Research scientist permanent position (Ingénieur de Recherches)

Monitoring the risks of disease emergence in forests

INRAE presentation

The French National Research Institute for Agriculture, Food and the Environment (INRAE) is a public research establishment under the dual authority of the Ministry of Agriculture and the Ministry of Research. INRAE is a major player in research and innovation created on 1 January 2020, resulting from the merger between INRA and IRSTEA. INRAE brings together a community of 12,000 people, with 268 research, service and experimental units, located in 18 centers throughout France. INRAE is one of the world’s leading institutions in agricultural and food sciences, plant and animal sciences, and ranks 11th in the world in ecology and the environment. In the face of population growth, climate change, resource scarcity and biodiversity decline, INRAE is building solutions for multi-performing agriculture, quality food and sustainable management of resources and ecosystems.

Working environment, missions and activities

You will be recruited in the Joint Research Unit (INRAE and University of Lorraine) Tree-Microbe Interactions (IAM), which has about 80 staff members, including 46 permanent staff members in three teams.

The IAM Unit’s research focuses on the biology and ecology of interactions between microorganisms and forest trees. It aims to improve our knowledge and understanding of the interactions between trees, fungi (pathogens, symbiotic and saprotrophic) and rhizospheric bacteria that contribute to the functioning and sustainability of forest ecosystems. The host team (Ecology of Forest Pathogenic Fungi), composed of 4 researchers, 2 engineers and assistant engineers and 4 technicians and technical assistants, develops research on the population biology of forest pathogenic fungi. The main research topics addressed are: (i) the determination of the main causes of emergence of forest diseases, (ii) the study of pathogen dispersal and its evolutionary consequences, (iii) the adaptation of pathogens to their hosts and (iv) the impact of emerging pathologies on forest ecosystems.

In this context, you will be in charge of developing innovative epidemiological surveillance methods for the early detection of new tree diseases in the natural environment, monitoring their emergence and assessing their impact on ecosystems. Targeted diseases will mainly be of fungal origin and will cover introductions of invasive parasites, pathogenicity evolution (linked to hybridization phenomena or resistance breakdown) and more gradual emergences linked to climate change or land use changes (especially host densities). Research will focus on a limited number of host-parasite pairs, which will also serve as study models for more fundamental work carried out in the UMR IAM (dispersion, adaptation, hybridization). It will involve experimental work in the field and in the laboratory: etiological characterization of diseases, inoculum detection and monitoring methods (based on quantitative PCR) and monitoring of epidemics and their long-term impact in the natural environment.

Your activity will be carried out in close coordination with the organizations in charge of epidemiological surveillance of forests (Forest Health Department, DSF) and agriculture (Plant Epidemiosurveillance Platform at Avignon) and of plant health risk assessment (ANSES Plant Health Laboratory), at the national level and locally in Nancy. More broadly, you will participate in national and international (cross-border networks, European projects, IUFRO working groups) scientific networks in the field of forest health.

Trips over several days with overnight stays in France and Europe are to be expected.

Training and skills required

PhD in population biology and/or plant epidemiology.

You ideally have a solid background in population biology and/or plant epidemiology. Your possible complementary skills in forest ecology and/or fungi biology will be appreciated, but are not essential. Your practical experience in the use of molecular tools for diagnosis, detection and quantification (quantitative PCR) will be appreciated. Skills in statistics and GIS (Geographic Information Systems) will be appreciated. You have good written (publications and scientific reports) and oral (meetings, conferences) communication skills and ability to communicate to non-academic audiences. You have a good command of written and spoken English and at least basic knowledge of French. You are independent, self-confident, curious and rigorous. You have a good sense of organization and an ability to work in a team and to supervise people (technicians, trainees).

Your quality of life at INRAE

By joining INRAE, you will benefit from:

– 30 days of annual leave + 15 days “Reduction of Working Time” (for a full time job);

– support for parenthood: CESU childcare, leisure benefits;

– skills development schemes: training, career guidance;

– social support: advice and listening, social aid and loans;

– holiday and leisure services: holiday vouchers, accommodation at preferential rates;

– sports and cultural activities;

– collective catering.

