Écologie Microbienne

Ce travail a pour objet d'explorer des voies de recherches pour l'amelioration du suivi et la connaissance des mecanismes biochimiques de la methanisation par voie seche. Il s'agit d'une technologie d'avenir pour la gestion des dechets et la production d'energie. Sont etudies : la caracterisation de la matiere organique (MO), les intermediaires de reaction, les mecanismes d'inhibition, les activites hydrolytiques. Un reacteur de laboratoire a ete mis au point pour mimer les conditions industrielles. La MO des dechets solides contient 3 compartiments de biodegradabilite et de solubilite decroissante. Il en decoule 3 etapes de degradation de vitesse decroissante qui peuvent etre attribuees a des activites hydrolytiques differentes. L'accumulation d'AGV et d'hydrolases sont des indicateurs d'un desequilibre entre l'acidogenese et la methanogenese suite a une surcharge ou l'inhibition par NH3. Celle-ci est accrue par le pH et peut etre...

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

The waste of organic matter comes primarily from the food industries, (of the domestic activities, slaughter-house...) and from urban waste water. This waste constitutes an environmental nuisance to take in charge for the durable safeguard of our environment. The valorisation of this organic matter would be a judicious solution to reduce their harmful effects. In addition, the application of a process of bioconversion 'anaerobic digestion' makes it possible to combine the treatment of this waste and the production of a renewable energy which is biogas. This gas rich in methane CH4 has a significant energy capacity and can be used in many applications like: heating, cooking, production of electricity, lighting and as a bio-carburant and being able to be injected into the gas network for domestic use. Our work consists in studying the anaerobic digestion of domestic waste (kitchen waste) and more particularly the influence of the pH on the biogas yield. During this study, we f...

Sur les sols pauvres en nutriments, les plantes de la famille des légumineuses (soja, luzerne, trèfle, haricot, etc.) peuvent survivre grâce à la symbiose fixatrice d'azote, qu'elles établissent avec des bactéries de la famille des Rhizobiaceae. Un dialogue moléculaire contrôle la mise en place de cette symbiose. En plus des processus permettant l'infection de la plante par son symbiote, il existe différentes voies de régulation négative, dont le contrôle de la prolifération bactérienne. Lors de cette thèse, nous avons caractérisé un signal issu de la plante Medicago sativa (hôte de Sinorhizobium meliloti) qui permet de contenir cette infection. Plus précisément, nous avons déterminé qu'il s'agissait d'une protéine, sensible à la température, très minoritaire dans un extrait aqueux de feuilles. Sa masse moléculaire est comprise entre 20 et 95 kDa, et son Pi est supérieur à 9. Ces caractéristiques permettront de déterminer sa structure après plusieurs étapes de purification. Nous avons également étudié l'effet secondaire de ce signal inducteur génique sur la production et la structure des exopolysaccharides (EPS) de S. meliloti. Nous avons constaté que la production d'EPS augmentait lorsque le signal était perçu par la bactérie, sans modification significative de leur structure. Toutefois, les EPS sont des composés connus pour être impliqués dans la mise en place de la symbiose. Si leur rôle symbiotique est bien connu, leur relation structure/activité reste floue. Nous avons donc étudié ces relations à partir des EPS produits par Rhizobium sullae, qui interagit symbiotiquement avec la légumineuse Hedysarum coronarium (sainfoin). Ce couple symbiotique a été choisi, car il présente un fort intérêt agronomique. En effet, le sainfoin colonise les zones arides et semi-désertiques du pourtour méditerranéen. Nous avons effectué la caractérisation structurale complète (GC-MS, ESI-MS, MS/MS, RMN 1D et 2D) de l'unité répétitive des EPS de R. sullae, ce qui a permis de constater qu'ils étaient composés d'environ 30% de fucose. Ce monosaccharide est très rarement présent dans les EPS de bactéries fixatrices d'azote. Dans le cadre de l'étude des relations structure/activité, nous avons déterminé qu'un tel taux de fucose améliore la mise en place de la symbiose. Nous avons également étudié le rôle des EPS de R. sullae dans la résistance à la sècheresse. Nous avons ainsi observé que les EPS de forte masse molaire (particulièrement visqueux) augmentent la résistance à la sècheresse, mais que la présence de fucose n'avait que peu d'influence.

