Les écologistes reconnaissent depuis longtemps que les organismes sont soutenus par le flux, l’emmagasinage et le renouvellement d’énergie et de matériel de l’écosystème, puisqu’ils sont nécessaires au métabolisme biologique et à la construction de biomasse. L’importance des organismes dans la régularisation des processus écosystémiques est maintenant de plus en plus considérée. Situé au centre des chaînes trophiques aquatiques, le zooplancton influence les flux d’énergie et de matériel dans les écosystèmes. Plusieurs de leurs caractéristiques sont connues comme étant de bons indicateurs de leur effet sur l’environnement, notamment leur taille, contenu corporel et taux métabolique. La plupart de ces caractéristiques peuvent être appelées « traits fonctionnels ». Alors que l’emploi des traits devient de plus en plus populaire en écologie des communautés aquatiques, peu ont su utiliser cette approche afin de concrètement lier la structure des communautés zooplanctoniques aux processus écosystémiques. Dans cette étude, nous avons colligé les données provenant d’une grande variété de littérature afin de construire une base de données sur les traits du zooplancton crustacé contribuant directement ou indirectement aux flux de C, N et P dans les écosystèmes. Notre méta-analyse a permis d’assembler plus de 9000 observations sur 287 espèces et d’identifier par le fait même ce qu’il manque à nos connaissances. Nous avons examiné une série de corrélations croisées entre 16 traits, dont 35 étaient significatives, et avons exploré les relations entre les unités taxonomiques de même qu’entre les espèces marines et d’eaux douces. Notre synthèse a entre autres révélé des patrons significativement différents entre le zooplancton marin et dulcicole quant à leur taux de respiration et leur allométrie (masse vs. longueur corporelle). Nous proposons de plus une nouvelle classification de traits liant les fonctions des organismes à celles de l’écosystème. Notre but est d’offrir une base de données sur les traits du zooplancton, des outils afin de mieux lier les organismes aux processus écosystémiques et de stimuler la recherche de patrons généraux et de compromis entre les traits. / Ecologists have long recognized that organisms are sustained by the flux, storage and turnover of ecosystem energy, which fuels biological metabolism, and material, used to construct biomass. Over the past three decades, the importance of individual organisms in regulating ecosystem processes, such as consumer-driven nutrient cycling, has been increasingly recognized. Occupying a central position in aquatic food webs, zooplankton are known to influence other trophic levels and exert a strong influence on energy fluxes or material processing in ecosystems. Several species’ characteristics have been pointed out as being good indicators, or predictors, of the effect of zooplankton on their environment, including individual body size, corporal stoichiometry and specific physiological rates. Most of these characteristics can also be termed “functional traits”. While the use of traits has recently gained popularity amongst aquatic community ecologists, few have applied this approach to concretely link zooplankton community structure to ecosystem processes. In the present study, we compiled data from a wide variety of literature to construct a database of crustacean zooplankton species and their traits contributing directly or indirectly to C, N or P ecosystem fluxes. Our literature search yielded over 9000 empirical observations on 287 different species and thereby allowed identification of knowledge gaps in the literature. We explored trait relationships amongst taxonomic units and between marine and freshwater habitats. Of all cross-correlations tested among 16 zooplankton traits, 35 were significant, with most traits being related to body mass. Our synthesis revealed significantly different patterns between freshwater and marine zooplankton respiration and allometry (body mass vs. length). We propose a novel trait classification scheme according to both organismal and ecosystem functions. Our goal is to provide a database for zooplankton functional traits, tools to link organisms to ecosystem processes, and to promote a search for general patterns and trade-offs amongst traits.

La mise en place d’une agriculture plus durable nécessite une compréhension de l’impact des pratiques de gestion sur le fonctionnement des agroécosystèmes et sur la fourniture de services écosystémiques. En représentant près de 68% des terres agricoles mondiales et contribuant à la subsistance de plus de 800 millions de personnes, les prairies sont l’un des agroécosystèmes où l’optimisation des pratiques agricoles apparaît comme cruciale. Ce travail de thèse porte sur le chaulage, une pratique agricole connue pour lutter contre les effets de l’acidification des sols – qu’elle soit naturelle ou induite par la gestion – mais dont l’efficacité est variable en prairie permanente. De fait, la littérature documentant l’impact du chaulage en prairie permanente est limitée et ne prend en compte que rarement la multifonctionnalité de ces agroécosystèmes. Par une approche intégrant différents types d’expérimentations, mon travail de thèse a cherché à répondre à ce besoin et à renforcer les connaissances du chaulage sur le fonctionnement de l’écosystème prairial. Le développement d’expérimentations au champ (in situ), en conditions semi-contrôlées (mésocosmes) et d’incubations de sol au laboratoire (microcosmes) a permis d’explorer les effets du chaulage sur les différents compartiments de l’écosystème prairial (végétation, microorganismes, sol) ainsi que l’influence de facteurs modulant ces effets. Dans l’ensemble des expérimentations, le chaulage a effectivement augmenté le pH des sols. Toutefois, cette amélioration du statut acido-basique du sol ne s’est pas toujours traduite par une augmentation de la productivité du fourrage ou des biomasses microbiennes et racinaires. Mes travaux ont montré que le chaulage contribue aux émissions de gaz à effet de serre par différentes voies (réémission du carbone apporté sous forme de chaulage et stimulation de la minéralisation) et peut potentiellement réduire les émissions de CO2 à l’échelle de la respiration de l’écosystème. Collectivement mes résultats soulignent l’importance du contexte pédoclimatique sur l’impact du chaulage en prairie permanente, et la difficulté d’extrapoler les effets du chaulage, en particulier sur la production de fourrage et les émissions de gaz à effet de serre, d’une échelle d’étude fine à l’échelle de la parcelle en prairie permanente. L’efficacité du chaulage semble dépendre du type d’amendement et de son dosage et peut également interagir avec d’autres pratiques de gestion telles que la fertilisation azotée et le niveau d’intensité de gestion. / The development of sustainable agriculture requires greater understanding of the impact of management practices on agroecosystem functioning, and on the ecosystem services provided by these agroecosystems. Representing