A restauração da Mata Atlântica tem sido considerada prioridade nas iniciativas de manutenção da biodiversidade. Adicionalmente, há consenso de que os parâmetros para avaliação da restauração ecológica devem mensurar o retorno de funções ecológicas. O estudo de interações planta-visitante floral pode ser um caminho adequado para avaliar a eficiência das práticas de restauração, visto que estas interações desempenham função crítica na dinâmica e diversidade da comunidade. Variações na diversidade de espécies de plantas e de seus visitantes florais podem alterar a freqüência de interação entre as espécies, definir a estrutura das redes de interação, determinando os níveis de generalização e especialização na comunidade. Neste contexto, a tentativa de restaurar florestas tropicais pela adição de espécies arbóreas pode ter efeitos sobre a estrutura, estabelecimento de grupos funcionais e níveis de generalização na rede de interação entre flores e visitantes florais. O objetivo principal deste trabalho é o de comparar redes de interação planta-visitante floral em florestas tropicais restauradas após 5 anos do plantio das arbóreas, florestas regeneradas naturalmente e remanescentes de floresta atlântica em uma área sob domínio da Mata Atlântica no sudeste do Brasil. Para atingir esse objetivo, essas florestas foram comparadas quanto suas diversidades estruturais e funcionais em relação aos seguintes aspectos: 1) Riqueza e atributos de história de vida (formas de vida, sistemas sexuais, modos de polinização e de dispersão); 2) redes de interação plantavisitante floral; 3) Grau de generalização e especialização das redes de interação; 4) robustez quanto à perda de espécie em redes de interação, e 5) Formação de grupos funcionais seguindo características florais e de freqüência de visitas. Para cada aspecto avaliamos a contribuição das espécies plantadas. Florestas restauradas tiveram a maior riqueza de espécies em flor, porém com menor similaridade florística com outras florestas locais. A similaridade em abundâncias relativas de arbustos e lianas com outras categorias de florestas indicou a inclusão de outras formas de vida além de árvores nas florestas restauradas. Porém, a alta abundância relativa de árvores nas florestas regeneradas naturalmente também indicou o potencial de regeneração natural em florestas 15 degradadas. A maior diversidade de modos de polinização biótica e de dispersão de sementes nas florestas restauradas veio das plantas regenerantes espontaneamente. Não houve diferenças significativas quanto às métricas de redes de interação flores e visitantes entre os tratamentos, porém houve uma tendência de maior especialização dessas interações nas florestas nativas e maior robustez à perda de espécies em florestas restauradas. Além disso, plantas regenerantes espontaneamente receberam significantemente mais visitas nas florestas regeneradas naturalmente do que em florestas restauradas, sugerindo que árvores plantadas podem estar reduzindo visitação às flores da vegetação regenerante espontânea, possivelmente competindo por visitantes florais. Em relação à diversidade funcional, 21 grupos funcionais baseados em atributos florais foram estabelecidos entre todas as espécies em flor, onde as espécies da floresta restaurada dominaram três grandes grupos e a floresta nativa apresentou representantes distribuídos equitativamente pelos grupos, sem dominância. Pólen foi a variável que mais contribui para diferenciação dos grupos. As espécies plantadas formaram grupos funcionais exclusivos nas florestas restauradas, contribuindo para uma maior diversificação em atributos funcionais florais em tais comunidades, porém não mais do que a diversificação funcional trazida pelas plantas regenerantes espontaneamente. Redes de interação entre grupos funcionais de plantas e categorias taxonômicas de visitantes reforçaram que os visitantes florais parecem não seguir fielmente grupos funcionais por atributos florais. Considerando que as florestas regeneradas naturalmente apresentaram alta abundância relativa de árvores, não apresentaram diferenças significativas quanto às métricas de redes de interação planta-visitantes florais com as florestas restauradas e que a regeneração natural na região estudada ocorre em grande intensidade, sugerimos que seja dada importância relevante às plantas regenerantes espontaneamente em projetos de restauração. Cabe ressaltar que avaliamos restauração após 5 anos da implantação. Assim, todas as conclusões tiradas deste estudo necessitarão ser acompanhada em estudos futuros. / Restoration of the Brazilian Atlantic Forest has been considered priority in initiatives to maintain biodiversity. Additionally, there is consensus that the parameters to evaluate restoration should address the return of ecological processes. The study of flower-visitor interactions can be a reasonable way to evaluate restoration practice, considering that these interactions have critical