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Ultramafic (i.e. serpentine) soils are widespread in the Balkans and particularly in Albania. They account for a large part of plant endemism in that region and host several hyperaccumulator species, which are characterized by leaf nickel concentrations frequently above 1%. This rich nickel hyperaccumulating flora could serve as candidate to be used in phytoextraction and agromining. Despite recent interest in metal hyperaccumulating plants and agromining, very few studies have investigated the bacterial diversity and the influence of environmental factors on microbial gene profiles in the rhizosphere of hyperaccumulator plants growing on ultramafic soils. Because rhizospheric bacteria could be crucial to the success of phytoremediation, we studied a total of 48 nickel-hyperaccumulating plants which were sampled from four species that are widespread in Albania: Noccaea ochroleuca, Odontarrhena smolikana, O. rigida and O. chalcidica. All samples were taken from the ultramafic regions of Librazhd and Pogradec in eastern Albania in October 2015. Our study shows that Proteobacteria, Actinobacteria and Acidobacteria dominated the soil bacterial communities. Of these three phyla, only Proteobacteria was relatively abundant. This study underlines the influence of soil Cation Exchange Capacity on the bacterial community's diversity and structure. Based on the predicted metagenomes, the genes belonging to amino acid, lipid and carbohydrate metabolisms were identified as major gene families. Our study sheds some light on our understanding of how bacterial communities are structured within and affect the rhizosphere of hyperaccumulator plants from ultramafic soils in Albania.

Plant genetic variation, through its phenotypic display, can determine the composition of below ground microbial communities. Variation within a species is increasingly acknowledged to have substantial ecological consequences, particularly through trophic cascades. We hypothesized that the intraspecific genotypic variation of the tree host might impact the phylogenetic composition of its rhizospheric microbial communities, by favouring particular clades, that might be further reflected in ecosystem process rates. We tested whether the intraspecific genotypic variation of Pinus pinaster modulates nutrient cycling by determining the phylogenetic structure of its symbiotic ectomycorrhizal fungi and rhizospheric bacteria. We sequenced fungal and bacterial molecular markers and reconstructed phylogenies in the rhizosphere of P. pinaster trees belonging to three genotypic variants (Mediterranean, Atlantic, African) in three 45-year-old common garden experiments, and measured seven soil enzymatic activities. Local effects, based on differences in elevation and soil conditions across sites, were strong predictors of the ectomycorrhizal and bacterial communities thriving in tree’s rhizosphere. Across-site variation also explained differences in phosphorus cycling. We detected, however, a significant effect of the plant genotype on the phylogenetic structure of the root-associated microbiota that was consistent across sites. The most productive Mediterranean plant genotype sheltered the most distinct root microbiome, with the dominant Basidiomycetes and Proteobacteria having a strong influence on the phylogenetic microbial community structure and associating with an enhanced hydrolysis of celluloses, hemicelluloses and chitin. Beneath the less productive Atlantic genotype, the less abundant Ascomycetes and up to thirteen bacterial phyla shaped the phylogenetic microbial structure, and predicted the rates of peptidase. Ectomycorrhizal fungi explained the activity of cellulases and protease, and bacteria that of hemicellulases and chitinase, suggesting functional complementarity. Synthesis. This is the first report using three-replicated long-term common gardens in mature forests to disentangle plant genotype- and site-specific drivers of the rhizospheric microbiome and its enzymatic potential. We concluded that intraspecific variation in primary producers leaves a phylogenetic signature in mutualists and decomposers that further modulate key steps in carbon and nitrogen cycles. These results emphasize the ecological relevance of plant intraspecific diversity in determining essential plant–soil feedbacks that control ecosystem productivity and performance., This work was supported by the projects MyFUNCO (CGL2011‐29585‐C02‐02), and Microfac (CGL2014‐58333‐P) funded by the Spanish Ministry for Economy and Competitiveness (MINECO), as well as by the LABoratoire d'EXcellence Arbre (LABEX Arbre, INRA‐Nancy). L.P.‐I. held a pre‐doctoral fellowship and M.G. a Ramón y Cajal contract, both awarded by the Spanish Ministry of Economy and Competitiveness‐MINECO.

