A aplicação da digestão anaeróbia aparece como opção para processamento da vinhaça, visto que por meio deste processo é possível aliar a recuperação de energia (hidrogênio e metano) ao enquadramento ambiental deste resíduo sem interferir em suas qualidades como biofertilizante. Nesse sentido, este trabalho avaliou a aplicação da digestão anaeróbia da vinhaça em sistema combinado acidogênico e metanogênico. Inicialmente, avaliou-se a influência de materiais suportes (argila expandida, carvão vegetal, cerâmica porosa e polietileno de baixa densidade) na produção de hidrogênio, em reatores de leito empacotado (APBR) operados em condição mesofílica (25°C) (Etapa 1). De uma forma geral, apenas traços de hidrogênio foram observados nos reatores preenchidos com partículas de carvão vegetal e cerâmica porosa (2 - 7,9 mL-H2.d-1.L-1 reator). Por outro lado, os valores para a produção volumétrica de hidrogênio (PVH) nos reatores com argila expandida e polietileno de baixa densidade foram dez vezes superior (74,3 - 84,2 mL-H2.d-1.L-1 reator), todavia, estatisticamente iguais. O critério de seleção do material suporte ocorreu com base em relatos na literatura que indicaram rebaixamento do leito e entupimento da saída de reatores APBR preenchidos com argila expandida. Portanto, o polietileno de baixa densidade foi escolhido como melhor opção dentre os suportes avaliados. Não obstante, a baixa relação C/N da vinhaça associada à microaeração do sistema (presença de microrganismos anóxicos) afetou severamente os reatores APBR com diferentes materiais suportes, levando-os à falência. Na segunda etapa, adotou-se a operação dos APBR preenchidos com polietileno de baixa densidade, em condição termofílica (55°C) a fim de diminuir o rendimento da biomassa acidogênica e a solubilidade do oxigênio. Adicionalmente, foi avaliada influência da Carga Orgânica Volumétrica aplicada (COVa - 36,4 - 108,6 kg- DQO.m-3.d-1), por meio da variação do Tempo de Detenção Hidráulica (TDH - 8 - 24 h). Produção contínua de hidrogênio foi observada em todos os reatores operados em condição termofílica (Etapa 2). Nessa etapa, estabeleceu-se a condição ótima de operação com COVa de 84,2 kg-DQO.m-3.d-1 e TDH de 10 h, resultando em PVH de valor 575,3 mL-H2.d-1.L-1 reator e rendimento de hidrogênio (Y1H2) de 1,4 mol-H2.mol-1 carboidratos totais. Na Etapa III, essas condições foram impostas na operação do APBR, resultando em aumento de 18,2% e 14,2% nos valores de PVH e Y1H2, respectivamente, em relação aos dados obtidos na Etapa II. Em paralelo, foram operados dois reatores metanogênicos do tipo manta de lodo (UASB), compondo um sistema único (UASB) e um sistema combinado (APBR/UASB). A produção de energia no sistema combinado foi 25,7% superior ao observado no sistema único. A eficiência de remoção da matéria orgânica total e solúvel aumentou de 60,7 ± 0,3% e 72,6% ± 1,2% no sistema único e 74,6 ± 0,3% e 96,1 ± 1,7% no sistema combinado, respectivamente, sob COVa de 25 kg-DQO.m-3.d-1 (calculada para os sistemas metanogênicos). / Anaerobic digestion application appears as an option for sugar cane vinasse processing, since via this process it is possible to combine the energy recovery (hydrogen and methane) to the environmental framework of this residue without interfering in their qualities as biofertilizer. In this sense, this study evaluated the application of anaerobic digestion of vinasse in two-stage system (acidogenic and methanogenic). Initially, it was evaluated the influence of support material (expanded clay, charcoal, porous ceramics, and low-density polyethylene) on hydrogen production in acidogenic packed bed reactors (APBR) operated under mesophilic condition (25°C) (Phase 1). In general, only traces of hydrogen were observed in APBR filled with charcoal and porous ceramics particles (2 - 7.9 mL-H2.d-1.L-1 reactor). On the other hand, in APBR with expanded clay and low-density polyethylene as support, the values for volumetric hydrogen production (VHP) were ten times higher (74.3 - 84.2 mL-H2.d-1.L-1 reactor), however, statistically equal. The selection criteria of support material was based on reports in the literature that indicated bed lowering and clogging in APBR outlet with expanded clay as support. Therefore, the low-density polyethylene was chosen as the best support among those evaluated. Nevertheless, the low C/N ratio of vinasse associated to microaeration condition in the systems (presence of microorganisms anoxic) severely affected the APBR with different support materials, leading them to bankruptcy. In the second phase, it was adopted the operation of APBR filled with low density polyethylene in thermophilic conditions (55°C) in order to reduce the acidogenic biomass yield and oxygen solubility. Moreover, it was evaluated the influence of organic loading rate (OLR - 36.4 to 108.6 kg-COD.m-3.d-1) by hydraulic retention time varying (HRT - 8 - 24 h). Continuous hydrogen production was observed in all reactors operated at 55°C (Phase 2). In this phase, it was established the optimum condition of operation, OLR of 84.2 kg-COD.m-3.d-1 and HRT of 10 h, resulting in values for PVH and hydrogen yield (Y1H2) of 575.3 mL-H2.d-1.L-1 reactor and 1.4 mol-H2.mol-1 total carbohydrates, respectively. In Phase III, these conditions were imposed on the operation of the APBR, resulting in an increase of 18.2% and 14.2% in the values of PVH and Y1H2, respectively, compared to the data obtained in Phase II. In parallel, two methanogenic reactors were operated (Up-flow Anaerobic Sludge Blanket UASB type), which composed a single stage system (UASB) and a two-stage system (APBR/UASB). The energy production in the two-stage system was 25.7% higher compared to the single stage system. The values for total and soluble organic matter removal were 60.7 ± 0.3% and 72.6 ± 1.2% to single stage system and 74.6 ± 0.3% and 96.1 ± 1.7% to two-stage system, respectively, at OLR of 25 kg-COD.m-3.d-1 (calculated for the methanogenic reactors).

