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Home > Research Teams > Rhizosphere


Team leaders : PRIGENT-COMBARET Claire

Coleader : MOËNNE-LOCCOZ Yvan

Team :

Permanent members

ALMARIO Juliana Researcher (CR), CNRS
COMTE Gilles Professor (Pr), UCB
DORE Jeanne Ingeneer, CNRS
GERIN Florence Tech, UCB
LEGENDRE Laurent Professor (PR), St-Etienne
MOËNNE-LOCCOZ Yvan Professor (Pr), UCB
MULLER Daniel Lecturer (MCF), UCB
PRIGENT-COMBARET Claire Research Director (DR), CNRS
REY Marjolaine Assistant Engineer (AI), CNRS
WISNIEWSKI-DYÉ Florence Professor (Pr), UCB

Non permanent members

GRUET Cécile- PhD Student (2019-2022)
MANRIQUEZ Beatriz PhD Student (2017-2020)
RIEUSSET Laura PhD Student/ATER (2016-2020)
TODOROVIC Irena PhD Student (2019-2012) Co-tutel between University of Belgrade and University of Lyon


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.

Job advertisement

A Research Engineer position (30 months) is available in the UMR CNRS 5557 Ecologie Microbienne Lyon, Team Rhizosphere, at University Lyon 1 to develop and implement methods for analyzing the
biocontrol activity of a bacterial product against the growth of Orobanche parasitic weeds.
Posted : 15/04/2020 - Expiration Date : 30/06/2020
Funds : ANR Ecophyto-19-ECOM-0002-01 Weeds-Biocontrol
Contact : Claire Prigent-Combaret (claire.prigent-combaret

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


  • Hugoni, M., Nunan, N., Thioulouse, J., Dubost, A., Abrouk, D., Martins, J.M.F., Goffner, D., Prigent-Combaret, C., Grundmann, G., 2021. Small-Scale Variability in Bacterial Community Structure in Different Soil Types. Microbial Ecology.


  • Czarnes, S., Mercier, P.-E., Lemoine, D.G., Hamzaoui, J., Legendre, L., 2020. Impact of soil water content on maize responses to the plant growth-promoting rhizobacterium Azospirillum lipoferum CRT1. Journal of Agronomy and Crop Science n/a.

  • Habbadi, K., Duplay, Q., Chapulliot, D., Kerzaon, I., Benkirane, R., Benbouazza, A., Wisniewski-Dyé, F., Lavire, C., Achbani, E.H., Vial, L., 2020. Characterization and phylogenetic diversity of Allorhizobium vitis isolated from grapevine in Morocco. Journal of Applied Microbiology 128, 828-839.

  • Lebot, V., Kaoh, J., Legendre, L., 2020. High-Throughput Analysis of Flavokawains in Kava (Piper methysticum Forst. f.) Roots, Chips and Powders and Correlations with Their Acetonic Extracts Absorbance. Food Analytical Methods 13, 1583-1593.

  • Rieusset, L., Rey, M., Muller, D., Vacheron, J., Gerin, F., Dubost, A., Comte, G., Prigent‐Combaret, C., 2020. Secondary metabolites from plant‐associated <i>Pseudomonas</i> are overproduced in biofilm. Microbial Biotechnology 13, 1562-1580.

  • Valente, J., Gerin, F., Le Gouis, J., Moënne‐Loccoz, Y., Prigent–Combaret, C., 2020. Ancient wheat varieties have a higher ability to interact with plant growth‐promoting rhizobacteria. Plant, Cell & Environment 43, 246-260.

  • Valette, M., Rey, M., Doré, J., Gerin, F., Wisniewski-Dyé, F., 2020. Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria. Physiology and Molecular Biology of Plants 26, 2537-2551.


  • Alonso, L., Pommier, T., Kaufmann, B., Dubost, A., Chapulliot, D., Doré, J., Douady, C.J., Moënne‐Loccoz, Y., 2019. Anthropization level of Lascaux Cave microbiome shown by regional-scale comparisons of pristine and anthropized caves. Molecular Ecology 28, 3383-3394.

  • 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.

  • 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.

  • Diel, B., Dequivre, M., Wisniewski‐Dyé, F., Vial, L., Hommais, F., 2019. A novel plasmid-transcribed regulatory sRNA, QfsR, controls chromosomal polycistronic gene expression in Agrobacterium fabrum. Environmental Microbiology 21, 3063-3075.

  • 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.

  • Kopecky, J., Samkova, Z., Sarikhani, E., Kyselková, M., Omelka, M., Kristufek, V., Divis, J., Grundmann, G., Moënne-Loccoz, Y., Sagova-Mareckova, M., 2019. Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab. Scientific Reports 9, 14883.

