Thesis (M.S.)--University of Missouri-Columbia, 2007. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on May 12, 2009) Includes bibliographical references.

No description available.

O objetivo principal do presente estudo foi avaliar a diversidade bacteriana endofítica cultivável associada a plantas de Citrus sinensis (L.) Osbeck sintomáticas e assintomáticas para a doença Greening, com destaque para Methylobacterium spp. Simultaneamente, como objetivo secundário, foi realizado o estudo da comunidade bacteriana endofítica de Methylobacterium spp. presente em plantas de laranja doce com e sem sintomas da Clorose Variegada dos Citros (CVC). Assim, em período chuvoso (novembro de 2008 e fevereiro de 2009) e seco (maio de 2009) foram amostradas dez plantas sadias e dez plantas doentes (Greening e/ou CVC), em dois municípios citrícolas da região central do estado de São Paulo. A confirmação da presença e/ou ausência dos fitopatógenos Candidatus Liberibacter americanus, Ca. L. asiaticus e Ca. L africanus, agentes causadores do Greening e, também, de Xylella fastidiosa, agente causador da CVC foram realizadas para todas as amostras pela técnica PCR a partir da utilização de iniciadores específicos para os respectivos fitopatógenos. Em relação à comunidade bacteriana estudada, foi realizado o isolamento e posterior quantificação do número de unidades formadoras de colônia (UFCs) totais e de Methylobacterium, caracterizadas pela presença de coloração rósea. A análise do sequenciamento parcial da região do gene 16S DNAr e agrupamentos filogenéticos dos isolados amostrados foram as metodologias adotadas para a geração dos resultados. Os resultados revelaram que a quantidade de Methylobacterium spp. isoladas em plantas sintomáticas para as doenças Greening e CVC foi expressivamente superior em relação as plantas sadias, destacando-se as espécies M. fujisawaense e M. radiotolerans, que foram os filotipos mais encontrados nas referidas amostras. As amostras vegetais coletadas em período seco, também, apresentaram maior presença da comunidade metilotrófica. A observação dos resultados da comunidade endofítica cultivável total associada a plantas sintomáticas e assintomáticas para Greening, mostrou que não houve diferenças relevantes quanto as UFCs encontradas nas plantas doentes e sadias. Foram encontradas as classes: Actinobacteria, Alfaproteobacteria, Betaproteobacteria, Gamaproteobacteria e Firmicutes e os gêneros mais frequentes foram Brevundimonas, Alcaligenes e Pantoea. Em relação às características adaptativas de Methylobacterium spp. quanto a situações de estresses, foram verificadas in vitro a produção da enzima ácido aminociclopropano-1-carboxilato deaminase (ACCd) e tolerância aos metais pesados cádmio e chumbo. Dos 62 isolados avaliados, 63% foram capazes de utilizar a molécula de 1-aminociclopropano-1-carboxilato (ACC) como fonte de nitrogênio para seu desenvolvimento. Os testes para tolerância ao metais pesados revelaram que apenas 3 isolados foram capazes de crescer em meio CHOI suplementado com sulfato de cádmio nas concentrações de 2,5 e 5,0 mM. Somente dois isolados se mostraram tolerantes ao chumbo, presente no meio CHOI suplementado com nitrato de chumbo nas concentrações 2,5 mM. Já em 5 mM, apenas um isolado foi capaz de se desenvolver. Os resultados, apresentados mostram a importância de Methylobacterium spp., sobre a comunidade endofítica cultivável de citros em dois diferentes patossistema avaliados, uma vez que em ambos foi observada uma maior quantidade de isolados do gênero em plantas doentes, sugerido uma associação com os respectivos fitopatógenos. A produção de ACCd por Methylobacterium está relacionada entre outros fatores, a interrupção da rota de síntese do etileno, composto relacionado ao estresse vegetal. Assim, a grande quantidade de Methylobacterium em plantas doentes e a produção de ACCd pelas mesmas, possivelmente, estão relacionadas ao favorecimento do patógeno mediante a redução da capacidade de resposta da planta / The aiming of this study was the evaluation of the diversity of endophytic culturable bacterial community associated with Huanglongbing (HLB) symptomatic and no-symptomatic Citrus sinensis (L.) Osbeck plants, highlighting the Methylobacterium spp. Simultaneously, it was evaluated the endophytic Methylobacterium community in sweetie orange with and without Citrus Variegated Chlorosis (CVC) symptoms. Thus, it was sampled ten healthy and no-health plants with HLB and CVC symptoms in raining (November 2008 and February are 2009) and dryed (may 2009) seasons in two provinces at São Paulo State. The presence or absence of the plant-pathogens Candidatus Liberibacter americanus, Ca. L. asiaticus e Ca. L africanus, HLB agents and Xylella fastidiosa, CVC agent, was confirmed using specific primer by PCR for all plant samples. The bacterial communities was accessed by isolation and posteriori