This review establishes basic knowledge about the taxonomic and metabolic diversity of hydrogen producers in fermentation bioprocesses, and emphasizes the crucial role of interactions between effective producers, negative effectors inhibiting or outcompeting hydrogen production, and positive contributors facilitating the ecosystem function, with the final objective to propose bioengineering strategies and microbial resource management to enhance bioprocess function.

Qu'elles reçoivent ma profonde reconnaissance et mes remerciements sincères. Je tiens à remercier tous les membres du jury d'avoir accepté d'y participer. J'adresse mes remerciements à M. le Professeur Ahmed LEBRIHI, à MM. Le Hong Khanh et Dao Huy Phong qui m'ont aidé et encouragé dans la recherche d'un financement de cette thèse. Je tiens à remercier l'Ambassade de France au Vietnam et le Gouvernement Français de m'avoir fait confiance en m'octroyant une bourse de doctorat. Mes remerciements vont aussi à M. Nguyen Hoang Phuong, à M. Raymond Kraemer et à Anh Liem-Chi Huong qui m'ont apporté aide et soutien lors de mes séjours en France. Je n'oublie pas l'accueil amical de toutes les personnes des laboratoires en France et au Vietnam :

En début de chaque chapitre, un sommaire détaillé présente son contenu. Remerciements 1 En premier lieu, j'aimerais exprimer toute ma gratitude à mon directeur de thèse, Madame S. Castanier-Perthuisot de l'Université d'Angers, qui a su me soutenir par ses conseils, ses encouragements, sa disponibilité et bien plus encore.

Xanthomonas albilineans, the causal agent of sugarcane leaf scald, is a bacterial plant pathogen that is mainly spread by infected cuttings and contaminated harvesting tools. However, some strains of this pathogen are known to be spread by aerial means and are able to colonize the phyllosphere of sugarcane before entering the host plant and causing disease. The objective of this study was to identify the molecular factors involved in the survival or growth of X. albilineans on sugarcane leaves. We developed a bioassay to test for the attachment of X. albilineans on sugarcane leaves using tissue-cultured plantlets grown in vitro. Six mutants of strain XaFL07-1 affected in surface polysaccharide production completely lost their capacity to survive on the sugarcane leaf surface. These mutants produced more biofilm in vitro and accumulated more cellular poly-β-hydroxybutyrate than the wild-type strain. A mutant affected in the production of small molecules (including potential biosurfactants) synthesized by nonribosomal peptide synthetases (NRPSs) attached to the sugarcane leaves as well as the wild-type strain. Surprisingly, the attachment of bacteria on sugarcane leaves varied among mutants of the rpf gene cluster involved in bacterial quorum sensing. Therefore, quorum sensing may affect polysaccharide production, or both polysaccharides and quorum sensing may be involved in the survival or growth of X. albilineans on sugarcane leaves.

Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we sh...

The symbiotic association (plant-soil-microorganisms) has an important role in nitrogen (N) and phosphorus (P) uptake. The main objective of this study is to assess the potential of fungal and rhizobial symbionts as well as the importance of plant-soil-microorganism interactions on microbial dynamics. The upland rice and the beans were cultivated in mono or in co-culture using the rhizospheric soil of the upland rice and beans collected on plots treated with different levels of organic and mineral fertilizers. What about saying: Microbial (fungal and rhizobial) inoculate were constituted by root fragments (rice or bean) collected from previous crop and coded as I1 (root fragments from rice), I2 (root fragments from bean) and I3 (mixed root fragments from rice and bean). The results showed that soils inoculated with I1 and I3, were characterized by high phosphatase activity. These two treatments enhance also the amount of nitrogen and phosphorus in the aerial part of upland rice intercropped with bean. These results suggest that the bean with its symbiont can be considered as ecological engineers that stimulate the biological functioning of soils and is beneficial for upland rice cultivation.

