PhD Defense : François Maillard

François Maillard soutiendra publiquement ses travaux de thèse portant sur :
Le rôle des communautés microbiennes dans la dégradation de la matière organique en forêt dans un contexte d’exportation intense de biomasse 
 
Dirigés par Marc Buée et Dominique Gérant le 26 octobre à 9h00
Salle de conférence
Centre INRA Grand Est – Nancy
Champenoux
Jury
Patricia Luis, Maître de Conférences, Université de Lyon (Rapporteur)
François Buscot, Prof. Dr., Helmholtz Centre for Environmental Research (Rapporteur)
Daniel Epron, Professeur des Universités, Université de Lorraine (Examinateur)
François Rineau, Prof. Dr., University of Hasselt (Examinateur)
 
Résumé :
En Europe, le bois est la première source d’énergie renouvelable. La transition énergétique se traduit par une intensification de l’exploitation des forêts. L’effet de ces pratiques sylvicoles sur les communautés microbiennes du sol est encore peu étudié. Au cours de ma thèse, j’ai évalué les conséquences d’une manipulation artificielle de matière organique en forêt tempérée sur la diversité fonctionnelle et taxonomique des communautés bactériennes et fongiques telluriques dans six sites expérimentaux (réseau expérimental MOS). Parallèlement, une caractérisation fonctionnelle des communautés microbiennes a également été réalisée dans un contexte proche des réalités de l’intensification des pratiques sylvicoles sous climat tropical en plantation d’Eucalyptus. Si certains descripteurs fonctionnels de la dégradation de la matière organique sont particulièrement informatifs, les activités microbiennes de dégradation de la chitine, polymère azoté des arthropodes et champignons, sont apparues très sensibles au retrait de matière organique. C’est pourquoi, par des approches de génomiques comparatives, nous avons cherché à estimer le potentiel chitinolytique des différentes guildes fongiques des sols. En conditions contrôlées, nous avons ensuite quantifié les capacités potentielles de mobilisation et de transfert du carbone et de l’azote, à partir d’une matière organique microbienne riche en chitine, par un champignon ectomycorhizien en symbiose avec son hôte. Enfin, la généricité des fonctions chitinolytiques d’un plus large spectre d’espèces fongiques ectomycorhiziennes a été évaluée par le couplage d’approches enzymatiques et isotopiques. L’ensemble de nos résultats met en lumière le rôle significatif des champignons ectomycorhiziens dans la mobilisation du carbone et de l’azote à partir de certaines formes de matière organique, et la nécessité de prendre en compte le compartiment microbien dans les études d’impact des pratiques sylvicoles.
 
Abstract:
One of the main usages of wood in Europe is renewable energy supply that implies intensification of forest management to respond to this increasing demand. However, the impact of intense forestry practices on soil microbial communities remains poorly investigated. In the frame of my PhD thesis, I evaluated effects of artificial organic matter removal on functional and taxonomical diversity of soil bacterial and fungal communities in temperate forest, using six experimental sites across France (INRA MOS experimental network). In parallel, I also characterised impact of intensified forest management practices on functional microbial communities in tropical plantation of Eucalyptus trees. This work permitted to identify several sensitive functional indicators of organic matter degradation. Notably, the degradation of chitin – a nitrogen polymer main component of arthropods and fungal cell walls – was revealed to be particularly sensitive to organic matter removal. Genomics and enzymatic approaches were then used to estimate chitinolytic potentials of the different genera of soil fungi. In controlled conditions, we were able to quantify ectomycorrhizal fungus carbon and nitrogen mobilisation and transfer capacities from chitin enriched organic matter to its host during symbiotic interaction. Finally, we evaluated chitinolytic functions of ectomycorrhizal fungi at large scale by combining enzymatic and isotopic approaches. Taken together, the results acquired in the frame of my PhD thesis, illustrate the significant role of ectomycorrhizal fungi in carbon and nitrogen mobilisation from organic matter. We particularly highlight that microbial compartment in soil must be considered in studies of forest management practices.

Seminar: F. Rineau

François RINEAU, Uhasselt (Belgium): more information here
Thursday 25th October (1:30 pm) Conference room at Champenoux- 
Titre:  « Using ecotron facility to study the effects of climate change on ecosystem services»

Article: Environmental microbiology

First evidences that the ectomycorrhizal fungus Paxillus involutus mobilizes nitrogen and carbon from saprotrophic fungus necromass E Akroume, F Maillard, C Bach, C Hossann, C Brechet, N Angeli, B Zeller, … Environmental microbiology

Summary

Fungal succession in rotting wood shows a surprising abundance of ectomycorrhizal (EM) fungi during the late decomposition stages. To better understand the links between EM fungi and saprotrophic fungi, we investigated the potential capacities of the EM fungus Paxillus involutus to mobilize nutrients from necromass of Postia placenta, a wood rot fungus, and to transfer these elements to its host tree. In this aim, we used pure cultures of P. involutus in the presence of labelled Postia necromass (15N/13C) as nutrient source, and a monoxenic mycorrhized pine experiment also, composed of labelled Postianecromass and P. involutus culture in interaction with pine seedlings. The isotopic labelling was measured in both experiments. In pure culture, P. involutus was able to mobilize N, but C as well, from the Postia necromass. In the symbiotic interaction experiment, we measured high 15N enrichments in all plant and fungal compartments. Interestingly, 13C remains mainly in the mycelium and mycorrhizas, demonstrating that the EM fungus transferred essentially N from the necromass to the tree. These observations reveal that fungal organic matter could represent a significant N source for EM fungi and trees, but also a C source for mycorrhizal fungi, including in symbiotic lifestyle.

