Different Medicago truncatula genotypes, expressing different phenotypes, modulate microbial functional genes in the rhizosphere

Plants host in their rhizosphere a remarkable diversity of microorganisms that in return promote plant growth and health. Thus, the plant microbiota emerges as a novel component that expand the capacity of plants to adapt to the environment, and thus pave the way for future breeding approaches.It is widely known that different plant species harbor different microbiota, but very few studies showed an impact of the plant genotypes on the microbiota. These contrasting results may depend on the choice of the tested genotypes.We formulate the hypothesis that only those plant genotypes showing high genetic diversity and expressing different phenotypes harbor different rhizosphere microbiota and a…

Editor for the Research Topic 'The Plant Holobiont Volume I: microbiota as part of the holobiont; challenges for agriculture' in Frontiers in Microbiology.

International audience

Drought stress impacts the microbiota mediating iron dynamic in the pea rhizosphere

Agroécologie, INRAE, Institut Agro, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, FranceMicrobiota, with their consortia of genomes, extend the genetic repertoires of host plants to form ‘extended genotypes’, resulting in extended host phenotypes. Trecently, the term ‘holobiont’, which encompasses the host plant plus its associated microbiota, has been proposedHow environmental properties impact both the plant and microbial components of the holobiont, and its phenotype, still remain to be explored.We addressed this question by testing the impact of different abiotic conditions (drought stress and soil pH) on plant and microbial phenotypes in relation to iron. Iron…

Biologie des communautés dans la rhizosphère : analyse des interactions plantes - champignons mycorhizogènes à arbuscules - bactéries

National audience

Strategies for analyzing interactions between arbuscular mycorrhiza and bacteria

National audience

Medicago species affect the community composition of arbuscular mycorrhizal fungi associated with roots

National audience; The symbiosis between plants and arbuscular mycorrhizal fungi (AMF) is ancient and involves 80% of terrestrial plant families. The symbiotic association between AMF and plants was described to be non specific. However, AMF were reported to influence plant community diversity and productivity. On the other way, the effect of plant genotypes belonging to closely related species on AMF diversity has not been explored so far. The aim of this work was to assess the impact of four different Medicago species, M. laciniata, M. murex, M. polymorpha and M. truncatula cv. Jemalong J5, on the composition of AM fungal community, when cultivated in a silty-thin clay soil (Mas d’Imbert,…

Interactions plantes/micro-organismes dans la rhizosphère

Prod 2018-76e EA SPE BIOME INRA AGROSUP; National audience; Chapitre 4. Interactions plantes/micro-organismes dans la rhizosphère La rhizosphère, un lieu d’échanges multiplesRecrutement des micro-organismes dans la rhizosphèreInteractions plantes/micro-organismes, une longue histoireMicrobiote rhizosphérique, des bénéfices pour la planteValorisation des interactions plantes/micro-organismes en agroécologieConclusion et perspectives Bibliographie résumé du livre : Les sols sont des milieux où évolue une myriade d’organismes différents, déterminant une série de fonctions, qui se traduisent en services écosystémiques essentiels pour l’humanité. Mieux connaitre ces organismes, leur biodiversité…

Ecology of arbuscular mycorrhizas : interactions plant - fungal genotypes and mycorrhizas - bacteria

Microdiversity of Burkholderiales associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula

The genetic diversity of bacterial communities associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula was characterized by two approaches. Firstly, phylogenetic analysis was performed on 164 partial 16S rRNA gene-intergenic spacer (IGS) sequences from operational taxonomic units previously shown to be preferentially associated with mycorrhizal roots. These sequences were distributed into three branches corresponding to Comamonadaceae, Oxalobacteraceae and Rubrivivax subgroups. Most sequences were obtained from mycorrhizal roots, indicating the preferential association of the corresponding families with mycorrhizal roots. A second phylogenetic analysis was performed on t…

Diversité et activités microbiennes dans la rhizosphère: des atouts majeurs en agroécologie

National audience; Les rhizodépôts libérés par les plantes stimulent une microflore abondante et active dans la rhizosphère. La diversité des communautés microbiennes correspondantes est influencée par la nature des rhizodépôts (composition, molécules signal) qui diffère selon les génotypes végétaux. Le coût pour la plante correspondant à la libération de ces rhizodépôts est contrebalancé par le bénéfice issu des effets positifs de certaines populations microbiennes rhizosphériques sur la croissance et la santé de la plante-hôte. La connaissance des traits végétaux impliqués dans la sélection de ces populations bénéfiques, au sein des communautés microbiennes telluriques, représente un enje…

Interactions between a mycorrhiza helper bacterium and arbuscular mycorrhizas

Pseudomonas fluorescens C7R12 was shown to promote arbuscular mycorrhization and to act as a ‘Mycorrhiza Helper Bacteria’ (MHB). The complex interactions between this model strain, Arbuscular Mycorrhizal (AM) fungi and host-plants were analysed by assessing the specificity of these interactions and by characterizing bacterial cell organization on mycorrhizal roots. Evaluation of the interaction specificity relied on the comparison of the bacterial effect on (i) the in vitro saprophytic growth of Glomus mosseae and Gigasopora rosea and (ii) the root colonization of two different plant species (Medicago truncatula and Lycopersicon esculentum) by the two AM fungal species. Characterization of …

Maîtrise et gestion de la biodiversité dans les sols: quelles perspectives ?