A aplicação da digestão anaeróbia aparece como opção para processamento da vinhaça, visto que por meio deste processo é possível aliar a recuperação de energia (hidrogênio e metano) ao enquadramento ambiental deste resíduo sem interferir em suas qualidades como biofertilizante. Nesse sentido, este trabalho avaliou a aplicação da digestão anaeróbia da vinhaça em sistema combinado acidogênico e metanogênico. Inicialmente, avaliou-se a influência de materiais suportes (argila expandida, carvão vegetal, cerâmica porosa e polietileno de baixa densidade) na produção de hidrogênio, em reatores de leito empacotado (APBR) operados em condição mesofílica (25°C) (Etapa 1). De uma forma geral, apenas traços de hidrogênio foram observados nos reatores preenchidos com partículas de carvão vegetal e cerâmica porosa (2 - 7,9 mL-H2.d-1.L-1 reator). Por outro lado, os valores para a produção volumétrica de hidrogênio (PVH) nos reatores com argila expandida e polietileno de baixa densidade foram dez vezes superior (74,3 - 84,2 mL-H2.d-1.L-1 reator), todavia, estatisticamente iguais. O critério de seleção do material suporte ocorreu com base em relatos na literatura que indicaram rebaixamento do leito e entupimento da saída de reatores APBR preenchidos com argila expandida. Portanto, o polietileno de baixa densidade foi escolhido como melhor opção dentre os suportes avaliados. Não obstante, a baixa relação C/N da vinhaça associada à microaeração do sistema (presença de microrganismos anóxicos) afetou severamente os reatores APBR com diferentes materiais suportes, levando-os à falência. Na segunda etapa, adotou-se a operação dos APBR preenchidos com polietileno de baixa densidade, em condição termofílica (55°C) a fim de diminuir o rendimento da biomassa acidogênica e a solubilidade do oxigênio. Adicionalmente, foi avaliada influência da Carga Orgânica Volumétrica aplicada (COVa - 36,4 - 108,6 kg- DQO.m-3.d-1), por meio da variação do Tempo de Detenção Hidráulica (TDH - 8 - 24 h). Produção contínua de hidrogênio foi observada em todos os reatores operados em condição termofílica (Etapa 2). Nessa etapa, estabeleceu-se a condição ótima de operação com COVa de 84,2 kg-DQO.m-3.d-1 e TDH de 10 h, resultando em PVH de valor 575,3 mL-H2.d-1.L-1 reator e rendimento de hidrogênio (Y1H2) de 1,4 mol-H2.mol-1 carboidratos totais. Na Etapa III, essas condições foram impostas na operação do APBR, resultando em aumento de 18,2% e 14,2% nos valores de PVH e Y1H2, respectivamente, em relação aos dados obtidos na Etapa II. Em paralelo, foram operados dois reatores metanogênicos do tipo manta de lodo (UASB), compondo um sistema único (UASB) e um sistema combinado (APBR/UASB). A produção de energia no sistema combinado foi 25,7% superior ao observado no sistema único. A eficiência de remoção da matéria orgânica total e solúvel aumentou de 60,7 ± 0,3% e 72,6% ± 1,2% no sistema único e 74,6 ± 0,3% e 96,1 ± 1,7% no sistema combinado, respectivamente, sob COVa de 25 kg-DQO.m-3.d-1 (calculada para os sistemas metanogênicos). / Anaerobic digestion application appears as an option for sugar cane vinasse processing, since via this process it is possible to combine the energy recovery (hydrogen and methane) to the environmental framework of this residue without interfering in their qualities as biofertilizer. In this sense, this study evaluated the application of anaerobic digestion of vinasse in two-stage system (acidogenic and methanogenic). Initially, it was evaluated the influence of support material (expanded clay, charcoal, porous ceramics, and low-density polyethylene) on hydrogen production in acidogenic packed bed reactors (APBR) operated under mesophilic condition (25°C) (Phase 1). In general, only traces of hydrogen were observed in APBR filled with charcoal and porous ceramics particles (2 - 7.9 mL-H2.d-1.L-1 reactor). On the other hand, in APBR with expanded clay and low-density polyethylene as support, the values for volumetric hydrogen production (VHP) were ten times higher (74.3 - 84.2 mL-H2.d-1.L-1 reactor), however, statistically equal. The selection criteria of support material was based on reports in the literature that indicated bed lowering and clogging in APBR outlet with expanded clay as support. Therefore, the low-density polyethylene was chosen as the best support among those evaluated. Nevertheless, the low C/N ratio of vinasse associated to microaeration condition in the systems (presence of microorganisms anoxic) severely affected the APBR with different support materials, leading them to bankruptcy. In the second phase, it was adopted the operation of APBR filled with low density polyethylene in thermophilic conditions (55°C) in order to reduce the acidogenic biomass yield and oxygen solubility. Moreover, it was evaluated the influence of organic loading rate (OLR - 36.4 to 108.6 kg-COD.m-3.d-1) by hydraulic retention time varying (HRT - 8 - 24 h). Continuous hydrogen production was observed in all reactors operated at 55°C (Phase 2). In this phase, it was established the optimum condition of operation, OLR of 84.2 kg-COD.m-3.d-1 and HRT of 10 h, resulting in values for PVH and hydrogen yield (Y1H2) of 575.3 mL-H2.d-1.L-1 reactor and 1.4 mol-H2.mol-1 total carbohydrates, respectively. In Phase III, these conditions were imposed on the operation of the APBR, resulting in an increase of 18.2% and 14.2% in the values of PVH and Y1H2, respectively, compared to the data obtained in Phase II. In parallel, two methanogenic reactors were operated (Up-flow Anaerobic Sludge Blanket UASB type), which composed a single stage system (UASB) and a two-stage system (APBR/UASB). The energy production in the two-stage system was 25.7% higher compared to the single stage system. The values for total and soluble organic matter removal were 60.7 ± 0.3% and 72.6 ± 1.2% to single stage system and 74.6 ± 0.3% and 96.1 ± 1.7% to two-stage system, respectively, at OLR of 25 kg-COD.m-3.d-1 (calculated for the methanogenic reactors).

