Fabrice ROUX
Research Director CNRS (co-head of the team)
ECOGEN
RESEARCH SUBJECTS
Fabrice Roux obtained his Ph.D. degree in 2004 on the management of herbicide resistance using Arabidopsis thaliana as an experimental model (under the supervision of Xavier Reboud, laboratory of Biology and Management of Weeds, INRAE Dijon). After his Ph.D., he spent one year as a junior lecturer in the laboratory of Genetics and Evolution of Plant Populations (GEPP, University of Lille 1) and worked on the evolution of early-flowering in plants. He then spent a too short period (only one year) in the laboratory of Joy Bergelson (University of Chicago), where he became interested in identifying the genetic basis of quantitative resistance in the pathosystem A. thaliana-Pseudomonas viridiflava. Recruited as a CNRS researcher in 2006 at the GEPP (University of Lille 1), he developed his own research theme on ecological genomics of adaptation in A. thaliana. In 2012, he then co-led the research theme 'Global change: from ecological genomics to community ecology’. The research of Fabrice mainly focused on (i) the identification of the genetic basis of complex adaptive traits with the desire to replace A. thaliana in an ecologically realistic context, and (ii) the study of adaptation at different spatial and temporal scales. Since July 2013, Fabrice joined the LIPME after obtaining a junior starting grant from the Labex TULIP (Toulouse). His current projects focus on ecological genomics of organism – organism interactions. He is particularly interested in identifying the genetic basis underlying coevolution in plant-microbiota-pathobiota pathogen and plant-plant interacting systems. Since 2021, he co-leds the team with Fabienne Vailleau.
Fabienne VAILLEAU
Research Director INRAE (co-head of the team)
ECOGEN
RESEARCH SUBJECTS
Fabienne Vailleau obtained her Ph.D. degree in 2003 at the University of Toulouse, Ph.D. realized at the LIPM in Dominique Roby’s group, on the Arabidopsis thaliana/Xanthomonas campestris pv. campestris pathosystem. After her Ph.D. she was Assistant Professor at the INP-ENSAT, where she set up the Medicago truncatula/Ralstonia solanacearum pathosystem. She was then recruited in Michel Petitprez’s group at the INP-ENSAT with a position of Associate Professor, where she continued her research on plant-bacteria interactions, giving lectures at the same time at INP-ENSAT in Plant Pathology and Weeds Science. From 2008 to 2015, she was the head of the 3rd year of specialization “Plant Agrobiosciences’. In 2008, Fabienne joined LIPM to perform her research in the group of Stéphane Genin and Christian Boucher. She worked on the post translational mechanisms required for the pathogenicity of the bacterium R. solanacearum. She obtained her Habilitation in 2016, and reoriented her projects on searching for plant proteins targeted and manipulated by R. solanacearum effectors, especially with approaches using association genetics. In 2020, she joined the team of Fabrice Roux to continue and integrate her work into a more global research theme in order to characterize and understand the molecular dialogue between the plant and its associated microbial cortege. In this context, she is currently developing a theme in the ECOGEN team on plant-microbiota-pathobiota interactions. Since 2021, she co-leds the team with Fabrice Roux.
Paloma DURÁN
Post-doc CNRS
ECOGEN
RESEARCH SUBJECTS
Paloma comes from Spain and studied Biology at the University of Salamanca. For her PhD, she moved to the MPIPZ in Cologne, Germany, and worked in the groups of Paul Schulze-Lefert and Stéphane Hacquard. There, she studied the multikingdom microbial communities associated with roots of natural Arabidopsis thaliana populations across Europe and the impact of microbial interactions on plant health. She was then then granted a Postdoctoral Fellowship with CEPLAS and moved to the group of Ruben Garrido Oter, also at the MPIPZ. There, she studied the microbiota composition and interactions at the phycosphere of the model microalgae Chlamydomonas reinhardtii, and investigated the microbial composition overlap with land plants. She is now part of the ECOGEN lab, where she will study the pathobiota of A. thaliana natural populations, investigating the host and microbial genetic factors, as well as environmental cues, that underlie these interactions.
Relevant publications
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Durán P. 2024. The core microbiota across the green lineage. Current Opinion in Plant Biology. 77 : 102487. https://doi.org/10.1016/j.pbi.2023.102487.
