Understanding mechanisms regulating the assembly of ecological communities is a major goal of community ecology. I combined experimental and theoretical approaches to investigate the influences of various ecological factors on the assembly of protist communities. My research included three experimental studies and one theoretical study. Two experimental studies used freshwater heterotrophic ciliated protists as model organisms to examine how species dispersal across local communities and functional and phylogenetic diversity of the species pool influence historical contingency of the assembled communities, respectively. The results of the first experiment showed that the differences in species colonization history led to alternative community states that substantially differed in species composition and abundances, regardless of the level of species dispersal. The results of the second experiment showed that historical contingency, measured by beta diversity and the strength of inhibitive priority effects decreased as phylogenetic and functional diversity of the species pool increased. In the third experimental study, I used the same model system and observed positive relationships between phylogenetic diversity and temporal stability of community biomass. These positive relationships are likely due to the reduced competition among species and increased asynchronous species responses to environmental changes under higher phylogenetic diversity. The theoretical study explored how phytoplankton and zooplankton coevolution drives species diversity patterns along productivity gradients in a mathematical model system. I explored the conditions for evolutionary divergence in phytoplankton and zooplankton and the consequent productivity-diversity relationships (PDR) using the theory of adaptive dynamics and numerical simulations. The results of numerical simulations showed that the coevolutionary dynamics of phytoplankton and zooplankton can generate transient unimodal or positive PDRs, and positive PDRs when the systems reach steady states. The findings of my research suggest an important role of traits and species ecological difference in understanding causes and consequences of biodiversity in community ecology.

It is increasingly being recognized that the soil microbes can mineralize recalcitrant soil organic matter (SOM) by using the fresh carbon (C) as a source of energy, a process called priming effect (PE). It has been shown mostly in lab incubations that PE can have important consequences for sequestration of organic C in soils. However, the importance of PE in C and N dynamics of ecosystems remains little known. The soil-plant interactions and rhizospheric processes can modulate the rates of PE and its consequences on C and N dynamics in an ecosystem. The objective of this thesis was to determine the role of PE in the C and N dynamics of permanent grasslands and the modulation of this role in response to management (plant clipping, fertilization) and global warming. Moreover, it was aimed to identify the microbial groups involved in PE and to unravel the way, e.g. absorption of N, root exudations and litter deposition, by which plant can induce PE. The thesis was based on a new approach allowing continuous dual labelling of multiple grassland plants with 13C- and 14C-CO2. The dual labelling permitted the separation of soil-derived CO2 from plant-derived CO2, the calculation of PE and the determination of mean age of soil-derived CO2-C. Moreover, phospholipids fatty-acids analysis (PLFA) permitted to correlate the variation of PE with changes in microbial community composition. Our work showed that the increased SOM mineralization under grasses was consistently two to three times more than that in bare soils (i.e. PE) over long term (511 days). This reveals that the PE plays key role in ecosystem CO2-C flux and indicates that a very large pool of SOM is under the control of PE. Moreover, we report that 15,000 years old organic C from an undisturbed deep soil can be mineralized after the supply of fresh C by living plants to soil microbes. This result supports the idea that the SOM in deep soils is stable due to the energy-limitation of microbes and the ‘inert' pool of organic C defined in current models is not so ‘inert' finally. The supply of N in soil-plant system through the use of fertilizer or legume decreased the PE suggesting that the C storage in soils is limited by nutrient supply. Similarly, plant clipping reduced the plant N uptake thereby PE. Collectively these results suggest synchronization between plant N uptake and SOM mineralization supporting the idea that soils under permanent plant cover function as a bank of nutrients for the plant, maximizing plant productivity and nutrient retention. An innovative method clearly showed that the root exudation is the major way by which grassland plants induce PE. Moreover, saprophytic fungi are suggested as the key actors in the mineralization of recalcitrant SOM & PE. Lastly, we developed a new theory on temperature response of SOM mineralization by taking into account the energy-limitation of microbes and the temperature-dependent inactivation of enzymes. This theory predicts a negative relationship between temperature and mineralization of recalcitrant SOM, which was supported by experimental results. This finding challenges the classical paradigm of positive relationship between temperature and recalcitrant SOM mineralization. Overall, these investigations on plant-soil systems reinforce the idea that PE and underlying mechanisms play a key role in ecosystem C and N dynamics and even suggest that this role was underestimated in lab experiments. / It is increasingly being recognized that the soil microbes can mineralize recalcitrant soil organic matter (SOM) by using the fresh carbon (C) as a source of energy, a process called priming effect (PE). It has been shown mostly in lab incubations that PE can have important consequences for sequestration of