Supplementation of trace metals such as Co and Ni may improve anaerobic digestion of organic material for biogas formation. Which trace metals that are needed and the quantity to apply are, at least partly, related to metal speciation and bioavailability. According to the common perception, metals have to be dissolved to be available for microbial uptake. However, the impact of trace metal speciation on bioavailability is still unclear. The purpose of the present study was to investigate the effect of Fe-, Co- and Ni-addition on the biogas process performance of stillage-fed lab-scale biogas tank reactors. Metal speciation was determined by sequential extraction (SE), extraction of acid volatile sulfides (AVS) and continuously extracted metals (AVS-Me). Sulfur forms, which may be associated to metal speciation, were studied with S XANES (sulfur X-ray absorption near edge structure). The effect of different Co- and Ni-concentrations on process microflora composition was examined with quantitative PCR (qPCR) and 454-pyrosequencing. The results showed that Co- and Ni-supplementation stimulated and stabilized the biogas process performance by increasing methane production and substrate utilization and by establishing low concentrations of volatile fatty acids. 10-20% of the total Co-amount was found in the dissolved phase, which shows that Co was relatively available for microbial uptake. Nickel was entirely associated to organic matter/sulfides and AVS, and was therefore considered to be non-bioavailable. Nevertheless, Ni-supplementation had stimulatory effects on the biogas process performance. This implies that Ni was available for microbial uptake despite its extensive association to sulfides and that other mechanisms than solubility govern the availability of this trace metal. The microbial analyzes revealed that it was primarily the methane producers which were affected by the concentration of Co and Ni. At stimulatory Co- and Ni-concentrations, the archaeal methanogenic community was dominated by aceticlastic Methanosarcinales. At lower Co- or Ni-levels, when biogas process performance was poor, an increase in hydrogenotrophic Methanomicrobiales was observed. This indicates a shift in the methanogenic flora, from being dominated by acetate utilizers to increased importance of hydrogen utilizers, and that the former was more dependent on Co and Ni. / Tillsats av spårmetaller kan förbättra rötning av organiskt material till biogas. Typ och mängd av respektive spårmetall som behöver tillsättas för att uppnå stimulerande effekter, varierar mellan processer. Detta är delvis kopplat till specieringen och biotillgängligheten av metallerna. Endast fria metalljoner och vissa metallkomplex antas vara tillgängliga för mikrobiellt upptag. Det är dock i många fall oklart hur metallernas speciering påverkar biotillgängligheten. Syftet med föreliggande studie var därför att undersöka effekten av tillsats av Fe, Co och Ni för biogasproduktion från drank, en restprodukt i produktion av bioetanol från spannmål, samt att undersöka hur dessa metallers speciering påverkar deras biotillgänglighet. Effekten av tillsatserna av Fe, Co och Ni undersöktes på biogasreaktorer i lab-skala. Metallernas speciering bestämdes genom sekventiell extraktion (SE), extraktion av AVS (acid volatile sulfide) och kontinuerligt extraherade metaller (AVS-Me). Svavelformer med betydelse för metallspeciering studerades med S XANES (sulfur X-ray absorption near edge structure). Effekten av olika Co- och Ni-koncentrationer på processens mikroflora undersöktes molekylärbiologiskt med kvantitativ PCR (qPCR) och 454-pyrosekvensering. Resultaten visade att Co och Ni stimulerade och stabiliserade biogasprocessen genom ökad metanproduktion, ökad utrötningsgrad samt låga halter av flyktiga fettsyror i det studerade systemet. 10-20% av totala mängden Co återfanns i löst fas, vilket visar att Co var relativt lättillgängligt för mikroorganismerna. Nickel var däremot enbart bundet till organiskt material/sulfider och AVS och kunde alltså betraktas som otillgängligt. Trots detta hade även tillsatsen av Ni stimulerande effekter på biogasprocessen. Det innebär att mikroorganismerna har förmåga att komma åt Ni bundet i svårlösliga sulfidföreningar och att andra mekanismer än löslighet reglerar tillgängligheten av denna spårmetall. De molekylärbiologiska analyserna visade att framför allt de metanbildande mikroorganismerna påverkades av halten av Co och Ni. De halter, som gav välfungerande processer, dominerades helt av acetiklastiska Methanosarcinales. Vid lägre halter av Co eller Ni, då processerna gick sämre, tillkom vätgasutnyttjande metanogener. Det tyder på ett skift i bildningen av metan från att ha dominerats av acetatklyvning till att vätgasutnyttjarna fått större betydelse och att de förra är mer beroende av Co och Ni.

