Seminar: Guillaume Bilodeau

le 27 septembre, l’unité de mycologie accueillera Guillaume Bilodeau, un collègue scientifique du Canadian Food Inspection Agency qui travaille principalement sur l’identification et la caractérisation des champignons phytopathogènes (

Guillaume proposera un séminaire : “Détection / identification d’agents phytopathogènes réglementés utilisant des données de génomes et métagénomique ”

Le séminaire aura lieu en nos locaux de Pixérécourt, Malzéville, le 27 à 14h00.

BMC Genomics

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata D Armaleo, O Müller, F Lutzoni, ÓS Andrésson, G Blanc, HB Bode, … BMC genomics 20 (1), 60



Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution.


A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting.


The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloriswhile they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.

Article: Environmental Microbiology

Ascoma genotyping and mating type analyses of mycorrhizas and soil mycelia of Tuber borchii in a truffle orchard established by mycelial inoculated plants P Leonardi, C Murat, F Puliga, M Iotti, A Zambonelli Environmental Microbiology


Tuber borchii (the Bianchetto truffle) is a heterothallic Ascomycete living in symbiotic association with trees and shrubs. Maternal and paternal genotype dynamics have already been studied for the black truffles Tuber melanosporumand Tuber aestivum but not yet for T. borchii. In this study, we analysed maternal and paternal genotypes in the first truffle orchard realized with plants inoculated with five different T. borchii mycelia. Our aims were to test the persistence of the inoculated mycelia, if maternal and/or paternal genotypes correspond to inoculated mycelia and to assess the hermaphroditism of T. borchii. The mating type of each isolate as well as those of mycorrhizas, ascomata and extraradical soil mycelia was determined. Moreover, simple sequence repeat (SSR) profiles of maternal and paternal genotypes were assessed in 18 fruiting bodies to investigate the sexual behaviour of this truffle. The maternal genotypes of the fruiting bodies corresponded to those of the inoculated mycelia with only two exceptions. This confirmed that the inoculated mycelia persisted 9 years after plantation. As regards paternal partner, only two had the same genotype as those of the inoculated mycelia, suggesting hermaphroditism. Most of the new paternal genotypes originated from a recombination of those of inoculated mycelia.

Article: Environmental Microbiology

Multi‐omic analyses of exogenous nutrient bag decomposition by the black morel Morchella importuna reveal sustained carbon acquisition and transferring H Tan, A Kohler, R Miao, T Liu, Q Zhang, B Zhang, L Jiang, Y Wang, L Xie, … Environmental microbiology


The black morel (Morchella importuna Kuo, O’Donnell and Volk) was once an uncultivable wild mushroom, until the development of exogenous nutrient bag (ENB), making its agricultural production quite feasible and stable. To date, how the nutritional acquisition of the morel mycelium is fulfilled to trigger its fruiting remains unknown. To investigate the mechanisms involved in ENB decomposition, the genome of a cultivable morel strain (MimportunaSCYDJ1‐A1) was sequenced and the genes coding for the decay apparatus were identified. Expression of the encoded carbohydrate‐active enzymes (CAZymes) was then analyzed by metatranscriptomics and metaproteomics in combination with biochemical assays. The results show that a diverse set of hydrolytic and redox CAZymes secreted by the morel mycelium is the main force driving the substrate decomposition. Plant polysaccharides such as starch and cellulose present in ENB substrate (wheat grains plus rice husks) were rapidly degraded, whereas triglycerides were accumulated initially and consumed later. ENB decomposition led to a rapid increase in the organic carbon content in the surface soil of the mushroom bed, which was thereafter consumed during morel fruiting. In contrast to the high carbon consumption, no significant acquisition of nitrogen was observed. Our findings contribute to an increasingly detailed portrait of molecular features triggering morel fruiting.

Article: Mycorrhiza

New insights into black truffle biology: discovery of the potential connecting structure between a Tuber aestivum ascocarp and its host root A Deveau, P Clowez, F Petit, JP Maurice, F Todesco, C Murat, M Harroué, … Mycorrhiza 29 (3), 219-226


According to isotopic labeling experiments, most of the carbon used by truffle (Tuber sp.) fruiting bodies to develop underground is provided by host trees, suggesting that trees and truffles are physically connected. However, such physical link between trees and truffle fruiting bodies has never been observed. We discovered fruiting bodies of Tuber aestivum adhering to the walls of a belowground quarry and we took advantage of this unique situation to analyze the physical structure that supported these fruiting bodies in the open air. Observation of transversal sections of the attachment structure indicated that it was organized in ducts made of gleba-like tissue and connected to a network of hyphae traveling across soil particles. Only one mating type was detected by PCR in the gleba and in the attachment structure, suggesting that these two organs are from maternal origin, leaving open the question of the location of the opposite paternal mating type.