organic C in soils. However, the importance of PE in C and N dynamics of ecosystems remains little known. The soil-plant interactions and rhizospheric processes can modulate the rates of PE and its consequences on C and N dynamics in an ecosystem. The objective of this thesis was to determine the role of PE in the C and N dynamics of permanent grasslands and the modulation of this role in response to management (plant clipping, fertilization) and global warming. Moreover, it was aimed to identify the microbial groups involved in PE and to unravel the way, e.g. absorption of N, root exudations and litter deposition, by which plant can induce PE. The thesis was based on a new approach allowing continuous dual labelling of multiple grassland plants with 13C- and 14C-CO2. The dual labelling permitted the separation of soil-derived CO2 from plant-derived CO2, the calculation of PE and the determination of mean age of soil-derived CO2-C. Moreover, phospholipids fatty-acids analysis (PLFA) permitted to correlate the variation of PE with changes in microbial community composition. Our work showed that the increased SOM mineralization under grasses was consistently two to three times more than that in bare soils (i.e. PE) over long term (511 days). This reveals that the PE plays key role in ecosystem CO2-C flux and indicates that a very large pool of SOM is under the control of PE. Moreover, we report that 15,000 years old organic C from an undisturbed deep soil can be mineralized after the supply of fresh C by living plants to soil microbes. This result supports the idea that the SOM in deep soils is stable due to the energy-limitation of microbes and the ‘inert' pool of organic C defined in current models is not so ‘inert' finally. The supply of N in soil-plant system through the use of fertilizer or legume decreased the PE suggesting that the C storage in soils is limited by nutrient supply. Similarly, plant clipping reduced the plant N uptake thereby PE. Collectively these results suggest synchronization between plant N uptake and SOM mineralization supporting the idea that soils under permanent plant cover function as a bank of nutrients for the plant, maximizing plant productivity and nutrient retention. An innovative method clearly showed that the root exudation is the major way by which grassland plants induce PE. Moreover, saprophytic fungi are suggested as the key actors in the mineralization of recalcitrant SOM & PE. Lastly, we developed a new theory on temperature response of SOM mineralization by taking into account the energy-limitation of microbes and the temperature-dependent inactivation of enzymes. This theory predicts a negative relationship between temperature and mineralization of recalcitrant SOM, which was supported by experimental results. This finding challenges the classical paradigm of positive relationship between temperature and recalcitrant SOM mineralization. Overall, these investigations on plant-soil systems reinforce the idea that PE and underlying mechanisms play a key role in ecosystem C and N dynamics and even suggest that this role was underestimated in lab experiments.

Comprendre les relations entre écohydrologie et structure fonctionnelle des communautés végétales est une problématique croissante en écologie. Cette thèse a pour objectif d'analyser les effets d'un gradient de ressource édaphique sur la structure et le fonctionnement de parcours herbacés dans le sud de la France, en intégrant les niveaux de l'écosystème à la plante. Par modélisation du bilan hydrique, les différences d'utilisation de l'eau au niveau de l'écosystème ont été quantifiées pour cinq années contrastées révélatrices de la variabilité des propriétés des sols et du fonctionnement végétal. Utilisation de l'eau et productivité des plantes sont proportionnelles à la réserve utile des sols et à son taux de remplissage, suggérant un équilibre fonctionnel entre les communautés végétales et la disponibilité de l'eau locale. Par une approche ‘traits', nous avons ensuite montré que le ratio entre surface foliaire et surface racinaire totales de la communauté est le facteur déterminant une relation 'allométrique' entre évapotranspiration potentielle et capacité de prélèvements hydriques. La coordination entre les compartiments racinaire et aérien de la végétation dépend d'une suite d'adaptations architecturales et morphologiques. Des modifications d'abondances relatives spécifiques et le turn-over d'espèces génèrent une variabilité de morphologie et de fonctionnement des communautés permettant leur adaptation à des ressources limitées. Au niveau plante, une expérimentation de transplantation a permis de quantifier l'importance relative de la disponibilité hydrique et des interactions entre plantes sur la productivité individuelle de trois espèces-cibles. L'importance de la compétition s'est révélée plus élevée sous fort niveau de ressource et dépendait plus des relations hiérarchiques entre traits que de la biomasse. La compétition entre plantes affecte les axes de niche fonctionnelle des espèces de façon indépendante, avec une convergence de la ‘teneur en matière sèche des feuilles' pour des faibles valeurs mais une plus forte divergence fonctionnelle pour la ‘hauteur des plantes'. Cette approche fonctionnelle a permis d'éclairer le rôle de la diversité végétale dans la réponse des systèmes écologiques à des ressources hydriques variables. De plus, ces résultats sur les propriétés écohydrologiques des communautés naturelles peuvent contribuer à la conception d'agro-écosytèmes complexes mieux adaptés aux sécheresses intenses prévues dans le contexte actuel de changement climatique. / Understanding the relationships between ecohydrology and functional structure of plant communities is a timely issue in plant ecology. From ecosystem to species levels, this works investigated the effects of a resource availability gradient on the structure and functioning of Mediterranean rangelands in Southern France. Using a water-balance