Diversity and Evolution of the Phenazine Biosynthesis Pathway

ABSTRACT Phenazines are versatile secondary metabolites of bacterial origin that function in biological control of plant pathogens and contribute to the ecological fitness and pathogenicity of the producing strains. In this study, we employed a collection of 94 strains having various geographic, environmental, and clinical origins to study the distribution and evolution of phenazine genes in members of the genera Pseudomonas , Burkholderia , Pectobacterium , Brevibacterium , and Streptomyces . Our results confirmed the diversity of phenazine producers and revealed that most of them appear to be soil-dwelling and/or plant-associated species. Genome analyses and comparisons of phylogenies inf…

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…

L'agroécologie, un chantier prioritaire pour l'INRA

Interview de Philippe Lemanceau par Angela Bolis journaliste du Monde le 24 avril 2013 à 18 h 17 SPE EcolDur; National audience

La biodiversité des sols : un fantastique patrimoine à préserver et valoriser

Les sols sont des environnements vivants dans lesquels cohabitent des microorganismes et une faune particulièrement abondants. Ainsi, les organismes évoluant dans le sol (mammifères, insectes, arachnides, vers, mollusques, protozoaires, nématodes, champignons, bactéries,…) représentent une masse bien supérieure à celle de ceux vivant au-dessus du sol. Une poignée de terre (approximativement 200 g) contient 0,5 g de matière vivante ce qui correspond à environ 5 tonnes à l’hectare.Au-delà de cette biomasse considérable, les organismes du sol représentent une fortediversité. L’étude de cette biodiversité nécessite l’application de stratégies et méthodes d’analyses adaptées compte-tenu de la di…

The establishment of an introduced community of fluorescent pseudomonads in the soil and in the rhizosphere is affected by the soil type

Indigenous populations of fluorescent pseudomonads were previously shown to vary in two different soils (Châteaurenard and Dijon) and in the rhizosphere of a plant species (Linum usitatissimum L.) cultivated in these two soils. These differences could be related to the soil type and to their crop history. In the present study, the influence of the soil type on the diversity of fluorescent pseudomonads in bulk and rhizospheric soils was evaluated. The soils of Châteaurenard and Dijon were sterilized before being inoculated with the same community of fluorescent pseudomonads. Bacterial isolates from bulk and rhizospheric soils were characterized on the basis of their repetitive extragenic pal…

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…

Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management

Aim The spatial organization of soil microbial communities on large scales and the identification of environmental factors structuring their distribution have been little investigated. The overall objective of this study was to determine the spatial patterning of microbial biomass in soils over a wide extent and to rank the environmental filters most influencing this distribution.

Plateforme GenoSol : une structure logistique d'appui à la recherche sur la microbiologie des sols et de l'environnement

EA SPE GenoSol EcolDur CT3; Les communautés microbiennes du sol sont difficiles à caractériser. Ceci s’explique par une accessibilité plus ou moins importante des populations au sein d’une matrice hétérogène et structurée mais aussi par leur densité et diversité très importante qui rend difficile à résoudre l’information obtenue. Toutefois, grâce aux avancées méthodologiques qui ont eu lieu depuis une quinzaine d’années, les études d’écologie microbienne bénéficient maintenant d’une automatisation des outils moléculaires (extraction d’ADN, caractérisation du polymorphisme de l’ADN, séquençage haut débit, métagénomique, métaprotéomique…) permettant la caractérisation des ressources génétique…

Interaction between Medicago truncatula and Pseudomonas fluorescens: evaluation of costs and benefits across an elevated atmospheric CO2.

10 pages; International audience; Soil microorganisms play a key role in both plants nutrition and health. Their relation with plant varies from mutualism to parasitism, according to the balance of costs and benefits for the two partners of the interaction. These interactions involved the liberation of plant organic compounds via rhizodeposition. Modification of atmospheric CO2 concentration may affect rhizodeposition and as a consequence trophic interactions that bind plants and microorganisms. Positive effect of elevated CO2 on plants are rather well known but consequences for micoorganisms and their interactions with plants are still poorly understood. A gnotobiotic system has been devel…

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

National audience

Multitrophic interactions in the rhizosphere Rhizosphere microbiology: at the interface of many disciplines and expertises.

The rhizosphere – the soil compartment influenced by the root, including the root itself – is the most-active microbial habitat in soils. Indeed, the release by plant roots of a significant part of their photosynthates promotes microbial abundance and activities in the rhizosphere. This investment made by plants is paid back by microbial functions, which contribute to plant nutrition and protection against soil-borne diseases. Indeed, rhizosphere microorganisms play a major role in plant growth and health and, …

Impact of Bacterial Siderophores on Iron Status and Ionome in Pea

National audience; Including more grain legumes in cropping systems is important for the development of agroecological practices and the diversification of protein sources for human and animal consumption. Grain legume yield and quality is impacted by abiotic stresses resulting from fluctuating availabilities in essential nutrients such as iron deficiency chlorosis (IDC). Promoting plant iron nutrition could mitigate IDC that currently impedes legume cultivation in calcareous soils, and increase the iron content of legume seeds and its bioavailability. There is growing evidence that plant microbiota contribute to plant iron nutrition and might account for variations in the sensitivity of pe…

La vie dans les sols : du découpage taxonomique à l’intégration écologique

Prod 2018-76b équipe EA SPE BIOME INRA AGROSUP; National audience; 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, leurs interactions, ainsi que celles avec l’environnement, représente donc un enjeu majeur. L’écologie des sols plonge ses racines dans l’histoire naturelle. Cette vision écologique appliquée aux sols a la particularité d’intégrer au moins partiellement les apports des sciences du sol (physique, chimie, biochimie). Par le renouvellement des méthodes d’observations et d’analyses (notamment molécul…

Methods for studying root colonization by introduced beneficial bacteria

e-Book; Some free-living rhizobacteria are considered as potential biocontrol and plant growth-promoting agents. Successful application of beneficial bacteria as microbial inoculants requires their presence and activity at the appropriate level, but even more, at the right time and place. Various markers are described in the literature to differentiate introduced bacteria from indigenous microflora and to visualize them. These markers are presented together with the methods currently applied to quantify bacterial densities and to characterize the distribution of introduced bacteria. The methods to quantify bacterial densities are either based on bacterial cultivation or not. Different types…

Global Soil Biodiversity Atlas

SPE EA Pôle BIOME The Atlas is divided in 8 chapters covering all the aspects of soil biodiversity: - Chapter I: The soil habitat - Chapter II: Diversity of soil organisms - Chapter III: Geographical and temporal distribution - Chapter IV: Ecosystem functions and services - Chapter V: Threats - Chapter VI: Interventions - Chapter VII: Policy, education and outreach - Chapter VIII: Conclusions Soil biodiversity experts from all over the world are involved in the project aiming at the creation of a reference publication not only for soil biodiversity researchers but also policy makers and general public.; International audience; The Global Soil Biodiversity Initiative (GSBI) and the Joint Res…

Valuing biodiversity and biotic interactions for crop protection in agroecology

SPEBIOMEGESTADINRA; Valuing biodiversity and biotic interactions for crop protection in agroecology. 12. European Fondation for Plant Pathology (EFPP) & 10. French Society for Plant Pathology Conference ‘Deepen Knwoledge in Plant Pathology for Innovative Agro-Ecology’

Biodiversité des sols et interactions biotiques, des enjeux majeurs en agroécologie

Interactions between Pisum sativum & pseudomonads, consequences on plant iron nutrition and growth and immunity

Pea has a high potential in agroecology, however, it may suffer from a susceptibility to iron deficiency in calcareous soils. This susceptibility varies depending on cultivars. Pseudomonad siderophores, pyoverdines (pvd), were shown to promote iron nutrition in Arabidopsis and tobacco. The hypothesis was therefore raised that variation in iron susceptibility between pea cultivars could be related to differences in their ability to recruit fluorescent pseudomonads (fp) contributing to siderophore-mediated iron nutrition. Our aims were to compare i) the impact of a susceptible (S) and a tolerant (T) cultivar of pea on fp biodiversity with a focus on their pvd, and in return ii) the impact of …

Soils as a Key Component of the Critical Zone 6

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 through the development of experimental approaches and modeling, a…

Strategies for analyzing interactions between arbuscular mycorrhiza and bacteria

National audience

Iron acquisition from Fe-pyoverdine by Arabidopsis thaliana.