National audience

Participation à la fête de la nature et de la biodiversité au Jardin des Sciences du Parc de l’Arquebuse à Dijon le dimanche 21 mai 2017

Functional Core microbiota: identification and involvement in plant nutrition

Plants host in their rhizosphere a remarkable diversity of microorganisms that in return can promote plant growth and health. The microbiota that is systematically associated with a given plant genotype is called the core microbiota. However, the core microbiota has been mostly defined on taxonomic basis, whilst the microbiota recruited by the plant in different environments seems to share greater functional similarity and the concept of core functional microbiota has been proposed accordingly. The purpose of the PhD thesis is to give evidence of the existence of a core functional microbiota. The PhD thesis aims to: (i) assess the impact of different plant genotypes on the rhizosphere funct…

POSITIF : Promouvoir la tolérance du pois aux stress abiotique (Fer) et biotique (phytopathogène) via les interactions biotiques dans la rhizosphère

Shotgun metagenomics sequencing of the rhizosphere microbiota associated to seven ecotypes of Medicago truncatula

International audience; Healthy plants host a remarkable diversity of microorganisms known as plant microbiota, which provide host services such as pathogen protection and nutrient acquisition. Thus, plant microbiota emerges as a trait that extends the capacity of plants to adapt to their environment. So far, microbial community profiling has mostly allowed the description of the phylogenetic structure of plant microbiota, whereas functional insights were mostly obtained from experiments using model strains. Thus, the plant impact on the microbial functional genes pool in the rhizosphere remains largely unknown. The goals of the study were to (i) compare the functional genes pool of the rhi…

Combining molecular microbial ecology with ecophysiology and plant genetics for a better understanding of plant-microbial communities' interactions in the rhizosphere.

18 pages; International audience

Plant/micro-organism interactions in the rhizosphere. Chap 4

Prod 2018-76i EA SPE BIOME INRA AGROSUP; International audience; Soils are environments where a myriad of different organisms evolve, determining a series of functions which translate into ecosystem services that are essential for humanity. Improving our understanding of these organisms, their biodiversity and their interactions with each other, as well as with the environment, represents a major challenge. Soil ecology has its roots in natural history. The ecological approach focused on soils is notable for integrating, at least partially, the contributions of soil sciences (physics, chemistry, biochemistry). By renewing methods of observation and analysis (especially molecular ones) and t…

Holobiont interactions occurring in pea-wheat intercropping impact both plant phenotype and the associated microbiota

Identification of bacterial groups preferentially associated with mycorrhizal roots of Medicago truncatula

ABSTRACT The genetic structures of bacterial communities associated with Medicago truncatula Gaertn. cv. Jemalong line J5 (Myc + Nod + ) and its symbiosis-defective mutants TRV48 (Myc + Nod − ) and TRV25 (Myc − Nod − ) were compared. Plants were cultivated in a fertile soil (Châteaurenard, France) and in soil from the Mediterranean basin showing a low fertility (Mas d'Imbert, France). Plant growth, root architecture, and the efficiency of root symbiosis of the three plant genotypes were characterized in the two soils. Structures of the bacterial communities were assessed by automated-ribosomal intergenic spacer analysis (A-RISA) fingerprinting from DNA extracted from the rhizosphere soil an…

Améliorer et utiliser les associations bénéfiques plantes x microorganismes

Le sol est considéré comme l’habitat majeur de la biosphère terrestre. Les microorganismes représentent une partie importante de la biodiversité du sol. Certains champignons et bactéries interagissent de façon bénéfique, directement ou indirectement, avec les plantes. Ces microorganismes du sol apparaissent comme des acteurs clés de ces services écosystémiques rendus par la nature à la société humaine. Les champignons mycorhiziens à arbuscules (CMA) jouent un rôle essentiel dans l’absorption d’éléments nutritifs de la plupart des espèces végétales, dans la séquestration du carbone, dans l’agrégation des particules dans le sol, et la tolérance des plantes vis à vis des stress biotiques et ab…

Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping

International audience; Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume i…

Colonization of adventitious roots ofMedicago truncatulabyPseudomonas fluorescensC7R12 as affected by arbuscular mycorrhiza