modeling approach, differences in water-use at the ecosystem level were quantified across five contrasting years, accounting for the variability in both soil characteristics and vegetation functioning. Plant water-use and productivity scaled with soil water storage capacity and its filling rate, suggesting a functional equilibrium between plant communities and local water availability. Using a trait-based approach, we then showed that the ratio of total leaf area of the community on total root area determined an allometric relationship between potential evapotranspiration and water uptake capacity. The “coordination” between above- and belowground compartment of the vegetation was achieved by a suite of architectural and morphological adaptations. Modifications of species relative abundances and species turn-over explained morphological and functioning adaptations to cope with limiting resources. Finally at species level, a removal experiment allowed to quantify the relative importance of water limitations and effects of plant-plant interaction on individual plant productivity of three target species of graminoïds. The importance of competition increased with soil resource availability and depended more on trait-trait hierarchical distances among species than standing biomass. Competition among plants affects the axes of the functional niche of species independently, leading to the convergence of leaf dry matter content towards low values but to greater functional divergence for plant height. Overall, this functional approach provided an integrative understanding of the role of plant diversity in the response of ecological systems to changes in water availability. Furthermore, these results on ecohydrological properties of natural communities can contribute to the design of complex agro-ecosystem better adapted to intense droughts predicted under climate change.

Les prairies permanentes peuvent fournir une grande diversité de services écosystémiques. Elles se trouvent dans des conditions contrastées en termes de gestion et de climat en Europe. Cette diversité de conditions induit une grande variété de types de prairies différant par leur végétation et leur fourniture en services écosystémiques. Certains travaux suggèrent que le fonctionnement des écosystèmes prairiaux peut être directement relié à des critères de diversité fonctionnelle végétale. Ces critères, qui pourraient être utilisés pour évaluer les services écosystémiques, sont influencés par la gestion et le climat. L'objectif de ce doctorat est d'évaluer les effets de la gestion et du climat sur la diversité fonctionnelle végétale liée à des services écosystémiques des prairies permanentes. La première étape a consisté à sélectionner 29 critères de diversité fonctionnelles liés à 8 services écosystémiques (quantité de fourrage, qualité du fourrage, stabilité de la production de fourrage, conservation de la biodiversité, pollinisation, la séquestration du carbone, résistance à la sécheresse et fertilité azotée). Cette sélection a été faite à partir d'interviews d'experts et d'une revue de la littérature. La deuxième étape a consisté à évaluer différentes inexactitudes dans le calcul des 29 critères de diversité fonctionnelle à partir de bases de traits fonctionnels et différents jeux de relevés botaniques. La troisième étape a consisté à évaluer les critères de diversité fonctionnelle à partir des données de gestion et de climat, en utilisant notamment la technique mathématique des forêts de Breiman. Les résultats montrent que les variables climatiques ont généralement plus d'effet sur la diversité fonctionnelle que celles de gestion. En outre, pour certaines conditions climatiques, la gestion n'affecte pas certains critères de diversité fonctionnelle. Parmi les 29 critères de diversité fonctionnelle, seulement 8 critères avaient plus de 40% de leur variance expliquée par la gestion et le climat / Permanent grasslands can provide a large diversity of ecosystem services. They are found in contrasted conditions in terms of management and climate in Europe. These conditions induce a wide variety of grassland types that differ in their vegetation and are expected to differ with respect to the provision of ecosystem services. Because ecosystem functioning in grassland has been shown to be linked to plant functional diversity criteria, we put forward that these functional diversity criteria can be used to evaluate the provision of ecosystem services. These criteria are influenced by the management and the climate. The overall objective of this PhD program is to assess the effects of management and climate on the plant functional diversity related to ecosystem services of permanent grasslands. The first step of the PhD program was to select 29 functional diversity criteria related to 8 ecosystem services (quantity of forage, forage quality, stability of the forage production, biodiversity conservation, pollination carbon sequestration, dryness resistance and nitrogen fertility). This selection was made using experts' interview and literature survey. The second step was to evaluate inaccuracies in the calculation of the 29 functional diversity criteria from functional trait databases and different sets of botanical surveys. The third step was to estimate the functional diversity criteria from management and climate data using "Random Forests" methodology. The results show that the climatic variables had generally more effect on the functional diversity than the management ones. Furthermore, for some climatic conditions, the management does not affect some functional diversity criteria. Among the 29 functional diversity criteria, only 8 have more than 40 % of their variance explained by the management and climate variables

