Author Archives: eric

Article: FEBS letters

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Structural snapshots along the reaction mechanism of the atypical poplar thioredoxin‐like2. 1 K Chibani, F Saul, C Didierjean, N Rouhier, A Haouz FEBS letters

Abstract

Plastidial thioredoxin (TRX)‐like2.1 proteins are atypical thioredoxins possessing a WCRKC active site signature and using glutathione for recycling. To obtain structural information supporting the peculiar catalytic mechanisms and target proteins of these TRXs, we solved the crystal structures of poplar TRX‐like2.1 in oxidized and reduced states and of mutated variants. These structures share similar folding with TRXs exhibiting the canonical WCGPC signature. Moreover, the overall conformation is not altered by reduction of the catalytic disulfide bond or in a C45S/C67S variant that formed a disulfide‐bridged dimer possibly mimicking reaction intermediates with target proteins. Modeling of the interaction of TRX‐like2.1 with both NADPH‐ and ferredoxin‐thioredoxin reductases (FTR) indicates that the presence of Arg43 and Lys44 residues likely precludes reduction by the plastidial FTR.

PhD position: Ecology and genomics of the bacterial communities

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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; http://mycor.nancy.inra.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: http://mycor.nancy.inra.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 20th 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.

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Sciences en Lumière

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Les arbres : sont-ils vraiment intelligents ? /// Projection-débat Sciences en Lumière à Lorry-Mardigny

 

Visuel_2018-03-23_LorryMardigny_Arbres-1Les arbres occupent près d’un tiers des terres émergées de la planète. Indispensables à notre survie, ils sont en particulier nos meilleurs alliés face au réchauffement climatique. Pourtant, nous ignorons presque tout d’eux. Loin d’être figés dans leur monde végétal, les arbres ont en fait une vie bien plus riche qu’il n’y paraît. Ils communiquent, s’entraident, se défendent, ils bougent même ! Les arbres seraient-ils dotés d’une certaine forme d’intelligence ? C’est la thèse défendue par un forestier allemand, Peter Wohlleben, dont le livre, « La vie secrète des arbres » est devenu un succès planétaire, vendu à plus d’1 million d’exemplaires. Le reportage « Le Monde Secret des Arbres » de Raphaële Schapira et Vincent Barral (documentaire d’« Envoyé spécial » du jeudi 26 octobre 2017) nous fera voyager des forêts de hêtres millénaires d’Allemagne jusqu’aux centres de thérapie forestière du Japon, en passant par les laboratoires de l’INRA qui étudient la perception des mouvements par les arbres, voyage au coeur de l’univers secret et fascinant des arbres. Au cours de cette soirée, Marc Buée et Pascal Frey, tous deux Directeurs de Recherche dans l’Unité Mixte de Recherche « Interactions Arbres-Microorganismes » à l’INRA de Nancy et spécialistes des arbres, animeront un débat avec le public à l’issue de la projection de ce documentaire, afin de tenter d’y voir clair entre science, croyances et interprétations abusives.

Un film de Raphaële Schapira et Vincent Barral (30’/France/2071/France Télévisions)

Soirée accompagnée par Marc BUEE et Pascal FREY, Directeurs de Recherche à L’Unité Mixte de Recherche “Interactions Arbres-Microorganismes” à l’INRA Grand-Est

Vendredi 23 mars 2018 – 20:30
Salle des fêtes 28 rue de Metz Lorry-Mardigny  France

Postdoctoral position

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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

 

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Functional Ecology Conference

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“Functional Ecology Conference” to be held in Nancy April 2018

The International Conference on Functional Ecology will be held in april 2018 in Nancy. The call for abstracts is open until 15 March. Researchers, engineers and PhD students are invited to register!

Highlight innovative actions, future research and applications! This is the objective of the International Conference on Functional Ecology 2018. This event will bring together scientists specialized in the functional ecology of organisms, populations, communities and ecosystems.

FEC2018 aims to take stock of research in functional ecology, focusing on material and energy flows and mobilizing long-term observation, experimentation and modelling. Global changes, threats to biodiversity, and remediation of degraded ecosystems will be addressed in the case of forest, natural, cultivated and urban ecosystems. It is also a space for interaction between experienced researchers, young researchers, engineers,… and research facility.

The program has just been announced: submit your abstract!

The event is composed of five daily sessions and a workshop on AnaEE France infrastructures. Registrations are open and you can now submit an abstract. All levels of research and ecosystem types (crops, grasslands, shrubs, forests, marines, lakes, rivers, urban and mining ecosystems) will be considered. Several sessions will be devoted to the functioning of forest ecosystems, which will be the main theme this year. Sessions will be delivered in English.

