A cana-de-açúcar é uma das principais culturas do Brasil e nos últimos anos está recebendo especial atenção devido ao crescente aumento da área cultivada e produção de etanol para uso como biocombustível. Considerando-se sua importância econômica e a possibilidade do uso de plantas geneticamente modificadas, essa cultura tem se tornado foco de pesquisas relacionadas à produtividade e sustentabilidade. Neste contexto, o estudo de comunidades microbianas associadas à cana-de-açúcar é de fundamental importância, pois além dessas comunidades desempenharem importante papel funcional na interação com a planta, os estudos realizados nas condições tropicais são limitados. Comunidades de fungos e bactérias associadas à cana-de-açúcar geneticamente modificada IMI-1 e sua isolinha convencional SP80-1842 foram sistematicamente isoladas de plantas cultivadas em área experimental em Piracicaba, SP, Brasil. Por meio de isolamento e PCR-denaturing gradient gel electrophoresis (PCR-DGGE) foi verificado que a transgenia não afeta a diversidade da comunidade fúngica associada à cana-deaçúcar. A diversidade dessas comunidades foi descrita e caracterizada molecularmente. O fungo Fusarium moniliforme apresentou alta freqüência de isolamento e também foi observado que o gene da endopoligalacturonase, pgIII, desempenha um importante papel no tipo de associação, endofítica ou patogênica, do F. moniliforme e a planta. O complexo Burkholderia cepacia constitui uma importante fração da comunidade de bactérias associada à cana-de-açúcar no Brasil e isolados deste complexo são capazes de inibir o crescimento do patógeno F. moniliforme. Análises filogenéticas indicaram que os isolados de bactérias endofíticas de Burkholderia são proximamente relacionados com linhagens-tipo do complexo B. cepacia isoladas de pacientes de fibrose cística. / In Brazil, the sugarcane is one of the most important cultivated crops. The sugarcane has received increased interest in the last years because of increase of the cultivated area and ethanol production to be used as biofuel. Considering its economical importance and the possibility of the use of the genetically modified plants; this crop has become the aim of current research for productivity and sustainability. In this context, the work on microbial communities associated with sugarcane is remarkable, because both, these communities play important functional role in the interaction with the plant, and studies performed in tropical conditions are limited as well. Fungal and bacterial communities associated with genetically modified sugarcane IMI-1 and its conventional isoline SP80-1842 were systematically isolated from plants cultivated in an experimental area in Piracicaba, SP, Brazil. The fungal communities associated with sugarcane were accessed by means of cultivation approach and PCR-denaturing gradient gel electrophoresis; the results revealed that these communities are not affected by transgeny. The microbial communities\' diversity was characterized and identified by using molecular tools. The fungus Fusarium moniliforme showed high frequency in association with the plant and it was observed that the endopolygalacturonase gene, pgIII, plays important role in order to determine the sort of association, either endophytic or pathogenic, between F. moniliforme and the host. The Burkholderia cepacia complex is an integral part of the endophytic bacterial community of sugarcane in Brazil and isolates of this complex are able to control F. moniliforme growth. Phylogenetic analyses indicated that the endophytic Burkholderia are closely related to clinical isolates of the B. cepacia complex isolated from cystic fibrosis patients.

