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Accueil > Equipes de Recherche > Rhizosphère > Rhizophere

Rhizophere

Team leaders : PRIGENT-COMBARET Claire

Coleader : MOËNNE-LOCCOZ Yvan

Team :

Permanent members

COMTE Gilles Professor (Pr), UCB
GERIN Florence Tech, UCB
GRUNDMANN Geneviève Lecturer (MCF), UCB
LEGENDRE Laurent Professor (PR), St-Etienne
MOËNNE-LOCCOZ Yvan Professor (Pr), UCB
MULLER Daniel Lecturer (MCF), UCB
PRIGENT-COMBARET Claire Research Scientist (CR), CNRS
REY Marjolaine Assistant Engineer (AI), CNRS
WISNIEWSKI-DYÉ Florence Professor (Pr), UCB

Non permanent members

ALONSO Lise PhD Student (2014-2017)
BESSET-MANZONI Yoann PhD Student (2015-2018)
JACQUEMOND Isaline PhD Student (2014-2017)
LAFAY Xavier PhD Student (2017-2020)
MERCIER Pierre-Edouard Tech (contract)
RIEUSSET Laura PhD Student (2016-2019)
ROZIER Camille PhD Student (2014-2017)
VALENTE Jordan PhD Student (2015-2018)
VALETTE Marine PhD Student (2015-2018)

 

The study of prokaryote-eukaryote interactions in Ecology usually focuses on parasitism and mutualism (such as interactions involving Rhizobium or Frankia and plants). In comparison, microorganisms involved in associative symbiosis or cooperations (defined as facultative interactions with reciprocal benefits) are widespread in numerous ecosystems, more abundant and more diverse than those involved in mutualism. However, these associative interactions remain poorly understood.

 
Figure 1 : Confocal microscopy pictures showing the root hair colonization of Poaceae by the bacterium Azospirillum labelled with EGFP

The Rhizosphere team focuses on the associative symbiosis between Plant Growth-Promoting Rhizobacteria (PGPR) and plant roots. PGPR are well adapted to the rhizosphere, i.e. the volume of soil located in the close vicinity of plant roots and characterized by the presence of root exudates (rhizodeposits). PGPR colonize rhizosphere through the use of root exudates as growth substrates, but unlike most other rhizospheric bacteria they exert a beneficial effect on plants, via a diversity of interaction mechanisms (Vacheron et al 2013 Front Plant Sci 4:356).

 
Figure 2 : Plant-beneficial effects of plant growth promoting rhizobacteria (PGPR)

The positive effects of PGPR on plants can be direct when bacteria stimulate root growth or induce systemic resistance, or indirect when PGPR counteract phytopathogens (antagonism). Thus, PGPR are interesting models for studying bacterial adaptation to a eukaryotic host. Moreover, PGPR are of biotechnological interest in agronomy (increase of plant yield, decrease of nitrogen inputs through phytostimulation, biocontrol of root diseases).

 

To understand plant-beneficial mechanisms of bacteria cooperating with plant, as well as the role of cooperation in microbial rhizosphere functioning, we develop three research themes.

 
Figure 3 : Research themes
  • The first theme deals with the characterization of genomic, physiological and ecological properties which define cooperative bacteria. We aim to understand the emergence of PGPR and of their plant-beneficial functions. To respond to this objective, we develop comparative genomics and molecular phylogeny approaches.
  • The second theme focuses on the characterization of beneficial effects of cooperative bacteria on the host plant, taking into account both phystostimulators (Azospirillum model) and biocontrol bacteria (Pseudomonas model). We aim at identifying new plant-beneficial mechanisms. We are also studying the plant physiological responses to the PGPR, by taking into account the plant genetic variability (Drogue et al 2014 Front Plant Sci 5:607).
  • The third theme deals with the role of plant-PGPR cooperation within rhizosphere microbial community and rhizosphere functioning, with a particular focus on micro-spatialisation of bacterial populations in soil, the relation between microbial diversity and functioning, and disease-suppressive soils.