Article: Scientific reports

A rust fungal effector binds plant DNA and modulates transcription MB Ahmed, KCG dos Santos, IB Sanchez, B Petre, C Lorrain, MB Plourde, … Scientific Reports 8 (1), 14718

Abstract

The basidiomycete Melampsora larici-populina causes poplar rust disease by invading leaf tissues and secreting effector proteins through specialized infection structures known as haustoria. The mechanisms by which rust effectors promote pathogen virulence are poorly understood. The present study characterized Mlp124478, a candidate effector of M. larici-populina. We used the models Arabidopsis thalianaand Nicotiana benthamiana to investigate the function of Mlp124478 in plant cells. We established that Mlp124478 accumulates in the nucleus and nucleolus, however its nucleolar accumulation is not required to promote growth of the oomycete pathogen Hyaloperonospora arabidopsidis. Stable constitutive expression of Mlp124478 in A. thalianarepressed the expression of genes involved in immune responses, and also altered leaf morphology by increasing the waviness of rosette leaves. Chip-PCR experiments showed that Mlp124478 associats’e with the TGA1a-binding DNA sequence. Our results suggest that Mlp124478 exerts a virulence activity and binds the TGA1a promoter to suppress genes induced in response to pathogen infection.

Article: New Phytologist

Oxidative protein folding: state‐of‐the‐art and current avenues of research in plants. AJ Meyer, J Riemer, N Rouhier. New Phytologist

Summary

Disulfide bonds are post‐translational modifications crucial for the structure and function of thousands of proteins. Their formation and isomerization, referred to as oxidative folding, require specific protein machineries found in oxidizing subcellular compartments, namely the endoplasmic reticulum and the associated endomembrane system, the intermembrane space of mitochondria and the thylakoid lumen of chloroplasts. At least one protein component is required for transferring electrons from substrate proteins to an acceptor that is usually molecular oxygen. For oxidation reactions, incoming reduced substrates are oxidized by thiol‐oxidoreductase proteins (or domains in case of chimeric proteins), which are usually themselves oxidized by a single thiol oxidase, the enzyme generating disulfide bonds de novo. By contrast, the description of the molecular actors and pathways involved in proofreading and isomerization of misfolded proteins, which require a tightly controlled redox balance, lags behind. Herein we provide a general overview of the knowledge acquired on the systems responsible for oxidative protein folding in photosynthetic organisms, highlighting their particularities compared to other eukaryotes. Current research challenges are discussed including the importance and specificity of these oxidation systems in the context of the existence of reducing systems in the same compartments.

Seminar: C. Bonnot

  • 28 septembre 2018 – 13h30 INRA (LGEF): Clémence Bonnot (IAM ecogeno) “Characterisation of the nutritional signals regulating the establishment and maintenance of ectomycorrhizal symbiosis (ECM) in Pop

Article: Environmental Microbiology

Oak extractive‐induced stress reveals the involvement of new enzymes in the early detoxification response of Phanerochaete chrysosporium AJ Fernández‐González, N Valette, A Kohler, S Dumarçay, R Sormani, … Environmental microbiology

Summary

Extensive evidence showed that the efficiency of fungal wood degradation is closely dependent on their ability to cope with the myriad of putative toxic compounds called extractives released during this process. By analyzing global gene expression of Phanerochaete chrysosporium after short oak extractive treatment (1, 3 and 6h), we show that the early molecular response of the fungus concerns first mitochondrial stress rescue followed by the oxidation and finally conjugation of the compounds. During these early responses, the lignolytic degradative system is not induced, rather some small secreted proteins (SSP) could play an important role in cell protection or signaling. By focusing on the functional characterization of an hitherto uncharacterized glutathione transferase, we show that this enzyme interacts with wood molecules suggesting that it could be involved in the detoxification of some of them, or act as a scavenger to prevent their cytosolic toxicity and favor their transport.

Article : Fungal Ecology

From leaf to continent: The multi-scale distribution of an invasive cryptic pathogen complex on oak ML Desprez-Loustau, M Massot, M Toïgo, T Fort, AGA Kaya, J Boberg, …Fungal Ecology 36, 39-50

Abstract

The spatial distribution and niche differentiation of three closely related species (Erysiphealphitoides, Erysiphe quercicola and Erysiphe hypophylla) causing oak powdery mildew was studied at scales ranging from the European continent, where they are invasive, to a single leaf. While E. alphitoides was dominant at all scales, E. quercicola and E. hypophylla had restricted geographic, stand and leaf distributions. The large-scale distributions were likely explained by climatic factors and species environmental tolerances, with E. quercicola being more frequent in warmer climates and E. hypophylla in colder climates. The extensive sampling and molecular analyses revealed the cryptic invasion of E. quercicola in nine countries from which it had not previously been recorded. The presence of the three species was also strongly affected by host factors, such as oak species and developmental stage. Segregation patterns between Erysiphe species were observed at the leaf scale, between and within leaf surfaces, suggesting competitive effects.

Article: Proceedings of the IUFRO conference

Genomics, transcriptomics, and effectoromics of the poplar leaf rust fungus Melampsora larici-populina B Petre, S Hacquard, A Persoons, N Saveleva, E Tisserant, E Morin, …In: Schoettle, Anna W.; Sniezko, Richard A.; Kliejunas, John T., eds …

Description

Melampsora larici-populina is causing leaf rust disease in poplar (Populus spp.) worldwide and poses serious problems to poplar breeders in France and in northern Europe. As with other rust fungi, its obligate biotroph status hinders laboratory investigations. Understanding the biology of rust fungi and deciphering the molecular mechanisms underlying biotrophy have long been a problem. Most of the knowledge gained was largely descriptive and limited to a few rust species; only recently has substantial progress been made in the characterization of avirulence determinants of the flax rust Melampsora lini.