quantification of colony forming unit (CFU) to total and Methylobacterium group that was identified according its pink coloration. To the identification and phylogenetic clusterization of the isolates was partially sequenced the 16S DNAr gene. The results showed a higher amount of isolated Methylobacterium spp. from symptomatic plants to HLB and CVC than healthy plant. M. fujisawaense and M. radiotolerans were present in these samples. The plants sampled in dryed season showed a high amount of methilotrific isolates. It was not observed a significant difference of the amount of total bacteria isolated from HLB symptomatic and no-symptomatic plants The identified classes was: Actinobacteria, Alfaproteobacteria, Betaproteobacteria, Gamaproteobacteria and Firmicutes. Brevundimonas, Alcaligenes and Pantoea were the most frequent genera. It was verified the acid aminocyclopropane-1-carboxylate deaminase (ACCd) production and the lead and cadmium tolerance as the adaptative characteristic of Methylobacterium to stress conditions. 63% of the 62 evaluated isolates were able to use the aminocyclopropane-1-carboxylate (ACC) as nitrogen source. Just 3 isolates were able to grow in supplemented CHOI media at 2.5 e 5.0 mM of sulphate of cadmium. Two isolates showed lead tolerance in the same media supplemented with nitrate of lead at 2.5 mM and just one at 5.0mM.The results showed the importance of Methylobacterium spp. to citrus culturable endophytic community in two pathossystem. In both the amount of methylotrofic isolates was higher in symptomatic plants, suggesting its association with the plant-pathogens. The Methylobacterium ACCd production has a relationship with the breaking of ethylen route. This compound is associated with vegetal stress. For this reason the high amount of Methylobacterium from symptomatic plants and the ACCd production probably is correlated with the disease development under the reduction of plant response capacity

Le chlorométhane est le plus abondant des composés organo-halogénés dans l’atmosphère et il est impliqué dans la destruction de l’ozone dans la stratosphère. Les sources et les puits de chlorométhane restent mal évalués. Bien que synthétisé et utilisé de manière industrielle, il est principalement produit naturellement, avec comme sources majeures les émissions provenant des végétaux et plus particulièrement de la phyllosphère, qui correspond aux parties aériennes des plantes. Certaines bactéries épiphytes de la phyllosphère sont des méthylotrophes capables d’utiliser des composés organiques sans liaison carbone-carbone comme le méthanol et le chlorométhane comme unique source de carbone et d’énergie pour leur croissance. La plupart des bactéries chlorométhane-dégradantes isolées jusqu’à présent utilisent une voie métabolique pour leur croissance sur chlorométhane appelée voie cmu (pour chloromethane utilisation), caractérisée par l’équipe. L’objectif principal de cette thèse a été de déterminer si des bactéries de la phyllosphère peuvent jouer le rôle de filtre pour l’émission de chlorométhane par les plantes. Dans ce but, un modèle de laboratoire a été mis en place, constitué de la plante Arabidopsis thaliana connue pour produire du chlorométhane par une réaction impliquant le gène HOL1, et la bactérie Methylobacterium extorquens CM4, souche de référence pour l’étude du métabolisme de dégradation du chlorométhane, qui possède la voie cmu et dont le génome complet a été séquencé et analysé. Des variants d’A. thaliana avec différents niveaux d’expression du gène HOL1 (le type sauvage, le mutant homozygote « knock-out » hol1 et un variant HOL1-OX avec surexpression) ont été sélectionnés par PCR et qPCR. Des souches bactériennes chlorométhane-dégradantes ont été isolées à partir de la phyllosphère d’A. thaliana, dont il a été montré qu’elles possèdent la voie cmu. Un bio-rapporteur bactérien pour le chlorométhane a été construit à l’aide d’un plasmide exploitant la région promotrice du gène conservé de la déshalogénase (cmuA) de la souche M. extorquens CM4. Il présente une réponse fluorescente rapide, sensible, et spécifique aux méthyl-halogénés de manière concentration-dépendante. L’application du bio-rapporteur aux trois variants d’A. thaliana étudiés suggère des niveaux d’émissions de chlorométhane différents. L’analyse, par qPCR et qRT-PCR, de l’ADN métagénomique extrait de la surface des feuilles a montré une corrélation entre la proportion relative de bactéries portant le gène cmuA et l’exprimant dans cet environnement, et l’expression du gène HOL1. Ces résultats indiquent qu’une production de chlorométhane, même très modeste par rapport aux fortes émissions de méthanol par A. thaliana, confère un avantage sélectif pour les bactéries épiphytes chlorométhane-dégradantes. Ces dernières pourraient ainsi bien jouer un rôle de filtre pour les émissions de chlorométhane de la phyllosphère vers l’atmosphère. En