nearly 68% of world's agricultural surfaces and contributing to the livelihoods of more than 800 million people, grasslands are one of the major agroecosystems where optimized agricultural practices are of concern. This PhD focuses on liming, a well-known practice for counteracting soil acidification (due to ongoing natural processes or accelerated by management practices), but which has variable efficiency in permanent grasslands. Indeed, liming effects on grassland are poorly documented and existing studies rarely take into account grassland multifunctionality. My thesis uses an integrated approach to improve the knowledge of liming impacts on grassland functioning. Different types of experiments – in the field (in situ), in semi-controlled conditions (mesocosms) and laboratory soil incubations (microcosms) – were used to study liming effects on different grassland compartments (vegetation, microorganisms, soil) along with possible interacting factors. Liming effectively increased soil pH in all the experiments. However, improving pH status did not always lead to greater forage production or increases in microbial and root biomass. My results showed that liming can enhance greenhouse gas emissions through several pathways (reemission of lime-derived carbon or stimulation of carbon mineralization), but may also reduce CO2 emissions from ecosystem respiration. Collectively, my findings emphasize the importance of pedoclimatic conditions for liming impacts on permanent grasslands and highlight the difficulty of upscaling liming effects, particularly on forage production and greenhouse gas emissions. The efficiency of liming appears to depend on the type and dose of soil improvers and can also interact with other management practices such as nitrogen fertilization and management intensification.

O presente trabalho consistiu na produção de uma síntese sobre os principais aspectos do ciclo biogeoquímico do carbono, envolvendo aspectos recentes do efeito estufa na atmosfera, sendo também contextualizadas as políticas públicas e seus mecanismos sócio-econômicos; inserida num contexto atual, das mudanças climáticas, intimamente relacionadas à Convenção-Quadro das Nações Unidas sobre Mudança do Clima, Protocolo de Kyoto e Mecanismos de Desenvolvimento Limpo. Os ecossistemas terrestres prestam enorme contribuição de serviços ambientais ao homem na forma de oferta de água, alimentos e insumos gerais. Estes ganhos são sustentáveis na medida em que haja um equilíbrio estável entre a entrada e saída de certas variáveis. Ainda não se entende satisfatoriamente a funcionalidade dos ecossistemas naturais e sua plena interação com o clima, nas escalas local, regional e global; portanto, é uma responsabilidade social antecipar o entendimento dessa relação, antes que tudo se transforme. Não se sabe ao certo todas as conseqüências do aumento excessivo na temperatura terrestre, mas são esperadas alterações profundas em diversos ecossistemas, por exemplo: descongelamento das calotas polares e o conseqüente alagamento de regiões costeiras, alterações de intensidade e freqüência de chuvas, e alteração do metabolismo vegetal. São também previstas conseqüências na mudança das zonas climáticas e agrícolas e o desaparecimento de espécies sensíveis a esta mudança de temperatura. Procurando atingir o objetivo final da Convenção-Quadro das Nações Unidas sobre Mudança do Clima, em Kyoto – Japão, foi proposto o Protocolo de Kyoto, no sentido de possibilitar alcançar a estabilização das concentrações de gases de efeito estufa na atmosfera, num nível que não interfira perigosamente no sistema climático. Estabelece metas e prazos para controlar num primeiro esforço os principais gases de efeito estufa. Foram estabelecidos três mecanismos para auxiliar os países desenvolvidos no cumprimento de suas metas de redução ou limitação de emissões de gases de efeito estufa. Um desses mecanismos foi definido como Mecanismo de Desenvolvimento Limpo - MDL, sua implementação interessa particularmente aos países em desenvolvimento, pois permitirá a transferência de recursos e tecnologias para a redução de emissões. Neste contexto, exigi-se da classe cientifica respostas mais precisas e rápidas do entendimento de todos os processos envolvidos. O acompanhamento de projetos é importante, gerando informações para análises técnicas, científicas, sociais, ambientais e econômicas, que serão demandadas nas futuras negociações relativas à mitigação da mudança do clima. / The present work intends to present a synthesis of the information which is distributed in several areas. It approaches the main aspects of the global carbon cycle, including the recent greenhouse effect in the atmosphere, also including the political argumentation and the socioeconomic mechanisms associated. The work also brings a critical revision of the framework related to the United Nations Framework Convention on the Climate Change, the Kyoto Protocol and the Clean Development Mechanism. The terrestrial ecosystems provide enormous contribution of environmental services to the human beings in terms of water, foods, and general inputs supplies. The sustainability of this provision relies on the maintenance of the input/output equity of matter and energy throughout time. There is still no clear understanding of the natural ecosystems functioning and their interactions with climate in a broad perspective, from local to regional and global scales. Therefore it is a social responsibility to anticipate the understanding of this relation, before everything changes. The effects on the ecosystems of the temperature increase in the Earth surface are not fully understood, but strong changes are expected and some are already being measured in several ecosystems, for instance: mountain glaciers and the ice cap in the North Pole are declining, with foreseeable consequences of increasing sea level and flooding of coastal areas; changes in the cycle and intensity of rain events; changes in plant metabolism and distribution of agricultural species, interfering in food production and safety. The Kyoto Protocol was proposed aiming to achieve the objectives of the United Nations Framework Convention on the Climate Change, building the legal and political background for the Nations to lessen and stabilize the concentrations of greenhouse gases in the atmosphere. The Protocol established mechanisms for reduction and mitigation of greenhouse gases emissions including developed and developing countries. In terms of economical and technological gains, the Clean Development Mechanism – CDM, was one of the proposed mechanism of the Kyoto Protocol, which is particularly interesting to the developing countries. This mechanism allows resources and technologies transference for the reduction of GHG emissions in developing countries. In this context, the scientific community is an important component to bring more precise and fast answers to the understanding of all of the processes related to the actual influence of the Human kind in the planet.