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Loo E.P.I.*, Durán P.*, Pang T.Y., Westhoff P., Deng C., Durán C., Lercher M., Garrido-Oter R. & Frommer W.B. 2024. Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis. Cell Host & Microbe 32, 1–14. https://doi.org/10.1016/j.chom.2024.02.014. *Authors contributed equally to this work.
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Durán, P., Flores-Uribe, J., Wippel, K., Zhang, P., Guan, R., Melkonian, B., Melkonian, M. & Garrido-Oter, R. 2022. Nat Commun 13, 406.
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Thiergart, T., Durán, P., Ellis, T. et al. 2020. Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nat. Ecol. Evol. 4, 122–131.
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Durán, P., Thiergart, T., Garrido-Oter, R., Agler, M., Kemen, E., Schulze-Lefert, P., & Hacquard, S. 2018. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell, 175(4), 973-983.
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Hassani, M. A., Durán, P., & Hacquard, S. 2018. Microbial interactions within the plant holobiont. Microbiome, 6(1), 58.
Mathieu HANEMIAN
Researcher INRAE
ECOGEN
RESEARCH SUBJECTS
During my 1st postdoc in Olivier Loudet's team at INRA Versailles, I used quantitative genetics combined with high throughput phenotyping to identify the genetic and molecular bases of vegetative growth in A. thaliana. The use of natural variation in these experiments led me to work on the ecological reasons of plant adaptation and in evolutionary biology. I did a 2nd postdoc in Cris Kuhlemeier's team at the University of Bern, where I studied the influence of pollinators on speciation in the Petunia genus, combining quantitative genetics, functional genomics and molecular biology.
I joined the ECOGEN team as a researcher since October 2019, to work on the molecular mechanisms involved in natural variation of the response to other plant species in A. thaliana. This is a fascinating subject because despite the importance of the interactions between plants in shaping plant communities, we know very little about the mechanisms of adaptation and co-evolution between them. In addition, a better understanding of these interactions may be useful for the agroecological transition.
TRAINING
2006 - BSc Sciences, Technologies, Health major in Biology - University of Burgundy, France
2007 - MSc (1st year) Sciences & Plant Technologies - University of Burgundy, France
2008 - MSc (2nd year) Microbiology-Agrobiosciences - University Toulouse III, France
2012 - PhD in Plant-Microbe Interactions - University Toulouse III, France
COMMITTEE MEMBER
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Member of the LIPME sustainable development committe (2020-)
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Member of the LIPME lab council (2021-)
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Member of the pedagogic council of the labex (2020-), with a particular focus on the Guided Tour and Junior Lab modules from the international TULIP master « Functional Biology and Ecology »
SCIENTIFIC PRODUCTION
CONNECTIONS
HOBBY
Gardening (where I most probably learn more about plants than during research work!)
Hiking
Claudia BARTOLI-KAUTSKY
Researcher INRAE
ECOGEN
RESEARCH SUBJECTS
I completed my PhD in microbial ecology at the Plant Pathology Laboratory in Avignon. During my thesis, I focused on understanding the emergence of diseases caused by the phytopathogenic bacterium Pseudomonas syringae in kiwi plants. In September 2014, I joined the LIPME in Fabrice Roux's team. During my postdoctoral research in this team, I studied microbiota variation in wild populations of Arabidopsis thaliana and highlighted a relationship between microbiota diversity and the diversity of pathogen populations (also known as the pathobiota). In 2016, I undertook a second postdoctoral position in Benoît Lefebvre’s team, focusing on interactions between fungi and bacteria in wheat. In 2018, I was recruited as a research scientist at INRAE in the IGEPP laboratory in Rennes. My current project primarily focuses on studying the co-evolution between plants and their microbiota. For this, I use the Brassica rapa fast cycling model. In January 2025, I joined the ECOGEN team, where I am also developing projects aimed at leveraging microorganisms (particularly fungi, my passion!) for biocontrol and biostimulation.
