Os ecossistemas campestres co-evoluíram com distúrbios como a herbivoria e o fogo. Assim, estes fatores são importantes no surgimento e manutenção de características da comunidade, podendo modificar os processos de sucessão. Em áreas perturbadas, as sementes que persistem no solo participam da regeneração natural. Diante da alta taxa de conversão dos campos nativos no sul do Brasil em áreas de uso intensivo (lavoura ou plantios de espécies arbóreas), bem como do manejo pastoril com alta pressão animal, aumenta o interesse em estudos relacionados ao banco de sementes do solo (BSS), buscando compreender a sua função nas comunidades vegetais e na regeneração de áreas degradadas. O conhecimento já existente sobre BSS em biomas campestres do hemisfério sul ainda é incipiente. Grande parte dos trabalhos feitos em campos sul-americanos compararam o BSS entre áreas de vegetação pastejadas e áreas abandonadas, sendo poucos os que utilizaram diferentes intensidades de pastejo, apesar de efeitos claros de diferentes intensidades de pastejo sobre a composição e estrutura da vegetação. Em vista disto, foi avaliado, neste trabalho, o BSS em um experimento em campo submetido a diferentes intensidades de pastejo, em duas estações (primavera e outono), utilizando o método de emergência de plântulas. Também foi feito o levantamento da vegetação estabelecida para avaliar a similaridade com o BSS. Em total, foram encontradas 103 espécies no BSS e 162 na vegetação estabelecida. No BSS, a porcentagem de espécies de caráter ruderal foi alta. Diferenças significativas em termos de densidade e riqueza do BSS foram encontradas somente entre o tratamento com maior intensidade de pastejo e os demais. De forma geral, a semelhança entre o BSS e a vegetação estabelecida foi baixa. Assim, estes resultados indicam que o BSS tem um papel limitado na recuperação da vegetação campestre típica após distúrbios mais severos e que, aparentemente, a intensidade do manejo não tem um impacto muito grande para o BSS. Apesar disso, o BSS é importante pelo armazenamento das características naturais dos ambientes, agregando funções à regeneração da comunidade vegetal. / Grassland ecosystems co-evolved with disturbances such as fire and herbivory, and these factors are important for emergence and maintenance of community features areas. After disturbances, the seeds that persist in the soil contribute to regeneration processes. However, increasing conversion of natural grasslands into areas of intensive use (agriculture and exotic tree plantations), as well as overgrazing make the study of the regeneration of grassland vegetation after these severe disturbances an important research topic. Our knowledge on the role of the soil seed bank (SSB) in grassland biomes in the southern hemisphere still is incipient. The majority of studies realized in South American grassland compared the SSB between grazed and abandoned areas, and few consider different intensities of grazing, despite clear effects of different grazing intensities on vegetation composition and structure. In view of this, in this study, the SSB was evaluated in a grassland experiment under different intensities of grazing in two seasons (spring and autumn), using the seedling emergence method. In spring, a survey of the established vegetation was conducted to evaluate the similarity with the SSB. In total, we found 103 species in the SSB and 162 in established vegetation. The SSB was mostly composed of ruderal species. Grass species dominant in aboveground vegetation were largely absent in the SSB. Significant differences regarding SSB richness and density were only found between the treatment with higher intensity of grazing and the others, and overall composition did not differ among treatments. In general, the similarity between the SSB and established vegetation was low. Our results indicate that the SSB has a limited role in the recovery of natural grassland vegetation after more severe disturbances. Apparently, the intensity of management does not have a very large impact on the SSB or on the similarity between SSB and established vegetation. Nevertheless, the SSB is important for storage the natural characteristics of environments, adding functions to the regeneration of the plant community.