Sustainability is one of the biggest goals of humankind in the new millennium. An increasing global demand on agricultural products stimulates agricultural expansion in Brazil, especially in the Southwestern Amazon, namely in the Cerrado and Amazon biomes. A better understanding of biogeochemical cycles and their influence on natural and agricultural systems is key to achieve environmental sustainability and improve agricultural efficiency. These biogeochemical cycles are driven by microbes, and the aim of this thesis was to correlate microbial functional group abundances with differences in carbon, nitrogen, and greenhouse gas cycles in response to land use changes in Southwestern Amazon soils. This work was performed at the University of São Paulo, Brazil, and at the University of Massachusetts Amherst, USA, while the candidate was enrolled in Ph.D. programs at both universities. The thesis is composed of five studies. The first study shows that land use change from Cerrado and forest to agriculture (soybean, Glycine max (L. Merrill), in succession with other crops) or pasture (Brachiaria brizantha (Hochst. ex A. Rich.) did not reduce soil microbial diversity but changed microbial structure. The second study, a physicochemical background for this land use conversion, describes the alteration of C and N stocks, soil chemical parameters, and microbiological parameters such as biomass, biological C stocks, and changes in the abundance of prokaryotes and fungi. In the third and fourth studies microcosm experiments depict how the agricultural change to soybean and Brachiaria alter the original microbial structure found in forest or cerrado. These studies focused on abundances of key biogeochemical genes (amoA, nirK, nirS, norB, nosZ, mcrA, and pmoA) and correlated gene copy abundances with C, N, and GHG measurements. In the fifth study, in situ soil surveys and GHG samplings were used to characterize the changes from forest to pasture (B. brizantha, 25 years) or soybean crop system (for 2 years or 25 years in succession). We found correlations between genes and processes, indicating that gene abundances provide important microbial information for the understanding of the targeted biogeochemical cycles. Land use, rather than plant species, promotes alterations in microbial gene abundances and processes. During the survey period, forest exhibited higher microbial activity, resulting in higher nitrate availability and N2O emissions. These processes were correlated with higher abundances of process related genes. Nitrate and N2O emissions were lower in agricultural and pasture soils. CO2 emission was higher in the two-year-old soybean plot. The forest and two-year-old soybean plots acted as a sink for CH4, while the pasture plots represented a source of it. The results validated the use of gene abundance determination as a valuable tool to better understand C, N, and GHG processes. The genes nirK, nosZ, and 16S rRNA presented the best correlations with the processes. A larger temporal and spatial analysis is needed to infer statements on the processes dynamics due to land use change. For the first time gene abundance measurements were used to integrate the C, N and GHG cycles, giving insights into land use changes in Southwestern Amazon / Sustentabilidade é um dos maiores objetivos da humanidade no novo milênio. Uma demanda crescente por produtos agrícolas tem estimulado a expansão agrícola no Brasil, especialmente no Sudoeste da Amazônia, nos biomas Cerrado e Amazônia. Um melhor entendimento dos ciclos biogeoquímicos e suas influências em sistemas naturais e agrícolas é chave para se alcançar sustentabilidade ambiental e aumentar eficiência agrícola. Esses ciclos biogeoquímicos são guiados por microrganismos, e o objetivo dessa tese foi correlacionar abundância de grupos funcionais de microrganismos com carbono, nitrogênio e gases de efeito estufa (GEE) em resposta a mudança do uso da terra em solos do sudoeste da Amazônia. Esse trabalho foi realizado na Universidade de São Paulo e na Universidade de Massachusetts Amherst enquanto o doutorando esteve matriculado nas duas universidades. A tese é composta de cinco estudos. O primeiro estudo mostra que a mudança no uso da terra de Cerrado e floresta para agricultura (soja, Glycine max (L. Merrill), em sucessão com outros cultivos) ou pastagem (Brachiaria brizantha (Hochst. ex A. Rich.) não reduz diversidade microbiana, mas muda sua estrutura. O segundo estudo descreve as alterações nos estoques de C, N, parâmetros químicos e microbiológicos da conversão de Cerrado para agricultura e pastagem. No terceiro e no quarto estudos, microcosmos foram usados para avaliar a influência de soja e braquiária na microbiota dos solos. Genes chaves dos processos biogeoquímicos (amoA, nirK, nirS, norB, nosZ, mcrA, e pmoA) foram quantificados e correlacionados com C, N e GEE. No quinto estudo, coletas in situ de solo e gases foram usadss para caracterizar a mudança do uso da terra de floresta para pastagem (braquiária, 25 anos) e para agricultura (soja, segundo ano, e soja, 25 anos, em sucessão com outras culturas). Correlações entre genes e processos foram encontradas, indicando que abundância gênica fornece importantes informações para o entendimento dos ciclos biogeoquímicos. Mudança no uso da terra como um todo, mais do que a mudança de vegetação, promove as alterações na abundância gênica e processos do solo. Durante o período de coleta, floresta exibiu maior atividade microbiana, resultando em maior disponibilidade de nitrato e emissão de N2O. Esses processos correlacionam com maior abundância dos genes relacionados aos processos. Quantidades de nitrato e N2O foram menores em agricultura e pastagem. As emissões de CO2 foram maiores na área de soja de segundo ano. Os solos de floresta e soja de segundo ano se mostraram como drenos de metano, enquanto que a pastagem foi uma fonte de emissão. Os resultados validam o uso de abundância gênica como uma técnica valiosa para um melhor entendimento dos ciclos do C, N e GEE. Os genes nirK, nosZ, e 16S rRNA apresentaram as melhores correlações com os processos. Uma análise temporal e espacial mais abrangente é necessária para generalizações sobre a dinâmica dos processos na região estudada. Pela primeira vez abundância gênica foi usada para integrar os ciclos do C, N e GEE, colaborando para um melhor entendimento dos processos relacionados à mudança no uso da terra no sudoeste da Amazônia