Os micro-organismos que habitam o trato digestivo dos ruminantes têm uma profunda influência no desenvolvimento e funcionamento do animal hospedeiro. O rúmen abriga comunidades microbianas complexas dominadas por bactérias que participam de um processo eficiente de degradação dos materiais que compõem a parede celular vegetal. Por esta razão, o microbioma do rúmen representa uma fonte inexplorada de enzimas hidrolíticas com potencial aplicação na produção de combustíveis a partir da biomassa lignocelulósica. Nós usamos a plataforma Ion Torrent (PGM) para acessar o microbioma do rúmen de quatro animais da raça Santa Inês submetidos a uma dieta base. A fim de descrever a estrutura da comunidade microbiana no rúmen de ovinos e explorar o seu potencial como uma fonte de genes de degradação da biomassa, usamos a abordagem de sequenciamento do gene RNA ribossomal 16S (rRNA), utilizando Ion Tags, e a abordagem de sequenciamento metagenômico shotgun (DNA total), respectivamente. Além disso, medimos parâmetros químicos do ambiente do rúmen, relacionados a cada animal, incluindo pH, Degradabilidade da Matéria Orgânica (OMD), Produção total de Gás (GP) e Emissões de Metano (CH4), a fim de buscar correlações entre estas variáveis químicas e os grupos bacterianos. Em termos de estrutura da comunidade microbiana (bacteriana), encontramos Bacteroidetes como o filo dominante, seguido por Firmicutes, Proteobacteria e Actinobacteria. Alguns táxons foram correlacionados com os parâmetros químicos, como as famílias Corynebacteriaceae e Streptococcaceae, que foram positivamente correlacionadas com OMD; e a família Streptomycetaceae, negativamente correlacionada com GP e CH4. Algumas glicosil hidrolases conhecidas foram identificadas, como Endo-1,4-beta-glucanases, Beta-D-glicosídioglicohidrolases e outras foram designadas como putativas. Estas descobertas mostram interações ecológicas entre os grupos microbianos e funções importantes do rúmen, assim como o potencial do rúmen de ovinos para a descoberta de novas enzimas celulolíticas. / The microorganisms inhabiting the digestive tracts of ruminants have a profound influence on the host animal development and functioning. The rumen harbors complex microbial communities dominated by bacteria, which participate in an efficient process to digest plant cell wall materials. For this reason, the rumen microbiome represents an untapped source of hydrolytic enzymes with potential application for fuel production from lignocellulosic biomass. We used the Ion Torrent (PGM) platform to access the rumen microbiome of four animals of Santa Inês breed under a base diet. In order to describe the structure of the microbial community in the sheep rumen and explore its potential as a source of biomass-degrading genes, we used 16S ribosomal RNA (rRNA) Ion Tags sequencing approach and shotgun metagenomic sequencing (total DNA) approach, respectively. Furthermore, we measured rumen chemical environmental parameters related to each animal, including pH, Organic Matter Degradability (OMD), Total Gas Production (GP) and Methane emissions (CH4) in order to search for correlations between these chemical variables and bacterial groups. In terms of microbial (bacterial) community structure, we found Bacteroidetes as the dominant phylum in sheep rumen microbiome, followed by Proteobacteria, Firmicutes and Actinobacteria. Some taxa were correlated with the environmental parameters, like the Corynebacteriaceae and Streptococcaceae families, which was positively correlated with OMD, and the Streptomycetaceae family, negatively correlated with GP and CH4. Some known glycoside hydrolases were identified, such as Endo-1,4-betaglucanases, Beta-D-glucoside glucohydrolases and others were designated as putative ones. These findings show ecological interactions among microbial groups and important rumen functions, as well as the potential of the sheep rumen for the discovery of new cellulolytic enzymes.

Os micro-organismos que habitam o trato digestivo dos ruminantes têm uma profunda influência no desenvolvimento e funcionamento do animal hospedeiro. O rúmen abriga comunidades microbianas complexas dominadas por bactérias que participam de um processo eficiente de degradação dos materiais que compõem a parede celular vegetal. Por esta razão, o microbioma do rúmen representa uma fonte inexplorada de enzimas hidrolíticas com potencial aplicação na produção de combustíveis a partir da biomassa lignocelulósica. Nós usamos a plataforma Ion Torrent (PGM) para acessar o microbioma do rúmen de quatro animais da raça Santa Inês submetidos a uma dieta base. A fim de descrever a estrutura da comunidade microbiana no rúmen de ovinos e explorar o seu potencial como uma fonte de genes de degradação da biomassa, usamos a abordagem de sequenciamento do gene RNA ribossomal 16S (rRNA), utilizando Ion Tags, e a abordagem de sequenciamento metagenômico shotgun (DNA total), respectivamente. Além disso, medimos parâmetros químicos do ambiente do rúmen, relacionados a cada animal, incluindo pH, Degradabilidade da Matéria Orgânica (OMD), Produção total de Gás (GP) e Emissões de Metano (CH4), a fim de buscar correlações entre estas variáveis químicas e os grupos bacterianos. Em termos de estrutura da comunidade microbiana (bacteriana), encontramos Bacteroidetes