Les travaux présentés dans ce mémoire ont été réalisés à l'UMR Agronomie et Environnement INPL-ENSAIA-INRA de Nancy. Je tiens à exprimer, au travers de ces quelques lignes, toute ma reconnaissance envers les personnes qui ont contribué directement ou indirectement à ce travail. Je tiens avant tout a exprimer toute ma gratitude envers Mademoiselle Séverine Piutti, Maître de Conférences, et Monsieur Emile Benizri, Professeur à l'ENSAIA, qui m'ont offert l'opportunité de réaliser cette thèse. Je les remercie notamment pour le temps qu'ils m'ont consacré notamment pour la lecture du manuscrit, des articles en préparation, ainsi que pour les conseils avisés qu'ils m'ont prodigués. Je voudrais vivement remercier les chercheurs qui ont participé au jury de cette thèse :

Introduction: Ochratoxin A (OTA) is a toxic secondary metabolite produced by fungi of the genera Aspergillus and Penicillium. It has been shown to have carcinogenic and immunotoxic properties in rats and to be responsible for human and animal kidney pathologies. OTA content in coffee was shown to be closely link to harvesting conditions, postharvest processing conditions and especially dry processing, storage and transportation conditions. Purpose: Fairly little is known about the conditions for contamination by fungi responsible for OTA production, their propagation and conditions for OTA production. Biodiversity and dynamics of fungal populations linked to OTA production could be studied by PCR-DGGE genetic fingerprinting with the aim to understand the effects of postharvest processing on the microbiota. Results: DGGE fingerprints analyzed by multivariate analysis showed an evolution of the fungal microflora of coffee during the different stages of the postharvest treatments (wet and dry processes) by extraction and amplification of 26S (yeasts) and 28S rDNA (filamentous fungi). PCR-DGGE stages were optimized: extraction and amplification, repeatability and sensitivity methodology applied to fungi were tested. Conclusion: PCR-DGGE is a rapid molecular technique to monitor the dynamics of coffee microbial populations (fungi and yeast). Significance of study: PCR-DGGE is a promising tool in order to investigate OTA production in coffee beans.

Un grand nombre d'espèces microbiennes, issues d'environnements variés, peuvent produire du biohydrogène par voie fermentaire. Le potentiel des cultures mixtes microbiennes est particulièrement intéressant au regard de leur large flexibilité métabolique permettant d'envisager d'utiliser des ressources organiques complexes issues du traitement de la biomasse. Toutefois, la diversité microbienne des cultures mixtes est également source d'instabilité des procédés via l'expression de métabolismes bactériens multiples pouvant conduire notamment à une reconsommation du bioH2 produit. A ce jour, peu de moyens d'actions, et essentiellement des modifications physico-chimiques, permettent d'assurer l'optimisation des procédés continus de production de biohydrogène. Les recherches menées ont permis d'identifier puis d'utiliser des espèces-clés situées au coeur des réseaux métaboliques en tant que contrôleur biologique des écosystèmes microbiens, et ceci en améliorant la stabilité et les rendements de conversion en biohydrogène.

The new European regulation 178/2002 imposes the determination of the geographical origin in the traceability process of foodstuffs at the moment of commercial transactions. In practice, it is difficult to determine with accuracy the geographical origin of foodstuffs. For this purpose, the total analysis of fungal communities in samples of coffee is used. In the present study the molecular technique using 28S rDNA profiles generated by PCR-DGGE was used in order to detect the variation in fungal community structures of coffee from five different locations in West and Coastal plain in Cameroon and the effect of treatment and coffee species on these fungal profiles. When the 28S rDNA profiles were analyzed by multivariate analysis, distinct microbial communities were detected. The band profiles obtained from different samples of coffee and specific for each location and could be used as a bar code to certify the origin of the coffee. This method is a new traceability tool which provides coffee products with a unique biological bar code and makes it possible to trace back the coffee to their original location.