Dans les environnements côtiers, soumis à l’impact des marées noires, les microorganismes jouent un rôle crucial dans le devenir des hydrocarbures pétroliers. Toutefois, de nombreux facteurs influencent les activités microbiennes, notamment par les organismes bioturbateurs qui modifient la pénétration de l’oxygène dans les sédiments. Le travail de la thèse vise à mieux comprendre l’impact d’une pollution pétrolière sur les communautés microbiennes dans des sédiments bio turbés. Il s’agissait de comparer les remaniements structuraux de la communauté microbienne liée à la contamination pétrolière dans des sédiments présentant une faible et une forte activité de bioturbation. Des sédiments marins ont été maintenus en microcosmes durant 9 mois et soumis à quatre conditions : (i) pas de traitement (contrôle), (ii) pétrole, (iii) bioturbation et (iv) pétrole et bioturbation. Les efficacités de dégradation des hydrocarbures pétroliers se sont révélées similaires dans les deux types de sédiments. Par des approches moléculaires, la diversité taxonomique et fonctionnelle des communautés microbiennes totales et métaboliquement actives a été évaluée au cours du temps. Les communautés microbiennes ont subi d’importants remaniements structuraux spécifiques à chaque traitement. Nous suggérons que le fonctionnement global de la communauté est modifié par l’activité bioturbatrice sans pour autant modifier l’activité de dégradation. Ces travaux ont mis en évidence une redondance fonctionnelle de l’activité de biodégradation des hydrocarbures pétroliers des communautés microbiennes. L’isolement de communautés hydrocarbonoclastes a permis de confirmer cette redondance fonctionnelle. / Coastal areas such as mudflats are affected by oil spills. In these environments, microorganisms play a crucial role in the fate of petroleum hydrocarbons. However, many factors influence microbial activities, especially the bioturbating organisms, which altered the oxygen penetration in sediments. The present work attempts to better understand the impact of petroleum contamination on microbial community associated with petroleum contamination in sediments with low and high bioturbation activity. This study is based on microcosm experiments with a device simulating tidal cycles. Marine sediments were maintained for 9 months in microcosms and subjected to four conditions: (i) no treatment (control), (ii) oil, (iii) bioturbation and (iv) oil and bioturbation. Chemical, microbiological and biological analyses were conducted throughout the experiment. The efficiencies of degradation of petroleum hydrocarbons were similar in both sediments. By molecular approaches, we assessed the dynamic of the functional and taxonomic diversity of the total and metabolically active communities during the oil contamination. Microbial communities showed significant structural rearrangements specific for each treatment that resulted in distinct microbial communities in both sediments. Hence, the overall microbial community structure was changed by bioturbating activity without changing the degradation capacity revealing a functional redundancy of the biodegradation capacity of hydrocarbons. This result was further supported by the isolation and characterization of hydro carbonoclastic communities.

Ubiquitaires et très anciens, les communautés des tapis microbiens font preuve de capacités métaboliques et adaptatives très importantes. Situés en zone côtières, ces écosystèmes peuvent être soumis à des contaminations pétrolières. Dans ce contexte, cette étude vise d’une part à décrire la structure et le fonctionnement de tapis microbiens et d’autre part à comprendre l’impact d’une contamination pétrolière sur ces écosystèmes. Cette étude porte sur deux tapis microbiens de l’étang de Berre aux paramètres physico-Chimiques proches mais présentant des contaminations pétrolières contrastées. Le fonctionnement du système étant tributaire d’autres facteurs tels que la lumière et les saisons, les variations saisonnières et nycthémérales ont été prises en compte dans cette étude. Un accent particulier a également été porté sur le cycle du soufre de par son importance en milieu marin. Les résultats de cette étude mettent en évidence des structures de communautés différentes entre les deux tapis au niveau global, la séparation spatiale prévalant sur la séparation saisonnière. La fraction active de la communauté du site contaminé présente une évolution linéaire tandis que celle du site témoins suit pour sa part les variations saisonnières. Au niveau du site contaminé une augmentation de l’expression des gènes impliqués dans la dégradation des hydrocarbures couplée à une biodégradation des hydrocarbures suggère que le tapis contaminé est adapté à la contamination pétrolière. Malgré les différences de structures et d’activités de dégradation, des profils métaboliques très semblables sont cependant observables entre les deux tapis, avec des fonctions similaires laissant supposer une redondance fonctionnelle. Des variations saisonnières et nycthémérales ont également été observées avec notamment des Desulfobulbaceae plus abondantes au printemps et plus actives en journée. Des études culturales ont été réalisées en parallèle. Elles permettront d’appréhender de manière complémentaire la dynamique des communautés des sulfato-Réducteurs au sein du tapis et de mieux comprendre les variations mises en évidence dans cette étude. / Ubiquist and very ancient, the microbial mats communities demonstrate very important metabolic and adaptive capacities. Located in the coastal area, these ecosystems may be subject to oil contamination. In this context, the aim of this study is on one hand to describe the structure and functioning of microbial mats and on the other to understand the impact of oil contamination on these ecosystems. This study focused on two microbial mats from the Berre lagoon with close physical chemical parameters but with contrasted hydrocarbon contamination levels. The functioning of the system is dependent on other factors such as light and seasons, diurnal and seasonal variations were taken into account in this study. Special emphasis was placed on the sulfur cycle due to its importance in the marine environments. The results of this study highlighted different communities’ structures at the global level between both mats, the spatial variation prevailed on seasonal variation. The active part of the community from the contaminated site shows a linear trend while that one of the uncontaminated site follows the seasonal variations. The contaminated site shows genes involved in hydrocarbon degradation more expressed coupled to a hydrocarbon biodegradation suggesting that the contaminated mat is adapted to the petroleum contamination. Despite these differences in the structure and the degradation capacities, very similar metabolic profiles are observed between the two mats with similar functions, suggesting functional redundancy. Seasonal and diurnal variation was also observed, the Desulfobulbaceae were particularly more abundant in spring and more active during the day. A complementary cultural approach will allow to better understanding the dynamics of sulfate-Reducers communities in the mat and comprehending these variations.

