This master thesis deals with polyhydroxyalkanoates (PHA) and their role in bacterial biofilms. In the theoretical part the polyhydroxyalkanoates, bacterial biofilm and the relationship between them were reviewed. The experimental part focused on differences in PHA production by planktonic and biofilm cells. In order to study selected topic, bacterial strains of Burkholderia cepacia and Burkholderia sacchari were cultivated using a CDC biofilm reactor. The attention was paid to quantity and especially to the form in which PHA occurs in planktonic and biofilm cells. Results of Raman spectroscopy have shown that PHA exists exclusively in native amorphous form in planktonic bacterial cells. On the other hand, in biofilm PHA occurs also in a partially crystalline form. In addition, the resistance of planktonic and biofilm cells against various stress factors and the effect of osmotic stress on PHA production was tested too. According to the results of the experiment, when the bacteria were exposed to different stress factors (high temperature, low temperature, presence of detergent and so forth) biofilm cells showed a higher stress resistance than planktonic cells. Apart from slowing cell growth and reproduction, increased osmotic pressure in the culture medium also caused decrease of PHA production. In addition, planktonic cells responded to external stimuli more sensitively than biofilm ones.

Dans cette thèse, les applications des plasmas à basse température à la pression atmosphérique sont discutées. En particulier, la bio-décontamination des bactéries planctoniques et biofilms bactériens sur des surfaces planes et complexe sont réalisées par des décharges corona de l'air et de plasma d'argon. Dans ce travail, nous caractérisons trois sources de plasma qui sont utilisées pour la décontamination d'Escherichia coli. CC corona décharges dans l'air - corona streamer positive et négative des impulsions Trichel ont été utilisés pour la décontamination des bactéries planctoniques et biofilms bactériens. Dans certaines expériences de l'eau a été électro-pulvérisée sur des échantillons de haute tension électrode. Bio-décontamination des biofilms bactériens a été réalisée sur des lames en verre, pendant 15 min le traitement de plasma a été rendu majorités des bactéries incultivables. Selon la microscopie confocale à balayage laser de biofilms colorées par kit de la viabilité, une partie de ces bactéries incultivables restait viables, seulement les couches les plus supérieures du biofilm ont été tuées. La deuxième source de plasma est corona décharge pulsée propagé à l'intérieur du tube de quartz longue et étroite où l'argon sec ou l'argon avec de la vapeur d'eau coulait à la pression atmosphérique. Ce type de décharge et a une application potentielle dans la décontamination des surfaces intérieures des cathéters ou d'autres dispositifs longs et tubulaires ou pourrait fournir un plasma à basse température sur des distances longues à l'intérieur du corps humain. Tout d'abord, cette source de plasma à basse température a été caractérisée par ses paramètres électriques, et ensuite, une spectroscopie d'émission optique identifiés l'émission de plasma UV-B de radical hydroxyle excité en particulier avec l'argon humide. L'effet de cette UV-B a été testé sur des bactéries planctoniques et a été découvert pour causer jusqu'à un dommage substantiel encore plus loin en aval du tube. La source de plasma d'argon dernière doit aller qui utilise l'argon saturé sec, humide ou de l'eau en tant que gaz de travail. Cette décharge a été principalement utilisée pour la décontamination biofilm, et nous avons reçu des résultats similaires comme décharges corona CC. / In this PhD thesis, applications of lowtemperature plasmas at atmospheric pressure are discussed. In particular, bio-decontamination of planktonic bacteria and bacterial biofilms on flat and complex surfaces by air corona discharges and argon plasma. In this work, we characterize three plasma sources which are used for decontamination of Escherichia coli. DC corona discharges in air - positive streamer corona and negative Trichel pulses were used for decontamination of planktonic bacteria and bacterial biofilms. In some experiments water was electrosprayed onto samples from high voltage electrode. Bio-decontamination of bacterial biofilms was carried out on glass cover slides, within 15 min plasma treatment most of the bacteria were rendered uncultivable. Part from these uncultivable bacteria remained viable only top layers of the biofilm were killed, according to confocal laser scanning microscopy of biofilms stained by live/dead viability kit. The secondplasma source was pulsed corona discharge propagated inside the long narrow quartz tube in which dry argon or argon with water vapor was flowing at atmospheric pressure. This type of discharge has a potential application in decontamination of inner surfaces of catheters or other long tubular devices or could able to deliver low-temperature plasma on longer distances inside the human body. Firstly, this low-temperature plasma source was characterized by its electrical parameters, then, an optical emission spectroscopy of plasma identified UV B emission form excited hydroxyl radical especially with humid argon working gas. The effect of this UV B was tested on planktonic bacteria and was found out to cause up to a substantial damage even further downstream the tube. The last plasma source has argon jet which used dry, humid or water saturated argon as a working gas. This discharge was predominantly used for biofilm decontamination, where we received similar results as with DC corona discharges.