How to apply

Download the applicant’s guide (in French only).

Note the profile number: IR20-ECOFA-1

Register here.

Job category: Ingénieur de Recherches

Closing date for registration: May 12, 2020

For more information about the position, please contact:

Dr Pascal FREY

Mobile: 33 631 45 94 07



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PhD Position : Are phytohormones key regulators of root microbiome of poplar trees ?”

The successful applicant will work within the frame of a joint project Plant-Microbe Interface ( between INRA-Nancy-Lorraine and US-DOE-Oak-Ridge National Laboratory (ORNL). The PMI project is directed towards understandingthe dynamic interface that exists between plants, microbes and their environment, using Populus as a model tree and its microbial consortia. The main goals of this joint project are: 1) to define the progression of molecular events that leads to selective, mutualistic plant-microbe partnerships and determine the general applicability of these mechanisms across the spectrum of potential microbiome members;  2) to identify and evaluate the components of the chemical environment that structure the community and 3) to understand the response of the community to biotic and abiotic stresses.

The specific objectives of the thesis are (i) to analyze the respective role of the signaling pathways of major phytohormones (SA, JA, GA, ethylene) in the regulation of root microbiome using poplar as a model system, (ii) to measure the functional consequences of microbiome alteration by these hormonal signaling pathways in terms of nutrition and stress response of poplar. Poplar is an interesting model for several reasons: first, it has an important place in the French forest economy and secondly, its roots are colonized by fungi with distinct functional capacities: (mycorrhizas and endophytes) Finally, it is the only temperate tree that can be genetically manipulated to test hypotheses. In this case, we will investigate whether poplar phytohormones have a structuring role in the composition of root microbial communities.

The main questions that the PhD Student will address are: Which roles do phytohormones play in the structuring of fungal and bacterial communities of poplar roots ? What are the functional consequences of root microbiome alterations? The following two hypotheses will be tested: (i) poplar phytohormones regulate the colonization of the root system by its microbiome; (ii) the modulation of the root microbiome and in particular the endophyte/mycorrhizal balance by phytohormones affects the poplar’s nutrition and resistance to stress.

more information : here


 Claire Veneault-Fourrey / Aurélie Deveau
 INRA Nancy / University of Lorraine
 /

Send Application before 2019 March 15th
If selected, date for interview: 2019 March 26th
If successful, starting date of PhD: 2019 May 1st

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PhD position on poplar rust

English version: see below

Titre du sujet de thèse :

Caractérisation évolutive et fonctionnelle d’un locus d’avirulence chez l’agent de la rouille du peuplier

Encadrants :

Pascal FREY (DR2, HDR), directeur de la thèse

Sébastien Duplessis (DR2, HDR), co-directeur de la thèse

Laboratoire d’accueil :

UMR Interactions Arbres – Microorganismes

INRA/Université de Lorraine

Centre INRA Grand Est Nancy

54280 Champenoux

Université d’inscription de l’étudiant en thèse : Université de Lorraine

Financement : Région Grand Est et ANR.

Résumé de la thèse

L’objectif de la thèse proposée est d’étudier les mécanismes sous-jacents à l’évolution de la pathogénicité d’un agent pathogène, Melampsora larici-populina, responsable de la rouille du peuplier. Grâce à une étude d’association pangénomique (GWAS), nous avons récemment identifié un locus dans le génome de M. larici-populina, qui pourrait correspondre au locus d’avirulence Avr7, dont la mutation est responsable du contournement de la résistance R7 du peuplier. L’objectif de la thèse sera d’étudier cette région génomique et de valider fonctionnellement le locus d’intérêt. Il s’agirait alors du premier gène d’avirulence identifié chez ce champignon. Plusieurs approches complémentaires sont envisagées : (i) une approche de génomique comparative afin de préciser le polymorphisme dans cette région ; (ii) une approche de transcriptomique afin de préciser l’expression du gène d’avirulence et des gènes co-exprimés ; (iii) une approche de génomique fonctionnelle pour tenter d’exprimer la protéine correspondante dans un système hétérologue et de rechercher son interactant dans les cellules végétales. Ces approches originales, mais néanmoins bien maitrisées par l’unité d’accueil, ont pour ambition d’apporter une meilleure compréhension de l’évolution des génomes des agents pathogènes afin d’aider à la définition de stratégies de sélection des plantes (en particulier le peuplier) pour une résistance durable.