Sustainability is one of the biggest goals of humankind in the new millennium. An increasing global demand on agricultural products stimulates agricultural expansion in Brazil, especially in the Southwestern Amazon, namely in the Cerrado and Amazon biomes. A better understanding of biogeochemical cycles and their influence on natural and agricultural systems is key to achieve environmental sustainability and improve agricultural efficiency. These biogeochemical cycles are driven by microbes, and the aim of this thesis was to correlate microbial functional group abundances with differences in carbon, nitrogen, and greenhouse gas cycles in response to land use changes in Southwestern Amazon soils. This work was performed at the University of São Paulo, Brazil, and at the University of Massachusetts Amherst, USA, while the candidate was enrolled in Ph.D. programs at both universities. The thesis is composed of five studies. The first study shows that land use change from Cerrado and forest to agriculture (soybean, Glycine max (L. Merrill), in succession with other crops) or pasture (Brachiaria brizantha (Hochst. ex A. Rich.) did not reduce soil microbial diversity but changed microbial structure. The second study, a physicochemical background for this land use conversion, describes the alteration of C and N stocks, soil chemical parameters, and microbiological parameters such as biomass, biological C stocks, and changes in the abundance of prokaryotes and fungi. In the third and fourth studies microcosm experiments depict how the agricultural change to soybean and Brachiaria alter the original microbial structure found in forest or cerrado. These studies focused on abundances of key biogeochemical genes (amoA, nirK, nirS, norB, nosZ, mcrA, and pmoA) and correlated gene copy abundances with C, N, and GHG measurements. In the fifth study, in situ soil surveys and GHG samplings were used to characterize the changes from forest to pasture (B. brizantha, 25 years) or soybean crop system (for 2 years or 25 years in succession). We found correlations between genes and processes, indicating that gene abundances provide important microbial information for the understanding of the targeted biogeochemical cycles. Land use, rather than plant species, promotes alterations in microbial gene abundances and processes. During the survey period, forest exhibited higher microbial activity, resulting in higher nitrate availability and N2O emissions. These processes were correlated with higher abundances of process related genes. Nitrate and N2O emissions were lower in agricultural and pasture soils. CO2 emission was higher in the two-year-old soybean plot. The forest and two-year-old soybean plots acted as a sink for CH4, while the pasture plots represented a source of it. The results validated the use of gene abundance determination as a valuable tool to better understand C, N, and GHG processes. The genes nirK, nosZ, and 16S rRNA presented the best correlations with the processes. A larger temporal and spatial analysis is needed to infer statements on the processes dynamics due to land use change. For the first time gene abundance measurements were used to integrate the C, N and GHG cycles, giving insights into land use changes in Southwestern Amazon / Sustentabilidade é um dos maiores objetivos da humanidade no novo milênio. Uma demanda crescente por produtos agrícolas tem estimulado a expansão agrícola no Brasil, especialmente no Sudoeste da Amazônia, nos biomas Cerrado e Amazônia. Um melhor entendimento dos ciclos biogeoquímicos e suas influências em sistemas naturais e agrícolas é chave para se alcançar sustentabilidade ambiental e aumentar eficiência agrícola. Esses ciclos biogeoquímicos são guiados por microrganismos, e o objetivo dessa tese foi correlacionar abundância de grupos funcionais de microrganismos com carbono, nitrogênio e gases de efeito estufa (GEE) em resposta a mudança do uso da terra em solos do sudoeste da Amazônia. Esse trabalho foi realizado na Universidade de São Paulo e na Universidade de Massachusetts Amherst enquanto o doutorando esteve matriculado nas duas universidades. A tese é composta de cinco estudos. O primeiro estudo mostra que a mudança no uso da terra de Cerrado e floresta para agricultura (soja, Glycine max (L. Merrill), em sucessão com outros cultivos) ou pastagem (Brachiaria brizantha (Hochst. ex A. Rich.) não reduz diversidade microbiana, mas muda sua estrutura. O segundo estudo descreve as alterações nos estoques de C, N, parâmetros químicos e microbiológicos da conversão de Cerrado para agricultura e pastagem. No terceiro e no quarto estudos, microcosmos foram usados para avaliar a influência de soja e braquiária na microbiota dos solos. Genes chaves dos processos biogeoquímicos (amoA, nirK, nirS, norB, nosZ, mcrA, e pmoA) foram quantificados e correlacionados com C, N e GEE. No quinto estudo, coletas in situ de solo e gases foram usadss para caracterizar a mudança do uso da terra de floresta para pastagem (braquiária, 25 anos) e para agricultura (soja, segundo ano, e soja, 25 anos, em sucessão com outras culturas). Correlações entre genes e processos foram encontradas, indicando que abundância gênica fornece importantes informações para o entendimento dos ciclos biogeoquímicos. Mudança no uso da terra como um todo, mais do que a mudança de vegetação, promove as alterações na abundância gênica e processos do solo. Durante o período de coleta, floresta exibiu maior atividade microbiana, resultando em maior disponibilidade de nitrato e emissão de N2O. Esses processos correlacionam com maior abundância dos genes relacionados aos processos. Quantidades de nitrato e N2O foram menores em agricultura e pastagem. As emissões de CO2 foram maiores na área de soja de segundo ano. Os solos de floresta e soja de segundo ano se mostraram como drenos de metano, enquanto que a pastagem foi uma fonte de emissão. Os resultados validam o uso de abundância gênica como uma técnica valiosa para um melhor entendimento dos ciclos do C, N e GEE. Os genes nirK, nosZ, e 16S rRNA apresentaram as melhores correlações com os processos. Uma análise temporal e espacial mais abrangente é necessária para generalizações sobre a dinâmica dos processos na região estudada. Pela primeira vez abundância gênica foi usada para integrar os ciclos do C, N e GEE, colaborando para um melhor entendimento dos processos relacionados à mudança no uso da terra no sudoeste da Amazônia