Chapitre 2National audienceMilk quality management for cheese production in the French J&Orthern Alps. In the French northern Alps, a number of cheese varieties considered as traditional products of local agriculture are protected by a label of origin (appellation contrôlée). Elaboration of milk quality for cheese-making is a fairly complex process and is based on the diversity of milk qualities supplied by farmers to the processing firms. To control and guarantee this quality, appropriate methodology must be developed to analyse the strategies of firms and of producers, the relationships between these actors, and the production systems. The authors make the assumption that systems modelling coupled with a typological approach will enable to develop decision-making aids. In the Beaufort cheese area, differences in milk quality strategies of cheese-making firms result from difficulties in meeting their own specifie needs while respecting the "Beaufort identity".Dans la fili...

National audienceA typology of 129 milk samples collected by two cooperatives to make Beaufort cheese, showed various associations in their milk characteristics (fat content, protein content, somatic cell count, bacteria count, breakdown of monthly milk bulk, annual milk bulk). Production practices were studied in 34 dairy farms. Feeding factors and calving periods were found to have an influence on the milk’s chemical composition. The bacteria counts in milk depended on the sanitation of the milking equipment. Farming practices, premilking udder preparation and cubicle mats were associated with somatic cell count. The variability of the different milk characteristics and the relations amongst them underlines the diversity in both farming practices and the control systems currently in place. Relationships between milk types and farming systems demonstrates the utility of proposing quality guidelines that are adapted to the diversity of dairy farmingUne typologie des laits livrés par...

Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology.

Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we sh...

The microbial composition of different types,in ecosystems (including agro-ecosystems), has been investigated in a rapidly growing number of studies in the past few years. The importance of microorganisms, regarding the maintenance and stability of nutrients in agroecosystems, is a key to maintain the sustainability of a crop. Molecular tools to study microbial communities are possible through many methods such as RISA, DGGE, TGGE, clone libraries, T-RFLP, RAPD, SSCP and more recently NGS (Next-Generation Sequencing). DGGE is widely employed to characterize the diversity and the community dynamics of microorganisms in the environment, making possible to find out specific groups through functional genes, allowing access to data that cannot be obtained by cultural methods. The aim of this paper is to review the functional groups related to agroecosystems and to indicate the critical choice of DNA primers pairs and targeted DNA regions that may be used in PCR-based methods such as the DGGE technique in order to evaluate the microbial communities in a variety of environments.

L’examen des echantillons d’aliment de betail de differentes origines (Ain M’lila, El Harrouch, Guelma et El khroub) a abouti a 166 isolats regroupes en 13 genres. La methode de diffusion sur un milieu gelose utilisee pour la detection des substances produites par les isolats, permit l’analyse de plusieurs souches sur la meme boite. Les resultats sur l’activite antibacterienne montrent une action inhibitrice elevee des isolats Aspergillus flavus , A. fumigatus ,  A. ochraceus , Penicillium chrysogenum, P. cyclopium  et P. viridicatum par rapport aux autres isolats. La recherche de l’activite catalytique a vise a etablir une  eventuelle correlation entre les deux secretions.