Taking into account the strong iron competition in the rhizosphere and the high affinity of pyoverdines for Fe(III), these molecules are expected to interfere with the iron nutrition of plants, as they do with rhizospheric microbes. The impact of Fe-pyoverdine on iron content of Arabidopsis thaliana was compared with that of Fe-EDTA. Iron chelated to pyoverdine was incorporated in a more efficient way than when chelated to EDTA, leading to increased plant growth of the wild type. A transgenic line of A. thaliana overexpressing ferritin showed a higher iron content than the wild type when supplemented with Fe-EDTA but a lower iron content when supplemented with Fe-pyoverdine despite its inc…

Analysis of the role of nitric oxide (NO) in the cross‐regulation between immunity, growth and iron homeostasis in plants

Studies performed in our Agroecology Department show that the immune response of plants is linked to their iron nutrition and is modulated by pyoverdine, a siderophore produced by the plant beneficial rhizobacteria Pseudomonas fluorescens C7R12. Accordingly, Arabidopsis thaliana plantlets exposed to iron deficiency and treated with pyoverdine in its iron non‐chelated structure (apo‐pyo) show an enhanced growth but a decreased immune response capacity. We hypothesize that nitric oxide (NO), a universal signaling molecule, is a key component of the regulation of the immune response in plants exposed to apo‐pyo and to the C7R12 strain. We checked by fluorescence microscopy that NO is actually …

Reciprocal interactions between plants and fluorescent pseudomonads in relation to iron in the rhizosphere

SPE EA Section 15 : Engineering the rhizosphere: The "biased rhizosphere" concept Ouvrage en 2 volumes Résumé du livre : Molecular Microbial Ecology of the Rhizosphere covers current knowledge on the molecular basis of plant-microbe interactions in the rhizosphere. Also included in the book are both reviews and research-based chapters describing experimental materials and methods. Edited by a leader in the field, with contributions from authors around the world, Molecular Microbial Ecology of the Rhizosphere brings together the most up-to-date research in this expanding area, and will be a valuable resource for molecular microbiologists and plant soil scientists, as well as upper level stud…

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant differenc…

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…

Effect of 2,4-Diacetylphloroglucinol on Pithium : cellular responses and variation in sensitivity among propagules and species

International audience

Comment définir la transition agroécologique à l’échelle territoriale ?. Vidéo youtube réalisée dans le cadre du programme PSDR. Création Peyrard M. Animation Laroche C., Lemoine M.C.

Traduction de la métagenomique des agrosystemes en services écologiques

International audience; En affectant les communautés microbiennes présentes dans le sol, les pratiques agricoles mettent en péril la biodiversité des agrosystèmes. La génomique environnementale est un nouveau moyen d’améliorer nos connaissances sur ces derniers et ce faisant, de concevoir des systèmes agricoles plus respectueux de l’environnement.

Distribution and diversity of type III secretion system-like genes in saprophytic and phytopathogenic fluorescent pseudomonads

Type three secretion systems (TTSSs) are protein translocation mechanisms associated with bacterial pathogenicity in host plants, and hypersensitive reactions in non-host plants. Distribution and diversity of TTSS-like genes within a collection of saprophytic and phytopathogenic fluorescent pseudomonads were characterized. This collection included 16 strains belonging to 13 pathogenic species, and 87 strains belonging to five saprophytic species isolated from plant rhizosphere and soil. Presence of conserved hypersensitive reaction/pathogenicity (hrp) genes (hrc RST) was assessed both by PCR using primers designed to amplify the corresponding sequence and by dot-blot hybridization using a P…

Colonization pattern of primary tomato roots by Pseudomonas fluorescens A6RI characterized by dilution plating, flow cytometry, fluorescence, confocal and scanning electron microscopy

Early colonization of primary tomato roots, grown in vitro, by Pseudomonas fluorescens A6RI, introduced by seed bacterization, was monitored for 7 days in three different root zones (zone A, apex+elongation+young hairy zone; zone B, hairy zone; zone C, old hairy zone+collar). Bacterial quantification was assessed by enumeration of (i) colony forming units (cfu) after dilution plating and of (ii) total bacterial cells by flow cytometry. Bacterial distribution and organization in the root zones were analyzed by fluorescence, confocal and scanning electron microscopy. For all sampling dates and zones, the densities of total bacterial cells were significantly higher than those of the cfu. The k…

Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5

International audience; The genetic structure of bacterial and fungal communities was characterized in the rhizosphere of Medicago truncatula Gaertn. cv. Jemalong line J5 at five developmental stages (three vegetative and two reproductive stages), and in three compartments (bulk soil, rhizosphere soil and root tissues). The genetic structure of microbial communities was determined by cultivation-independent methods using directly extracted DNA that was characterized by automated ribosomal intergenic spacer analysis (ARISA). Principal component analyses (PCA) indicate that, for all developmental stages, the genetic structure of microbial communities differed significantly by compartment, wit…

Compréhension et valorisation des interactions entre plantes et microorganismes telluriques : Un enjeu majeur en agroécologie

Influence of pea genotype on root associated fluorescent pseudomonads, impact on plant iron nutrition

International audience; Pea has a high potential in agroecology because of its ability to fix atmospheric nitrogen and for Humannutrition due to the high amino-acids content of its seeds. However, pea can suffer from a susceptibility toiron deficiency in calcareous soils as expressed by chlorosis symptoms. Previous studies have shown thatsiderophores of model strains of fluorescent pseudomonads (fp), pyoverdines, promote iron nutrition ofarabidopsis and tobacco. We hypothesized that susceptibility to iron deficiency of pea is at least partly dueto its ability to select fluorescent pseudomonad that promote differentially plant nutrition thanks to theirsiderophores.To identify siderophores po…

Fluorescent pseudomonads harboring type III secretion genes are enriched in the mycorrhizosphere of Medicago truncatula

Type III secretion systems (T3SSs) of Gram-negative bacteria mediate direct interactions with eukaryotic cells. Pseudomonas spp. harboring T3SS genes (T3SS+) were previously shown to be more abundant in the rhizosphere than in bulk soil. To discriminate the contribution of roots and associated arbuscular mycorrhizal fungi (AMF) on the enrichment of T3SS+ fluorescent pseudomonads in the rhizosphere of Medicago truncatula, their frequency was assessed among pseudomonads isolated from mycorrhizal and nonmycorrhizal roots and from bulk soil. T3SS genes were identified by PCR targeting a conserved hrcRST DNA fragment. Polymorphism of hrcRST in T3SS+ isolates was assessed by PCR-restriction fragm…

Comment le microbiote des sols peut-il servir à l’amélioration des cultures ?

Prod 2019-148 SPE BIOME INRA

Contribution of fluorescent pseudomonads to iron nutrition and health of pea

Effect of primary mild stresses on resilience and resistance of the nitrate reducer community to a subsequent severe stress

International audience; The factors regulating soil microbial stability (e.g. resistance and resilience) are poorly understood, even though microorganisms are essential for ecosystem functioning. In this study, we tested whether a functional microbial community subjected to different primary mild stresses was equally resistant or resilient to a subsequent severe stress. The nitrate reducers were selected as model community and analysed in terms of nitrate reduction rates and genetic structure by narG PCR-restriction fragment length polymorphism fingerprinting. Heat, copper and atrazine were used as primary stresses and mercury at a high concentration as a severe stress. None of the primary …

Connaître les sols français pour mieux les gérer

National audience

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…

Optimisation de la procédure d'extraction d'ADN des sols pour caractériser la diversité microbienne tellurique par le pyroséquençage des gènes ribosomiques

Depuis plusieurs années, les communautés microbiennes du sol (bactériennes et fongiques) sont étudiées au travers de leur ADN. Le mode d’extraction de l’ADN du sol revêt donc une importance capitale pour décrire la biodiversité microbienne. A ce jour, de nombreuses procédures d’extraction d’ADN (commerciales ou non) des sols sont disponibles et utilisées. Il est cependant difficile de comparer les résultats d’études ayant utilisés différents protocoles d’extraction. L’emploi d’une méthode d’extraction standardisée est donc devenu indispensable pour comparer les résultats de différents laboratoires, comme la norme “ISO-11063: Soil quality – Method to directly extract DNA from soil” développé…

Fitness in soil and rhizosphere of Pseudomonas fluorescens C7R12 compared with a C7R12 mutant affected in pyoverdine synthesis and uptake.

