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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


  • Almario J, et al. 2017. Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism. Frontiers in Microbiology. 8. doi: 10.3389/fmicb.2017.01218.

  • Guyonnet JP, et al. 2017. The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites. FEMS Microbiology Ecology. 93. doi: 10.1093/femsec/fix022.

  • Keshavarz-Tohid V, et al. 2017. Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of a bean from Iran for controlling Rhizoctonia solani. Research in Microbiology. doi: 10.1016/j.resmic.2017.08.002.

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

  • 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. doi: 10.1128/genomeA.00122-17.

  • 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. doi: 10.1128/genomeA.00122-17.


  • BORLAND S, PRIGENT-COMBARET C, WISNIEWSKI-DYE F. 2016. Bacterial hybrid histidine kinases in plant-bacteria interactions. Microbiology. doi: 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. doi: 10.1038/srep21690.

  • Cormier F, et al. 2016. Breeding for increased nitrogen-use efficiency: a review for wheat (T. aestivum L.). Plant Breeding. 135:255-278. doi: 10.1111/pbr.12371.

  • Joffard N, Legendre L, Gibernau M, Pascal L. 2016. Differential accumulation of Volatile Organic Compounds (VOCs) by leaves and roots of two Guianese Philodendron species, P. fragrantissimum Kunth and P. melinonii Brongn. Chemistry & Biodiversity. n/a-n/a. doi: 10.1002/cbdv.201600415.

  • 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. doi: 10.1016/j.jfca.2016.04.009.

  • 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. 1-8. doi: 10.1007/s00248-016-0810-0.

  • Mommer L, Hinsinger P, Prigent-Combaret C, Visser EJW. 2016. Advances in the rhizosphere: stretching the interface of life. Plant and Soil. 407:1-8. doi: 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. doi: 10.1016/j.jfca.2016.07.004.

  • 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.

  • Vacheron J, et al. 2016. Expression on roots and contribution to maize phytostimulation of 1-aminocyclopropane-1-decarboxylate deaminase gene acdS in Pseudomonas fluorescens F113. Plant and Soil. 1-16. doi: 10.1007/s11104-016-2907-0.

  • Vacheron J, et al. 2016. Fluorescent Pseudomonas Strains with only Few Plant-Beneficial Properties Are Favored in the Maize Rhizosphere. Plant Biotic Interactions. 1212. doi: 10.3389/fpls.2016.01212.


  • Bardon C, et al. 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. doi: 10.1111/1462-2920.13062.
  • Bardon C, Poly F, Piola F, Haichar FZ, Comte G. 2015. Utilisation de proanthocyanidines pour lutter contre la dénitrification.

  • Benabdelkader T, et al. 2015. Functional characterization of terpene synthases and chemotypic variation in three lavender species of section Stoechas. Physiologia Plantarum. 153:43-57. doi: 10.1111/ppl.12241.

  • Bérard A, et al. 2015. Rhizosphere: a leverage for tolerance to water deficits of soil microflora ? In: Vol. 17 p. 9481.

  • Borland S. 2015. Rôle des systèmes à deux composants dans l'adaptation de la bactérie phytostimulatrice Azospirillum à la rhizosphère. (Accessed no date).

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

  • Christina M, et al. 2015. Allelopathic effect of a native species on a major plant invader in Europe. The Science of Nature. 102:1-8. doi: 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. In: Biological Nitrogen Fixation. De Bruijn, FJ. John Wiley & Sons, Inc: Hoboken, NJ, USA p. 1047-1054.

  • Doussan C, et al. 2015. Crop systems and plant roots can modify the soil water holding capacity. In: Vol. 17 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. doi: 10.1016/j.resmic.2015.06.008.

  • Lebot V, Lawac F, Michalet S, Legendre L. 2015. Characterization of taro [Colocasia esculenta (L.) Schott] germplasm for improved flavonoid composition and content. Plant Genetic Resources. 1-9. doi: 10.1017/S1479262115000581.

  • Lebot V, Legendre L. 2015. HPTLC screening of taro hybrids ( <i>Colocasia esculenta</i> (L.) Schott) with high flavonoids and antioxidants contents Bachem, C. Plant Breeding. 134:129-134. doi: 10.1111/pbr.12225.
  • Moënne-Loccoz Y, et al. 2015. Significance of maize diversification for symbiotic interactions between roots and soil bacteria. In: communication orale: Montpellier, France p. .

  • Moja S, et al. 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. doi: 10.1080/11263504.2015.1014006.

  • 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. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. 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. In: communication orale: Maastricht , Pays-Bas p. .

  • 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, et al. 2015. Plant growth-promoting properties of Pseudomonas biocontrol agent producing 2,4 diacetylphloroglucinol. In: Natural Products and Biocontrol. p. .
  • Vacheron J, et al. 2015. Functional interactions between co-occurring plant beneficial activities from PGPR: which impact on plant growth? In: communication orale: Liège - Belgique p. .

  • Wisniewski-Dyé F, et al. 2015. Core and Accessory Genomes of the Diazotroph Azospirillum. In: Biological Nitrogen Fixation, 2 Volume Set. p. 253.

  • Wisniewski-Dyé F, Vial L. 2015. Cell–Cell Communication in Azospirillum and Related PGPR. In: Handbook for Azospirillum. Cassán, FD, Okon, Y, & Creus, CM. Springer International Publishing p. 263-285.

  • Youenou B, et al. 2015. Comparative genomics of environmental and clinical <i>Stenotrophomonas maltophilia</i> strains with different antibiotic resistance profiles. Genome Biology and Evolution. evv161. doi: 10.1093/gbe/evv161.


  • Almario J, Gobbin D, Défago G, Moënne-Loccoz Y, Rezzonico F. 2014. Prevalence of type III secretion system in effective biocontrol pseudomonads. Research in Microbiology. doi: 10.1016/j.resmic.2014.03.008.

  • Almario J, Muller D, Défago G, Moënne-Loccoz Y. 2014. Rhizosphere ecology and phytoprotection in soils naturally suppressive to Thielaviopsis black root rot of tobacco. Environmental Microbiology. n/a-n/a. doi: 10.1111/1462-2920.12459.

  • Bardon C, et al. 2014. Evidence for biological denitrification inhibition (BDI) by plant secondary metabolites. New Phytologist. 204:620-630. doi: 10.1111/nph.12944.

  • Bouffaud M-L, Poirier MA, Muller D, Moënne-Loccoz Y. 2014. Root microbiome relates to plant host evolution in maize and other Poaceae. Environmental Microbiology. n/a–n/a. doi: 10.1111/1462-2920.12442.

  • 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. doi: 10.1098/rspb.2014.0848.

  • 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. doi: 10.1038/srep06261.

  • Campillo T, et al. 2014. Analysis of hydroxycinnamic acids degradation in <i>Agrobacterium fabrum<i/> reveals a CoA-dependent, beta-oxidative deacetylation pathway. Applied and Environmental Microbiology. AEM.00475-14. doi: 10.1128/AEM.00475-14.

  • Donn S, et al. 2014. Rhizosphere microbial communities associated with Rhizoctonia damage at the field and disease patch scale. Applied Soil Ecology. 78:37-47. doi: 10.1016/j.apsoil.2014.02.001.

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