Cotesia congregata est une guêpe parasitoïde qui se développe à l’intérieur de la larve du Lépidoptère, Manduca sexta. Ce parasitoïde a développé une stratégie de virulence qui utilise un symbionte viral de la famille des Polydnavirus nommé Cotesia congregata bracovirus. Mon travail de thèse a permis de caractériser le dialogue moléculaire au cours de l’interaction par des approches de transcriptomique à haut débit et de physiologie. Ces travaux ont permis d’établir la première carte fonctionnelle du génome viral et de visualiser l’ensemble des gènes de M. sexta régulés au cours du parasitisme. La régulation des gènes de l’immunité a révélé que le parasitisme n’empêche pas l’induction de peptides antimicrobiens, mais entraine la sous-expression de gènes impliqués dans la réponse cellulaire. De plus j’ai pu mettre en évidence une réduction du nombre de cellules adhérentes au cours de l’interaction et décrire l’induction d’un phénotype de type apoptose d’une catégorie de cellules immunitaires. Ces résultats permettent d’identifier des gènes acteurs de l’interaction et apportent de nouvelles connaissances relatives aux interactions hôtes-parasitoïdes. / Cotesia congregata is a parasitoid wasp that develops inside the lepidopteran larvae, Manduca sexta. This parasitoid wasp has evolved virulence strategies using an obligate viral symbiont from the Polydnavirus family named Cotesia congregata bracovirus. My thesis work has allowed us to characterize the molecular dialogue during the interaction by physiological and high-throughput transcriptomic approaches. This work allowed to obtain the first functional map of the viral genome and to identify all M. sexta genes regulated during parasitism. Regulation of immune genes revealed that parasitism does not prevent induction of antimicrobial peptides, but leads to the down-regulation of genes involved in the cellular response. Moreover, I was able to demonstrate a reduction in the number of adherent cells during the interaction and to describe this induction as an apoptosis-like phenotype targeting a specific population of immune cells. These findings open the way to the identification of candidate genes involved in this particular interaction and provide new insights into host-parasitoid interactions in general.

Infestações com Rhipicephalus microplus, o carrapato dos bovinos, causam enormes prejuízos econômicos para a pecuária. Os carrapatos estão desenvolvendo resistência aos carrapaticidas que, além dessa desvantagem, deixam resíduos em carne e leite. Vacinas anticarrapato representam uma alternativa sustentável de controle de infestações, mas as atualmente disponíveis têm efeitos parciais e transitórios. Surge, assim, a necessidade de identificar novos antígenos vacinais. Para alcançar esse objetivo este trabalho explora o fato de que bovinos apresentam fenótipos contrastantes e herdáveis de infestações que são específicos de certas raças. Além disso, o nível de imunidade do hospedeiro afeta a transcrição de genes de glândulas salivares do carrapato, órgão que produz proteínas que medeiam o parasitismo. A hipótese de trabalho é a que os diferentes níveis da imunidade anticarrapato do hospedeiro afetam, também, a composição salivar do parasita. Assim, em carrapatos alimentando-se em hospedeiros resistentes as proteínas que são cruciais ao parasitismo poderão estar ausentes ou deficientes na sua saliva e por isso os carrapatos não terminam sua refeição de sangue. A neutralização dessas mesmas proteínas pela imunidade humoral pode ter o mesmo efeito e por isso, essas proteínas constituem bons antígenos vacinais. Assim, o objetivo do trabalho foi identificar novos antígenos vacinais em saliva de fêmeas e glândulas salivares de ninfas, machos e fêmeas de carrapatos alimentados em hospedeiros resistentes e suscetíveis, bem como em larvas não alimentadas oriundas de ovos de fêmeas alimentadas nestes mesmos hospedeiros. Para isso, foram empregadas abordagens de sequenciamento de nova geração \"RNA-Seq\" (454) e abordagens proteômicas, como análise diferencial em gel (DIGE) e Western Blots (imunoproteoma) seguido de sequenciamento de massa, além da tecnologia de identificação de proteínas multidimensionais (ou Multidimensional Protein Identification Technology, MudPIT) para descrever o proteoma das glândulas salivares e da saliva de fêmeas. A análise transcriptômica resultou no sequencimanto de 1.999.086 reads que permitiu identificar e classificar 11.676 sequências codificadoras (CDS), muitas das quais (3.600 CDS) contêm peptídeo sinal que é indicativo de secreção, portanto podendo estar presente na saliva e Resumo Gustavo Rocha Garcia apresentar função importante na hematofagia. Por meio de MudPIT, identificamos 321 proteínas salivares diferentes, além de 126 proteínas no DIGE e 266 proteínas nos imunoproteomas. Muitas dessas proteínas podem ser consideradas antígenos potenciais por estarem associadas com a hematofagia/parasitismo, tais como proteases, nucleases, inibidores de proteases, peptídeos antimicrobianos, proteínas de fixação, entre outros, inclusive proteínas ainda não caracterizadas. A maioria dos genes codificantes dessas proteínas está mais expressa em carrapatos alimentados em hospedeiros suscetíveis, principalmente em carrapatos machos. Além disso, muitas dessas proteínas não são reconhecidas por soros bovinos, inclusive soros de bovinos infestados, embora soros de bovinos infestados e resistentes ao carrapato apresente a maioria das reatividades. O conjunto dos resultados sugere que em nível de proteína a composição da saliva também é afetada pelos diferentes níveis de imunidade dos hospedeiros, além de variar com o ciclo de vida do carrapato. Desse modo, concluímos que as estratégias de investigação empregadas foram satisfatórias para identificar um conjunto de antígenos salivares do carrapato R. microplus que representam proteínas alvos para compor vacinas multicomponentes anticarrapato. / Infestation with Rhipicephalus microplus, the cattle tick, causes huge economic losses to livestock. Ticks