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.

Context

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; https://mycor.iam.inrae.fr/IAM/), 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: https://mycor.iam.inrae.fr/IAM/?page_id=727) and Marie-Pierre TURPAULT (BEF; DR2 INRA and HdR: https://www6.nancy.inra.fr/bef/Personnel/Scientifiques/Marie-Pierre-TURPAULT).

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

Coordonnées e-mail :

stephane.uroz@inra.fr

Téléphone   : Renseignements

Stéphane Uroz 03.83.39.40.81

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.

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

Project

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

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) 

JOB TITLE

Research engineer in bioinformatics and data analysis

http://jobs.inra.fr/offers/emploi_perm/concours/ce-it/?campagne=23129&intitule=concours&concours=105069

Environment

The position is open in the “Trees / Microorganisms Interactions” research Unit (INRA / Lorraine University) (https://mycor.iam.inrae.fr/IAM/?page_id=2000).

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).

CONTEXT AND ACTIVITIES

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.

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.

Requirements

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

Application

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.

Contact

Claude Murat, INRA Centre Nancy-Lorraine, UMR1136, 54280 Champenoux, France, claude.murat@nancy.inra.fr

Fabienne Malagnac, University Paris-Sud, UMR 9198, 91400 Orsay cedex, France, fabienne.malagnac@u-psud.fr

Francesco Paolocci, CNR Perugia, IBBR, Via Madonna Alta, 130, 06128 Perugia, Italy, francesco.paolocci@ibbr.cnr.it

Research Teams’ Publications

https://mycor.iam.inrae.fr/IAM/?page_id=318

http://www.i2bc.paris-saclay.fr/spip.php?article69

http://ibbr.cnr.it/ibbr/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

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: https://mycor.iam.inrae.fr/IAM/) 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 (https://mycor.iam.inrae.fr/IAM/?page_id=17). 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: Melanie.Morel@univ-lorraine.fr, phone: +33 3 83 68 42 28.

Institution: INRA, UMR IAM, Lab of Excellence ARBRE

Location: Nancy, France

Job Description: 

A postdoctoral researcher position is available immediately in the lab of Francis Martin at the Tree-Microbe Interactions Department at INRA in Nancy, France. Martin’s lab uses computational approaches to study how saprotrophic and symbiotic (mycorrhizal) fungi evolve and adapt to their environments. Ongoing projects fall into the following broad areas: 1) Studying the emergence of the symbiotic mutualism in fungal and tree species by phylogenomics; 2) Characterization of symbiosis-related genes by using comparative transcriptomics; and 3) Deciphering genomic signatures of fungal adaptations to carbon decay and sequestration in forest habitats by metatranscriptomics. More information about Martin’s lab.

Qualified applicant must have a Ph.D. in bioinformatics, computational biology, computer science, evolutionary biology or a related field with background and strong interest in molecular evolution of Fungi. The ideal candidate will already have some experience working with large genomic data sets from sequenced fungi or plants. This position requires a high level of proficiency in programming skills, and experience applying computational methods to genomic data is highly desirable. Applicants must possess good communication skills and be fluent in both spoken and written English (or French). Strong skills in the use of unix-based computer softwares, critical thinking, problem-solving abilities, and the ability to work semi-independently are also required. The responsibilities will include pipeline development for analyses of next-generation data sets and utilization of high-performance computing facilities.

The successful candidate should anticipate contributing to a variety of ongoing collaborative research projects with the Joint Genome Institute, including the 1000 Fungal Genomes project and the Mycorrhizal Genomics Initiative, with teams across France, Europe and the United States. In addition to becoming a part of a vibrant research and educational environment, the incumbent can take advantage of professional development programs offered by Laboratory of Excellence ARBRE.

The initial appointment is for one year with the possibility of renewal for up to two additional years contingent upon performance and funding. Review of applications will begin immediately and continue until the position is filled. Start date is July 1st, 2016 at the latest.

Interested applicants should send a single PDF file containing CV, one-page statement of research interests and contact information of three referees to Francis Martin at fmartin[at]nancy.inra.fr.