role in the dynamics and diversity of communities. Variations in the diversity of plant species and their flower visitors could modify frequency of interactions between species; define the structure of interaction networks, and determine generalization and specialization levels in the community as well. In this context, the attempt to restore tropical forests by planting native trees can affect the structural and functional diversity and generalization level in flower-visitor networks. The main objective of this research is to compare flower-visitor networks in 5-year-old restored forests, naturally regenerated forests and native forests in an Atlantic Forest domain in southeastern Brazil. We compared these forests in relation to: 1) Richness of species and life history traits (growth form, sexual system, biotic pollination modes and dispersal modes); 2) Flower-visitor networks; 3) Generalization and specialization levels in ecological networks; 4) Robustness to species loss in ecological networks; and 5) Functional groups by floral traits and visitation frequencies of flower visitors. We evaluated the contribution of planted species on each of these aspects. Restored forests had the highest floristic richness of species in flower, but little floristic similarity with other native local forests. Similarity in the relative abundance of shrubs and lianas among habitat categories indicated the possibility of annexation of other life forms than trees in restored forests. But the presence of high relative abundance of trees in the naturally regenerated forests also indicated the potential of natural regeneration of the degraded forests. Biotic pollination and dispersal modes tended to be more diverse in restored forests, but it comes as a result of the addition of spontaneously regenerated plants to this forest. There were no significant differences in the metrics of flower-visitor networks between forest categories, although there was a trend towards high specialization of 17 interactions between flower and visitors in native forests and high robustness of species loss in restored forests. In addition, spontaneously regenerated plants received significantly more visits in the naturally regenerated forests than in restored forests, suggesting that the planted trees may reduce the visitation to the spontaneously regenerated vegetation, possibly by competing for flower visitors. With regard to functional diversity, 21 functional groups based on floral traits were recognized when all species in flower was pooled. Species of restored forests were dispersed mainly among three groups, while species from native forests were spread among all groups with almost the same number of species per group. Pollen was the variable that most contributed for grouping species. Planted trees species formed exclusive functional groups, contributing for higher diversification of floral trait to the community. However, this diversification was not higher than provided by spontaneous regenerated plants. Interaction networks between plant functional groups and taxonomic categories of flower visitors ensured that flower visitors do not seem to follow the grouping formed by floral traits. Considering that naturally regenerated forests had high relative abundance of trees, were not different from restored forests in relation to network metrics and that natural regeneration was intense in the region, we suggest paying relevant attention to spontaneous regenerated plants in restoration projects. We would like to point out that we evaluated five-year-old restored forests and there is still need to track these forests in the future.

Foram realizados dois experimentos para avaliação de aditivos microbianos na ensilagem de forragens tropicais. No primeiro experimento avaliou-se o efeito de doses crescentes de Lactobacillus buchneri, em diferentes tempos de armazenamento, sobre o valor nutritivo, perfil fermentativo e estabilidade aeróbia de silagens de milho. No segundo experimento avaliou-se o efeito de L. buchneri, de forma exclusiva, ou em combinação com Lactobacillus plantarum, em silagens de milho, cana-de-açúcar e capim elefante cv. Napier. O tratamento das silagens de milho com L. buchneri não afetou a contagem de fungos filamentosos, com decréscimo nas contagens com maiores tempos de armazenamento. Os teores de ácido lático decresceram com o aumento da dose de L. buchneri. Os maiores períodos de armazenamento resultaram em decréscimo na contagem de BAL, e maiores valores de pH. O tempo de armazenamento diminuiu as leveduras na silagem de milho. Maiores tempos de armazenamento propiciaram maiores tempos para atingir a temperatura máxima e a perda da estabilidade aeróbia. As silagens com doses superiores de L. buchneri apresentaram perda de estabilidade em momento posterior às silagens dos tratamentos controle e LB1x105. O maior tempo de armazenamento da silagem de milho resultou em maior valor nutritivo e perfil