are developing resistance to acaricides that, besides this disadvantage, leave residues in meat and milk. The anti tick vaccines represent a sustainable alternative of the infestations control, but the currently available has partial and transient effects. Thus arises the need to identify new vaccine antigens. To achieve this goal, this work explores the fact that cattle exhibit contrasting phenotypes and inheritable of infestations that are specific to certain breeds. Furthermore, the level of immunity of the host affects gene transcription tick salivary gland, organ that produces proteins that mediate the parasitism. The working hypothesis is that different levels of anti tick immunity of host affect also the salivary composition of the parasite. So in ticks feeding on resistant hosts the proteins that are crucial to parasitism may be absent or deficient in their saliva, and by this the ticks do not finish your meal blood. The neutralization of these same proteins by humoral immunity can have the same effect and by this, these proteins are good vaccine antigens. So, the aim of the study was to identify new vaccine antigens in saliva from females and salivary glands of nymphs, males and females of ticks fed on resistant and susceptible hosts as well as in unfed larvae originating from eggs of females fed on these same hosts. To this, were employed sequencing approaches of new generation \"RNA-Seq\" (454) and proteomic approaches, such as differential analysis in gel (DIGE) and Western Blots (immunoproteomics) followed by sequencing mass, besides the Multidimensional Protein Identification Technology (MudPIT) to describe the proteome of the salivary glands and saliva of females. The transcriptomics analysis identified 11,676 coding sequences (CDS), many of which (3,600 CDS) contain predicted signal peptide indicative of secretion, therefore may be present in saliva and provide an important function in blood feeding. Through MudPIT, we identify 321 different salivary proteins, besides 126 proteins in DIGE and 266 proteins in immunoproteomics. Many of these proteins may be considered as potential antigens to be associated with the blood meal/ parasitism, such as proteases, nucleases, protease inhibitors, antimicrobial peptides, proteins of attachment, among Abstract Gustavo Rocha Garcia others, including proteins not yet characterized. Most of the genes encoding of these proteins are more expressed in ticks fed on susceptible hosts, especially in male ticks. Moreover, many of these proteins are not recognized by bovine sera, including sera from infested hosts, although sera from infested and resistant host to tick present the most reactivities. The overall results suggest that in protein level, the composition of saliva is also affected by the different levels of immunity of the host, besides vary with the tick life cycle. Thus, we conclude that the research strategies employed were satisfactory to identify a set of tick salivary antigens from R. microplus that represent target proteins for composing anti tick multicomponent vaccines.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-09-15T12:46:42Z No. of bitstreams: 1 fernandaalvesdefreitasguedes.pdf: 2011976 bytes, checksum: 6684b1525d9f87a2f6e72eadaa42fc34 (MD5) / Approved for entry into archive by Diamantino Mayra (mayra.diamantino@ufjf.edu.br) on 2016-09-26T20:18:53Z (GMT) No. of bitstreams: 1 fernandaalvesdefreitasguedes.pdf: 2011976 bytes, checksum: 6684b1525d9f87a2f6e72eadaa42fc34 (MD5) / Made available in DSpace on 2016-09-26T20:18:53Z (GMT). No. of bitstreams: 1 fernandaalvesdefreitasguedes.pdf: 2011976 bytes, checksum: 6684b1525d9f87a2f6e72eadaa42fc34 (MD5) Previous issue date: 2011-02-28 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Lippia alba, também conhecida popularmente como erva cidreira, é uma espécie amplamente distribuída pelas Américas podendo ser encontrada por praticamente todo o Brasil. Muito usada pela medicina popular para o tratamento de problemas gastrointestinais e respiratórios, a folha desta espécie produz um óleo essencial rico em terpenos, principalmente mono e sesquiterpenos. Estes compostos não são apenas de interesse farmacológico, como também industrial. A composição deste óleo pode variar em função de fatores abióticos e também de variações genotípicas. Diante da complexidade da síntese destes compostos a proposta deste trabalho foi uma ampla caracterização do transcriptoma de folha de Lippia alba, além da identificação de prováveis enzimas envolvidas na síntese de terpenos. Para isso, foi feito um sequenciamento deste transcriptoma usando a plataforma 454 (Roche) seguido de uma montagem de novo. Esta plataforma tem sido cada vez mais utilizada para o sequenciamento de transcriptomas numa abordagem conhecida como RNA-Seq. O sequenciamento de biblioteca preparada a partir de RNA total em 1/8 de placa gerou 104.631 leituras com comprimento médio de 184,48bp num total de 19.302.161 bases. Foram feitas montagens das leituras usando 2 diferentes assemblers a fim de compará-las. Com o Newbler 2.5 foi possível montar 2.686 contigs com comprimento médio de 349bp, enquanto o SeqMan2.2 gerou 13.448 contigs com média de 284bp. Em seguida, foi feita a anotação funcional com o Blast2GO para os contigs obtidos nas duas montagens, tendo sido anotados 51,49% e 30,88%, respectivamente, dos contigs do Newbler e do SeqMan. Por fim, a análise das sequências anotadas revelou algumas enzimas potencialmente envolvidas com a síntese de terpenos. Os resultados obtidos neste estudo pioneiro sobre a espécie comprovam que as tecnologias NGS podem ser uma ferramenta bastante eficiente para o sequenciamento de transcriptomas e servirão como referência para o preparo mais específico de novas bibliotecas. Futuros sequenciamentos devem contribuir para uma melhor cobertura do transcriptoma permitindo a descoberta inclusive de transcritos raros. / Lippia alba, popularly known as erva cidreira, is widely distributed throughout the Americas and can be found through almost whole