increased with C-addition, but only when fish were absent. Interaction effects between these top-down and bottom-up drivers were evident in middle of the food web, which is seldom examined in this type of study. Although the energy pathway from bacteria to higher consumers is generally longer than from phytoplankton to higher trophic levels, increased BP still stimulated the biomass of rotifers, calanoid copepods and YOY fish. However, this appeared to be mediated by intermediate bacterial grazers such as flagellates and ciliates. Light was an important driver of crustacean zooplankton biomass (paper IV), but the light:nutrient hypothesis was inadequate to predict the mechanisms behind the decrease in zooplankton biomass at low light. Instead, it appeared that reduced edibility of the phytoplankton community under low light conditions and reduced BP most strongly affected zooplankton biomass. Thus, the LNH may not apply in oligotrophic lakes where PPr is primarily N-limited, Daphnia is rare or absent and mixotrophic phytoplankton are abundant. N, P, C and light manipulations have very different effects on different parts of the pelagic food web. They influence the relative rates of PPr and BP, affect phytoplankton community composition, alter the biomass of higher trophic levels and change pathways of energy transfer through the pelagic food web. This thesis adds valuable information as to how major changes in these resources will affect food web structure and function under different environmental conditions and future climate scenarios. / Lake ecosystem response to environmental change

Ecological communities are collections of species bound together by their influences on one another. Community structure, therefore, refers to the way in which these influences are organised. As a result, ecologists are mainly interested in the factors driving the structure, functioning, and persistence of communities. The traditional focus, however, has been on the feeding relationships among species (direct trophic interactions), whereas relationships mediated by a third species or the environment (indirect interactions) have been largely overlooked. I investigated the role of indirect interactions in structuring communities through a series of field experiments in a diverse assemblage of arthropods living on a Brazilian shrub species. I experimentally reduced the abundance of the commonest galler on the shrub and found that the perturbation resonated across the food web, affecting its structure and robustness. Since there was no potential for these effects to be propagated directly or indirectly via the documented trophic links, the effects must have spread non-trophically and/or through trophic links not included in the web. Thus, I investigated non-trophic propagation of effects in the system. I demonstrate that hatched galls of the commonest galler, which serve as habitat for other species, can mediate non-trophic interactions that feedback to the galler modifying its interactions with parasitoids and inquiline aphids. I performed further manipulative experiments, excluding ants, live galls and hatched galls, to reveal mechanisms for the non-trophic interaction modifications observed in this system. Finally, I explored how non-trophic interaction modification could affect the structure and stability of a discrete ecological community in the field. I investigated how the densities of certain pairs of groups relate to each other, and how their relationship changes in relation to a third group. Then, I assembled an "effect network" revealing, for the first time in an empirical community, a hidden web of non-trophic indirect interactions modifying the direct interactions and modifying each other. Overall, the thesis presents evidence that communities are strongly interconnected through non-trophic indirect interactions. This is one of the first empirical demonstrations of the context-dependent modification of interactions via non-trophic interactions. However, determining the mechanisms behind such interaction modifications may be unfeasible. Understanding how the observed effects relate to community structuring requires shifting our focus from bipartite interaction networks to a more holistic approach.