perspective, de nouvelles expériences complémentaires, basées sur l’analyse par génomique comparative des souches chlorométhane-dégradantes également effectuée dans le cadre du projet et sur une analyse par séquençage à haut-débit initiée dans ce travail, sont proposées pour améliorer la compréhension des mécanismes d’adaptation des bactéries chlorométhane-dégradantes dans la phyllosphère. / Chloromethane is the most abundant halocarbon in the environment, and responsible for substantial ozone destruction in the stratosphere. Sources and sinks of chloromethane are still poorly constrained. Although synthesized and used industrially, chloromethane is mainly produced naturally, with major emissions from vegetation and especially the phyllosphere, i.e. the aerial parts of plants. Some phyllosphere epiphytes are methylotrophic bacteria which can use single carbon compounds such as methanol and chloromethane as the sole source of carbon and energy for growth. Most chloromethane-degrading strains isolated so far utilize the cmu pathway for growth with chloromethane which was characterized by the team. The main objective of this work was to investigate whether epiphytes may act as filters for plant emissions of chloromethane, by using a laboratory bipartite system consisting of the model plant Arabidopsis thaliana, known to produce chloromethane mainly by way of the HOL1 gene, and the reference chloromethane-degrading bacterial strain Methylobacterium extorquens CM4, possessing the cmu pathway and of known genome sequence. Three A. thaliana Col-0 variants with different levels of expression of HOL1, i.e. the wild-type strain, its homozygous HOL1 knockout mutant hol1 and an HOL1-OX HOL1 overexpressor, were selected using PCR and qRT-PCR. Chloromethane-degrading strains were isolated from the A. thaliana phyllosphere, and shown to contain the cmu pathway. A plasmid-based bacterial bioreporter for chloromethane was constructed which exploits the promoter region of the conserved chloromethane dehalogenase gene cmuA of strain CM4. It yields rapid, highly sensitive, specific and methyl halide concentration-dependent fluorescence. Application of the bioreporter to the three A. thaliana variants differing in expression of HOL1 investigated in this work suggested that they indeed synthesize different levels of chloromethane. Analysis by qPCR and qRT-PCR of metagenomic DNA from the leaf surface of these variants showed that the relative proportion and expression of cmuA in this environment paralleled HOL1 gene expression. Taken together, the results obtained indicate that even minor amounts of chloromethane produced by A. thaliana in the face of large emissions of methanol may provide a selective advantage for chloromethane-degrading methylotrophic bacteria in the phyllosphere environment. This suggests that chloromethane-degrading epiphytes may indeed act as filters for emissions of chloromethane from plants. Further experiments are envisaged to further assess the adaptation mechanisms of chloromethane-degrading bacteria in the phyllosphere, building upon the comparative genomic analysis of chloromethane-degrading strains which was also performed in this work, and on the preliminary investigations using high-throughput sequencing that were initiated.

O objetivo principal do presente estudo foi avaliar a diversidade bacteriana endofítica cultivável associada a plantas de Citrus sinensis (L.) Osbeck sintomáticas e assintomáticas para a doença Greening, com destaque para Methylobacterium spp. Simultaneamente, como objetivo secundário, foi realizado o estudo da comunidade bacteriana endofítica de Methylobacterium spp. presente em plantas de laranja doce com e sem sintomas da Clorose Variegada dos Citros (CVC). Assim, em período chuvoso (novembro de 2008 e fevereiro de 2009) e seco (maio de 2009) foram amostradas dez plantas sadias e dez plantas doentes (Greening e/ou CVC), em dois municípios citrícolas da região central do estado de São Paulo. A confirmação da presença e/ou ausência dos fitopatógenos Candidatus Liberibacter americanus, Ca. L. asiaticus e Ca. L africanus, agentes causadores do Greening e, também, de Xylella fastidiosa, agente causador da CVC foram realizadas para todas as amostras pela técnica PCR a partir da utilização de iniciadores específicos para os respectivos fitopatógenos. Em relação à comunidade bacteriana estudada, foi realizado o isolamento e posterior quantificação do número de unidades formadoras de colônia (UFCs) totais e de Methylobacterium, caracterizadas pela presença de coloração rósea. A análise do sequenciamento parcial da região do gene 16S DNAr e agrupamentos filogenéticos dos isolados amostrados foram as metodologias adotadas para a geração dos resultados. Os resultados revelaram que a quantidade de Methylobacterium spp. isoladas em plantas sintomáticas para as doenças Greening e CVC foi expressivamente