Discover the program!

Submit an abstract online

Local and national partnership

The 2018 session is organised by INRA Grand Est-Nancy and the AgroParisTech-Nancy centre with the support of AnaEE France, AnaEE Europe and the Nancy-Freiburg-Zürich international network (NFZ. forestnet). The University of Lorraine and the CNRS are also partners. This conference is a continuation of the “functional ecology days” held in recent years.

Keywords: Functional ecology, conference, ecosystem, animal, plant

CONTACT

Contact the organizers by email: functionnal-ecology-contact@inra.fr

WEBSITE: https://journees.inra.fr/functionalecologyconference/

PhD defense: C. Lorrain

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PhD defense the 28th of March at 1.30 p.m. in the conference room of the INRA center in Champenoux.

Cécile Lorrain
soutiendra publiquement ses travaux de thèse portant sur :
L’analyse moléculaire de l’interaction peuplier-Melampsora spp.
Dirigés par Sébastien Duplessis et Arnaud Hecker
le 28 mars à 13h30
Salle de conférence
Centre INRA Grand Est – Nancy
Champenoux

Résumé:

La maladie de la rouille foliaire du peuplier est causée par des espèces de champignons de la famille des Melampsoraceae et de l’ordre des Pucciniales. Trois espèces infectent principalement les peupleraies en France : Melampsora larici-populina qui est la plus agressive, Melampsora allii-populina et Melampsora medusae f. sp. deltoidae. Dans leurs cycles de vie, ces trois espèces partagent les peupliers comme hôtes communs pour assurer leur multiplication clonale au cours de l’été et elles infectent des hôtes différents pour réaliser leur cycle sexué au cours du printemps. Chez les champignons pathogènes biotrophes obligatoires comme les Pucciniales, la sécrétion de molécules appelées effecteurs conditionne le succès d’infection de la plante hôte. Ainsi, les effecteurs permettent de manipuler les fonctions cellulaires de l’hôte et de contourner son système immunitaire. Comprendre le rôle fondamental de ces molécules dans la cellule-hôte est une des questions clés de la biologie des effecteurs. Au cours de cette thèse, des approches de génomique, de transcriptomique et de caractérisation fonctionnelle et structurale d’effecteurs candidats ont été déployées afin de contribuer à l’analyse moléculaire de l’interaction entre peupliers et Melampsora spp. Premièrement, l’analyse du transcriptome de M. larici-populina au cours de son cycles sexué a mis en évidence que les protéines sécrétées sont surreprésentées parmi les gènes surexprimés dans les basides et au cours de l’infection de l’hôte mélèze. La comparaison des transcriptomes de M. larici-populina lors de l’infection des deux hôtes, le peuplier et le mélèze, révèle la présence d’une majorité de gènes exprimés communément chez les deux hôtes et une fraction exprimée spécifiquement chez chacun des deux hôtes. Ainsi, nous révélons des gènes codant de petites protéines sécrétées qui pourraient être associés à la spécificité d’hôte. Deuxièmement, le séquençage du génome de M. allii-populina et sa comparaison au génome de M. larici-populina a révélé une expansion de sa taille (336 Mb contre 110 Mb). Cette dernière est associée à l’invasion du génome par de nombreux éléments transposables qui représentent près de 75% du génome et par un enrichissement en gènes par rapport à M. larici-populina (23 089 gènes contre 19 550). Cependant, les répertoires de gènes potentiellement impliqués dans le processus infectieux sont proportionnellement sensiblement similaires entre les deux espèces. Les quelques différences observées pourraient être associées à la spécificité d’hôte (Populus spp./Larix spp. dans un cas et Populus spp./Allium spp. dans l’autre) et à l’adaptation à des hôtes alternants différents. Troisièmement, des cribles effectoromiques réalisés sur un répertoire d’effecteurs candidats de M. larici-populina ont révélé deux candidats d’intérêt. Nous avons mis en place des approches fonctionnelles pour tenter d’élucider leur rôle dans l’interaction avec le peuplier. Nous avons ainsi pu produire l’effecteur MLP124017 qui interagit avec des protéines de la famille Topless-related proteins et résoudre sa structure tridimensionnelle qui présente une similarité à des protéines nuclear transport factor 2 like qui sont des protéines cargo transportant diverses molécules entre le noyau et le cytoplasme. L’effecteur Chloroplast-Targeted Protein MLPCTP1 est adressé vers et est localisé dans les chloroplastes via un peptide de transit dans le système hétérologue Nicotiana benthamiana et nous montrons une localisation similaire chez le peuplier et l’arabette. Les fonctions de ces effecteurs restent encore à déterminer mais les travaux amorcés dans cette thèse ouvrent de nouvelles perspectives quant à la diversité et au rôle des effecteurs chez les Pucciniales.