Brazil. This species is largely used in folk medicine to treat gastrointestinal and respiratory problems, especially leaves, which produce an essential oil rich in terpenes, mainly mono-and sesquiterpenes. These compounds are not only of pharmacological interest, as well as industrial. Composition of essencial oil can vary depending on the developmental stage, the plant part and other abiotic factors. However, genotypic variations also contribute to oil composition variation. Given the complexity of terpenes synthesis, including diversity of enzymes involved in these metabolic pathways, the purpose of this work was a L. alba leaf transcriptome characterization, in addition to identifying some enzymes probably involved in terpene synthesis. For that, it was made a transcriptome sequencing using 454 platform (Roche) followed by a de novo assembly. This platform, along with other NGS technologies, has been increasingly used for transcriptome sequencing in an approach known as RNA-Seq. Sequencing of a library prepared from total RNA in 1/8 plate generated 104,631 reads with average length of 184.48 bp and a total of 19,302,161 bases. Read assemblies were made using two different assemblers in order to compare them. While Newbler 2.5, proprietary software platform, assembled 2686 contigs with average length of 349bp, SeqMan2.2 generated 13,448 contigs with an average of 284bp. Then, functional annotation was performed with Blast2GO for all contigs from both assemblies; 51.49% and 30.88% of contigs, respectively, from Newbler and SeqMan were annotated. Finally, analysis of annotated sequences revealed some enzymes potentially involved in terpene synthesis. Results obtained from this pioneering study on the species show that NGS technology can be a very efficient tool for transcriptome sequencing and they will serve as reference for preparation of other more specific libraries. New sequencings should contribute to a better coverage of this transcriptome, allowing discovery of even rare transcripts.

Abstract Disturbance may shift microbial communities from one state to another. However, species differ in their ecological characteristics and their abilities to withstand disturbance. No single species or individuals of a species exist alone, but they are parts of complex interaction networks including species above- and belowground. In boreal and subarctic forests, almost all plants and a high number of fungi form mycorrhizas at the plant roots. In mycorrhiza, the fungal partner harvests nutrients for the host plant and, in return, gains carbon from the plant. In general, these common associations benefit both partners, but as heterotrophs, fungi are dependent on carbon photosynthesized by plants, whereas plants can survive alone as autotrophs. In addition to mycorrhizal fungi, also other fungi, such as endophytes, saprotrophs and pathogens, live in and on plant roots. This thesis concerns the impacts of disturbance on fungi living in plant roots and in soil near the roots. I hypothesized that i) root-associated fungal (RAF) and soil fungal communities and colonization types change after disturbance, that ii) the observed shifts relate to disturbance intensity and that iii) they co-occur with changes in soil conditions and vegetation. Changes in RAF were studied as changes in root fungal colonization, or in fungal community composition. The latter were detected with next-generation sequencing methods. The responses of RAF to disturbance seemed to be context dependent and related to sources of fungal communities (e.g. soil, RAF networks), environmental conditions (e.g. soil pH and nutrients) and host performance. It seems that abundances of those RAF species, which are present in the roots first (priority effect), may be increased by disturbance. Research produced new information related to ecological roles of the genera Phialocephala and Meliniomyces. Altogether, the results indicate connections between both abiotic and biotic environments and RAF, and host species viability and RAF. / Tiivistelmä Häiriöt voivat siirtää eliöyhteisön tilasta toiseen. Lajien ominaisuudet ja häiriönsietokyvyt eroavat toisistaan. Mikään laji tai yksilö ei elä yksin, vaan lajit ovat osa maan ylä- ja alapuolelle ulottuvia monimutkaisia vuorovaikutusverkostoja. Boreaalisissa ja subarktisissa metsissä lähes kaikki kasvit ja useat sienet muodostavat sienijuuren eli mykorritsan. Mykorritsassa sieniosakas hankkii isäntäkasville ravinteita ja saa vastavuoroisesti kasvilta hiiltä. Tavallisesti nämä vuorovaikutussuhteet hyödyttävät molempia sienijuuren osakkaita, mutta toisenvaraisina (heterotrofeina) sienet ovat riippuvaisia kasvien yhteyttämästä hiilestä, kun taas tuottajina (autotrofeina) kasvit voivat elää itsenäisesti. Mykorritsasienten lisäksi kasvien juurissa elää yleisesti myös muita sieniä kuten endofyyttejä, saprotrofeja ja patogeeneja. Tämä väitöskirja käsittelee häiriön vaikutuksia sieniin, jotka elävät kasvien juurissa ja juuria ympäröivässä maassa. Hypoteesieni mukaan i) juurissa ja maassa elävien sienten yhteisöt ja kolonisaatiotyypit muuttuvat häiriön jälkeen, ii) muutokset liittyvät häiriön voimakkuuteen ja iii) muutokset tapahtuvat samanaikaisesti maan olosuhteiden ja kasvillisuuden muutoksien kanssa. Juurissa elävien sienten esiintymisen muutokset tutkittiin sienten kolonisaation tai yhteisörakenteen muutoksina. Sieniyhteisöt selvitettiin NGS-menetelmien avulla. Juurissa elävien sienten vasteet häiriöön vaikuttavat olevan tilannesidonnaisia ja liittyvän sienilajien lähteisiin (esim. maa, juurisieniverkostot), ympäristömuuttujiin (esim. maan pH, ravinteet) ja isäntäkasvin menestymiseen. Häiriö voi vahvistaa juurissa ensimmäisenä läsnä olevien sienilajien menestymistä (prioriteettivaikutus). Uutta tietoa tuotettiin Phialocephala ja Meliniomyces –sienisukujen ekologiasta, jota tunnetaan huonosti. Kaiken kaikkiaan, tulokset osoittavat yhteydet sekä elottoman ja elollisen ympäristön ja juurten sieniyhteisön että isäntäkasvin elinkyvyn ja juurten sieniyhteisön välillä.

