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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Menu Logo Principal CBGP Cirad IRD SupAgro Muse

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Jean-François Martin

Jean-François MARTIN
755 avenue du Campus Agropolis
CS 30016
34988 Montferrier sur Lez cedex

Associate Professor, Montpellier SupAgro, department Biology and Ecology

MARTIN Jean-François

Thematic group : Origin and characterization of biodiversity 

Curriculum Vitae

  • Since January2003 Associate Professor, Montpellier SupAgro/CBGP – department Biology and Ecology
  • 2002 – 2003 Postdoc position, European Biological Control Laboratory (USDA)
  • 2000 – 2002 Postdoc position, CSIRO European Laboratory
  • 1999 - 2000 Postdoc position LECA (CNRS)

Teaching activities

Most of my teaching activities take place within the framework of the initial training of the two engineering programs and the 3A master's degree of the institution. These teaching activities are found in the three years of training up to options. The common thread that structures my commitment is, wherever possible, to focus on the dual entry Ecology and Evolution to understand the organization and functioning of biodiversity at all scales. Through my interventions or my organizational responsibilities, my general objective is to optimize the coherence of the disciplines related to ecology and evolution in our courses and to encourage students to reflect on the biological interactions that govern not only agrosystems but more generally ecosystems by integrating various levels of life organization and by promoting integrative approaches to ecology. The concepts I wish to transmit during the students' curriculum range from awareness of the complexity of biological systems in the first year to the analysis of biotic interactions in the various modules in which I participate and/or lead afterwards.
Ongoing Research

I am clearly focused today on the functioning of Arthropod communities, mainly in agrosystems, through the study of ecological interaction networks at the Arthropods/Plant community level. This approach to ecosystem functioning through the analysis of interaction networks makes it possible to address a large number of questions raised in the field of ecology in general and biological control in particular. We work on these themes in different systems, through several research contracts (ANR, Fondation Agropolis, collaborative agreement with the Australian CSIRO). This theme is expanding rapidly, has great potential and answers both central conceptual questions in Ecology but also directly addressable societal questions.

  • Flagship project STRADIV (2015-2019) : System approach for the TRAnsition to bio-DIVersified agroecosystems, from process analysis to multi-scale co-conception with actors. Work-package co-leader . Responsible for a postdoc.
  • Sonchus oleraceus biocontrol collaborative project with CSIRO (2017-2020) : Using classical biological control and innovative trophic interactions reconstruction with molecular metabarcoding approaches. Co-responsible for a posdoc, an assitant engineer and a phD student.

Beyond those main themes, I am involved in several methodological projects implying the used and development of methods based on high throuput sequencing technologiesin the context of biodiversity characterization.

Teaching at Montpellier SupAgro (192 hours) bioinformatics, Evolution and Ecology from L3 to M2.

  • Co-Head of L3 AI Biodiversity from gene to ecosystem (5 ECTS)
  • Co-head of M1 Dominante 3 Biodiversity (2 ECTS)
  • Co-Head of M1 Evolutionary applications in Agriculture (3 ECTS)
  • Co-Head of M1 Junior research Lab (8 ECTS)
  • Head of M2 Bioinformatics through Practice (1 ECTS)


  • participant in the project MOOC NECTAR with a training module focused on environmental barcoding
  • Leader for the project GENPOP : french speaking e-learning level L3 and M1 with focus on population genetics

International Workshops

  • NextGen european Workshop. Trainer on HTS methodologies and amplicon sequencing

Collectives responsibilities

  • Elected member of the council at Department Biology and Ecology, Montpellier SupAgro
  • Elected member of the professors council, Montpellier SupAgro