PhD since 2008

  • Zo ANDRIANJAKA. 2008. Intérêt de l’utilisation et de la manipulation de la diversité microbienne rhizosphérique dans la lutte contre la phanérogame parasite du genre Striga.
  • Mickaël BOYER. 2008. Rôle du quorum-sensing et prévalence des bactériophages chez la bactérie phytostimulatrice Azospirillum.
  • Christophoros KARANIKAS. 2008. Selection and biochemical analysis of high-yielding oleoresin genotypes of Pinus halepensis mill. Thèse Université de Thessalonique, Grèce (codirection).
  • Martina Kyselkova. 2008. Caractérisation par puce à ADN taxonomique de la communauté bactérienne rhizosphérique associée aux sols résistant à la maladie de la pourriture noire des racines.
  • Stéphanie Texier. 2008. Etude de la dispersion et du contrôle écologique de populations de bactéries fécales bovines dans les sols des écosystèmes pâturés de montagne ; conséquences en terme de transferts sol-eaux de surface et de risques de contamination microbiologique des eaux. Thèse Université de Savoie (codirection).
  • Marta Toth-Dobrone. 2008. Accumulation et dissémination secondaire des métaux lourds extraits de sols miniers et industriels par Ambrosia elatior, son pollen et la microflore associée. Thèse Université de Debrecen, Hongrie (codirection).
  • Olivier COUILLEROT. 2009. Compatibilité des bactéries phytobénéfiques Azospirillum et Pseudomonas dans la rhizosphère.
  • Emeline COMBES-MEYNET. 2010. Impact des signaux rhizosphériques sur l’expression des gènes phytobénéfiques chez les bactéries symbiotiques associatives.
  • Vincent WALKER. 2010. Impact de l’inoculation de microorganismes phytobénéfiques sur le métabolisme secondaire de Zea mays L.
  • Marie-Lara BOUFFAUD. 2011. Diversité génétique et capacité du maïs à recruter des populations bactériennes rhizosphériques phytobénéfiques.
  • Amel CHAMAM. 2011. Etude de la spécificité de l’interaction entre le riz (Oriza sativa) et la bactérie phytostimulatrice Azospirillum lipoferum.
  • Juliana ALMARIO. 2012. Relation entre la propriété phytoprotectrice de synthèse de 2,4 diacétylphloroglucinol par les Pseudomonas fluorescents dans la rhizosphère, et la résistance des sols à la maladie de la pourriture noire des racines de tabac.
  • Benoit DROGUE. 2013. Spécificité de la coopération phytostimulatrice Azospirillum-céréales.
  • Maxime BRUTO. 2014. Analyse génomique des modes d’action des bactéries phytobénéfiques : origines, distribution et transferts procaryotes-eucaryotes

 Research paper since 2008

2018



  • Besset-Manzoni, Y., Rieusset, L., Joly, P., Comte, G., Prigent-Combaret, C., 2018. Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies. Environmental Science and Pollution Research 1-18. https://doi.org/10.1007/s11356-017-1152-2

2017



  • 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. https://doi.org/10.3389/fmicb.2017.01218
  • Anne-Emmanuelle, H., Hasna, B., Antoine, B., Marjolaine, R., Guillaume, M., Laetitia, C.-G., Gilles, C., Aude, H.-B., 2017. Control of Endophytic Frankia Sporulation by Alnus Nodule Metabolites. Molecular Plant-Microbe Interactions 30, 205–214.


  • Bardon, C., Poly, F., Haichar, F.Z., Le Roux, X., Simon, L., Meiffren, G., Comte, G., Rouifed, S., Piola, F., 2017. Biological denitrification inhibition (BDI) with procyanidins induces modification of root traits, growth and N status in Fallopia x bohemica. Soil Biology and Biochemistry 107, 41-49. https://doi.org/10.1016/j.soilbio.2016.12.009


  • Guyonnet, J.P., Vautrin, F., Meiffren, G., Labois, C., Cantarel, A.A.M., Michalet, S., Comte, G., Haichar, F.Z., 2017. The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites. FEMS Microbiology Ecology 93. https://doi.org/10.1093/femsec/fix022


  • Joffard, N., Legendre, L., Gibernau, M., Pascal, L., 2017. Differential Accumulation of Volatile Organic Compounds by Leaves and Roots of Two Guianese Philodendron Species, P. fragrantissimum Kunth and P. melinonii Brongn. Chemistry & Biodiversity 14, e1600415. https://doi.org/10.1002/cbdv.201600415
  • Kasrati, A., Alaoui Jamali, C., Spooner-Hart, R., Legendre, L., Leach, D., Abbad, A., 2017. Chemical Characterization and Biological Activities of Essential Oil Obtained from Mint Timija Cultivated under Mineral and Biological Fertilizers. Journal of analytical methods in chemistry 2017.

  • Kasrati, A., Alaoui Jamali, C., Spooner-Hart, R., Legendre, L., Leach, D., Abbad, A., 2017. Chemical Characterization and Biological Activities of Essential Oil Obtained from Mint Timija Cultivated under Mineral and Biological Fertilizers. Journal of Analytical Methods in Chemistry.