Os ecossistemas campestres co-evoluíram com distúrbios como a herbivoria e o fogo. Assim, estes fatores são importantes no surgimento e manutenção de características da comunidade, podendo modificar os processos de sucessão. Em áreas perturbadas, as sementes que persistem no solo participam da regeneração natural. Diante da alta taxa de conversão dos campos nativos no sul do Brasil em áreas de uso intensivo (lavoura ou plantios de espécies arbóreas), bem como do manejo pastoril com alta pressão animal, aumenta o interesse em estudos relacionados ao banco de sementes do solo (BSS), buscando compreender a sua função nas comunidades vegetais e na regeneração de áreas degradadas. O conhecimento já existente sobre BSS em biomas campestres do hemisfério sul ainda é incipiente. Grande parte dos trabalhos feitos em campos sul-americanos compararam o BSS entre áreas de vegetação pastejadas e áreas abandonadas, sendo poucos os que utilizaram diferentes intensidades de pastejo, apesar de efeitos claros de diferentes intensidades de pastejo sobre a composição e estrutura da vegetação. Em vista disto, foi avaliado, neste trabalho, o BSS em um experimento em campo submetido a diferentes intensidades de pastejo, em duas estações (primavera e outono), utilizando o método de emergência de plântulas. Também foi feito o levantamento da vegetação estabelecida para avaliar a similaridade com o BSS. Em total, foram encontradas 103 espécies no BSS e 162 na vegetação estabelecida. No BSS, a porcentagem de espécies de caráter ruderal foi alta. Diferenças significativas em termos de densidade e riqueza do BSS foram encontradas somente entre o tratamento com maior intensidade de pastejo e os demais. De forma geral, a semelhança entre o BSS e a vegetação estabelecida foi baixa. Assim, estes resultados indicam que o BSS tem um papel limitado na recuperação da vegetação campestre típica após distúrbios mais severos e que, aparentemente, a intensidade do manejo não tem um impacto muito grande para o BSS. Apesar disso, o BSS é importante pelo armazenamento das características naturais dos ambientes, agregando funções à regeneração da comunidade vegetal. / Grassland ecosystems co-evolved with disturbances such as fire and herbivory, and these factors are important for emergence and maintenance of community features areas. After disturbances, the seeds that persist in the soil contribute to regeneration processes. However, increasing conversion of natural grasslands into areas of intensive use (agriculture and exotic tree plantations), as well as overgrazing make the study of the regeneration of grassland vegetation after these severe disturbances an important research topic. Our knowledge on the role of the soil seed bank (SSB) in grassland biomes in the southern hemisphere still is incipient. The majority of studies realized in South American grassland compared the SSB between grazed and abandoned areas, and few consider different intensities of grazing, despite clear effects of different grazing intensities on vegetation composition and structure. In view of this, in this study, the SSB was evaluated in a grassland experiment under different intensities of grazing in two seasons (spring and autumn), using the seedling emergence method. In spring, a survey of the established vegetation was conducted to evaluate the similarity with the SSB. In total, we found 103 species in the SSB and 162 in established vegetation. The SSB was mostly composed of ruderal species. Grass species dominant in aboveground vegetation were largely absent in the SSB. Significant differences regarding SSB richness and density were only found between the treatment with higher intensity of grazing and the others, and overall composition did not differ among treatments. In general, the similarity between the SSB and established vegetation was low. Our results indicate that the SSB has a limited role in the recovery of natural grassland vegetation after more severe disturbances. Apparently, the intensity of management does not have a very large impact on the SSB or on the similarity between SSB and established vegetation. Nevertheless, the SSB is important for storage the natural characteristics of environments, adding functions to the regeneration of the plant community.

