Orientadores: Ricardo Ribeiro Rodrigues, Flavio Antonio Maes dos Santos / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-21T20:07:39Z (GMT). No. of bitstreams: 1 Garcia_LeticiaCouto_D.pdf: 4213297 bytes, checksum: 251e5ae3edee734a1c9d00ebaa020ca4 (MD5) Previous issue date: 2012 / Resumo: A busca pela restauração de ambientes degradados tem sido um desafio em todas as regiões do planeta e há consenso de que estudos ecológicos podem contribuir para o aprimoramento da prática da restauração. No entanto, pouco se conhece sobre a trajetória dos ecossistemas em processo de restauração, especialmente quanto ao restabelecimento da diversidade de espécies e de suas funções nos processos ecológicos. O objetivo da pesquisa proposta foi verificar se há ou não a previsibilidade da recuperação de atributos ao longo do tempo, no que tange à diversidade de espécies, estrutura da vegetação, grupos funcionais, diversidade e redundância funcional e oferta de recursos para a fauna, em comunidades vegetais de matas ciliares em restauração em comparação com um ecossistema de referência. O objeto de estudo foram matas ciliares em região de Floresta Estacional Semidecidual, na região central do Estado de São Paulo, cujos plantios utilizaram elevada diversidade inicial. Foram amostrados mensalmente todos os indivíduos em reprodução de todas as formas de crescimento e a sua fenologia durante dois anos (353 espécies). Nestes indivíduos foram levantadas as características estruturais e reprodutivas, como: formas de crescimento, altura e área basal, fenologia, tipos florais, cores e tamanho das flores, índice de originalidade floral, síndromes de dispersão, cores e tamanhos dos frutos. Partiu-se da premissa de que o restabelecimento dos descritores estudados indica uma evolução positiva e autônoma dos ecossistemas em processo de restauração rumo à sua sustentabilidade. Alguns desses descritores se restabeleceram com o tempo, tais como a estrutura da vegetação, proporção de grupos sucessionais, diversidade de espécies arbóreas e sua funcionalidade e originalidade floral, quantidade de flores e frutos produzidos. Porém, ações de manejo adaptativo podem ser necessárias com vistas a suprir eventuais lacunas funcionais, principalmente no que tange às formas de vida não-arbóreas, devendo essas serem introduzidas, já que foram insuficientemente representadas, principalmente em áreas bastante fragmentadas. Desse modo, o manejo adaptativo dessas áreas poderá auxiliar na recuperação desses descritores. Para as futuras áreas que serão implantadas, a consideração desses fatores e o planejamento prévio de quais espécies, características funcionais e formas de vida a serem plantadas serão de grande relevância. Para completar o trabalho, acreditamos que aliar o conhecimento adquirido com políticas públicas e com a legislação ambiental nacional é indispensável. Desse modo, discutimos também o projeto de alteração da lei do Código Florestal brasileiro e os efeitos que poderão ocorrer na conservação e restauração dos ecossistemas nacionais / Abstract: Throughout the world there is large scale environment degradation. Hence, restoration of degraded areas has been a challenge. There is a consensus that ecological studies can contribute to improve the practice of restoration. However, there is a knowledge lack about the trajectory of ecosystems' under restoration; in particular, regarding re-establishment of species diversity and its function in the ecological process. The aim of the present study is to verify whether riparian forest communities under restoration recover their attributes over time, such as species diversity, structure, plant functional groups, functional diversity and redundancy and resource provision for fauna compared to a reference forest. We studied riparian forests of the seasonal semideciduous forest domain, in the Atlantic Forest Biome, São Paulo State, SE, Brazil. These areas were restored using a high diversity of species during the planting process. We sampled all reproductive individuals of all growth forms and followed their phenology monthly for two years (353 species). We measured reproductive and structural plant traits such as growth form, size, basal area, reproductive phenology, floral types, flower color and size, dispersal syndrome, fruit color and size. We assumed that recover of the studied descriptors indicates positive and autonomous advancement in ecosystem restoration towards its sustainability. Several of these attributes were re-established over time, such as the vegetation structure, ecological sucessional group proportion, species diversity of trees and their flower functionality and originality, as well as the amount production of flowers and fruits. On the other hand, adaptive