  • Keshavarz-Tohid, V., Taheri, P., Muller, D., Prigent-Combaret, C., Vacheron, J., Taghavi, S.M., Tarighi, S., Moënne-Loccoz, Y., 2017. Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani. Research in Microbiology 168, 760-772. https://doi.org/10.1016/j.resmic.2017.08.002


  • Lassalle, F., Planel, R., Penel, S., Chapulliot, D., Barbe, V., Dubost, A., Calteau, A., Vallenet, D., Mornico, D., Bigot, T., Guéguen, L., Vial, L., Muller, D., Daubin, V., Nesme, X., 2017. Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. Genome Biology and Evolution 9, 3413-3431. https://doi.org/10.1093/gbe/evx255


  • Lebot, V., Lawac, F., Michalet, S., Legendre, L., 2017. Characterization of taro [Colocasia esculenta (L.) Schott] germplasm for improved flavonoid composition and content. Plant Genetic Resources 15, 260-268. https://doi.org/10.1017/S1479262115000581


  • Lemanceau, P., Blouin, M., Muller, D., Moënne-Loccoz, Y., 2017. Let the Core Microbiota Be Functional. Trends in Plant Science 22, 583-595. https://doi.org/10.1016/j.tplants.2017.04.008


  • Lhuissier, T., Mercier, P.-E., Michalet, S., Lebot, V., Legendre, L., 2017. Colorimetric assessment of kava (Piper methysticum Forst.) quality. Journal of Food Composition and Analysis 59, 27-34. https://doi.org/10.1016/j.jfca.2017.02.005


  • Rozier, C., Hamzaoui, J., Lemoine, D., Czarnes, S., Legendre, L., 2017. Field-based assessment of the mechanism of maize yield enhancement by Azospirillum lipoferum CRT1. Scientific reports 7, 7416. https://doi.org/10.1038/s41598-017-07929-8

  • 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. https://doi.org/10.1094/MPMI-07-17-0185-R


  • 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. https://doi.org/10.1128/genomeA.00122-17

2016



  • Bardon, C., Poly, F., Piola, F., Pancton, M., Comte, G., Meiffren, G., Haichar, F.Z., 2016. Mechanism of biological denitrification inhibition (BDI): procyanidins induce an allosteric transition of the membrane-bound NO3-reductase through membrane alteration. FEMS Microbiology Ecology 92, fiw034. https://doi.org/10.1093/femsec/fiw034


  • BORLAND, S., PRIGENT-COMBARET, C., WISNIEWSKI-DYE, F., 2016. Bacterial hybrid histidine kinases in plant-bacteria interactions. Microbiology 162, 1715-1734. https://doi.org/10.1099/mic.0.000370


  • Bouffaud, M.-L., Renoud, S., Moënne-Loccoz, Y., Muller, D., 2016. Is plant evolutionary history impacting recruitment of diazotrophs and nifH expression in the rhizosphere? Scientific Reports 6, 21690. https://doi.org/10.1038/srep21690


  • Cormier, F., Foulkes, J., Hirel, B., Gouache, D., Moënne-Loccoz, Y., Le Gouis, J., 2016. Breeding for increased nitrogen-use efficiency: a review for wheat (T. aestivum L.). Plant Breeding 135, 255-278. https://doi.org/10.1111/pbr.12371


  • Lebot, V., Michalet, S., Legendre, L., 2016. Identification and quantification of phenolic compounds responsible for the antioxidant activity of sweet potatoes with different flesh colours using high performance thin layer chromatography (HPTLC). Journal of Food Composition and Analysis 49, 94-101. https://doi.org/10.1016/j.jfca.2016.04.009


  • Lebot, V., Legendre, L., 2016. Comparison of kava (Piper methysticum Forst.) varieties by UV absorbance of acetonic extracts and high-performance thin-layer chromatography. Journal of Food Composition and Analysis 48, 25-33. https://doi.org/10.1016/j.jfca.2016.01.009

  • Lebot,, V., Legendre, L., 2016. Comparison of kava (<i>Piper methysticum</i> Forst.) varieties by UV absorbance of acetonic extracts and high-performance thin-layer chromatography 48, 25-33.


  • Michelland, R., Thioulouse, J., Kyselková, M., Grundmann, G., 2016. Bacterial Community Structure at the Microscale in Two Different Soils. Microbial Ecology 72, 1-8. https://doi.org/10.1007/s00248-016-0810-0


  • Michelland, R., Thioulouse, J., Kyselková, M., Grundmann, G.L., 2016. Bacterial Community Structure at the Microscale in Two Different Soils. Microbial Ecology 72, 717-724. https://doi.org/10.1007/s00248-016-0810-0


  • 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. https://doi.org/10.1007/s11104-016-3040-9


  • Muñoz-Cuervo, I., Malapa, R., Michalet, S., Lebot, V., Legendre, L., 2016. Secondary metabolite diversity in taro, Colocasia esculenta (L.) Schott, corms. Journal of Food Composition and Analysis 52, 24-32. https://doi.org/10.1016/j.jfca.2016.07.004

  • Rozier, C., Erban, A., Hamzaoui, J., Prigent-Combaret, C., Comte, G., Kopka, J., Czarnes, S., Legendre, L., 2016. Xylem Sap Metabolite Profile Changes During Phytostimulation of Maize by the Plant Growth-Promoting Rhizobacterium, Azospirillum lipoferum CRT1. Metabolomics (Los Angel) 6, 2153–0769.