International audience; Fluorescent pseudomonads have evolved an efficient strategy of iron uptake based on the synthesis of the siderophore pyoverdine and its relevant outer membrane receptor. The possible implication of pyoverdine synthesis and uptake on the ecological competence of a model strain (Pseudomonas fluorescens C7R12) in soil habitats was evaluated using a pyoverdine minus mutant (PL1) obtained by random insertion of the transposon Tn5. The Tn5 flanking DNA was amplified by inverse PCR and sequenced. The nucleotide sequence was found to show a high level of identity with pvsB, a pyoverdine synthetase. As expected, the mutant PL1 was significantly more susceptible to iron starva…

Expression communes de gènes de M. truncatula lors de la mycorhization, la nodulation et l'interaction avec une rhizobactérie bénéfique

National audience

The Pseudomonas fluorescens Siderophore Pyoverdine Weakens Arabidopsis thaliana Defense in Favor of Growth in Iron-Deficient Conditions

SPE EA BIOME IPM UB INRA; International audience; Pyoverdines are siderophores synthesized by fluorescent Pseudomonas spp. Under iron-limiting conditions, these high-affinity ferric iron chelators are excreted by bacteria in the soil to acquire iron. Pyoverdines produced by beneficial Pseudomonas spp. ameliorate plant growth. Here, we investigate the physiological incidence and mode of action of pyoverdine from Pseudomonas fluorescens C7R12 on Arabidopsis (Arabidopsis thaliana) plants grown under iron-sufficient or iron-deficient conditions. Pyoverdine was provided to the medium in its iron-free structure (apo-pyoverdine), thus mimicking a situation in which it is produced by bacteria. Rema…

Soil microbial diversity at the scale of the French national territory

Cryo-méthodes appliquées à l’étude des interactions entre plantes et Pseudomonas Fluorescents en relation avec le fer dans la rhizosphère

SPEBAPEAIPMBIOmE; Cryo-méthodes appliquées à l’étude des interactions entre plantes et [i]Pseudomonas Fluorescents[/i] en relation avec le fer dans la rhizosphère. 7. Journées Scientifiques et Techniques du Réseau des Microscopistes de l'INRA (RμI)

Characterization and transcriptional analysis of Pseudomonas fluorescens denitrifying clusters containing the nar, nir, nor and nos genes

In this study, we report the cloning and characterization of denitrifying gene clusters of Pseudomonas fluorescens C7R12 containing the narXLDKGHJI, nirPOQSM, norCB and nosRZDFYL genes. While consensus sequences for Fnr-like protein binding sites were identified in the promoter regions of the nar, nir, nor and nos genes, consensus sequences corresponding to the NarL binding sites were identified only upstream the nar genes. Monitoring by mRNA analysis the expression of the narG, nirS, norB and nosZ structural genes suggests a sequential induction of the denitrification system in P. fluorescens.

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…

Common gene expression in Medicago truncatula roots in response to Pseudomonas fluorescens colonization, mycorrhiza development and nodulation

International audience

Optimisation du pyroséquençage haut-débit pour caractériser la diversité taxonomique des communautés bactériennes des sols

Affiche, résumé; International audience; La diversité microbienne d’un sol (que l’on estime entre 100 000 et 1 000 000 d’espèces différentes par gramme de sol) est difficile à caractériser. Toutefois, d’importantes avancées en biologie moléculaire, comme le développement du pyroséquençage, ont permis d'obtenir plusieurs centaines de milliers de séquences à partir d’un ADN méta-génomique. Ces nouveaux développements permettent maintenant de caractériser la diversité des communautés microbiennes du sol en se basant sur un marqueur phylogénétique comme l'ADNr 16S, aussi appelée MetaTaxogénomique (Maron et coll., 2011). Toutefois, dans un contexte ou l’écologie microbienne du sol commence à s’a…

Notre futur passe par les légumineuses. Enquête Les Echos de la planète.

National audience

Chapter 12 Role of Iron in Plant–Microbe Interactions

Iron is an essential micronutrient for plants and associated microorganisms. Iron nutrition of these organisms relies on the soil supply. However, bioavailability of iron in cultivated soils is low. Plants and microorganisms have thus evolved active strategies of iron uptake based on acidification, chelation, and/or reduction processes. Iron acquisition by these organisms leads to complex interactions ranging from mutualism to competition. In the rhizosphere, plants support abundant and active microbial communities through the release of rhizodeposits. Iron uptake by these microorganisms and by the host plant decrease even more the concentration of iron in solution. Therefore, there is an i…

Plant growth-promoting rhizobacteria present status and future prospects

International audience; Fluorescent pseudomonads have been widely tested for their ability to promote plant growth and to suppress soilborne diseases. Their efficacy is both related to their activity and to their density in the rhizosphere. To enable the introduction of a number of bacterial cells high enough to allow the expression of their beneficial activities, the strain must be produced at a low cost. In order to optimise the inoculum production of the biocontrol agent Pseudomonas fluorescens C7R12, different combinations of carbon, nitrogen and yeast extract including the reference King's B medium (KB) were compared using a central composite design. Among the different growing media t…

La rhizosphère

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 …

Effect of fusaric acid and phytoanticipins on growth of rhizobacteria and Fusarium oxysporum

International audience

Soil as a Support of Biodiversity and Functions

The soil is a major reservoir of biological diversity on our planet. It also shelters numerous biological and ecological processes and therefore contributes to the production of a considerable number of ecosystem services. Among the ecological, social and economic services identified, the role of soil as a reservoir of diversity has now been well established, along with its role in nutrient cycling, supporting primary productivity, pollution removal and storing carbon. Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have resulted in modifications of the diversity of the indigenous m…

Presence of DNA sequences characteristic of type III secretion systems in biocontrol Pseudomonas fluorescens strain C7R12

International audience

Diversity of root-associated fluorescent pseudomonads as affected by ferritin overexpression in tobacco

A transgenic tobacco overexpressing ferritin (P6) was recently shown to accumulate more iron than the wild type (WT), leading to a reduced availability of iron in the rhizosphere and shifts in the pseudomonad community. The impact of the transgenic line on the community of fluorescent pseudomonads was assessed. The diversity of 635 isolates from rhizosphere soils, rhizoplane + root tissues, and root tissues of WT and P6, and that of 98 isolates from uncultivated soil was characterized. Their ability to grow under iron stress conditions was assessed by identifying their minimal inhibitory concentrations of 8-hydroxyquinoline for each isolate, pyoverdine diversity by isoelectrofocusing and ge…

Enhancing biological control by combining microorganisms

International audience

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

National audience

Plateforme CA-SYS : un dispositif de recherche INRA pour l'agroécologie, video Youtube

CA-SYS est une plateforme de recherche et d'expérimentation de l'INRA, collaborative, pour expérimenter l'agroécologie à différentes échelles. Projet collaboratif de l'UMR Agroécologie (INRA Bourgogne Franche-Comté) et de l'UE Domaine d'Epoisses, CA-SYS propose de tester sur 120ha une diversité de systèmes agro-écologiques en semis-direct ou avec travail du sol possible, tous sans pesticides, afin d’éprouver la pertinence de la réduction d’usage des intrants de synthèse au profit d’une valorisation des interactions biotiques au sein d’un environnement parcellaire riche en infrastructures paysagères (bandes enherbées, bandes fleuries, quelques haies, arbres isolés).

Diversity of TonB-dependent outer-membrane proteins in plant-associated strains of Pseudomonas fluorescens

International audience; Genomic sequences of ten strains of plant-associated Pseudomonas spp. were surveyed for the presence of TonB-dependent outer-membrane proteins (TBDPs), which function in the uptake of substrates from the environment by many Gram-negative bacteria. The ten strains represent P. fluorescens, P. chlororaphis, and P. synxantha isolated from the phyllosphere, rhizosphere or soil. 14 to 45 TBDPs were identified in each strain, and phylogenetic analysis of the TBDPs identified five that are conserved across all ten genomes. Comparisons to proteins with known functions allowed the assignment of putative roles in uptake of heme, vitamin B12, copper, and the siderophore ferrich…

Dijon Métropole et la transition alimentaire

National audience; La santé commence dans l’assiette et les collectivités reprennent la main. Exemple à Dijon Métropole qui se veut territoire démonstrateurde la transition vers un système alimentaire durable. En 2019, Dijon ouvrira les portes de la Cité internationale de la gastronomie et du vin, dont l’une des missions sera de valoriser le repas gastronomique des Français et mettre en avant les climats de Bourgogne, tous deux inscrits au patrimoine mondial de l’Unesco. Dans le même temps, Dijon veut devenir un territoire modèle du « système alimentaire durable de 2030 ». Derrière ce titre se cache un projet innovant qui fait partie des vingt-quatre lauréats de l’appel à projets gouverneme…

Biogeography of soil microbial communities: a review and a description of the ongoing french national initiative

International audience; Microbial biogeography is the study of the distribution of microbial diversity on large scales of space and time. This science aims at understanding biodiversity regulation and its link with ecosystem biological functioning, goods and services such as maintenance of productivity, of soil and atmospheric quality, and of soil health. Although the initial concept dates from the early 20th century (Beijerinck (1913) De infusies en de ontdekking der backterien, in: Jaarboek van de Knoniklijke Akademie van Wetenschappen, Muller, Amsterdam), only recently have an increasing number of studies have investigated the biogeographical patterns of soil microbial diversity. A such …

Shifts in microbial diversity through land use intensity as drivers of carbon mineralization in soil

10 pages; International audience; Land use practices alter the biomass and structure of soil microbial communities. However, the impact of land management intensity on soil microbial diversity (i.e. richness and evenness) and consequences for functioning is still poorly understood. Here, we addressed this question by coupling molecular characterization of microbial diversity with measurements of carbon (C) mineralization in soils obtained from three locations across Europe, each representing a gradient of land management intensity under different soil and environmental conditions. Bacterial and fungal diversity were characterized by high throughput sequencing of ribosomal genes. Carbon cycl…

Iron dynamics in the rhizosphere as a case study for analysing interactions among soils, plants and microbes

International audience

The impact of the plant-associated siderophore ornicorrugatin on Arabidopsis thaliana

International audience; Most microorganisms produce siderophores when they are faced with iron-limiting conditions. Fluorescent pseudomonads produce a yellow-green, fluorescent siderophore, called pyoverdine. Besides pyoverdine, sev-eral other secondary siderophores, which have a relatively lower affinity for iron, have been identified in Pseu-domonas spp. Examples are pyochelin, pseudomonine and thioquinolobactin (Cornelis and Matthijs 2002). An atypical set of secondary siderophores, due to their lipopeptidic nature, are the siderophores corrugatin (Risse et al., 1998), ornicorrugatin (Matthijs et al., 2008) and histicorrugatin (Matthijs et al., 2016). These siderophores consist out of an…

Ecological Function and Biodiversity Indicators in European Soils EcoFINDERS

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…

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality -- Method to directly extract DNA from soil samples"

International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …

Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques.