Les écosystèmes lacustres sont de plus en plus soumis à de multiples perturbations mais leur réponse est encore trop rarement considérée de façon globale. En effet, au travers d'un jeu d'interactions complexes, chaque perturbation peut moduler l'intensité de l'impact des autres sur les lacs, et de ce fait, leur réponse. Dans ce contexte, ce travail doctoral est axé sur l'approfondissement de notre compréhension de la réponse des lacs à un contexte de perturbations multiples, sur le long terme. Pour cela, trois grands lacs profonds (le lac Léman, du Bourget et d'Annecy), soumis à une perturbation régionale similaire (i.e., le réchauffement climatique) et à deux perturbations locales (i.e., les changements dans le statut trophique et dans les pratiques de gestion piscicole) d'intensités différentes, ont été choisis. La réponse de ces lacs à ces changements a été abordée au travers d'une approche paléolimnologique, basée sur les cladocères. En effet, la capacité de ceux-ci à intégrer les changements temporels dans le réseau trophique pélagique en réponse aux trois perturbations environnementales en fait un modèle adéquat pour reconstruire les changements à l'échelle de la communauté pélagique. Plus précisément, nous avons abordé (i) les changements dans les communautés de cladocères, au cours du siècle dernier, en réponse aux trois perturbations environnementales et (ii) l'impact de ces perturbations sur les stratégies de reproduction des Daphnies. Cependant, le manque de connaissance dans les grands lacs profonds sur la représentativité des communautés sources de cladocères par les assemblages de restes archivés dans les sédiments a tout d'abord conduit à faire un point méthodologique. Ce dernier a abouti à la mise en évidence de différences dans le niveau de représentation de communautés sources de cladocères selon le type de restes utilisés. La composition taxonomique et la structure en taille des restes parthénogénétiques (i.e., exosquelettes) reflètent relativement bien celle des communautés sources. Quant aux éphippies (œufs de dormance), elles se révèlent des indicateurs fiables pour reconstruire les comportements de reproduction. Suite à ces résultats, les reconstructions paléolimnologiques des communautés de cladocères montrent que leur trajectoire écologique était contrôlée par des interactions complexes entre les trois pertubations différentes, selon les périodes de temps et entre les lacs. De plus, la réponse des communautés de cladocères au climat était différente entre les trois lacs comme une fonction de l'intensité des forçages locaux. Ces observations suggèrent qu'il est important d'inclure le rôle des perturbations locales dans la prédiction de l'impact futur des changements climatiques sur les lacs. L'impact des perturbations environnementales sur le comportement de reproduction des Daphnies est tel que des évènements d'hybridation interspécifique ont été observés. Cependant, ces évènements d'hybridation sont issus de sensibilité aux trois perturbations environnementales différentes entre les espèces de Daphnies. / Lake ecosystems are increasingly subjected to multiple perturbations but their response is too rarely considered in overall. But, though a complex set of interactions, each perturbation can modulate the intensity of the impact of each other on lakes, and thus their response. In this context, this work is focused on deepening our understanding of the response of lakes in a context of multiples perturbations, over the long-term. We studied this response performing a paleolimnological approach (based on cladoceran) on three large, deep lakes (Lakes Geneva, Bourget and Annecy) submitted to a similar regional perturbation (i.e., climate warming) and varying intensities of two local perturbations (i.e., changes in nutrient inputs and fisheries managment practices). The ability of cladoceran to integrate the temporal changes in the pelagic food web in response to three environmental perturbations makes them a suitable model to reconstruct changes in the whole pelagic community. Specifically, we addressed (i) changes in cladoceran communities, during the last century, in response to three environmental perturbations and (ii) the impact of these perturbations on reproductive behavior of Daphnia. However, the lack of knowledge in large, deep lakes on the representativity of source cladoceran communitites by fossil assemblages in sediments firstly led to a methodological calibration. This last showed that the represention level of source communities was different according to the type of remain. Parthenogenetic remain assemblages (i.e., exoskeleton) reflect accurately the taxonomical and size structure of source communities in contrast to ephippia which are reliable proxy to reconstruct reproductive behavior. Following these results, the paleolimnological reconstructions of cladoceran communities showed that their ecological trajectories are controlled by complex interactions between the three perturbations, according to time periods and lakes. Moreover, the response of cladoceran communties to climate was different between the three lakes as a function of the intensity of local forcings. These observations suggest that it is important to include the role of local perturbations in predicting the future impact of climate change on lakes. The impact of environmental perturbations on the reproductive behavior of Daphnia is such that interspecific hybridization events were observed. However, these hybridization events were the result of different sensitivity to perturbations among Daphnia species.

A food web comprises exchanges of matter and energy that occur among species and between biotic and abiotic environment. Given that abiotic components form the basal resources, the approach of this work consists of evaluating the effects of nutrients input in strategic models that describe food web and chain dynamics. Its focus lies on the determination of the nature of equilibrium populations as well as on their dynamics for different functional responses. Strategic models that describe the behavior of interactive populations under nutrient inputs are an important basis for outlining general phenomena that occur in community dynamics. / Uma rede trófica reúne as trocas de matéria e energia que ocorrem entre as espécies e entre o meio biótico e abiótico. Visto que os componentes abióticos formam a fonte de recursos basais, a abordagem deste trabalho consiste na avaliação dos efeitos da entrada de nutrientes alóctones em modelos estratégicos que descrevem a dinâmica de redes e cadeias tróficas, concentrando-se na determinação das características das populações de equilíbrio e das dinâmicas das espécies com diferentes respostas funcionais. Modelos estratégicos que contêm informações acerca do comportamento de populações interativas frente à entrada de nutrientes são uma base importante no delineamento de fenômenos gerais que podem ocorrer dentro da dinâmica de comunidades.