management actions may be necessary in order to afford any functional gaps, especially in regard to forms of non-tree species that should be introduced since they have been underrepresented, particularly in landscapes very fragmented. Thereby, adaptive management of these areas may assist the recovery of these descriptors. Consideration of these factors and prior planning of which species and grow forms should be planted will be of great relevance for areas that will be implemented in the future. We also believe that combining the knowledge acquired with public policy and the national environmental legislation is essential. Hence, we discussed the proposal bill to the Brazilian Forest Code and the effects that may occur in conservation and restoration of national ecosystems, where several current protected areas may lose protection and it will be a setback for conservation and restoration of Brazilian forests / Doutorado / Biologia Vegetal / Doutor em Biologia Vegetal

The current ecological hypothesis states that the soil type (e.g., chemical and physical properties) determines which microbes occupy a particular soil and provides the foundation for soil provenance studies. As human profiles are used to determine a match between evidence from a crime scene and a suspect, a soil microbial profile can be used to determine a match between soil found on the suspect’s shoes or clothing to the soil at a crime scene. However, for a robust tool to be applied in forensic application, an understanding of the uncertainty associated with any comparisons and the parameters that can significantly influence variability in profiles needs to be determined. This study attempted to address some of the most obvious uncertainties of soil provenance applications such as spatial variability, temporal variability, and marker selection (i.e., taxa discrimination). Pattern analysis was used to validate the ecological theories driving the soil microbial biogeography. Elucidating soil microbial communities’ spatial and temporal variability is critical to improve our understanding of the factors regulating their structure and function. Microbial profiling and bioinformatics analyses of the soil community provided a rapid method for soil provenance that can be informative, easier to perform, and more cost effective than approaches using traditional physico-chemical data. This study also showed that stable profiles may allow comparison between evidence and a possible crime scene despite the time lapse (4 years) between sample collections, however, this is dependent on the analysis method, site, vegetation, and level of disturbance. Marker selection was also an important consideration for profiling. Even though Fungi look promising for single taxon soil discrimination, the additional markers can help discriminate between a wide variety of soil types. As in human identification, the more DNA markers queried the greater the discrimination power. Lastly, this study illustrated a novel method to query the iron relating genes and ability to design a novel marker that can easily be used to profile the functional diversity of a soil community to enhance soil classification. Overall this research demonstrated the potential and effectiveness of using microbial DNA from soil, not just for comparison, but also for intelligence gathering to pinpoint the geographic origin of the soil.

O funcionamento dos ecossistemas é o fluxo de matéria e de energia ao longo dos seus componentes bióticos e abióticos. A manutenção de tal funcionamento é crucial para promover os serviços ecossistêmicos dos quais a humanidade depende. Atividades antrópicas, como a agricultura e a urbanização podem alterá-los significativamente e, por isso, o entendimento dos impactos positivos e negativos de tais alterações bem como o desenvolvimento de ferramentas de avaliação da biodiversidade são importantes para a conservação. A diversidade funcional é um componente da diversidade biológica que leva em conta o papel que cada espécie desempenha no ecossistema e, portanto, deve refletir o funcionamento do ecossistema de forma mais acurada. Esta tese teve por objetivos relacionar o funcionamento do ecossistema e os seus serviços a ações antrópicas, bem como propor a abordagem funcional como indicadora da biodiversidade de áreas naturais. No primeiro capítulo, avalio padrões espaciais e temporais da exposição dos tipos de vegetação que ocorrem no Brasil à luz artificial, um dos principais símbolos da urbanização e da vida moderna. Os resultados mostram que a maioria deles apresenta alguma porcentagem de sua área expostos à luz artificial. Em alguns deles, porém, ainda é possível encontrar o brilho natural do céu noturno, o que nos permite sugerir a elaboração de