Coralie FUERTES
Technician, CNRS
ECOGEN
RESEARCH SUBJECTS
Coralie obtained a bachelor degree in genome and biotechnology for plant breeding from the University of Toulouse in September 2023. As part of this degree, she did an internship with the ECOGEN and ENOD teams on plant-plant interactions between Arabidopsis thaliana and Medicago truncatula. She was supervised by Matthias Benoit and Mathieu Hanemian. In December 2023, she was hired in the ECOGEN team to work on the ERC PATHOCOM project as a research technician. She will participate in setting up bacterial collections that will be used to test for interactions within the bacterial pathobiota of Arabidopsis thaliana, but also between the pathobiota and the microbiota of Arabidopsis thaliana.
Tifaine FOLLETTI
Engineer INRAE
ECOGEN - RLE
RESEARCH SUBJECTS
Tifaine graduated with a Master’s degree in Tropical Plants Biotechnology in Montpellier University in 2021. During her studies she took a year’s break (between Master 1 and Master 2) during which she worked as engineer assistant in SPI team at LIPME with Mireille Chabaud. She worked on research of resistance against a parasitic plant: the broomrape on sunflower. After obtaining her Master’s degree she took a short-term contract as biotechnology engineer at SYNGENTA where she worked on the improvement of a mitochondrial DNA extraction protocol on barley. Since april 2022 she joined the LIPME between two teams, ECOGEN and RLE, to work on the PATHOSYM ANR project.
Chrystel GIBELIN-VIALA
Engineer Assistant INRAE
ECOGEN
RESEARCH SUBJECTS
Chrystel Gibelin-Viala was recruited at INRA Poitou-Charentes in 2000. She worked in the molecular biology laboratory of URP3F, unit which study the functioning of the forage crop on grassland. She joined the LIPME in 2009 in the group of Clare Gough and Julie Culimore, where she studied the arbuscular mycorrhizal symbiosis using potential mutants of mycorrhization. She also developed genetic approaches to dissect the host range control in the rhizobium-legume symbiosis. Since January 2020, she joined the team of Fabrice Roux, ECOGEN (Ecological genomics of adaptation in plant communities). Her main missions are focused on the plant-microbiota-pathobiota interactions, one of the ECOGEN team themes of research. One of her main objectives is to contribute to characterize and understand the molecular dialog between Arabidopsis thaliana and its microbial cortege. Chrystel has skills in molecular biology (DNA extraction, PCR, genotyping), microscopy, plant biology (plant supply, plant experimentation, phenotyping), microbiology.
Baptiste MAYJONADE
Engineer INRAE
ECOGEN
RESEARCH SUBJECTS
Baptiste obtained a Master degree at the University of Limoges in 2010. He spent two years in the laboratory of molecular biology of Limagrain Europe (Chappes). In the context of molecular breeding and marker-assisted selection, he developed molecular markers on crops. In 2012, he joined the LIPME to work on the genetics and genomics of response to biotic and abiotic stresses in sunflower. He was in charge of projects related to transcriptomics and genomics. He was also involved in the development of technologies in molecular biology. Since September 2015, he has a permanent position in the ECOGEN team. He is responsible for the genomic, ecological and phenotypic characterization of 168 populations of Arabidopsis thaliana located southwest of France, and their associated plant and microbial communities. To do this, it implements innovative methodologies, in particular based on the most recent high-throughput sequencing technologies.
Roxane Lion
Engineer Assistant, CNRS
ECOGEN
RESEARCH SUBJECTS
After obtaining a Professional License in Molecular Biology at the IUT of Mont-de-Marsan, Roxane was recruited on a fixed-term contract at INRA in Bordeaux within the Fruit Biology and Pathology unit. She worked in the Virology team on the ANR Potymove project where she studied the genes involved in resistance to the TuMV virus as well as its movement in the Arabidopsis thaliana model. Since November 2021, she has joined the ECOGEN team to work on the ERC Pathocom project.
Rémi DUFLOS
PhD student
ECOGEN
RESEARCH SUBJECTS
Rémi Duflos obtained two master degrees in 2021, the first one at INP-ENSAT University (Toulouse, France) in AgroBiosciences and the second one at Paul Sabatier University (Toulouse, France) in Plant Biology. He performed his Master internship in the ECOGEN team, under the supervision of Fabienne Vailleau and Fabrice Roux. The goal of this project was the establishment of a genomic map of local adaptation in Arabidopsis thaliana to its most abundant bacterial species in the leaf compartment in south-west of France. His PhD project follows this internship with (i) the functional validation of candidates genes underlying QTLs identified in A. thaliana during his Master internship, and (ii) the identification, in Pseudomonas koreensis, of genes that mediate the genetic and molecular dialog with A. thaliana.