Chapter 2 The sea surface microlayer is a biogenic thin layer, comprising less than one millimeter of the ocean surface. This surface layer has gained much attention due to its dampening effect on ocean capillary ripples. The chemistry of the air-sea interface has been studied for decades; however, the structure and function of the marine bacterial community within the sea surface microlayer are still understudied. Although various sea surface microlayer sampling techniques were developed over the past decades, aseptic bacterial sampling in the open ocean is a rather challenging task. In this study, a new approach is presented. It is designed for bacterial sampling of the sea surface microlayer, which intends to reduce sampling contamination from the vessel, subsurface water and the investigators. A 47mm polycarbonate membrane was utilized at each sampling site. In addition, the metagenomic approach using the new generation 454 high-throughput DNA sequencing system was employed to compensate for the small sample size. Two sample sets were collected in summer 2010 and fall 2011 from the sea surface microlayer and underlying water (20 cm deep). A contamination assessment was carried out to determine that contamination might have been caused during the use of the sampling techniques. A total of 14,120 bacterial 16S rRNA gene sequences with an average length of 437.8 bp were obtained. A total of 1,254 Operational Taxonomic Units (OTUs) were constructed and 268 genera were identified. The results indicated that the bacterial compositions of the sea surface microlayer samples were distinct from those of the underlying water samples. This experiment demonstrated that the new generation sequencing platform and microbial metagenomics analysis software together served as powerful tools to gain a deeper understanding of microbial communities within the sea surface microlayer. Furthermore, it is suggested that the newly employed sampling methods could be used to obtain a snapshot of bacterial community structure as well as environmental conditions. Chapter 3 Synthetic aperture radar (SAR) remote sensing captures various fine-scale features on the ocean surface such as coastal discharge, oil pollution, vessel traffic, algal blooms and sea slicks. Although numerous factors potentially affect the SAR imaging process, the influence of biogenic and anthropogenic surfactants has been suggested as one of the primary parameters, especially under relatively low wind conditions. Surfactants have a tendency to dampen the short gravity-capillary ocean waves causing the sea surface to smoothen, thus allowing the radar to detect areas of surfactants. Surfactants are found in sea slicks, which are the accumulation of organic material shaped as elongated bands on the ocean’s surface. Sea slicks are often observable with the naked eye due to their glassy appearance and can also be seen on SAR images as dark scars. While the sources of surfactants can vary, some are known to be associated with marine bacteria. Countless numbers of marine bacteria are present in the oceanic environment, and their biogeochemical contributions cannot be overlooked. Not only do marine bacteria produce surfactants, but they also play an important role in the transformation of surfactants. In this study, we profiled the surfactant-associated bacteria composition within the biogenic thin layer of the ocean surface more commonly referred as the sea surface microlayer (SML). Bacterial samples were collected from the SML for comparative analysis from both within and outside of sea slick areas as well as the respective underlying subsurface water. The bacterial microlayer sampling coincided with SAR satellite, RADARSAT-2, overpasses to demonstrate the simultaneous in-situ measurements during a satellite image capture. The SML sampling method was designed to enable aseptic bacterial sampling. A 47 mm polycarbonate membrane was utilized at each sampling site to obtain a snapshot of the bacterial community structure at a specific space and time. Also, a new generation high-throughput sequencing method was employed to compensate for the small sample size acquired. A total of 27,006 nucleotide sequences (16S rRNA genes) with an average 437.8 bp in length were analyzed. The results revealed the presence of industrially important surfactant-producing marine bacteria, Acinetobacter, Bacillus, Corynebacterium and surfactant-degrading marine bacteria, Escherichia. In addition, Pseudomonas was detected which can be either a producer, decomposer or both. Recognizing that there is still a large number of marine bacterial species that have not been taxonomically classified nor recognized as surfactant-associated species, the effects on SAR imaging due to a high number of surfactant-associated marine bacteria is expected. This study has provided the basis for the biological importance for fine-scale synthetic aperture satellite imaging. Moreover, this new approach is expected to have applications in monitoring biological and chemical properties of the sea surface across the globe.