políticas de desenvolvimento de distribuição de luz com foco no mínimo impacto, ao contrário das políticas de mitigação adotadas por países onde a iluminação é excessivamente difundida. No segundo capítulo mapeio padrões espaciais e temporais da provisão de dois serviços ecossistêmicos (polinização e estoque de carbono) e um serviço ambiental (espaço para viver) e avalio os impactos da agricultura sobre estes serviços, na área coberta pelo cerrado, na região central do Brasil. Os serviços ecossistêmicos avaliados descaíram significativamente ao longo do tempo e a região conhecida como MATOPIBA (entre os estados do Maranhão, Tocantins, Piauí e Bahia) foi identificada como um importante remanescente. Por isso, recomendo a criação de unidades de conservação de proteção integral na área. Identifiquei também sobreposição da disponibilidade destes serviços com áreas indígenas, o que ressalta a importância da manutenção destas áreas para a disponibilidade dos serviços. No terceiro capítulo exploro, por meio de revisão bibliográfica, o status da diversidade funcional na literatura científica no campo da Conservação Biológica. Os resultados permitiram visualizar o paradigma da transferência de conhecimento e identificar o potencial desta abordagem para elaboração de indicadores da biodiversidade. Por fim, no quarto capítulo, estabeleço uma lista de espécies de plantas que podem ser indicadoras da diversidade funcional em áreas cobertas por cerradão no estado de São Paulo. Tais indicadores devem ser usados em conjunto para monitoramento e diagnóstico da biodiversidade quando o objetivo é manter o funcionamento do ecossistema. As conclusões do estudo contribuem para elucidar a interferência das atividades antrópicas nos ecossistemas naturais, para levantar formas de minimizá-los e para aprimorar as formas de avaliação da biodiversidade. / Ecosystem functioning is the flow of energy and matter through the biotic and abiotic ecosystems components. The maintenance of this functioning is essential to the ecosystem services provisioning upon which humans depend. Anthropogenic activities such as agriculture and urbanisation may change it. Thus, conservation strategies rely on the understanding of the positives and negatives impacts from this changes and on the development of measurements of biodiversity. Functional diversity is a biodiversity component which considers the role of each species in the ecosystem, and, as a consequence, may reflect the ecosystem functioning more accurately. This thesis aims the establishment of the relationships between ecosystem functioning, ecosystem services and anthrogenic activities as well as purpose functional approach as biodiversity indicator of natural areas. In the first chapter, I assessed spatial and temporal patterns of exposition of the Brazilian vegetation types to the artificial light which is one of the urbanisation symbols. The results show that most of them are affected by artificial light. However, in some of them it is still possible to find a natural sky background, which allow suggesting the formulation of light distribution policies focused on minimal impact instead of mitigation, as adopted by countries where light is excessively widespread. In the second chapter, I mapped spatial and temporal patterns of two ecosystem services provisioning (pollination and carbon stocks) and one environmental service (living space) and assessed the impacts of agriculture in these services in Cerrado area, in the central region of Brazil. The ecosystem services I assessed declined significatively over time and the MATOPIBA region (around Maranhão, Tocantins, Piaui, and Bahia States) was identified as an important remint. Thus I recommended the creation of strictly protected areas in that region. I also identify overlap of these services with indigenous land, highlighting its importance for the ecosystem services provisioning. In the third chapter I explored through literature survey, the status of functional diversity in the scientific literature related to the Biological Conservation field. The results allow visualise the paradigm of knowledge transfer and identify the potential use of this approach for developing indicators of biodiversity. Finally, in the fourth chapter, we established a list of plant species that are functional diversity indicators in cerradão areas in São Paulo State. These indicators should be use as a set for the monitoring and diagnosis of biodiversity when the goal is to maintaining ecosystem functioning. The conclusions of the study contribute to clarify some lack of knowledge concerned to the impacts of human activities on ecosystem functioning, to raise means to minimise them, and to improve means of ecological integrity assessment.