Comprendre les mécanismes d'assemblages des communautés est l'une des principales questions en écologie et biogéographie. Elle est également essentielle pour prédire les conséquences des changements globaux sur la distribution future de la biodiversité. Les communautés écologiques sont la résultante de facteurs interagissant à plusieurs échelles spatiales et temporelles. En outre, ces processus peuvent affecter différemment les composantes taxonomique, fonctionnelle et phylogénétique de la biodiversité. Nous étudions ici les processus écologiques qui structurent les communautés de poissons de récif, l'un des assemblages de vertébrés les plus diversifié sur Terre. Les facettes taxonomique et fonctionnelle de ces assemblages ont été étudiées au travers de plusieurs échelles spatiales. Nos objectifs sont (i) d'identifier les facteurs structurant les assemblages de poissons de récif à différentes échelles (du régional au local), (ii) d'évaluer dans quelles mesures les processus structurant les groupes taxonomiques et fonctionnels sont consistants entre eux et (iii) de comprendre la distribution de la rareté fonctionnelle dans les assemblages de poissons de récif. Deux bases de données ont été utilisées : (1) une base de données sur les caractéristiques fonctionnelles et les distributions globales de plus de 6000 espèces de poissons dans six régions biogéographiques ; (2) un ensemble de données comprenant les occurrences de 1 474 espèces de poissons sur 9 681 échantillons obtenus le long de transects (comptages visuels en scaphandre autonome) de 40m² à travers 252 sites dans plusieurs régions biogéographiques. Dans l'océan Atlantique, la structure taxonomique et fonctionnelle des communautés de poissons a une signature biogéographique, avec une différence marquée entre les espèces des récifs biogènes riches (dans les Caraïbes et composée des petites espèces) et les régions périphériques dominées par des espèces plus grandes. L'environnement joue également un rôle important dans la structuration des assemblages dans d'autres domaines biogéographiques. Alors que la composition taxonomique des communautés est principalement liée à l'isolement des récifs, la structure fonctionnelle est influencée par la disponibilité de l'habitat à l'échelle locale. Encore une fois, il y a une plus grande contribution des petites espèces dans les sites les plus riches alors que les grandes espèces dominent en périphérie, suite à la plus forte capacité de colonisation des grandes espèces. Les assemblages présentent des structures fonctionnels emboîtées. Plus précisément les sites pauvres en diversité fonctionnelle, ici mesurée en nombre d'entités fonctionnelles différentes, sont des sous-ensembles des sites riches. Cette structure résulte de l'interaction entre les capacités de dispersion/colonisation des espèces et/ou des besoins en ressources, ainsi que des gradients d'isolement et de surface. Malgré la présence de groupes fonctionnels essentiels et de redondance dans les assemblages de poissons, la majorité des espèces dans les communautés sont rares. De plus, les espèces rares occupent une large proportion de la gamme de traits fonctionnels et effectuent souvent des fonctions uniques. Selon les scénarios simulant la perte d'espèces rares (de 8 à plus de 200 espèces rares / moyenne : 78,2 ± 62), il y aurait une perte élevée - 80 % dans un seul site - de la diversité fonctionnelle. Nos résultats révèlent que les processus au sein d'un domaine biogéographique sont responsables d'une structuration taxonomique et fonctionnelle. De plus, le rôle essentiel de la capacité de colonisation de l'espèce met en évidence l'importance de la connectivité pour le maintien de la structure fonctionnelle des communautés de poissons de récif. Enfin, la contribution des espèces rares à la diversité fonctionnelle montre que ces taxons doivent être protégés afin de maintenir l'ensemble des fonctions et services des écosystèmes. / Understanding the mechanisms of community assembly is one of the main questions in ecology and biogeography, and is essential for predicting the implications of future biodiversity loss. It is known that an array of processes operating at different spatial and temporal scales interact to produce ecological communities. These processes may affect differently the multiple components of communities: the taxonomic, functional and phylogenetic components. Here we investigate the patterns and processes structuring one of the most diverse vertebrate assemblages on Earth: reef fishes. Reef fish assemblages were assessed across multiple spatial scales, under a taxonomic and functional perspective. Our main objectives included: (i) the identification of determinants of structure in reef fish assemblages across scales (regional to local); (ii) assessing to which extent the processes behind assemblage structures are consistent for taxonomic and functional groups; (iii) understanding the patterns of functional rarity in reef fish assemblages at a global scale. Two databases were utilized: (1) an extensive database on the functional traits and the global distributions of over 6,000 reef fish species across six marine biogeographic regions; (2) a dataset comprising the occurrences of 1,474 fish species over 9,681 underwater visual transects of 40m2 across 252 sites, also throughout the major biogeographic regions. Within the Atlantic Ocean, the taxonomic and functional structure of reef fish assemblages exhibit a biogeographic fingerprint, with a marked discrimination between species rich biogenic reefs – primarily in the Caribbean, where communities were dominated by small invertebrate feeders – and poorer peripheral regions dominated by larger species with more diverse diets. At the regional scale, both historical events and environmental characteristics (coral reefs vs. periphery) have played a role in structuring both components of assemblages. The role of environment features also holds for the structure of assemblages in other biogeographic realms (i.e. Indo-Pacific and Tropical Eastern Pacific). While the taxonomic composition of assemblages is mainly related to reef isolation, the functional structure is influenced by local habitat availability. Again, there is a greater