Most of microorganisms are ubiquitously able to live in both planktonic and biofilm states, which can be applied to dissolve the energy and environmental issues (e.g., producing biofuels and purifying waste water), but can also lead to serious public health problems. To better harness microorganisms, plenty of studies have been implemented to investigate the metabolism of planktonic and/or biofilm cells via multi-omics approaches (e.g., transcriptomics and proteomics analysis). However, these approaches are limited to provide the direct description of intracellular metabolism (e.g., metabolic fluxes) of microorganisms. Therefore, in this study, I have applied computational modeling approaches (i.e., 13C assisted pathway and flux analysis, flux balance analysis, and machine learning) to both planktonic and biofilm cells for better understanding intracellular metabolisms and providing valuable biological insights. First, I have summarized recent advances in synergizing 13C assisted pathway and flux analysis and metabolic engineering. Second, I have applied 13C assisted pathway and flux analysis to investigate the intracellular metabolisms of planktonic and biofilm cells. Various biological insights have been elucidated, including the metabolic responses under mixed stresses in the planktonic states, the metabolic rewiring in homogenous and heterologous chemical biosynthesis, key pathways of biofilm cells for electricity generation, and mechanisms behind the electricity generation. Third, I have developed a novel platform (i.e., omFBA) to integrate multi-omics data with flux balance analysis for accurate prediction of biological insights (e.g., key flux ratios) of both planktonic and biofilm cells. Fourth, I have designed a computational tool (i.e., CRISTINES) for the advanced genome editing tool (i.e., CRISPR-dCas9 system) to facilitate the sequence designs of guide RNA for programmable control of metabolic fluxes. Lastly, I have also accomplished several outreaches in metabolic engineering. In summary, during my Ph.D. training, I have systematically applied computational modeling approaches to investigate the microbial metabolisms in both planktonic and biofilm states. The biological findings and computational tools can be utilized to guide the scientists and engineers to derive more productive microorganisms via metabolic engineering and synthetic biology. In the future, I will apply 13C assisted pathway analysis to investigate the metabolism of pathogenic biofilm cells for reducing their antibiotic resistance. / Ph. D.

Traditionally, differential-equation models for population dynamics have considered organisms as "fixed" entities in terms of their behaviour and characteristics. However, there have been many observations of adaptivity in organisms, both at the level of behaviour and as an evolutionary change of traits, in response to the environmental conditions. Taking such adaptiveness into account alters the qualitative dynamics of traditional models and is an important factor to be included, for example, when developing reliable model predictions under changing environmental conditions. In this thesis, we consider piecewise-smooth and smooth dynamical systems to represent adaptive change in a 1 predator-2 prey system. First, we derive a novel piecewise-smooth dynamical system for a predator switching between its preferred and alternative prey type in response to prey abundance. We consider a linear ecological trade-off and discover a novel bifurcation as we change the slope of the trade-off. Second, we reformulate the piecewise-smooth system as two novel 1 predator-2 prey smooth dynamical systems. As opposed to the piecewise-smooth system that includes a discontinuity in the vector fields and assumes that a predator switches its feeding strategy instantaneously, we relax this assumption in these systems and consider continuous change in a predator trait. We use plankton as our reference organism because they serve as an important model system. We compare the model simulations with data from Lake Constance on the German-Swiss-Austrian border and suggest possible mechanistic explanations for cycles in plankton concentrations in spring.

O objetivo da presente tese é o de documentar, em escala milenar, as variações paleoclimáticas e paleoceanográficas superficiais do Atlântico Sul Ocidental desde o Último Máximo Glacial. Com esta finalidade, foram obtidas estimativas de paleotemperatura, paleossalinidade e paleoprodutividade baseadas na análise de fauna de foraminíferos planctônicos, isótopos estáveis de oxigênio e carbono em Globigerinoides ruber e nove datações de radiocarbono em amostras de um testemunho coletado na Bacia de Santos. Os dados foram complementados com a reanálise de outro testemunho previamente coletado em outro setor da mesma Bacia. Os resultados demonstram que as mudanças paleoceanográficas registradas no período analisado podem ser parcialmente explicadas por variações na exportação de calor e sal para o hemisfério norte relacionadas à atividade da célula de transporte meridional e à configuração das correntes superficiais associadas à circulação atmosférica. Outra parte significativa da variabilidade parece estar relacionada à intensidade do Sistema de Monção da América do Sul resultante de variações na insolação de acordo com o ciclo de precessão. Os principais desvios da tendência de variação da composição isotópica da água do mar esperada em função das mudanças de insolação coincidem com os grandes pulsos de degelo ocorridos em torno de 19, 14 e 8,2 mil anos AP. / The goal of this thesis is to document the paleoclimatic and paleoceanographic changes occurred at the millennial scale since the Last Glacial Maximum at the surface Western South Atlantic. Paleotemperature, paleosalinity and paleoproductivity estimates were obtained for this purpose based on faunal changes of foraminifera assemblages, carbon and oxygen stable isotopes in Globigerinoides ruber and nine radiocarbon datings in a core retrieved at Santos Basin. These data were supplemented by the reanalysis of a second core previously analyzed from a different sector of the same basin. The results demonstrate that paleoceanographic changes recorded in the analyzed period may be partially explained by changes in the heat and salt export to the northern hemisphere related to the meridional overturning cell and the surface currents related to atmospheric circulation. Another significant portion of the observed variability seems to be related to changes in the strength of the South American Monsoon System resulting from insolation changes according to the precessional cycle. The main departures from the expected trend of variation in the isotopic composition of seawater related to insolation changes coincide with great meltwater pulses occurred around 19, 14, and 8.2 kyr BP.