This thesis deals with biodiversity-productivity relationship in desmid communities. Biodiversity is found to be changing globally. The biodiversity-productivity relationship is therefore an important research topic. Three aspects of biodiversity are thought to play an important role: species richness, functional diversity and phylogenetic diversity. It is known that in general, productivity is positively correlated with diversity. Interactions between different metrics of biodiversity are known less. Existing studies have shown that these interactions might be present. In general, biodiversity-productivity studies were mostly focused on plants. Less is known about other organisms, including algae. In this work I explore the relationship between overyielding and functional or phylogenetic diversity on a species richness gradient of desmid communities. I conducted an artificial biodiversity- ecosystem functioning experiment using combinations of two to 12 desmid species. Communities differed in the diversity aspects. I had measured the biomass growth. For the analysis, I have used the overyielding index, which is based on a comparison of a polyculture production with the production expected based on monoculture yields. The relationship of overyielding on functional diversity depended on species...

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Numerous studies have evaluated the relationship between biodiversity and productivity, with general trends suggesting a positive relationship. While most studies only use species richness, this study also analyzed how productivity changes with functional diversity and Shannon’s diversity index. Functional diversity gives important context to the examination of biodiversity-productivity relationships due to the direct link between organisms’ functional traits and their role in a given ecosystem. This study used data from the USDA Forest Service Forest Inventory and Analysis (FIA) database collected in Alabama, Louisiana, and Mississippi to estimate plot-level productivity and diversity. Structural equation modeling was used to determine the strength of the relationship between measures of diversity and forest productivity. This study found that species richness had the greatest influence on forest productivity, but it was largely an indirect effect mediated by stand density. This study could be expanded spatially to include more forest types for comparison of trends.

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Les réchauffements climatiques associés aux activités anthropiques ont soumis les écosystèmes arctiques à des changements rapides qui menacent leur stabilité à court terme. La diminution dramatique de la banquise arctique est une des conséquences les plus concrètes de ce réchauffement. Dans ce contexte, comprendre et prédire comment les systèmes arctiques évolueront est crucial, surtout en considérant comment les flux de carbone (C) de ces écosystèmes - soit des puits nets, soit des sources nettes de CO2 pour l'atmosphère - pourraient avoir des répercussions importantes sur le climat. Le but de cette thèse est de dresser un portrait saisonnier de l’activité bactérienne afin de déterminer l’importance de sa contribution aux flux de carbone en Arctique. Plus spécifiquement, nous caractérisons pour la première fois la respiration et le recours à la photohétérotrophie chez les microorganismes du golfe d’Amundsen. Ces deux composantes du cycle du carbone demeurent peu décrites et souvent omises des modèles actuels, malgré leur rôle déterminant dans les flux de C non seulement de l’Arctique, mais des milieux marins en général. Dans un premier temps, nous caractérisons la respiration des communautés microbiennes (RC) des glaces de mer. La connaissance des taux de respiration est essentielle à l’estimation des flux de C, mais encore limitée pour les milieux polaires. En effet, les études précédentes dans le golfe d’Amundsen n’ont pas mesuré la RC. Par la mesure de la respiration dans les glaces, nos résultats montrent des taux élevés de respiration dans la glace, de 2 à 3 fois supérieurs à la colonne d'eau, et une production bactérienne jusqu’à 25 fois plus importante. Ces résultats démontrent que la respiration microbienne peut consommer une proportion significative de la production primaire (PP) des glaces et pourrait jouer un rôle important dans les flux biogéniques de CO2 entre les glaces de mer et l’atmosphère (Nguyen et Maranger, 2011). Dans un second temps, nous mesurons la respiration des communautés microbiennes pélagiques du golfe d’Amundsen pendant une période de 8 mois consécutif, incluant le couvert de glace hivernal. En mesurant directement la consommation d'O2, nous montrons une RC