International audience; This work is the first report on the use of DNA-, RNA-SIP approaches to elucidate the dynamics and the diversity of bacterial populations actively assimilating C derived from plant residues labelled at more than 90% (13)C. Wheat-residues, were incorporated and incubated into soil microcosms for 28 days. At the end of the incubation time, no more than 55% of the total CO(2) released was (13)C-labelled, suggesting the occurrence of an important priming effect process. After 7 days, more than 30% of the whole DNA extracted were labelled, allowing an efficient separation of labelled from unlabelled DNA using density gradient centrifugation. The genetic structure of bacte…

Influence du système de sécrétion de type III bactérien dans les intéractions plantes-Pseudomonas spp. fluorescents non pathogènes

http://prodinra.inra.fr/record/271693SPEEAEcolDurCT3; L’objectif de cette thèse a été de contribuer à faire progresser les connaissances sur les interactions bénéfiques entre les plantes et les microorganismes en évaluant la contribution des systèmes de sécrétion de type III (SST3). Une synthèse des connaissances disponibles relatives aux SST3 chez les Pseudomonas non pathogènes, saprotrophes ou mutualistes, montre que les SST3 ne sont pas cantonnés aux interactions parasites ou pathogènes avec les plantes. Dans la première étude expérimentale, nous avons utilisé différents génotypes de Medicago truncatula Gaertn. cv. Jemalong capables (Myc+) ou non (Myc-) d’établir une symbiose mycorhizien…

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

La pyoverdine, un sidérophore produit par la souche bénéfique du sol Pseudomonas fluorescens C7R12, impacte l’homéostasie du fer et promeut la croissance aux dépens des réactions de défense d’Arabidopsis thaliana cultivée en condition de carence en fer

Microbial Biogeography at the scale of France by the use of molecular tools applied to the French soil quality monitoring network (RMQS)

Are soils suppressive to fungal diseases the sources of biocontrol agents ?

Soils suppressive to soil-borne diseases are defined by a low disease incidence in spite of the presence of a virulent pathogen and a susceptible plant. In many cases, the inhibition of the disease development relies on the activity of the resident soil microbiome. Suppressiveness can be transmitted to conducive soil by mixing a small amount of suppressive soil into the conducive one. To identify microbial taxons linked to the suppressive phenotype of soils, culture independent-based methods have been employed to analyze and compare microbial diversities in two different soils suppressive (respectively conducive) to either Fusarium wilt of flax or Rhizoctonia diseases of sugar beet. Metagen…

Rôle de la nitrate réductase et de la pyoverdine dans la compétence tellurique et rhizosphérique de la souche Pseudomonas fluorescens C7R12

National audience

Les sols au cœur de la zone critique 6

Philippe Lemanceau est directeur de recherche à l’INRA où il dirige l’UMR Agroécologie. Il est microbiologiste du sol et spécialiste de la biodiversité des sols et des interactions plantes/micro-organismes.Manuel Blouin est professeur en écologie à AgroSup Dijon et membre de l’UMR Agroécologie. Ses recherches concernent l’effet des organismes du sol sur la croissance, le développement et la santé des plantes.; International audience; 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, leurs interactions, ainsi qu…

The beneficial rhizosphere : a necessary strategy for microplant production

Society's expectation that plant production systems will become more compatible with the environment requires the development of an agriculture with low chemical inputs. With microplants, this can be achieved successfully by the introduction of beneficial microorganisms, particularly those developing in the rhizosphere. Inoculation with mycorrhizal fungi has provided a wide range of examples of the usefulness of this technology. Recent results indicate that this application could be improved by combining mycorrhizal inoculation with other soil microbes with complementary beneficial effects. It is proposed that multimicrobial biotization is a valuable development for microplant technology.

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…

Soil suppressiveness to plant diseases

Prod 2018-286 SPE BIOmE IPM INRA; International audience

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

SST3 : similarités et différences entre P. fluorescens cliniques et environnementaux

Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

National audience

Defense Responses of Fusarium oxysporum to 2,4-Diacetylphloroglucinol, a Broad-Spectrum Antibiotic Produced by Pseudomonas fluorescens

A collection of 76 plant-pathogenic and 41 saprophytic Fusarium oxysporum strains was screened for sensitivity to 2,4-diacetylphloroglucinol (2,4-DAPG), a broad-spectrum antibiotic produced by multiple strains of antagonistic Pseudomonas fluorescens. Approximately 17% of the F. oxysporum strains were relatively tolerant to high 2,4-DAPG concentrations. Tolerance to 2,4-DAPG did not correlate with the geographic origin of the strains, formae speciales, intergenic spacer (IGS) group, or fusaric acid production levels. Biochemical analysis showed that 18 of 20 tolerant F. oxysporum strains were capable of metabolizing 2,4-DAPG. For two tolerant strains, analysis by mass spectrometry indicated…

Implication of pyoverdines in the interactions of fluorescent pseudomonads with soil microflora and plant in the rhizosphere

Soils are known to be oligotrophic environments whereas soil microflora is mostly heterotrophic in such way that microbial growth in soil is mainly limited by the scarce sources of readily available organic compounds (Wardle 1992). Therefore, in soils, microflora is mostly in stasis (fungistasis/bacteriostasis) (Lockwood 1977). In counterpart, plants are autotrophic organisms responsible for the primary production resulting from the photosynthesis. A significant part of photosynthetates are released from plant roots to the soil through a process called rhizodeposition. These products, i.e. the rhizodeposits, are made of exudates, lysates, mucilage, secretions and dead cell material, as well…

Agroécologie : Concilier performances agronomique et environnementale

Une approche territoriale associant des enjeux de production en amont et de durabilité des systèmes alimentaires en aval : système alimentaire durable pour la métropole de Dijon

National audience; Présentation de l'Atelier :Les protéines sont des macronutriments majeurs dans l’alimentation des hommes et des animaux. Or la production de protéines végétales est toujours déficitaire en France qui a recours à des importations pour couvrir ses besoins.Les légumineuses contiennent plus de protéines que les céréales. En outre, leur culture contribue à la mise en œuvre de systèmes moins demandeurs en intrants qui peuvent ainsi, seuls, en rotation ou en mélange, contribuer efficacement à la démarche one health, vers une meilleure santé globale des hommes, des animaux, des cultures et de l’environnement. Améliorer la qualité des protéines végétales, tout en maintenant voire …

Response of soil bacterial community structure to successive perturbations of different types and intensities

SummaryIn soil, genetic structure modifications of indigenousbacterial community consecutively to a severe stress(mercury contamination) were delayed when thecommunity was pre-exposed to various minor per-turbations (heat, copper and atrazine). Such minorperturbations induced transitory community struc-ture modifications leading to an increase of commu-nity stability towards a severe mercury stress. Theseresults illustrated well the short-term pre-adaptationprocess for bacterial community hypothesizing thatcommunity submitted to perturbations become moreresistant to withstand another stress. Compared with other environmental matrices of the bio-sphere, soils are considered as the main reservo…

Colonization of Plant Roots by Pseudomonads and AM Fungi: A Dynamic Phenomenon, Affecting Plant Growth and Health

Because of their enormously large range of plant hosts and role in plant nutrition, arbuscular mycorrhizal (AM) fungi represent an extraordinarily fascinating field of study. Plant growth promotion effects by AM fungi were described as early as 1900 (Sthal 1900) and several data obtained in the second half of the last century support the idea that these microrganisms can act as biocontrol agents (BCA). The extent of root colonization is variable in different plants and under different environmental conditions (Giovannetti and Hepper 1985). Some effects of AM colonization on plants have been reported to be dependent on the degree of root colonization, while others have not. Root exudation an…