Os ecossistemas campestres co-evoluíram com distúrbios como a herbivoria e o fogo. Assim, estes fatores são importantes no surgimento e manutenção de características da comunidade, podendo modificar os processos de sucessão. Em áreas perturbadas, as sementes que persistem no solo participam da regeneração natural. Diante da alta taxa de conversão dos campos nativos no sul do Brasil em áreas de uso intensivo (lavoura ou plantios de espécies arbóreas), bem como do manejo pastoril com alta pressão animal, aumenta o interesse em estudos relacionados ao banco de sementes do solo (BSS), buscando compreender a sua função nas comunidades vegetais e na regeneração de áreas degradadas. O conhecimento já existente sobre BSS em biomas campestres do hemisfério sul ainda é incipiente. Grande parte dos trabalhos feitos em campos sul-americanos compararam o BSS entre áreas de vegetação pastejadas e áreas abandonadas, sendo poucos os que utilizaram diferentes intensidades de pastejo, apesar de efeitos claros de diferentes intensidades de pastejo sobre a composição e estrutura da vegetação. Em vista disto, foi avaliado, neste trabalho, o BSS em um experimento em campo submetido a diferentes intensidades de pastejo, em duas estações (primavera e outono), utilizando o método de emergência de plântulas. Também foi feito o levantamento da vegetação estabelecida para avaliar a similaridade com o BSS. Em total, foram encontradas 103 espécies no BSS e 162 na vegetação estabelecida. No BSS, a porcentagem de espécies de caráter ruderal foi alta. Diferenças significativas em termos de densidade e riqueza do BSS foram encontradas somente entre o tratamento com maior intensidade de pastejo e os demais. De forma geral, a semelhança entre o BSS e a vegetação estabelecida foi baixa. Assim, estes resultados indicam que o BSS tem um papel limitado na recuperação da vegetação campestre típica após distúrbios mais severos e que, aparentemente, a intensidade do manejo não tem um impacto muito grande para o BSS. Apesar disso, o BSS é importante pelo armazenamento das características naturais dos ambientes, agregando funções à regeneração da comunidade vegetal. / Grassland ecosystems co-evolved with disturbances such as fire and herbivory, and these factors are important for emergence and maintenance of community features areas. After disturbances, the seeds that persist in the soil contribute to regeneration processes. However, increasing conversion of natural grasslands into areas of intensive use (agriculture and exotic tree plantations), as well as overgrazing make the study of the regeneration of grassland vegetation after these severe disturbances an important research topic. Our knowledge on the role of the soil seed bank (SSB) in grassland biomes in the southern hemisphere still is incipient. The majority of studies realized in South American grassland compared the SSB between grazed and abandoned areas, and few consider different intensities of grazing, despite clear effects of different grazing intensities on vegetation composition and structure. In view of this, in this study, the SSB was evaluated in a grassland experiment under different intensities of grazing in two seasons (spring and autumn), using the seedling emergence method. In spring, a survey of the established vegetation was conducted to evaluate the similarity with the SSB. In total, we found 103 species in the SSB and 162 in established vegetation. The SSB was mostly composed of ruderal species. Grass species dominant in aboveground vegetation were largely absent in the SSB. Significant differences regarding SSB richness and density were only found between the treatment with higher intensity of grazing and the others, and overall composition did not differ among treatments. In general, the similarity between the SSB and established vegetation was low. Our results indicate that the SSB has a limited role in the recovery of natural grassland vegetation after more severe disturbances. Apparently, the intensity of management does not have a very large impact on the SSB or on the similarity between SSB and established vegetation. Nevertheless, the SSB is important for storage the natural characteristics of environments, adding functions to the regeneration of the plant community.

Etant donné le rôle clé des grands herbivores sur la diversité végétale spécifique et fonctionnelle, notre objectif était de mieux comprendre la relation entre l'herbivorie et les communautés végétales principalement à une échelle spatiale fine, afin de concilier des objectifs de gestions des populations et de conservation de la flore. Pour cela, nous avons abordé cette problématique en intégrant des approches taxonomiques et fonctionnelles, et en étudiant les interactions aux niveaux inter- et intra-spécifiques. Nous avons combiné les informations de trois bases de données : (1) des données de régime alimentaire issus d'analyses d'ADN metabarcoding réalisées sur des faeces de chamois (Rupicapra rupicapra), chevreuil (Capreolus capreolus) et mouflons (Ovis gmelini musimon) du Massif des Bauges, (2) des données sur les caractéristiques des communautés végétales (composition floristique, biomasse, phénologie), (3) des données de traits fonctionnels des plantes. L'analyse de variabilité intra-spécifique des