importante, mesurable tout au long de l’année et dépassant largement les apports en C de la production primaire. Globalement, la forte consommation de C par les communautés microbiennes suggère une forte dépendance sur recyclage interne de la PP locale. Ces observations ont des conséquences importantes sur notre compréhension du potentiel de séquestration de CO2 par les eaux de l’Océan Arctique (Nguyen et al. 2012). Dans un dernier temps, nous déterminons la dynamique saisonnière de présence (ADN) et d’expression (ARN) du gène de la protéorhodopsine (PR), impliqué dans la photohétérotrophie chez les communautés bactérienne. Le gène de la PR, en conjonction avec le chromophore rétinal, permet à certaines bactéries de capturer l’énergie lumineuse à des fins énergétiques ou sensorielles. Cet apport supplémentaire d’énergie pourrait contribuer à la survie et prolifération des communautés qui possèdent la protéorhodopsine. Bien que détectée dans plusieurs océans, notre étude est une des rares à dresser un portrait saisonnier de la distribution et de l’expression du gène en milieu marin. Nous montrons que le gène de la PR est présent toute l’année et distribué dans des communautés diversifiées. Étonnamment, l’expression du gène se poursuit en hiver, en absence de lumière, suggérant soit qu’elle ne dépend pas de la lumière, ou que des sources de photons très localisées justifie l’expression du gène à des fins sensorielles et de détection (Nguyen et al., soumis au journal ISME). Cette thèse contribue à la compréhension du cycle du C en Arctique et innove par la caractérisation de la respiration et de l’efficacité de croissance des communautés microbiennes pélagiques et des glaces de mer. De plus, nous montrons pour la première fois une expression soutenue de la protéorhodopsine en Arctique, qui pourrait moduler la consommation de C par la respiration et justifier son inclusion éventuelle dans les modélisations du cycle du C. Dans le contexte des changements climatiques, il est clair que l'importance de l’activité bactérienne a été sous-estimée et aura un impact important dans le bilan de C de l'Arctique. / Arctic ecosystems are undergoing rapid changes, primarily due to unprecedented climatic warming as a function of anthropogenic activities, which threaten their short-term stability. One of the most dramatic impacts has been the loss and change in annual sea ice. Understanding and predicting how these systems will evolve is crucial, especially if considering how carbon (C) fluxes from these ecosystems – either net sinks or net CO2 sources for the atmosphere – could have important repercussions on global climate. The objective of this thesis is to establish a seasonal portrait of bacterial activity to characterize its contribution to Arctic carbon fluxes. Specifically, we quantify for the first time microbial respiration in sea-ice and the water column and explore the use of photoheterotrophy by microorganism over an annual cycle in the Amundsen Gulf of the Arctic Ocean. These components of carbon cycling remain poorly understood and infrequently directly measured. As a consequence they are either extrapolated or omitted from models, despite their significant role in C dynamics not only in the Arctic, but also in marine systems in general. First, we characterise respiration in sea-ice microbial communities (CR). An understanding of respiration rates is essential for accurate estimation of C fluxes, but the role of respiration in sea ice is poorly understood. This work represents the first comprehensive evaluation of respiration in polar sea ice to date. Using novel O2 consumption measurements in sea-ice, we found high respiration rates in sea-ice, 2 to 3 times higher than in the water column and bacterial production rates up to 25 times higher. These results show that microbial respiration can consume a significant portion of sea ice primary production (PP) and play a key role in biogenic CO2 fluxes between sea-ice and the atmosphere (Nguyen and Maranger, 2011). Second, we measure respiration of pelagic microbial communities of Amundsen Gulf over an eight-month period, including under the winter ice-cover. By measuring directly O2 consumption, we show high CR, measurable over the whole year and greatly surpassing C inputs from PP. Globally, high C consumption by microbial communities supports a high reliance on internal recycling of local PP. These observations have important consequences on our understanding of the CO2 sequestering potential of the Arctic Ocean (Nguyen et al., 2012) Finally, we describe the seasonal patterns in presence (DNA) and expression (RNA) of the proteorhodospin (PR) gene, involved in bacterial photoheterotrophy. The PR gene, combined