To combat pests of crops (herbivores and pathogens) new pathways have been explored, in particular biological control. Used the nature and its organisms to regulate the populations of pathogens, that is the goal of the biological fight also called biocontrol. Among the organisms commonly found in biocontrol are micro-organisms, be they fungi or bacteria. These microorganisms have very interesting capabilities for farmers and agronomists. Indeed, studies have shown that they are able to interact with plants to allow a better growth and health of it.Then, in this thesis, we were interested in bacteria to find alternative methods of struggle with Fusarium graminearum, a pathogen of cereals responsible for high yield losses, especially thanks to the production of mycotoxins that will make the seeds unfit for human and animal consumption.Through an original approach of keeping noninhibitory strains in vitro for in planta tests, we have been able to show the limitations of in vitro selection. Thanks to the metabolic exploration of a particularly efficient strain, we have also been able to highlight potential new antifungal molecules. Through a model strain, we explored the mechanisms of the establishment of systemic resistance in wheat induced by bacteria. And finally, we have explored the potential of bacterial combinations in wheat protection that seems to represent a real future in the world of biocontrol.The work done is in line with the needs of new resources to limit the use of pesticides, but also in a need to better understand the tripartite interactions between wheat, pathogen and beneficial bacteria, Pour lutter contre les nuisibles des cultures (herbivores et pathogènes), de nouvelles voies ont été explorées et en particulier la lutte biologique. Utilisé la nature et ses organismes pour réguler les populations de pathogènes, tel est le but de la lutte biologique aussi appelé biocontrôle. Parmi les organismes couramment retrouvés dans le biocontrôle se trouve les micro-organismes, que cela soit des champignons ou des bactéries. Ces micro-organismes possèdent des capacités très intéressante pour des agriculteurs et agronomes. En effet, des études ont montré qu’ils étaient capables d’interagir avec les plantes pour permettre une meilleure croissance et santé de celle-ci. Alors, dans cette thèse, nous nous sommes intéressés aux bactéries pour trouver des méthodes de luttes alternatives à Fusarium graminearum, un pathogène des céréales responsables de fortes pertes de rendements, en particulier grâce à la production de mycotoxines qui va rendre les grains impropres à la consommation humaine et animales. Par l’intermédiaire d’une approche original consistant à garder des souches non-inhibitrice in vitro pour des tests in planta, nous avons pu montrer les limites de la sélection in vitro. Grâce à l’exploration métaboliques d’une souche particulièrement efficace, nous avons aussi pu mettre en évidence de potentiels nouvelles molécules antifongiques. Par l’intermédiaire d’une souche modèle, nous avons explorer les mécanismes de la mise en place d’une résistance systémique chez le blé induite par les bactéries. Et enfin, nous avons exploré le potentiel des combinaisons de bactéries dans la protection du blé qui semble représenter un vrai futur dans le monde du biocontrôle. Les travaux effectués s’inscrivent dans les besoins de nouvelles ressources pour limiter l’utilisation des pesticides, mais aussi dans un besoin de mieux comprendre les interactions tripartite entre blé, pathogène et bactéries bénéfiques

Six bacterial strains were isolated from the oak-Scleroderma citrinum ectomycorrhizosphere in acidic and nutrient-poor forest soil for their high efficacy to weather minerals. Four of the six isolates, PML1(12)T and PML1(4), PML1(14) and PML1(16), were further characterized extensively. They were Gram negative, obligate aerobic, motile, non spore forming and rod-shaped. The major fatty acids of strain PML1(12)T were cyclo-C17:0, cyclo-C19:0-ω8c, C16:0 and C18:1-ω7c. The GC content of the DNA was 60.8%. The 16S rRNA and GyrB analyses showed that the four PML strains formed a distinct phylogenetic lineage within the genus Caballeronia, most closely related to Caballeronia udeis. This result was confirmed by whole-genome phylogeny analyses done on strain PML1(12)T. The results of digital DNA–DNA relatedness further supported the separation of the new isolates from closely related species. Morphological, chemotaxonomic properties were also consistent with the description of the genus Caballeronia. It is therefore proposed that strains PML1(12)T and PML1(4), PML1(14) and PML1(16) be recognized as a novel species, for which the name Caballeronia mineralivorans sp. nov. is proposed. The type strain is PML1(12)T (= DSM 104028 and LMG 2991).

