Lichens are, in most cases, sensitive to anthropogenic factors such as air pollution, global warming, forestry and fragmentation. Two studies are included in this thesis. The first is an evaluation of the importance of old oak for the rare epiphytic lichen Cliostomum corrugatum (Ach.) Fr. This study analysed whether C. corrugatum was limited by dispersal or restricted to tree stands with an unbroken continuity or the substrate old oaks. The results provide evidence that the investigated five populations in Östergötland, Sweden, of C. corrugatum exhibit substantial gene flow, an effective dispersal and a small genetic variation between the sites. Most of the genetic variation was within the populations. Thus, C. corrugatum is more dependent of the substrate old oaks, rather than limited by dispersal. The second study investigated possible range shift of some common macrolichens, due to global warming, from 64 sites in southern Sweden comparing the two years 1986 and 2003. The centroid of three lichen species had moved a significant distance, all in a north east direction: Hypogymnia physodes (L.) Nyl. and Vulpicida pinastri (Scop.) J.-E. Mattsson and M. J. Lai on the tree species Juniperus communis L. (50 and 151 km, respectively) and H. physodes on Pinus sylvestris L. (41 km). Considering also the non-significant cases, there is strong evidence for a prevailing NE direction of centroid movement.

Relevant information is essential for finding solutions in Integrated Water Management (IWM). Complex water systems and a need for increasing integration of sectors, actors and scales in IWM require new methods for developing and managing such information. This thesis investigates the role of information within the IWM process, as well as the main challenges for development of representative, accessibleand harmonized information. Results show how information needs and the information production process for IWM may be systematized, and indicate a large potential for information system development for IWM. However, in order to reach the full potential, today’s limited and heterogeneous water information needs to become more comprehensive, transparent, interoperable, dynamic, scalable and openly accessible. Large pressures on water systems are found in coastal catchment areas that are unmonitored across the local to the global scale, indicating a large importance of these areas for nutrient and pollutant loading. The globally accessible runoff data from catchment areas that are rich in pressures from population, agriculture and general economic activity further exhibit a rapidly declining trend during recent years. Major water system changes may therefore pass unnoticed if analyzed on the basis of openly accessible runoff global data. Furthermore, large discrepancies are found between land cover databases, which may result in major uncertainties in quantification of water and evapotranspiration flows. Identified information challenges may be relatively easily overcome by making better use of available information, while other challenges such as development of consistent baselines of core data and a possible re-prioritization of water-environmental monitoring programs may be both difficult and costly.

<p>Lichens are, in most cases, sensitive to anthropogenic factors such as air pollution, global warming, forestry and fragmentation. Two studies are included in this thesis. The first is an evaluation of the importance of old oak for the rare epiphytic lichen Cliostomum corrugatum (Ach.) Fr. This study analysed whether C. corrugatum was limited by dispersal or restricted to tree stands with an unbroken continuity or the substrate old oaks. The results provide evidence that the investigated five populations in Östergötland, Sweden, of C. corrugatum exhibit substantial gene flow, an effective dispersal and a small genetic variation between the sites. Most of the genetic variation was within the populations. Thus, C. corrugatum is more dependent of the substrate old oaks, rather than limited by dispersal. The second study investigated possible range shift of some common macrolichens, due to global warming, from 64 sites in southern Sweden comparing the two years 1986 and 2003. The centroid of three lichen species had moved a significant distance, all in a north east direction: Hypogymnia physodes (L.) Nyl. and Vulpicida pinastri (Scop.) J.-E. Mattsson and M. J. Lai on the tree species Juniperus communis L. (50 and 151 km, respectively) and H. physodes on Pinus sylvestris L. (41 km). Considering also the non-significant cases, there is strong evidence for a prevailing NE direction of centroid movement.</p>

The aim of this study is to investigate the components of religion and spirituality in the specific context of "Fryshuset" – a multicultural and glocal arena. Against the backdrop of contemporary researchers such as Heelas and Woodhead and their hypothesis about the "spiritual revolution" and a "new spirituality", as well as the postmodern discussion about "the return of God", this study discusses how religious change can be understood in the context of Fryshuset. The theoretical point of departure is taken in a hermeneutical method where Fleck´s theory about "thought-collective" and Gidden´s theory about the "duality of structure" are used in order to understand and describe the dialectical relationship between individual and social structure. The method used in this study is qualitative. The interviews are made of six individuals representing different social projects at Fryshuset. By analyzing the material from the field study through theories on religious change, three areas are identified: "The subjective turn" Religion and spirituality A Cosmopolitan interpretation of life  The result of this study is that the religiosity among the interviewed can be described through Taylor’s understanding of the "subjective turn". Furthermore they are also part of a "double subjective turn" understood as an internalized subjective turn. Despite the fact that a lot of what the informants describe corresponds to Heelas and Woodheads theories of "subjective life spirituality" it is not relevant to talk about a "spiritual revolution". However, according to Beckford´s theories about religion as a "cultural resource" it can be described as a kind of new spirituality which is used in order to act and think global. The individuals use religion and spirituality as a cultural resource in their formation of a larger cosmopolitan interpretation of life.