superior em relação as plantas sadias, destacando-se as espécies M. fujisawaense e M. radiotolerans, que foram os filotipos mais encontrados nas referidas amostras. As amostras vegetais coletadas em período seco, também, apresentaram maior presença da comunidade metilotrófica. A observação dos resultados da comunidade endofítica cultivável total associada a plantas sintomáticas e assintomáticas para Greening, mostrou que não houve diferenças relevantes quanto as UFCs encontradas nas plantas doentes e sadias. Foram encontradas as classes: Actinobacteria, Alfaproteobacteria, Betaproteobacteria, Gamaproteobacteria e Firmicutes e os gêneros mais frequentes foram Brevundimonas, Alcaligenes e Pantoea. Em relação às características adaptativas de Methylobacterium spp. quanto a situações de estresses, foram verificadas in vitro a produção da enzima ácido aminociclopropano-1-carboxilato deaminase (ACCd) e tolerância aos metais pesados cádmio e chumbo. Dos 62 isolados avaliados, 63% foram capazes de utilizar a molécula de 1-aminociclopropano-1-carboxilato (ACC) como fonte de nitrogênio para seu desenvolvimento. Os testes para tolerância ao metais pesados revelaram que apenas 3 isolados foram capazes de crescer em meio CHOI suplementado com sulfato de cádmio nas concentrações de 2,5 e 5,0 mM. Somente dois isolados se mostraram tolerantes ao chumbo, presente no meio CHOI suplementado com nitrato de chumbo nas concentrações 2,5 mM. Já em 5 mM, apenas um isolado foi capaz de se desenvolver. Os resultados, apresentados mostram a importância de Methylobacterium spp., sobre a comunidade endofítica cultivável de citros em dois diferentes patossistema avaliados, uma vez que em ambos foi observada uma maior quantidade de isolados do gênero em plantas doentes, sugerido uma associação com os respectivos fitopatógenos. A produção de ACCd por Methylobacterium está relacionada entre outros fatores, a interrupção da rota de síntese do etileno, composto relacionado ao estresse vegetal. Assim, a grande quantidade de Methylobacterium em plantas doentes e a produção de ACCd pelas mesmas, possivelmente, estão relacionadas ao favorecimento do patógeno mediante a redução da capacidade de resposta da planta / The aiming of this study was the evaluation of the diversity of endophytic culturable bacterial community associated with Huanglongbing (HLB) symptomatic and no-symptomatic Citrus sinensis (L.) Osbeck plants, highlighting the Methylobacterium spp. Simultaneously, it was evaluated the endophytic Methylobacterium community in sweetie orange with and without Citrus Variegated Chlorosis (CVC) symptoms. Thus, it was sampled ten healthy and no-health plants with HLB and CVC symptoms in raining (November 2008 and February are 2009) and dryed (may 2009) seasons in two provinces at São Paulo State. The presence or absence of the plant-pathogens Candidatus Liberibacter americanus, Ca. L. asiaticus e Ca. L africanus, HLB agents and Xylella fastidiosa, CVC agent, was confirmed using specific primer by PCR for all plant samples. The bacterial communities was accessed by isolation and posteriori quantification of colony forming unit (CFU) to total and Methylobacterium group that was identified according its pink coloration. To the identification and phylogenetic clusterization of the isolates was partially sequenced the 16S DNAr gene. The results showed a higher amount of isolated Methylobacterium spp. from symptomatic plants to HLB and CVC than healthy plant. M. fujisawaense and M. radiotolerans were present in these samples. The plants sampled in dryed season showed a high amount of methilotrific isolates. It was not observed a significant difference of the amount of total bacteria isolated from HLB symptomatic and no-symptomatic plants The identified classes was: Actinobacteria, Alfaproteobacteria, Betaproteobacteria, Gamaproteobacteria and Firmicutes. Brevundimonas, Alcaligenes and Pantoea were the most frequent genera. It was verified the acid aminocyclopropane-1-carboxylate deaminase (ACCd) production and the lead and cadmium tolerance as the adaptative characteristic of Methylobacterium to stress conditions. 63% of the 62 evaluated isolates were able to use the aminocyclopropane-1-carboxylate (ACC) as nitrogen source. Just 3 isolates were able to grow in supplemented CHOI media at 2.5 e 5.0 mM of sulphate of cadmium. Two isolates showed lead tolerance in the same media supplemented with nitrate of lead at 2.5 mM and just one at 5.0mM.The results showed the importance of Methylobacterium spp. to citrus culturable endophytic community in two pathossystem. In both the amount of methylotrofic isolates was higher in symptomatic plants, suggesting its association with the plant-pathogens. The Methylobacterium ACCd production has a relationship with the breaking of ethylen route. This compound is associated with vegetal stress. For this reason the high amount of Methylobacterium from symptomatic plants and the ACCd production probably is correlated with the disease development under the reduction of plant response capacity