como o filo dominante, seguido por Firmicutes, Proteobacteria e Actinobacteria. Alguns táxons foram correlacionados com os parâmetros químicos, como as famílias Corynebacteriaceae e Streptococcaceae, que foram positivamente correlacionadas com OMD; e a família Streptomycetaceae, negativamente correlacionada com GP e CH4. Algumas glicosil hidrolases conhecidas foram identificadas, como Endo-1,4-beta-glucanases, Beta-D-glicosídioglicohidrolases e outras foram designadas como putativas. Estas descobertas mostram interações ecológicas entre os grupos microbianos e funções importantes do rúmen, assim como o potencial do rúmen de ovinos para a descoberta de novas enzimas celulolíticas. / The microorganisms inhabiting the digestive tracts of ruminants have a profound influence on the host animal development and functioning. The rumen harbors complex microbial communities dominated by bacteria, which participate in an efficient process to digest plant cell wall materials. For this reason, the rumen microbiome represents an untapped source of hydrolytic enzymes with potential application for fuel production from lignocellulosic biomass. We used the Ion Torrent (PGM) platform to access the rumen microbiome of four animals of Santa Inês breed under a base diet. In order to describe the structure of the microbial community in the sheep rumen and explore its potential as a source of biomass-degrading genes, we used 16S ribosomal RNA (rRNA) Ion Tags sequencing approach and shotgun metagenomic sequencing (total DNA) approach, respectively. Furthermore, we measured rumen chemical environmental parameters related to each animal, including pH, Organic Matter Degradability (OMD), Total Gas Production (GP) and Methane emissions (CH4) in order to search for correlations between these chemical variables and bacterial groups. In terms of microbial (bacterial) community structure, we found Bacteroidetes as the dominant phylum in sheep rumen microbiome, followed by Proteobacteria, Firmicutes and Actinobacteria. Some taxa were correlated with the environmental parameters, like the Corynebacteriaceae and Streptococcaceae families, which was positively correlated with OMD, and the Streptomycetaceae family, negatively correlated with GP and CH4. Some known glycoside hydrolases were identified, such as Endo-1,4-betaglucanases, Beta-D-glucoside glucohydrolases and others were designated as putative ones. These findings show ecological interactions among microbial groups and important rumen functions, as well as the potential of the sheep rumen for the discovery of new cellulolytic enzymes.

The boreal forest area around Flin Flon, MB, and Creighton, SK, has been the site of a metal mining and smelting complex since the 1930s. Smelter emissions, coupled with forest logging, forest fires, and subsequent soil erosion, have led to severe vegetation dieback and the development of soils containing a mixture of metals in varying concentrations. In affected areas, existing vegetation typically is stunted. Limestone applications to affected soils have served to increase pH and, in some instances, the vegetation has responded positively; however, in some areas limestone application has failed to restore vegetation, leading to an interest in examining the suitability of other soil amendments to affect revegetation in these areas. Typically revegetation programs focus on aboveground vegetation responses; however, healthy plant growth often is dependent on the presence of an equally healthy soil microbial community. Thus, this study attempted to link revegetation success with responses of the soil microbial community structure to various soil amendments. Two studies were conducted to determine the influence of soil amendments (biochar, municipal and manure compost, glauconite, and an arbuscular mycorrhizal/ectomycorrhizal inoculant) on plant growth and microbial community structure in two soils from the Flin Flon area, classified as containing high and low metal concentrations. The two studies evaluated the growth of boreal forest understory species American vetch (Vicia americana) and tufted hairgrass (Deschampsia caespitosa) and overstory species jack pine (Pinus banksiana) and trembling aspen (Populus tremuloides) after addition of soil amendments, and the subsequent effects on microbial community structure. Greenhouse experiments evaluated plant growth for a period of 8 weeks (understory species) or 19 weeks (overstory species), after which plants were analyzed for changes in biomass and metal accumulation in plant tissue. Soils were analyzed for available metal concentrations, as well as microbial biomass carbon and nitrogen, and phospholipid fatty acid concentration, which is a measure of microbial community structure. Significant effects were seen on plant growth and microbial community structure due to the metal concentrations in the soil, but no one amendment consistently impacted plant growth or metal uptake, or any measured microbial parameter. The results of this study indicate the variability of plant growth and microbial functioning in soils from the study site, as well as the inherent challenges associated with revegetating heavy metal affected soils, and underline the need for further research on plant growth and microbial community structure at this site.

