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Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Members - Quantitative Immunity in Plants

Dr. Dominique Roby, DR1 CNRS group leader

Dominique ROBY

Dominique did her PhD in the Laboratory of Plant Physiology in Toulouse; her work concerned the study of defense mechanisms triggered by fungal elicitors in plants and the signalling role of ethylene. She was then recruited in 1982 as a CNRS researcher to work on the regulation of chitinase genes in plants upon fungal infection. After 4 years, she moved to Rutgers University (USA) and then to the Department of Agricultural Products of E. DuPont de Nemours (USA) where she investigated the role and transcriptional regulation of chitinase genes in plant immunity. Then she joined the LIPM in 1990 and started a group in collaboration with Yves Marco, working on plant-bacteria interactions, and more paticulatrly on plant genes involved in the control of the Hypersensitive Response, a form of programmed cell death for which there was still very limited information. The main goals of her research, in collaboration with Sylvain Raffaele, are now to identify  key components of quantitative resistance in Arabidopsis to two agronomically important pathogens: Xanthomonas campestris and Sclerotinia slerotiorum. This programme is developped in tight collaboration with Fabrice Roux team, interested in identifying the genetic basis underlying coevolution in plant - pathogen and plant – plant interacting systems.

Dominique is presently coordinator of the LabEx TULIP (https://www.labex-tulip.fr/Le-LabEx) and Deputy Head of INRA Division - Plant Health & Environment  (http://www.spe.inra.fr/)

 

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Dr Sylvain Raffaele, CR1 INRA co-group leader

Sylvain Raffaele

I obtained my Ph.D in 2006 from the University Paul Sabatier of Toulouse (France). My work carried out at the Plant-Microbe Interactions Laboratory (LIPM), in the group of Drs. Dominique Roby and Yves Marco, revealed the role of a class of plant lipids in the response to pathogenic bacteria. I started my postdoctoral studies at the University of Bordeaux (France) in the group of Sébastien Mongrand, working on Remorin proteins and the role of plant membrane microdomains in virus propagation. Between 2008 and 2012 my research in the group of Sophien Kamoun group at The Sainsbury Laboratory, Norwich (UK), focused on the genomics of the potato blight pathogen Phytophthora infestans. I have been appointed in 2012 as an independent INRA researcher at the LIPM, Toulouse. I am currently leading a multidisciplinary research programme aiming at understanding of the molecular mechanisms underlying plant quantitative disease resistance and fungal pathogenicity in the Arabidopsis thaliana – Sclerotinia sclerotiorum pathosystem.

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Dr Adelin Barbacci

Adelin Barbacci

After masters in engineering sciences and artificial intelligence, I started my research by designing algorithms to decrease computation time for real time rendering of complex 3D forest scenes (INRIA Nancy / CIRAD Montpellier).

I continued my research  during a Ph.D at AgroParisTech by studying how plants defies gravity to survive  thanks to mechanoperception and tension wood. My work at INRA Nancy, in Gérard Nepveu/Mérièm Fournier/Thiéry Constant ‘s group, concerned the study of gravitropic movement in mature beech trees. As spatial organization of trees in space appeared of major importance in gravitropic movement, I joined the Xiaopeng Zhang’s group in LIAMA at Beijing in 2009. My first postdoctoral studies aimed at reconstructing 3D trees architecture from partial data obtained with LIDAR. I joined Bruno Moulia’s team at INRA Clermont-Ferrand in 2010 to work on movements of trees caused by wind. I was recruited in 2011 in Marc Lahaye’s group at INRA Nantes to work on relationships between mechanical properties of plant tissues and cell wall composition.

I joined the LIPM in 2016 to work on thigmoimmunity in which mechanoperception, mechanical properties of cell wall and turgor pressure play a central role.

Dr Carine Huard-Chauveau, INRA engineer

Carine CHAUVEAU

During her PhD in the Protein Biochemistry and Structure laboratory, INRA Jouy-en Josas, Carine worked on the characterization of peptidoglycan hydrolases of Lactococcus lactis. She was then recruited in the Small Ruminant Pathology unit of Sophia-Antipolis laboratory of ANSES (French Agency for food, environmental, and occupational health and safety). She joined the LIPM in 2005. She is now involved in the characterization of genes controlling quantitative resistance of Arabidopsis to Xanthomonas campestris pv campestris (ANR projects Quantirex 2009-2013 ;  ANR projects Riposte 2014-2018).

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Mehdi Khafif, INRA research assistant

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Mehdi obtained a Master in Plant Biology from the University of Montpellier. He worked at the ISV (Institute of Plant Sciences) in Gif-sur-Yvette on plant tolerance to abiotic stresses. Then he moved in 2006 to the URGV (Unite de Recherche en Génomique Végetale Evry) in A. Bendahmane’s team to work in collaboration with O. Voinnet on the  positional mapping of genes involved in miRNA action. He joined the group of D. Roby in 2009. He is working on the indentification of key genes involved Hypersensitive Response and/or the resistance ofArabidopsis to Xanthomonas campestris pv campestris.  He is also involved in the set-up of the plant highthrouput phenotyping platform « Toulouse Plant Microbe Phenotyping » .