Understanding the role of forests in the cycling of methane (CH4) and carbon dioxide (CO2) is of importance to the elucidation of global greenhouse gas budgets. Previous studies have shown aerated forests soils to be net sinks of atmospheric CH4 and sources of carbon dioxide. While much research has focused on the role of forest soils as CO2 sources and CH4 sinks, few studies have utilized 13C-isotope studies to clarify the nature of subsurface CO2 production and CH4 consumption. The present study, carried out in 3 temperate forest environments on Vancouver Island during 2006 and 2007, and a boreal forest in northern Quebec in 2005, is intended to address this paucity of information. The isotope and concentration data corroborates previous studies in suggesting that both temperate and boreal forest environments act as net CH4 sinks and CO2 sources. No clear evidence of methanogenesis is apparent in either Vancouver Island or northern Quebec, where the isotopic composition of subsurface CH4 is influenced by diffusive and biological fractionation. Near-surface photosynthetic uptake may have a strong influence on the isotopic composition of soil CO2 and the resultant fluxes, acting to reduce apparent fluxes due to CO2 consumption. Intra-site variability of CH4 and CO2 fluxes indicates that the use of two static chambers in a single site, while sufficient for the confirmation of gas uptake or emission, may be less adequate in the determination of actual rates of efflux/influx. Future studies should address this by either sampling a larger area, installing a greater number of chambers, or by utilizing entirely different methods, such as the use of eddy covariance techniques.

Le déclin mondial des anguilles tempérées est lié aux effets synergiques de multiples pressions anthropiques. Cependant, la complexité du cycle de vie des anguilles et leurs incroyables capacités d’adaptation font qu’il est très difficile de connaître le poids relatif de chacune des pressions. Les anguilles tempérées sont trois espèces catadromes qui ont de très grandes aires de répartition pendant leurs phases de croissance continentales. Leurs panmixies et les longues dérives larvaires passives sont des freins aux adaptations locales, cependant on observe des patrons spatiaux de traits d’histoire de vie corrélés aux gradients environnementaux, à l’échelle du bassin versant et de son aire de répartition. Ce doctorat vise à (i) démontrer si ces patrons spatiaux d’histoire de vie sont le résultat de deux réponses adaptatives : le polymorphisme génétique et la plasticité phénotypique adaptative, et (ii) à réévaluer l’effet des différentes composantes du changement global en prenant en compte ces réponses adaptatives. Dans ce cadre, GenEve el, un modèle d’optimisation individu-centré a été développé. Ce modèle postule que la sélection de l’habitat dépendant du génotype et la plasticité phénotypique sont deux mécanismes permettant de faire face à l’hétérogénéité environnementale. Avec de telles hypothèses, le modèle permet de reproduire les patrons spatiaux observés concernant la longueur à l’argenture, le sexe-ratio et la distribution des écotypes. Par la suite, différents types des pressions anthropiques - les pêcheries de civelles et d’anguilles argentées, les obstacles à la migration de montaison et les mortalités dues aux turbines hydroélectriques - ont été intégrés dans le modèle.L’objectif a été d’évaluer leurs impacts sur l’échappement, à la fois en nombre, mais aussi sur différents attributs comme le sexe-ratio, la répartition entre génotypes, la longueur à l’argenture