contribution of small-bodied species in the most species-rich locations; and large-bodied species prevailing in peripheral assemblages, a pattern related to species' colonization capacity. Reef fish assemblages across most regions depicted significantly functional nested structures, attributed to functional redundancy – different species constitute a number of key functional entities. The nested structure results from the interaction between species' dispersal/colonization capabilities and/or resource requirements, with isolation and area gradients. Despite the existence of key functional groups and redundancy, the majority of species are rare (low abundance or occupancy). Also, rare species fulfil much of the range of functional traits within reef fish communities and often perform unique roles. Under scenarios of rare species loss (from 8 to over 200 rare species/ mean: 78.2±62) there would be high functional diversity erosion in the majority of reef fish communities, this level reaching up to 80% of functional diversity in one location. However the extent to which these functional groups actually contribute to ecosystem functioning is unknown. Our results reveal that within-realm processes, such as evolutionary histories, have shaped the taxonomic and functional structure of assemblages in each realm. Moreover, the key role of species' colonization capacity highlights the importance of connectivity to the maintenance of the functional structure across reef fish communities. Finally, the contribution of rare species to functional diversity indicates that protecting these taxa is essential to maintain ecosystem functioning and services in reef fish communities.

A escassez de trabalhos acerca dos impactos causados por mosaicos agrícolas sobre a biodiversidade dificulta a criação de estratégias de conservação, havendo necessidade de informações acerca da ecologia e comportamento de espécies da fauna. Nesse contexto o presente estudo objetivou: 1) determinar a composição e estrutura de assembleias de mamíferos de médio e grande em uma paisagem agrícola de Mata Atlântica; 2) avaliar o padrão de alimentação da onça-parda (Puma concolor) por meio da análise de isótopos estáveis (SIA) em dois mosaicos agrícolas; 3) analisar por meio da diversidade funcional (FD) assembleias de mamíferos em remanescentes florestais distribuídos nas principais regiões biogeográficas da Mata Atlântica, e identificar limiares ecológicos para a conservação. Para o inventário, foram selecionados oito remanescentes florestais na Região Metropolitana de Campinas (RMC), São Paulo. Os dados foram coletados por busca ativa (visualizações e vestígios), resultando no registro de 34 espécies de mamíferos, sendo 27 de médio e grande porte, quatro de pequeno porte, e três exóticas. Sete espécies se encontram ameaçadas de extinção, com registros inéditos de Myrmecophaga tridactyla e Lycalopex gymnocercus. A riqueza e a composição de espécies registradas apontaram a RMC como importante para a conservação da mastofauna. Foram analisados isotopicamente (carbono e nitrogênio) pelos de onças-pardas, obtidos a partir de amostras fecais coletadas por busca ativa em remanescentes florestais inseridos em paisagens agrícolas no interior do estado de São Paulo. Houve maior consumo de presas C3 (~47% dos indivíduos) na área com maior proporção de vegetação nativa, e maior consumo de presas C4 (~40% dos indivíduos) para a área onde é predominante a matriz agrícola. Foi constatado o consumo de presas com dieta baseada em itens alimentares dos remanescentes e da matriz agrícola, sugerindo alta plasticidade comportamental das onças-pardas e de suas presas ocupando áreas fortemente impactadas pelo homem. A ferramenta isotópica apresentou informações pioneiras sobre ecologia trófica, podendo contribuir na elaboração estratégias de conservação em áreas antropizadas. Para a análise da FD e identificação dos limiares foi utilizado um banco de dados composto por 49 assembleias de mamíferos, criado a partir de dados primários e secundários de inventários, sendo selecionadas 38 características das espécies para o cálculo. A existência de limiares foi verificada utilizando a função \"segmented\", disponível no programa R. A FD apresentou-se diferente para assembleias com o mesma riqueza de espécies, indicando que filtros ambientais podem influenciar nos valores. O incremento gradual na FD devido ao aumento da área dos remanescentes mostrou uma relação positiva, possivelmente ligada a maior complexidade e heterogeneidade de áreas maiores. Foram identificados dois limiares (52 e 1244 ha), criando três situações funcionalmente distintas, tanto críticas quanto mais estáveis, permitindo definir e propor formas de ação específicas. Assembleias presentes entre os limiares apresentaram incremento funcional significativo entre FD e o aumento da área dos remanescentes, e ações visando à restauração e melhorias na configuração da paisagem devem ser incentivadas. Conclui-se, portanto, que tanto a SIA quanto a FD, podem ser consideradas importantes ferramentas para delinear estratégias e ações em prol da conservação da mastofauna. / The scarcity of studies regarding the impacts of agricultural mosaics on biodiversity hinders the creation of conservation strategies and a need for information concerning the ecology and behavior of wildlife species. In this context, the present study aimed to: 1) determine the composition and structure of mammal assemblages of medium and large sized in an agricultural landscape at Atlantic Forest; 2) evaluate the puma (Puma concolor) feeding pattern through analysis of stable isotopes (SIA) in two agricultural mosaics; 3) analyze mammal assemblages by functional diversity (FD) in forest remnants distributed in major biogeographic regions of the Atlantic Forest, and identify ecological thresholds for conservation. For mammal\'s inventory, eight forest remnants were selected in Campinas Metropolitan Region (RMC), São Paulo state. Data were collected through