O presente trabalho consistiu na produção de uma síntese sobre os principais aspectos do ciclo biogeoquímico do carbono, envolvendo aspectos recentes do efeito estufa na atmosfera, sendo também contextualizadas as políticas públicas e seus mecanismos sócio-econômicos; inserida num contexto atual, das mudanças climáticas, intimamente relacionadas à Convenção-Quadro das Nações Unidas sobre Mudança do Clima, Protocolo de Kyoto e Mecanismos de Desenvolvimento Limpo. Os ecossistemas terrestres prestam enorme contribuição de serviços ambientais ao homem na forma de oferta de água, alimentos e insumos gerais. Estes ganhos são sustentáveis na medida em que haja um equilíbrio estável entre a entrada e saída de certas variáveis. Ainda não se entende satisfatoriamente a funcionalidade dos ecossistemas naturais e sua plena interação com o clima, nas escalas local, regional e global; portanto, é uma responsabilidade social antecipar o entendimento dessa relação, antes que tudo se transforme. Não se sabe ao certo todas as conseqüências do aumento excessivo na temperatura terrestre, mas são esperadas alterações profundas em diversos ecossistemas, por exemplo: descongelamento das calotas polares e o conseqüente alagamento de regiões costeiras, alterações de intensidade e freqüência de chuvas, e alteração do metabolismo vegetal. São também previstas conseqüências na mudança das zonas climáticas e agrícolas e o desaparecimento de espécies sensíveis a esta mudança de temperatura. Procurando atingir o objetivo final da Convenção-Quadro das Nações Unidas sobre Mudança do Clima, em Kyoto – Japão, foi proposto o Protocolo de Kyoto, no sentido de possibilitar alcançar a estabilização das concentrações de gases de efeito estufa na atmosfera, num nível que não interfira perigosamente no sistema climático. Estabelece metas e prazos para controlar num primeiro esforço os principais gases de efeito estufa. Foram estabelecidos três mecanismos para auxiliar os países desenvolvidos no cumprimento de suas metas de redução ou limitação de emissões de gases de efeito estufa. Um desses mecanismos foi definido como Mecanismo de Desenvolvimento Limpo - MDL, sua implementação interessa particularmente aos países em desenvolvimento, pois permitirá a transferência de recursos e tecnologias para a redução de emissões. Neste contexto, exigi-se da classe cientifica respostas mais precisas e rápidas do entendimento de todos os processos envolvidos. O acompanhamento de projetos é importante, gerando informações para análises técnicas, científicas, sociais, ambientais e econômicas, que serão demandadas nas futuras negociações relativas à mitigação da mudança do clima. / The present work intends to present a synthesis of the information which is distributed in several areas. It approaches the main aspects of the global carbon cycle, including the recent greenhouse effect in the atmosphere, also including the political argumentation and the socioeconomic mechanisms associated. The work also brings a critical revision of the framework related to the United Nations Framework Convention on the Climate Change, the Kyoto Protocol and the Clean Development Mechanism. The terrestrial ecosystems provide enormous contribution of environmental services to the human beings in terms of water, foods, and general inputs supplies. The sustainability of this provision relies on the maintenance of the input/output equity of matter and energy throughout time. There is still no clear understanding of the natural ecosystems functioning and their interactions with climate in a broad perspective, from local to regional and global scales. Therefore it is a social responsibility to anticipate the understanding of this relation, before everything changes. The effects on the ecosystems of the temperature increase in the Earth surface are not fully understood, but strong changes are expected and some are already being measured in several ecosystems, for instance: mountain glaciers and the ice cap in the North Pole are declining, with foreseeable consequences of increasing sea level and flooding of coastal areas; changes in the cycle and intensity of rain events; changes in plant metabolism and distribution of agricultural species, interfering in food production and safety. The Kyoto Protocol was proposed aiming to achieve the objectives of the United Nations Framework Convention on the Climate Change, building the legal and political background for the Nations to lessen and stabilize the concentrations of greenhouse gases in the atmosphere. The Protocol established mechanisms for reduction and mitigation of greenhouse gases emissions including developed and developing countries. In terms of economical and technological gains, the Clean Development Mechanism – CDM, was one of the proposed mechanism of the Kyoto Protocol, which is particularly interesting to the developing countries. This mechanism allows resources and technologies transference for the reduction of GHG emissions in developing countries. In this context, the scientific community is an important component to bring more precise and fast answers to the understanding of all of the processes related to the actual influence of the Human kind in the planet.