Candidature :

Envoyer un CV, une lettre de motivation et les coordonnées de 2 personnes de référence à Pascal Frey ( et Sébastien Duplessis ( avant le 1er septembre 2018.

Compétences recherchées

Le(la) candidat(e) devra avoir de bonnes compétences en génétique, génomique, bioinformatique et en biologie moléculaire. Il(elle) devra avoir des connaissances de base en écologie et un intérêt pour la biologie évolutive et la pathologie végétale. Un goût prononcé pour le travail en équipe est indispensable.


Title of the thesis

Evolutionary and functional characterization of an avirulence locus in the poplar rust fungus.


Pascal FREY (Senior scientist), main supervisor

Sébastien DUPLESSIS (Senior scientist), co-supervisor

Host laboratory

Department of Tree – Microbe Interactions

INRA / University of Lorraine

INRA Grand Est Nancy research centre

54280 Champenoux

Funding : Region Grand Est and ANR (French National Research Agency). Duration 3 years. Monthly net salary about €1400.

Thesis summary

The objective of this thesis is to study the mechanisms underlying the evolution of pathogenicity of the poplar rust fungus, Melampsora larici-populina. Through a genome-wide association study (GWAS), we recently identified a locus in the genome of M. larici-populina, which could correspond to the avirulence locus Avr7, whose mutation is responsible for R7 resistance breakdown in poplar. The objective of the thesis will be to study in fine details this genomic region and to functionally validate this avirulence locus. This would be the first avirulence gene identified in this biotrophic fungal species. Several complementary approaches will be engaged: (i) a comparative genomics approach in order to list the polymorphisms in this region; (ii) a transcriptomic approach to clarify the expression of the avirulence gene and the co-expressed genes; (iii) a functional genomic approach to attempt to express the corresponding protein in a heterologous system and to search for its interactant in plant cells. These original approaches, but nevertheless well mastered by the proposing team, aim to provide a better understanding of the evolution of the pathogen genomes in order to help define plant selection strategies for durable resistance, especially for poplar.


Send CV, cover letter and contact details of two referees to Pascal Frey ( and Sébastien Duplessis ( before September 1, 2018.

Required skills

The candidate should have good skills in genetics, genomics, bioinformatics and molecular biology. He/she should have basic knowledge in ecology and an interest in evolutionary biology and plant pathology. A taste for teamwork is essential. Knowledge of French will be an asset but is not mandatory.


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Offre de CCD de 2 ans niveau Ingénieur d’Etudes

Comment identifier les foyers de Phytophthora ramorum en France ?

Encadrants : Benoit Marçais, UMR IAM, INRA-Nancy & Renaud Ioos, Laboratoire de la Santé des Végétaux, ANSES Nancy


Phytophthora ramorum est un parasite polyphage infectant des arbres de familles très diverses (en particulier Lauracées, Fagacées, Ericacées et Pinacées). Il a été initialement décrit pour ses dégâts sur Fagacées dans l’ouest des USA (« Sudden Oak Death »). Mais, il a ultérieurement démontré sa capacité à provoquer des épidémies sévères sur des hôtes sur lesquels il n’était pas du tout attendu : alors que le hêtre a une sensibilité reconnue et était la cible attendue de l’épidémie en Europe, l’essence fortement impactée en Grande-Bretagne a finalement été le mélèze du japon (« Sudden Larch Death »). Toutefois, des Fagacée tels que le chêne vert et surtout le châtaignier restent des candidats possibles pour un développement ultérieur de l’épidémie car, comme le mélèze, ils peuvent multiplier l’inoculum et présentent une sensibilité de l’écorce significative. Ce parasite représente donc un risque majeur et est classé comme organisme de quarantaine en Europe (soumis à éradication).