Abstract To date, plant endophytic bacteria have mainly been studied in roots of crop plants. However, shoot-associated endophytes are less diverse than root-associated ones. Hence, endophytic bacteria of plant shoots evolved different traits, than root colonizers, especially with types of host tissues infected and patterns of growth and development. This study found Methylobacterium extorquens colonized pine seedlings similarly to stem-colonizing rhizobia of other plants. M. extorquens DSM13060 was isolated from meristematic cells in shoot tip cultures of Scots pine (Pinus sylvestris L.). M. extorquens infected the plant stem through epidermis or stomatal apertures, forming infection pockets in the root and stem epidermis, or cortex. Post-infection, thread-like infection structures passed through the endoderm, invading vascular tissues. This led to systemic colonization of above and below ground-parts, observed in in vitro grown Scots pine. A novel mechanism enabling development of endophyte-host symbiosis is discovered within the M. extorquens – Scots pine model. This mechanism involves ability of M. extorquens to produce polyhydroxybutyrates (PHB) to protect itself from host-induced oxidative stress during infection. Upon initial colonization on the host surface, M. extorquens DSM13060 consumes methanol as a carbon source, using it to biosynthesize PHB. PHB are then degraded, upon host infection, by PHB depolymerases (PhaZ) to yield methyl-esterified 3-hydroxybutyrate oligomers. These oligomers have substantial antioxidant activity towards host-induced oxidative stress, enabling the bacterium to bypass host defenses and colonize further tissues. The bacteria can also store PHBs for future protection. The capacity for PHB production and, thus, protection from oxidative stress, is discovered in a wide taxonomic range of bacteria. This study also shows meristematic endophytes are important in growth and development of their hosts. Unlike many bacterial root endophytes, M. extorquens DSM13060 does not induce plant growth through hormones. However, this bacterium can colonize the interior of living host cells, where it aggregates around the nucleus of the host plant. M. extorquens DSM13060 genome encodes nucleomodulins, eukaryotic-like transcription factors, which may intervene in host transcription and metabolism. / Tiivistelmä Kasvin sisällä elävien endofyyttisten bakteerien tutkimus on perinteisesti keskittynyt viljelykasveihin ja niiden juuristoon. Kasvien maanpäällisissä versoissa elävät endofyytit eroavat merkittävästi juuriston bakteereista lajirikkauden suhteen. Versoissa eläville bakteereille on todennäköisesti kehittynyt erilaisia sopeumia kuin juuriston endofyyttilajeille. Endofyyttinen Methylobacterium extorquens DSM13060 elää männyn silmujen kasvusolukossa lisäten isäntäkasvin kasvua. Tässä tutkimuksessa M. extorquens –bakteerin todettiin siirtyvän männyn taimiin samoja mekanismeja käyttäen kuin Rhizobium –suvun typensitojabakteerit. Metylobakteeri tunkeutui isäntäkasviin aktiivisesti soluseinien läpi tai varren ilmarakojen kautta muodostaen mikropesäkkeitä juuren ja varren pinnoille, sekä infektiotaskuja kuorisolukkoon. Bakteeri eteni infektiolankojen avulla endodermin ohi johtosolukoihin, mikä mahdollisti bakteerin siirtymisen muualle taimeen. M. extorquens käytti kasvin pinnalla runsaana olevaa metanolia hiilenlähteenään, varastoiden sen solujen sisäiseksi polyhydroksibutyraatti (PHB) polymeeriksi. Infektion myöhemmissä vaiheissa bakteeri hajotti varastoidun polymeerin PHB-depolymeraasientsyymien (PhaZ) avulla lyhyiksi rasvahappoketjuiksi. Nämä metyloidut 3-hydroksibutyraatin oligomeerit suojasivat bakteeria isäntäkasvin puolustuksen tuottamilta happiradikaaleilta mahdollistaen infektion etenemisen. Tutkimuksessa saatujen tulosten perusteella endofyytin solunsisäinen energiavarasto, PHB, toimii pelkistävänä varastona ympäristön hapettavaa stressiä vastaan. Löytö osoitti uudenlaisen antioksidatiivisen puolustumekanismin, joka on levinnyt laajalle bakteerikunnassa ja liittyy yleisesti bakteerien kykyyn sietää vaikeita olosuhteita. Toisin kuin useat juurissa elävät bakteeriendofyytit, M. extorquens ei lisää isäntäkasvin kasvua tuottamalla kasvihormoneja. Bakteeri kykenee elämään männyn elävien solujen sisällä tumien läheisyydessä. M. extorquens DSM13060 genomi sisältääkin useita geenejä, jotka koodaavat nukleomoduliineja, eukaryoottisolujen säätylytekijöiden kaltaisia entsyymejä, joiden avulla bakteeri todennäköisesti vaikuttaa isäntäkasvin aineenvaihduntaan. Vastaavaa vaikutusmekanismia ei ole aikaisemmin kuvattu endofyyteillä. Tutkimus korostaa aiemmin tuntemattomien meristemaattisten bakteeriendofyyttien merkitystä isäntäkasvin kasvussa ja erilaistumisessa.