This research assessed the seasonal effects of contrasting tillage and crop rotation systems on soil ammonia oxidizing bacteria (AOB) and archaea (AOA). Four different cropping systems under till and no-till were analyzed in a 30 year-old agricultural field trial. Samples were collected during the 2010 growing season at times corresponding with agronomic events. Nucleic acids were preserved in the field and subsequently analyzed by quantitative real-time polymerase chain reactions (qPCR). Tillage decreased AOB activity and abundance in the plow layer (0-15 cm) immediately after fall moldboard plow events, but observed AOB dynamics at other times suggest tillage had a long-term distribution effect across depth (0-30 cm). AOA abundance was significantly greater in no-till plots at all times indicating tillage had longer-term effects on these communities. Crop rotation had minimal effect on AOB and AOA, but there was a noted yield advantage for corn following wheat, regardless of tillage treatment. / OMAFRA Highly Qualified Personnel Program, NSERC

Climate change is likely to alter plant species composition and interactions between plants and soil microbes that together dictate the quantity and quality of forage produced in pastures, the base of animal production in central Kentucky. This study assessed the seasonal dynamics of soil microbes and their response to increased temperature (+3oC) and growing season precipitation (+30% of the mean annual). Total soil microbial biomass, community composition, enzyme activities, potential carbon mineralization, and catabolic responses to selected substrates were measured seasonally in the different climate treatments. In this system, seasonal variability was a dominant driving factor for all the soil microbial characteristics that I investigated. Summer maxima and winter minima were identified in the active microbial biomass, while soil microbial community structure differed between each season. Extracellular enzyme activities were generally highest in either the spring or summer, while seasonal patterns for each substrate were unique across catabolic response profiles. Climate treatments produced few significant main or interactive effects on the soil microbial biomass and function. This resiliency, coupled with evidence of functional redundancy, suggests that central Kentucky pasture ecosystems may be well-equipped to handle future environmental stress associated with climate change and to maintain critical ecosystem services.

Submitted by Socorro Pontes (socorrop@ufersa.edu.br) on 2017-11-23T13:00:29Z No. of bitstreams: 1 JoelmaMPL_DISSERT.pdf: 1767206 bytes, checksum: c5b6652a65db20c661f3ad0f021c09fe (MD5) / Made available in DSpace on 2017-11-23T13:00:30Z (GMT). No. of bitstreams: 1 JoelmaMPL_DISSERT.pdf: 1767206 bytes, checksum: c5b6652a65db20c661f3ad0f021c09fe (MD5) Previous issue date: 2017-07-21 / The coalho cheese is considered a cultural patrimony and has great social and economic importance for the northeastern Brazilian region. The evaluation of the microbiological conditions of this product becomes fundamental for the affirmation of food safety and investigation of the real characteristics that make this kind of cheese so peculiar. The objective of the study was to identify the microbial community of coalho cheese. Metagenomic target DNA was extracted from eight samples of coalho cheese, four of which were made from pasteurized milk and four from raw milk. The DNA of the samples was sequenced by the next generation sequencing technology using the 16S and 18S rDNA gene as the basis for the identification of the organisms. Sequencing analyzes revealed several prokaryotic pathogenic microorganisms such as Rothia dentocariosa, Elizabethkingia meningoseptica and Bacillus cereus, as well as bacterial genera belonging to the microbiota previously described as Lactobacillus, Lactococcus, Escherichia, Enterococcus. Several fungi, such as Candida tropicalis, Candida parapsilolis, Pichia membranifaciens, Tritirachium oryzae, Malassezia furfur and Kluyveromyces marxianus were identified in the eukaryotic research, as well as microorganisms that had not yet been described in rennet cheeses such as Vibrio rumoienses, Ruminococcus flavefaciens, Piscicoccus intestinalis and Dekkera bruxellensis / O queijo de coalho é considerado um patrimônio cultural e tem grande importância social e econômica para a região nordeste brasileira, por isso a avaliação das condições microbiológicas desse produto torna-se fundamental para a afirmação da segurança alimentar e investigação das reais características que fazem com que esse tipo de queijo apresente sabores, texturas e aromas tão peculiares. A partir disso, o objetivo do trabalho foi identificar a comunidade microbiana