Sonia SILVA
Engineer, CNRS
ECOGEN
RESEARCH SUBJECTS
Sonia obtained a Master's degree in Biotechnology, Molecular Biology and Microbiology at the Toulouse’s University. Then, she worked during two years for TWB (Toulouse White Biotechnology) in the High Throughput Strain Engineering platform where she worked on bacterial, yeast and micro-algae genetic engineering. Since March 2022, she joined the ECOGEN team to work on the ERC Pathocom project.
Personal link
Shantala MOUNICHETTY
Post-doc CNRS
ECOGEN
RESEARCH SUBJECTS
Shantala obtained a bachelor's degree in cell biology and physiology, as well as a Master's specialized in plant-microorganism interactions, from the Université Paul Sabatier. She then completed her PhD in the Quantitative Plant Immunity (QIP) team at LIPME. Her work focused on the study of virulence mechanisms in the broad host-spectrum plant pathogenic fungus, Sclerotinia sclerotiorum. During her thesis, she studied the role of a fungal transcription factor involved in both carbon metabolism and infection of the Brassicaceae model plant, Arabidopsis thaliana. More specifically, her work highlighted the role of this transcription factor in the detoxification of a defense compound produced by A. thaliana, camalexin, during infection of the plant by the fungus. She has now joined the ECOGEN team as a postdoctoral researcher and is working on the ERC PATHOCOM project.
Antoine VAJOU
Post-doc CNRS
ECOGEN
RESEARCH SUBJECTS
Antoine graduated from the Université Paris Cité (Paris Diderot) in 2020 with a degree in molecular and cellular biology, specializing in microbiology with a second major in mycology. He carried out an end-of-study project at the Institut Pasteur in Paris within the CNRMA research unit (National Reference Center Invasives Mycoses and Antifungals), focusing on the persistence of the yeast Cryptococcus neoformans against antifungal agents. His PhD, obtained in 2023, is a continuation of his research into the adaptation of organisms to their environment. He studied phenotypic plasticity and adaptive potential in the phytopathogenic fungus Fusarium graminearum in response to environmental change. A subject that combines phenotypic plasticity and association genetics, as well as genotypic plasticity via experimental evolution. He has been part of the ECOGEN laboratory since 2025, working on the PATHOCOM ERC and studying pathogens interactions between them and their modulation by the plant microbiota, the plant genetic and the environment.
Marine PAPIN
Post-doc CNRS
ECOGEN
RESEARCH SUBJECTS
Marine obtained a bioengineering degree in Clermont Ferrand before working at the AFMB (Aix-Marseille University) on the structure and interactions of proteins by crystallography techniques. She then moved to Dijon for her PhD at UMR Agroecologie of INRAe. Her PhD focused on improving the survival of a bacterial inoculant strain using recurrent inoculations strategies while assessing the effect on maize growth and the impact on soil microbial communities. She joined ECOGEN team on the Pathocom ERC project since April 2025 to study the types of interaction between Arabidopsis thaliana pathogens during plant infection and their genetic determinants
Léonie FALGOUS
PhD student
ECOGEN
RESEARCH SUBJECTS
After graduating as an agricultural engineer from the École d'Ingénieurs de Purpan in Toulouse in 2024, I am now pursuing my doctorate in the ECOGEN team at LIPME. Before I did my Master internship in the same team, supervised by Fabrice Roux and Mathieu Hanemian, where I studied the natural genetic variation in the response to competition in Arabidopsis thaliana against different competitors.
My thesis, entitled “ Study of intercrop productivity in market gardening and its relation with soil and microbiota ”, is supervised by Mathieu Hanemian (researcher, LIPME) and Camille Dumat (teacher-researcher, ENSAT-DYNAFOR). I'm working on crop associations in market gardening. The aim of this research is to better understand the interactions between plants, soils and environmental factors in order to optimize these associations. This work is based on a participatory science approach, in collaboration with market gardeners, gardeners and researchers, in order to generate interdisciplinary scientific field data integrating the complexity of socio-agronomic processes.