English version: see below

Titre du sujet de thèse :

Architecture génétique de traits d’histoire de vie liés au pouvoir pathogène de l’agent de la rouille du peuplier.

Encadrants :

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

Fabien HALKETT (CR1), co-encadrant

Stéphane DE MITA (CR2), co-encadrant

Laboratoire d’accueil :

UMR Interactions Arbres – Microorganismes

INRA/Université de Lorraine

Centre INRA Nancy-Lorraine

54280 Champenoux

https://mycor.iam.inrae.fr/IAM/

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

Ecole doctorale : RP2E (Ressources, Procédés, Produits, Environnement)

Financement (acquis) : INRA Département EFPA (Ecologie des Forêts, Prairies et milieux Aquatiques) & Région Lorraine

Résumé de la thèse

L’objectif de la thèse est d’étudier l’architecture génétique de traits d’histoire de vie liés au pouvoir pathogène de l’agent de la rouille du peuplier, Melampsora larici-populina. Nous faisons l’hypothèse que l’agressivité du champignon risque d’augmenter suite au déploiement au champ de nouveaux cultivars de peuplier portant des résistances quantitatives. L’objectif général de cette thèse est de mieux comprendre le potentiel d’évolution de l’agressivité des agents pathogènes, afin d’alimenter la réflexion sur les stratégies de sélection de résistances durables, en particulier chez le peuplier.

Contexte et enjeux

Le peuplier constitue une production importante en Europe pour le bois d’industrie et sa contribution à des filières énergétiques est en nette progression. La rouille du peuplier, causée par le champignon pathogène Melampsora larici-populina constitue la principale contrainte phytosanitaire de la populiculture en Europe et dans le monde. La sélection de variétés de peupliers résistants à la rouille était basée pendant des décennies sur la sélection d’hybrides F1 interspécifiques, portant majoritairement des résistances qualitatives monogéniques et dominantes, basées sur la relation gène-pour-gène. Cependant, les déploiements successifs au champ de cultivars de peuplier à résistances qualitatives se sont soldés par les contournements systématiques de ces résistances par l’agent pathogène, témoignant de leur caractère non durable à moyen et long terme (Xhaard et al., 2011). La connaissance du déterminisme génétique des facteurs de virulence qui causent les contournements de résistance serait souhaitable, tant sur le plan fondamental (interactions entre loci d’avirulence et loci de résistance) que sur le plan appliqué (stratégies de gestion spatio-temporelle des résistances qualitatives).

Depuis une vingtaine d’années, la recherche de résistances plus durables a conduit les améliorateurs à s’orienter vers la sélection de résistances quantitatives, à déterminisme génétique plus complexe. Cependant, la résistance quantitative peut également s’éroder du fait de l’augmentation de l’agressivité des agents pathogènes, définie comme la composante quantitative du pouvoir pathogène (Pariaud et al., 2009). Par conséquent, il est primordial d’étudier l’évolution potentielle des traits d’agressivité et leurs éventuels compromis évolutifs (Lannou, 2012).

De plus, la sélection de traits favorables peut conduire à des trade-offs, c’est-à-dire des compromis entre traits d’histoire de vie (Laine & Barrès, 2013). Les trade-offs entre traits peuvent refléter des stratégies d’adaptation de l’agent pathogène à l’hôte (compétition et/ou dispersion) suivant les traits sur lesquels les individus investissent prioritairement (Pariaud et al., 2009) et peuvent donc jouer un rôle primordial au cours des processus épidémiques. L’étude de ces trade-offs entre traits quantitatifs peut ainsi permettre de mieux comprendre les paramètres qui conditionnent une épidémie.

Hypothèses de travail et objectifs de la thèse

L’hypothèse principale est que l’agressivité de M. larici-populina pourrait augmenter suite au déploiement de nouveaux cultivars de peuplier portant des résistances quantitatives. Par conséquent, une connaissance de l’architecture de ces traits et de leurs trade-offs éventuels devrait permettre d’orienter les stratégies de sélection pour des résistances durables (McDonald & Linde, 2002).