do queijo de coalho. Para isso, o DNA metagenômico do queijo foi extraído de oito amostras de queijo de coalho, sendo quatro feitas a partir do leite pasteurizado e quatro feitas a partir do leite cru. O DNA das amostras foi sequenciado pela tecnologia de próxima geração da Illumina utilizando como base para a identificação dos organismos o gene rDNA 16S e 18S. As análises do sequenciamento revelaram vários exemplares de microrganismos patógenos procarióticos como Rothia dentocariosa, Elizabethkingia meningoseptica e Bacillus cereus, assim como gêneros de bactérias próprias da sua microbiota previamente descrita como Lactobacillus, Lactococcus, Escherichia, Enterococcus. Na investigação dos eucarióticos foram identificados diversos fungos como a Candida tropicalis, Candida parapsilolis, Pichia membranifaciens, Tritirachium oryzae, Malassezia furfur e Kluyveromyces marxianus, além dos microrganismos que ainda não tinham sido descritos em queijos coalho como o Vibrio rumoienses, Ruminococcus flavefaciens, Piscicoccus intestinalis e Dekkera bruxellensis / 2017-11-23

A cana-de-açúcar é uma das principais culturas do Brasil e nos últimos anos está recebendo especial atenção devido ao crescente aumento da área cultivada e produção de etanol para uso como biocombustível. Considerando-se sua importância econômica e a possibilidade do uso de plantas geneticamente modificadas, essa cultura tem se tornado foco de pesquisas relacionadas à produtividade e sustentabilidade. Neste contexto, o estudo de comunidades microbianas associadas à cana-de-açúcar é de fundamental importância, pois além dessas comunidades desempenharem importante papel funcional na interação com a planta, os estudos realizados nas condições tropicais são limitados. Comunidades de fungos e bactérias associadas à cana-de-açúcar geneticamente modificada IMI-1 e sua isolinha convencional SP80-1842 foram sistematicamente isoladas de plantas cultivadas em área experimental em Piracicaba, SP, Brasil. Por meio de isolamento e PCR-denaturing gradient gel electrophoresis (PCR-DGGE) foi verificado que a transgenia não afeta a diversidade da comunidade fúngica associada à cana-deaçúcar. A diversidade dessas comunidades foi descrita e caracterizada molecularmente. O fungo Fusarium moniliforme apresentou alta freqüência de isolamento e também foi observado que o gene da endopoligalacturonase, pgIII, desempenha um importante papel no tipo de associação, endofítica ou patogênica, do F. moniliforme e a planta. O complexo Burkholderia cepacia constitui uma importante fração da comunidade de bactérias associada à cana-de-açúcar no Brasil e isolados deste complexo são capazes de inibir o crescimento do patógeno F. moniliforme. Análises filogenéticas indicaram que os isolados de bactérias endofíticas de Burkholderia são proximamente relacionados com linhagens-tipo do complexo B. cepacia isoladas de pacientes de fibrose cística. / In Brazil, the sugarcane is one of the most important cultivated crops. The sugarcane has received increased interest in the last years because of increase of the cultivated area and ethanol production to be used as biofuel. Considering its economical importance and the possibility of the use of the genetically modified plants; this crop has become the aim of current research for productivity and sustainability. In this context, the work on microbial communities associated with sugarcane is remarkable, because both, these communities play important functional role in the interaction with the plant, and studies performed in tropical conditions are limited as well. Fungal and bacterial communities associated with genetically modified sugarcane IMI-1 and its conventional isoline SP80-1842 were systematically isolated from plants cultivated in an experimental area in Piracicaba, SP, Brazil. The fungal communities associated with sugarcane were accessed by means of cultivation approach and PCR-denaturing gradient gel electrophoresis; the results revealed that these communities are not affected by transgeny. The microbial communities\' diversity was characterized and identified by using molecular tools. The fungus Fusarium moniliforme showed high frequency in association with the plant and it was observed that the endopolygalacturonase gene, pgIII, plays important role in order to determine the sort of association, either endophytic or pathogenic, between F. moniliforme and the host. The Burkholderia cepacia complex is an integral part of the endophytic bacterial community of sugarcane in Brazil and isolates of this complex are able to control F. moniliforme growth. Phylogenetic analyses indicated that the endophytic Burkholderia are closely related to clinical isolates of the B. cepacia complex isolated from cystic fibrosis patients.