  • 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. https://doi.org/10.1007/s11104-016-2907-0


  • 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. https://doi.org/10.3389/fpls.2016.01212

2015



  • Bardon, C., Piola, F., Haichar, F.Z., Meiffren, G., Comte, G., Misery, B., Balby, M., Poly, F., 2015. Identification of B-type procyanidins in <i>Fallopia</i> spp. involved in biological denitrification inhibition (BDI): B-type procyanidins from Fallopia involved in BDI. Environmental Microbiology. https://doi.org/10.1111/1462-2920.13062
  • Bardon, C., Poly, F., Piola, F., Haichar, F.Z., Comte, G., 2015. Utilisation de proanthocyanidines pour lutter contre la dénitrification. 1552258.


  • Benabdelkader, T., Guitton, Y., Pasquier, B., Magnard, J.L., Jullien, F., Kameli, A., Legendre, L., 2015. Functional characterization of terpene synthases and chemotypic variation in three lavender species of section Stoechas. Physiologia Plantarum 153, 43-57. https://doi.org/10.1111/ppl.12241

  • Bérard, A., Ruy, S., Coronel, A., Toussaint, B., Czarnes, S., Legendre, L., Doussan, C., 2015. Rhizosphere: a leverage for tolerance to water deficits of soil microflora ?, dans: . Présenté à EGU General Assembly Conference Abstracts, p. 9481.

  • Borland, S., 2015. Rôle des systèmes à deux composants dans l'adaptation de la bactérie phytostimulatrice Azospirillum à la rhizosphère.


  • 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. https://doi.org/10.1186/s12864-015-1962-x


  • 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. https://doi.org/10.1007/s00425-015-2382-5


  • Christina, M., Rouifed, S., Puijalon, S., Vallier, F., Meiffren, G., Bellvert, F., Piola, F., 2015. Allelopathic effect of a native species on a major plant invader in Europe. The Science of Nature 102, 1-8. https://doi.org/10.1007/s00114-015-1263-x


  • Wisniewski-Dyé, F., Vial, L., Burdman, S., Okon, Y., Hartmann, A., 2015. Phenotypic Variation in <i>Azospirillum</i> spp. and Other Root-Associated Bacteria, dans: de Bruijn, F.J. (éd.), Biological Nitrogen Fixation. John Wiley & Sons, Inc, Hoboken, NJ, USA, p. 1047-1054.

  • Doussan, C., Cousin, I., Berard, A., Chabbi, A., Legendre, L., Czarnes, S., Toussaint, B., Ruy, S., 2015. Crop systems and plant roots can modify the soil water holding capacity, dans: . Présenté à EGU General Assembly Conference Abstracts, p. 9285.


  • Lassalle, F., Muller, D., Nesme, X., 2015. Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis. Research in Microbiology. https://doi.org/10.1016/j.resmic.2015.06.008


  • Lebot, V., Legendre, L., 2015. HPTLC screening of taro hybrids ( <i>Colocasia esculenta</i> (L.) Schott) with high flavonoids and antioxidants contents. Plant Breeding 134, 129-134. https://doi.org/10.1111/pbr.12225
  • 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.


  • Moja, S., Guitton, Y., Nicolè, F., Legendre, L., Pasquier, B., Upson, T., Jullien, F., 2015. Genome size and plastid trnK-matK markers give new insights into the evolutionary history of the genus Lavandula L. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology 1-9. https://doi.org/10.1080/11263504.2015.1014006
  • Muller, D., 2015. Compartimentalisation de la communauté bactérienne le long des racines dans la rhizosphère du maïs.

  • Muñoz Cuervo, I., 2015. Évaluation de la diversité du contenu phytochimique de trois espèces à racines et tubercules amylacées tropicales, le taro, la grande igname et le manioc. Lyon 1.


  • Normand, P., Caumette, P., Goulas, P., Pujic, P., Wisniewski-Dyé, F., 2015. Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions in Natural or Anthropized Environments, dans: Bertrand, J.-C., Caumette, P., Lebaron, P., Matheron, R., Normand, P., Sime-Ngando, T. (Éd.), Environmental Microbiology: Fundamentals And Applications. Springer Netherlands, p. 293-351.
  • 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.

  • Vacheron, J., 2015. Sélection des rhizobactéries phytostimulatrices par la plante : impact sur la distribution des propriétés phytobénéfiques chez les Pseudomonas fluorescents. Lyon 1.
  • 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.

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