active search (visualizations and tracks), resulting in the record of 34 mammal species, 27 medium and large size, four of small size, and three exotic. Seven species are threatened with extinction, with novel records of Myrmecophaga tridactyla and Lycalopex gymnocercus for this region. The species richness and composition pointed RMC as an important area for mammal\'s conservation. Carbon and nitrogen stable isotopes were analyzed in pumas hair, obtained from fecal samples collected by active search in forest remnants embedded in agricultural landscapes in São Paulo state. There was a higher consumption of C3 prey (~ 47% of individuals) in the area with the highest proportion of forest coverage, and greater consumption of C4 prey (~ 40% of individuals) where the agricultural matrix was predominant. Was observed the consumption of prey with diet based on food items from both forest remnants and agricultural matrix, suggesting high behavioral plasticity of puma\'s and their prey\'s occupying areas heavily impacted by man. Stable isotopes contributed with pioneer information on trophic ecology, aiming the development of new conservation strategies in anthropogenic areas. A database consisting of 49 mammal\'s assemblages, created from primary and secondary data of inventories, was used for FD analysis and threshold\'s identification. 38 specie\'s traits were selected for FD calculation. The thresholds existence was verified using the \"segmented\" function, available on R program. FD was different between mammal assemblages with the same species richness, indicating that environmental filters may affect its values. The gradual increment in FD, due to the increase in forest remnants area, presented a positive relationship, possibly linked to the increased complexity and heterogeneity of large areas. Two thresholds (52 and 1244 ha) were identified, creating three functionally distinct situations, both critical as more stable, allowing to define and propose for each one specific ways of action. Mammal\'s assemblages found between the thresholds showed significant functional increment considering the relationship between FD and forest remnants area, and actions aiming biological restoration and improvements in the landscape configuration should be encouraged. It was concluded, therefore, that both SIA as the FD can be considered important tools to outline strategies and actions for mammal\'s conservation.

A expansão da agricultura tem levado a utilização intensiva de agrotóxicos para o controle de pragas agrícolas que apresentam sérios riscos de contaminação tanto de ambientes aquáticos como terrestres. A contaminação da biota do solo pode causar efeitos sobre diversos processos ecossistêmicos tendo em vista a importância que estes organismos desempenham na estrutura do solo. O objetivo dessa pesquisa foi avaliar os possíveis efeitos do inseticida/acaricida Kraft 36EC sobre a composição da fauna edáfica total e sobre a composição da comunidade de colêmbolos utilizando os atributos funcionais, em uma escala temporal, durante dois períodos amostrais. De forma geral, ambas as estações apresentaram diferenças na composição da fauna edáfica ao longo do tempo, nos dois tratamentos. Os colêmbolos foram os organismos mais sensíveis ao inseticida. As variáveis ambientais (temperatura e umidade) influenciaram nos efeitos do inseticida/acaricida sobre os organismos, principalmente em situações extremas. Os índices de diversidade [média por atributo (mT) e diversidade funcional (FD)] com as morfoespécies de colêmbolos, demostraram que o inseticida acaricida reduziu a diversidade funcional. Tais resultados estavam relacionados com a dominância de espécies epiedáficas (superficiais), em relação as hemiedáficas (mais afetadas pelo inseticida), principalmente no vigésimo primeiro dia. A atividade alimentar (teste bait lamina) foi reduzida ao longo do período de exposição. Os resultados obtidos mostraram que mesmo em doses recomendadas o inseticida/acaricida afetou a composição da fauna edáfica. Além disso, esse trabalho demonstrou a importância de pesquisas que avaliam não apenas dados taxonômicos como também a estrutura funcional das comunidades edáficas. Nesse sentido, podemos predizer possíveis alterações dos agrotóxicos sobre os processos ecossistêmicos. / The expansion of agriculture has led to the intensive use of pesticides for the control of agricultural pests that present serious risks of contamination in both aquatic and terrestrial environments. Contamination of soil biota by these pollutants can have effects on various ecosystem processes in view of the importance that these organisms play in the soil structure. The objective of this research was to evaluate the possible effects of the acaricide insecticide Kraft 36EC on the composition of the total soil fauna and on the composition of the community of collembolans using the functional traits, over time, during the dry and rainy season. In general, there are differences in the composition of the edaphic fauna over time, in both treatments. The collembolans were the most sensitive to insecticidal organisms. Environmental variables can influence the effects on organisms, especially in extreme situations.The diversity index [average per attribute (mT) and functional diversity (FD)] with morphospecies collembolan, showed that the insecticide reduced functional diversity. These results were related to the dominance of epiedaphic species (surface), in relation to hemiedaphic (more affected by insecticide), especially in the twenty-first day. Feeding activity (test blade bait) was reduced over the exposure period. The results showed that even at recommended doses the insecticide affected the composition of the edaphic fauna. In addition, this work has demonstrated the importance of research that evaluates not only taxonomic data but also the functional structure of edaphic communities. In this way, it is possible to predict possible changes in agrochemicals on ecosystem processes.