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Dr Ullrich Dubiella,  Post-Doctoral fellow

 I started to investigate platen-pathogen interactions during my Diploma thesis in the group of Thorsten Nuernberger at the University of Tuebingen. During my PhD in the group of Tina Romeis at the Free University Berlin I studied the function of calcium-dependent protein kinases after pathogen attack.I spend the last for years at Indiana University (USA). Primarily, I was working in the lab of Roger Innes on the recognition of the receptor-like cytoplasmic kinase PBS1 by the R-protein RPS5. Furthermore I worked in the lab of Roger Hangarter, investigating the molecular mechanisms underlying the light-dependent movement of chloroplasts. Here in Toulouse I will investigate the role of the atypical kinase RKS1 in quantitative disease resistance responses in the group of Dominique Roby.

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Dr Stefan Kusch,  Post-Doctoral fellow

From 2007 to 2013, I studied at Georg-August University in Göttingen (Germany) and obtained my Master’s degree in Microbiology and Biochemistry. Here, I already worked on plant-microbe interactions. In particular, my master’s thesis entailed in silico and pathological characterization of an effector from the Arabidopsis powdery mildew Erysiphe cruciferarum.From 2013 to 2017, I pursued my Ph.D. at the RWTH Aachen University (Germany), where I focussed on the family of Mildew resistance Locus O (MLO) proteins. My work comprised for example the study of a barley powdery mildew isolate infecting barley mlo mutant plants that are otherwise fully and stably resistant to powdery mildew. I gained experience with the CRISPR system, quantitative plant pathology, phylogenetic and statistical analysis, analysis of RNA-Seq data, and advanced cloning methodologies.I joined the LIPM in 2017 to establish a reliable transformation and CRISPR pipeline in Sclerotinia sclerotiorum, and to characterize S. sclerotiorum virulence factors determining infection outcome and host specificity.

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Dr Rémi Peyraud,  Post-Doctoral fellow

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I studied biochemistry at the universities of Limoges and Toulouse (France). Then, I obtained my PhD in September 2011 at ETH Zürich (Switzerland) under the supervision of Julia Vorholt. During my PhD I elucidated the ethylmalonyl-CoA pathway in Methylobacterium extorquens, a glyoxylate cycle variant using 13C labeling metabolomics. Getting interested in system biology I performed the reconstruction of the genome-scale metabolic network of this methylotrophic epiphyte. I joined in February 2012 (EMBO Long term Fellowship) the team of Stéphane Genin to tackle the system-level reprogramming of the embedded metabolic and regulatory networks of Ralstonia solanacearum during infection. Now, I joined the team of Sylvain Raffaele to deploy system biology approaches on Sclerotinia sclerotiorium in order to decipher the metabolic adaptation of the pathogen on the plant.

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Dr Justine Sucher,  Post-Doctoral fellow

I studied plant biotechnology at the Université Paul Sabatier in Toulouse where I graduated my master. I did my master thesis in the group of Evans Lagudah in CSIRO (Australia) and in the group of Graham Moore in the JIC (UK) and learned a lot about plant breeding by the use of resistance genes. From October 2012 to January 2017 I performed my PhD thesis at the University of Zurich, in the group of Beat Keller where I studied the quantitative and durable resistance mechanism through the Lr34 wheat gene. In April 2017 I joined the QIP group with Sylvain Raffaele as post-doc and work on the effect of climate variation on quantitative resistance, using the model host plant Arabidopsis thaliana and the necrotrophic fungus Sclerotiniasclerotinium.

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Thomas Badet, PhD student

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Thomas obtained a Master in Plant Bioscience at Paul Sabatier Toulouse University. For his PhD project, Thomas is working on the Arabidopsis Sclerotinia pathosystem, looking for new actors of plant quantitative disease resistance.

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Delplace Florent, PhD student

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During my Master 1 and Master 2 in Plant Biology at the  University Paul Sabatier in Toulouse (France), I did  internships under the supervision of Dominique Roby on the  "identification of RKS1 dependent signaling pathways components , RKS1 being an atypical kinase conferring in Arabidopsis thaliana quantitative disease resistance to the pathogenic bacteria Xanthomonas campestris. Now as a PhD student, I am invloved in the extension of the same project. However I am also developping a new axis, aiming at the characterization of the leaf microbiota in relation to the signaling components involved in quantitative disease resistance. My thesis, under the supervision of Dominique Roby and Fabrice Roux is funded by the INRA (Division PPlant Health and Environment - SPE) and the Occitanie region.

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Marielle Barascud, Marie-Curie Grant research assistant

Marielle obtained a Master in Plant Biosciences from the University Paul Sabatier of Toulouse in 2003. Then she worked for almost 2 years in D.Barker’s group at the LIPM, contributing to the construction of a collection of insertion mutants of Medicago truncatula.Then, she joined the production-sequencing department of a private lab, Millegen, during nearly 6 years.Since the begining of 2014, she returned to the LIPM, in the group of D. Roby and Y. Marco, working on a project to study quantitative disease resistance against Sclerotinia sclerotiorum, led by Sylvain Raffaele.

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Florent Delplace, Master student

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.During my Master 1 and Master 2 in Plant Biology at the  University Paul Sabatier in Toulouse (France), I did  internships under the supervision of Dominique Roby on the  "identification of RKS1 dependent signaling pathways components , RKS1 being an atypical kinase conferring in Arabidopsis thaliana quantitative disease resistance to the pathogenic bacteria Xanthomonas campestris. Now as a PhD student, I am invloved in the extension of the same project. However I am also developping a new axis, aiming at the characterization of the leaf microbiota in relation to the signaling components involved in quantitative disease resistance. My thesis, under the supervision of Dominique Roby and Fabrice Roux is funded by the INRA (Division PPlant Health and Environment - SPE) and the Occitanie region.

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