Mycorrhiza helper bacteria: a promising model for the genomic analysis of fungal-bacterial interactions

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Linking diversity to function: highlight on the mineral weathering bacteria

International audienceWhat is the best way to identify new functions for which we currently know nothing? Here, we discuss the importance of combining cultivation-dependent and -independent approaches to identify new functions and new genes. We argue that although the cultivationdependent approach is presently viewed as an "old fashioned", focusing only on a limited proportion of the total bacterial communities, it remains essential to the characterization as well as the discovery of new potential functions in bacteria. This will allow us to highlight potential model bacterial strains for further genomic and genetic studies and to identify genes of interest. By illustrating an example of a function for which our current knowledge is so far limited, mineral weathering, we highlight different steps necessary to study of the mineral weathering bacterial communities, decipher their respective role as well as their distribution in various ecological niches of the soil

Altération bactérienne des minéraux dans les écosystèmes forestiers pauvres en nutriments (Analyse des communautés bactériennes et identification des mécanismes impliqués)

Dans les écosystèmes forestiers pauvres en nutriments, les minéraux du sol constituent la principale source de nutriments inorganiques nécessaires à leur bon fonctionnement. Néanmoins ces nutriments ne sont pas directement accessibles aux racines des arbres. C'est l'action conjointe de facteurs abiotiques, comme le pH ou la circulation de l'eau, et biotiques comme les racines ou les microorganismes du sol dont les bactéries, qui vont conduire à l'altération de ces minéraux. A ce jour, nos connaissances sur les communautés bactériennes impliquées dans le processus d'altération et leur distribution dans des sols forestiers restent limitées, notamment à des habitats tels que la rhizosphère et la mycorhizosphère. Les objectifs de cette thèse étaient de caractériser les communautés bactériennes colonisant les minéraux du sol et leur aptitude à altérer les minéraux et enfin d'identifier les gènes bactériens impliqués. La combinaison d'approches cultivable, non cultivable et de biogéochimie sur des minéraux enterrés pendant 4 ans dans un sol forestier, a démontré que leur surface était colonisée par des communautés bactériennes spécifiques, capables d'altérer les minéraux et présentant des capacités métaboliques limitées, suggérant que ce support pourrait être considéré comme un habitat : la minéralosphère. La relation minéral/bactéries a été testée in situ via un amendement minéral sur une plantation et a mis en évidence l'impact de la disponibilité en nutriments sur la structuration des communautés bactériennes capables d'altérer les minéraux. L'étude génétique réalisée sur la souche modèle PML1(12) a révélé l'implication de plusieurs mécanismes dans la fonction altérationIn nutrient-poor forest ecosystems, minerals are the main source of inorganic nutrients for the long lasting functioning of the forests. However, these nutrients are not directly accessible to the tree roots. It is the joined action of abiotic factors, such as pH and water circulation, and biotic factors such as tree roots and soil microorganisms, and notably bacteria, which leads to the solubilisation of these minerals. To date, our knowledge of the bacterial communities involved in the mineral weathering process and their distribution in forest soils is very limited and remains restricted to habitats such as the rhizosphere and mycorrhizosphere. The goals of this PhD thesis were to characterise the mineral associated bacterial communities, their ability to weather minerals and finally to identify the bacterial genes involved in the mineral weathering process. The combination of geochemical, cultivation-dependent and -independent approaches applied on minerals grounded in a forest soil during 4 years, revealed that the mineral associated bacterial communities were specific, able to weather minerals and had restricted metabolic abilities. These results suggest that minerals could be considered as a true ecological habitat: the mineralosphere. The mineral/bacteria relationship was tested in situ through a mineral amendment applied on a small-scale plantation, which has highlighted that the nutrient availability impacted the functional structure of the mineral weathering bacterial communities. At least, random mutagenesis applied on a model mineral weathering bacterial strain revealed that its mineral weathering ability resulted from several molecular mechanismsMETZ-SCD (574632105) / SudocNANCY1-Bib. numérique (543959902) / SudocNANCY2-Bibliotheque electronique (543959901) / SudocNANCY-INPL-Bib. électronique (545479901) / SudocSudocFranceF

Déterminisme moléculaire des interactions entre le champignon ectomycorhizien Laccaria bicolor S238N et des bactéries du sol