moyenne, et la production globale d’oeufs. Les résultats montrent que la pression qui induit la plus forte mortalité directe n’a pas forcément la plus forte influence sur la biomasse féconde et n’exerce pas nécessairement la pression sélective la plus forte sur les écotypes. Le modèle met aussi en évidence que la plasticité phénotypique peut être source de résilience pour la population et qu’elle atténue l’effet de certaines pressions, mais pas de toutes. Cela suggère également que la gestion ne doit pas seulement se concentrer sur les nombres de survivants et les mortalités directes, mais aussi sur la protection de la diversité au sein des populations. Finalement, un modèle démo-génétique est décrit pour résumer notre compréhension des populations d’anguilles. Un tel modèle pourra être utilisé à l’avenir pour explorer les conditions écologiques dans lesquelles le polymorphisme génétique et la plasticité phénotypique ont été sélectionnés à travers des générations et fournir de nouvelles recommandations pour la conservation des espèces d’anguilles en voie d’extinction. / The worldwide decline of temperate eels is due to a synergistic combination of several anthropogenic pressures. However, eels display very specific life-cycles and amazing adaptation capacities that impair our ability to assess the relative effects of each pressure. Temperate eels are three catadromous species with large spatially distribution area during their continental growth stage. Their panmixia and the passive larval drifts impair the possibility of local adaptation; however life history spatial patterns are correlated with environmental gradients at both river catchment and distribution area scales. ThisPhD aims (i) to explore whether these life history spatial patterns may result from two adaptive responses: genetic polymorphism and adaptive phenotypic plasticity, and (ii) to revisit the effect of different components of global change in consideration to these adaptive responses. In this context,GenEveel, an individual-based optimization model was developed. The model postulates that genetic dependent habitat selection and phenotypic plasticity are mechanisms to address environmental heterogeneity. With such assumptions, the model was able to mimic observed spatial patterns in length-at-silvering, sex ratio and distribution of ecotypes. Moreover, different types of anthropogenic pressures (glass eel fishery, silver eel fishery, obstacles to upstream migration, and mortality due to hydropower facilities) were integrated in the model. Then, the model was used to assess their impacts on the number of escapees and their attributes: sex ratio, repartition between genotypes, mean lengthat-silvering, and overall egg production. The results showed that the pressure that induces the highest direct mortality has not necessarily the greatest influence on the spawning biomass and does not necessarily exert the strongest selective pressure on the ecotypes. This demonstrates that phenotypic plasticity can be a source of resilience for the population and mitigates the effect of some but not all the pressures. It also suggests that management should not only focus on numbers and direct mortalitybut on the preservation of diversity within populations. Finally, a demo-genetic model is described summarizing our understanding of eel populations. Such model can be used in the future to explore the ecological conditions in which genetic polymorphism and phenotypic plasticity have been selected through generations and provide new insights for the conservation of endangered eel species.