Submitted by Biblioteca de Pós-Graduação em Geoquímica BGQ (bgq@ndc.uff.br) on 2017-09-27T14:22:18Z No. of bitstreams: 1 Dissertac...pdf: 4004750 bytes, checksum: c28f16763d698bcdf286109327f4a3a0 (MD5) / Made available in DSpace on 2017-09-27T14:22:18Z (GMT). No. of bitstreams: 1 Dissertac...pdf: 4004750 bytes, checksum: c28f16763d698bcdf286109327f4a3a0 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Universidade Federal Fluminense. Instituto de Química. Programa de Pós-Graduação em Geoquímica, Niterói, RJ / A porção equatorial Oeste do Atlântico Sul é uma região-chave para o estudo das variabilidades climáticas, já que esta área é a principal saída de calor e sal para as altas latitudes do hemisfério norte através da Corrente Norte do Brasil. Esta transferência inter-hemisférica é um dos fatores cruciais para o funcionamento da circulação termohalina no oceano Atlântico, conhecida como Atlantic Meridional Overturning Circulation (AMOC). Baseado nisto, o objetivo deste trabalho é apresentar uma reconstrução da temperatura da superfície do mar (TSM) ao longo dos últimos 40.000 anos, em um intervalo que engloba o Ultimo Máximo Glacial (UMG) e o Holoceno. Para isto, foram empregados três testemunho sedimentares recuperados na margem Nordeste do Brasil. Dois destes testemunhos (MC 17/2 e MC 11/1) tiveram sua cronologia combinada, para juntos formarem um registro único do Holoceno. O terceiro testemunho (MC 10/3) enfoca o UMG e a fase de degelo até o início do Holoceno. Como proxies para a reconstrução paleoceanográfica da TSM foram empregados o isótopo estável de oxigênio (δ18Oc) do foraminífero planctônico Globigerinoides ruber (branco 250 – 300 μm), a Técnica do Análogo Moderno (TAM) e a análise faunística da assembleia de foraminíferos planctônicos na fração 150 μm. Os resultados para o UMG mostram a existência de dois cenários distintos que se separam em 21 k anos AP. Antes desta data condições mais frias na ordem de 2 ºC existiram na região, como ficou evidenciado pelos valores mais positivos do δ18Oc, pelas menores TSM reconstruídas pela TAM e pela maior abundância de foraminíferos planctônicos relacionados a produtividade e profundidade, como Globigerina glutinata, Neogloboquadrina dutertrei, Globorotalia truncatulinoides (dextral e sinistral) e Globorotalia inflata. Após 21 k anos AP uma forte transição ocorre no δ18Oc e na abundância absoluta de foraminíferos planctônicos, indicando a entrada de condições mais quentes na região, principalmente durante o evento Heinrich 1 (H1) e o Younger Dryas (YD). Este intervalo, que inclui a fase de degelo e parte do Holoceno é marcado pela redução das espécies relacionada a produtividade e profundidade e pelo aumento das espécies de águas quentes e superficiais. O retorno da espécie Globorotalia menardii em 21 k anos AP pode indicar a reativação do transporte de águas quentes do Oceano Índico para o Atlântico Sul realizado pela Corrente das Agulhas durante a fase de degelo. Os dados apresentados aqui demonstram que o Atlântico equatorial Oeste responde a entrada de água doce no Atlântico Norte e ao transporte de águas quentes via Corrente das Agulhas, e que o balanço destes dois fatores foi crucial para o retorno da AMOC no fim do UMG. Os resultados para o Holoceno mostraram que a região vem sofrendo um aumento progressivo da TSM da ordem de 1 ºC principalmente após o Holoceno médio, onde alterações nos padrões orbitais podem ter modificado a distribuição da energia solar no planeta. Análises