Significatant publications during the last five years

  1. Jakub Kreisinger, Lucie Schmiedová, Adéla Petrželková, Oldřich Tomášek, Marie Adámková, Romana Michálková, Jean‐François Martin, Tomáš Albrecht: Fecal microbiota associated with phytohaemagglutinin‐induced immune response in nestlings of a passerine bird. Ecology and Evolution 09/2018; 8(19)., DOI:10.1002/ece3.4454
  2. Vincent Lesieur, Jean-François Martin, Hariet L. Hinz, Boris Fumanal, Rouhollah Sobhian, Marie-Claude Bon: Implications of a phylogeographic approach for the selection of Ceutorhynchus assimilis as a potential biological control agent for Lepidium draba. Biological Control 05/2018; 123., DOI:10.1016/j.biocontrol.2018.05.001
  3. Emmanuel Guivier, Jean-François Martin, Nicolas Pech, Arnaud Ungaro, Rémi Chappaz, André Gilles: Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species. Microbial Ecology 09/2017;, DOI:10.1007/s00248-017-1077-9
  4. Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R. J. Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles: Challenges and advances for transcriptome assembly in non-model species. PLoS ONE 09/2017; 12(9):e0185020., DOI:10.1371/journal.pone.0185020
  5. Emmanuel Corse, Emese Meglécz, Gaït Archambaud, Morgane Ardisson, Jean-François Martin, Christelle Tougard, Rémi Chappaz, Vincent Dubut: A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies. Molecular Ecology Resources 08/2017; 17(6)., DOI:10.1111/1755-0998.12703
  6. Sylvain Piry, Catherine Wipf-Scheibel, Jean-François Martin, Maxime Galan, Berthier: High throughput amplicon sequencing to assess within- and between-host genetic diversity in plant viruses. DOI:10.1101/168773
  7. Lucie Kropáčková, Hana Pechmanová, Michal Vinkler, Jana Svobodová, Hana Velová, Martin Těšičký, Jean-François Martin, Jakub Kreisinger: Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major). PLoS ONE 06/2017; 12(6):e0179945., DOI:10.1371/journal.pone.0179945
  8. Lucie Kropáčková, Martin Těšický, Tomáš Albrecht, Jan Kubovčiak, Dagmar Čížková, Oldřich Tomášek, Jean-François Martin, Lukáš Bobek, Tereza Králová, Petr Procházka, Jakub Kreisinger: Co-diversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence. Molecular Ecology 04/2017; 26(19)., DOI:10.1111/mec.14144
  9. Jakub Kreisinger, Lucie Kropáčková, Adéla Petrželková, Marie Adámková, Oldřich Tomášek, Jean-François Martin, Romana Michálková, Tomáš Albrecht: Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird. Frontiers in Microbiology 02/2017; 8(e0123933)., DOI:10.3389/fmicb.2017.00050
  10. M. E. Maggia, Yves Vigouroux, J. F. Renno, Fabrice Duponchelle, E. Desmarais, J. Nunez, C. García-Dávila, F. M. Carvajal-Vallejos, Emmanuel Paradis, Jean-Francois Martin, Cédric Mariac: DNA Metabarcoding of Amazonian Ichthyoplankton Swarms. PLoS ONE 01/2017; 12(1):e0170009., DOI:10.1371/journal.pone.0170009
  11. Vincent Lesieur, Jean-François Martin, David K. Weaver, Kim A. Hoelmer, David R. Smith, Wendell L. Morrill, Nassera Kadiri, Frank B. Peairs, Darren M. Cockrell, Terri L. Randolph, Debra K. Waters, Marie-Claude Bon: Phylogeography of the wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae): implications for pest management. PLoS ONE 12/2016; 11(12):e0168370., DOI:10.1371/journal.pone.0168370
  12. V. Lesieur, M. Jeanneau, J. F. Martin, M. C. Bon: Development and characterization of 11 microsatellite markers in the root-gall-forming weevil, Ceutorhynchus assimilis (Coleoptera: Curculionidae). Applied Entomology and Zoology 04/2016; 51(3)., DOI:10.1007/s13355-016-0414-7
  13. Antoine Fraimout, Anne Loiseau, Donald K. Price, Anne Xuéreb, Jean-François Martin, Renaud Vitalis, Simon Fellous, Vincent Debat, Arnaud Estoup: New set of microsatellite markers for the spotted-wing Drosophila suzukii (Diptera: Drosophilidae): A promising molecular tool for inferring the invasion history of this major insect pest. European Journal of Entomology 07/2015; 112(4)., DOI:10.14411/eje.2015.079
  14. Gregory Mollot, Pierre-François Duyck, Pierre Lefeuvre, Françoise Lescourret, Jean-François Martin, Sylvain Piry, Elsa Canard, Philippe Tixier: Cover Cropping Alters the Diet of Arthropods in a Banana Plantation: A Metabarcoding Approach. PLoS ONE 04/2014; 9(4):e93740., DOI:10.1371/journal.pone.0093740
  15. Emese Meglécz, Nicolas Pech, André Gilles, Vincent Dubut, Pascal Hingamp, Aurélie Trilles, Rémi Grenier, Jean‐François Martin: QDD version 3.1: A user-friendly computer program for microsatellite selection and primer design revisited: Experimental validation of variables determining genotyping success rate. Molecular Ecology Resources 04/2014; 14(6)., DOI:10.1111/1755-0998.12271