Le présent travail a pour objectif de caractériser la flore de neuf échantillons de farine de maïs Zea mays (L.)] achetés sur trois marchés d'Abidjan (Adjamé, Yopougon, Abobo). Méthodologie et résultats : A l'issue de l'inoculation du milieu de culture PDA avec les différentes suspensionsdilutions de farine, cinq genres de champignons ont été isolés et identifiés à des pourcentages variés. A Adjamé, Aspergillus niger est respectivement présent à 41, 45 et 33,33 % ; Fusarium sp. à 33, 35, 66,66 % ; 36,84 % à Abobo chez la 1 ère vendeuse et 33,33 %, 25 % respectivement chez la 1 ère et la 3 ème vendeuse à Yopougon. A yopougon Penicillium sp. est présent sur la 1 ère (16,66 %) et la 2 ème (40 %) farine et sur la 1 ère (21,05 %) farine à Abobo. Aspergillus flavus a été isolé sur les farines 2 (10 %) et 1 (31,57 %) respectivement à Adjamé et à Abobo. Botrytis sp. était présent à Adjamé, Yopougon et Abobo respectivement sur les farines 1 et 2 (25 %, 10 %) ; 3 (25 %) et sur 1 (10,52 %). La présence de ces champignons a entrainé la détérioration des farines en provenance d'Adjamé et de la farine 1 achetée à Abobo. En fonction des marchés, le pourcentage moyen d'apparition le plus élevé est attribué à Fusarium sp. (44,88 %) à Adjamé, ensuite à Mucor sp. (28,33 %) à Yopougon puis à Aspergillus flavus (10,52 %) à Abobo. Conclusion et application des résultats : Les farines achetées sur les trois marchés renferment toutes des champignons parmi lesquels figurent les genres Aspergillus, Penicillium et Fusarium reconnus comme producteurs de mycotoxines. Ces derniers sont peu volatiles, très stables à l'acidité et à la chaleur. Il est donc important que des mesures d'hygiène rigoureuse soient observées au moulin, au cours du séchage et de la conservation de la farine afin que le consommateur soit à l'abri de toute intoxication.

Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored ...

Introductions multiples et mélange à l’origine de l’expansion continentale du champignon pathogène du bananier Mycophaerella fijiensis en Amérique centrale : un test statistique utilisant le calcul bayésien approché. — La reconstruction des histoires d’invasions est l’un des principaux défis de la biologie des invasions. L’ascomycète Mycophaerella fijiensis, agent causal de la maladie des raies noires des bananiers, en provenance d’Asie du Sud-Est, a commencé à envahir le continent américain en 1972 et est aujourd’hui présent dans toutes les régions productrices de bananes d’Amérique. Dans une précédente étude de la structure génétique des populations à l’échelle mondiale, nous supposions que l’invasion américaine pourrait avoir résulté d’introductions multiples et de mélange. Ici, nous avons cherché (i) à tester statistiquement cette hypothèse, et (ii) à inférer les caractéristiques démo-génétiques de cette introduction, en utilisant une technique de choix de scénario par calcul ba...

Diseases transmitted between wildlife and livestock may have significant impacts on local farmers" health, livestock health and productivity, overall national economies, and conservation initiatives, such as Transfrontier Conservation Areas in Southern Africa. However, little is known on local farmers" awareness of the potential risks, and how they perceive the role played by wildlife in the epidemiology of these diseases. We investigated the knowledge base regarding livestock diseases of local cattle owners living at the periphery of conservation areas within the Great Limpopo TFCA and the Kavango-Zambezi TFCA in Zimbabwe, using free-listing and semi-structured questionnaires during dipping sessions. The results suggest that information related to cattle diseases circulates widely between cattle farmers, including between different socio-cultural groups, using English and vernacular languages. Most respondents had an accurate perception of the epidemiology of diseases affecting their livestock, and their perception of the potential role played by wildlife species was usually in agreement with current state of veterinary knowledge. However, we found significant variations in the ranking of livestock diseases between sites, and owners" perceptions were not directly related with the local abundance of wildlife. In contrast, awareness of zoonotic risks and of the potential increase in TADs with the establishment of TFCAs, seemed low. We recommend the establishment of a One health program, including information and awareness on zoonotic diseases, with increased participation of communities at a local level in the prioritization of disease control and surveillance.

The new European regulation 178/2002 imposes the determination of the geographical origin in the traceability process of foodstuffs at the moment of commercial transactions. In practice, it is difficult to determine with accuracy the geographical origin of foodstuffs. For this purpose, the total analysis of fungal communities in samples of coffee is used. In the present study the molecular technique using 28S rDNA profiles generated by PCR-DGGE was used in order to detect the variation in fungal community structures of coffee from five different locations in West and Coastal plain in Cameroon and the effect of treatment and coffee species on these fungal profiles. When the 28S rDNA profiles were analyzed by multivariate analysis, distinct microbial communities were detected. The band profiles obtained from different samples of coffee and specific for each location and could be used as a bar code to certify the origin of the coffee. This method is a new traceability tool which provides coffee products with a unique biological bar code and makes it possible to trace back the coffee to their original location.