L’objectif central de la thèse proposée est d’étudier l’architecture génétique des traits d’histoire de vie qualitatifs (facteurs de virulence) et quantitatifs (composantes d’agressivité) chez l’agent de la rouille du peuplier. Pour cela, les techniques de NGS (Next Generation Sequencing) seront utilisées.

Les objectifs détaillés de ce projet de thèse seront :

1. de cartographier les facteurs de virulence et les QTL d’agressivité par une approche de re-séquençage de descendances (autofécondations et allofécondations) obtenues par croisements contrôlés de M. larici-populina (Pernaci et al., 2014 ; Pernaci 2015).
2. de cartographier ces mêmes traits qualitatifs et quantitatifs par une approche de GWAS (Genome-Wide Association Study ; Hamblin et al., 2011) sur des populations naturelles de M. larici-populina.
3. d’étudier les compromis évolutifs (trade-offs) entre ces traits, qui peuvent conditionner l’adaptation de M. larici-populina aux résistances du peuplier.

Publications récentes des responsables de la thèse, en rapport avec le projet proposé :

Pernaci, M., De Mita, S., Andrieux, A., Pétrowski, J., Halkett, F., Duplessis, S., and Frey, P. (2014). Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. Frontiers in Plant Science 5, 454.

Persoons, A., Morin, E., Delaruelle, C., Payen, T., Halkett, F., Frey, P., De Mita, S., and Duplessis, S. (2014). Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors. Frontiers in Plant Science 5, 450.

Barrès, B., Dutech, C., Andrieux, A., Halkett, F., and Frey, P. (2012). Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure. Molecular Ecology 21, 4996-5008.

Xhaard, C., Barrès, B., Andrieux, A., Bousset, L., Halkett, F., and Frey, P. (2012). Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Molecular Ecology 21, 2383-2398.

Xhaard, C., Fabre, B., Andrieux, A., Gladieux, P., Barrès, B., Frey, P., and Halkett, F. (2011). The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication. Molecular Ecology 20, 2739-2755.

Autres références bibliographiques

Hamblin, M.T., Buckler, E.S., and Jannink, J.L. (2011). Population genetics of genomics-based crop improvement methods. Trends Genet 27, 98-106.

Laine, A.L., and Barrès, B. (2013). Epidemiological and evolutionary consequences of life-history trade-offs in pathogens. Plant Pathology 62, 96-105.

Lannou, C. (2012). Variation and selection of quantitative traits in plant pathogens. Annual Review of Phytopathology 50, 319-338.

McDonald, B.A., and Linde, C. (2002). Pathogen population genetics, evolutionary potential, and durable resistance. Annual Review of Phytopathology 40, 349-379.

Pariaud, B., Ravigné, V., Halkett, F., Goyeau, H., Carlier, J., and Lannou, C. (2009). Aggressiveness and its role in the adaptation of plant pathogens. Plant Pathology 58, 409-424.

Pernaci, M. (2015). Etude des traits d’histoire de vie de Melampsora larici-populina, agent de la rouille du peuplier : de leur déterminisme génétique à leurs conséquences évolutives. Thèse de Doctorat, Université de Lorraine, 200 p.

Candidature :

Envoyer un CV, une lettre de motivation et les coordonnées de 2 personnes de référence à Pascal Frey (pascal.frey@nancy.inra.fr) avant le 1er octobre 2015.

Compétences recherchées

Le(la) candidat(e) devra avoir de bonnes compétences en génétique (génétique quantitative, génétique des populations, génomique) et en bioinformatique. 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

Genetic architecture of pathogenicity-associated life history traits in the poplar rust fungus.