Une des solutions alternatives les plus fiables contre la raréfaction des ressources en eau et la dégradation de leur qualité est la réutilisation des eaux usées. Aujourd'hui la technologie membranaire basse et haute pression s'impose comme la technologie de choix pour la production directe et indirecte d'eau potable du fait de la très haute qualité de l'eau produite. Néanmoins, le colmatage des membranes, affectant techniquement et économiquement les filières de traitement, reste aujourd'hui l'un des principaux défis. Les objectifs de cette thèse sont d'améliorer la compréhension du colmatage membranaire dans le recyclage des eaux usées en étudiant le rôle de la qualité de l'effluent secondaire sur le développement du colmatage et l'impact du colmatage sur la qualité de l'eau produite. Afin d'atteindre ces objectifs, une meilleure connaissance de la qualité des effluents secondaires et de leur impact sur les procédés membranaires s'avère indispensable. Les différentes fractions organiques des effluents ont été caractérisées à l'aide de techniques innovantes telles que la spectroscopie de fluorescence à 3 dimensions (EEM) et la chromatographie liquide couplée à une détection carbone (LC-OCD). Une unité à échelle pilote, composée d'ultrafiltration suivie d'une osmose inverse à deux étages, a été mise en place sur deux sites distincts. Plusieurs doses de monochloramine ont été testées (0 à 2 mg/L NH2Cl) afin de donner des recommandations d'optimisation de traitement. / One of the most reliable alternative solutions to water shortage and scarcity in urban areas is potable reuse of what would otherwise be considered "waste" water. The combination of low and high-pressure membrane processes is the favoured technology for direct and indirect potable water recycling due to the very high water quality produced. Despite the fact that membrane technology is well established, membrane fouling remains a major challenge affecting plant operation technically and economically. This thesis aims to contribute to the understanding of membrane fouling in water reuse by investigating the importance of the feed water quality on fouling development and the impact of the fouling on the treated water quality. In order to achieve these objectives, it was important to develop better knowledge of the impact of feed water quality on the membrane process. The organic composition of the effluents was successfully differentiated with the use of advanced analytical tools such as fluorescence excitation emission matrix (EEM) and liquid chromatography-organic carbon detection (LC-OCD). To evaluate water quality impact on membrane fouling, a membrane pilot unit consisting of ultrafiltration and a two stage reverse osmosis train was operated on two different sites. Different monochloramine dosages (0 to 2 mg/L NH2Cl) were applied and their impact on RO membrane performance was studied in order to provide recommendations for plant design.