Phytophthora ramorum a été identifié en Bretagne en 2017 dans plusieurs peuplements de mélèzes. Le projet proposé est centré sur le développement de méthodes permettant d’identifier de façon fiable les foyers de P. ramorum en Bretagne afin d’optimiser les mesures de gestion de ces derniers. L’accent sera mis sur la capacité à détecter le parasite le plus précocement possible dans divers supports (air, eau, litière, plante), soit par isolement mycologique, soit par méthode de détection moléculaire (qPCR), dans le but d’améliorer la surveillance du parasite en milieu naturel, en particulier dans les cours d’eau, et de limiter sa propagation. Dans un second temps, l’hypothèse que le mélèze est le seul hôte compétent à considérer sera testée. Pour cela, la capacité de différents ligneux à être infectés, à produire de l’inoculum en milieu naturel et a permettre la persistance du parasite dans l’environnement sera évaluée en ciblant préférentiellement les hôtes potentiels (châtaignier, chêne vert, frêne, rhododendron, viornes, myrtille, robinier …).

Pour réaliser ce projet, nous recrutons un(e) ingénieur(e) d’étude pour une durée de 2 ans à partir d’Août ou Septembre 2018. Le candidat(e) sera en charge des développements méthodologiques sur les techniques de détection à partir de tissus infectés ou d’eau de rivière (méthodes moléculaires ou de mycologie) et de la prospection de terrain (plusieurs semaines de déplacement dans le Finistère par ans). Une formation ou une expérience de travail en laboratoire (techniques de biologie moléculaire et de microbiologie) et / ou de travail sur le terrain dans le domaine de la protection des plantes est demandée. Le poste sera basé à l’INRA Grand Est à Champenoux.

Contact : ;

La date limite de candidature est fixée au 15/07/18.

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PhD Position

English version below

Offre de thèse : Identification et caractérisation d’enzymes microbiennes pour la dépollution de bois traités.

Chaque année en France, 1,4 Mt de déchets sont produites sous forme de bois traités. Actuellement, aucune filière de recyclage de ces bois n’est disponible à cause de la toxicité des composés utilisés en amont pour leur préservation. L’objectif de ce projet est de développer une nouvelle stratégie utilisant des microorganismes et/ou des enzymes microbiennes comme biocatalyseurs pour l’élimination des composés toxiques dans les bois traités dans le but de (i) limiter l’impact de ces molécules sur l’environnement et la santé humaine, et (ii) à terme pouvoir utiliser cette source importante de déchets comme biomasse valorisable au niveau industriel. L’hypothèse de travail est basée sur le fait que certains microorganismes isolés ou en consortium possèdent des capacités accrues de résistance aux fongicides utilisés, des systèmes enzymatiques performants pour la dégradation de molécules complexes, et la capacité de sécréter des sidérophores pour le piégeage des métaux. Le travail du candidat recruté consistera à tester les capacités de champignons et bactéries à dépolluer des bois traités et comprendre les mécanismes moléculaires impliqués grâce à des approches de génomique, transcriptomique et protéomique. Ces approches à grande échelle permettront de sélectionner des protéines candidates qui seront produites en système hétérologue et caractérisées plus finement au niveau biochimique et fonctionnel.

L’Unité Mixte de Recherche INRA/Université de Lorraine 1136 Interactions Arbres/Micro-organismes (IAM) étudie la biologie et l’écologie des interactions entre micro-organismes et arbres forestiers. Les recherches de l’Unité visent à améliorer notre connaissance et notre compréhension des interactions qui s’établissent entre les arbres, les champignons et les bactéries rhizosphériques, et qui contribuent au fonctionnement et à la durabilité des écosystèmes forestiers.

L’UMR IAM  est organisée en trois équipes soutenues par des plateaux techniques :

Equipe Réponse aux stress et régulation redox

Equipe Ecogénomique des interactions

Equipe Ecologie des champignons pathogènes forestiers

L’Unité IAM fait partie du Laboratoire d’Excellence ARBRE et est reconnue par l’ “AgreenSkills mobility programme“.

Le candidat s’intégrera dans l’équipe Réponse aux stress et régulation redox de l’UMR IaM 1136 située sur le campus de la Faculté des Sciences et Technologie de l’Université de Lorraine à Vandoeuvre-lès-Nancy. Des compétences en microbiologie et biologie moléculaire sont requises. Des compétences en biochimie et bioinformatique seraient un avantage supplémentaire.