La présente étude se propose d'analyser les diverses valorisations possibles de la Biométhanisation rurale appliquée aux déjections bovines. Le diagnostic mis en oeuvre a concerné la productivité gazeuse ainsi que certains paramètres de dépollution environnementale, de croissance et de fertigation des plants en pépinière maraîchère. Les résultats préliminaires ont montré que le conditionnement du biogaz rural produit a permis d'améliorer les performances énergétiques relevées. L'utilisation de la tourbe mélangée avec du méthacompost bovin comme substrat de culture a donné des résultats encourageants vis-à-vis de la croissance en hauteur des plants de piment. De plus, le jus de process bovin, dilué à raison de 75% d'eau, a présenté une capacité fertilisante intéressante, en plus de l'absence observée de flétrissement. Cependant, en termes de valorisation environnementale, le processus de Biométhanisation adopté n'a pas permis de réduire la charge polluante des MES et de la DBO 5 de manière satisfaisante.

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Blights and cankers of fruit trees caused by Pseudomonas syringae generate significant economic losses worldwide. Given the epiphytic lifestyle of P. syringae orchard ground covers represent a potential source of inoculum of P. syringae for fruit trees. They also represent a reservoir of bacterial diversity that could be beneficial for plant health via natural antagonistic and competitive interactions within the microbial flora. This microbial reservoir could be exploited for the development of ecological engineering practices, specifically the management of ground covers to reduce their negative impact on plant health and in particular as a source of pathogenic strains of P. syringae. Within the species P. syringae there is a very high genetic variability, and strains are distributed into 13 phylogroups (Berge et al., 2014) with very marked differences in pathogenicity among some of these phylogroups. Until now the only method for phylogenetic identification was the sequencing of s...

Microbially mediated arsenic release from Holocene and Pleistocene Cambodian aquifer sediments was investigated using microcosm experiments and substrate amendments. In the Holocene sediment, the metabolically active bacteria, including arsenate-respiring bacteria, were determined by DNA stable-isotope probing. After incubation with 13 C-acetate and 13 C-lactate, active bacterial community in the Holocene sediment was dominated by different Geobacter spp.-related 16S rRNA sequences. Substrate addition also resulted in the enrichment of sequences related to the arsenate-respiring Sulfurospirillum spp. 13 C-acetate selected for ArrA related to Geobacter spp. whereas 13 C-lactate selected for ArrA which were not closely related to any cultivated organism. Incubation of the Pleistocene sediment with lactate favoured a 16S rRNA-phylotype related to the sulphate-reducing Desulfovibrio oxamicus DSM1925, whereas the ArrA sequences clustered with environmental sequences distinct from those identified in the Holocene sediment. Whereas limited As(III) release was observed in Pleistocene sediment after lactate addition, no arsenic mobilization occurred from Holocene sediments, probably because of the initial reduced state of As, as determined by X-ray Absorption Near Edge Structure. Our findings demonstrate that in the presence of reactive organic carbon, As(III) mobilization can occur in Pleistocene sediments, having implications for future strategies that aim to reduce arsenic contamination in drinking waters by using aquifers containing Pleistocene sediments.

The microbial composition of different types,in ecosystems (including agro-ecosystems), has been investigated in a rapidly growing number of studies in the past few years. The importance of microorganisms, regarding the maintenance and stability of nutrients in agroecosystems, is a key to maintain the sustainability of a crop. Molecular tools to study microbial communities are possible through many methods such as RISA, DGGE, TGGE, clone libraries, T-RFLP, RAPD, SSCP and more recently NGS (Next-Generation Sequencing). DGGE is widely employed to characterize the diversity and the community dynamics of microorganisms in the environment, making possible to find out specific groups through functional genes, allowing access to data that cannot be obtained by cultural methods. The aim of this paper is to review the functional groups related to agroecosystems and to indicate the critical choice of DNA primers pairs and targeted DNA regions that may be used in PCR-based methods such as the DGGE technique in order to evaluate the microbial communities in a variety of environments.