  • Lebot, V., Michalet, S., Legendre, L., 2019. Kavalactones and Flavokavins Profiles Contribute to Quality Assessment of Kava (Piper methysticum G. Forst.), the Traditional Beverage of the Pacific. Beverages 5, 34.

  • Meyer, T., Thiour-Mauprivez, C., Wisniewski-Dyé, F., Kerzaon, I., Comte, G., Vial, L., Lavire, C., 2019. Ecological Conditions and Molecular Determinants Involved in Agrobacterium Lifestyle in Tumors. Frontiers in Plant Science 10, 978.

  • Miotto-Vilanova, L., Courteaux, B., Padilla, R., Rabenoelina, F., Jacquard, C., Clément, C., Comte, G., Lavire, C., Ait Barka, E., Kerzaon, I., Sanchez, L., 2019. Impact of <i>Paraburkholderia phytofirmans</i> PsJN on grapevine phenolic metabolism. International Journal of Molecular Sciences 20, 5775.

  • Rondeau, M., Esmaeel, Q., Crouzet, J., Blin, P., Gosselin, I., Sarazin, C., Pernes, M., Beaugrand, J., Wisniewski-Dyé, F., Vial, L., Faure, D., Clément, C., Barka, E.A., Jacquard, C., Sanchez, L., 2019. Biofilm-Constructing Variants of Paraburkholderia phytofirmans PsJN Outcompete the Wild-Type Form in Free-Living and Static Conditions but Not In Planta. Applied and Environmental Microbiology 85.

  • Rozier, C., Gerin, F., Czarnes, S., Legendre, L., 2019. Biopriming of maize germination by the plant growth-promoting rhizobacterium Azospirillum lipoferum CRT1. Journal of Plant Physiology 237, 111-119.

  • Valette, M., Rey, M., Gerin, F., Comte, G., Wisniewski-Dyé, F., 2019. A common metabolomic signature is observed upon inoculation of rice roots with various rhizobacteria. Journal of Integrative Plant Biology.


  • Alonso, L., Creuzé des Châtelliers, C., Trabac, T., Dubost, A., Moënne-Loccoz, Y., Pommier, T., 2018. Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave. Microbiome 6, 216.

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

  • 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.

  • Bouffaud, M.-L., Renoud, S., Dubost, A., Moënne-Loccoz, Y., Muller, D., 2018. 1-Aminocyclopropane-1-carboxylate deaminase producers associated to maize and other Poaceae species. Microbiome 6.

  • Chiapusio, G., Jassey, V.E.J., Bellvert, F., Comte, G., Weston, L.A., Delarue, F., Buttler, A., Toussaint, M.L., Binet, P., 2018. Sphagnum Species Modulate their Phenolic Profiles and Mycorrhizal Colonization of Surrounding Andromeda polifolia along Peatland Microhabitats. Journal of Chemical Ecology.

  • Doussan, C., Bérard, A., Czarnes, S., Legendre, L., Legouis, J., Ruy, S., Guix, N., 2018. Do Plant Roots Modify The Soil Water Retention Properties of Rhizospheric Soil ? Evidences from the field and controlled conditions. AGU Fall Meeting Abstracts 23.

  • 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.

  • 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.

  • Meyer, T., Renoud, S., Vigouroux, A., Miomandre, A., Gaillard, V., Kerzaon, I., Prigent-Combaret, C., Comte, G., Moréra, S., Vial, L., Lavire, C., 2018. Regulation of hydroxycinnamic acid degradation drives <i>Agrobacterium fabrum</i> lifestyles. Molecular plant-microbe interactions: MPMI.

  • 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.

  • Zidat, T., Dufour, A.-B., Meiffren, G., Gabirot, M., Comte, G., Allainé, D., 2018. Anal scent gland secretions inform on sexual maturity, sex and social status in the Alpine marmot, Marmota marmota (Rodentia: Sciuridae): a role in intrasexual competition in cooperative breeders? Biological Journal of the Linnean Society 125, 229-239.


  • 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.

  • 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.

  • 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.

  • Hay, A.E., Boubakri, H., Buonomo, A., Rey, M., Meiffren, G., Cotin-Galvan, L., Comte, G., Herrera-Belaroussi, A., 2017. Control of Endophytic Frankia Sporulation by Alnus Nodule Metabolites. Molecular Plant-Microbe Interactions 30, 205-214.

  • 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.

  • 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.

  • 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.

  • 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.

  • Lemanceau, P., Blouin, M., Muller, D., Moënne-Loccoz, Y., 2017. Let the Core Microbiota Be Functional. Trends in Plant Science 22, 583-595.

  • 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.

  • 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.

  • 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.

  • 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.

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