espectrais sobre os dados mostram uma série de periodicidade quase cíclicas centradas em 4.1 – 3.8 kyr, 1.5 – 1.0 kyr, ~ 700 yr, 570 – 560 yr, ~ 390 yr, ~350 yr e ~ 330 yr e podem refletir a ação de forçantes climáticas externa (variabilidade solar) e internas (sistema oceano-atmosfera) transmitidas pela circulação termohalina globalmente. / The western equatorial Atlantic is a key region for the study of climate variability, as this area is the main source of heat and salt toward high latitudes of northern Atlantic through the North Brazil Current. This interhemispheric transfer is one of the crucial factors for the thermohaline circulation in the Atlantic Ocean, known as Atlantic Meridional Overturning Circulation (AMOC). Based on this, the aim of this work is to show a reconstruction of sea surface temperature (SST) over the last 40,000 years, into a range that comprises the Last Glacial Maximum (LGM) and Holocene. For this, we used three sedimentary records recovered in Northeast Brazilian margin. Two of these records (MC 17/2 e MC 11/1) were combined to generate a single record of Holocene. The last record comprises the LGM until the early Holocene. As proxies for the reconstruction of SST were employed the oxygen stable isotope (δ18Oc) of planktonic foraminifera Globigerinoides ruber (white 250 – 300 μm), the Modern Analogue Technique (MAT) and the assemblage of planktonic foraminifera in the size-fraction of 150 μm. The results for the LGM showed the existence of two different scenarios that were separated at 21 kyr BP. The heavier oxygen values recorded prior to 21 kyr BP demonstrated that the Last Glacial Maximum was up to 2ºC colder than Holocene. After 21 kyr BP, a strong shift to lighter values indicated the onset of warmer conditions during deglacial, especially during Heinrich event 1 and the Younger Dryas. The planktonic foraminifera assemblage as species related to productive or deep waters confirmed the conditions indicated by the oxygen composition; i.e., Globigerinita glutinata, Neogloboquadrina dutertrei, Globorotalia truncatulinoides (left and right coiling) and Globorotalia inflata were more abundant prior to 21 kyr BP. With the increase in the sea surface temperature after 21 kyr BP, the abundance of these species was reduced, particularly for G. glutinata and G. inflata, and the abundance of species found in warmer waters increased, especially for Globigerinella siphonifera. The species Globorotalia menardii, which was absent in the Last Glacial Maximum, reappeared after 21 kyr BP, which may have been a response to the Agulhas Leakage that released warmer waters into the South Atlantic at the beginning of deglacial. The data presented here indicate that the western equatorial Atlantic responded to the meltwater pulse at high latitudes of the northern Atlantic and to warm waters from the Indian Ocean. The balance between these two factors was crucial to the development of the Atlantic Meridional Overturning Circulation at the end of the LGM. The results of Holocene showed that the region has suffered a gradual increase in SST of around 1 ºC, mainly after the mid-Holocene, where changes orbital patterns may have changed the distribution of solar energy on the planet. Spectral analyzes on the data demonstrated a series of periodicities centered at 4.1 – 3.8 kyr, 1.5 – 1.0 kyr, ~ 700 yr, 570 – 560 yr, ~ 390 yr, ~350 yr e ~ 330 yr and can be related of climate forcing transmitted globally by the thermohaline circulation.