Les conséquences des récents changements environnementaux sont déjà observables sur les écosystèmes du monde entier et menacent la biodiversité. Dans l'objectif de conserver les bénéfices que nous procurent les écosystèmes, l'enjeu est de comprendre et prédire la dynamique spatiale et temporelle des paysages et de la biodiversité afin de mieux anticiper les changements possibles et adapter les décisions de conservation. En zone de montagne, où l'environnement est très hétérogène, les effets combinés des modifications du climat et de l'agriculture sont susceptibles d'avoir un impact important sur les écosystèmes. La présente thèse a pour objectif principal de caractériser les espèces et les habitats vulnérables aux changements climatiques et changements d'utilisation des terres dans les Alpes Françaises. Elle apporte sa contribution en se basant sur des données accumulées par le Conservatoire Botanique National Alpin et le Parc national des Ecrins (PNE), et en utilisant trois angles d'approche complémentaires. Dans une première partie, les cadres théoriques expliquant la coexistence des espèces et leur répartition spatiale ont été testés empiriquement. Les patrons de rareté des plantes des Alpes françaises ont ainsi été reliés aux caractéristiques des espèces, mettant en évidence les compromis entre différentes stratégies fonctionnelles. Une seconde analyse de la répartition de 21 espèces cibles a démontré la différence entre les facteurs expliquant la présence d'une espèce à un endroit donné et ceux expliquant son abondance. Cette analyse a également permis de souligner l'importance de la dispersion et mis en évidence des dynamiques source-puits chez certaines espèces. La deuxième partie s'appuie sur les mêmes cadres théoriques et a consisté à développer un modèle dynamique de la structure et de la diversité de la végétation. Ce modèle a été calibré et validé sur la végétation du PNE. Une troisième partie porte son attention sur les évolutions possibles de la végétation sous plusieurs scénarios de changements climatiques et d'utilisation des terres. Les simulations ont montré qu'il est nécessaire de considérer la dynamique temporelle du fait que les conséquences d'un changement climatique peuvent être observées bien après la phase du changement. D'autre part, l'analyse a montré les effets conjugués que peuvent avoir les changements climatiques et la déprise agricole sur la structure de la végétation. Un tel modèle ouvre la voie à l'exploration de multiples scenarios, en permettant non seulement de décrire des paysages futurs potentiels mais aussi les états de transition qui devraient y mener. / On-going global changes have already affected ecosystems and threaten the biodiversity all over the world. In order to maintain the ecosystems services provided to humans and adapt conservation planning, the challenge is to improve our understanding of the mechanisms underlying the maintenance of biodiversity and to predict its response to global changes. In mountainous areas, where the environment is very heterogeneous, the modifications of both climate and land use are expected to strongly influence the landscapes and current biodiversity. This PhD thesis has for main objective to assess the vulnerability of species and habitat to environmental changes in the French Alps. It uses three different approaches and relies on the large databases accumulated by two institutions: the National Alpine Botanical Conservatory and the Ecrins National Park (PNE). The first part of the PhD confronts theoretical hypotheses for species coexistence to observations and describes the characteristics of the regional flora. The species ecological niche breadth has been estimated and related to other rarity facets and trade-off between plant functional strategies. A second analysis disentangles the drivers of the presence or the local abundance of 21 focal species and highlights the importance of the dispersion and the source-sink dynamics. The second part is based on the same conceptual background and aims to develop a dynamic model of the vegetation structure and diversity. The model has been validated for the vegetation of the PNE. The last part proposes an application of this dynamic model to provide multiple biodiversity scenarios in respect to change in both climate and land management. The simulations showed that the consequences of climate change might be visible only after a certain time-lag, demonstrating the interest of considering the spatial but also temporal vegetation dynamics. Furthermore, the analysis pointed out the importance of the interplay effects between climate and land use abandonment. Such a model should pave the way for the exploration of multiples scenarios and will be able to describe not only the potential future landscapes but also the transition states leading to it.