Contact : Mélanie Morel-Rouhier

Email :

Site Web :

English version:

 Identification and characterization of microbial enzymes for wood decontamination.

 1.4 Mt of wood wastes are produced each year in France and no recycling is possible because of the toxicity of the products used for wood preservation. The main objective of the proposal is to develop a new strategy using microorganisms and/or microbial enzymes as biocatalysts for wood decontamination. The aim is to (i) limit the impact of the toxic compounds on the environment and human health and (ii) be able to recycle and valorize wood waste biomass. The working hypothesis is based on the fact that microorganisms either as single species or in consortium exhibit increased ability to resist to the toxic compounds, possess efficient enzymatic systems for complex molecules degradation and are able to secrete siderophores for metal sequestration. The PhD project will be to test the ability of fungi and bacteria to detoxify wood waste and understand the molecular mechanisms involved in the process, thanks to genomic, transcriptomic and proteomic approaches. These global analyses will help identifying molecular actors for further biochemical and functional characterization after production and purification of the recombinant proteins in heterologous systems.

Research projects performed by the UMR INRA/Lorraine University 1136 «Interactions Arbres-Microorganismes » are dedicated to the biology and the ecology of the interactions between microorganisms and forest trees.

The ultimate goals of these projects are to improve our knowledge and our understanding of the interactions that take place between trees, fungi and bacteria, and that contribute to the sustainable functioning of forest ecosystems.

The Department is organized into three teams:

  • Stress response and redox regulation team
  • Ecogenomics of Interactions team
  • Ecology of forest pathogenic fungi team

and is supported by technical platforms

IAM is member of the Lab of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems (ARBRE) and is recognized by the AgreenSkills mobility programme for the quality of the support offered to postdoctoral research fellows that have been awarded an AgreenSkills Fellowship

The candidate will join the team « Stress response and redox regulation » located at the Faculty of Science and Technology (Lorraine University) at Vandoeuvre-lès-Nancy. Skills in microbiology and molecular biology are required. Skills in biochemistry and bioinformatics could be an advantage.

Contact : Mélanie Morel-Rouhier

Email :

Web site :

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PhD position: Ecology and genomics of the bacterial communities

Title: Ecology and genomics of the bacterial communities associated to minerals in forest soils 

PhD position at INRA

Key words: low-input ecosystems, minerals, mineral weathering, minerals, bacteria, environmental microbiology

 Profile and skills required:

The candidate will have skills in microbial ecology, molecular biology, bacteriology, and possibly in biostatistics / bioinformatics. The candidate needs to be motivated by academic research.


In temperate regions, minerals and rocks represent one the main source of nutritive cations in the soil of low-input ecosystems such as forests. In such nutrient-poor and non-amended environments, the access and the recycling of the nutritive cations are key processes for tree growth and productivity. However, these nutritive cations are almost inaccessible to the tree roots as they are entrapped into the organic matter (OM) or into the soil minerals/rocks. Consequently, the mineral weathering process is essential as it allows the restoration of soil fertility and provides the inorganic nutrients for tree growth. This aspect is especially reinforced in managed forests where the nutrients coming from the OM are lost during wood exportation. In this context, the soil mineral/rock interfaces and their associated microbiome are essential for the replenishment of the soil fertility. However, all the minerals/rocks do not have the same chemical composition (nutritive interest) and the same physico-chemical properties (reactivity). Indeed, some minerals/rocks are highly weatherable and nutritive (i.e., apatite), while some others are recalcitrant and poorly nutritive (i.e., quartz). Consequently, the impact of these different minerals on nutrient cycling and plant nutrition can strongly vary. While, the implication of microorganisms in the mineral weathering process and plant nutrition is established, the intrinsic parameters (i.e., mineral properties) and the extrinsic parameters (i.e., the environmental factors) regulating this implication as well as the molecular mechanisms involved remain unknown or poorly understood.