microbiológico favorável quanto à fermentação e estabilidade em aerobiose. Inoculação com L. buchneri (NCIMB 40788) reduz a sobrevivência de leveduras durante a fase de armazenamento e o crescimento durante a exposição ao oxigênio, melhorando a estabilidade aeróbia da silagem em ambiente tropical. Doses mais elevadas poderiam compensar parcialmente o menor tempo de armazenamento das silagens. No segundo experimento, o tratamento das silagens de milho com L. buchneri (LB), exclusivamente, ou associado com L. plantarum (LB+LP) não afetou as variáveis relacionadas com o valor nutritivo das silagens. As concentrações de ácido acético nas silagens de milho foram superiores no tratamento controle. Nas silagens de cana-de-açúcar, o tratamento LB apresentou maiores teores de MS e DVIVMO. O tratamento controle apresentou maior população de bactérias ácido láticas, e menor valor de pH. A silagem de cana-de-açúcar sem aditivo atingiu o pico de temperatura após o tratamento LB, sendo esse pico superior na silagem aditivada. Foram observadas menores perdas de matéria seca e produção de gases nas silagens aditivadas, resultando assim em maior recuperação de MS no tratamento LB. Foi observado maior tempo para atingir a temperatura máxima e menor acúmulo de temperatura até o quinto dia de exposição aeróbia no tratamento controle. A temperatura máxima atingida durante a exposição aeróbia foi superior no tratamento LB. Nas silagens de capim, as silagens do tratamento LB+LP apresentaram maiores teores de MS, e menor teor de PB. Foi observada maior população de bactérias ácido láticas nas silagens do tratamento LB+LP. A inoculação com L. buchneri, sozinho, ou em associação com L. plantarum não foi eficiente em melhorar a qualidade e estabilidade aeróbia das forragens avaliadas. / Two trials were conducted for the evaluation of microbial additives on tropical forages ensiling. At the first trial the effect of increasing L. buchneri doses, and different storage periods on the fermentation profile, aerobic stability and nutritive value of corn silage were evaluated. At the second trial the effect of L. buchneri with or without L. plantarum was evaluated on the fermentation profile, aerobic stability and nutritive value of corn, sugarcane and tropical grass silages. Silages inoculation with L. buchneri did not affect the filamentous funghi counts, with decreased counts with higher storage periods. Lactic acid content was influenced only by treatment, with decrease in concentrations as the L. buchneri dose increased. Lactic acid bacteria, yeasts, pH, butyric and acetic acid were influenced by both treatment and storage period. Higher storage periods resulted in decreased LAB counts and higher pH values. Storage time decreased yeast count in corn silage. For the dry matter losses, gas losses and maximum temperature there was no treatment effect, only storage period effect, decreasing along time. It was observed an increase in effluent production with higher storage time. Time to reach maximum temperature, AC5 and AC10 were influenced by both treatment and storage period. Higher storage periods resulted in higher time to reach the maximum temperature and to break the aerobic stability. Silages with the higher L. buchneri doses showed stability breakdown after control and LB1x105 silages. The higher storage period of corn silages resulted in higher nutritive value and microbial profile favorable to the fermentation and stability during aerobic exposure. Inoculation with Lactobacillus buchneri (NCIMB 40788) reduces the survival of yeasts during the storage phase, and its growth during oxygen exposure, improving silage aerobic stability in tropical regions. Higher doses could partly compensate the lower storage time in silages. In the second trial, inoculation of corn silages with L. buchneri (LB), alone or in association with L. plantarum (LB+LP) did not affect the variables related to the silage nutritive value. Acetic acid content of corn silages was higher for the control treatment. In sugarcane silages, LB treatment showed higher DM content and IVTOMD. Control treatment showed higher lactic acid bacteria counts, and lower pH. Sugarcane silage with no additive reached temperature peak after LB treatment, with this peak being higher at the additivated silage. There were observed lower dry matter losses and gas production in LB silages, resulting in higher dry matter recovery. It was observed higher time to reach maximum temperature and lower temperature accumulation until fifth day of aerobic exposure for the control treatment. Maximum temperature reached during aerobic exposure was higher for LB treatment. In tropical grass silages, LB+LP silages showed higher DM and lower CP contents. It was observed higher lactic acid bacteria in LB+LP treatment. Inoculation with L. buchneri, alone or in association with L. plantarum was not efficient in improving quality and aerobic stability of evaluated forages.