Muitos fatores, como variações sazonais, tipos de tecido vegetal, cultivares e espécies de hospedeiro, tipo de solo, interação com microrganismos benéficos ou patógenos entre outros, afetam a estrutura e a composição da comunidade bacteriana das plantas. A introdução de plantas geneticamente modificadas (PGM) foi somada ao conjunto desses fatores, podendo acarretar efeitos diretos e indiretos sobre a comunidade bacteriana. Cana-de-açúcar é uma cultura de grande importância no Brasil; a área de cultivo está em expansão devido aos incentivos para a produção de álcool. Uma bactéria potencialmente importante para a cultura de cana-de-açúcar é a Methylobacterium, um importante endófito de diversas culturas de interesse econômico e que, em cana-de-açúcar, pode melhorar a germinação de sementes, promover um aumento do peso da planta e da área foliar, além do número de internódios. Dessa forma, o trabalho teve como objetivos: i) avaliar os efeitos da canade- açúcar transgênica resistente a insetos e a herbicida sobre a comunidade bacteriana associada; ii) avaliar se o suposto efeito causado pela cana-de-açúcar transgênica resistente a herbicida deriva diretamente do transgene ou dos tratos culturais diferenciados aos quais a planta transgênica é submetida; iii) avaliar a interação entre Methylobacterium spp. e cana-de-açúcar. Analisando a densidade bacteriana das plantas de cana-de-açúcar convencionais e transgênicas não foi possível constatar diferenças relacionadas à introdução dessas plantas. Analisando somente quanto ao manejo de ambos os experimentos, foi possível observar que diferenças em trato cultural ou manejo de plantas, decorrentes ou não da transgenia, podem influenciar a comunidade bacteriana. Por meio de ARDRA, foi possível observar distribuição diferenciada dos ribotipos com a introdução das PGMs. No experimento realizado somente com plantas transgênicas para resistência a Imazapyr, foi possível notar que, em 17 meses, a presença da planta transgênica e a aplicação do herbicida Imazapyr podem ter resultado na redução da densidade bacteriana associada à rizosfera de cana-de-açúcar. Por meio de DGGE, foi visto que o estado fisiológico da planta foi a maior fonte de variação. Novamente por meio de ARDRA, foram observados ribotipos cuja presença foi afetada pelo cultivo da planta transgênica. Esses ribotipos diferentemente distribuídos poderiam resultar em alterações na atividade bacteriana dessas plantas, uma vez que esses ribotipos podem representar grupos funcionais importantes. A colonização de Methylobacterium spp. em cana-de-açúcar foi analisada por meio de microscopia eletrônica de varredura, reisolamento e microscopia óptica de fluorescência. Foi visto que as linhagens utilizadas colonizam cana-de-açúcar, sendo que os pontos de maior colonização são os flanges cuticulares e as regiões pilosas da raiz. Outros estudos são necessários para o melhor aproveitamento dessa bactéria na cultura de cana-de-açúcar. / Many factors, such as seasonal variations, kinds of vegetal tissue, cultivares and host species, kind of soil, interaction with beneficial or pathogen microorganisms, among others, affect the structure and composition of plants bacterial community. The introduction of genetically modified plants (GMP) was added to the set of these factors, making it possible to cause direct and indirect effects on the bacterial community. Sugarcane is a very important crop in Brazil; the cultivation area is expanding due to incentives to alcohol production. A potentially important bacterium for sugar cane cultivation is the Methylobacterium, which is an important endophyte for several cultures of economic interest and which can improve seed germination in sugar cane, promote an increase of plant weight and foliar area, and also the internodes. Thus, the work had as objectives: i) to assess the effects of transgenic sugarcane resistant to insects and herbicide on the associated bacterial community; ii) to assess if the presumed effect caused by transgenic sugarcane resistant to herbicides derives directly from the transgene or differentiated cultural handlings to which the genetically modified plant is undertaken; iii) to assess the interaction between Methylobacterium ssp. and sugarcane. Analyzing the bacterial density of conventional and transgenic sugarcane