Dans les agroécosystèmes, la biodiversité fonctionnelle et la biodiversité associée fournissent de nombreux services à l'homme dont la pollinisation, la régulation biologique et le cycle des nutriments. L'association des cultures est une pratique agricole qui augmente la diversité des plantes dans les agroécosystèmes, fournit des ressources alimentaires alternatives et structure les communautés des arthropodes. Elle favorise les prédateurs généralistes pour la régulation biologique des ravageurs. Cette étude vise à comprendre comment la diversité des plantes, à l'échelle de la parcelle, structure les réseaux trophiques des arthropodes et peut participer à améliorer la régulation biologique des ravageurs. Tout d'abord, une méta-analyse a été réalisée afin de rechercher la relation générale liant la diversité végétale considérée à l'échelle locale et le contrôle des insectes ravageurs par les prédateurs généralistes. Ensuite, sur un réseau de 20 parcelles paysannes de la région de Njombé au Cameroun, nous avons étudié l'effet de la diversité des plantes cultivées sur la structure du réseau trophique des arthropodes. Les résultats ont montré que l'abondance des prédateurs était positivement corrélée avec la diversité des plantes alors que celle des herbivores était négativement corrélée avec la diversité des plantes. L'effet inverse de la diversité des plantes sur les abondances des prédateurs et des herbivores suggère que des effets top-down structurent la communauté des arthropodes dans les parcelles de plantain. Enfin, l'effet de trois cultures couramment associées au plantain (maïs Zea mays, macabo Xanthosoma sagittifolium, et pistache Lagenaria siceraria) sur i) la structure de la communauté des fourmis et ii) les dégâts de Cosmopolites sordidus ont été étudiés dans un essai réalisé en station expérimentale. Les trois cultures associées ont eu un effet significatif sur l'abondance de tous les taxa de fourmis collectés mais le sens et la magnitude de cet effet ont varié selon les taxa. Cela montre le levier que constituent les cultures associées pour structurer la communauté des prédateurs généralistes de l'agroécosystème. Les abondances de tous les taxa de fourmis étaient également corrélées avec les dégâts de C. sordidus. Les abondances de Camponotus spp., Monomorium spp., Paratrechina longicornis et Tetramorium sp. étaient négativement corrélées avec les dégâts de C. sordidus montrant leur potentiel de régulation de ce ravageur. Cette étude à l'échelle de la communauté de l'agroécosystème suggère qu'il est nécessaire de prendre en compte les effets de la diversité végétale à tous les niveaux trophiques pour espérer maximiser le service de régulation des ravageurs.Mots clés : Diversité des plantes, cultures associées, réseaux trophiques, arthropodes, fourmis, structure de la communauté / Functional diversity and associated biodiversity in agroecosystems provide and promote important services to human society such as pollination, biological control, and nutrient cycling. Intercropping is a practical way to increase plant diversity in agroecosystems and participates to provide alternative foods and to structure arthropod communities, including generalist predators involved in pest control. To better understand how plant diversity structures the arthropod food web and how the control of pest may be optimized, we first made one meta-analysis to understand the mechanisms linking plant diversity to pest control by generalist predators at local scale. We second studied the effect of plant diversity on the arthropod community in contrasted plantain fields. We showed that predator abundance was positively correlated with plant diversity while herbivore abundance was negatively correlated with plant diversity. This strong and inverse effect of plant diversity on herbivore and predator abundance suggests that top-down forces structure the arthropod community in plantain fields and that it should be possible to structure the predator community to better control herbivores including pests. In a third step, we measured the effect of combinations of three associated crops maize Zea mays, cocoyam Xanthosoma sagittifolium and gourd Lagenaria siceraria as intercrops on ant community structure and then the effect relation between ant abundances with Cosmopolites sordidus damages. The three associated plants had a significant effect on abundance of all ant species but in different magnitudes and with either negative or positive effect showing that the selection of plant species that are intercropped is an efficient way to structure the ant community. The abundances of all species of ants were positively or negatively correlated with the damages of C. sordidus larvae. The abundances of Camponotus spp., Monomorium spp., Paratrechina longicornis and Tetramorium sp. were negatively correlated to C. sordidus damage. These ants appear to be the best candidates for C. sordidus control. These findings will help in the design of plantain agroecosystems that enhance pest control services.Keywords: Plant diversity, intercropping, arthropod food webs, ants, interspecific interactions, habitat structure