Tropical savannas and woodlands are the dominant vegetation cover in Southern Africa covering 4 million km2. Their large spatial extent means they are potentially a globally important store of biomass carbon with implications for global climate, and an area of high biodiversity value. They provide natural resources such as food, fuel and timber that help sustain the livelihoods of over 100 million people. The ability of these savanna woodlands to maintain these important ecological functions is under question due to increases in land use and land cover change. This thesis addresses a set of science questions aimed at (i) improving our knowledge of the amount of carbon and biodiversity stored in these ecosystems and how they co-vary, (ii) how these variables are spatially distributed at landscape scales and the factors which underlie these patterns, and (iii) how they respond over time to human disturbance. In Chapter 2 I examine how patterns in aboveground woody carbon storage (AGC) are linked to differences in forest structure, tree species diversity and floristic composition across a recently established network of 25 permanent sample plots in south-east Tanzania. Large stems were a significant contributor to plot-level AGC stocks with the top 3% of individuals (>40cm) in terms of size containing 35% of the total measured C. This data can potentially be used to simplify future measurements of biomass in these systems. Tree species diversity was positively related to AGC indicating the potential to align forest conservation efforts. The linear relationship suggests a functional relationship between the variables and is consistent with ecological theory on niche complementarity and selection effects, however based on the available data the mechanisms underlying this relationship can only be theorised. Changes in tree species composition were also noted across plots with differences in vegetation structure between plots explaining 16% of the variation in composition, with environmental differences related to climate and soils explaining only 3%. In Chapter 3, the focus shifts to understanding larger-scale spatial patterns in AGC. Field plots are spatially limited in this regard, therefore radar remote sensing data was used to generate a map of AGC in order to improve our knowledge on what principally controls its spatial variability at landscape scales. Results showed that factors related topography, climate and soils explained very little of the variation in C stocks across the landscape (r2 = 15 – 20%). Differences in slope angle and topographic position were important in discriminating between low biomass savannas and moderate biomass woodlands, while differences in annual precipitation were more important in separating woodlands and denser forests. A large proportion of the variation in C stocks (~80%) was unexplained highlighting the role of unmeasured variables. It is suggested that fire may play a key role in shaping patterns in tree species composition and C stocks across these landscapes. This data has important implications for a local REDD+ project which is aiming to generate carbon credits through improved fire management. In the second part of the thesis the attention shifts to understanding the long-term ecological impacts of shifting cultivation and the sensitivity and resilience of these woodlands to anthropogenic change. In Chapter 4 I examined how carbon stored in trees and soils recover across a 40-year chronosequence of abandoned agricultural land, and how this patchy disturbance impacts spatial pattern in tree species composition and diversity. I show that re-growing woodlands can act as carbon sinks through the accumulation of woody biomass (0.83 tC ha-1 yr-1), with soil texture having no clear impact on accumulation rates. Re-growing woodlands were also found to contain considerable biodiversity value by promoting novel species assemblages. Bulk soil carbon stocks appeared to be largely unaffected by the full cycle of shifting cultivation. However in Chapter 5 I show evidence of a previously unquantified legacy effect of land clearance on soil CO2 production with more recently abandoned fields (c. 6 years) exhibiting significantly higher efflux rates than the older abandonments (15 -25 years) and mature woodlands. Total soil nitrogen was the most important predictor of soil respiration across the plots (r2 = 0.3) followed by fine root density (r2 = 0.12). Soils in the younger sites were found to be more nitrogen rich which was used to explain the greater CO2 fluxes in these areas, however, it is still unclear why this pattern exists. The thesis concludes by discussing the wider implications of the results, as well as outlining further work needed to solidify some of the conclusions drawn in this thesis.