Purpose : This work was conducted to determine whether Nickel-resistant rhizosphere bacteria (NiRRB) affected the Ni uptake and hyperaccumulation by Noccaea caerulescens. Material and methods : Ni-resistant bacterial strains (10 mM Ni), Bacillus pumilus and Micrococcus spp., were originally isolated from the rhizosphere of N. caerulescens (Brassicaceae) collected from serpentine Ni-rich soil in the Vosges mountains (France). They served to inoculate axenic seeds of N. caerulescens, which were then sown aseptically into sterile soil Magenta boxes and cultured under controlled conditions. Results and discussion : Cultures inoculated with NiRRB showed a disappearance of chlorosis signs and a significant increase of the aerial biomass compared to the axenic control (1.5-fold higher). Despite the drastic decrease of the water-extractable Ni in the soil (80 %) at the end of the growth, there was no significant effect on Ni accumulation by N. caerulescens compared to the axenic control. A highly significant promoting effect on plant growth (fourfold higher) and an increase of Ni accumulation (65-fold higher) by N. caerulescens were shown in cultures with native microorganisms (nonsterile control) compared to the axenic control. Conclusions : The NiRRB strains used in this study reduced Ni bioavailability in the soil and did not improve the Ni uptake by N. caerulescens. Nevertheless, they induced promoting effects on the growth of this plant. They could serve as an effective metal-immobilizing and growth-promoting bioinoculant for plants in Ni-stressed soils. Optimal growth and Ni uptake by N. caerulescens requires the presence of native microbial community.

International audience; Lateral gene transfers (LGT), species to species transmission of genes by means other than direct inheritance from a common ancestor, have played significant role in shaping prokaryotic genomes and are involved in gain or transfer of important biological processes. Whether LGT significantly contributed to the composition of an animal genome is currently unclear. In nematodes, multiple LGT are suspected to have favored emergence of plant-parasitism. With the availability of whole genome sequences it is now possible to assess whether LGT have significantly contributed to the composition of an animal genome and to establish a comprehensive list of these events. We generated clusters of homologous genes and automated phylogenetic inference, to detect LGT in the genomes of root-knot nematodes and found that up to 3.34% of the genes originate from LGT of non-metazoan origin. After their acquisition, the majority of genes underwent series of duplications. Compared to the rest of the genes in these species, several predicted functional categories showed a skewed distribution in the set of genes acquired via LGT. Interestingly, functions related to metabolism, degradation or modification of carbohydrates or proteins were substantially more frequent. This suggests that genes involved in these processes, related to a parasitic lifestyle, have been more frequently fixed in these parasites after their acquisition. Genes from soil bacteria, including plant-pathogens were the most frequent closest relatives, suggesting donors were preferentially bacteria from the rhizosphere. Several of these bacterial genes are plasmid-borne, pointing to a possible role of these mobile genetic elements in the transfer mechanism. Our analysis provides the first comprehensive description of the ensemble of genes of non-metazoan origin in an animal genome. Besides being involved in important processes regarding plant-parasitism, genes acquired via LGT now constitute a substantial proportion of protein-coding genes in these nematode genomes.

International audience; The main effects of antagonistic rhizobacteria on plant pathogenic fungi are antibiosis, fungistasis or an indirect constraint through the induction of a plant defence response. To explore different biocontrol mechanisms, an in vitro confrontation assay was conducted with the rhizobacterium Pseudomonas fluorescens Pf29Arp as a biocontrol agent of the fungus Gaeumannomyces graminis var. tritici (Ggt) on wheat roots. In parallel with the assessment of disease extension, together with the bacterial and fungal root colonization rates, the transcript levels of candidate fungal pathogenicity and plant-induced genes were monitored during the 10-day infection process. The bacterial inoculation of wheat roots with the Pf29Arp strain reduced the development of Ggt-induced disease expressed as attack frequency and necrosis length. The growth rates of Ggt and Pf29Arp, monitored through quantitative polymerase chain reaction of DNA amounts with a part of the Ggt 18S rDNA gene and a specific Pf29Arp strain detection probe, respectively, increased throughout the interactions. Bacterial antagonism and colonization had no significant effect on root colonization by Ggt. The expression of fungal and plant genes was quantified in planta by quantitative reverse transcription-polymerase chain reaction during the interactions thanks to the design of specific primers and an innovative universal reference system. During the early stages of the tripartite interaction, several of the fungal genes assayed were down-regulated by Pf29Arp, including two laccases, a β-1,3-exoglucanase and a mitogen-activated protein kinase. The plant host glutathione-S-transferase gene was induced by Ggt alone and up-regulated by Pf29Arp bacteria in interaction with the pathogen. We conclude that Pf29Arp antagonism acts through the alteration of fungal pathogenesis and probably through the activation of host defences

Effects of soil type on rhyzospheric and endophitic bacterial communities associated to cherry rootstock Colt (Prunusavium). 10. Symposium on Bacterial Genetics and Ecology - Coexisting on a Changing Planet (BAGECO 10)