O objetivo do presente estudo foi investigar a resposta da assembleia de foraminíferos planctônicos frente às variações paleoceanográficas superficiais na porção oeste do Atlântico Sul, o qual desempenha um papel fundamental na Célula de Revolvimento Meridional do Atlântico (AMOC, Meridional Overturning Circulation). Para esta finalidade, foi analisado um registro sedimentar marinho contínuo desde o Último Máximo Glacial até o presente, com base na assembleia de foraminíferos planctônicos, isótopos de oxigênio e na razão Mg/Ca. Adicionalmente, foram avaliadas as variações na ocorrência e na geoquímica dos dois morfotipos de G. ruber (branca), principal espécie utilizada em estudos paleoceanográficos de regiões tropicais e subtropicais. Os resultados mostraram que as diferenças geoquímicas e de abundância relativa dos morfotipos de G. ruber branca evidenciam dois grupos de espécimes ecologicamente distintos, confirmando que o morfotipo sensu stricto calcifica em menores profundidades com relação ao morfotipo sensu lato e que reconstituições paleoceanográficas baseadas no uso não-seletivo dos morfotipos poderiam ser tendenciosas. A Análise Fatorial realizada nos dados de abundância relativa dos foraminíferos planctônicos identificou 4 fatores principais: o Fator 1, representado pelas espécies G. tenella, G. calida, e G. rubescens e relacionado com a temperatura subsuperficial; o Fator 2, representado pelas espécies N. incompta, N. dutertrei e G. truncatulinoides, relacionado com a profundidade da termoclina; o Fator 3, representado pela espécie G. bulloides, associado com o processo de ressurgência e o Fator 4, representado pelas espécies G. ruber e G. glutinata, associado com a intensidade da Corrente do Brasil. As variações mais expressivas de paleotemperatura e paleosalinidade da superfície do mar e da fauna de foraminíferos planctônicos estão relacionadas com os eventos climáticos abruptos do Hemisfério Norte ocorridos durante a deglaciação, tendo sido moduladas pelas variações de arranjo e intensidade da AMOC. Durante os eventos frios Heinrich 1 e Younger Dryas, relacionados a um enfraquecimento da AMOC, foi observado um aumento das paleotemperatura e paleosalinidade e da intensidade da Corrente do Brasil (Fator 4). Contrariamente, durante o evento quente Bolling-Allerod, a paleotemperatura e a paleosalinidade diminuíram expressivamente, como resposta à retomada da AMOC, e houve aumento da produtividade e presença de uma termoclina mais rasa (Fatores 2 e 3). Sugere-se ainda, que entre 26 e 15 ka houve um deslocamento para norte da Confluência Brasil-Malvinas, possivelmente alcançando a latitude da área de estudo (∼23°S), inferido pela presença da espécie G. inflata. Durante o Holoceno, também foi registrada variação significativa na intensidade da Corrente do Brasil, indicada pelos valores máximos do Fator 4 em torno de 7 ka. O reaparecimento das espécies do plexo G. menardii se deu em 8 ka, assim como o aumento das espécies de foraminíferos planctônicos subsuperficiais, indicado pelo Fator 1. Essas mudanças no Holoceno foram atribuídas à entrada efetiva das águas quentes e salinas do Oceano Índico via vazamento das Agulhas, as quais foram essenciais para o restabelecimento da AMOC moderna. / The objective of the present study was to investigate the response of the planktonic foraminiferaassemblage to the superficial paleoceanographic variations in the western South Atlantic, which plays a key role in the AMOC. For this purpose, a continuous marine sedimentary record was analyzed from the Late Glacial Maximum to the present, based on the planktonic foraminifera assemblage, oxygen isotopes and the Mg/Ca ratio. In addition, variations in the occurrence and geochemistry of the two morphotypes of G. ruber (white) were evaluated. This is the main species used in paleoceanographic studies of tropical and subtropical regions. The results showed that the geochemical and relative abundance differences between the G. ruber morphotypes show two ecologically distinct groups of specimens, confirming that the morphotype sensu stricto calcifies at lower depths with respect to the morphotype and sensu lato, and paleoceanographic and paleoceanographic reconstructions using non-selective mixture of morphotypescould potentially be biased. The Factorial Analysis identified four factors: Factor 1, represented by G. tenella, G. calida, and G. rubescens, is related to the subsurface temperature; Factor 2, represented by N. incompta, N. dutertrei and G. truncatulinoides is related to the depth of the thermocline; Factor 3, represented by G. bulloides, is related toupwelling; and Factor 4, represented by G. ruber and G. glutinata, is related to the intensity of the Brazil Current. The results showed that the most significant variations of paleotemperature and paleosalinity and the planktonic foraminifera assemblage are related to the abrupt climatic events of the Northern Hemisphere occurred during deglaciation and were modulated by variations in AMOC arrangement and intensity. During the cold events Heinrich 1 and Younger Dryas, related to a weakening of the AMOC, an increase of paleotemperature and paleosalinity and intensity of the Brazil Current (Factor 4) in the western portion of the South Atlantic was observed. Conversely, during the hot event Bolli-Allerod, paleotemperature and paleosalinity decreased expressively, as a response to AMOC resumption, with increased productivity and presence of a shallower thermocline (Factors 2 and 3). It is also suggested that between 26 and 15 ka there was a displacement to the north of the Brazil-Malvinas Confluence, possibly reaching the latitude of the study area (∼23°S), inferred by the presence of the G. inflata. Along the Holocene, there was also a significant variation in the intensity of the Brazil Current, indicated by the maximum values of Factor 4 around 7ka. The reappearance of G. menardii plexus occurred in 8ka, as well as the increase of the species of subsurface planktonic foraminifera, indicated by Factor 1. These changes in the Holocene were attributed to the effective entrance of the hot and saline waters from the Indian Ocean via the Agulhas Leakage, which were essential for the reestablishment of the modern AMOC.