Tropical ecosystems are some of the most diverse and productive ecosystems on the planet. These ecosystems are also some of the most threatened worldwide and this is largely driven by agricultural expansion. Predicting biotic responses to such forms of environmental change is a challenge that requires an increased understanding of the factors structuring these communities in both pristine environments as well as environments that are undergoing environmental change. Studying patterns in the spatial structure of communities can provide important insights into ecological and evolutionary processes structuring communities. Combining such approaches with analyses of the distribution of activity and the genomic content of communities can help us better understand relationships between community structure and function. I explore the topics of microbial spatial scaling, activity, and gene content in both pristine tropical rainforest environments as well as tropical regions undergoing agricultural conversion. I first pose a fundamental question in microbial spatial ecology, i.e. why do microorganisms tend to show weaker spatial patterns than macro-organisms? I show that trees and soil microorganisms differ in the rates at which their communities change over space. I test the hypothesis that low rates of spatial turnover in microbial communities are an artifact of how we assess the community structure of microbial communities and show that sampling extent is likely the main driver of these differences. Next, I examine a Central Africa ecosystem that is undergoing conversion to agriculture. I show that there are numerous indications of biotic homogenization in these soil microbial communities and that the active fraction of the community shows a more pronounced response to environmental change. Finally, I examine two microbial processes in the Amazon Basin that have been reported to change following conversion to agriculture: methane production and methane consumption. I investigate changes to the genes and taxa involved in these processes and propose a new conceptual framework for how these processes might be changing. Work in this thesis contributes to a broader understanding of the spatial and functional ecology of tropical microorganisms and offers perspectives useful for those interested in predicting and mitigating the impacts of environmental change on these communities. / 2019-02-17

Gravity waves play a fundamental role in driving the large-scale circulation of the atmosphere. They are influenced both by the variation in their sources and the filtering effects of the winds they encounter as they ascend through the atmosphere. In this thesis we present new evidence that gravity waves play a key role in coupling the troposphere, stratosphere and mesosphere. In particular, we examine the connection of gravity waves to two important large-scale oscillations that occur in the atmosphere, namely the Madden-Julian Oscillation (MJO) in the troposphere and the Mesospheric Semi-Annual Oscillation (MSAO). We present the first ever demonstration that the MJO acts to modulate the global field of gravity waves ascending into the tropical stratosphere. We discover a significant correlation with the MJO zonal-wind anomalies and so suggest that the MJO modulates the stratospheric gravity-wave field through a critical-level wave-filtering mechanism. Strong evidence for this mechanism is provided by consideration of the winds encountered by ascending waves. The Ascension Island meteor radar is used for the first time to measure momentum fluxes over the Island. These measurements are then used to investigate the role of gravity-wave in driving a dramatic and anomalous wind event that was observed to occur during the first westward phase of the MSAO in 2002. Gravity waves are shown to play an important role in driving this event, but the observations presented here also suggest that the current theory of the mechanism describing these anomalous mesospheric wind events is not valid. Both of these studies highlight the critical importance of gravity waves to the dynamics of the atmosphere and highlight the need for further work to truly understand these waves, their processes and their variability.

Orientadora: Telma Teresinha Berchielli Moreno / Banca: Euclides Braga Malheiros / Banca: Ives Cláudio da Silva Bueno / Resumo: Os sistemas de formulação de dietas para ruminantes exigem a avaliação de alimentos como forrageiras, pois essas são as principais fontes de nutrientes em condições tropicais. Por essa razão, é necessário o desenvolvimento de metodologias que sejam rápidas e ao mesmo tempo eficientes na avaliação de forragens para o funcionamento dos sistemas produtivos. O objetivo deste trabalho foi avaliar em duas épocas do ano o efeito de idade de corte (28, 35 e 42 dias), no valor nutritivo de três espécies forrageiras tropicais de grande utilização na alimentação de bovinos em pastejo no Brasil: capim-Tanzânia (Panicum maximum Jacq. cv. Tanzânia), o capim-Marandu (Brachiaria brizantha cv. Marandu), e o Tifton 85 (Cynodon spp), através da composição química, o fracionamento de proteína e carboidratos, a digestibilidade e a produção de