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Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Members - Endosymbiotic infection and nodule development

Dr. Fernanda de Carvalho-Niebel, CR1 CNRS, co-group leader


Fernanda performed her PhD in the Laboratory of Genetics (Ghent University, Belgium) directed by Dirk Inzé and Marc Van Montagu. Her work focused on the study of the regulation and function of a gene encoding Pathogenesis-Related ß-1,3-glucanase. During her PhD she also discovered and characterized an original form of Post-Transcriptional Gene Silencing (PTGS) in plants resulting from dose-dependent co-suppression of homologous genes. As an EMBO and EC post-doctoral fellow, she joined the group of Pascal Gamas/Julie Cullimore at the LIPM and worked on the identification and characterization of novel early nodulin genes from the model legume Medicago truncatula, including a rhizobial Nod factor (NF)-elicited gene encoding an annexin calcium-binding protein. More detailed studies on this gene were pursued in David Barker’s group at the LIPM after her recruitment by the CNRS. Since 2002, Fernanda’s research has been focused on the study of the molecular mechanisms underlying symbiotic host gene expression, which led to her identify NF-signaling components directly involved in host gene transcription. Her present research is centred in the characterization of a small family of ERN transcription factors mediating NF-dependent host gene expression (see above). Fernanda is now group leader of the Endosymbiotic infection and nodule development (ENOD) team together with Andreas Niebel .


Dr. Andreas Niebel, DR2 CNRS, co-group leader

Andreas NIEBEL

Andreas obtained his PhD at the University of Ghent in 1994 in the Lab of Marc van Montagu under the supervision of Dirk Inzé and Godelieve Gheysen. His research project involved identifying and characterizing genes such as the cell cycle regulator gene cdc2a, which are expressed in the giant feeding cells elicited in roots of potato, tobacco and Arabidopsis by plant endoparasitic nematodes. As an EMBO postdoctoral fellow he then moved to the LIPM to work on the legume-Rhizobium symbiotic interaction, where he was subsequently recruited by the CNRS (CR2). Andreas initially studied rhizobial Nod factor perception using biochemical and molecular approaches in the group of Julie Cullimore. In 2000, he joined the group of Pascal Gamas and contributed to the study of the symbiotic transcriptome of Medicago truncatula, especially during early steps of this symbiotic interaction. As a member of the Barker-Gamas team he is particularly interested in a group of transcription factors belonging to the CCAAT-box binding factor family, also known as HAP (Heme activating protein) that act as key regulators of rhizobial infection and nodule development and possibly also Nod factor signal transduction. In addition he also studies the symbiotic microtranscriptome and in particular several microRNAs that control early symbiotic signaling and/or nodule development. Andreas is now group leader of the Endosymbiotic infection and nodule development (ENOD) team together with Fernanda de Carvalho-Niebel.


Dr. David Barker, DR2 INRA


After obtaining his PhD at Imperial College, London, studying the structure and functional specificity of key components of protein synthesis, the aminoacyl tRNA synthetases, David obtained an EMBO fellowship to continue research in this field at the CNRS Institute of Molecular and Cellular Biology at Strasbourg. David then obtained a junior scientist position (4 years) at the National Institute of Medical Research, London, studying the cell-cycle regulation of DNA ligase genes in both budding and fission yeasts. After a 1-year post-doc at the LIPM, David was recruited by INRA (1987) with the objective of identifying novel plant genes expressed during the early stages of the root symbiosis between legume plants and nitrogen-fixing rhizobia. During this period David also contributed with other colleagues at the LIPM to the establishment of Medicago truncatula as a model legume, and to the development of parallel studies on the important arbuscular mycorrhizal symbiosis. David's current research interests are focused on understanding the molecular and cellular mechanisms underlying plant-microbe signaling and the unique processes of transcellular host infection which characterize the endosymbiotic associations involving both rhizobia and arbuscular mycorrhizal fungi.


Dr. Pascal Gamas, DR1 CNRS

Pascal GAMAS

The first seven years of Pascal’s scientific career were devoted to studies on bacterial transposable elements. His PhD (Michael Chandler’s lab, Toulouse University), focused on the insertion sequence IS1, after which he was recruited by the CNRS (CR2) in 1986. He then studied the transposon Tn7 as a post-doc in Nancy L. Craig’s lab at the University of California, San Francisco, USA. Returning to France, Pascal switched to plant biology to work on the Rhizobium-legume symbiosis. He joined  Julie Cullimore’s group at the LIPM in 1990 (co-PI from 1997 to 2007) in order to develop global approaches aimed at identifying Medicago truncatula genes transcriptionally activated by Sinorhizobium meliloti or purified rhizobial Nod factors. He thus established with co-workers a collection of transcriptomics tools in M. truncatula, including standard cDNA sequencing, differential display analysis, subtractive probes or libraries, macro and microarrays and most recently RNA-seq approaches. Pascal is particularly interested in identifying and characterizing transcriptional regulators, notably transcription factors that control early to late nodulation stages, as well as their regulation networks. Pascal was the LIPM Director from 2003 to 2010.