Predators exert strong direct and indirect effects on ecological communities by intimidating their prey. Non-consumptive effects (NCEs) of predators are important features of many ecosystems and have changed the way we understand predator-prey interactions, but are not well understood in some systems. For my dissertation research I combined a variety of approaches to examine the effect of predation risk on herbivore foraging and reproductive behaviors in a coral reef ecosystem. In the first part of my dissertation, I investigated how diet and territoriality of herbivorous fish varied across multiple reefs with different levels of predator biomass in the Florida Keys National Marine Sanctuary. I show that both predator and damselfish abundance impacted diet diversity within populations for two herbivores in different ways. Additionally, reef protection and the associated recovery of large predators appeared to shape the trade-off reef herbivores made between territory size and quality. In the second part of my dissertation, I investigated context-dependent causal linkages between predation risk, herbivore foraging behavior and resource consumption in multiple field experiments. I found that reef complexity, predator hunting mode, light availability and prey hunger influenced prey perception of threat and their willingness to feed. This research argues for more emphasis on the role of predation risk in affecting individual herbivore foraging behavior in order to understand the implications of human-mediated predator removal and recovery in coral reef ecosystems.

Establishing historical water velocities is a goal of Everglades restoration because of their role maintaining landscape topographic relief. However, flows may also change the trophic state of marshes by phosphorus loading. I used fatty acid (FA) and stoichiometric data to quantify how increased sheet flow altered the relative heterotrophic and autotrophic contributions to aquatic consumers in a field experiment that introduced flowing water to an Everglades marsh in November, 2014. Algal taxonomic composition was different between pre-flow and flow sampling, marked by increases in the nutrient exploiting Mougeotia species (green algae) during flow sampling. Dietary tracer FAs in consumers reflected changes in algal resources, including an increase in green algae-derived and a decrease in bacteria-derived FAs. These food web responses indicate that establishing historic water velocity in degraded wetlands can shift the origins of organic matter from a more detrital to more algal supported web.

Changes of habitats are amongst the main drivers of evolutionary processes. Corresponding shifts in the behaviour and life history traits of species might in turn also alter ecosystem attributes. The reproduction of Western European fire salamanders (Salamandra salamandra), in small pond habitats instead of first order streams, is one example of a recent local adaptation. Since fire salamander larvae are important top-predators in these fish free habitats, their presence likely changes various aspects of ecosystem functioning. Here, it was analysed how the ecological performance of salamander larvae in ponds in the Kottenforst in Western Germany changed in comparison to sympatric stream populations. Further, it was analysed how their presence in ponds influenced key ecosystem attributes such as prey density and diversity and aquatic-terrestrial linkage. To assess the impact of the life cycle shifts in salamanders on the pond functioning, detailed investigations of salamander larvae population dynamics, phenology, and macroinvertebrate community development in ponds were combined with experimental manipulations of the salamander presence. In the first part of this study, the impact of pond presence of fire salamanders in terms of ecosystem functioning focussing on aquatic terrestrial subsidy transfer was calculated. The study could show, that the adaptation of fire salamanders to breed in pools led to strong increases of animal-mediated import of terrestrial matter into the aquatic habitats. The hypothesis about the impact on macroinvertebrate communities derived from these calculations was then tested experimentally. It was shown, that presence of salamander larvae could influence some taxa of macroinvertebrates but they had only limited effects on the food web structure in their aquatic habitats. Yet, a high relevance of the subsidy exchange from aquatic to terrestrial and its high relevance for the predator persistence in the system could again be confirmed. Moreover, it was demonstrated, that the larval behaviour and performance could have a high inter-annual variability as a reaction to contrasting ecosystem constraints in comparison to the stream habitats. A fact that integrally separates the pond ecotype from stream ecotype conspecifics.

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