with the retinal chromophore, allows bacteria to capture energy from light towards energetic or sensory purposes. This additional energy source could contribute to the survival and proliferation of bacterial communities expressing the gene in the highly variable polar environment. Although PR has been found in many oceans, this study represents a unique time-series that follows the seasonal distribution and expression of the gene in a natural marine system. We show that the PR gene was present over the whole study period and widely distributed in diverse bacterial communities. Surprisingly, we observed continued PR expression over winter, in the absence of sunlight. This suggests either that the PR’s expression does not depend on light or, that other very localized photon sources could justify PR expression for detection and sensory functions (Nguyen et al., submitted to the ISME journal). This thesis contributes to the understanding of Arctic carbon cycling and includes several novel elements such as the characterization of respiration and bacteria growth efficiency in both pelagic and sea-ice habitats. The use of an alternative C pathway by bacteria in the Polar ocean was also explored for the first-time in a time-series. The observed sustained expression of the PR gene in the Arctic could modulate C consumption by respiration and justify its inclusion in future models of C cycling. In a context of climate change, it is clear that bacterial activity has been underestimated and how this will change in a warmer Arctic will have a significant impact in the ecosystem’s overall C budget.

Ce mémoire visait à déterminer si un petit parc périurbain, en l’occurrence le Parc national du Mont-Saint-Bruno, est parvenu à maintenir l’intégrité de sa flore au cours des trente dernières années en dépit de pressions humaines croissantes et de perturbations naturelles passées, en plus d’identifier les principaux changements floristiques survenus au cours de cette période et les facteurs responsables. Pour répondre à ces objectifs, une étude historique a été réalisée, en comparant un inventaire floristique ancien (1977) à un inventaire récent (2013). Mes résultats montrent d’abord une forte croissance de la diversité alpha indigène au cours des 35 dernières années, accompagnée d’un déclin significatif de la diversité bêta (30%). Malgré cette homogénéisation taxonomique, la diversité fonctionnelle de la flore forestière s’est accrue, la rendant probablement plus résiliente aux événements perturbateurs. D’autre part, mes analyses ont révélé la progression de traits fonctionnels souvent associés à des habitats forestiers intensément broutés, révélant une certaine influence du cerf de Virginie sur la composition et la structure de la flore forestière. Enfin, mes résultats ont montré que les herbiers botaniques se révèlent être une alternative fiable aux méthodes traditionnelles pour documenter et évaluer l’impact des grands herbivores sur la morphologie des plantes broutées. Au final, cette étude a montré que les petites aires protégées périurbaines peuvent jouer un rôle majeur dans la préservation de la diversité floristique d’habitats forestiers d’intérêt, particulièrement lorsque leur statut de protection permet d’encadrer de manière stricte les activités humaines. / This study aimed to determine whether a small suburban park, namely the Mont-Saint-Bruno National Park, managed to maintain the integrity of its flora over the last thirty years despite increasing human pressures and past natural disturbances, in addition to identify the main floristic changes during this period and the drivers of observed changes. To do so, a historical study was conducted by comparing past (1977) and recent (2013) floristic surveys. First, a striking increase in alpha diversity, driven mostly by native species and associated with a significant decline (30%) in the beta diversity over the last 35 years was found. Despite this taxonomic homogenization, the functional diversity of forest flora has increased, probably increasing its resistance to disruptive events. Furthermore, analyses revealed the progression of functional traits associated with overbrowsed forest habitats, revealing some influence of white-tailed deer on the composition and structure of the forest flora. Finally, my study also showed that herbarium specimens can be used as a reliable alternative to traditional methods to document and assess the impact of large herbivores on browsed plants morphology. In conclusion, this study showed that small suburban protected areas can play a major role in the preservation of the floristic diversity of rich forest habitats, particularly when their status strictly frames human activities.