gases in vitro. Nas duas épocas o Tifton 85 apresentou os maiores conteúdos de parede celular, fibra em detergente neutro (FON), fibra em detergente neutro corrigida para cinzas e proteína (FONcp), fibra em detergente ácido (FOA), lignina (LlG), carboidratos totais (CHOS totais), fração B2 e C dos carboidratos (69,36; 62,19; 32,09; 4,09; 78,31; 54,25 e 9,82%, respectivamente) e menores coeficientes de digestibilidade in vitro da matéria seca (OIVMS) e digestibilidade in vitro da matéria orgânica (OIVMO) 49,33 e 45,35% respectivamente, alem de menor produção de gases após 96h de incubação 225,49mL g-1 MS. O valor nutritivo (composição química, digestibilidade e produtos da digestão) da Brachiaria brizantha foi superior nas duas épocas do ano e nas idades de corte avaliadas nas condições deste trabalho comparada com Tanzânia e Tifton 85. / Abstract: In the tropics, diet formulation systems for ruminants require the forages evaluation, as they are the main source of nutrients for the animais. For this reason, the development of practical and efficient methodologies to evaluate forages is crucial for a better result of the production systems. The aim of the present work was to evaluate the cutting age effect (28, 35 and 42 days) in three different forage species which are largely used for the nutrition of cattle raised under pasture conditions in Brazil: Tanzania grass (Panicum maximum Jacq. cv. Tanzânia), Marandu grass (Brachiaria brizantha cv. Marandu) and Tifton 85 (Cynodon spp). compared based on the chemical composition, protein and carbohydrate fractions, digestibility and in vitro gas production of the forages. In the two different periods of the year Tifton 85 had the highest cellular wall components, neutral detergent fiber (NDF), neutral detergent fiber with corrections for mineral and protein (NDFcp), acid detergent fiber (ADF), lignin (LlG), total carbohydrates (CHOS), fraction B2 and C of the CHO (69,36; 62,19; 32,09; 4,09; 78,31; 54,25 e 9,82%, respectively), and the lower in vitro dry matter digestibility (IVDMD) 49,33%, in vitro organic matter digestibility (IVOMD) 45,35%, and the gas production 225,49mL g-1 MS. The forage nutritive value (the potential degradability (PD), the effective degradability (ED). Considering the two periods of the year and the three cutting ages investigated in the present study, the nutritive value (chemical composition, digestibility and nature of digested products) of Marandugrass was superior in comparison to Tanzaniagrass and Tifton 85. / Mestre

Sementes de cupuaçu (Theobroma grandiflorum (Willd. ex Spreng.) K, Schum.) são recalcitrantes e requerem conhecimento sobre os fatores que afetam a manutenção da qualidade. Assim, o objetivo desse estudo foi avaliar os efeitos do teor de água das sementes e da temperatura do ambiente na manutenção da qualidade das sementes em três ensaios. Inicialmente foram avaliados os efeitos do dessecamento na qualidade das sementes; posteriormente, os efeitos das temperaturas de 10°C, 15°C e 20°C foram avaliados sobre as sementes armazenadas por períodos de zero, cinco, 10, 15, 20 e 25 horas; finalmente, os efeitos dos graus de umidade (59,4%, 51,6%, 42,4%, 35,4% e 28,7%) e das temperaturas (20°C e ambiente não controlado) em sementes acondicionadas em sacos de polietileno foram avaliados em intervalos de 15 dias, durante dois meses. Para todos os ensaios foram realizadas avaliações de umidade, germinação e vigor. A dessecação de sementes de cupuaçu até 41,4% de água não afeta a sua qualidade fisiológica e, ao atingirem 14,6% de água as sementes morrem. Entre as temperaturas testadas, a de 20°C foi a que proporcionou melhor desempenho das sementes durante o armazenamento. A combinação do grau de umidade de 59,4% e temperatura de 20°C, juntamente as combinações do grau de umidade de 51,6% e temperaturas 20°C e ambiente não controlado, possibilitam o armazenamento das sementes por até 60 dias. / Cupuassu (Theobroma grandiflorum (Willd. ex Spreng.) K, Schum.) has recalcitrant seeds which require knowledge on the factors that affect their quality during the storage. The objective of this study was to verify the effects of seed moisture content and ambient temperature during the storage. Firstly, it was evaluated the effects of desiccation on seed quality. Afterward, it was evaluated the effects of temperatures (10°C, 15°C and 20°C) and storage periods (zero, five, 10, 15, 20 and 25 hours). Finally, it was evaluated the effects of seed moisture contents (59.4%, 51.6%, 42.4%, 35.4% and 28.7%) and temperatures (20°C and ambient with no control temperature) on packed seeds in polyethylene bags evaluated at intervals of 15 days for two months. For all experiments it was quantified seed moisture content, germination and vigor. Cupuassu seeds can be desiccated to as low as 41.4% of moisture content with no reduction of the physiological quality, and at 14.6 of moisture content all seeds were dead. Temperature of 20°C was that which maintain initial seed quality for 25 hours. Association of the seed moisture content 59.4% with temperature of 20°C and moisture content of 51.6% with 20°C and ambient with no control temperature make possible seed storage for 60 days.