Atividades humanas podem causar degradação e impedir que serviços ambientais cheguem á sociedade. Evitá-la demanda constante monitoramento, que pode ser realizado com indicadores ambientais. Buscamos selecionar indicadores da exploração de petróleo nas comunidades microbianas de riachos da Amazônia, Mata Atlântica, Cerrado e Caatinga. Avaliamos as diversidades taxonômica (Sequenciamento 16S) e funcional (GeoChip 5.0M) e comparamos os resultados de amostras de água, sedimento, biofilme e solo das margens de riachos influenciados por campos de petróleo com áreas de referência. Todas as estações apresentaram alta riqueza, baixa similaridade taxonômica e alta similaridade funcional. Impactos da atividade de exploração de petróleo foram relacionados ao uso do solo e não à contaminação por hidrocarbonetos, já que as estações não tinham histórico de vazamentos. Os indicadores identificados não foram atreldos a grupos taxonômicos ou atividades metabólicas específicas, sendo mais promissora a utilização de um conceito baseado em sequencias genéticas indicadoras. / Human activities can cause degradation and prevent environmental services from reaching society. Avoid it demand constant monitoring, which can be carried out with environmental indicators. We sought to select indicators of oil exploration in the microbial communities of streams in the Amazon, Atlantic Forest, Cerrado and Caatinga morphoclimatic domains. We evaluated taxonomic (16S Sequencing) and functional (GeoChip 5.0M) diversity and compared the results from water, sediment, biofilm and soil (from the margins of streams) samples influenced by oil fields with reference areas. All of them presented high richness, low taxonomic similarity and high functional similarity. Impacts of the oil exploration activity are related to the use of soil and not to hydrocarbon contamination, since the sampling stations we choose are historically not affected by oil spills. The indicators we identified are not related to taxonomic groups or specific metabolic activities, and the use of a concept based on indicator sequences is more promising.

La forte croissance des populations humaines a engendré une intensification des milieux, surtout agricoles pour l’alimentation et l’élevage, résultant en une plus grande appropriation de la productivité primaire nette. La productivité primaire étant à la base des réseaux trophiques et écologiques, toute modification de ce processus essentiel est susceptible d’avoir de fortes conséquences sur la biodiversité. Par ailleurs, l’intensification est un processus complexe dont les trois dimensions – intrants, extrants et système – sont rarement étudiées de concert. Le cadre conceptuel et méthodologique HANPP (Human Appropriation of Net Primary Production) proposé par Helmut Haberl et collaborateurs en 2007, a pour objectif de quantifier différents paramètres de l’intensification. Dans un premier temps, les liens entre des composantes d’HANPP et d’autres indices d’intensification (i.e. HNV, IC/ha) ont été explorés afin de mieux interpréter la variabilité d’HANPP et ses composantes. HANPP semble lié à la fois aux dimensions « système » et « extrants » de l’intensité d’usage des sols et apparait comme complémentaire aux autres indicateurs testés. Dans un second temps, je me suis intéressée à la relation entre HANPP et biodiversité, à travers deux taxons complémentaires par leurs fonctions écosystémiques, i.e. les oiseaux et chiroptères. Grâce à l’utilisation de données issues de programmes de sciences participatives en France métropolitaine, j’ai pu montrer que l’intensification : i) diminuait la richesse spécifique, l’abondance et la masse moyenne des communautés de chiroptères, et ii) simplifiait la structure des communautés aviaires par l’abaissement du niveau trophique et de la régularité fonctionnelle, au bénéfice de spécialistes des milieux agricoles. Par ailleurs, j’ai pu observer que la réponse de la biodiversité pouvait grandement varier selon l’indicateur et/ou la facette (taxonomique ou fonctionnelle) étudiée. A travers mes analyses, j’ai pu clarifier les conditions d’utilisation du cadre méthodologique HANPP. J’ai également identifié des régions et types de paysage où l’intensité d’usage des sols peut coexister avec la biodiversité. L’ensemble de ces résultats forme le support à une discussion sur les opportunités pour concilier efforts de conservation et intensification. / The strong growth of Human populations has led to the intensification of land uses and land covers, especially in agricultural lands for food production and livestock, resulting in a higher appropriation of net primary productivity. As primary productivity is the root of food webs and ecological networks, any change in this essential process is likely to have a strong impact on