Advisors:

Pascal FREY (Senior scientist), main supervisor

Fabien Halkett (Junior scientist), co-supervisor

Stéphane DE MITA (Junior scientist), co-supervisor

Host laboratory

Department of Tree – Microbe Interactions

INRA / University of Lorraine

INRA Nancy-Lorraine Research Centre

54280 Champenoux

https://mycor.iam.inrae.fr/IAM/

 Funding (acquired): INRA EFPA Scientific division (Ecology of Forests, Grasslands and Aquatic environments) & Region Lorraine. Duration 3 years. Monthly net salary about €1400.

 Thesis summary

The aim of the thesis is to study the genetic architecture of life history traits related to pathogenicity in the poplar rust fungus, Melampsora larici-populina. We assume that the aggressiveness of the fungus may increase following the deployment in the field of new poplar cultivars with quantitative resistance. The general objective of this thesis is to better understand the potential evolution of aggressiveness in pathogens, to fuel the debate on sustainable resistance breeding strategies, especially in poplar.

Context and challenges

Poplar is an important product for the wood industry worldwide and its contribution to energy systems has increased recently. Poplar rust, caused by the pathogenic fungus Melampsora larici-populina, is the main phytosanitary constraint for commercial poplar cultivation in Europe and worldwide. In the last 50 years many rust-resistant cultivars were bred and released, but each of the qualitative resistance genes (i.e. major resistance genes) released have been overcome by pathogen evolution within a short period (Xhaard et al., 2011). Qualitative resistance is particularly subject to breakdown by pathogen evolution for perennial hosts, such as poplar trees, because of the wide inequality between the pathogen’s rapid generation time and the time needed to deploy new host varieties. Knowledge of the genetic determinism of the virulence factors leading to resistance breakdown would be beneficial both from an academic perspective (e.g. to decipher interactions between avirulence loci and resistance loci) and from an applied perspective (e.g., for determining strategies of spatiotemporal management of qualitative resistance).

The failure of qualitative resistances to control poplar rust has prompted breeders to search for quantitative resistance, which is supposed to be more durable. However quantitative resistance can also be challenged by the evolution of aggressiveness, which is the quantitative component of pathogenicity, determined by several disease-associated traits (Pariaud et al., 2009). Thus it is of primary importance to assess the potential evolution of aggressiveness traits in the pathogen and the potential trade-offs between these traits (Lannou, 2012; Laine & Barrès, 2013).

Working hypotheses and objectives of the thesis

The main hypothesis is that the aggressiveness of M. larici-populina could increase following the deployment of new poplar cultivars with quantitative resistance. Therefore, knowledge of the architecture of aggressiveness traits and their potential trade-offs would be useful in order to guide breeding strategies towards durable resistance (McDonald & Linde, 2002).

The central aim of the proposed thesis is to study the genetic architecture of qualitative (virulence factors) and quantitative (aggressiveness components) traits in the poplar rust fungus. To this aim, whole-genome re-sequencing techniques will be used.

The detailed objectives of this PhD project will be:

1. To map avirulence loci and aggressiveness QTLs through whole-genome re-sequencing of selfed and/or outcrossed progenies obtained from controlled crosses of M. larici-populina (Pernaci et al, 2014; Pernaci 2015).
2. To map the same kind of qualitative and quantitative traits through an approach of Genome-Wide Association Study (GWAS; Hamblin and al., 2011) in natural populations of M. larici-populina.
3. To assess the potential trade-offs between those traits, which can condition the adaptation of the pathogen to the resistance of the host.

 Recent publications of the thesis advisors in relation to the proposed project

Pernaci, M., De Mita, S., Andrieux, A., Pétrowski, J., Halkett, F., Duplessis, S., and Frey, P. (2014). Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. Frontiers in Plant Science 5, 454.

Persoons, A., Morin, E., Delaruelle, C., Payen, T., Halkett, F., Frey, P., De Mita, S., and Duplessis, S. (2014). Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors. Frontiers in Plant Science 5, 450.

Barrès, B., Dutech, C., Andrieux, A., Halkett, F., and Frey, P. (2012). Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure. Molecular Ecology 21, 4996-5008.

Xhaard, C., Barrès, B., Andrieux, A., Bousset, L., Halkett, F., and Frey, P. (2012). Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Molecular Ecology 21, 2383-2398.