O objetivo do presente estudo foi investigar a resposta da assembleia de foraminíferos planctônicos frente às variações paleoceanográficas superficiais na porção oeste do Atlântico Sul, o qual desempenha um papel fundamental na Célula de Revolvimento Meridional do Atlântico (AMOC, Meridional Overturning Circulation). Para esta finalidade, foi analisado um registro sedimentar marinho contínuo desde o Último Máximo Glacial até o presente, com base na assembleia de foraminíferos planctônicos, isótopos de oxigênio e na razão Mg/Ca. Adicionalmente, foram avaliadas as variações na ocorrência e na geoquímica dos dois morfotipos de G. ruber (branca), principal espécie utilizada em estudos paleoceanográficos de regiões tropicais e subtropicais. Os resultados mostraram que as diferenças geoquímicas e de abundância relativa dos morfotipos de G. ruber branca evidenciam dois grupos de espécimes ecologicamente distintos, confirmando que o morfotipo sensu stricto calcifica em menores profundidades com relação ao morfotipo sensu lato e que reconstituições paleoceanográficas baseadas no uso não-seletivo dos morfotipos poderiam ser tendenciosas. A Análise Fatorial realizada nos dados de abundância relativa dos foraminíferos planctônicos identificou 4 fatores principais: o Fator 1, representado pelas espécies G. tenella, G. calida, e G. rubescens e relacionado com a temperatura subsuperficial; o Fator 2, representado pelas espécies N. incompta, N. dutertrei e G. truncatulinoides, relacionado com a profundidade da termoclina; o Fator 3, representado pela espécie G. bulloides, associado com o processo de ressurgência e o Fator 4, representado pelas espécies G. ruber e G. glutinata, associado com a intensidade da Corrente do Brasil. As variações mais expressivas de paleotemperatura e paleosalinidade da superfície do mar e da fauna de foraminíferos planctônicos estão relacionadas com os eventos climáticos abruptos do Hemisfério Norte ocorridos durante a deglaciação, tendo sido moduladas pelas variações de arranjo e intensidade da AMOC. Durante os eventos frios Heinrich 1 e Younger Dryas, relacionados a um enfraquecimento da AMOC, foi observado um aumento das paleotemperatura e paleosalinidade e da intensidade da Corrente do Brasil (Fator 4). Contrariamente, durante o evento quente Bolling-Allerod, a paleotemperatura e a paleosalinidade diminuíram expressivamente, como resposta à retomada da AMOC, e houve aumento da produtividade e presença de uma termoclina mais rasa (Fatores 2 e 3). Sugere-se ainda, que entre 26 e 15 ka houve um deslocamento para norte da Confluência Brasil-Malvinas, possivelmente alcançando a latitude da área de estudo (∼23°S), inferido pela presença da espécie G. inflata. Durante o Holoceno, também foi registrada variação significativa na intensidade da Corrente do Brasil, indicada pelos valores máximos do Fator 4 em torno de 7 ka. O reaparecimento das espécies do plexo G. menardii se deu em 8 ka, assim como o aumento das espécies de foraminíferos planctônicos subsuperficiais, indicado pelo Fator 1. Essas mudanças no Holoceno foram atribuídas à entrada efetiva das águas quentes e salinas do Oceano Índico via vazamento das Agulhas, as quais foram essenciais para o restabelecimento da AMOC moderna. / The objective of the present study was to investigate the response of the planktonic foraminiferaassemblage to the superficial paleoceanographic variations in the western South Atlantic, which plays a key role in the AMOC. For this purpose, a continuous marine sedimentary record was analyzed from the Late Glacial Maximum to the present, based on the planktonic foraminifera assemblage, oxygen isotopes and the Mg/Ca ratio. In addition, variations in the occurrence and geochemistry of the two morphotypes of G. ruber (white) were evaluated. This is the main species used in paleoceanographic studies of tropical and subtropical regions. The results showed that the geochemical and relative abundance differences between the G. ruber morphotypes show two ecologically distinct groups of specimens, confirming that the morphotype sensu stricto calcifies at lower depths with respect to the morphotype and sensu lato, and paleoceanographic and paleoceanographic reconstructions using non-selective mixture of morphotypescould potentially be biased. The Factorial Analysis identified four factors: Factor 1, represented by G. tenella, G. calida, and G. rubescens, is related to the subsurface temperature; Factor 2, represented by N. incompta, N. dutertrei and G. truncatulinoides is related to the depth of the thermocline; Factor 3, represented by G. bulloides, is related toupwelling; and Factor 4, represented by G. ruber and G. glutinata, is related to the intensity of the Brazil Current. The results showed that the most significant variations of paleotemperature and paleosalinity and the planktonic foraminifera assemblage are related to the abrupt climatic events of the Northern Hemisphere occurred during deglaciation and were modulated by variations in AMOC arrangement and intensity. During the cold events Heinrich 1 and Younger Dryas, related to a weakening of the AMOC, an increase of paleotemperature and paleosalinity and intensity of the Brazil Current (Factor 4) in the western portion of the South Atlantic was observed. Conversely, during the hot event Bolli-Allerod, paleotemperature and paleosalinity decreased expressively, as a response to AMOC resumption, with increased productivity and presence of a shallower thermocline (Factors 2 and 3). It is also suggested that between 26 and 15 ka there was a displacement to the north of the Brazil-Malvinas Confluence, possibly reaching the latitude of the study area (∼23°S), inferred by the presence of the G. inflata. Along the Holocene, there was also a significant variation in the intensity of the Brazil Current, indicated by the maximum values of Factor 4 around 7ka. The reappearance of G. menardii plexus occurred in 8ka, as well as the increase of the species of subsurface planktonic foraminifera, indicated by Factor 1. These changes in the Holocene were attributed to the effective entrance of the hot and saline waters from the Indian Ocean via the Agulhas Leakage, which were essential for the reestablishment of the modern AMOC.