La symbiose ectomycorhizienne a un effet bénéfique sur la nutrition et le développement des arbres. Dans les sols, les champignons ectomycorhiziens interagissent continuellement avec des communautés bactériennes qui peuvent avoir une action bénéfique, neutre ou antagoniste vis-à-vis du champignon. Parmi ces bactéries, une attention particulière a été portée au cours de ces dernières années sur les bactéries auxiliaires de la mycorhization qui favorisent la symbiose ectomycorhizienne. La souche auxiliaire Pseudomonas fluorescens BBc6R8 améliore la survie pré-symbiotique et la croissance du champignon ectomycorhizien Laccaria bicolor S238N, et favorise son établissement en symbiose avec le Douglas. Mais les mécanismes moléculaires sous-jacents sont inconnus. A l aide d un dispositif de confrontation bactérie-champignon in vitro et d outils transcriptomiques, nous avons analysé les réseaux de gènes fongiques impliqués dans l interaction entre P. fluorescens BBc6R8 et L. bicolor S238N ainsi que le degré de spécificité de la réponse du champignon. De plus, nous avons examiné le rôle joué par certains métabolites fongiques et bactériens dans l interaction : thiamine, tréhalose, système de sécrétion de type III. Nos résultats suggèrent que l effet auxiliaire de la souche BBc6R8 soit dû à une combinaison de mécanismes : d une part une amélioration du statut nutritionnel du mycélium, d autre part une préparation des racines et des hyphes à l infection mycorhienne.Ectomycorrhizal fungi have a beneficial impact on tree nutrition and growth by forming symbiotic associations with roots. In their natural environment, they interact physically and metabolically with soil bacterial communities that are beneficial, neutral or antagonistic to the fungus. Since the 80ies, a specific interest has been given to bacterial strains that improve the formation of ectomycorrhizal symbiosis, so-called mycorrhiza helper bacteria. The strain Pseudomonas fluorescens BBc6R8 is particularly efficient to enhance the establishment of Douglas fir - Laccaria bicolor S238N mycorrhizal symbiosis, by improving the survival and the growth of the pre-symbiotic mycelium in soil. We have used both a global and a targeted approach to investigate the molecular mechanisms of this helper effect. In a first step, we have analysed, using an in vitro assay, the morphological and the transcriptomic responses of the ectomycorrhizal fungus to the presence of the helper bacteria at different time of the interaction. Then we have assessed the question of the specificity of the fungal response by studying the effect of non-helper bacterial strains on the fungal behaviour. Finally, we have focused on the role played by several key molecules in the interaction: thiamine, trehalose and the type III secretion system. We suggest that the bacterial strain would exert its helper effect through a combination of mechanisms: an improvement of the nutritional status of the fungus and a preparation of both the plant and the ectomycorrhizal fungus to the root infection.NANCY1-Bib. numérique (543959902) / SudocSudocFranceF

Des bactéries à la rescousse des champignons symbiotiques

National audienceLes champignons symbiotiques jouent un rôle majeur dans la nutrition des arbres. Cette symbiose est loin d’être une simple interaction bipartite entre plantes et champignons ; des bactéries interviennent en effet dans le processus de formation des mycorhizes. Si les mécanismes en jeu restent méconnus, le développement récent des techniques de génomique permet néanmoins d’espérer de nombreux progrès dans ce domaine

Inter-kingdom encounters: recent advances in molecular bacterium–fungus interactions

International audienceInteractions between bacteria and fungi are well known, but it is often underestimated how intimate and decisive such associations can be with respect to behaviour and survival of each participating organism. In this article we review recent advances in molecular bacterium–fungus interactions, combining the data of different model systems. Emphasis is given to the positive or negative consequences these interactions have on the microbe accommodating plants and animals. Intricate mechanisms of antagonism and tolerance have emerged, being as important for the biological control of plants against fungal diseases as for the human body against fungal infections. Bacterial growth promoters of fungal mycelium have been characterized, and these may as well assist plant-fungus mutualism as disease development in animals. Some of the toxins that have been previously associated with fungi are actually produced by endobacteria, and the mechanisms that lie behind the maintenance of such exquisite endosymbioses are fascinating. Bacteria do cause diseases in fungi, and a synergistic action between bacterial toxins and extracellular enzymes is the hallmark of such diseases. The molecular study of bacterium–fungus associations has expanded our view on microbial communication, and this promising field shows now great potentials in medicinal, agricultural and biotechnological application

Tiques, bactéries, maladie et projets participatifs

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Root-Associated Bacteria Contribute to Mineral Weathering and to Mineral Nutrition in Trees: a Budgeting Analysis

The principal nutrient source for forest trees derives from the weathering of soil minerals which results from water circulation and from plant and microbial activity. The main objectives of this work were to quantify the respective effects of plant- and root-associated bacteria on mineral weathering and their consequences on tree seedling growth and nutrition. That is why we carried out two column experiments with a quartz-biotite substrate. The columns were planted with or without pine seedlings and inoculated or not with three ectomycorrhizosphere bacterial strains to quantify biotite weathering and pine growth and to determine how bacteria improve pine growth. We showed that the pine roots significantly increased biotite weathering by a factor of 1.3 for magnesium and 1.7 for potassium. We also demonstrated that the inoculation of Burkholderia glathei PML1(12) significantly increased biotite weathering by a factor of 1.4 for magnesium and 1.5 for potassium in comparison with the pine alone. In addition, we observed a significant positive effect of B. glathei PMB1(7) and PML1(12) on pine growth and on root morphology (number of lateral roots and root hairs). We demonstrated that PML1(12) improved pine growth when the seedlings were supplied with a nutrient solution which did not contain the nutrients present in the biotite. No improvement of pine growth was observed when the seedlings were supplied with all the nutrients necessary for pine growth. We therefore propose that the growth-promoting effect of B. glathei PML1(12) mainly resulted from the improved plant nutrition via increased mineral weathering

Effect of plants and soil bacteria on mineral weathering

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The effect of plants and soil bacteria on mineral weathering

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