Une nouvelle méthodologie fondée sur l’interfaçage de la géochimie et de la biologie a été utilisée pour étudier la durabilité d’un système d’agriculture irriguée face aux changements globaux (climat et urbanisation). L’étude de sa durabilité nécessite une vision dynamique spatio-temporelle de l’évolution d’un agrosystème irrigué, ici le système « irrigation – prairie (plante) – sol – nappe ». Pour cela, deux démarches sont utilisées : l’étude de terrain et la modélisation. L’étude de terrain comprend des suivis temporels et spatiaux de la qualité des eaux de surface, de la nappe phréatique et de la qualité du foin des prairies. La modélisation consiste en un modèle biogéochimique prenant en compte l’ensemble des compartiments réactionnels du système. Le fil directeur est constitué par les mécanismes d’acquisition de la composition chimique de l’eau lors de son transfert dans le sol depuis eau d’irrigation jusqu’à l’eau de nappe. Ces mécanismes sont étudiés du double point de vue de leurs bilans géochimiques et des réactions sol / solution. L’acquisition de données porte ainsi sur : (1) la composition chimique des eaux d’irrigation et des eaux souterraines de la nappe ; (2) la minéralogie des sols ; (3) la nature des engrais apporté ; (4) la quantité des éléments chimiques prélevés et exportés par les plantes. Le modèle biogéochimique consiste à interfacer le modèle de culture STICS et le modèle de géochimie PHREEQC. Ce modèle est capable de rendre compte de l’évolution des eaux lors de leur parcours dans le sol et de mettre en évidence les processus majeurs qui déterminent la qualité de l’eau ; en sortie, il permet d’établir des indicateurs géochimiques pertinents pour la gestion du système. Cette méthode est appliquée aux prairies irriguées en la Crau, au Sud de France. Le système d’irrigation gravitaire par les eaux de la Durance depuis le 16e siècle sur la Crau a construit un système agricole durable en amenant des alluvions sur les terres irriguées, sur lequel poussent les prairies (le foin de Crau (AOP)). De plus cette irrigation participe à plus de 70% au renouvellement des eaux de la nappe phréatique. L’analyse des données sur une longue durée (1960-2013), l’acquisition de données récentes et la modélisation montrent l’originalité et la durabilité de cet agrosystème irrigué et sa résilience face à une augmentation de température de 2°C, tant en ce qui concerne les rendements que la qualité du foin. Cependant dans la perspective des changements globaux, les prévisions tablent sur une disponibilité en eau pour l’irrigation en diminution, de plus des changements d’occupation du sol (10% de la surface totale), avec une réduction des prairies irriguées. Ceci risque de remettre en cause la durabilité de l’agrosystème irrigué et partant l’approvisionnement en eau à partir de la nappe de toute l’économie locale (300 000 habitants, les industries lourdes du site de Fos-sur-Mer). / A new methodology based on geochemistry and biology interfacing to study the sustainability of an irrigated agriculture system in the face of global changes (climate and urban sprawl). It requires construction of a spatio-temporal view of the ”irrigation - meadow (plant) - soil - groundwater” system evolution. Thereby two approaches are used : the field study and the modeling. The field study includes temporal and spatial survey of waters quality, plant quality and used fertilizers. The modeling consists of a biogeochemical model taking into account all the factors reaction of the system. The main theme is the mechanisms of acquiring the chemical composition of water during its transfer the soil horizon from irrigation water to groundwater. These mechanisms are studied from the double point of view of their geochemical balances and soil / solution reactions. The data acquisition thus relates to : (1) the chemical composition of irrigation water and groundwater ; (2) the soil mineralogy ; (3) the nature of the provided fertilizer ; (4) quantity of chemical elements uptaken by plants. The biogeochemical model consists in interfacing the crop model (STICS) and the geochemical model (PHREEQC). This model is able to perform the chemical evolution of waters during their pathway in the soil and to highlight the major processes that determine the water quality ; in output, it makes it possible to establish geochemical indicators relevant to the system management. The Crau is chosen as a demo area, South France, its grassland production is based on surface irrigation via channels withdrawn from the Durance River. Irrigation water is rich in minerals and trace elements thanks to alluvium brought, on which produce high quality hay that is regulated under appellation control since 1997. Additionally, this irrigation recharge the aquifer by 70% But it is threatened by global changes, which ultimately risks to compromising the sustainability of the irrigated grassland system. Data analysis over a long term (1960-2013), the acquisition of recent data and modeling show the originality and durability of this irrigated agrosystem and Its resilience to an increase in temperature by about 2°C, both in terms of yields and hay quality. However, according to future scenarios, declining of irrigation water is forecasted, and changes in land use by 10% of the total area, with a reduction in irrigated grassland areas. This may jeopardize the sustainability of the the irrigated agrosystem and thus the water supply for local use (300 000 inhabitants, the heavy industries of the Fos-sur-Mer site).