Le plancton constitue l’essentiel de la biomasse pélagique et est un acteur majeur des cycles biogéochimiques globaux qui régulent le système Terre. Il comprend l'ensemble des organismes portés par les courants, des bactéries aux méduses géantes. La communauté n'est que très rarement étudiée dans son ensemble mais plutôt par fraction. L’expédition Tara Oceans constitue le premier effort de collecte simultané de toutes les classes de taille de plancton à l’échelle de l’océan global. Pour démontrer la faisabilité de cette approche à grande échelle, des échantillons hebdomadaires de plancton, depuis les bactéries jusqu’au macroplancton gélatineux, ont d’abord été analysés en combinant plusieurs instruments d’imagerie sur une période de 10 mois, en un site de référence (point B) dans la rade de Villefranche sur mer. L’imagerie nous a permis de comparer 1) l’information fonctionnelle définie comme l’agrégation de taxons en 18 Groupes Ecologiques de Plancton (GEP), et 2) la structure en taille des communautés échantillonnées sur un intervalle de taille de 6 ordres de grandeur (0.1 µm à 10000 µm). La communauté planctonique au point B évolue en une succession écologique complexe impliquant tous les groupes planctoniques, depuis les bactéries jusqu’aux prédateurs gélatineux du macroplancton. Des évènements impulsifs, tels que des coups de vent, déclenchent des réorganisations de la communauté par un jeu d’interactions entre des contrôles « bottom-up » et « top-down ». Toutefois, le biovolume planctonique total ne varie que d’un seul ordre de grandeur au cours de la période échantillonnée. De même, la structure en taille des communautés planctoniques totales ne varie pas significativement au cours du temps. La stabilité du biovolume total et de la structure en taille suggère que des mécanismes structurant et de compensation forts maintiennent les communautés planctoniques dans un intervalle de biomasse restreint. Le couplage entre données de taille et de taxonomie révèle une réorganisation du réseau trophique entre l’été et l’hiver. En hiver, Le réseau trophique microplancton-zooplancton est dominé par la fonction de broutage. En été, le réseau trophique microplancton-zooplancton est dominé par la fonction de prédation (chaetognathes et gélatineux carnivores). En été, ce réseau trophique s’organise en deux chaines trophiques parallèles et distinctes discriminées par des relations de taille entre proies et prédateurs. Cette réorganisation souligne le rôle clef du zooplancton et de la prédation dans la structuration des communautés planctoniques. Parallèlement à cette analyse temporelle en un point fixe, nous avons montré l’existence de types caractéristiques de communautés zooplanctoniques, associés à des conditions environnementales distinctes, à partir des échantillons de l’expédition Tara Oceans, à l’échelle globale. En utilisant la même méthodologie que pour l’analyse de la dynamique temporelle, nous avons identifié trois types de communautés mésozooplanctoniques à l’échelle globale selon le type d’environement: 1) des communautés associées aux environnements productifs (upwellings côtiers et équatoriaux), 2) des communautés associées aux zones de minimum d’oxygène (OMZs, « Oxygen Minimum Zones »), et 3) des communautés associées aux gyres océaniques oligotrophes. Ce travail constitue une première typologie des communautés zooplanctoniques, structurées en taille et GEP, à l’échelle globale. Il sera complété dans le futur par l’intégration de données issus des autres compartiments planctoniques, et de données d’export vertical de matière organique particulaire pour affiner les estimations des relations qui existent entre phytoplancton, zooplancton et flux biogéochimiques. / Plankton constitutes the bulk of pelagic biomass and plays a major role in the global biogeochemical cycles that regulate the earth system. It encompasses all the organisms that drift with the water masses movements, from bacteria to giant medusae. Studies of the entire community are scarce, and plankton has been traditionally studied by fractions. The Tara Oceans expedition is the first attempt to simultaneously collect plankton in every size classes at the global scale. To demonstrate the feasibility of this approach, samples of plankton from bacteria to gelatinous macroplankton were collected weekly over ten months at a reference site (point B), in Villefranche Bay, northwestern Mediterranean, and analyzed using imaging techniques. Imaging enabled us to compare 1) the functional taxonomic information as derived from the analysis of 18 Plankton Ecological Groups (PEGs), and 2) the size structure of the same planktonic community over 6 orders of magnitude in size. The plankton dynamics at point B are