<div>A tropical cyclone (TC) vortex is an immense, coherent, organized-convective system. Beneath this large-scale organization, is a litany of azimuthally asymmetric convective motions that exist on a spectrum of scales. These asymmetries are especially dominant during periods when the vortex undergoes critical transitions in its intensity and structure. However, the precise nature of influence of the organization of asymmetries on TC intensity change remains an enigma. The inherent difficulty in predicting their behavior is because asymmetries may arise due to different external or intrinsic sources and occur at different spatial and temporal scales while several complex mechanisms act near-simultaneously to dictate their evolution in time. As a result, multiple pathways are possible for a TC vortex that is influenced by these asymmetries. Our preliminary investigations using numerical models made it apparent that there wasn't a single, unifying way to address this problem. In this thesis, I outline multiple novel techniques of diagnosing and predicting which of the many pathways are likely for a TC vortex that is influenced by azimuthal asymmetries. </div><div> </div><div> First, using three-dimensional numerical simulations of a pair of sheared and non-sheared vortices, I demonstrate the diagnostic potential of the juxtaposition in the azimuthal phasing of: </div><div>(i) the asymmetrically distributed vertical eddy flux of moist-entropy across the top of the boundary layer, and the radial eddy flux of moist-entropy within the boundary layer; and (ii) eddy relative vorticity, eddy moist-entropy, and vertical velocity throughout the depth of the vortex. </div><div> </div><div> Second, I introduce an energetics-based diagnostic framework that computes the energy transactions occurring at asymmetries across various length-scales in the wavenumber domain. By applying it to select cases, this thesis uncovers the relative importance of all the energy pathways that support or disrupt the growth of asymmetries within the vortex. Contrary to the traditional explanations of convective aggregation/disaggregation and axi/asymmetrization through barotropic mean-eddy transactions, my thesis reveals that the growth or disruption of asymmetries are predominantly due to (i) the baroclinic conversion from available potential to kinetic energy at individual scales of asymmetries and (ii) the transactions of kinetic energy across asymmetries of different length scales. </div><div> </div><div>Finally, this thesis introduces two further diagnostic frameworks targeted at tackling the problem of real-time forecasting of TC rapid intensity changes. The first is an empirical framework which examines symmetric and asymmetric convection and other state variables within the vortex, and in the environment across a suite of TCs and identifies a set of `important' variables that are significantly different during time periods that precede a rapid intensification as opposed to a rapid weakening. My framework then ranks the variables identified based on how significantly they influence a rapid intensity change in a TC and the amplification factor of any associated variability. We recommend that future observational, and consequent TC modeling and data assimilation efforts prioritize the highest ranked variables identified here. </div><div><br></div><div>The second is a stochastic model wherein a scale-specific stochastic term is added to the equations describing the energy transactions within the TC vortex. By simulating a stochastic forcing that may arise from any scale, I compute the probability of the vortex transitioning into a rapidly intensifying or a rapidly weakening configuration across an ensemble of scenarios. </div><div><br></div><div>In summary, this thesis introduces and applies a variety of diagnostic techniques that help determine the impact of azimuthal asymmetries on TC intensity evolution.</div>

Forests are a critical biome but are under threat from unprecedented global change. The need to understand forest dynamics across spatial, temporal and biological scales has never been greater. Critical to this will be understanding how the demographic rates of individuals translate into patterns of species diversity, biomass and carbon turnover at much larger scales. In this thesis, I present a modelling framework focussed on demography. In Chapter 2, I introduce methods for translating forest inventory data into population models that account for the size-dependency of vital rates and persistent differences in individual performance. Outbreaks of forest pest and pathogens are increasing in frequency and severity, with consequences for biodiversity and forest structure. In Chapter 3, I explore the impact of ash dieback on the community dynamics of a British woodland, describing a spatially explicit individual based model that captures the effect of an opening of the canopy on local competitive interactions. Chapter 4 introduces methods to infer the impact of historical deer herbivory on the juvenile survival of forest trees. The approach is generalisable and could be applied to any forest in which patterns of regeneration and community structure have been impacted by periodic disturbance (e.g. forest fires). Finding meaningful ways of incorporating species diversity into global vegetation models is increasingly recognised as a research priority. In Chapter 5, I explore the diversity of demographic rates in a tropical forest community and identify groups of species with similar life history strategies. I discuss the potential of integrating demographic and physiological traits as a way to aggregate species for inclusion in global models. In summary, translating measurements of individuals into population dynamics provides opportunities to both explore small-scale community responses to disturbance events, and to feed into much larger scale vegetation models.