La phyllosphère est l’habitat fourni par la partie foliaire des plantes. De nombreuses espèces microbiennes - pathogènes, saprophytes ou mutualistes des plantes - peuplent cet environnement. Ce compartiment microbien influence donc la dynamique et la structure des communautés végétales. L’objectif principal de cette thèse était d’étudier les effets potentiels du changement climatique sur la structure des assemblages fongiques de la phyllosphère des arbres forestiers, et sur la niche écologique des espèces fongiques pathogènes des arbres forestiers. Nous avons pour cela utilisé deux approches, i) l’étude de gradients altitudinaux et ii) la construction de modèles de niche bioclimatique.Les assemblages fongiques de la phyllosphère des arbres forestiers étant encore peu connus, nous avons dans un premier temps décrit leur diversité et quantifié leur variabilité spatiale à l’échelle d’une parcelle forestière.Nos résultats montrent que la phyllosphère d’un arbre forestier abrite quelques centaines d’espèces fongiques, avec quelques espèces dominantes et beaucoup d’espèces rares. Les facteurs structurant ces assemblages incluent à la fois des facteurs abiotiques et biotiques : la température apparaît comme la variable climatique la plus explicative le long d’un gradient altitudinal ; à l’échelle d’une parcelle, la proximité génétique entre arbres est plus déterminante que leur distance géographique.L’analyse des modèles de niche des champignons pathogènes forestiers à l’échelle de la France met en évidence des limitations climatiques, les pluies estivales étant une variable explicative importante.Toutefois, plusieurs espèces introduites occupent déjà la plus grande part de la distribution de leur hôte,sans limitation apparente par le climat. Les effets du changement climatique sur la plupart des pathogènes s’exerceront d’abord indirectement par des effets dépressifs très importants sur l’abondance de leurs arbres-hôtes. Seuls les pathogènes adaptés au biotope méditerranéen verraient leur impact s’accroitre. / Phyllosphere is the habitat provided by the leaves of living plants. Many microbial species -pathogens, saprophytes or mutualists of plants - inhabit this environment. These microbes therefore influence the dynamics and structure of plant communities. The main objective was to study the potential effects of climate change on the structure of phyllosphere fungal assemblages, and on the ecological niche of pathogenic fungal species of forest trees. We used two approaches, i) the study of altitudinal gradients and ii) the construction of bioclimatic niche models. Since phyllosphere fungal assemblages of forest trees are still poorly known, we first described their diversity and quantified their spatial variability at the scale of a forest stand.Our results show that the phyllosphere of a forest tree houses hundreds of fungal species, with few dominant species and many rare species. Factors structuring these assemblages include both abiotic and biotic factors: the temperature appears as the most explanatory variable along an elevation algradient. At the scale of a forest stand, the genetic proximity between trees is more important than the geographic distance. Analysis of the bioclimatic niche models of pathogenic fungi forest at the French scale highlights some climatic limitations, and the summer rainfall is an important explanatory variable. However, many introduced species already occupy the distribution of their host, without apparent climatic limitation. The effects of climate change on most pathogens will be exercised indirectly by very important depressive effects on the abundance of their host trees. Only pathogens adapted to the Mediterranean biotope would increase their impact.

Arbuscular mycorrhizal fungi (AMF) play an important role in nutrient cycling and growth of flax (Linum usitatissimum L.). However, limited information is available regarding the symbiotic association between flax and AMF in field environments. A study was conducted to survey AMF communities colonizing flax grown in Saskatchewan. Additionally, field and growth chamber studies investigated the impact of AMF inoculation on nutrient uptake and growth of flax. Eighteen commercial flax fields were surveyed to assess mycorrhizal colonization of flax and to assess the impact of agricultural practices and soil abiotic factors on AMF activity. The flax root-associated AMF communities were explored using a 454 sequencing method, together with microscopic-based measurements of root AMF colonization and soil spore density. High levels of root colonization were detected in most flax fields. Of the 222 AMF operational taxonomic units (OTUs) identified in flax roots, 181 OTUs clustered as Funneliformis-Rhizophagus, 19 as Claroideoglomus, 14 as Paraglomus, six as Diversisporales and two as Archaeospora. Results suggest that tillage influenced the composition of AMF communities colonizing flax, and reduced relative AMF abundance and species richness. Additionally, AMF community characteristics were related to soil abiotic factors such as pH, EC, available phosphorus and nitrogen. Field experiments were conducted over two years (two sites per year) using a commercial AMF inoculant applied at three rates (0, 1X, and 2X the recommended rate) with or without P fertilizer (16.8 kg ha-1). The response of flax cultivars to AMF inoculation was examined in a growth chamber experiment. In addition, 454 sequencing was employed to examine the impact of AMF inoculation on root-associated AMF communities. Under field conditions, only one site showed increased root colonization with AMF inoculation. Flax responded to AMF inoculation differently under different field conditions. At the two sites with intermediate initial soil P level, evidence of increased above-ground biomass and plant nutrient uptake with AMF inoculation was observed. However, such an effect was not detected when P fertilizer was combined with the inoculation. At a low P site and an irrigated site, P application accounted for all of the increases in plant nutrient uptake and biomass of flax, whereas no responses to AMF inoculation were detected. The 454 sequencing revealed different inoculation-induced changes in the diversity and composition of root-associated AMF communities between sites, which was possibly related to different field environments and native AMF communities. In the growth chamber, AMF inoculation resulted in general increases of plant nutrient uptake among cultivars, but only one cultivar showed enhanced biomass with inoculation. The diversity of AMF communities colonizing different flax cultivars was generally reduced by AMF inoculation. Community composition shifted under AMF inoculation, and the shifts appeared to be cultivar specific. These results suggested that benefits of AMF inoculation in flax production are limited and currently not predictable, and the degree of response is likely dependent on a myriad of soil and environmental conditions.