Corentin CHALAS
PhD student
ECOGEN
RESEARCH SUBJECTS
I'm currently a PhD student in the ECOGEN team at LIPME, after graduating with a Master's degree in Plant Biology, “Plant-Microbe Interaction for Plant Health” in 2024, and a Bachelor's degree in Life Sciences, “Biodiversity Sciences” in 2022, from the Université Claude Bernard Lyon 1.
My thesis topic is “Eco-functional genomics of interspecific diversity of the beneficial microbiota of Arabidopsis thaliana”, under the supervision of Fabienne VAILLEAU and Carine CHAUVEAU. The aim of my thesis is to identify and functionally validate bacterial genes conferring beneficial effects on A. thaliana, by studying interspecific natural variation in a collection of over 1000 bacterial strains from the South-West of France. One of the main objectives of my thesis is to identify new bacterial genetic and molecular mechanisms involved in natural variation between wild bacterial species on plant biostimulation.
I had the opportunity to do my Master 1 and 2 internships in this team, under the supervision of Rémi DUFLOS, Fabienne VAILLEAU and Fabrice ROUX.
- In 2023 during my Master 1 internship (2 months) on beneficial plant-bacteria interactions, I studied the response of five natural accessions of A. thaliana to single inoculations or co-inoculations of pairs of 4 OTUs (Operational Taxonomic Units) of commensal bacteria of the phyllosphere.
- In 2024 during my Master 2 internship (6 months) on the identification and functional validation of Pseudomonas siliginis genes involved in the promotion of A. thaliana growth, by studying the natural intraspecific genetic variation of 74 strains of P. siliginis and starting the generation of bacterial mutants.
Former members
Visiting scientists
Hanna Susi (University of Helsinki) 2022
Quanjing Zheng 2023 (PhD student from the University of Copenhagen)
Post-docs
Claudia Bartoli (2014-2016)
Ullrich Dubiella (2015-2018)
Tatiana Vernié (2017-2018)
Florent Delplace (2020-2021)
Alexandre Perrat (2022-2024)
PhD students
Romain Villoutreix (2010-2013)
Etienne Baron (2011-2014)
Lea Frachon (2014-2017)
Cyril Libourel (2015-2019)
Nathalie Aoun (2016-2019)
Lorenzo Favale (2017)
Jaishree Subrahmaniam (2017-2020)
Florent Delplace (2017-2020)
Nargess Razavi (2017-2021)
Choghag DEMIRJIAN (2019 - 2022)
Daniela Ramirez-Sanchez (2019-2022)
Marie Invernizzi (2020-2024)
Rémi Duflos (2021-2024)
Technical staff
Rémi Zamar (2018 - 2022)
Oriane Besset (2022 - 2023)
Mégane Fenaux (2025)
Students
Cyril Libourel - Master 2 (2015)
Eve Coutant - Master 1 (2015)
Arnaud Chevalier-Mairet - Master 1 (2016)
Wijmer Taeken - Master 1 (2016)
Thomas Dussarat - Master 1 (2017)
Arnaud Chevalier-Mairet - Master 2 (2018)
Laurie Thailades - Master 1 (2019)
Marie Invernizzi - Master 2 (2019)
Louis Uhlmann - Vocational degree (2020)
Alexandre Boubegtitène - Master 2 (2021)
Paul Baumet - Master 1 (2021)
Manon Pradel - Master 1 (2021) + Master 2 (2022)
Corentin Chalas - Master 1 (2023)
Irene Leccia - Stage de césure (2023)
Leo Zbierski - BTS 1ère et 2ème année (2023)
Elena Dangla - Master 2 (2023)
Anais Botello - Master 2 (2023)
Clara Lapasse - Licence professionnelle (2024)
Audrey Vidal - L3 (2024)
Pauline Faure - BUT 2ème année (2024)
Edwin Wagner - Master 1 (2024)
Lila Rigolot - Master 1 (2024)
Matteo Antoine - Master 1 (2024)
Léonie Falgous - Master 2 (2024)
Corentin Chalas - Master 2 (2024)
Otto Bohm - Master 2 (2025)
Vincent Garrigues - Master 2 (2025)