Beaucoup de parasites à cycle complexe ont développé la capacité d’altérer le phénotype de leurs hôtes. Il est reconnu que ces modifications d’apparence ou de comportement sont responsables d’une augmentation de la probabilité de prédation de l’hôte intermédiaire par l’hôte définitif. Ce phénomène de manipulation parasitaire peut avoir de nombreuses conséquences à l’échelle de l’écosystème, modifiant les interactions entre les populations d’hôtes et bouleversant leur rôle écologique. Cependant, les parasites manipulateurs sont peu étudiés sur le plan écologique, et l’effet de l’environnement sur l’interaction entre ces parasites et leurs hôtes, notamment en termes de manipulation, est encore largement inconnu. Au cours de cette thèse, j’ai étudié l’effet de l’environnement sur l’interaction entre les gammares, des crustacés amphipodes de grande importance écologique dans les rivières, et leurs parasites acanthocéphales. Mes travaux ont montré que les conditions de ressources alimentaires et de température subies par les hôtes durant le développement des parasites influençaient plusieurs paramètres de l’infection mais n’affectaient pas la manipulation en termes d’utilisation de refuges. Toutefois, tandis que la géotaxie ne dépendait pas non plus de la température, l’impact des parasites sur la phototaxie des gammares était plus fort à haute température. De plus, mes travaux ont montré que l’impact conjoint de la température et des parasites pouvait modifier le rôle détritivore des gammares. Dans un contexte de changements globaux, ces travaux permettent de mieux comprendre l’importance de l’impact des parasites sur leurs hôtes et en prévoir les conséquences écologiques. / Many parasites with complex life cycle have developed the ability to alter the phenotype of their hosts. It is recognized that such changes in appearance and behavior are responsible for an increase in the probability of predation of their intermediate hosts by their definitive hosts. This phenomenon of parasite manipulation can have numerous consequences at the scale of the ecosystem, modifying the interactions between host populations and altering their ecological role. However, manipulative parasites received little attention from an ecological point of view. Thus, the effect of the environment on the interaction between these parasites and their hosts, in particular in terms of manipulation, is largely unknown. In this thesis, I studied the effect of the environment on the interaction between gammarids – ecologically important crustacean amphipods in rivers – and their acanthocephalan parasites. My experiments showed that the conditions of food resources and temperature experienced by gammarids during the development of their parasites influenced several infection parameters, but did not affect behavioral manipulation in terms of use of refuges. Nevertheless, while the geotaxis was not either effected by temperature, the impact of parasites on gammarids phototaxis was stronger at high temperature. Moreover, my studies showed that the cumulative effect of temperature and parasitism could alter the shredder role of gammarids. In a context of global changes, this work provides a better understanding of the importance of the impact of parasites on their hosts, allowing to make previsions on their subsequent ecological consequences.

The demise of reef-building corals potentially lies on the horizon, given ongoing climate change amid other anthropogenic environmental stressors. If corals cannot acclimatize or adapt to changing conditions, dramatic declines in the extent and health of the living reefs are expected within the next half century. The primary and proximal global threat to corals is climate change. Reef-building corals are dependent upon a nutritional symbiosis with photosynthetic dinoflagellates belonging to the group Symbiodinium. The symbiosis between the cnidarian host and algal partner is a stress-sensitive relationship; temperatures just 1°C above normal thermal maxima can result in the breakdown of the symbiosis, resulting in coral bleaching (the loss of Symbiodinium and/or associated photopigments) and ultimately, colony death. As ocean temperatures continue to rise, corals will either acclimatize or adapt to changing conditions, or will perish. By experimentally preconditioning the coral Acropora millepora via sublethal heat treatment, the coral acquired thermal tolerance, resisting bleaching during subsequent hyperthermal stress. The complex nature of the coral holobiont translates to multiple possible explanations for acclimatization: acquired thermal tolerance could potentially originate from the host itself, the Symbiodinium, or from the bacterial community associated with the coral. By examining the type of in hospite Symbiodinium and the bacterial community prior acclimation and after thermal challenge, it is shown that short-term acclimatization is not due to a distinct change in the dinoflagellate or prokaryote community. Though the microbial partnerships remain without considerable flux in preconditioned corals, the host transcriptome is dynamic. One dominant pattern was the apparent tuning of gene expression observed between preconditioned and non-preconditioned treatments, showing a modulated transcriptomic response to stress. Additionally several genes were upregulated in association with thermal tolerance, including antiapoptotic genes, lectins, and oxidative stress response genes. Upstream of two of these thermal tolerance genes, inhibitor of NFκB and mannose-binding lectin, DNA polymorphisms were identified which vary significantly between the northern and southern Great Barrier Reef. The impact of these mutations in putative promoter regions remains to be seen, but variation across thermally-disparate geography serves to generate hypotheses regarding the role of regulatory element evolution in a coral adaptation context.