Pseudomonas fluorescens C7R12 was previously shown to promote colonization of Medicago truncatula roots by Glomus mosseae BEG12. To gain more insight into the interaction between C7R12 and BEG12, the cell organization of C7R12 was characterized on adventitious roots mycorrhized or not with BEG12 and on extraradical hyphae. Bacterial cell observations were made using the immuno-fluorescence technique and confocal laser scanning microscopy. Five types of cell organization, so-called organization types (OT), were identified: small or large single cells, cells by pair and cells in microcolonies or in strings. The frequencies of each OT on the roots were expressed as the percentage of observatio…

Ecologie du microbiote rhizosphérique impliqué dans la dynamique du fer et conséquences sur la teneur en fer des plantes

Le pois représente une espèce particulièrement intéressante en agroécologie pour sa capacité à fixer l’azote atmosphérique, ainsi que pour sa contribution à la diversification des cultures, telles que les cultures associées pois-blé. Une de limitations majeures à la culture du pois est son rendement irrégulier, dû, entre autre, à sa sensibilité à la carence en fer. Le pois est également intéressant pour l’alimentation humaine, compte tenu de la richesse en protéines de ses graines. La part d’alimentation humaine reposant sur les protéines végétales est grandissante, il est donc indispensable de garantir la teneur en fer de ces produits pour limiter la propagation de l’anémie, qui est déjà u…

Determinism and genetic diversity of pea intercropping ability in peawheat association

Intercropping pea (Pisum sativum) with cereals stabilizes the yield and overall quality of the products in the context of low-input cropping conditions thanks to a more efficient use of resources through interspecific competitive interactions [1] . In order to develop this cropping system which increases the sustainability of agroecosystems, we have launched a survey of pea genetic variability for intercropping ability. Field experiments were carried out over two years using 11 phenotypically diverse pea genotypes associated with two contrasted wheat varieties (height, precocity). We characterized several functional architecture and phenology traits potentially impacting the interactions am…

Toward an integrated approach for studying plant-microbe interactions in the rhizosphere: from genomic to proteomic

International audience

Variable and core functional microbiota associated with seven Medicago truncatula genotypes

The rhizosphere microbiota emerges as a novel component that expands plant adaptation to its environment, and thus paves the way for future breeding approaches. Knowledge regarding the "functional core microbiota", which refers to the microbial taxa bearing essential functions for holobiont fitness, is required to move forward in this area. The aim of the present study was to compare the functional microbiota recruited by different plant genotypes in order to identify itscore and variable components. Seven genotypes of Medicago truncatula (DZA315-16, DZA315-26, DZA045-6, F83005-5, SA028064, Jemalong A17 and J6), representatives of a core collection of 184 genotypes, were studied. Functional…

Caractérisation fonctionnelle des partenaires de l’association pois/blés pour l’optimisation d’agro-écosystèmes durables via le levier génétique

Effect of arbuscular mycorrhiza establishment on the genetic structure and diversity of bacteria in the rhizosphere of Medicago truncatula

National audience; The rhizosphere is the volume of soil which is influenced by plant root activity. Plant roots release 20% of the photosynthates into the rhizosphere. This process sustains the development of an active free living microflora in the rhizosphere compared to the bulk soil. Plants establish also symbiotic associations with soil microorganisms. Arbuscular mycorrhizas (AM) are mutualistic symbioses between soil fungi and plant roots. AM contribute to plant adaptation to low fertility environments. AM are established by 80% of terrestrial plant families including major crop plants. AM are also ancient symbiosis (400 million years). AM are known to be non-specific associations. Ho…

Interactions durables entre plantes et microorganismes dans les sols

National audience

EFfORT : Ecologie et Fonctionnement du micrObiote Rhizosphérique impliqué dans l’amélioration de la nuTrition en fer du pois

Qu’attendre des recherches en microbiologie du sol ?

SPE EA EcolDur GenoSol MERS IPM Résumé du livre : La fertilité des sols est au carrefour des enjeux de sécurité alimentaire, de protection de l’environnement et de rentabilité économique de l’activité agricole. Cet ouvrage présente les résultats d’une réflexion prospective sur le contexte de la fertilisation dans les 5-10 ans à venir. Il définit les besoins en termes de méthodes et d'outils pour la gestion des cycles biogéochimiques et le raisonnement de la fertilisation en agriculture. Mots clés du livre : agriculture - agronomie - eau - effluent - engrais - environnement - fertilisation - pollution - prévention - production végétale - prospective - sol Description du chapitre 10 (partie 3…

Changes in gene expression during adaptation of Listeria monocytogenes to the soil environment

project SEST 009; International audience; Listeria monocytogenes is a ubiquitous opportunistic pathogen responsible for listeriosis. In order to study the processes underlying its ability to adapt to the soil environment, whole-genome arrays were used to analyse transcriptome modifications 15 minutes, 30 minutes and 18 h after inoculation of L. monocytogenes EGD-e in soil extracts. Growth was observed within the first day of incubation and large numbers were still detected in soil extract and soil microcosms one year after the start of the experiment. Major transcriptional reprofiling was observed. Nutrient acquisition mechanisms (phosphoenolpyruvate-dependent phosphotransferase systems and…