Xhaard, C., Fabre, B., Andrieux, A., Gladieux, P., Barrès, B., Frey, P., and Halkett, F. (2011). The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication. Molecular Ecology 20, 2739-2755.

 Other references

Hamblin, M.T., Buckler, E.S., and Jannink, J.L. (2011). Population genetics of genomics-based crop improvement methods. Trends Genet 27, 98-106.

Laine, A.L., and Barrès, B. (2013). Epidemiological and evolutionary consequences of life-history trade-offs in pathogens. Plant Pathology 62, 96-105.

Lannou, C. (2012). Variation and selection of quantitative traits in plant pathogens. Annual Review of Phytopathology 50, 319-338.

McDonald, B.A., and Linde, C. (2002). Pathogen population genetics, evolutionary potential, and durable resistance. Annual Review of Phytopathology 40, 349-379.

Pariaud, B., Ravigné, V., Halkett, F., Goyeau, H., Carlier, J., and Lannou, C. (2009). Aggressiveness and its role in the adaptation of plant pathogens. Plant Pathology 58, 409-424.

Pernaci, M. (2015). Etude des traits d’histoire de vie de Melampsora larici-populina, agent de la rouille du peuplier : de leur déterminisme génétique à leurs conséquences évolutives. Thèse de Doctorat, Université de Lorraine, 200 p.

 Application

Send CV, cover letter and contact details of two referees to Pascal Frey (pascal.frey@nancy.inra.fr) before 1 October 2015.

 Required skills

The candidate should have good skills in genetics (quantitative genetics, population genetics, genomics) and bioinformatics. 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.

Sujet de thèse : Ecologie des Phytophthora en forêts Néotropicales

Contexte et les enjeux :
Les forêts néotropicales offrent une diversité considérable d’espèces d’arbres, à la fois à l’échelle locale et régionale (Steege et al. 2013). Cette extraordinaire diversité reste encore source de nombreux inventaires et ces communautés d’arbres abritent une diversité microbienne largement aussi considérable mais très peu étudiée. Les facteurs qui sous-tendent la distribution des ces espèces végétales sont par conséquent peu connus et le rôle relatif que jouent la biogéographie, les facteurs abiotiques, et biotiques dans la limitation des distributions des espèces de plantes reste un sujet de discussion. En particulier, l’amplitude de la diversité fongique et des ennemies microbiens naturels, comme les Phytophthora, ainsi que leur degré d’interaction avec les arbres hôtes restent obscures (Schimann et al. soumis).
Le présent sujet de thèse s’inscrit dans le projet de recherche NEBEDIV (ANR blanc), qui vise à améliorer notre compréhension du rôle que joue la plante hôte dans la structuration des communautés microbiennes, et réciproquement l’influence des microorganismes dans le maintien de la diversité végétale par des relations de dépendance et d’interactions positives ou négatives. Ainsi, par des analyses, à l’échelle de la parcelle, de plus d’une centaine de communautés d’arbres à travers l’Amazonie et de leurs communautés fongiques associées, le projet NEBEDIV doit constituer une évaluation unique de la diversité de la forêt tropicale à travers de larges gradients géographiques et environnementaux. Dans ce contexte, par l’étude de différents gradients spatio-temporels, le projet de thèse vise une mise en lumière des corrélations et préférences d’hôte entre les communautés d’arbres et les Phytophthora. En effet, les Phytophthora sont des oomycètes, catégorie de microorganismes apparentés aux algues, et ils constituent une classe très importante d’agents pathogènes telluriques des plantes. Ils sont très peu étudiés en milieu tropical humide, et en particulier dans les forêts néotropicales. La thèse se propose donc d’explorer ces communautés d’Oomycètes et de déterminer si leur composition est contrôlée principalement par l’hôte ou par l’environnement. En retour, sur la base des d’hypothèses développées par Janzen (1970) et Connell (1971), la connaissance des interactions biotiques entre les arbres tropicaux et les phytophthora devrait contribuer à expliquer les patterns de distribution des plantes et la régulation négative de leur densité par les liens spécifiques potentiellement établis avec leurs ennemis naturels.