Dr. Joëlle Fournier, CR1 CNRS


During her PhD at Toulouse University, Joëlle worked on the role of lipoxygenases in defense responses of tobacco upon infection by the oomycete Phytophthora parasitica in the group of Marie-Thérèse Esquerré-Tugayé. She joined the CNRS in 1992 to continue her work in this group on the participation of lipoxygenases and the oxylipin pathway in plant defense and resistance against pathogens. In 2005, Joëlle moved to the field of symbiotic plant-microbe interactions in David Barker’s group, where she initiated a project on the cellular mechanisms and dynamics associated with the initial stages of Medicago truncatula root entry by the N-fixing endosymbiont Sinorhizobium meliloti. Rhizobial infection involves the de novo formation of apoplastic compartments called infection threads which host the microsymbiont. Joëlle has developed in vivo approaches for time-lapse studies on infection thread formation in root hairs using laser confocal microscopy associated with ER- or PM-targeted fluorescent markers and fluorescent S. meliloti strains. Her current research is focused on the dynamics of cell wall deposition/modification at infection initiation sites and she is also involved in studies of the in vivo spatio-temporal dynamics of early nodulins during endosymbiotic interface construction.


Dr. M-Françoise Jardinaud, MCF ENSAT-INPT

Marie-Françoise JARDINAUD

Françoise obtained her PhD at the Graduate School of Life Sciences of Toulouse in 1994 in the Biotechnology and Plant Improvement Department under the supervision of André Souvré and Gilbert Alibert. She developed new methods for genetic transformation of Brassica and maize microspores. She then moved to CSIRO (Plant Industry, Canberra Australia) where she worked from 1994 to 1995 as post doctoral fellow on the Arabidopsis thaliana flowering gene FLF in Liz Denis’ lab. In 1996, she initiated a new research program funded by the “Australian Rice Growers company” aimed at increasing the iron content of rice seeds. In 2000, she was recruited by CIMMYT (El Batan, Mexico DF) as an associate scientist to study maize drought tolerance in Jean Marcel Ribaut’s group. In 2001, she returned to France after being recruited as an associate professor by the Graduate School of Life Sciences of Toulouse. Françoise first worked on the molecular characterization of sunflower embryogenesis in the Biotechnology and Plant Improvement Department. In 2005, her interest shifted to plant-microbe interactions and in particular the association between the soil-born pathogen Ralstonia solanacearum and Medicago truncatula. Françoise focused her research activities on the relationships between symbiotic and pathogenic plant-microbe interactions. She then joined the Barker-Gamas team in 2009 to work on transcriptional regulators common to both symbiotic and pathogenic interactions.


Dr. Mireille Chabaud, IR1 INRA

Mireille CHABAUD

Mireille is “ingénieur agronome” (equivalent to Masters degree) from the National School of Agronomy in Montpellier (Ecole Nationale d’Agronomie de Montpellier). She was initially employed by the research company Graines Caillard, France, using in vitro culture for vegetable breeding and then moved to Biotechnica International Inc., Boston, USA, with the goal of optimizing genetic transformation of alfalfa (Medicago sativa). Mireille was then recruited by INRA as a research engineer at the LIPM in Thierry Huguet’s group to work on A. tumefaciens-mediated transformation of the model legume M. truncatula. She then obtained her PhD on this topic and has also contributed to various other aspects of M. truncatula transformation (notably root transformation via A. rhizogenes). Mireille then joined the group of David Barker to work on the arbuscular mycorrhizal symbiosis and in particular the development of cellular dynamics approaches using laser confocal microscopy associated with plant fluorescent markers. More recently she has contributed to the development of fluorescent “cameleon” calcium reporters to study calcium signaling during early stages of endosymbiotic interactions.


Sandra Moreau, IE2 CNRS


Sandra obtained a Masters degree in Plant Biotechnology at the Paris 7 University in 2001. She worked for one year at INRA Versailles in Loïc Lepiniec’s lab, studying seed transcription factors, and then for 18 months at the URGV (Plant Genomics Research), Evry, on positional cloning projects. Sandra was recruited by the CNRS in 2004, and joined P. Gamas’ group at the LIPM where she was in charge of transcriptomics approaches in Medicago truncatula. She notably established microarray analyses (in collaboration with H. Küster, Bielefeld University, Germany), Affymetrix chip analyses (in collaboration with S. Balzergue, URGV Evry), large scale quantitative RT-PCR analyses on 384 plates (using the Toulouse Genopole facilities). Sandra is also involved in the functional characterization of symbiotic transcription factors using molecular and reverse genetics approaches, under P. Gamas’ supervision. Her current projects include the characterization of the efd-1 mutant in symbiotic and pathogenic interactions (with M-F. Jardinaud) and the identification of EFD binding sites on DNA (with F. de Carvalho-Niebel).


