The overall aim of this thesis was to elucidate the relative importance of the bacterial and fungal energy channels within the soil food web and to differentiate and appreciate the differences in niche of the soil fauna when affected by differing land management. Feeding niche of the soil fauna is ambiguous and has been previously determined by observation, inference or biochemical studies. One method that can determine feeding preferences in situ is the use of stable isotopes. Stable isotopes trace the passage of C and N through different trophic levels, both at natural abundance and by the addition of a pulse of enrichment. The work described within this thesis describes the development of methods of culturing and labelling organisms for use in stable isotope studies. Bacteria, protozoa and fungi were cultured with stable isotopes enriched to 99 atom% and their growth and survival monitored. Utilising stable isotope enriched organisms means that empirical testing of the feeding interactions can occur and that differences between the bacterial and fungal energy channels can be explored. Two field sites were chosen to assess how management changes affect the food web, both sites were historically grassland with the same soil type, but one was converted to a willow woodland twenty years ago. The results of these studies have shown, at natural abundance a grassland and woodland habitat with very different stable isotope signatures, reflecting plant and soil composition, as well as differences in trophic niche and C drivers. The introduction of enriched bacteria illustrated that bacterial feeding was more widespread than normally portrayed in food web diagrams. The introduction of enriched protozoa highlighted that protozoan feeding by soil fauna was more prevalent in the grassland habitat; reflecting differences in linkages between trophic levels within the two habitats. Methods were also developed to “grow” enriched fungal hyphae back into soil food webs in a comparable way to the investigation of the bacterial energy channel. Different species of saprotrophic fungi were found to fractionate to differing extents when grown on the same natural abundance media and the fungus Absidia cylindrospora's growth was impacted when grown on a dually enriched medium. We can now infer that the bacterial energy channel is not as divergent from the fungal energy channel as previously hypothesised. The majority of soil fauna were found to be omnivorous through empirical results, consuming bacteria and protozoa, even when they were considered to be fungal feeders by the literature. The different habitats within the study were found to have different C drivers, with roots and soil being the primary driver in the grassland whilst litter was in the woodland, consequently favouring different food webs. This work makes a first step in measuring the contribution of the different feeding channels and feeding interactions occurring within the different trophic levels in the two habitats and shows the effect that one change in management has had over the entire faunal assemblage.

En dépit de la ré-oligotrophisation de nombreux lacs d'Europe du nord au cours des deux dernières décennies, les développements massifs de cyanobactéries toxiques, telle que Planktothrix rubescens, adaptée aux écosystèmes mésotrophes, sont encore largement observés. Parmi les cyanotoxines produites par cette espèce, les microcystines (MCs) sont les toxines les plus fréquemment rencontrées et sont reconnues comme des molécules perturbatrices de tous les compartiments trophiques des écosystèmes lacustres. Ces blooms toxiques affectent notamment les lacs péri-alpins pour lesquels des risques de contaminations des populations piscicoles exploitées ont été démontrés. Cependant, il existe encore un manque de connaissances important tant concernant les voies de transfert de ces toxines au sein des réseaux trophiques limniques, que leurs effets physiologiques sur les populations de poisson. Dans le cadre de ce travail de thèse, deux modèles de poissons, dont les répartitions spatiales verticales diffèrent (juvéniles de perche et corégones), ont été considérés. Les objectifs principaux ont été traités d'une part au travers d'une approche expérimentale (par gavage) visant à analyser les processus d'accumulation et de détoxification, ainsi que les effets génotoxiques des MCs sur ces deux espèces modèles. Les réponses physiologiques ainsi étudiées ont permis de mettre en évidence que les juvéniles de perche et les corégones sont capables de détoxifier une partie des MCs ingérées, mais cependant des effets génotoxiques sont observés suite à l'exposition des poissons aux MCs. D'autre part, des approches écosystémiques ont permis (1) d'explorer les effets potentiels de la présence du bloom sur la répartition spatiale des poissons (2) d'évaluer les niveaux de contaminations par les MCs pour les deux espèces de poisson en tenant compte de la variabilité saisonnière (3) d'identifier les principaux vecteurs zooplanctoniques de MCs jusqu'aux poissons. Les résultats acquis montrent que les filaments de P. rubescens constituent une ressource alimentaire en période de bloom pour les organismes zooplanctoniques brouteurs et qu'un transfert de MCs est possible jusqu'aux espèces zooplanctoniques prédatrices et in fine jusqu'aux poissons. Nos résultats mettent également en avant que les voies de contaminations ainsi que les intensités de contamination des poissons peuvent varier aussi bien à l'échelle saisonnière que journalière. Ces variations sont expliquées à la fois par les changements de régime alimentaire des poissons, les variations journalières de la production de MCs par P. rubescens, et les abondances et distributions verticales des différentes proies zooplanctoniques. A l'issue de ce travail, la part importante du transfert trophique des MCs jusqu'aux poissons a été vérifiée dans les cas des contaminations chroniques qui caractérisent les conditions de blooms des lacs péri-alpins (concentrations en cyanobactéries et en toxines modérées à fortes au cours de plusieurs mois). / Many deep peri-alpine lakes which are currently under re-oligotrophication are impacted by Planktothrix rubescens blooms. Among cyanotoxins produced by P. rubescens, microcystins (MCs) are the most commonly studied and are involved in many ecological disturbances. In peri-alpine lakes, these blooms might affect exploited fish species due to toxin contaminations. However, there is still a lack of knowledge regarding both transfer pathways of the toxin and their physiological effects on fish populations. In this work, two models of fish populations were considered (Young-Of-Year (YOY) perch and whitefish which exhibit distinct vertical distributions). The main objectives were on the one hand investigated through an experimental approach to analyze on the two model species, accumulation and detoxification processes as well as genotoxic effects of MCs. From these experiments, we showed that YOY perch and whitefish were able to detoxify part of the MCs but that genotoxic effects were still observed. On the other hand, ecosystemic approaches allowed (1) to explore the potential effects of the presence of bloom on the spatial distribution of fish, (2) to assess the levels of contamination by MCs for both fish species taking into account the seasonal variability, (3) to identify the main zooplanktonic vectors of MCs to fish. Our results revealed that the filaments of P. rubescens are a food resource for zooplankton grazers, and that a trophic transfer of MCs exists from herbivorous to their zooplanktonic predators and in fine to fish. Our results also highlight that the contamination pathways and their intensities could vary both at seasonal and daily scales. These variations are explained by both changes in fish diet, daily variations in the production of MCs by P. rubescens, and abundances and vertical distributions of zooplanktonic preys. Overall, we highlighted the importance of MCs trophic transfer in fish intoxication in the case of chronic contaminations observed in peri-alpine lakes (moderate to severe cyanobacteria/toxins concentrations over several months).