plants it was not possible to see differences related to the introduction of these plants. Analyzing only in relation to the handling of both experiments, it was possible to see that differences in cultural wielding or handling of plants derived or not from transgenia can influence the bacterial community. By means of ARDRA, it was possible to see a differentiated distribution of ribotypes with the introduction of GMPs. In the experiment made only with transgenic plants for Imazapyr resistance, it was possible to see that in 17 months, the presence of the transgenic plant and the application of Imazapyr herbicide can bring result regarding the bacterial density reduction associated to sugarcane rizosphere. By means of DGGE, it was seen that the physiological status of the plant was the greatest variation source. Again, by means of ARDRA, ribotypes whose presence was affected by transgenic plant cultivation were observed. If distributed differently, these ribotypes can represent important functional groups. The Methylobacterium ssp. Colonization in sugarcane was analyzed and by means of scanning electronic microscopy, re-isolation, and fluorescence optical microscopy. It was observed that the utilized lineages colonize sugarcane being cuticle flange and perilous regions of root the highest colonization points. Other studies are needed to a better good use of this bacterium in sugarcane culture.

La symbiose Methylobacterium nodulans / Crotalaria podocarpa est une symbiose originale. En effet, la méthylotrophie, propriété remarquable de la bactérie, s'exprime à l'apex du nodule et modifie localement le métabolisme : une dégradation apicale marquée des tissus est observée suite à une digestion des parois végétales, libérant du méthanol directement utilisable par la bactérie. Grâce à ce métabolisme, le bactéroïde -de taille et de forme inhabituellement grandes- fournirait l'énergie nécessaire à l'activité de la nitrogénase, et permettrait à la plante d'accumuler des réserves carbonées sous forme d'amyloplastes dans les cellules infectées. Cette propriété méthylotrophique bactérienne apporte également à la plante-hôte un gain de biomasse (>40 % par rapport aux mutants non méthylotrophes). En revanche, à l'échelle de l'espèce, la crotalaire n'est pas avantagée, en termes de fixation d'azote, à s'associer avec M. nodulans ou avec Bradyrhizobium sp., autre genre bactérien décrit en symbiose avec ces plantes. L'originalité de cette association symbiotique se situe également au niveau du dialogue moléculaire : les gènes nod de M. nodulans sont insensibles aux isoflavones, flavonoïdes inducteurs des Bradyrhizobium, mais sont induits par les flavanones et les flavones. L'analyse phylogénétique des gènes nod révèle que M. nodulans forme une branche particulière avec Methylobacterium sp. 4-46 et Burkholderia tuberum STM678, isolées de nodules de Légumineuses appartenant à la tribu des Crotalariae. Au niveau du signal bactérien, une structure unique de facteur Nod a été caractérisée chez M. nodulans ORS2060T : MnV(C18:1, S). Enfin, si la symbiose fonctionnelle M. nodulans/ Crotalaria a été identifiée seulement chez trois espèces de ce genre, la capacité du partenaire bactérien à former des pseudonodules avec d'autres Crotalaria laisse entrevoir un rôle clé de plusieurs composés pendant le processus d'infection suggérant différents mécanismes moléculaires impliqués dans la spécificité d'hôte.

A long-standing question in evolutionary biology is whether adaptation will typically proceed through a few mutations with large selective effects or many mutations with small effects. Many studies have implicated few loci of major effect, but it has been predicted that small-effect mutations should exist and contribute to adaptation. However, such mutations have not been found in many studies, either because they do not exist or because the experimental design limited their detection. To determine the effects and types of mutations contributing to adaptation, I studied laboratory and wild populations of bacteria. I characterized the distribution of the effect sizes in laboratory populations of an aerobic bacterium, Methylobacterium extorquens, and studied the types of genetic changes associated with adaptation to a novel host in wild populations of Mycoplasma gallisepticum.