Avec la mondialisation et l'industrialisation de l'alimentation, la fraude et les cas de contamination des aliments peuvent avoir un impact international et entraîner des conséquences de grande envergure à la fois sur l'économie et la santé des consommateurs (Cubero-Leon et al., 2014). La fraude et l'authentification sont donc devenues des sujets émergents dans le secteur alimentaire. D'autant que les fraudes sont de plus en plus sophistiquées pour contourner au mieux les contrôles et donc de plus en plus difficiles à détecter par des analyses classiques. Les aliments issus de l'agriculture biologique (AB ou bio) font d'ailleurs partie des aliments qui risquent le plus de faire l'objet de fraude. Mais la traçabilité des aliments est principalement garantie par des moyens administratifs (règlement UE 178/2002). C'est pourquoi il est nécessaire de recourir à des techniques analytiques avancées pour détecter les produits non-conformes et pour garantir la traçabilité et l'authenticité des aliments, notamment ceux issus de l'AB. Notre étude est basée sur l'hypothèse que les traitements, associés à différents types d'agriculture, ont un impact mesurable sur la microflore des aliments. L'objectif principal était de pouvoir utiliser l'environnement microbien des aliments pour les discriminer en fonction de leur mode de production. La PCR-DGGE, un outil moléculaire d'écologie microbienne, pourrait servir à discriminer les modes de production d'aliments par analyse des profils génétiques des ADNr bactériens et fongiques. L'analyse des profils génétiques microbiens de nectarines, pêches, bananes et de pommes a montré qu'il était possible de différencier les fruits en fonction de leur mode de production. La robustesse de notre méthodologie a été démontrée en comparant les résultats obtenus sur deux années de récolte successives. Létude des variation intra-parcellaires ont également permis de démontrer que les fruits bio pouvaient être différenciés des conventionnels indépendamment de leur position dans la parcelle (centre vs bord) ou encore sur l'arbre. Les différences observées au niveau de la structure des communautés microbiennes étaient donc suffisamment importantes pour conclure que les traitements appliqués ont un impact significatif sur ces communautés. De plus, l'identification des espèces microbiennes obtenues après PCR-DGGE et NGS a révélé que certains groupes microbiens (fongiques et bactériens) pourraient être spécifiques aux aliments bio. Cependant, l'effet terroir est un critère important à prendre en compte dans la mise en place d'un outil d'authentification des aliments bio. Une application sur le terrain serait donc difficile à prévoir si elle est parcelle-spécifique. Cette étude s'inscrit à la base de la mise au point d'un outil analytique qui pourrait permettre de répondre aux besoins des professionnels de l'industrie alimentaire en termes d'authenticité et de sûreté alimentaire, en particulier pour aider les organismes certificateurs à contrôler et authentifier les aliments bio. Cette étude a également permis d'enrichir les connaissances actuelles sur l'écosystème microbien des fruits en fonction des pratiques agricoles. / Globalization of trades and industrialization of food have increased the occurrence of food fraud. Cases of food contamination now have a global impact and lead to far-reaching consequences both on the economy and the health of consumers (Cubero-Leon et al., 2014). Thus, fraud and authentication became important topics in the food sector. Especially as food frauds are becoming more sophisticated to bypass controls and are therefore more difficult to detect by classical approaches. Organic foods are part of foods that are the most likely to be subject of fraud. But traceability of foods is mainly performed by administrative means (UE Regulation 178/2002). That is why it is necessary to resort advanced analytical techniques to detect non-compliant products and to ensure traceability and authentication of foods, including those from organic agriculture. Our study is based on the hypothesis that treatments associated to various farming types have a measurable impact on food microflora. That is why, the main objective of this study was to use the microbial environment of foods to discriminate them according to their production mode. PCR-DGGE, a molecular tool of microbial ecology, could be used as to discriminate food production modes using bacterial and fungal rDNA profiles. The analysis of microbial genetic profiles of nectarines, peaches, bananas and apples showed that it was possible to differentiate fruits according to their farming types. It was possible to verify the robustness of our methodology by comparing results obtained on two successive harvest years. We estimated also the intra-plot variations and observed that organic apples could be discriminated from conventional ones independently upon their position in the field (centre or border) or even on the tree. The observed differences in microflora between organic and conventional apples were significant enough to conclude that the applied treatments have a significant impact on this microflore. Furthermore, the analysis of DNA sequences obtained from PCR-DGGE and NGS allowed some microbial groups (fungal and bacterial) to be identified as specific to organic foods. However, the “terroir effect” is an important criterion to take into account for the implementation of an authentication tool for organic products. So, an application in the field would be difficult to predict if it is plot-specific. This study constitutes the basis for the development of an analytical tool that could meet the needs of food industry professionals in terms of authenticity and food safety, especially to assist certifying bodies to control and authenticate organic food products. This study enabled also to enrich the existing knowledge on the microbial ecosystem of fruits from different agricultural practices.