Témoignage sous forme de questions-réponses

International audience; Résumé de l'ouvrage :Prolongements des exploitations agricoles, les coopératives agricoles ont toujours accompagné l’évolution de l’agriculture et des agriculteurs. Elles accompagnent ainsi aujourd’hui les changements en cours chez leurs adhérents en apportant leur contribution à la transition agroécologique. Les actions de développement menées par les coopératives présentent une grande diversité, à travers des actions collectives, techniques, liées à leur territoire. La recherche de la reconnaissance et de la valorisation économique de ces évolutions est aussi un axe majeur des démarches entreprises dans toutes les filières. Ce recueil d’expériences constitue un pan…

Les apports de la génomique à l'agroécologie: Bilan des projets financés sur la période 2005 -2019 et perspectives pour la recherche

Les fiches projets ont été rédigées par les porteurs de projets et coordonnées par Jannatul Mia et Isabelle Hippolyte. Relecture scientifique et conseils : Thierry Doré, Christophe Salon; International audience

Major advances in knowledge and practice to preserve and value functions of European soils

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…

EcoFINDERS, Ecological Function and Biodiversity Indicators in European Soils

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…

Antibiotiques et environnement conclusions et perspectives

Siderophore typing, a powerful tool for the identification of fluorescent and nonfluorescent Pseudomonas

ABSTRACT A total of 301 strains of fluorescent pseudomonads previously characterized by conventional phenotypic and/or genomic taxonomic methods were analyzed through siderotyping, i.e., by the isoelectrophoretic characterization of their main siderophores and pyoverdines and determination of the pyoverdine-mediated iron uptake specificity of the strains. As a general rule, strains within a well-circumscribed taxonomic group, namely the species Pseudomonas brassicacearum , Pseudomonas fuscovaginae , Pseudomonas jessenii , Pseudomonas mandelii , Pseudomonas monteilii , “ Pseudomonas mosselii ,” “ Pseudomonas palleronii ,” Pseudomonas rhodesiae , “ Pseudomonas salomonii ,” Pseudomonas syringa…

Identification of Traits Implicated in the Rhizosphere Competence of Fluorescent Pseudomonads: Description of a Strategy Based on Population and Model Strain Studies

E-book; International audience; The lack of consistency of the beneficial effects of inoculated fluorescent pseudomonads has often been related to their bad survival in the rhizosphere. In this review, we describe the strategy followed over the last decade to study traits involved in the rhizosphere competence of these bacteria. The diversity of indigenous populations associated with plant roots was first compared to that of populations associated with uncultivated soils in order to identify traits that discriminate these populations. The involvement of these bacterial traits in the rhizosphere competence was then assessed by comparing the competitiveness of a wild-type strain to that of mu…

Platform GenoSol: a new tool for conserving and exploring soil microbial diversity

International audience; Soils are the principal reservoirs of microbial diversity and represent a core component of terrestrial ecosystems. There is an increasing demand for assessing the impact of agricultural and industrial practices on the environment at large scales in a context of global change. To address this demand, taxonomic and functional diversity of soil microbial communities, and their stability over time need to be characterized for predicting soil quality upon human activities, the evolution of this quality being expected to affect environment quality and public health. Recent methodological progresses have led to the development and automation of molecular biological tools (…

Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe

Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, gra…

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…

Effect of the host-plant and the soil-type on the diversity of soilborne populations of fluorescent pseudomonds and of Fusarium oxysporum

International audience

Diversité microbienne du sol: un enjeu majeur en agroécologie

La connaissance des populations microbiennes du sol et la compréhension de leurs relations complexes avec la plante constituent des voies de progrès majeures pour l’évolution des pratiques agricoles vers des systèmes de cultures moins consommateurs en intrants de synthèse et plus respectueux de l’environnement.

Soil biodiversity monitoring in Europe : ongoing activities and challenges

International audience; The increasing interest in soil biodiversity and its protection includes both the biodiversity conservation issues and the mostly unknown economic and ecological values of services provided by soil biodiversity. Inventory and monitoring are necessary tools for the achievement of an adequate level of knowledge regarding soil biodiversity status and for the detection of biodiversity hot spots as well as areas where current levels of biodiversity are under threat of decline. In this paper the main tools and methodological approaches for soil biodiversity measurement are presented. Technical aspects related to the inventory and monitoring activities at a large spatial sc…

Territoires et transitions agro-alimentaires, regards croisés : Dijon Métropole et Reggio Emilia

National audience

Involvement of nitrate reductase and pyoverdine in competitiveness of Pseudomonas fluorescens strain C7R12 in soil

ABSTRACT Involvement of nitrate reductase and pyoverdine in the competitiveness of the biocontrol strain Pseudomonas fluorescens C7R12 was determined, under gnotobiotic conditions, in two soil compartments (bulk and rhizosphere soil), with the soil being kept at two different values of matric potential (−1 and −10 kPa). Three mutants affected in the synthesis of either the nitrate reductase (Nar − ), the pyoverdine (Pvd − ), or both (Nar − Pvd − ) were used. The Nar − and Nar − Pvd − mutants were obtained by site-directed mutagenesis of the wild-type strain and of the Pvd − mutant, respectively. The selective advantage given by nitrate reductase and pyoverdine to the wild-type strain was as…

Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt

Natural disease-suppressive soils provide an untapped resource for the discovery of novel beneficial microorganisms and traits. For most suppressive soils, however, the consortia of microorganisms and mechanisms involved in pathogen control are unknown. To date, soil suppressiveness to Fusarium wilt disease has been ascribed to carbon and iron competition between pathogenic Fusarium oxysporum and resident non-pathogenic F. oxysporum and fluorescent pseudomonads. In this study, the role of bacterial antibiosis in Fusarium wilt suppressiveness was assessed by comparing the densities, diversity and activity of fluorescent Pseudomonas species producing 2,4-diacetylphloroglucinol (DAPG) (phlD+) …

3. Colloque Rhizosphère : programme et résumés des communications

National audience

Analysis of the cross‐regulation between immunity, growth and iron homeostasis in plants

The existence of a tightly regulated balance between growth and immunity in plants has recently emerged. In this study, we challenged this concept thanks to the biological model pyoverdine-Arabidopsis thaliana. Pyoverdine is a siderophore produced by the plant growth promoting rhizobacteria Pseudomonas fluorescens C7R12. Under iron deficiency, P. fluorescens excretes the iron free form of pyoverdine (apo‐pyo) in the soil. Once chelated with iron (ferri‐pyo), the complex is internalized by the bacteria. We demonstrated that Arabidopsis thaliana plants treated by apo‐pyo in a medium containing or not iron internalize pyoverdine. Interestingly, apo‐pyo-treated plants did not show a typical gro…

Report on the interaction between pea and fluorescent pseudomonads and the potential impact on the plant iron nutrition

Présence de séquences d'ADN caractéristiques de systèmes de sécrétion de type III chez l'agent de lutte biologique Pseudomonas fluorescens C7R12

National audience

Variation in the TonB-dependent outer-membrane proteins in plant-associated strains of Pseudomonas fluorescens

International audience; Genomic sequences of ten strains of plant-associated Pseudomonas spp. were surveyed for the presence of TonB-dependent outer-membrane proteins (TBDPs), which function in the uptake of substrates from the environment by many Gram-negative bacteria. The ten strains represent P. fluorescens, P. chlororaphis, and P. synxantha isolated from the phyllosphere, rhizosphere or soil. 14 to 45 TBDPs were identified in each strain, and phylogenetic analysis of the TBDPs identified five that are conserved across all ten genomes. Comparisons to proteins with known functions allowed the assignment of putative roles in uptake of heme, vitamin B12, copper, and the siderophore ferrich…

CA-SYS: A long term experimental platform on agroecology at various scales

National audience; The French National Institute for Agricultural Research (INRA) has established an ambitious, multiscale, agricultural experimental infrastructure (the CA-SYS platform) as a collaboration between the Research Unit, Agroécologie (Dijon, eastern France), and the Experimental Research Unit, Domaine d’Epoisses (20 km next to Dijon). CA-SYS covers an area of 120 ha, and is divided into 47 fields, each of which has drainage and can be irrigated, and will be initiated in autumn 2018. The aims of CA-SYS are to: i) design and evaluate new agroecological systems; ii) study the transition from current farming systems towards these new agroecological systems, with goals that include a…

Biological control of fusarium wilts: Toward development of commercial products

105 ref., chap. 2; International audience

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

International audience

Les sols au coeur de la zone critique 6, écologie

Prod 2018-76a équipe EA SPE BIOME INRA AGROSUP; 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, leurs interactions, ainsi que celles avec l’environnement, représente donc un enjeu majeur. L’écologie des sols plonge ses racines dans l’histoire naturelle. Cette vision écologique appliquée aux sols a la particularité d’intégrer au moins partiellement les apports des sciences du sol (physique, chimie, biochimie). Par le renouvellement des méthodes d’observations et d’analyses (notamment moléculaires), le développ…

Foreword

Evolution of the phenazine biosynthesis pathway and diversity of phenazine-producing Pseudomonas spp. in dryland wheat-producing areas of washington state

Metabolic fate of a bacterial siderophore in Arabidopsis thaliana and Pisum sativum in relationship with iron status in plants