Le processus de dégradation anaérobie de la matière organique est un phénomène naturel largement répandu sur terre (ex. marais, lacs, rizières, systèmes digestifs d'animaux et humains). Une très grande diversité microbienne est entretenue durant ce processus, traduisant une diversité de voies métaboliques impliquées. Lorsqu'elle est complète, la digestion anaérobie aboutie à la formation de biogaz (mélange de méthane et de dioxyde de carbone). En termes de biotechnologie, le traitement par voie anaérobie de pollutions organiques permet de réduire le volume de déchets en générant du méthane valorisable sous plusieurs formes (électricité, chaleur, gaz naturel, biocarburant). Cependant, les digesteurs industriels sont optimisés pour un fonctionnement à 35°C ou à 55°C, ce qui nécessite un apport exogène d'énergie de maintenance. Ainsi, les travaux de thèse se sont intéressés à l'étude de la capacité d'adaptation de divers écosystèmes anaérobies industriels couvrant u...

L’émergence de pathogènes dans l’eau destinée à la consommation humaine représente une préoccupation majeure en matière de santé publique pour les industriels et les pouvoirs publics concernés. Parmi ces pathogènes, certains sont d’origine fécale (Cryptosporidium, Campylobacter ou bien les rotavirus), alors que d’autres vivent dans l’environnent naturel (Legionella, Pseudomonas, Aeromonas ou bien les mycobactéries). Dans l’optique de mettre en place une analyse des risques liés à la présence de ces pathogènes, il est important d’accroître nos connaissances sur l’écologie de ces microorganismes et de développer des outils d’analyse afin de réaliser une meilleure surveillance sanitaire. Par conséquent, l’écologie microbienne du réseau de distribution d’eau potable doit être étudiée en détail, particulièrement vis-à-vis des propriétés physiologiques et la diversité des espèces microbiennes présentes, afin de mieux comprendre les interactions entre les espèces communément rencontrées et...

The symbiotic association (plant-soil-microorganisms) has an important role in nitrogen (N) and phosphorus (P) uptake. The main objective of this study is to assess the potential of fungal and rhizobial symbionts as well as the importance of plant-soil-microorganism interactions on microbial dynamics. The upland rice and the beans were cultivated in mono or in co-culture using the rhizospheric soil of the upland rice and beans collected on plots treated with different levels of organic and mineral fertilizers. What about saying: Microbial (fungal and rhizobial) inoculate were constituted by root fragments (rice or bean) collected from previous crop and coded as I1 (root fragments from rice), I2 (root fragments from bean) and I3 (mixed root fragments from rice and bean). The results showed that soils inoculated with I1 and I3, were characterized by high phosphatase activity. These two treatments enhance also the amount of nitrogen and phosphorus in the aerial part of upland rice intercropped with bean. These results suggest that the bean with its symbiont can be considered as ecological engineers that stimulate the biological functioning of soils and is beneficial for upland rice cultivation.

The new European regulation 178/2002 imposes the determination of the geographical origin in the traceability process of foodstuffs at the moment of commercial transactions. In practice, it is difficult to determine with accuracy the geographical origin of foodstuffs. For this purpose, the total analysis of fungal communities in samples of coffee is used. In the present study the molecular technique using 28S rDNA profiles generated by PCR-DGGE was used in order to detect the variation in fungal community structures of coffee from five different locations in West and Coastal plain in Cameroon and the effect of treatment and coffee species on these fungal profiles. When the 28S rDNA profiles were analyzed by multivariate analysis, distinct microbial communities were detected. The band profiles obtained from different samples of coffee and specific for each location and could be used as a bar code to certify the origin of the coffee. This method is a new traceability tool which provides coffee products with a unique biological bar code and makes it possible to trace back the coffee to their original location.