Lisa Frances, TCN INRA


In 1999, Lisa obtained a two-year bioengineering University diploma in Agronomy (DUT) at the Technological University Institute in Perpignan and in 2000 a Plant Biotechnology degree at ENFA/Paul Sabatier University. Lisa then worked as a technician in the molecular biology laboratories of BIOGEMMA Biotech Company (Clermont-Ferrand, France) and RAGT GENETIQUE (Rodez, France). Lisa was recruited as a technician by INRA in 2005 and joined the LIPM to take charge of the DNA sequencing service of the laboratory. Lisa also joined the Barker-Gamas team to work on the research project run by Fernanda de Carvalho-Niebel on the functional characterization of ERN transcription factors. Lisa is involved in different aspects of this research project but has particularly contributed to the study of the transcription properties of ERN factors using both N. benthamiana- and M. truncatula-based  assays, and to the study of protein interactions using yeast two-hybrid and BiFC approaches.


Agnès Lepage, TCE CNRS

Agnès joined the CNRS in 1990. She first worked in the Lab of Cell Physiology in Paris attempting to identify a vaccine against the HIV virus. In 1992 she joined the Institut Jacques Monod (Paris) where she was in charge of the production and microinjection of different animal cell cultures. In 1996 she moved to Toulouse where she joined the Centre for Developmental Biology (CBD) and developed her skills in molecular biology and cytology studying Drosophila melanogaster development. In 2007 she joined the Barker-Gamas team at the LIPM where she studies the role of HAP (CCAAT-box binding factor) transcription factors during the legume-Rhizobium symbiosis under the direction of Andreas Niebel.

Iltaf Abdou-Pavy, CDD IE CNRS

Iltaf Abdou-Pavy

Iltaf obtained a master’s degree in September 2014, in plant biotechnology from the University of Toulouse III. Following her graduation, she joined the LIPM, in the Stephane Genin's group, under the supervision of Fabienne Vailleau. Iltaf contributed to a project on Ralstonia solanacearum pathogenicity. In May 2015, she integrated David Barker/Pascal Gamas' team. Iltaf contributes to the tasks of the ANR "SYMActino" project involving living-tissue microscopy studies of Frankia (nitrogen-fixing filamentous bacteria) infection of the actinorhizal host plant Casuarina glauca.


Martina Beck, Post Doctoral Fellow

Martina Beck

Martina obtained her PhD in 2009 in the group of Jozef Samaj and Diedrik Menzel at the Institute of Cellular and Molecular Botany of University Bonn. Her research focused on mitogen-activated-protein kinase (MAPK) signaling and its contribution to the remodeling of cytoskeletal elements during plant development, thereby discovering the important role of MAPKs in the regulation of microtubule structure and dynamics during cell elongation and cell divison in Arabidopsis thaliana. For her first PostDoc between 2010-2014, she moved at The Sainsbury Laboratory in Norwich (UK) in the group of Silke Robatzek to study the intracellular dynamics of a bacterial immune receptor in plants, setting up an automated high throughput imaging system to identify the intracellular trafficking pathway of this protein. This work was funded by a post doctoral fellowship of the German Research Council (DFG). Being awarded with a Tulip LABEX post-doctoral fellowship and an AgreenSkills (INRA) fellowship, she joined in April 2015 the group of David Barker/Pascal Gamas initiating a project which will investigate the role of cell-to-cell communication during early symbiotic infection processes. By combining in vivo microscopy with genetic approaches the project aims to unravel the role of plant specific structures essential for cellular communication, namely plasmodesmata, during symbiotic interactions.


Carolina Ripodas, Post Doctoral Fellow

Carolina Ripodas

Carolina obtained her PhD in 2015 in the group of Maria Eugenia Zanetti and Flavio Blanco at the Institute of Biotechnology and Molecular Biology of the National University of La Plata – Argentina. Her research focused on the characterization of NF-Y and GRAS transcription factors during the symbiotic association between Phaseolus vulgaris and Rhizobium etli. In the context of an ANR project entitled “NODCCAAT”, obtained by Andreas Niebel she joined the group of David Barker/Pascal Gamas in April 2016. In addition Carolina has been awarded with an AgreenSkills (INRA) fellowship. She initiated a postdoctoral project to thoroughly understand the mode of action of NF-Y transcription factors during nodule development in the model plant Medicago truncatula.


Maria-Fernanda Guerrero-Molina, Post Doctoral Fellow

Audrey Kelner, PhD Student

Audrey obtained a Master’s degree in June 2015 in plant science from the University of Toulouse III – Paul Sabatier. She joined the ENOD group in January 2015 for her Master's training and has, since October 2015 initiated her PhD thesis under the supervision of Fernanda de Carvalho-Niebel. By combining cutting-edge microscopy and genetic approaches she is investigating the real-time dynamics of nuclear signaling in plant cells undergoing symbiotic bacterial infection. By focusing on the key ERF transcription factor ERN1, Audrey is currently investigating its interconnection with other nuclear components during the reprogramming of host cells for endosymbiotic infection.