driven by a complex succession process involving all plankton groups, from bacteria to macroplanktonic gelatinous predators. Environmental impulsive events such as wind events trigger sharp community level reorganizations via interplay of bottom-up controls followed by top-down controls. However, the total biovolume of the planktonic community varies within only one order of magnitude over the period studied. In addition, the size structure of the entire community does not vary significantly over time. The total biovolume and size structure stability suggest that strong and compensative mechanisms drive community dynamics within a narrow range of biomass variation. The use of both taxonomic and size structured data reveals a reorganization of the food web between winter and summer. In winter and spring the microplanktoniczooplanktonic food web is shaped by the grazing function. In summer, it is shaped by the predation function (chaetognaths and gelatinous predators). In summer, the food web self organizes in two distinct food chains discriminated by size relations between predators and preys. This reorganization underlines the key role of zooplankton and predation in structuring planktonic communities. In parallel to this temporal dynamics study, we used the Tara Oceans expedition samples to study the global scale distribution of mesozooplankton. We showed that characteristic mesozooplanktonic communities were associated with distinct environmental conditions, at the global scale. Using a similar methodology as for the temporal study we found that three different mesozooplanktonic communities were associated with 1) productive environments (e.g. upwellings), 2) Oxygen Minimum Zones, and 3) Oligotrophic oceanic gyres. This work is the first typology of mesozooplanktonic communities at the global scale. It will be further developed in the future by the integration of other planktonic compartments and particulate organic matter fluxes data, to improve our knowledge on the relations between phytoplankton, zooplankton and particulate organic matter fluxes.

O objetivo da presente tese é o de documentar, em escala milenar, as variações paleoclimáticas e paleoceanográficas superficiais do Atlântico Sul Ocidental desde o Último Máximo Glacial. Com esta finalidade, foram obtidas estimativas de paleotemperatura, paleossalinidade e paleoprodutividade baseadas na análise de fauna de foraminíferos planctônicos, isótopos estáveis de oxigênio e carbono em Globigerinoides ruber e nove datações de radiocarbono em amostras de um testemunho coletado na Bacia de Santos. Os dados foram complementados com a reanálise de outro testemunho previamente coletado em outro setor da mesma Bacia. Os resultados demonstram que as mudanças paleoceanográficas registradas no período analisado podem ser parcialmente explicadas por variações na exportação de calor e sal para o hemisfério norte relacionadas à atividade da célula de transporte meridional e à configuração das correntes superficiais associadas à circulação atmosférica. Outra parte significativa da variabilidade parece estar relacionada à intensidade do Sistema de Monção da América do Sul resultante de variações na insolação de acordo com o ciclo de precessão. Os principais desvios da tendência de variação da composição isotópica da água do mar esperada em função das mudanças de insolação coincidem com os grandes pulsos de degelo ocorridos em torno de 19, 14 e 8,2 mil anos AP. / The goal of this thesis is to document the paleoclimatic and paleoceanographic changes occurred at the millennial scale since the Last Glacial Maximum at the surface Western South Atlantic. Paleotemperature, paleosalinity and paleoproductivity estimates were obtained for this purpose based on faunal changes of foraminifera assemblages, carbon and oxygen stable isotopes in Globigerinoides ruber and nine radiocarbon datings in a core retrieved at Santos Basin. These data were supplemented by the reanalysis of a second core previously analyzed from a different sector of the same basin. The results demonstrate that paleoceanographic changes recorded in the analyzed period may be partially explained by changes in the heat and salt export to the northern hemisphere related to the meridional overturning cell and the surface currents related to atmospheric circulation. Another significant portion of the observed variability seems to be related to changes in the strength of the South American Monsoon System resulting from insolation changes according to the precessional cycle. The main departures from the expected trend of variation in the isotopic composition of seawater related to insolation changes coincide with great meltwater pulses occurred around 19, 14, and 8.2 kyr BP.