Diseases transmitted between wildlife and livestock may have significant impacts on local farmers" health, livestock health and productivity, overall national economies, and conservation initiatives, such as Transfrontier Conservation Areas in Southern Africa. However, little is known on local farmers" awareness of the potential risks, and how they perceive the role played by wildlife in the epidemiology of these diseases. We investigated the knowledge base regarding livestock diseases of local cattle owners living at the periphery of conservation areas within the Great Limpopo TFCA and the Kavango-Zambezi TFCA in Zimbabwe, using free-listing and semi-structured questionnaires during dipping sessions. The results suggest that information related to cattle diseases circulates widely between cattle farmers, including between different socio-cultural groups, using English and vernacular languages. Most respondents had an accurate perception of the epidemiology of diseases affecting their livestock, and their perception of the potential role played by wildlife species was usually in agreement with current state of veterinary knowledge. However, we found significant variations in the ranking of livestock diseases between sites, and owners" perceptions were not directly related with the local abundance of wildlife. In contrast, awareness of zoonotic risks and of the potential increase in TADs with the establishment of TFCAs, seemed low. We recommend the establishment of a One health program, including information and awareness on zoonotic diseases, with increased participation of communities at a local level in the prioritization of disease control and surveillance.

Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored ...

Je tiens avant tout à remercier, le CIRAD ainsi que les différents responsables de programmes ou d'unités, je pense notamment à Christophe Montagnon, André Rouzière et Max Reynes. Ils m'ont permis, dans le cadre de la formation continue, cette évolution de carrière de Technicien Supérieur à Docteur en sciences des aliments, ceci en 10 ans. Je remercie Madame Florence Mathieu, Professeur à l'ENSAT de Toulouse d'avoir accepté de participer à ce jury et de juger ce travail en tant que rapporteur. Je remercie Monsieur Sevastianos Roussos, Directeur de Recherche à l'IRD d'avoir accepté de participer à ce jury et de juger ce travail en tant que rapporteur, mais aussi président du jury. Je remercie Monsieur Amaury Martinez, professeur à l'UCB d'avoir accepté de participer à ce jury et de juger ce travail en tant qu'examinateur. Je voudrais aussi remercier les personnes qui m'ont directement aidé dans mes travaux de thèse, comme Dominique, Jean Claude, Isabelle et Jean Christophe. Je n'oublierais pas les personnes qui m'ont aidé sur les autres activités de recherche et d'analyses, ce qui m'a laissé plus de temps pour mes travaux de thèse, je pense à Laurent, Renaud, Philippe et Philip, mais aussi Nathalie et Chantal. Je remercie aussi Oscar et Mirna, pour leur aide en ce qui concerne les échantillons de café du Mexique ainsi que les souches d'aspergillus isolées du café, et Mirna pour les travaux sur la PCR-DGGE effectués en commun. Ensuite il y a, tous les stagiaires et thésards qui ont contribué à ces résultats, Aly bien sûr, Nadège, Clémentine, Cyril, Carmen, Fabien. J'aurai une pensée particulière pour Erik. Je voudrais remercier aussi l'Université de Pau et des Pays de l'Adour, l'UNELLEZ, l'UCB, qui m'ont accompagné dans ce projet, et j'associe bien sur Amaury, Isabel,

The symbiotic association (plant-soil-microorganisms) has an important role in nitrogen (N) and phosphorus (P) uptake. The main objective of this study is to assess the potential of fungal and rhizobial symbionts as well as the importance of plant-soil-microorganism interactions on microbial dynamics. The upland rice and the beans were cultivated in mono or in co-culture using the rhizospheric soil of the upland rice and beans collected on plots treated with different levels of organic and mineral fertilizers. What about saying: Microbial (fungal and rhizobial) inoculate were constituted by root fragments (rice or bean) collected from previous crop and coded as I1 (root fragments from rice), I2 (root fragments from bean) and I3 (mixed root fragments from rice and bean). The results showed that soils inoculated with I1 and I3, were characterized by high phosphatase activity. These two treatments enhance also the amount of nitrogen and phosphorus in the aerial part of upland rice intercropped with bean. These results suggest that the bean with its symbiont can be considered as ecological engineers that stimulate the biological functioning of soils and is beneficial for upland rice cultivation.