Le concept de « service écosystémique », en plein essor depuis la publication du Millenium Ecosystem Assessment en 2005, a permis de souligner l'importance des performances non-marchandes des écosystèmes. En arboriculture, assurer une bonne productivité tout en préservant les ressources naturelles et la santé humaine est aujourd’hui un défi majeur, qui peut être analysé sous l’angle des services écosystémiques. Quels sont ces services au sein d’un verger de pommiers ? Comment les analyser ? Quels sont les liens - conflits et synergies - entre services écosystémiques multiples et comment les systèmes de culture modifient-ils les profils de services multiples? Ce travail de thèse vise à répondre à ces questions avec une démarche novatrice combinant mesures expérimentales, modélisation et analyse statistique. Suite à une analyse bibliographique des services écosystémiques pouvant être délivrés dans des vergers, cinq services ont été sélectionnés. Il s’agit de la production de fruits, de la disponibilité de l’azote dans le sol, de la régulation du climat reposant sur la prévention de la dénitrification de l’azote et sur la séquestration du carbone, de la maintenance et de la régulation du cycle de l’eau y compris de sa qualité, et de la régulation des bioagresseurs. Conjointement à ces services nous avons considéré les nuisances environnementales dues aux pesticides. Pour chaque service nous avons identifié les fonctions écosystémiques sous-jacentes ainsi que les pratiques agricoles et les conditions pédoclimatiques ayant un impact sur ces fonctions. Les services et fonctions ont été décrits par un ou plusieurs indicateurs et quantifiés à l’aide de modèles dans les cas suivants : (i) neuf systèmes de culture réels sur deux dispositifs expérimentaux dans le sud-est de la France et (ii) 150 systèmes de culture fictifs conçus à partir de la combinaison de cinq leviers de pratiques et de leurs modalités, dans des conditions pédoclimatiques identiques. Les deux modèles utilisés ont été STICS, un modèle générique de simulation du fonctionnement du sol et des cultures sous l’influence des pratiques, qui a nécessité une paramétrisation et une évaluation sur pommier à partir de mesures expérimentales, et IPSIM, une plateforme de modélisation simulant les effets des pratiques et des conditions du milieu sur les dégâts aux cultures causés par les bioagresseurs. IPSIM a été paramétré sur pommier, sur la base d’une importante étude bibliographique et à dires d’experts. Les simulations des modèles ont fait l’objet d’analyses statistiques simples dans le cas des systèmes de culture réels, et d’analyses multivariées à deux tableaux (analyse en composantes principales avec variables instrumentales) pour les systèmes de culture fictifs. Pour les neufs systèmes de culture réels, 14 liens importants entre services écosystémiques ont été identifiés, notamment des conflits comme celui entre la prévention de la dénitrification ou de la lixiviation de l’azote et la disponibilité de l’azote dans le sol à court terme, et des synergies, comme celle entre l’humidité du sol ou la séquestration du carbone et la disponibilité de l’azote dans le sol à court terme. Ces liens entre services sont expliqués par les fonctions écosystémiques sous-jacentes. La comparaison de profils de services entre systèmes a mis en évidence l’impact de pratiques agricoles sur certains services. Ainsi, sur un même site, une forte densité de plantation augmente la production de fruits et la séquestration du carbone. La fertilisation exclusivement sous une forme organique diminue la production de fruits via un stress azoté mais diminue également la lixiviation. Par ailleurs, les profils de services sont fortement influencés par les caractéristiques pédoclimatiques de chaque site. Ces résultats confortent la nécessité d’une prise en compte explicite de l’interdépendance ‘pratiques x conditions du milieu’ pour analyser les services. / The concept of « ecosystem service », which has been used increasingly since the publication of the Millennium Ecosystem Assessment in 2005, has highlighted the importance of ecosystem’s non-marketed performances. In orchards, ensuring high productivity while preserving natural resources and human health has become a real challenge that could be analyzed with the concept of ecosystem service. Which ecosystem services are delivered in an apple orchard? How to analyze them? What are the relationships - conflicts or synergies – among multiple ecosystem services and how do cropping systems change multiple ecosystem service profiles? This PhD work aims at answering those questions with an innovative approach combining experimental measures, modeling and statistical analysis.Based on a literature review of ecosystem services in orchards, five services were selected: fruit production, nitrogen availability in soil, climate regulation based on the prevention of nitrogen denitrification and on carbon sequestration, maintenance and regulation of water cycle, including water quality, and pest control. We also considered the environmental disturbances caused by the use of pesticides. For each service, we identified the underlying ecosystem functions as well as the agricultural practices and soil and climate conditions affecting these functions. Services and functions were described by one or multiple indicators and quantified using models in the case of (i) nine existing cropping systems on two experimental sites in southeastern France differing in terms of soil and climate conditions, and (ii) 150 virtual cropping systems designed out of the combination of five major agricultural practice levers and their modalities, in identical soil and climate conditions. The two models used were STICS, a generic soil-crop simulation model under the influence of practices which required a parameterization and an evaluation on apple orchards based on experimental measures, and IPSIM, a generic modeling framework simulating the impacts of agricultural practices and local conditions on crop injuries caused by pests. IPSIM was parameterized on apple orchards, based on an important literature review and expert opinions. Model simulations were analyzed with simple statistics in the case of the nine existing cropping systems and with two-table multivariate analyses (principal component analysis with instrumental variables) for virtual cropping systems.Concerning the existing cropping systems, 14 important relationships were identified among ecosystem services, especially conflicts, like the one between nitrogen denitrification or leaching prevention and soil nitrogen availability on the short term, and synergies such as the one between soil humidity or carbon sequestration and nitrogen availability on the short term. These relationships are explained by the underlying ecosystem functions. Comparing service profiles among cropping systems highlighted the impacts of agricultural practices on some services. That way, on a same site, a high planting density increases fruit production and carbon sequestration. An exclusively organic fertilization decreases fruit production through nitrogen stress but also nitrogen leaching in drained water. Furthermore, service profiles are strongly influenced by the soil and climate conditions of each site. These results strengthen the need to explicitly consider the ‘agricultural practices x soil and climate conditions’ interdependence in order to analyze ecosystem services. The results obtained with the virtual cropping systems simulations confirmed those of the existing ones and gave precision on the impacts of fertilization, irrigation and pest control for codling moth, rosy apple aphid and apple scab on ecosystem functions and services.