trois grands herbivores nous a permis de valider l'hypothèse de variation de niche (NVH) de Van Valen au niveau intra-spécifique mais aussi au niveau inter-spécifique, soit une relation positive entre la largeur de niche de l'espèce et sa variabilité intra-spécifique. Ensuite, grâce à deux populations de chamois d'alpage, l'une vivant en sympatrie avec le mouflon et l'autre vivant en allopatrie, nous avons pu mettre en évidence l'absence d'effets négatifs de la population introduite de mouflon sur le régime alimentaire de la population native de chamois, autant au niveau de la niche alimentaire taxonomique que fonctionnelle. L'analyse des critères de sélection alimentaire nous a finalement permis de mettre en avant des différences de critères de choix entre les deux espèces à certaines saisons, expliquant ainsi partiellement le partitionnement des niches taxonomiques et fonctionnelles entre les deux espèces. Par ailleurs, les scénarios proposés d'évolution de la sélection alimentaire au cours de l'année pour les deux espèces concordaient avec les caractéristiques morphologiques spécifiques à l'espèce d'ongulé. Finalement, contrairement à la littérature où aucune étude n'était capable de discriminer les effets directs et indirects des traits fonctionnels à cause de corrélations, nous avons pu, grâce à des analyses de pistes, démontrer que, dans la plupart des cas, les traits biomécaniques avaient un effet direct sur le choix alimentaire alors que les traits chimiques n'avaient qu'un effet indirect. Enfin, d'un point de vue méthodologique, nous conseillons l'utilisation d'indices d'azote fécaux uniquement dans l'étude de la variation à long terme de la qualité des régimes de manière spécifique à chaque espèce et chaque site, et non pas pour comparer des qualités de régime entre espèces ni pour étudier les variations fines à l'échelle intra-saisonnière. La complémentarité des approches nous a permis de mieux appréhender la structuration des communautés d'herbivores, et devrait nous aider à mieux évaluer l'état actuel et l'évolution des relations entre individus, entre espèces et avec leur environnement.Mots-clés : ongulés, interactions intra- et inter-spécifiques, approche taxonomique et fonctionnelle, ADN metabarcoding, NIRS, massif des Bauges, sélection alimentaire / Given the key role of large herbivores on species and functional plant diversity, we aimed at better understanding the relationship between herbivory and plant communities mainly at a fine-scale, in order to reconcile objectives of population management and plant conservation. For this purpose, we used both taxonomic and functional approaches, and studied interactions at the inter- and intra-specific levels. We combined information coming from three databases: (1) diet data from DNA-metabarcoding applied on chamois (Rupicapra rupicapra), roe deer (Capreolus capreolus) and mouflon (Ovis gmelini musimon) faeces from the Bauges Massif, (2) characteristics of plant communities (plant composition, biomass, phenology), (3) plant functional traits. Analyses of intra-specific variability of the three large herbivores allowed us to upscale the niche variation hypothesis (NVH) of Van Valen from the intra- to the inter-specific level, i.e. we observed a positive relationship between the species niche breadth and among-individual variation. Then, based on two chamois subpopulations living in pastures, one living in sympatry with the mouflon and the other living in allopatry, we revealed the absence of negative effects of the introduced mouflon population on native chamois population diet, both for the taxonomic and functional dietary niche. Analyses of diet selection criteria allowed us to highlight differences in choice criteria between chamois and mouflon in some seasons, which helped to explain the taxonomic and functional niche partitioning of the two species. Furthermore, the proposed scenario of the evolution of diet selection over the year for both species were consistent with ungulate-specific morpho-physiological features. Finally, contrary to the literature where no studies could discriminate the direct and indirect effects of functional traits on diet selection because of correlations, we used path analyses, which allowed us to show that in most cases, biomechanical traits had a direct effect on diet choices, whereas chemical traits had an indirect effect. Furthermore, from a methodological point of view, we advised to use nitrogen fecal indices only to study the evolution of species-specific and location-specific population long-term diet quality, but not to compare diet quality between species, nor to study slight fluctuations at the intra-seasonal level. The complementarity of the approaches allowed us to better account for the structuration of herbivore communities, which should help to better assess the actual state and the evolution of relationships among individuals, species and their environment.Key-words: ungulates, intra- and inter-specific interactions, taxonomic and functional approach, DNA metabarcoding, NIRS, Bauges Massif, diet selection