Orientador: Anita Jocelyne Marsaioli / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-13T13:06:45Z (GMT). No. of bitstreams: 1 Pomini_ArmandoMateus_D.pdf: 4501241 bytes, checksum: 249f7514962993874b22ddcad9831cc8 (MD5) Previous issue date: 2009 / As bactérias Gram-positivas e Gram-negativas possuem um mecanismo de comunicação química intra-específico conhecido como ¿quorum-sensing¿, regulando a expressão de uma vasta gama de atividades biológicas. As bactérias Gram-negativas utilizam acil-homosserina lactonas (acil-HSLs) como principais substâncias sinalizadoras. Na presente tese, relatamos a determinação da configuração absoluta do raro metabólito (S)-(-)-N-heptanoil-HSL produzida pela bactéria fitopatogênica Pantoea ananatis. A configuração absoluta desta substância foi determinada através da técnica de cromatografia gasosa com detecção por ionização em chama com coluna quiral, através de comparações de tempo de retenção e co-injeção com padrões sintetizados. Avaliou-se também a importância da configuração absoluta para a atividade antimicrobiana de acil-HSLs contra bactérias Gram-positivas (Bacillus subtilis, Bacillus cereus e Staphylococcus aureus). Curiosamente, o enantiômero não natural (R)-N-3-oxo-octanoil-HSL foi tão ativo quanto o produto natural (S). Estudou-se também as interações da (S)-N-3-oxo-octanoil-HSL com células de Agrobacterium tumefaciens NTL4(pZLR4) através da técnica de ressonância magnética nuclear de hidrogênio por diferença de transferência de saturação (STD-RMN), revelando que o primeiro evento de interação da substância com a célula ocorre com a região lipídica da membrana celular externa. Finalmente, realizou-se o estudo químico das substâncias sinalizadoras produzidas pela bactéria Methylobacterium mesophilicum, que ocorre simbioticamente com a bactéria Xylella fastidiosa nos vasos condutores de laranjeiras atacadas pela clorose variegada dos citros. Entre os vários resultados inéditos, reportamos a caracterização e síntese do produto natural inédito (S)-N-(2E)-dodecenoil-HSL e a primeira síntese do metabólito (S)-N-(2E, 7Z)-tetradecadienil-HSL. Outrossim, reportamos a primeira caracterização da configuração absoluta de cinco acil-HSLs naturais de cadeia longa. Realizou-se também estudos relacionados aos efeitos das acil-HSLs sintéticas contra bactérias Gram-positivas endofíticas da laranjeira. Adicionalmente, caracterizou-se a secreção de defesa do opilião Hoplobunus mexicanus. O repertório de defesa deste animal é composto por dois componentes voláteis de alta irritabilidade (2,5-dimetil-fenol e 2-metil-5-etil-fenol), além da tanatose e emissão de sons, uma característica inédita em opiliões / Gram-positive and Gram-negative bacteria use quorum sensing communication circuits to regulate a diverse array of physiological activities. In general, Gram-negative bacteria use acylated homoserine lactones (acyl-HSLs) as autoinducers, and Gram-positive bacteria use processed oligo-peptides. In the present work, we relate the absolute configuration determination of the rare metabolite (S)-(-)-N-heptanoyl-HSL produced by the phytopathogen Pantoea ananatis. The absolute configuration was determined by gas chromatography coupled to flame ionization detection with chiral column, through retention time comparison and co-injections with synthetic products. The importance of the absolute configuration for the antimicrobial activity of acyl-HSL against Gram-positive bacteria (Bacillus subtilis, Bacillus cereus and Staphylococcus aureus) was assessed. Curiously, non-natural (R)-N-3-oxo-octanoyl-HSL was as active as the natural product with (S) absolute configuration. The interaction of (S)-N-3-oxo-octanoil-HSL with Agrobacterium tumefaciens NTL4(pZLR4) cells was further studied using hydrogen nuclear magnetic resonance experiments with saturation transfer difference (STD-NMR) revealing that the first binding event is the diffusion through the lipidic part of the outer membrane. Finally, we have investigated the chemical study of the signaling substances produced by Methylobacterium mesophilicum, which co-occurs with Xylella fastidiosa in orange trees affected by the citrus variegated chlorosis disease. Among several results, we report herein the characterization and synthesis of a new natural product [(S)-N-(2E)-dodecenoyl-HSL], the first synthetic procedure for the rare (S)-N-(2E,7Z)-tetradecadienyl-HSL and the occurrence of a rare long, odd chain representative (N-tridecanoyl-HSL) in trace amounts. We report the first absolute configuration determination for five natural acyl-HSLs. We have also studied the effects of synthetic acyl-HSLs on Gram positive bacteria isolated from orange tissues. Additionally, the defensive secretion produced by the harvestman Hoplobunus mexicanus was characterized. The defensive repertory of this arachnid includes two irritating and volatile components (2,5-dimethyl-phenol and 2-methyl-5-ethyl-phenol), besides thanatosis and sound emission, a new behavioral artifice in opilionids / Doutorado / Quimica Organica / Doutor em Ciências