Despite its abundance, iron is weakly bioavailable for organisms due to its poor solubility in soils under aerobic conditions. Therefore, plants and other organisms have evolved mechanisms to efficiently assimilate iron from the soil. Non-grass plants use a strategy (strategy I) based on soil acidification, reduction of the Fe3+ in Fe2+ which incorporated in the roots by iron transporters. We previously showed (Shirley et al., 2011; Vansuyt et al., 2007) that iron nutrition and growth of a strategy I plant could be promoted by the ferric-complex of the pyoverdine (Fe-pvd), a siderophore produced by microorganisms. If pyoverdine was further localized in planta using different immunological t…

Microbial ecology of the rhizosphere

Part II. Selected MethodsPlant-microbe Chapitre 9 : Interactions and Soil Quality; International audience

Comparative genetic diversity of the narG, nosZ, and 16S rRNA genes in fluorescent Pseudomonads

ABSTRACT The diversity of the membrane-bound nitrate reductase ( narG ) and nitrous oxide reductase ( nosZ ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overa…

Ecological function and biodiversity indicators in European soils. Since for the environment

La biodiversité des sols : un fantastique patrimoine à préserver et valoriser

National audience

New perspectives and approaches in plant growth-promoting rhizobacteria research

International audience; In the context of increasing international concern for food and environmental quality, use of Plant Growth-Promoting Rhizobacteria (PGPR) for reducing chemical inputs in agriculture is a potentially important issue. PGPR are root-colonizing bacteria that exert beneficial effects on plant growth and development, but they can be also employed in the control of plant pathogens, for enhancing the efficiency of fertilizers, and for degrading xenobiotic compounds. This book provides an update by renowned international experts on the most recent advances in the ecology of these important bacteria, the application of innovative methodologies for their study, their interactio…

Acyl-homoserine lactone production is more common among plant-associated Pseudomonas spp. than among soilborne Pseudomonas spp.

ABSTRACT A total of 137 soilborne and plant-associated bacterial strains belonging to different Pseudomonas species were tested for their ability to synthesize N -acyl-homoserine lactones (NAHL). Fifty-four strains synthesized NAHL. Interestingly, NAHL production appears to be more common among plant-associated than among soilborne Pseudomonas spp. Indeed, 40% of the analyzed Pseudomonas syringae strains produced NAHL which were identified most often as the short-chain NAHL, N -hexanoyl- l -homoserine lactone, N -(3-oxo-hexanoyl)-homoserine lactone, and N -(3-oxo-octanoyl)- l -homoserine lactone (no absolute correlation between genomospecies of P. syringae and their ability to produce NAHL …

Free-living plant-beneficial microorganisms and soil quality.

CABI Publishing, Wallingford Oxon, UK,

EcoFINDERS Characterize biodiversity and the function of soils in Europe 23 partners in 10 European countries and China

National audience

Erosion of biodiversity affects the stability of soil microbial communities

Anthropogenic activities have led to a significant modification/reduction of biodiversity. By observing this erosion, the understanding of the relationship between biodiversity and ecosystem functioning has emerged as a central issue in ecological and environmental sciences during the last decade. This relationship between diversity-stability-function has been extensively studied by plant ecologists, but remains largely unexplored for soil microorganisms. In this context, we studied the impact of an erosion of biodiversity on the stability of soil microbial communities (i.e. resistance and resilience) in response to two perturbations: a residual metallic stress (mercury input at 20 ppm) and…

Leviers génétiques pour optimiser les interactions positives plantes micro-organismes

International audience

Rhizosphere: achievements and challenges

Reprinted from Plant and Soil, Vol.321, nos 1-2; International audience

Soil as support of biodiversity and functions

Chapitre 11 Section 3 EA SPE EcolDur GenoSol; The soil is a major reservoir of biological diversity on our planet. It also shelters numerous biological and ecological processes and therefore contributes to the production of a considerable number of ecosystem services. Among the ecological, social and economic services identified, the role of soil as a reservoir of diversity has now been well established, along with its role in nutrient cycling, supporting primary productivity, pollution removal and storing carbon. Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have resulted in modi…

Effect of ferritin overexpression in tobacco on the structure of bacterial and pseudomonad communities associated with the roots

The genetic structures of total bacterial and pseudomonad communities were characterized in rhizosphere soil and rhizoplane+root tissues of tobacco wild type and a ferritin overexpressor transgenic line (P6) by a cultivation-independent method using directly extracted DNA at the end of three consecutive plant cultures. The structure of total bacterial communities was characterized by automated ribosomal intergenic spacer analysis (A-RISA), and that of pseudomonad communities was characterized by PCR-restriction fragment length polymorphism (PCR-RFLP) from DNA amplified with specific primers. The structure of total bacterial communities was significantly modified in the rhizosphere soil by t…

Extraction of copper and iron from soil with siderophores of fluorescent pseudomonads

Due to the application for more than 100 years of copper to French vineyards to combat fungal diseases of vines copper levels have been reported in vineyard soils up to several hundred milligrams of copper/kg of soil. There are now concerns about the ecotoxicity effects of copper accumulation. One potential way to remediate copper accumulation is phytoextraction. Furthermore, there may be potential to enhance the phytoextraction process by augmenting the process using beneficial bacterial species. Our research has involved investigating the potential to use fluorescent pseudomonads, a key group of bacteria that produce siderophores (iron-scavenging compounds), to enhance phytoextraction of …

Suppression of Rhizoctonia root-of tomato by Glomus mosseae BEG12 and Pseudomonas fluorescens A6RI is associated with their effect on the pathogen growth and on the root morphogenesis

Importance de la biodiversité microbienne des sols dans la transition Agroécologique

Stability of soil microbial structure and activity depends on microbial diversity

Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity …

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…

Assessing genetic structure and diversity of airborne bacterial communities by DNA fingerprinting and 16S rDNA clone library

Abstract The density, genetic structure and diversity of airborne bacterial communities were assessed in the outdoor atmosphere. Two air samples were collected on the same location (north of France) at two dates (March 2003 (sample1) and May 2003 (sample 2)). Molecular culture-independent methods were used to characterise airborne bacterial communities regardless of the cell culturability. The automated-ribosomal intergenic spacer analysis (A-RISA) was performed to characterise the community structure in each sample. For both sampling dates, complex A-RISA patterns were observed suggesting a highly diverse community structure, comparable to those found in soil, water or sediment environment…

Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils.

The taxonomic position of eight fluorescent Pseudomonas strains isolated from bulk and rhizospheric soils, and from water was examined. These eight strains clustered in one phenon together with Pseudomomas mandelii (CFBP 4844T), but could still be differentiated from this type strain by four phenotypic features. The eight stains exhibited internal DNA-DNA hybridization values ranging from 60 to 100%, with deltaTm below 5 degrees C (3.9 and 4.3 degrees C) for the lowest values (60 and 66%). The percentages of hybridization with type or reference strains of other Pseudomonas species tested ranged from 12 to 60% (deltaTm = 5.5 degrees C), indicating that the eight isolates studied constituted …

Understanding and managing soil biodiversity: a major challenge in agroecology

Costs-benfits trade-off in the intercation between Medicago truncatula and Pseudomonas fluorescens C7R12 across atmospheric carbon dioxide modulation

The interactions between plants and soil microorganisms are mainly based on trophic relationships. The compounds exchanged represent cost for the organism produces them but a benefit for the one who receive those compounds. A mutualistic relation leads to stability in the cost-benefit balance resulting from a co-evolution between the two organisms. The cost corresponding for the release of carbon compounds by the plant would be offset by benefits in return corresponding for the activities of microorganisms that use them. We tested by an experimental way the effect of CO2 concentration on the interaction between M. truncatula and the bacterium P. fluorescens C7R12. The results allowed a best…

Soil carbon dynamics and nutrient cycling

Chapitre 7 Section 2 SPE EcolDur; The quantity of organic carbon in soil and the quantity and type of organic inputs have profound impacts on the dynamics of nutrients. Soil organic matter itself represents a large reservoir of nutrients that are released gradually through the action of soil fauna and microorganisms: this is especially important for the supply of N, P and S to plants, whether agricultural crops or natural vegetation. Organic matter also modifies the behaviour and availability of nutrients through a range of mechanisms including increasing the cation exchange capacity of soil, thus leading to greater retention of positively charged nutrient ions such as Ca, Mg, K, Fe, Zn and…

Chapter 4 Iron Dynamics in the Rhizosphere

Abstract Iron is an essential micronutrient for most organisms due to its role in fundamental metabolic processes. In cultivated soils, soil solution iron is mostly oxidized [Fe(III) species] unless local anoxic conditions develop. The concentration of these Fe(III) species is small in soil solution due to the low solubility of ferric oxides, oxyhydroxides, and hydroxides, which is minimal at neutral and alkaline pH. In the rhizosphere, iron concentration in the soil solution is even lower because of its uptake by aerobic organisms (plants and microorganisms), leading to a high level of competition for Fe(III). In order to face iron competition, these organisms have evolved active uptake st…

Biogeographical patterns of soil bacterial communities.

International audience; This study provides the first maps of variations in bacterial community structure on a broad scale based on genotyping of DNA extracts from 593 soils from four different regions of France (North, Brittany, South-East and Landes). Soils were obtained from the soil library of RMQS (Réseau de Mesures de la Qualité des Sols = French soil quality monitoring network). The relevance of a biogeographic approach for studying bacterial communities was demonstrated by the great variability in community structure and specific geographical patterns within and between the four regions. The data indicated that the distribution of bacterial community composition might be more relate…

Use of fonctional genes to quantify denitrifiers in the environment

 ; During the last decade, application of molecular methods using cultivation-independent approaches has provided new insights into the composition and structure of denitrifying communities in various environments. However, little is known about their abundance, and quantification is still performed using cultivation-based approaches, which are not only biased by the inability to cultivate of many micro-organisms but also fastidious and time-consuming. Two types of cultivation-independent approaches have recently been developed to quantify denitrifiers. The first type, which is based on the hybridization technique, comprises the use of Southern hybridization and DNA arrays. The second type,…

« PPHD » : A Platform For High Throughput Phenotyping of Plant/Plant and Plant/Microorganisms Interactions

International audience

Optimisation du pyroséquençage haut-débit pour caractériser la diversité taxonomique des communautés bactériennes des sols

La diversité microbienne d’un sol (que l’on estime à 100000 à 1000000 d’espè ces différentes par gramme de sol) est difficile à caractériser. Toutefois, d’importantes avancé es en biologie moléculaire (comme le développement du pyrosé quençage), ont permis d'obtenir plusieurs centaines de milliers de sé quences à partir d’un ADN métagénomique, permettant une meilleure caracté risation de la diversité des communautés microbiennes du sol. Toutefois, dans un contexte ou l’écologie microbienne du sol commence à s’accaparer les é chantillonnages de grande envergure (spatial et temporelle) afin de mieux hié rarchiser les processus et paramètres impliqués dans la diversification de ces communauté …

Influence du type de sol et du mode d’occupation des sols sur la quantité d’ADN extraite et la densité des communautés bactériennes indigènes

National audience

Temporal variability of airborne bacterial community structure in an urban area

International audience; Temporal airborne bacterial genetic community structure and meteorological factors were analysed above an urban area in the northwest of France from December 2003 to April 2004 with a sampling strategy considering different time intervals (from an hour to a month). Principal component analysis (PCA) of B-ARISA (Bacterial-Automated Ribosomal Intergenic Spacer Analysis) profiles revealed a hierarchy in the temporal variability of bacterial community: daily<weekly<seasonal. Co-inertia analysis between B-ARISA data and meteorological factors demonstrated the correlation between the seasonal variability in the bacterial community and climatic conditions such as temperatur…

La biodiversité : menaces et ressources

Prod 2019-147 SPE BIOME INRA; National audience

Antibiosis as a possible mechanism of soil suppressiveness to Fusarium wilts

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

Concepts and methods to assess phytosanitary quality of soils

Chapitre 9.4 : Plant-microbe interactions and soil quality; International audience

Effects of land use intensity on european soil bacterial, fungal and archaeal communities

Whilst the importance of soils and their contribution to ecosystem services provision are well recognised, there is a paucity of knowledge on how particular land-use practices affect different types of soil organisms, and subsequently whether this affects soil functioning. The seventh framework programme EcoFINDERS project (Ecological Function and Biodiversity Indicators in European Soils) aims to “Decipher the links between soil biodiversity, activities, functioning and ecosystem services”. Through this project we have examined soil microbes at a number of European locations ranging from Iberian grassland to boreal forest. At each field site a gradient of land-use intensification has been …

Reciprocal interactions between plants and fluorescent pseudomonads in relation with iron in the rhizosphere

communication orale invitée; absent

Translation of metagenomics agroecosystems in ecological services

National audience

Towards an integrated approach to the microbial ecology of soil

Vers la mise en place d’un dispositif expérimental en agroécologie à l’échelle d’une unité expérimentale : le cas du domaine d’Epoisses (INRA Dijon)

National audience; L’agroécologie est aujourd’hui un thème source de nombreuses publications visant à définir ce terme et à le faire exister comme une science, un mouvement ou un ensemble de pratiques. Faisant suite à la volonté politique et scientifique de l’INRA de développer des expérimentations ambitieuses sur cette thématique, l’UMR Agroécologie et l’UE d’Epoisses, posent aujourd’hui les bases d’un projet d’expérimentation en agroécologie à l’échelle d’un domaine expérimental de 130 ha en grandes cultures, avec modification des pratiques agricoles et mise en place d’infrastructures paysagères. Un groupe de travail composé d’agronomes, écologues, écophysiologistes, généticiens, expérime…

Compréhension et valorisation des interactions entre plantes et microorganismes telluriques : un enjeu majeur en agroécologie

National audience; La libération d’une part significative des produits de photosynthèse de la plante sous forme de rhizodépôts constitue une source majeure de composés organiques pour la microflore hétérotrophe du sol qui est principalement en état de stase du fait de la forte compétition nutritionnelle régnant au niveau du sol. Parmi l’immense biodiversité tellurique, la plante sélectionne des populations particulières bien adaptées à l’environnement rhizosphérique et qui diffèrent selon le génotype de la plante. Cette sélection repose sur l’aptitude des populations microbiennes à tirer au mieux profit des composés organiques libérés, mais également sur une signalisation moléculaire à l’or…

Interactions réciproques entre plantes et Pseudomonas fluorescents en relation avec le fer rhizosphèrique

Soil biodiversity and ecosystem functions across Europe: A transect covering variations in bio-geographical zones, land use and soil properties

Prod 2016-344 SPE BIOME CT? INRA

Involvement of pyoverdine and nitrate reductase in the soil and rhizospheric competence of biocontrol Pseudomonas fluorescens strain C7R12

International audience

Panorama du projet « Dijon Alimentation Durable 2030 »

National audience

Influence of pea genotype on root-associated pseudomonads, impact on the plant protection against fungal pathogens

International audience

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples"

International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …

Soil carbon, multiple benefits

Made available in DSpace on 2018-12-11T17:24:47Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-01-01 In March 2013, 40 leading experts from across the world gathered at a workshop, hosted by the European Commission, Directorate General Joint Research Centre, Italy, to discuss the multiple benefits of soil carbon as part of a Rapid Assessment Process (RAP) project commissioned by Scientific Committee on Problems of the Environment (SCOPE). This collaboration led to the publication of the SCOPE Series Volume 71 Soil Carbon: Science, Management and Policy for Multiple Benefits; which brings together the essential scientific evidence and policy opportunities regarding the global importa…

"Favoriser la consommation des légumineuses en restauration scolaire". Conférence lors du salon "Food Use Tech" à Dijon le 20 septembre 2018

Organisation d'un salon grand public pour montrer le champ d'action du projet Territoire d'Innovation "Alimentation Durable 2030" porté par la Métropole de Dijon.

Conservation of type III secretion system genes inBradyrhizobiumisolated from soybean

International audience; The distribution of rhcRST genes encoding the type III secretion system (T3SS) in a collection of Bradyrhizobium strains was characterized by PCR and Southern blot hybridization. The polymorphism of the corresponding sequences amplified by PCR was characterized by RFLP and sequencing together with those available in the databank. Genomic group I is characterized by the presence of Bradyrhizobium elkanii strains and group II by the presence of B. japonicum and B. liaoningense strains. Highly conserved T3SS-like genes were detected by PCR in all Bradyrhizobium strains isolated from soybean belonging to genomic group II, and in none of the strains belonging to genomic g…

Importance de la diversité des Pseudomonas rhizosphériques et de celle de leurs sidérophores dans la nutrition en fer de la plante hôte

Influence of pea genotype on root associated fluorescent pseudomonads, consequences for plant iron nutrition

Pea has a high potential in agroecology because of its ability to fix atmospheric nitrogen and in Human nutrition because of the high aminoacid content of its grains. However, pea may suffer from a susceptibility to iron deficiency in calcareous soils. This susceptibility varies depending on cultivars. Pseudomonad siderophores, pyoverdines (pvd), were shown to promote iron nutrition in Arabidopsis and tobacco. Thus, we hypothesize that variations in iron susceptibility between pea cultivars could be related to differences in their ability to recruit fluorescent pseudomonad (fp) contributing to siderophore-mediated iron nutrition. Our aims were to compare i) the impact of a susceptible (S) a…

Ensemble de Ressources Biologiques dédiées à l'Agroécologie (INRA, Dijon). Mieux connaître, conserver et utiliser les ressources du sol.

National audience; Les spécificités de la problématique biodiversité dans le domaine agricole sont directement liées à l'ensemble des ressources génétiques, qu'elles soient microbiennes, végétales ou animales, et nécessitent la prise en compte de ces multiples composantes, leur fonctionnalité et leurs interactions pour en assurer la conservation et la valorisation. Gérer ces ressources biologiques consiste à les préserver in situ, mais aussi, à les inventorier, les caractériser et les évaluer, les conserver ex situ éventuellement, les régénérer et les diffuser ainsi que les connaissances afférentes. En collaboration avec le CRB Ferdinand Cabanne (http://www.crbferdinandcabanne.fr/) du CHU d…

EcoFINDERS : caractériser la biodiversité et le fonctionnement des sols en Europe : 23 partenaires de 10 pays européens et la chine

Le chercheur Philippe Lemanceau récompensé pour l'ensemble de sa carrière.

National audience

Projets emblématiques de recherche et résultats opérationnels sur la biologie des sols agricoles

Le système alimentaire facteur de qualité environnementale et de cohésion sociale

Une métropole modèle d’un système alimentaire durable #TIGAalimentation Rencontre Inra au SIA 2018 : Territoires d’Innovation de Grandes Ambitions (TIGA) : Dijon, territoire modèle du système alimentaire durable 2030. L’enjeu de ce projet est de prouver que l’évolution des systèmes alimentaires représente une formidable opportunité pour la transformation des territoires en termes de qualité environnementale, de développement économique et au final de bien-être, de santé et de cohésion sociale. L’ambition est de faire de Dijon métropole un démonstrateur de succès de cette transition du système alimentaire à l’échelle territoriale. Cette ambition représente une rupture comparée aux initiative…

Morphogenetic modifications induced by Pseudomonas fluorescens A6RI and Glomus mosseae BEG12 in the root system of tomato differ according to plant growth conditions

Summary • The ability of fluorescent pseudomonads and glomalean fungi to promote plant growth has been reported many times. However, little is known of their effects on root morphogenesis. Growth and root morphogenesis were compared in tomato ( Lycopersicon esculentum ) plants inoculated or not with a model strain of Pseudomonas fluorescens (A6RI) or with the arbuscular mycorrhizal fungus Glomus mosseae (BEG12). • Plants were cultivated in a sandy-loam soil mixed with sand at two different ratios (2 : 1 and 1 : 2), in gnotobiotic conditions. Plant growth was evaluated by measuring root and shoot fresh weight, and various morphometric parameters were compared. • Growth of control plants was …

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…

Introduction à l'ouvrage "Les sols et la vie souterraine : des enjeux majeurs en agroécologie"

Cette notice concernant l'introduction de l'ouvrage :"Les sols et la vie souterraine : des enjeux majeurs en agroécologie"SPEEABIOME; Introduction à l'ouvrage "Les sols et la vie souterraine : des enjeux majeurs en agroécologie"

Effect of soil type and plant species on the fluorescent pseudomonads nitrate dissimilating community

International audience

Interaction Pisum sativum (pois)- Pseudomonas: Conséquences sur la nutrition en fer, la croissance et l’immunité de la plante hôte

SPEEABIOMEDOCT INRA; Le projet vise à progresser dans notre connaissances des interactions pois – Pseudomonas afin d’améliorer la nutrition en fer et la santé de la plante-hôte. Le pois représente un fort potentiel en agroécologie (symbiose fixatrice d’azote) et en nutrition humaine (graines riches en acides aminés). Cependant, sa culture est sensible à la carence en fer et à certains phytopathogènes. Pour promouvoir la nutrition en fer et la santé du pois, l’objectif est de valoriser les pyoverdines, sidérophores produits par les Pseudomonas spp. fluorescents, dont certains peuvent améliorer la nutrition en fer de plantes et sont responsables d’antagonisme envers des phytopathogènes. La st…

Soils as a key component of the critical zone 6 : ecology

Prod 2018-76h équipe EA SPE BIOME INRA AGROSUP; International audience

Les LL (Living Lab), pour qui, pour quoi, avec qui et avec quoi ?

Depuis une quinzaine d’année, des Living Labs sont apparus dans différents secteurs économiques comme le numérique ou la santé. Le rapport « Agriculture et innovation 2025 » recommandait en 2018 de créer des Living Labs pour l’agriculture et l’alimentation. Cette volonté s’est traduite dans l’appel à projets « Territoires d’Innovation » lancé dans le cadre du Grand Plan d’Investissement. 24 projets ont été retenus en 2019 et une douzaine concernent l’agriculture, l’alimentation et la forêt. Cette séance présente le concept de Living Lab et l’illustre au travers de l’exemple de deux Territoires d’Innovation.ObjectifsIl s’agit tout d’abord de présenter le concept. Les Living Lab sont une nouv…

Implication of pyoverdines in the interactions of fluorescent pseudomonads with soil microflora and plant in the rhizosphere

International audience

Monitoring microbial diversity in European soils: ongoing projects and challenges

SPEEcolDurGenoSolCT3communication orale invitée, résumé et slides; According to the Convention of Biological Diversity (Rio de Janeiro, 1992), biodiversity is the variation in life from genes to species, communities, ecosystems, and landscapes. Soils represent a huge reservoir of biodiversity which varies in terms of taxonomic richness, relative abundance and distribution according to soil types, climatic conditions, vegetation and land uses. The key functions supporting ecosystem services as identified in the Millennium Ecosystem Assessment (MEA, 2005) largely depend upon organisms that inhabit the soil. Thus, the design and implementation of a sustainable soil management strategy requires…

Actions et rétroactions : conséquences pour la gestion des sols

Prod 2018-76d équipe EA SPE BIOME INRA AGROSUP; National audience; Chapitre 9. Actions et rétroactions : conséquences pour la gestion des sols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 Sébastien BAROT, Manuel BLOUIN et Philippe LEMANCEAU 9.1. Émergence d’une compréhension éco-évolutive du fonctionnement des sols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 9.2. Vers une ingénierie des sols écologique et évolutive . . . . . . . . . . . 166 9.3. Bibliographie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 résumé du livre : Les sols sont des milieux où évolue une myriade d’organismes différents, déterminant…

Reciprocal interactions between plants and fluorescent pseudomonads in relation with iron in the rhizosphere

National audience; Although iron is the fourth element in the Earth’s crust, the availability of Fe(III) is limited in most cultivated soils due to their pH. In soil adhering to plant roots (rhizosphere), plants release a sgnificant part of their photosynthetates (rhizodeposits) that promote microbial density and activity. Iron uptake by this microflora and by plant roots contributes to decrease even more iron availability in the rhizosphere. In this competition context, plants and microbes have developed active strategies of iron uptake. In dicotyledon plants, this strategy involves (i) the excretion of protons, (ii) the reduction of Fe(III) by reductases, and (iii) plasmalemma transport o…

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

Les sols fournissent de nombreux services écosystémiques tels que : (i) la production primaire, (ii) la régulation des cycles géochimiques avec leurs conséquences sur la production agricole mais également sur le climat, (iii) la filtration et régulation de l’eau, (iv) la résistance aux maladies et ravageurs, (v) la régulation de la biodiversité végétale. Ces services sont rendus grâce au fonctionnement biologique des sols reposant sur les activités déterminées par la biodiversité tellurique. En dépit de l’importance du fonctionnement biologique des sols, notre connaissance de la biodiversité et des activités telluriques demeurent fragmentaires. Au niveau académique, l’enjeu des recherches d…

Fluorescent pseudomonad injectisomes and manipulation of plant defenses : biocontrol versus pathogenic rhizosphere agents

International audience

Relever les défis des relations agriculture et environnement par des approches participatives : une révolution amorcée !

Prod 2018-124 SPE EA BIOME INRA; National audience

Reciprocal interactions between plants and fluorescent pseudomonads in relation with iron in the rhizosphere

International audience; Iron is an essential element for plants and microbes. However, in most cultivated soils, the concentration of iron available for these living organisms is very low since its solubility is controlled by stable hydroxides, oxyhydroxides and oxides. The high demand for iron by plants and microorganisms in the rhizosphere together with its low availability in soils leads to a strong competition for this nutrient among living organisms. To face this competition, plants and microorganisms have developed active strategies of iron uptake. In non graminaceous plants (strategy I), iron uptake relies on acidification and reduction of Fe+++ in Fe++ which incorporated in the root…

Contribution of studies on suppressive soils to the identification of bacterial biocontrol agents and to the knowledge of their modes of action

International audience

Benefits of soil carbon: report on the outcomes of an international scientific committee on problems of the environment rapid assessment workshop

The outcomes of the discussion in the four working sessions showed that although there is an urgent need to improve soil carbon management and stocks, and despite the existing knowledge about good agricultural practices to achieve this goal, these are not put into practice effectively and globally. The apparent contradiction has to do with a mismatch of policies at different societal and geographical scales, and the low policy profile of SOC. All participants agreed in the need to bring SOC into the core of environmental policies at all levels and to improve the governance of policy actions by addressing the stakeholders in a more effective way. Fil: Banwart, Steven. University of Sheffield…