Objectives and methods

The PhD thesis will aim at determining the molecular mechanisms used by bacteria to weather minerals and to identify the environmental drivers involved in the interaction, the colonization and the weathering of minerals by bacterial communities in a context of nutrient-poor forest soil. The project is based on the hypothesis that minerals represent a nutritive reserve, an important reactive interface and microbial habitat for adapted microorganisms (i.e., the mineralosphere; Uroz et al., 2015). The molecular work (transcriptomic, proteomic, mutagenesis and cloning) will be done on an effective mineral weathering model bacterial strains (strain PMB3(1) of Collimonas), which genome is sequenced. The microbial ecology part will be done on mineral incubated in soil conditions since 2012 on the forest experimental site of Montiers. This part will be developed using soil sciences, culture-dependent (bacterial collection, functional bioassays) and -independent (metabarcoding targeting 16S rRNA genes) tools.

Labs and information on the supervision:

The candidate will integrate the mixt unite INRA/University of Lorraine IAM (Tree microbes interactions;, which aims at improving our knowledge and our understanding of the interactions that take place between trees, fungi, bacteria, and soil, and that contribute to the sustainable functioning of forest ecosystems. The candidate will be member of the Ecogenomic team. As the project is at the interface with the mineralogy and the soil science, the candidate will be also member of the Biogeochemistry of forest ecosystem (BEF) unit.

The PhD thesis will be supervised by Stephane UROZ (IAM/BEF; DR2 INRA and HdR: and Marie-Pierre TURPAULT (BEF; DR2 INRA and HdR:

To candidate, provide a recommendation letter as well as a CV to Stephane Uroz before the 20th of April.

Coordonnées e-mail :

Téléphone   : Renseignements

Stéphane Uroz

Some recent references on the topic

– Uroz, S.* and Oger, P. (2017) Caballeronia mineralivorans sp. nov., isolated from oak-Scleroderma citrinum mycorrhizosphere. Systematic and Applied Microbiology. In press.

– Colin, Y., Nicolitch, O., Turpault, M-P., Uroz, S.* (2017) Mineral type and tree species determine the functional and taxonomic structure of forest soil bacterial communities. Applied and Environmental Microbiology. 83(5). pii: e02684-16. doi: 10.1128/AEM.02684-16.

– Nicolitch, O., Colin, Y., Turpault, M-P., Uroz, S.* (2017) Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees. Soil Biology and Biochemistry. 103, 429-445.

– Uroz S.*, Oger P. , Tisserand E. , Cébron A., Turpault M-P., Buée M., De Boer W., Leveau J.H.J., and P. Frey-Klett. (2016) Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Scientific Reports. 6: 27756.

– Kelly, LC., Collin, Y., Tupault, M-P. and Uroz, S.* (2015) Mineral type and solution chemistry affect the structure and composition of actively growing bacterial communities as revealed by bromodeoxyuridine immunocapture and 16S rRNA pyrosequencing. Microbial Ecology. Volume 72, 428–442.

– Uroz, S.*, Kelly, L.C., Turpault, M-P., Lepleux, C., and P. Frey-Klett. (2015) The Mineralosphere concept: mineralogical control of bacterial communities. Trends in Microbiology. 23, 751–762. (IF=9.186)

– Uroz, S.*, Tech, J.J., Sawaya, N.A., Frey-Klett, P., and J.H.J. Leveau. (2014) Structure and function of bacterial communities in ageing soils: Insights from the Mendocino ecological staircase. Soil Biology and Biochemistry. 69, 265–274

– Uroz, S.*, Calvaruso, C., Turpault, MP and Frey-Klett, P. (2009) The microbial weathering of soil minerals: Ecology, actors and mechanisms. Trends in Microbiology. 17:378-387.

