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…

Additional file 3: of Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens

Mutagenesis of the quorum sensing determinants of pAtP4. All mutations were generated by the insertion of the same Gm resistance cassette that originated from p34S-Gm [39] either at the XbaI site of the cinI gene or at a reconstituted SphI site generated by the fusion of parts of cinR and cinX determinants in a synthetic ORF. (PDF 46Â kb)

Additional file 4: of Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens

The 32 differentially expressed genes identified by RNA-seq. Only changes above 3 fold with a p-value lower than 5 10 â 2 were considered significant. All differentially expressed genes were upregulated in P4 when compared to P4cinI. (PDF 285Â kb)

L’holobionte vigne, un levier biologique pour lutter contre les dépérissements ?

National audience

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…

L’holobionte « vigne » face au dépérissement ou quand le « vivre ensemble » n’est plus à l’équilibre

Prod 2019-165 SPE EA IPM BIOmE GenoSol INRA UB; National audience

Utilisation et possibilités de méthodes dites -omiques en viticulture

Additional file 2: of Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens

UPLC MS-MS solvent composition. The table provides the composition of the solvent mixture used in the UPLC MS-MS analyses of the concentrated extract of the culture supernatant of strain P4. (DOCX 14Â kb)

The holobiont, a biological lever to manage some declines of grapevine

International audience; The concept of a multicellular organism to describe complex organisms composed of groups of analogous cells called tissues and organs with specific functions, shows currently some limitations. An organism such as a plant does not live alone, but closely associated with different microbial communities making up its microbiomes. The microbiomes, specific to a tissue, interact with the plant and modulate some of its functions, including physiology and immunity. The host and the associated microbiomes define a holobiont, whose function is influenced by the spatio-temporal dynamics of their interactions. Thus, a dysfunction of the grapevine holobiont (linked for example t…

Répercussions spatiales de l’esca sur l’holobionte vigne : réponse du microbiome dans le continuum sol/feuilles

Dans le cadre du projet Holoviti (Plan National Dépérissement du Vignoble), l’holobionte vigne est étudié, dans le continuum sol - racines - parties aériennes (SRP), chez des ceps symptomatiques (S) ou asymptomatiques (AS) de la forme lente d’esca (tigrures foliaires). Ces recherches ont été réalisées sur une parcelle du château de Marsannay, située sur la commune de Couchey en Côte d’Or (21). Celle-ci a été choisie car elle présente simultanément trois types de dépérissements : deux liés à des agents pathogènes, respectivement viraux (agent du court-noué) et fongiques (agents de l’esca), et un lié à des dysfonctionnements physiologiques (porte-greffe 161-49C). Cette parcelle a été cartogra…

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…

Influence of the FanLeaf Virus on the grapevine holobiont : a study from the soil to the leaves

The grapevine FanLeaf (FL) corresponds to an infectious decline (nepovirus) which appears in patches within the plots. This disease leads to a progressive degeneration of grapevine plants which ultimately leads to the death. At present, about 60% of the French vineyard would be affected, of which 30% in an important way. Sixteen nepoviruses are responsible for grapevine degeneration or decline. Nevertheless, the Grapevine FanLeaf Virus (GFLV) is the main responsible agent. It is specifically transmitted from plant to plant by a soil-borne ectoparasitic nematode, Xiphinema index. The nematodes, by successively biting two neighboring plants whose roots are close, inoculate the virus from the …

Additional file 1: of Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens

Map of the genetic determinants involved in Ti plasmid conjugation in Agrobacterium strain C58. The functions of operons or genetic regions are as follows: acc, agrocinopine catabolism; arc, agrocinopine regulation of conjugation; noc, nopaline catabolism; tra, conjugative transfer region a; trb conjugative transfer region b; vir, virulence. Both the acc and arc operons are regulated by the repressor AccR. In the presence of agrocinopines A and B or in an accR mutant, the acc and arc operons are expressed. The expression of the arc operon permits the production of the QS regulator TraR. The production of the QS signal 3O,C8-HSL by the synthase TraI leads to an accumulation of the signal unt…

Le microbiote de la vigne : de nouveaux paradigmes et une perspective pour la vigne de demain

Prod 2018-253a SPE EA BIOmE IPM INRA UB; National audience

Influence du court noué sur la diversité fonctionnelle des champignons mycorhiziens à arbuscules dans des racines et du sol de vigne

Le court-noué (CN) correspond à un dépérissement infectieux (népovirus) qui apparaît par taches au sein des parcelles. Cette maladie entraîne une dégénérescence progressive de la vigne qui conduit in fine à la mort des ceps. A l’heure actuelle, environ 60% du vignoble national serait touché, dont 30% de façon importante. Seize népovirus sont responsables de dégénérescence ou de dépérissement de la vigne. Cependant, le Grapevine FanLeaf Virus (GFLV) est le principal agent responsable. Il est transmis spécifiquement de plante à plante par un nématode ectoparasite du sol, Xiphinema index. Les nématodes, en piquant successivement deux ceps voisins dont les racines sont proches, inoculent le vir…

Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens.

Background Agrobacterium tumefaciens strain P4 is atypical, as the strain is not pathogenic and produces a for this species unusual quorum sensing signal, identified as N-(3-hydroxy-octanoyl)-homoserine lactone (3OH,C8-HSL). Results By sequence analysis and cloning, a functional luxI-like gene, named cinI, has been identified on the At plasmid of A. tumefaciens strain P4. Insertion mutagenesis in the cinI gene and transcriptome analyses permitted the identification of 32 cinI-regulated genes in this strain, most of them encoding proteins responsible for the conjugative transfer of pAtP4. Among these genes were the avhB genes that encode a type 4 secretion system (T4SS) involved in the forma…

Additional file 5: of Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens

Differentially expressed genes. Xlsx. Four repeats are show for the mutant strain P4cinI (col. B to E) with repetition numbers (e.g. rep1_cinI) and three repeats for the wild type strain P4 (col. F to H), also with repetition numbers (e.g. rep1_P4). Average values are given for the mutant strain P4cinI (col. I) and the wild type strain P4 (col. J). Fold change and Log2 fold change are also shown (col. K and L) along with the raw p values and adjusted p values (col. M and N). (XLSX 15Â kb)