Les communautés végétales constituent des systèmes complexes au sein desquels de nombreuses espèces, pouvant présenter une large variété de traits fonctionnels, interagissent entre elles et avec leur environnement. En raison de la quantité et de la diversité de ces interactions les mécanismes qui gouvernent les dynamiques des ces communautés sont encore mal connus. Les approches basées sur la modélisation permettent de relier de manière mécaniste les processus gouvernant les dynamiques des individus ou des populations aux dynamiques des communautés qu'ils forment. L'objectif de cette thèse était de développer de telles approches et de les mettre en oeuvre pour étudier les mécanismes sous-jacents aux dynamiques des communautés. Nous avons ainsi développés deux approches de modélisation. La première s'appuie sur un cadre de modélisation stochastique permettant de relier les dynamiques de populations aux dynamiques des communautés en tenant compte des interactions intra- et interspécifiques et de l'impact des variations environnementale et démographique. Cette approche peut-être aisément appliquée à des systèmes réels et permet de caractériser les populations végétales à l'aide d'un petit nombre de paramètres démographiques. Cependant nos travaux suggèrent qu'il n'existe pas de relation simple entre ces paramètres et les traits fonctionnels des espèces, qui gouvernent pourtant leur réponse aux facteurs externes. La seconde approche a été développée pour dépasser cette limite et s'appuie sur le modèle individu-centré Nemossos qui représente de manière explicite le lien entre le fonctionnement des individus et les dynamiques de la communauté qu'ils forment. Afin d'assurer un grand potentiel d'application à Nemossos, nous avons apportés une grande attention au compromis entre réalisme et coût de paramétrisation. Nemossos a ainsi pu être entièrement paramétré à partir de valeur de traits issues de la littérature , son réalisme a été démontré, et il a été utilisé pour mener des expériences de simulations numériques sur l'importance de la variabilité temporelle des conditions environnementales pour la coexistence d'espèces fonctionnellement différentes. La complémentarité des deux approches nous a permis de proposer des éléments de réponse à divers questions fondamentales de l'écologie des communautés incluant le rôle de la compétition dans les dynamiques des communautés, l'effet du filtrage environnementale sur leur composition fonctionnel ou encore les mécanismes favorisant la coexistence des espèces végétales. Ici ces approches ont été utilisées séparément mais leur couplage peut offrir des perspectives intéressantes telles que l'étude du lien entre le fonctionnement des plantes et les dynamiques des populations. Par ailleurs chacune des approches peut être utilisée dans une grande variété d'expériences de simulation susceptible d'améliorer notre compréhension des mécanismes gouvernant les communautés végétales. / Plant communities are complex systems in which multiple species differing by their functional attributes interact with their environment and with each other. Because of the number and the diversity of these interactions the mechanisms that drive the dynamics of theses communities are still poorly understood. Modelling approaches enable to link in a mechanistic fashion the process driving individual plant or population dynamics to the resulting community dynamics. This PhD thesis aims at developing such approaches and to use them to investigate the mechanisms underlying community dynamics. We therefore developed two modelling approaches. The first one is based on a stochastic modelling framework allowing to link the population dynamics to the community dynamics whilst taking account of intra- and interspecific interactions as well as environmental and demographic variations. This approach is easily applicable to real systems and enables to describe the properties of plant population through a small number of demographic parameters. However our work suggests that there is no simple relationship between these parameters and plant functional traits, while they are known to drive their response to extrinsic factors. The second approach has been developed to overcome this limitation and rely on the individual-based model Nemossos that explicitly describes the link between plant functioning and community dynamics. In order to ensure that Nemossos has a large application potential, a strong emphasis has been placed on the tradeoff between realism and parametrization cost. Nemossos has then been successfully parameterized from trait values found in the literature, its realism has been demonstrated and it has been used to investigate the importance of temporal environmental variability for the coexistence of functionally differing species. The complementarity of the two approaches allows us to explore various fundamental questions of community ecology including the impact of competitive interactions on community dynamics, the effect of environmental filtering on their functional composition, or the mechanisms favoring the coexistence of plant species. In this work, the two approaches have been used separately but their coupling might offer interesting perspectives such as the investigation of the relationships between plant functioning and population dynamics. Moreover each of the approaches might be used to run various simulation experiments likely to improve our understanding of mechanisms underlying community dynamics.