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Postdoctoral position

Funded by the Lab of Excellence ARBRE :

A post-doc position is offered in the UMR Tree-Microbe Interactions and Biogeochemical Cycles in Forest Ecosystems Departments

postdoctoral position

Fate of lignin altered by Brown Rot And White rOt fungi


In forest ecosystems, the wood rotting Basidiomycota fungi play a central role in woody litter degradation. They are indeed the only microorganisms able to remove or circumvent the lignin barrier that hinders access to plant polysaccharides; the major plant tissues that can support microbial growth. Wood-rotting fungi are categorized as white rot or brown rot fungi. White rot fungi degrade all components of plant cell walls, including cellulose, hemicellulose and lignin, primarily using enzymatic systems. They cannot grow on lignin alone but mineralize a large proportion of it into CO2 and H2O, making energy-rich polysaccharides accessible to the fungi and other microorganisms. Brown rot fungi employ a different biodegradative strategy. They generate hydroxyl radicals by a chelator-mediated Fenton (CMF) reaction to remove all carbohydrate from plant tissues, leaving behind them modified lignin. These hydroxyl radicals depolymerize lignin and carbohydrate, enabling the diffusion of oligosaccharide into wood cell lumen where fungal enzymes are located. The brown rot fungi have been shown in recent molecular clock genomic analyses to have evolved from ancestral saprotrophic white rot fungi in a process accompanied by reduction of some cellulases and loss of all lignin-modifying enzymes. It has been suggested, but not verified, that brown rot fungi have cast off the energetically expensive enzyme system of lignocellulose degradation employed by the white rot fungi. In this context, we want to explore the relationship between the strategies developed by brown rot and white rot fungi and the persistence of altered wood residues. The proposed project pursues two main objectives. (i) to compare the energy cost and gains associated with the contrasted biodegradation strategies employed by white rot and brown rot fungi. (ii) to explore the relationships between the strategies developed by brown rot and white rot fungi and the chemical properties of the altered residues and their persistence in soil. This imply to focus on the mechanisms involved in the wood degradation by white rot and brown rot fungi, with a special emphasis on Fenton, and chelator-mediated Fenton reaction mechanisms


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Job: Research engineer in bioinformatics

Research engineer in bioinformatics and data analysis from microbial metagenomics research using microbial genomic resources

(INRA permanent position open in 2017 – application before 16th March)

IR BioInfo position_INRA-IAM_Nancy (Eng) 


Research engineer in bioinformatics and data analysis


The position is open in the “Trees / Microorganisms Interactions” research Unit (INRA / Lorraine University) (

The recruited person will work in collaboration with scientists of the unit and with a permanent bioinformatics engineer from the technical platform in bioinformatics. This person will develop an expertise in microbial metagenomics, and particularly in fungal metagenomics / metatranscriptomics, and he / she will be involved in national (National Research Agency, Meta-omics and Microbial Ecosystems (MEM) meta-program) and international research programs (US Department of Energy Joint Genome Institute; e.g. Metatranscriptomics of Forest Soil Ecosystems).


The huge microbial richness (bacteria and fungi) in forest soils remains little explored in spite of fundamental or applied research opportunities (understanding of the functioning of ecosystems, analysis of functional diversity, extended phenotype of host plants, forestry management, ecosystem services, bioenergy). The study of this microbial diversity and their trophic and functional interactions requires integrative approaches (“meta-omics”) and powerful analysis and data mining. The use and development of bioinformatics tools for New Generation Sequencing (NGS) data analysis from microbial (prokaryotic and eukaryotic) metagenomic and metatranscriptomic researches will require:

(i) to develop and use appropriate bioinformatics procedures

(ii) to store, search, and compare meta-omic data sets

(iii) to identify the gene networks and associated key functions (indicators) controlling these complex systems.

Finally, in interaction with colleagues of the technical platform, the recruited person will also lead and deploy the hardware and software architecture and its application (installation, assistance, training, evaluation).


SKILLS AND Personal Qualities

– PhD in biology, bioinformatics, computer science or Engineer degree from graduate schools or equivalent.

– Professional experience in biology and/or in genomics / metagenomics, ideally applied to microbiology, molecular ecology or plant / microbe physiology. Good knowledge of programming languages and tools for building / managing databases adapted to the analysis of recommended metagenomes.

– One or more proven experiments in (meta) comparative genomics of gene repertoires; Computer processing of sequencing data (HiSeq, MiSeq, PacBio …); Quantification of fungal gene expression (trimming, mapping, normalization); Differential expression and analysis of co-expression networks.

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Post-doc position

Using Ascobolus immersus as a genetic model for understanding the sexual reproduction of the truffle.