biodiversity. Besides, intensification is a complex process whose three dimensions - inputs, outputs and system - are rarely studied together. The conceptual and methodological framework of HANPP (Human Appropriation of Net Primary Production) proposed by Helmut Haberl and collaborators in 2007, aims to quantify different parameters of intensification. First, I explored the variability of HANPP components and their relationships to other intensification indices (i.e. HNV, IC / ha) to better interpret the variability of HANPP and its components. HANPP seems to be linked to both the "system" and "output" dimensions of land use intensity and appears to complement the other indicators considered. Then, I investigated the relationship between HANPP and biodiversity, focusing on two taxa complementary in their ecosystem functions, i.e. birds and bats. Using data from citizen-science programs occurring in metropolitan France, I showed that intensification: i) decreased species richness, abundance and the average mass of bats, and ii) simplified the structure of avian communities by lowering the average trophic level and functional regularity, to the benefit of farmland specialists. In addition, I observed that the response of biodiversity could widely vary depending on the indicator and / or facet (taxonomic or functional) studied. Through my analyzes, I was able to clarify the conditions of use of the HANPP methodological framework. I also identified areas and types of landscape where land use intensity can coexist with biodiversity. All of these results form the basis for a discussion on opportunities to reconcile conservation efforts with intensification.

Orientador: David Montenegro Lapola / Resumo: O impacto do aumento da concentração atmosférica de CO 2 sobre as florestas tropicais é incerto. Uma das fontes de incerteza está na má representação da diversidade funcional encontradas nestes ecossistemas pelos modelos de vegetação atuais. Este trabalho teve como objetivo investigar como a inclusão da representação da variabilidade dos atributos funcionais pode afetar o desempenho dos modelos vegetação e os impactos que o aumento da concentração atmosférica de CO 2 pode ter sobre as florestas tropicais, com foco nos processos de alocação, tempo de residência do carbono e armazenamento de carbono, bem como na diversidade funcional das mesmas. Para tal foi desenvolvido o modelo CAETÊ (Carbon and Ecosystem Functional-Trait Evaluation model) com foco no módulo que representa a alocação e o tempo de residência do carbono. Foram utilizadas duas versões do modelo: (i) versão beta: vegetação representada através de tipos funcionais de plantas (PFTs), a exemplo dos modelos de vegetação atuais, em que os atributos funcionais são invariantes no espaço e no tempo; (ii) versão final: os indivíduos são resultado da combinação aleatória de valores de atributos funcionais de modo a gerar uma ampla gama de estratégias de vida de planta (PLSs) que substituem os PFTs comumente utilizados. A versão final foi aplicada a um cenário de aumento de concentração de CO 2. A inclusão da variabilidade dos atributos funcionais (versão final) melhorou a capacidade do modelo em representar os fluxos bioge... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The effects of increasing atmospheric CO 2 concentrations on tropical forests remain largely uncertain. One of the sources of the uncertainties is the poor representation of functional diversity found in tropical ecosystems on vegetation models. Here we aimed to explore how the inclusion of functional diversity affects vegetation model performance and the impacts of increasing CO 2 on tropical forests, focusing on allocation, carbon residence time and carbon storage processes as well as on its functional diversity. For this purpose it was developed the CAETÊ model (Carbon and Ecosystem Functional-Trait Evaluation model) with focus on the module that represents carbon allocation and residence time. Two versions of the model were used: (i) beta version: vegetation represented through plant functional types (PFTs), just like current vegetation models, in which functional traits are invariant on space and time; (ii) final version: vegetation is represented through plant life strategies (PLSs) generated through random combinations of functional trait values which replace the commonly used PFTs. The final version was applied to an increased CO 2 scenario (+200 ppmv). The inclusion of functional diversity (final version) improved the model performance on representing biogeochemical fluxes and stocks, mainly on spatial patterns, compared to a low functional diversity version (beta version). The CO 2 increase has generated an increase on NPP, on GPP and on biomass, despite the biomass... (Complete abstract click electronic access below) / Mestre