Les invasions biologiques sont une cause majeure de perte de biodiversité à l’échelle mondiale. L’impact direct des espèces exotiques envahissantes (EEE) sur la structure et la composition des communautés a été bien documenté. Par contre, leur impact sur le fonctionnement des écosystèmes a été comparativement moins étudié. Dans le présent travail, j’ai mesuré sur le terrain et en conditions expérimentales l’impact de 7 espèces de plantes exotiques particulièrement envahissantes en Europe sur les propriétés chimiques du sol, sur la productivité et sur le stock d’éléments minéraux dans la biomasse. Malgré la diversité des groupes fonctionnels considérés dans notre échantillon (des espèces annuelles aux arbres), des impacts récurrents ont pu être mis en évidence. Les EEE ont toujours une biomasse et une productivité supérieures à celles de la végétation qu’elles envahissent. Il en va de même pour le stock d’éléments minéraux dans la biomasse aérienne. En ce qui concerne le sol, les traits fonctionnels des espèces ne permettent pas de prédire la direction et l’amplitude des impacts. Par contre, ces impacts sur le sol se sont révélés partiellement prévisibles en fonction des conditions écologiques initiales (contexte pédologique). La disponibilité des cations et du P et la concentration en C et N organiques augmentent suite à l’invasion dans les sites initialement pauvres alors que ces mêmes paramètres baissent dans les sites plus eutrophes au départ. Les EEE entraînent, dans une certaine mesure, une homogénéisation des conditions écologiques dans les écosystèmes envahis. <p>Dans un deuxième temps, je me suis attaché à identifier les mécanismes de l’impact de Fallopia japonica sur le cycle de l’azote. Cette espèce, perenne rhizomateuse, adopte une gestion très conservatrice de l’azote en retransloquant jusqu’à 80 % de l’azote des tiges et des feuilles vers le système racinaire en automne avant l’abscission des feuilles. La litière restituée est, de ce fait, pauvre en azote. Ce paramètre, combiné à une teneur élevée en lignine, explique sa faible vitesse de décomposition par rapport à celle de la végétation non envahie. Une grande partie de l’azote de l’écosystème tourne donc en cycle quasi fermé entre les organes de réserve et les parties aériennes de la plante, tandis que l’azote restant est en grande partie bloqué dans la nécromasse de la plante et est donc non disponible pour les espèces concurrentes indigènes. Ce mécanisme explique, sans doute, en partie le succès invasif de l’espèce.<p><p>A l’avenir, les implications des impacts sur le sol en terme de restauration des communautés devront être étudiées. L’hypothèse d’une influence positive de ces impacts sur l’aptitude compétitive des espèces envahissantes devra être testée. Enfin, une étude plus fonctionnelle des impacts de ces espèces dans des sites contrastés devrait permettre d’identifier les mécanismes impliqués./Biological invasions are a major cause of biodiversity loss worldwide. The direct impact of alien invasive species (AIS) on community structure and composition has been well documented. On the other hand, their impact on ecosystem functioning has been comparatively less studied. In this work, I measured, on the field and in experimental conditions, the impact of 7 highly invasive alien plant species in Europe on soil chemical properties, biomass and aboveground nutrient stock. Despite the high diversity in considered functional groups (from annuals to trees), recurring impacts have been found. AIS had always higher biomass and aboveground nutrient stocks than invaded resident vegetation. Concerning soil, species functional traits did not allow us to predict impact direction and intensity. On the other hand, impacts on soil were partially predictable based on initial ecological conditions (pedologic context). Thus, cations and P availability and organic C and N concentrations increased in initially poor sites and decreased in eutrophic ones. AIS tend to homogenize soil properties across invaded landscapes.<p>In a second part, i tried to identify the mechanisms of the impacts of Fallopia japonica on N cycling. This perrennial rhizomatous species manage N in a very conservative way. About 80 % of aboveground N is translocated to rhizomes before leaves abscission. The litter is therefore poor in N. This parameter combined with a high lignin concentration explains its slow decomposition rate compared to that of uninvaded vegetation. A big part of the ecosystem N is engaged in a nearly closed cycle between above and belowground organs while the remaining N is blocked in the necromass and is thus not available for the indigenous competitors. This mechanism probably explains the invasive success of this species.<p><p>In the future, the implications of soil properties modifications in terms of community restoration should be studied. The hypothesis of a positive influence of these modifications on the competitive ability of AIS should be tested. At last, a functional study of these soil impacts in contrasted sites should allow us to identify the implied mechanisms.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished