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Equipe de Recherche Rhizosphère

Claire Prigent-Combaret

Directrice de Recherche CNRS


  • Depuis 2017 : Directrice de Recherche CNRS
  • Depuis 2013 : Responsable de l’équipe Rhizosphère
  • De 2009 à 2013 : Responsable adjoint de l’équipe Rhizosphère
  • Depuis 2003 : Chercheur CNRS au sein du Laboratoir d’Ecologie Microbienne
  • Thèmes de recherches :
    1. Ecologie fonctionnelle et spécificité de la coopération PGPR-plantes.
    2. Interactions biotiques entre PGPR au sein des biofilms racinaires.
    3. Analyse moléculaire de la stimulation bactérienne de la croissance végétale.

Parcours scientifique

  • 2011 : Habilitation à diriger des Recherches de l’Université Lyon 1
  • 2000 : Doctorat de Microbiologie de l’Université Paris 7
  • 1996 : D.E.A. de Microbiologie de l’Université Paris 7
  • 1995 : Diplôme d’Ingénieur Biochimiste de l’INSA de Lyon


  • 2016-2019 : Co-diretion de la thèse de L. Rieusset (G. Comte, directeur, équipe ‘Rhizosphère’). Impact de la plante hôte sur le métabolisme bactérien et sur la coopération bactérienne dans la rhizosphère.
  • 2015-2018 : Direction de la thèse de J. Valente (Y. Moënne-Loccoz, co-directeur, équipe ‘Rhizosphère’). Phytostimulation des blés de sélection ancienne (pré-Révolution verte) et moderne (post-Révolution verte) par les bactéries PGPR (Plant Growth-Promoting Rhizobacteria)
  • 2015-2018 : Direction de la thèse de Y. Besset-Manzoni (P. Joly, co-directeur, société Biovitis). Sélection des nouveaux agents bactériens de phytoprotection et étude des mécanismes de protection du blé vis-à-vis de stress biotique et abiotique (CIFRE).
  • 2017 : Co-encadrement du M2R de B. Manriquez (D. Muller, encadrement). Caractérisation de nouvelles propriétés phytobénéfiques chez des PGPR Pseudomonas chlororaphis.


  • Vacheron, J., A. Dubost, D. Chapulliot, C. Prigent-Combaret, D. Muller. 2017. Draft genome sequence of Chryseobacterium sp. JV274 isolated from maize rhizosphere. Genome Announcements (In Press)
  • Rozier C, et al. 2016. Xylem Sap Metabolite Profile Changes During Phytostimulation of Maize by the Plant Growth-Promoting Rhizobacterium, Azospirillum lipoferum CRT1. 6:1-10.


    • Alori, E.T., Babalola, O.O., Prigent-Combaret, C., 2019. Impacts of Microbial Inoculants on the Growth and Yield of Maize Plant. The Open Agriculture Journal 13.
      Résumé : Impacts of Microbial Inoculants on the Growth and Yield of Maize Plant
      Mots-clés : #3.
      Pièce jointe Full Text PDF 840.4 ko (source)

    • Aremu, B.R., Prigent-Combaret, C., Babalola, O.O., 2019. Draft Genome Sequence of <i>Bacillus velezensis</i> Strain ZeaDK315Endo16. Microbiology Resource Announcements 8, e00136-19, /mra/8/46/MRA.00136-19.atom.
      Résumé : ABSTRACT Here, we report the draft genome sequence of the endophytic Bacillus velezensis strain ZeaDK315Endo16, isolated from DK315 maize from Lyon, France. B. velezensis ZeaDK315Endo16 exhibits a suppressive ability toward Fusarium graminearum , a widely known threat to maize production and quality.
      Mots-clés : #3.

    • Keshavarz-Tohid, V., Vacheron, J., Dubost, A., Prigent-Combaret, C., Taheri, P., Tarighi, S., Taghavi, S.M., Moënne-Loccoz, Y., Muller, D., 2019. Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov. Systematic and Applied Microbiology.
      Résumé : Bacteria of the Pseudomonas putida group are studied for a large panel of properties ranging from plant growth promotion and bioremediation to pathogenicity. To date, most of the classification of individual pseudomonads from this group relies on 16S RNA gene analysis, which is insufficient for accurate taxonomic characterization within bacterial species complexes of the Pseudomonas putida group. Here, a collection of 20 of these bacteria, isolated from various soils, was assessed via multi-locus sequence analysis of rpoD, gyrB and rrs genes. The 20 strains clustered in 7 different clades of the P. putida group. One strain per cluster was sequenced and results were compared to complete genome sequences of type strains of the P. putida group. Phylogenetic analyses, average nucleotide identity data and digital DNA hybridizations, combined to phenotypic characteristics, resulted in the proposition and description of four new species i.e. Pseudomonas alloputida Kh7 T (= LMG 29756 T = CFBP 8484 T) sp. nov., Pseudomonas inefficax JV551A3 T (= DSM108619 T = CFBP 8493 T) sp. nov., Pseudomonas persica RUB6 T (= LMG 29757 T = CFBP 8486 T) sp. nov. and Pseudomonas shirazica VM14 T (= LMG 29953 T = CFBP 8487 T) sp. nov.
      Mots-clés : #3, #ibio, GGDC, group, Pseudomonads genomes.


    • Bertrand, C., Prigent-Combaret, C., Gonzales-Coloma, A., 2018. Chemistry, activity, and impact of plant biocontrol products. Environmental Science and Pollution Research.
      Mots-clés : #3.

    • Ibrahim, N.A.G.A.A., Omar, M.N.A.M., El Heba, G.A.A., Moënne-Loccoz, Y., Prigent-Combaret, C., Muller, D., 2018. Draft Genome Sequence of Plant Growth-Promoting <i>Bacillus altitudinis</i> Strain PAE4. Microbiology Resource Announcements 7.
      Mots-clés : #3.

    • Jacquemond, I., Muggeo, A., Lamblin, G., Tristan, A., Gillet, Y., Bolze, P.A., Bes, M., Gustave, C.A., Rasigade, J.-P., Golfier, F., Ferry, T., Dubost, A., Abrouk, D., Barreto, S., Prigent-Combaret, C., Thioulouse, J., Lina, G., Muller, D., 2018. Complex ecological interactions of Staphylococcus aureus in tampons during menstruation. Scientific Reports 8, 9942.
      Résumé : Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons’ microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.
      Mots-clés : #3, #ibio.

    • Nonfoux, L., Chiaruzzi, M., Badiou, C., Baude, J., Tristan, A., Thioulouse, J., Muller, D., Prigent-Combaret, C., Lina, G., 2018. Impact of Currently Marketed Tampons and Menstrual Cups on Staphylococcus aureus Growth and Toxic Shock Syndrome Toxin 1 Production In Vitro. Applied and Environmental Microbiology 84, e00351-18.
      Résumé : Fifteen currently marketed intravaginal protection products (11 types of tampon and 4 types of menstrual cup) were tested by the modified tampon sac method to determine their effect on Staphylococcus aureus growth and toxic shock syndrome toxin 1 (TSST-1) production. Most tampons reduced S. aureus growth and TSST-1 production, with differences based on brand and composition, and the level of S. aureus growth was higher in destructured than in unaltered tampons. We observed higher levels of S. aureus growth and toxin production in menstrual cups than in tampons, potentially due to the additional air introduced into the bag by cups, with differences based on cup composition and size. IMPORTANCE Menstrual toxic shock syndrome is a rare but severe disease. It occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock syndrome toxin 1 using intravaginal protection, such as tampons or menstrual cups. Intravaginal protection induces TSS by the collection of catamenial products, which act as a growth medium for S. aureus. Previous studies evaluated the impact of tampon composition on S. aureus producing toxic shock syndrome toxin 1, but they are not recent and did not include menstrual cups. This study demonstrates that highly reproducible results for S. aureus growth and TSST-1 production can be obtained by using a simple protocol that reproduces the physiological conditions of tampon and cup usage as closely as possible, providing recommendations for tampon or cup use to both manufacturers and consumers. Notably, our results do not show that menstrual cups are safer than tampons and suggest that they require similar precautions.
      Mots-clés : #3, biofilm, elastomer, fiber, menstrual cup, Staphylococcus aureus, tampon, toxic shock syndrome toxin 1.


    • Almario, J., Bruto, M., Vacheron, J., Prigent-Combaret, C., Moënne-Loccoz, Y., Muller, D., 2017. Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism. Frontiers in Microbiology 8, 1218.
      Résumé : Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG+ Pseudomonas strains in the ‘P. corrugata’ and ‘P. protegens’ subgroups of the ‘Pseudomonas fluorescens’ group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG+ Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp. was investigated in sequenced genomes and type strains. Results showed that the DAPG+ Pseudomonas include species of the ‘P. fluorescens’ group, i.e. P. protegens, P. brassicacearum, P. kilonensis and P. thivervalensis, as expected, as well as P. gingeri in which it had not been documented. Surprisingly, they also include bacteria outside the ‘P. fluorescens’ group, as exemplified by Pseudomonas sp. OT69, and even two Betaproteobacteria genera. The phl operon-based phylogenetic tree was substantially congruent with the one inferred from concatenated housekeeping genes rpoB, gyrB and rrs. Contrariwise to current supposition, ancestral character reconstructions favored multiple independent acquisitions rather that one ancestral event followed by vertical inheritance. Indeed, based on synteny analyses, these acquisitions appeared to vary according to the Pseudomonas subgroup and even the phylogenetic groups within the subgroups. In conclusion, our study shows that the phl+ Pseudomonas populations form a polyphyletic group and suggests that DAPG biosynthesis might not be restricted to this genus. This is important to consider when assessing the ecological significance of phl+ bacterial populations in rhizosphere ecosystems.
      Mots-clés : #3, biocontrol agent, DAPG, Diacetylphloroglucinol, phl Operon, phlACBD genes.

    • Vacheron, J., Desbrosses, G., Renoud, S., Padilla-Aguilar, R.-M., Walker, V., Muller, D., Prigent-Combaret, C., 2017. Differential contribution of plant-beneficial functions from Pseudomonas kilonensis F113 to root system architecture alterations in Arabidopsis thaliana and Zea mays. Molecular Plant-Microbe Interactions MPMI–07.
      Résumé : Fluorescent pseudomonads are playing key roles in plant-bacteria symbiotic interactions due to the multiple plant-beneficial functions (PBFs) they are harboring. The relative contributions of PBFs to plant-stimulatory effects of the well-known PGPR Pseudomonas kilonensis F113 (formerly P. fluorescens F113) were investigated using a genetic approach. To this end, several deletion mutants were constructed: simple mutants ΔphlD (impaired in the biosynthesis of 2,4-diacetylphloroglucinol [DAPG]), ΔacdS (deficient in 1-aminocyclopropane-1-carboxylate [ACC] deaminase activity), Δgcd (glucose dehydrogenase deficient, impaired in phosphate solubilization), and ΔnirS (nitrite reductase deficient) and a quadruple mutant (deficient in the 4 PBFs mentioned above). Every PBF activity was quantified in the wild-type strain and the five deletion mutants. This approach revealed few functional interactions between PBFs in vitro. In particular, biosynthesis of glucose dehydrogenase severely reduced the production of DAPG. Contrariwise, the DAPG production impacted positively, but to a lesser extent, phosphate solubilization. Inoculation of the F113 wild-type strain on Arabidopsis thaliana Col-0 and maize seedlings modified the root architecture of both plants. Mutant strain inoculations revealed that the relative contribution of each PBF differed according to the measured plant traits, and that F113 plant-stimulatory effects did not correspond to the sum of each PBF relative contribution. Indeed, two PBF genes (ΔacdS and ΔnirS) had a significant impact on root system architecture from both model plants, whether in in vitro and in vivo conditions. The current work underlined that few F113 PBFs seem to interact between each other in the free-living bacterial cells, whereas they control in concert Arabidopsis thaliana and maize growth and development.
      Mots-clés : #3, #4.

    • Vacheron, J., Dubost, A., Chapulliot, D., Prigent-Combaret, C., Muller, D., 2017. Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere. Genome Announcements 5, e00122-17.
      Résumé : We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated from the rhizosphere of maize during a greenhouse experiment. JV274 harbors genes involved in flexirubin production (darA and darB genes), bacterial competition (type VI secretion system), and gliding (bacterial motility; type IX secretion system).
      Mots-clés : #3, #4, #ibio.


    • BORLAND, S., PRIGENT-COMBARET, C., WISNIEWSKI-DYE, F., 2016. Bacterial hybrid histidine kinases in plant-bacteria interactions. Microbiology 162, 1715-1734.
      Résumé : Two-component signal transduction systems (TCS) are essential for many bacteria to maintain homeostasis and adapt to environmental changes. TCS typically involve a membrane-bound histidine kinase (HK) that senses stimuli, autophosphorylates in the transmitter region and then transfers the phosphoryl group to the receiver domain of a cytoplasmic response regulator (RR) that mediates appropriate changes in bacterial physiology. Although usually found on distinct proteins, the transmitter and receiver modules are sometimes fused into a so-called hybrid HK (HyHK). Such structure results in multiple phosphate transfers that are believed to provide extra fine-tuning mechanisms and more regulatory checkpoints than classical phosphotransfers. HyHK-based regulation may be crucial for finely tuning gene expression in a heterogeneous environment such as the rhizosphere where intricate plant-bacteria interactions occur. In this review, we focus on roles fulfilled by bacterial HyHKs in plant-associated bacteria, providing recent findings of the mechanistic of their signaling properties. Recent insights in understanding additive regulatory properties fulfilled by the tethered receiver domain of HyHKs are also addressed.
      Mots-clés : #3.

    • Mommer, L., Hinsinger, P., Prigent-Combaret, C., Visser, E.J.W., 2016. Advances in the rhizosphere: stretching the interface of life. Plant and Soil 407, 1-8.
      Mots-clés : #3.

    • Vacheron, J., Combes-Meynet, E., Walker, V., Gouesnard, B., Muller, D., Moënne-Loccoz, Y., Prigent-Combaret, C., 2016. Expression on roots and contribution to maize phytostimulation of 1-aminocyclopropane-1-decarboxylate deaminase gene acdS in Pseudomonas fluorescens F113. Plant and Soil 407, 187-202.
      Résumé : Aims The plant-beneficial bacterium Pseudomonas fluorescens F113 harbours an acdS gene, which enables deamination of 1-aminocyclopropane-1-carboxylate. The impact of abiotic and biotic factors on the expression of this gene was assessed, as well as the plant-beneficial properties of F113 under different soil moistures. Methods An acdS-egfp biosensor was constructed in F113, validated in vitro and used to analyse, by microscopy, its expression on roots of Zea mays comparatively to Beta vulgaris. An acdS mutant was constructed and compared with the wild-type to characterize plant-beneficial effects of F113 on maize lines EP1 and FV2, under well-watered and water deficit conditions. Results Different patterns of root colonization and acdS expression were observed according to plant genotype. acdS rhizoplane expression was higher on Beta vulgaris, and on maize line FV2 and hybrid PR37Y15 than on maize line EP1 and teosinte. Strain F113 but not its acdS mutant promoted root growth of EP1 under well-watered conditions and germination of FV2 under water deficit conditions. Conclusions Maize lines differed in their ability to induce acdS expression and to respond to P. fluorescens F113. The maize line leading to higher acdS expression, FV2, was the one benefiting from inoculation under water deficit.
      Mots-clés : #3, #cesn, 1-aminocyclopropane-1-decarboxylate deaminase, acdS expression, ecology, Maize genotypes, Plant growth promotion, Plant Physiology, Plant Sciences, Soil Science & Conservation, Water deficit.

    • Vacheron, J., Moënne-Loccoz, Y., Dubost, A., Gonçalves-Martins, M., Muller, D., Prigent-Combaret, C., 2016. Fluorescent Pseudomonas Strains with only Few Plant-Beneficial Properties Are Favored in the Maize Rhizosphere. Plant Biotic Interactions 7, 1212.
      Résumé : Plant Growth-Promoting Rhizobacteria (PGPR) enhance plant health and growth using a variety of traits. Effective PGPR strains typically exhibit multiple plant-beneficial properties, but whether they are better adapted to the rhizosphere than PGPR strains with fewer plant-beneficial properties is unknown. Here, we tested the hypothesis that strains with higher numbers of plant-beneficial properties would be preferentially selected by plant roots. To this end, the co-occurrence of 18 properties involved in enhanced plant nutrition, plant hormone modulation, or pathogen inhibition was analyzed by molecular and biochemical methods in a collection of maize rhizosphere and bulk soil isolates of fluorescent Pseudomonas. Twelve plant-beneficial properties were found among the 698 isolates. Contrarily to expectation, maize preferentially selected pseudomonads with low numbers of plant-beneficial properties (up to five). This selection was not due to the predominance of strains with specific assortments of these properties, or with specific taxonomic status. Therefore, the occurrence of only few plant-beneficial properties appeared favorable for root colonization by pseudomonads.
      Mots-clés : #3, #cesn, #ibio, fluorescent Pseudomonas, Functional groups, Maize, PGPR, plant-beneficial properties.
      Note Note
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    • Borland, S., Oudart, A., Prigent-Combaret, C., Brochier-Armanet, C., Wisniewski-Dyé, F., 2015. Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum. BMC Genomics 16.
      Mots-clés : #3.

    • Chamam, A., Wisniewski-Dyé, F., Comte, G., Bertrand, C., Prigent-Combaret, C., 2015. Differential responses of Oryza sativa secondary metabolism to biotic interactions with cooperative, commensal and phytopathogenic bacteria. Planta.
      Mots-clés : #3, #cesn.


    • Bruto, M., Prigent-Combaret, C., Luis, P., Moënne-Loccoz, Y., Muller, D., 2014. Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes. Proceedings of the Royal Society B: Biological Sciences 281, 20140848.
      Résumé : Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.
      Mots-clés : #2, #3, adaptive horizontal transfer, inter-domain transfer, lateral gene transfer.

    • Bruto, M., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2014. Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Scientific Reports 4, 6261.
      Mots-clés : #3, #ibio.


    • Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2013. Effect of Clay Mineralogy on Iron Bioavailability and Rhizosphere Transcription of 2,4-Diacetylphloroglucinol Biosynthetic Genes in Biocontrol <i>Pseudomonas protegens</i>. Molecular Plant-Microbe Interactions 130213113028008.
      Résumé : Pseudomonas strains producing 2,4-diacetylphloroglucinol (DAPG) can protect plants from soil-borne phytopathogens and are considered the primarily reason for suppressiveness of morainic Swiss soils to Thielaviopsis basicola-mediated black root-rot disease of tobacco, even though they also occur nearby in conducive sandstone soils. The underlying molecular mechanism(s) accounting for this discrepancy are not understood. In this study, we assessed the hypothesis that the presence of iron-rich vermiculite clay (dominant in suppressive soils) instead of illite (dominant in neighboring conducive soils) translates into higher levels of iron bioavailability and transcription of Pseudomonas DAPG synthetic genes in the tobacco rhizosphere. Rhizosphere monitoring of reporter gene systems pvd-inaZ and phlA-gfp in Pseudomonas protegens respectively indicated that the level of iron bioavailability and the number of cells expressing phl genes (DAPG synthesis) were higher in vermiculitic than in illitic artificial soils. This was in accordance with the effect of iron on phlA-gfp expression in vitro, and indeed iron addition to the illitic soil increased the number of cells expressing phlA-gfp. Similar findings were made in presence of the pathogen T. basicola. Altogether, results substantiate the hypothesis that iron-releasing minerals may confer disease suppressiveness by modulating iron bioavailability in the rhizosphere and expression of biocontrol-relevant genes in antagonistic P. protegens.
      Mots-clés : #3.

    • Chamam, A., Sanguin, H., Bellvert, F., Meiffren, G., Comte, G., Wisniewski-Dyé, F., Bertrand, C., Prigent-Combaret, C., 2013. Plant secondary metabolite profiling evidences strain-dependent effect in the <i>Azospirillum–Oryza sativa</i> association. Phytochemistry 87, 65-77.
      Résumé : Azospirillum is a plant growth-promoting rhizobacterium (PGPR) able to enhance growth and yield of cereals such as rice, maize and wheat. The growth-promoting ability of some Azospirillum strains appears to be highly specific to certain plant species and cultivars. In order to ascertain the specificity of the associative symbiosis between rice and Azospirillum, the physiological response of two rice cultivars, Nipponbare and Cigalon, inoculated with two rice-associated Azospirillum was analyzed at two levels: plant growth response and plant secondary metabolic response. Each strain of Azospirillum (Azospirillum lipoferum 4B isolated from Cigalon and Azospirillum sp. B510 isolated from Nipponbare) preferentially increased growth of the cultivar from which it was isolated. This specific effect is not related to a defect in colonization of host cultivar as each strain colonizes effectively both rice cultivars, either at the rhizoplane (for 4B and B510) and inside the roots (for B510). The metabolic profiling approach showed that, in response to PGPR inoculation, profiles of rice secondary metabolites were modified, with phenolic compounds such as flavonoids and hydroxycinnamic derivatives being the main metabolites affected. Moreover, plant metabolic changes differed according to Azospirillum strain × cultivar combinations; indeed, 4B induced major secondary metabolic profile modifications only on Cigalon roots, while B510, probably due to its endophytic feature, induced metabolic variations on shoots and roots of both cultivars, triggering a systemic response. Plant secondary metabolite profiling thereby evidences the specific interaction between an Azospirillum strain and its original host cultivar.
      Mots-clés : #3, #cesn, Azospirillum, Oryza sativa, PGPR, Phenolic metabolites, Root colonization, Secondary metabolite profiling.

    • Couillerot, O., Ramírez-Trujillo, A., Walker, V., von Felten, A., Jansa, J., Maurhofer, M., Défago, G., Prigent-Combaret, C., Comte, G., Caballero-Mellado, J., Moënne-Loccoz, Y., 2013. Comparison of prominent <i>Azospirillum</i> strains in <i>Azospirillum–Pseudomonas–Glomus</i> consortia for promotion of maize growth. Applied Microbiology and Biotechnology 97, 4639-4649.
      Résumé : Azospirillum are prominent plant growth-promoting rhizobacteria (PGPR) extensively used as phytostimulatory crop inoculants, but only few studies are dealing with Azospirillum -containing mixed inocula involving more than two microorganisms. We compared here three prominent Azospirillum strains as part of three-component consortia including also the PGPR Pseudomonas fluorescens F113 and a mycorrhizal inoculant mix composed of three Glomus strains. Inoculant colonization of maize was assessed by quantitative PCR, transcription of auxin synthesis gene ipdC (involved in phytostimulation) in Azospirillum by RT-PCR, and effects on maize by secondary metabolic profiling and shoot biomass measurements. Results showed that phytostimulation by all the three-component consortia was comparable, despite contrasted survival of the Azospirillum strains and different secondary metabolic responses of maize to inoculation. Unexpectedly, the presence of Azospirillum in the inoculum resulted in lower phytostimulation in comparison with the Pseudomonas – Glomus two-component consortium, but this effect was transient. Azospirillum 's ipdC gene was transcribed in all treatments, especially with three-component consortia, but not with all plants and samplings. Inoculation had no negative impact on the prevalence of mycorrhizal taxa in roots. In conclusion, this study brought new insights in the functioning of microbial consortia and showed that Azospirillum – Pseudomonas – Glomus three-component inoculants may be useful in environmental biotechnology for maize growth promotion.
      Mots-clés : #3, #cesn, Chemistry and Materials Science.

    • Drogue, B., Sanguin, H., Borland, S., Prigent-Combaret, C., Wisniewski-Dyé, F., 2013. Genome wide profiling of <i>Azospirillum lipoferum</i> 4B gene expression during interaction with rice roots. FEMS Microbiology Ecology n/a–n/a.
      Résumé : Azospirillum-plant cooperation has been mainly studied from an agronomic point of view leading to a wide description of mechanisms implicated in plant growth-promoting effects. However, little is known about genetic determinants implicated in bacterial adaptation to the host plant during the transition from free-living to root-associated lifestyles. This study aims at characterizing global gene expression of Azospirillum lipoferum 4B following a 7-day-old interaction with two cultivars of Oryza sativa L. japonica (cv. Cigalon from which it was originally isolated, and cv. Nipponbare). The analysis was done on a whole genome expression array with RNA samples obtained from planktonic cells, sessile cells and root-adhering cells. Root-associated Azospirillum grow in an active sessile-like state and gene expression is tightly adjusted to the host plant. Adaptation to rice seems to involve genes related to ROS detoxification and multidrug efflux, as well as complex regulatory networks. As revealed by the induction of genes encoding transposases, interaction with root may drive bacterial genome rearrangements. Several genes related to ABC transporter and ROS detoxification display cultivar-specific expression profiles, suggesting host specific adaptation and raising the question of A. lipoferum 4B/rice cv. Cigalon co-adaptation.This article is protected by copyright. All rights reserved.
      Mots-clés : #3, Azospirillum, Cooperation, Plant growth-promoting rhizobacteria, rice, transcriptome.

    • Vacheron, J., Desbrosses, G., Bouffaud, M.-L., Touraine, B., Moënne-Loccoz, Y., Muller, D., Legendre, L., Wisniewski-Dyé, F., Prigent-Combaret, C., 2013. Plant growth-promoting rhizobacteria and root system functioning. Frontiers in Plant Science - Functional plant Ecology 4, 356.
      Résumé : The rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. Among the latter, plant growth-promoting rhizobacteria (PGPR) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. Modification of root system architecture by PGPR implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development of root hairs. PGPR also modify root functioning, improve plant nutrition and influence the physiology of the whole plant. Recent results provided first clues as to how PGPR signals could trigger these plant responses. Whether local and/or systemic, the plant molecular pathways involved remain often unknown. From an ecological point of view, it emerged that PGPR form coherent functional groups, whose rhizosphere ecology is influenced by a myriad of abiotic and biotic factors in natural and agricultural soils, and these factors can in turn modulate PGPR effects on roots. In this paper, we address novel knowledge and gaps on PGPR modes of action and signals, and highlight recent progress on the links between plant morphological and physiological effects induced by PGPR. We also show the importance of taking into account the size, diversity, and gene expression patterns of PGPR assemblages in the rhizosphere to better understand their impact on plant growth and functioning. Integrating mechanistic and ecological knowledge on PGPR populations in soil will be a prerequisite to develop novel management strategies for sustainable agriculture.
      Mots-clés : #3, #cesn, functional group, ISR, phytohormone, plant nutrition, plant-PGPR cooperation, rhizo-microbiome, rhizosphere.
      Note Note

    • Walker, V., Bruto, M., Bellvert, F., Bally, R., Muller, D., Prigent-Combaret, C., Moënne-Loccoz, Y., Comte, G., 2013. Unexpected Phytostimulatory Behavior for Escherichia coli and Agrobacterium tumefaciens Model Strains. Molecular Plant-Microbe Interactions 26, 495-502.
      Mots-clés : #3, #cesn.


    • Drogue, B., Doré, H., Borland, S., Wisniewski-Dyé, F., Prigent-Combaret, C., 2012. Which specificity in cooperation between phytostimulating rhizobacteria and plants? Research in Microbiology 163, 500-510.
      Résumé : Plant growth-promoting rhizobacteria (PGPR) are found in association with a large range of host plants. Although the subject of plant host specificity has been well studied in parasitic and mutualistic interactions, the question of whether phytostimulating rhizobacteria efficiently interact only with a specific host remains poorly discussed. This review presents elements suggesting the existence of specificity in three-step establishment of associative symbiosis between phytostimulating rhizobacteria and plants: bacterial attraction by the host plant, bacterial colonization of roots, and functioning of associative symbiosis.
      Mots-clés : #3, Adherence, Chemotaxis, Cooperation, Host specificity, Plant genotype, Plant growth-promoting rhizobacteria.

    • Drogue, B., Thomas, P., Balvay, L., Prigent-Combaret, C., Dorel, C., 2012. Engineering Adherent Bacteria by Creating a Single Synthetic Curli Operon. Journal of Visualized Experiments.
      Mots-clés : #3.

    • Prigent-Combaret, C., Sanguin, H., Champier, L., Bertrand, C., Monnez, C., Colinon, C., Blaha, D., Ghigo, J.-M., Cournoyer, B., 2012. The bacterial thiopurine methyltransferase tellurite resistance process is highly dependent upon aggregation properties and oxidative stress response: The TPMT Te <sup>R</sup> process. Environmental Microbiology 14, 2645-2660.
      Mots-clés : #3, #6.

    • Prigent-Combaret, C., Sanguin, H., Champier, L., Bertrand, C., Monnez, C., Colinon-Dupuich, C., Blaha, D., Ghigo, J.M., Cournoyer, B., 2012. The bacterial thiopurine methyltransferase tellurite resistance process is highly dependent upon aggregation properties and oxidative stress response. Environmental Microbiology.
      Mots-clés : #3, #6.

    • Prigent-Combaret, C., Zghidi-Abouzid, O., Effantin, G., Lejeune, P., Reverchon, S., Nasser, W., 2012. The nucleoid-associated protein Fis directly modulates the synthesis of cellulose, an essential component of pellicle–biofilms in the phytopathogenic bacterium <i>Dickeya dadantii</i>. Molecular Microbiology.
      Mots-clés : #3.

    • Wisniewski-Dyé, F., Lozano, L., Acosta-Cruz, E., Borland, S., Drogue, B., Prigent-Combaret, C., Rouy, Z., Barbe, V., Herrera, A.M., González, V., Mavingui, P., 2012. Genome Sequence of <i>Azospirillum brasilense</i> CBG497 and Comparative Analyses of <i>Azospirillum</i> Core and Accessory Genomes provide Insight into Niche Adaptation. Genes 3, 576-602.
      Mots-clés : #3, #7.


    • Combes-Meynet, E., Pothier, J.F., Moënne-Loccoz, Y., Prigent-Combaret, C., 2011. The <i>Pseudomonas</i> secondary metabolite 2, 4-diacetylphloroglucinol is a signal inducing rhizoplane expression of <i>Azospirillum</i> genes involved in plant-growth promotion. Molecular Plant-Microbe Interactions 24, 271–284.
      Mots-clés : #3.

    • Couillerot, O., Combes-Meynet, E., Pothier, J.F., Bellvert, F., Challita, E., Poirier, M.A., Rohr, R., Comte, G., Moënne-Loccoz, Y., Prigent-Combaret, C., 2011. The role of the antimicrobial compound 2, 4-diacetylphloroglucinol in the impact of biocontrol <i>Pseudomonas fluorescens</i> F113 on <i>Azospirillum brasilense</i> phytostimulators. Microbiology 157, 1694–1705.
      Résumé : Pseudomonads producing the antimicrobial metabolite 2,4-diacetylphloroglucinol (Phl) can control soil-borne phytopathogens, but their impact on other plant-beneficial bacteria remains poorly documented. Here, the effects of synthetic Phl and Phl+ Pseudomonas fluorescens F113 on Azospirillum brasilense phytostimulators were investigated. Most A. brasilense strains were moderately sensitive to Phl. In vitro, Phl induced accumulation of carotenoids and poly-β-hydroxybutyrate-like granules, cytoplasmic membrane damage and growth inhibition in A. brasilense Cd. Experiments with P. fluorescens F113 and a Phl− mutant indicated that Phl production ability contributed to in vitro growth inhibition of A. brasilense Cd and Sp245. Under gnotobiotic conditions, each of the three strains, P. fluorescens F113 and A. brasilense Cd and Sp245, stimulated wheat growth. Co-inoculation of A. brasilense Sp245 and Pseudomonas resulted in the same level of phytostimulation as in single inoculations, whereas it abolished phytostimulation when A. brasilense Cd was used. Pseudomonas Phl production ability resulted in lower Azospirillum cell numbers per root system (based on colony counts) and restricted microscale root colonization of neighbouring Azospirillum cells (based on confocal microscopy), regardless of the A. brasilense strain used. Therefore, this work establishes that Phl+ pseudomonads have the potential to interfere with A. brasilense phytostimulators on roots and with their plant growth promotion capacity.
      Mots-clés : #3, #cesn.

    • Dorioz, J.M., Quetin, P., Prigent-Combaret, C., Trévisan, D., 2011. Rôle des facteurs édaphiques et hydrométéorologiques dans la survie et le transfert de bactéries fécales bovines, à l’échelle bassin versant: cas de pâturages d’altitude.
      Mots-clés : #3.

    • Wisniewski-Dyé, F., Borziak, K., Khalsa-Moyers, G., Alexandre, G., Sukharnikov, L., Wuichet, K., Hurst, G.B., McDonald, W.H., Robertson, J.S., Barbe, V., Calteau, A., Rouy, Z., Mangenot, S., Prigent-Combaret, C., Normand, P., Boyer, M., Siguier, P., Dessaux, Y., Elmerich, C., Condemine, G., Krishnen, G., Kennedy, I., Paterson, A.H., González, V., Mavingui, P., Zhulin, I.B., 2011. Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments. PLoS Genet 7, e1002430.
      Résumé : Genome sequencing and analysis of plant-associated beneficial soil bacteria Azospirillum spp. reveals that these organisms transitioned from aquatic to terrestrial environments significantly later than the suggested major Precambrian divergence of aquatic and terrestrial bacteria. Separation of Azospirillum from their close aquatic relatives coincided with the emergence of vascular plants on land. Nearly half of the Azospirillum genome has been acquired horizontally, from distantly related terrestrial bacteria. The majority of horizontally acquired genes encode functions that are critical for adaptation to the rhizosphere and interaction with host plants.
      Mots-clés : #1, #3, #7.


    • Baudoin, E., Lerner, A., Mirza, M.S., El Zemrany, H., Prigent-Combaret, C., Jurkevich, E., Spaepen, S., Vanderleyden, J., Nazaret, S., Okon, Y., Moënne-Loccoz, Y., 2010. Effects of <i>Azospirillum brasilense</i> with genetically modified auxin biosynthesis gene <i>ipdC</i> upon the diversity of the indigenous microbiota of the wheat rhizosphere. Research in Microbiology 161, 219-226.
      Résumé : The phytostimulatory properties of Azospirillum inoculants, which entail production of the phytohormone indole-3-acetic acid (IAA), can be enhanced by genetic means. However, it is not known whether this could affect their interactions with indigenous soil microbes. Here, wheat seeds were inoculated with the wild-type strain Azospirillum brasilense Sp245 or one of three genetically modified (GM) derivatives and grown for one month. The GM derivatives contained a plasmid vector harboring the indole-3-pyruvate/phenylpyruvate decarboxylase gene ipdC (IAA production) controlled either by the constitutive promoter PnptII or the root exudate-responsive promoter PsbpA, or by an empty vector (GM control). All inoculants displayed equal rhizosphere population densities. Only inoculation with either ipdC construct increased shoot biomass compared with the non-inoculated control. At one month after inoculation, automated ribosomal intergenic spacer analysis (ARISA) revealed that the effect of the PsbpA construct on bacterial community structure differed from that of the GM control, which was confirmed by 16S rDNA-based denaturing gradient gel electrophoresis (DGGE). The fungal community was sensitive to inoculation with the PsbpA construct and especially the GM control, based on ARISA data. Overall, fungal and bacterial communities displayed distinct responses to inoculation of GM A. brasilense phytostimulators, whose effects could differ from those of the wild-type.
      Mots-clés : #3, #6, Azospirillum, Ecological impact, Genetically modified bacteria, Microbial community, PGPR, rhizosphere.

    • Couillerot, O., Poirier, M.A., Prigent-Combaret, C., Mavingui, P., Caballero-Mellado, J., Moënne-Loccoz, Y., 2010. Assessment of SCAR markers to design real-time PCR primers for rhizosphere quantification of <i>Azospirillum brasilense</i> phytostimulatory inoculants of maize. Journal of applied microbiology 109, 528–538.
      Mots-clés : #3, #7.

    • Fremaux, B., Prigent-Combaret, C., Beutin, L., Gleizal, A., Trevisan, D., Quetin, P., Jocteur-Monrozier, L., Rozand, C., 2010. Survival and spread of Shiga toxin-producing <i>Escherichia coli</i> in alpine pasture grasslands. Journal of applied microbiology 108, 1332–1343.
      Mots-clés : #3.

    • Miller, S.H., Browne, P., Prigent-Combaret, C., Combes-Meynet, E., Morrissey, J.P., O'gara, F., 2010. Biochemical and genomic comparison of inorganic phosphate solubilization in <i>Pseudomonas</i> species. Environmental Microbiology Reports 2, 403–411.
      Mots-clés : #3.

    • Trevisan, D., Dorioz, J.M., Poulenard, J., Quetin, P., Prigent-Combaret, C., Merot, P., 2010. Mapping of critical source areas for diffuse fecal bacterial pollution in extensively grazed watersheds. Water research 44, 3847–3860.
      Mots-clés : #3.


    • Couillerot, O., Prigent-Combaret, C., Caballero-Mellado, J., Moënne-Loccoz, Y., 2009. <i>Pseudomonas fluorescens</i> and closely-related fluorescent pseudomonads as biocontrol agents of soil-borne phytopathogens. Letters in applied microbiology 48, 505–512.
      Mots-clés : #3.

    • Richardson, A.E., Barea, J.M., McNeill, A.M., Prigent-Combaret, C., 2009. Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant and Soil 321, 305–339.
      Mots-clés : #3.


    • Fremaux, B., Prigent-Combaret, C., Delignette-Muller, M.L., Mallen, B., Dothal, M., Gleizal, A., Vernozy-Rozand, C., 2008. Persistence of Shiga toxin-producing <i>Escherichia coli</i> O26 in various manure-amended soil types. Journal of Applied Microbiology 104, 296–304.
      Mots-clés : #3.

    • Fremaux, B., Prigent-Combaret, C., Vernozy-Rozand, C., 2008. Long-term survival of Shiga toxin-producing<i> Escherichia coli</i> in cattle effluents and environment: An updated review. Veterinary microbiology 132, 1–18.
      Mots-clés : #3.

    • Fremaux, B., Prigent-Combaret, C., Vernozy-Rozand, C., 2008. Long-term survival of Shiga toxin-producing<i> Escherichia</i> coli in cattle effluents and environment: An updated review. Veterinary microbiology 132, 1–18.
      Mots-clés : #3.

    • Pothier, J.F., Prigent-Combaret, C., Haurat, J., Moënne-Loccoz, Y., Wisniewski-Dyé, F., 2008. Duplication of plasmid-borne nitrite reductase gene <i>nirK</i> in the wheat-associated plant growth-promoting rhizobacterium <i>Azospirillum brasilense</i> Sp245. Molecular plant-microbe interactions 21, 831–842.
      Mots-clés : #3.

    • Prigent-Combaret, C., Blaha, D., Pothier, J.F., Vial, L., Poirier, M.A., Wisniewski-Dyé, F., Moënne-Loccoz, Y., 2008. Physical organization and phylogenetic analysis of acdR as leucine-responsive regulator of the 1-aminocyclopropane-1-carboxylate deaminase gene acdS in phytobeneficial <i>Azospirillum lipoferum</i> 4B and other Proteobacteria. FEMS microbiology ecology 65, 202–219.
      Mots-clés : #3.

    • Sanguin, H., Kroneisen, L., Gazengel, K., Kyselková, M., Remenant, B., Prigent-Combaret, C., Grundmann, G., Sarniguet, A., Moënne-Loccoz, Y., 2008. Development of a 16S rRNA microarray approach for the monitoring of rhizosphere <i>Pseudomonas</i> populations associated with the decline of take-all disease of wheat. Soil Biology and Biochemistry 40, 1028–1039.
      Mots-clés : #3.

    • Texier, S., Prigent-Combaret, C., Gourdon, M.H., Poirier, M.A., Faivre, P., Dorioz, J.M., Poulenard, J., Jocteur-Monrozier, L., Moënne-Loccoz, Y., Trevisan, D., 2008. Persistence of Culturable Fecal Contaminants in Dairy Alpine Grassland Soils. Journal of environmental quality 37, 2299–2310.
      Mots-clés : #3.


    • Fremaux, B., Delignette-Muller, M.L., Prigent-Combaret, C., Gleizal, A., Vernozy-Rozand, C., 2007. Growth and survival of non-O157: H7 Shiga-toxin-producing <i>Escherichia coli</i> in cow manure. Journal of applied microbiology 102, 89–99.
      Mots-clés : #3.

    • Fremaux, B., Prigent-Combaret, C., Delignette-Muller, M.L., Dothal, M., Vernozy-Rozand, C., 2007. Persistence of Shiga toxin-producing <i>Escherichia coli</i> O26 in cow slurry. Letters in applied microbiology 45, 55–61.
      Mots-clés : #3.

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    Chapitre d’ouvrages


    • Vacheron, J., Combes-Meynet, E., Bellvert, F., Moënne-Loccoz, Y., Muller, D., Prigent-Combaret, C., 2015. Plant growth-promoting properties of Pseudomonas biocontrol agent producing 2,4 diacetylphloroglucinol, dans: Natural Products And Biocontrol.
      Mots-clés : #3, #cesn.

    • Vacheron, J., Renoud, S., Muller, D., Babalola, O.O., Prigent-Combaret, C., 2015. Alleviation of Abiotic and Biotic Stresses in Plants by Azospirillum, dans: Cassán, F.D., Okon, Y., Creus, C.M. (Éd.), Handbook For Azospirillum. Springer International Publishing, p. 333-365.
      Résumé : In the face of global changes, plants must adapt to a wide range and often combined biotic and abiotic stresses that seriously impaired plant growth and development. Plants develop complex strategies to deal with water stress conditions, soil fertility losses, soil pollutions, pests, and disease. Emerging evidence suggest the involvement of common hormonal players in plant defense signaling pathways triggered in response to biotic and abiotic stresses. Besides plant strategies, plant growth-promoting rhizobacteria (PGPR), which colonize the root system and establish cooperative interactions with plants can improve their growth and help them to adapt to and cope with multiple stresses including drought, salinity, heavy metal pollutions, and parasites. Accordingly, PGPR supply added values to the plant defense strategies by expressing many relevant functions for modulating the plant hormonal balance, increasing nutrients supply to the plant, improving the functional and physical properties of protective barriers against plant parasites. Among PGPR, Azospirillum strains were long viewed as biofertilizers and less as biocontrol agents. It is becoming evident that Azospirillum is able to protect plants against a myriad of detrimental conditions. This review provides an update of works regarding the ability of Azospirillum strains to alleviate plant stress and brings out the relevant involved plant-beneficial functions. Developing PGPR-based bio-inoculants is a promising strategy to improve the growth and health of crops and develop sustainable agriculture.
      Mots-clés : Eukaryotic Microbiology, Mycology.

    • Wisniewski-Dyé, F., Drogue, B., Borland, S., Prigent-Combaret, C., Borziak, K., Zhulin, I.B., Lozano, L., Gonzáles, V., Mavingui, P., 2015. Core and Accessory Genomes of the Diazotroph Azospirillum, dans: Biological Nitrogen Fixation, 2 Volume Set. p. 253.
      Mots-clés : #3, #7.


    • Drogue, B., Combes-Meynet, E., Moënne-Loccoz, Y., Wisniewski-Dyé, F., Prigent-Combaret, C., 2013. Control of the Cooperation Between Plant Growth-Promoting Rhizobacteria and Crops by Rhizosphere Signals, dans: Molecular Microbial Ecology Of The Rhizosphere, Two Volume Set. John Wiley & Sons, p. 281.
      Résumé : 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 students in microbiology, ecology, and agriculture.
      Mots-clés : #3, Science / Life Sciences / Microbiology.

    • Bruto, M., Prigent-Combaret, C., Luis, P., Hoff, G., Moënne-Loccoz, Y., Muller, D., 2013. Horizontal Acquisition of Prokaryotic Genes for Eukaryote Functioning and Niche Adaptation, dans: Pontarotti, P. (Éd.), Evolutionary Biology: Exobiology And Evolutionary Mechanisms. Springer Berlin Heidelberg, p. 165-179.
      Résumé : Horizontal gene transfer (HGT) is a major mechanism of evolution, in that it is pervasive and can dramatically affect lifestyle by allowing adaptation to specialized niches. Although research has mostly focused on HGT within prokaryotes, examples of inter-domain transfers from prokaryotes to eukaryotes are increasing, and such inter-domain HGT is emerging as a very significant component in ecological and evolutionary terms. Here, different cases of intra- and inter-domain HGT conferring an adaptive advantage to eukaryotes are reviewed to examine novel trends and HGT paradigms. Thus, HGT appears to play an important role in eukaryotic adaptation to specific environmental conditions, including in the ecological evolution toward parasitic lifestyles and pathogenesis. The diversity of prokaryotes and their genetic potential are emerging as a vast reservoir to foster rapid eukaryote evolution.
      Mots-clés : #2, #3, Animal Genetics and Genomics, Animal Systematics/Taxonomy/Biogeography, Biodiversity, evolutionary biology, HGT dynamic, Interdomain gene transfer, Lateral gene transfer (LGT), Plant Genetics & Genomics, Plant Systematics/Taxonomy/Biogeography.

    • Wisniewski-Dyé, F., Drogue, B., Borland, S., Prigent-Combaret, C., 2013. <i>Azospirillum</i>-Plant Interaction: from Root Colonization to Plant Growth Promotion, dans: Beneficial Plant-Microbial Interactions: Ecology And Applications. CRC Press.
      Résumé : Beneficial Plant-microbial Interactions: Ecology and Applications provides insight into the mechanisms underlying the interactions of plants and microbes, the ecological relevance and roles of these symbioses, the adaptive mechanisms of plant-associated microorganisms to abiotic stress and their contribution to plant stress tolerance, and the potential of these interactions as tools in agrobiotechnology. A team of authors with wide experience in the area contribute up-to-date reviews in nineteen chapters devoted to different ecological and applied aspects of the rhizobia-legume symbiosis, ecto- and endomycorrhizas, and plant associations with diazotrophic or adiazotrophic plant-growth promoting rhizobacteria. The book is intended for students, researchers and academic faculty members in the field of agrobiotechnology.
      Mots-clés : #3, Science / Life Sciences / Botany, Science / Life Sciences / Microbiology, Technology & Engineering / Agriculture / General.



    • Vacheron, J., Muller, D., Prigent-Combaret, C., 2012. Journal de bord des ARCs 2012/2013.
      Résumé : Brève dans le journal des ARC 2012

    Communications Orales


    • Moënne-Loccoz, Y., Walker, V., Bouffaud, M.L., Kyselková, M., Renoud, S., Vacheron, J., Comte, G., Gouesnard, B., Muller, D., Prigent-Combaret, C., 2015. Significance of maize diversification for symbiotic interactions between roots and soil bacteria, dans: . Présenté à EUCARPIA Meetings, communication orale, Montpellier, France.
      Mots-clés : #3, #cesn, #colloque.
    • Vacheron, J., Muller, D., Dubost, A., Moënne-Loccoz, Y., Prigent-Combaret, C., 2015. PGPR with multiple plant-beneficial functions : The more the better ?, dans: . Présenté à Rhizosphère 4, communication orale, Maastricht - Pays Bas.
      Mots-clés : #colloque, #ibio.
    • Vacheron, J., Muller, D., Dubost, A., Moënne-Loccoz, Y., Prigent-Combaret, C., 2015. Sélection des rhizobactéries phytostimulatrices par la plante : Impact sur la distribution des propriétés phytobénéfiques, dans: . Présenté à Journée de rencontre des doctorants, Ecole doctorale E2M2, communication orale, Lyon.
      Mots-clés : #colloque, #ibio.
    • Vacheron, J., Renoud, S., Padilla, R., Walker, V., Muller, D., Prigent-Combaret, C., 2015. Functional interactions between co-occurring plant beneficial activities from PGPR: which impact on plant growth?, dans: . Présenté à 10th International PGPR Workshop, communication orale, Liège - Belgique.
      Mots-clés : #3, #cesn, #colloque.


    • Vacheron, J., Muller, D., Prigent-Combaret, C., 2014. Impact of abiotic conditions on the distribution of plant-beneficial functions in fluorescent Pseudomonads, dans: . Présenté à 11ème Rencontre Plantes-bactéries, communication orale, Aussois, France.
      Résumé : La croissance des plantes est fortement influencée par les interactions qu’elles établissent avec les microorganismes du sol. Les plantes vont sélectionner via leurs exsudats racinaires, une communauté microbienne spécifique. En retour, certaines bactéries de cette communauté, qualifiées de PGPR (Plant Growth-Promoting Rhizobacteria) sont capables de stimuler la croissance de nombreuses céréales comme le maïs, grâce à l’expression d’une large variété de fonctions phytobénéfiques (Richardson et al. 2009 Plant Soil 321:305; Vacheron et al. 2013 Front. Plant Sci. 4:356). Aujourd’hui, la distribution de ces fonctions phytobénéfiques chez les bactéries est encore mal connue. Cependant, le séquençage récent de différents génomes de PGPR couplé à des approches de génomique comparative a montré qu’une même bactérie PGPR peut posséder plusieurs fonctions phytobénéfiques (i.e. fonctions co-occurentes). Des réseaux de régulation particuliers seraient impliqués dans le contrôle de l’expression de ces fonctions les unes par rapport aux autres, favorisant leur synergie et in fine leur efficacité sur le végétal (Bashan et de Bashan 2010 Adv. Agron. 108:77). Dans cette étude, la distribution de fonctions phytobénéfiques chez une collection d’isolats rhizosphériques, appartenant à un groupe bactérien bien connu dans la littérature pour comporter de nombreuses bactéries PGPR, le groupe des Pseudomonas fluorescents, a été considérée en prenant en compte le sol et la variété de maïs d’origine des isolats obtenus. Les premiers résultats montrent une influence d’au moins un des deux paramètres sur la répartition des fonctions phytobénéfiques chez ce groupe bactérien.
      Mots-clés : #colloque.


    • Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2012. Relation between landscape distribution of disease-suppressive soils, iron bioavailability for biocontrol Pseudomonas on roots, and rhizosphere expression of genes for 2,4-diacetylphloroglucinol synthesis, dans: . Présenté à 14th International Symposium on Microbial Ecology ISME14, Copenhagen, Denmark.
      Mots-clés : #colloque.
    • Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2012. Effect of clay mineralogy on the plant-protecting activity of Pseudomonas in the rhizosphere, dans: . Présenté à 2nd meeting of Ph.D. students in Ecology, Evolution, Microbiology and Modelization, Villeurbanne, France.
      Mots-clés : #colloque.
      Note Note
    • Bruto, M., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2012. Etude génomique des déterminants codant les propriétés phytobénéfiques des Protéobactéries, dans: . Présenté à 10th Plant-Bacteria Interactions Meeting, Aussois, France.
      Résumé : Le développement et la croissance des plantes sont fortement influencés par les symbioses mutualistes ou associatives avec des bactéries du sol. Parmi elles, les symbioses associatives (coopérations) restent mal connues, car elles impliquent une grande diversité de taxons bactériens et de propriétés phytobénéfiques. Notre objectif est de comprendre, par des approches génomiques, la distribution et l'évolution des gènes codant des propriétés phytobénéfiques chez les Proteobactéries en symbiose associative avec la plante. Vingt de ces gènes parmi les plus emblématiques ont été recherchés dans les génomes séquencés de bactéries symbiotiques associatives, mais aussi de bactéries mutualistes ou parasites de plantes (BLAST). La majorité des gènes étudiés présente une distribution dépendante de la phylogénie, comme par exemple ph/D (synthèse de 2,4- diacétylphloroglucinol) chez les Pseudomonadaceae, le type d'interaction biotique étant d'importance moindre. Néanmoins, certains gènes sont davantage ubiquistes, comme acdS (désamination de l'l-aminocyclopropane-1- carboxylate) et pqqABCD (production de pyrroloquinoline). Une approche couplant génomique comparative et analyse phylogénétique est en cours pour estimer les transferts horizontaux, que nous avons mis en évidence dans le cas d' hcnB (synthèse d'acide cyanhydrique) et de ses orthologues putatifs. Ces résultats illustrent l'intérêt des approches de génomique pour mieux comprendre la diversité et l'évolution des bactéries favorisant la croissance des plantes
      Mots-clés : #3, #colloque.
    • Vacheron, J., Bellvert, F., Moënne-Loccoz, Y., Muller, D., Prigent-Combaret, C., 2012. Evaluation of 2,4-diacetylphloroglucinol fluorescent Pseudomonas for plant growth promotion, dans: . Présenté à The World Congress On Biostimulants, communication orale, Strasbourg, France.
      Mots-clés : #3, #cesn, #colloque.



    • Renoud, S., 2015. Effect of Azospirillum inoculation on the abundance and genetic diversity of key phytobeneficial microbial functional groups in the maize rhizosphere, dans: . Présenté à Rhizosphere4, communication orale, Maastricht , Pays-Bas.
      Mots-clés : #3, #cesn, #poster.


    • Walker, V., 2014. Symbiomaize Project: Effect of maize diversification on its associative symbiosis with P. fluorescens rhizobacteria, dans: . Présenté à 15ème Rencontre du Groupe Régional de Recherche en Microbiologie des Interactions, communication orale, Villeurbanne, France.
      Mots-clés : #3, #cesn, #poster.


    • Vacheron, J., 2012. Développement de nouveaux inoculants bactériens agricoles stimulateurs de la croissance des céréales, dans: . Présenté à Journée de rencontre des doctorants, E2M2, communication orale, Villeurbanne, France.
      Mots-clés : #3, #cesn, #poster.