Orientador: Carlos Magno Castelo Branco Fortaleza / Coorientador: Lenice do Rosário de Souza / Banca: Anna Sara S. Levin / Banca: Elisei Alves Waldman / Banca: Maria de Lourdes Ribeiro de Souza da Cunha / Banca: Adriano Dias / Resumo: Estudos recentes identificaram comportamento sazonal de alguns microrganismos implicados na etiologia das Infecções Hospitalares ou Relacionadas à Assistência em Saúde (IH/IRAS). A maior parte desses estudos foi conduzida em países de clima temperado. Para identificar a sazonalidade de patógenos hospitalares em uma região tropical, nós conduzimos um estudo ecológico e um caso-controle, envolvendo hemoculturas positivas de presumível origem hospitalar (colhidas após o terceiro dia de internação) do Hospital das Clínicas da Faculdade de Medicina de Botucatu no período de 2005 a 2010. O estudo foi realizado em duas fases. No estudo ecológico, foram realizadas: (a) comparações de incidência de bacteremias por microrganimos ou grupos específicos em meses "quentes/úmidos" (outubro-março) e "frios/secos" (abril a setembro); (b) análise de regressão para identificar relação entre temperatura e umidade médias e incidência mensal de bacteremias; (c) análise de séries temporais para identificação de sazonalidade.No "casocontrole", foram abordados fatores climáticos (temperatura e umidade médias dos sete dias que precederam a coleta de cada hemocultura) para identificar preditores do isolamento de microrganismos e grupos específicos, em modelo de regressão logística. Os resultados demonstraram consistência entre as diversas abordagens, identificando para três grupos (Gram-negativos como um todo, Acinetobacter baumannii e Enterobacter spp) um aumento de incidência nos meses "quentes/úmidos", relação significante entre temperatura média mensal e incidência e sazonalidade em modelos estocásticos. Neste último teste, também se detectou sazonalidade para estafilococos coagulase-negativa, aparentemente não relacionada a fatores climáticos. No estudo de base individual ("caso-controle") identificamos correlação entre temperaturas elevadas na semana anterior ... / Abstract: Recent studies identified seasonal behavior of some microorganisms implicated in the etiology of Healthcare-associated Infections (HAIs). Most of these studies were conducted in developed countries with temperate climate. In order to identify the seasonality of nosocomial pathogens in a tropical region, we conducted an ecological study involving positive blood cultures of suspected nosocomial origin (collected after the third day of hospitalization) in the Hospital das Clinicas from Faculdade de Medicina de Botucatu in the period 2005-2010. The study was conducted in two phases. In the first ("ecologic study") we performed: (a) comparisons of the incidence of bacteremia caused by specific organisms or groups during "warm" (October to March) and "cold" (April to September) months; (b) regression analysis, aimed at identifying the association between temperature and humidity and the average monthly incidence of bacteremia, (c) time series analysis. In the second phase, ("casecontrol"), weather factors (temperature and humidity averages of the seven days preceding the collection of each blood cultures) were addressed in order to identify predictors of isolation of specific microorganisms and groups in the logistic regression model. The results showed consistency between the various approaches. Three groups (Gram-negative as a whole, Acinetobacter baumannii and Enterobacter spp) presented increased incidence in "warm" months, significant relation between mean temperature and monthly incidence and seasonality in stochastic models. Those models also detected seasonality for coagulase-negative staphylococci, apparently not related to climatic factors. In individualbased analysis ("case-control") we identified correlation between high temperatures in the past week and recovery of Gram-negatives in general, and among these, A. baumannii. The findings are consistent with the literature, showing ... / Mestre