Doctorate thesis of Montpellier University


Thursday october 27 at 2h pm, Amphi Philippe Lamour


Plant – microbiota molecular dialogue: analysis of root and bacterial exudates, and evolution of root exudation function during wheat domestication and improvement

Doctoral school : GAIA – Biodiversité, Agriculture, Alimentation, Environnement, Terre, Eau
Spéciality : BIDAP – Biologie, Interactions, Diversité Adaptative des Plantes
University : Université Montpellier
Reasearch unit : IPSiM –  Institut des Sciences des Plantes de Montpellier


Jury :

M. Guillaume BECARD Université Paul Sabatier UT3, Toulouse – Rapporteur
M. Yvan MOENNE-LOCCOZ Université de Lyon – Rapporteur
M. Ali ALKHATIB Université Internationale Libanaise – Examinateur
Mme Brigitte BRUNEL Institut Agro Montpellier – Examinatrice
M. Pierre PETRIACQ Université de Bordeaux – Examinateur

M. Jean-Benoît  PELTIER INRAE – Directeur de thèse
M. Ali CHOKR Université libanaise – Co-directeur de thèse
Mme Israa DANDACHE Université Libanaise – Co-encadrante de thèse
Mme Loubna EL ZEIN Université Libanaise – Invitée
M. Pierre ROUMET INRAE – Invité

Abstract :

The classical model of industrialized agriculture, based on the unbridled use of inputs, is now widely considered unsustainable because it generates biodiversity erosion and multiple pollutions. The use of plant growth promoting rhizobacteria (PGPR) as biofertilizers is considered as a way to reduce the current dependence on hazardous agrochemicals. Our working hypothesis is that during the domestication of crops, human migrations and then selection have distanced crops from their original microbiota having co-evolved with them for thousands of years and that some plant-microbiota interaction capacities may have been altered. As these interaction capacities are generated by exchanges of water-soluble or volatile signals, we analyzed the root exudation profiles of different wheat subspecies recapitulating the main stages of domestication from the wild emmer (T. t. dicoccoides), the cultivated emmer (T. t. dicoccum) and the durum wheat (T. t. durum) showing almost exclusively secondary metabolites such as benzoxazinoids, peptides and phytohormones with notable variations between subspecies. In parallel, we isolated diazotrophic PGPR bacteria from the rhizosphere of a wild emmer accession isolated from a refuge area in Lebanon, a region part of the Fertile Crescent from where wheat originated and was domesticated. These bacteria showed a PGPR effect on modern durum wheat under nitrogen limitation, with a 50% increase in total seed nitrogen content. The culture supernatant of these strains was brought in contact with the root system of hydroponically grown modern wheat seedlings and aletred root development differently with a strong increase in length and density of root hairs observed when exudates of one of the tested strains were added. Analysis of the profile of these bacterial exudates revealed again mainly secondary metabolites including many antibiotics, peptides potentially mimicking phytohormones and proteins of the secretory pathway forming vesicles from the outer membrane and enclosing enzymatic activities such as proteases and secondary metabolites. Finally, endophytic bacteria from wild wheat seeds have been isolated and the study of their in-situ localization is in progress thanks to GFP labeling. In conclusion, wheat subspecies showed rich and different exudation profiles.Modern wheat seems to have retained the ability to interact with PGPR bacteria which can alter root growth, including that of the root hairs.

Key words: Wheat domestication, Root exudates, Bacterial exudates, Endophytic bacteria, Diazotrophs, PGPR, Metabolomics, Proteomics.