Abstract:

The poplar rust disease is caused by fungi belonging to the order Pucciniales in the family Melamsporaceae. Three main species cause damages in poplar plantations in France: Melampsora larici-populina, which is the most aggressive, Melampsora allii-populina and Melampsora medusae f. sp. deltoidae. During their life cycles, these three fungi share poplars as main host in which they achieve their clonal multiplication during summer and they infect different alternate hosts to complete their sexual reproduction in spring. In fungal obligate biotrophs like rust fungi, the success of host infection is conditioned by the secretion of molecules called effectors. Effectors allow the pathogen to manipulate host cell processes and to evade the plant immune system. A key question in effector biology is to understand how these molecules function in the host cell. In the frame of this PhD thesis, genomics, transcriptomics, functional and structural approaches were used to contribute to the molecular analysis of the poplar-Melamspora spp. interaction. Firstly, the transcriptome analysis of M. larici-populina during its sexual cycle highlighted that small-secreted proteins were over-represented among genes up-regulated in basidia and during larch infection. Comparison of M. larici-populina transcriptomes during infection of the two hosts, poplar and larch, revealed that a majority of the genes are commonly expressed on both hosts and a fraction is specifically expressed on each host. Small-secreted protein genes specifically expressed on each host maybe related to host specificity. Secondly, the sequencing of the M. allii-populina genome and the comparison with M. larici-populina revealed a size expansion in M. allii-populina (336Mb vs. 110Mb). This expansion is mostly due to the invasion of the genome by numerous transposable elements that represent more than 75% of the genome and by a gene enrichment compared to M. larici-populina (23,089 and 19,550 genes, respectively). However, catalogues of gene potentially involved in the infection process are proportionally similar between the two species. The few differences observed could be linked to host specificity (Populus spp./Larix spp. on one hand and Populus spp./Allium spp. on the other hand) and adaptation to their different hosts. Thirdly, effectoromic screens developed on a panel of M. larici-populina candidate effectors revealed two candidates of interest. We set up a pipeline of functional approaches in order to elucidate their role in the interaction with poplar. We produced the candidate effector MLP124017 that interacts with proteins of the Topless-related proteins family and solved its structure that presents similarities with nuclear transport factor 2 like proteins. These proteins are cargos that transport diverse molecules between the nucleus and cytosol in plant cells. The effector Chloroplast-Targeted Protein MLPCTP1 is addressed and translocated inside chloroplasts through a transit peptide in the heterologous system Nicotianana benthamiana and we showed that the same localization occurs in poplar and in Arabidopsis. The functions of these two effectors remain to be determined but the functional characterization initiated in this thesis opens new perspectives in term of diversity and roles of effectors in rust fungi.

Article: FEMS Microbiology Ecology

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Tracking the invasion: dispersal of Hymenoscyphus fraxineus airborne inoculum at different scales. M Grosdidier, R Ioos, C Husson, O Cael, T Scordia… FEMS Microbiology Ecology.

Summary

Ash dieback is caused by an invasive pathogen, Hymenoscyphus fraxineus, which emerged in Europe in the 1990s and jeopardizes the management of ash stands. Although the biological cycle of the pathogen is well understood, its dispersal patterns via airborne spores remain poorly described. We investigated the seasonal and spatial patterns of dispersal in France using both a passive spore-trapping method coupled with a real-time PCR assay and reports of ash dieback based on symptom observations. Spores detection varies from year to year, with a detection ability of 30 to 47%, depending on meteorological conditions, which affect both production of inoculum and efficiency of the trapping. Nevertheless, our results are consistent and we showed that sporulation peak occurred from June to August and that spores were detected up to 50-100 km ahead of the disease front, proving the presence of the pathogen before any observation of symptoms. The spore dispersal gradient was steep, most of inoculum remaining within 50 m of infected ashes. Two dispersal kernels were fitted using Bayesian methods to estimate the mean dispersal distance of H. fraxineus from inoculum sources. The estimated mean distances of dispersal, either local or regional scale, were 1.4 km and 2.6 km, respectively, the best fitting kernel being the inverse power-law. This information may help to design disease management strategies.