Job description: The successful applicant will work for a joint project between INRA-Nancy-Lorraine, University Paris Sud and CNR-IBBR Perugia.

The aims of the project AscoTube are to 1) use Ascobolus immersus as a genetic model species to assess the truffle strains recognition in vitro and 2) better understand the truffle sexual reproduction in situ.

The successful applicant is expected:

1) to set cassettes and transform A. immersus with mating type genes from both Tuber melanosporum and Tuber indicum, previously identified by means of genomic and genetic tools;

2) to test the intra and inter specific recognition of these genes;

3) to follow the dynamics of strains of different mating type in the soils of truffle a plantation, in the root system and in the fructification.


PhD in Microbiology or Molecular biology or related science.

Experience in molecular genetics, molecular biology as well as knowledge on fungal genetic transformation, soil DNA extraction and quantitative PCR will be an advantage.

Communicate in English with other members of the lab as well as other members of the project.

Working language(s): English, French and Italian


Applicants should submit (1) a cover letter describing their research interests and background, (2) a detailed CV , and (3) the contact details of three referees.


Claude Murat, INRA Centre Nancy-Lorraine, UMR1136, 54280 Champenoux, France,

Fabienne Malagnac, University Paris-Sud, UMR 9198, 91400 Orsay cedex, France,

Francesco Paolocci, CNR Perugia, IBBR, Via Madonna Alta, 130, 06128 Perugia, Italy,

Research Teams’ Publications

Employer: INRA Nancy-Lorraine

Department & Research Team: Tree-microbe-interactions UMR1136

Place of work: Nancy /France, Orsay/France (for short period) and Perugia/Italy (for 3-6 months)

Duration: 12 months starting September 2016

Salary & Working hours: INRA Post-Doc depending on experience, 38.5h/week

Application deadline: July 15th, 2016




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Post-doc position

Towards new eco-friendly strategies to limit fungal attacks on plants and wood

Project: The adaptive capacity of a target population of fungi is intimately correlated with the selective pressure exerted by its local niche. This is due to the chemical specificity of these niches, which could be rich in secondary metabolites in the case of plants or rich in lignin-derived compounds in the case of wood. We have shown that lignolytic fungi have expanded detoxification systems composed by cytochrome P450 monooxygenases (P450s) and conjugating enzymes, allowing them to detoxify a large panel of toxic compounds that could be released during the wood degradation process. These enzymes are known to be highly versatile (i.e. they accept various substrates), with high catalytic promiscuity (i.e. only small sequence variations could modify their catalytic properties and the type of reactions catalyzed). Hence, by rapidly acquiring new functions under environmental pressures (neofunctionalization), these enzymes are part of the mechanisms developed by fungi to adapt to their changing environment. Thus, thanks to their efficient detoxification and antioxidant systems, fungi are amazing organisms able to resist hostile environments.

This project aims both at evaluating the antifungal capacity of various environmental extracts from plants and wood, and at delineating the underlying molecular mechanisms explaining the growth phenotypes of various fungal strains observed in presence of the tested extracts. By coupling these two approaches, we expect identifying natural extracts with antifungal activity and deciphering how they affect fungal metabolism. The expected results could help better understanding fungal physiology, evolutionary history and adaptation, knowledge that are required for developing new eco-friendly strategies to limit fungal attacks on crops and on wood material.

Required skills: This project combines genomic, transcriptomic, physiological, biochemical and chemical approaches. The candidate needs to have a strong expertise in molecular biology, fungal microbiology and bioinformatics. For this project, he will benefit from the expertise of many scientists in the research unit (see website: with a strong background in these disciplines and from external existing collaborations for sample extraction and chemical analyses, fungal genetic transformation, or for protein structural analysis.

Place of work: Stress Responses and Redox Regulation” team ( Faculty of sciences, Vandoeuvre-lès-Nancy, France

Form of employment: Temporary employment for one year funded by the Région Lorraine and Lorraine University, possibly renewable and starting in autumn 2016.

Applicants should sent a CV, including the names and contact details of three referees, and a covering letter addressing the selection criteria to Dr Mélanie Morel-Rouhier, e-mail:, phone: +33 3 83 68 42 28.

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