Objectifs et directions de recherche :
Ce projet de thèse adresse donc plusieurs questions: i) quelles sont les contributions relative des filtres environnementaux (habitats, climat, sol, géographie) dans la structure des communautés d’arbres ? ii) comment s’associent les communautés de phytophthora et de plantes, à différentes échelles spatiales ? iii) quels sont les réseaux d’interactions (positifs ou négatifs) entre ces deux types de communautés ? iv) la modélisation de la beta-diversité végétale peut-elle supporter l’hypothèse Janzen Connell en forêt néotropicale ?
Nous utiliserons un dispositif mis en place dans le cadre du projet ANR NEBEDIV (Natural-Enemy mediated tree Beta-Diversity across south American rain forests). Quatorze familles végétales seront étudiées dans trois habitats différents : sables blancs, « terra firma » et bas-fonds (Coll. Christopher Baraloto et Heidy Schimann, UMR EcoFoG, Kourou). A partir d’une collection de souches de Phytophthora, isolées en Guyane française, la description des différents taxa sera réalisée par typage moléculaire sur plusieurs loci. Différents marqueurs seront ainsi comparés pour les analyses phylogénétiques. Dans un second temps, une description préliminaire des communautés de phytophthora, par séquençage à haut débit, sera réalisée en utilisant les barcodes les plus informatifs, pour validation. Ce type de démarche est pour l’instant encore en développement, comme l’indique nos récents travaux (Coince et al. 2013). Après sélection définitive des marqueurs, l’étude sera élargie à l’ensemble des sites du projet NEBEDIV (Guyane, Brésil et Pérou). Les analyses de diversité des communautés de phytophthora se feront alors conjointement aux analyses phylogénétiques des arbres hôtes, à partir des racines échantillonnées sur chaque juvénile inventorié. L’exploitation des résultats permettra d’identifier les déterminants de la structure des communautés (biotique ou/et environnementaux). Cette étude sera élargie à l’analyse des réseaux d’interaction dans un contexte spatial : construction de réseaux de co-occurrence (interactions directes et indirectes, interactions positives et négatives), en collaboration avec Hélène Morlon (IBENS, ENS, UMR 8197).

Contacts et candidatures (avant le 15 juillet 2015):
Directeur de thèse : Marc Buée, DR INRA, (buee@nancy.inra.fr) et Benoît Marcais, DR INRA (marcais@nancy.inra.fr)
Financement: ANR / métaprogramme INRA Méta-omiques des Ecosystèmes Microbiens (MEM)

Coince A., Cael O., Bach C., Lengelle J., Cruaud C., Gavory F., Marcais B., Buée M. (2013). Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest. Fungal Ecology, 6 : 223-235.
Connell JH. (1971) On the role of natural enemies in preventing competitive exclusion in some marine animals. Proceedings of the Advanced Study Institute on Dynamics of Numbers in Population. Oosterbeek, Wageningen, Holland: P.J. Den Boer & G.R. Grandwell, 298–312.
Janzen DH. (1970). Herbivores and the number of Tree Species in Tropical Forests. American naturalist 104: 501–528.
Schimann H, Bach C, Lengelle J, Louisanna E, Barantal S, Murat C and Buée M. Tree selectivity of non-mycorrhizal fungal communities in Neotropical rainforest soils (soumis).
Steege, ter, H., Pitman, N.C.A., Sabatier, D., Baraloto, C., Salomão, R.P., Guevara, J.E., et al. (2013). Hyperdominance in the Amazonian tree flora. Science 342: 1243092.

La campagne de recrutement des ATER 2014-2015 est lancée.
Elle se termine le 25 mai à minuit.
Les candidats doivent postuler sur GALAXIE par l’application ALTAIR
Ils recevront un identifiant et un mot de passe pour pouvoir déposer leur dossier de candidature sur l’application Esup-Dematec