Article: Food Microbiology

Are bacteria responsible for aroma deterioration upon storage of the black truffle Tuber aestivum: A microbiome and volatilome study M Vahdatzadeh, A Deveau, R Splivallo Food Microbiology, 103251


Truffle fungi, luxurious food items with captivating aromas, are highly valued in the culinary world. However, truffles are perishable and their aroma undergoes deep changes upon storage. Additionally, truffle aroma might be partially derived from microbes. Hence, we investigated here the influence of storage on two factors, namely the volatile profile and bacterial community composition in the black truffle Tuber aestivum. The possible linkage among those factors was further explored.

Our results demonstrate important changes in the volatile profiles of truffles over nine days of storage at room temperature. In the same time frame, dominant bacterial classes characteristic of fresh truffles (α-Proteobacteriaβ-Proteobacteria, and Sphingobacteria classes) were gradually replaced by food spoilage bacteria (γ-Proteobacteria and Bacilli classes). Freshness and spoilage volatile markers (i.e. dimethyl sulfide (DMS), butan-2-one, 2- and, 2- and 3-methylbutan-1-ol, and 2-phenylethan-1-ol) were identified. Lastly, network analysis showed correlations between those markers and specific bacterial classes typical of fresh and spoiled truffles.

Overall, our results demonstrate the profound effect of storage on the aroma and bacterial community composition of truffles and highlight how the gradual replacement of the commensal microbiome by spoilage microbes mirrors shifts in aroma profile and the possible loss of fresh truffle flavor.

Article: Fungal Biology and Biotechnology

Increasing access to microfluidics for studying fungi and other branched biological structures LJ Millet, J Aufrecht, J Labbé, J Uehling, R Vilgalys, ML Estes, … Fungal Biology and Biotechnology 6 (1), 1


Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have the potential to resolve the underlying mechanisms of growth and transport in these complex branched living systems. Microfluidics provide controlled environments and improved optical access for real-time and high-resolution imaging studies that allow high-content and quantitative analyses. Studying growing branched structures and the dynamics of cellular interactions with both biotic and abiotic cues provides context for molecule production and genetic manipulations. To make progress in this arena, technical and logistical barriers must be overcome to more effectively deploy microfluidics in biological disciplines. A principle technical barrier is the process of assembling, sterilizing, and hydrating the microfluidic system; the lack of the necessary equipment for the preparatory process is a contributing factor to this barrier. To improve access to microfluidic systems, we present the development, characterization, and implementation of a microfluidics assembly and packaging process that builds on self-priming point-of-care principles to achieve “ready-to-use microfluidics.”


We present results from domestic and international collaborations using novel microfluidic architectures prepared with a unique packaging protocol. We implement this approach by focusing primarily on filamentous fungi; we also demonstrate the utility of this approach for collaborations on plants and neurons. In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi.


This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures.

PhD position in population genetics and modeling

Title of the thesis:
Study and inference of dispersion during clonal colonization waves in the poplar rust fungus

Pascal FREY (Senior scientist), director of the thesis
Fabien HALKETT (Junior scientist), co-director of the thesis

Host laboratory
Department of Tree – Microbe Interactions, INRA / University of Lorraine, INRA Grand Est Nancy research centre, 54280 Champenoux

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

Thesis summary
The main objective of this thesis is to study the conditions of emergence of spatial genetic structures during waves of clonal propagation. The thesis proposes to explore this question both theoretically, using simulation, but also empirically, using datasets collected in a particular ecological system. This ecological system allows us studying recurrent invasive dynamics. In the Durance River valley, which forms a veritable ecological corridor, clonal epidemics of poplar rust develop each year, spreading from upstream to downstream along the wild poplar riparian forest. This ecological system has already been well described by the host team and many data are available for the realization of the thesis. This project aims to form an original and significant contribution, not only to the study of clonal population genetics (with the ultimate goal of developing a dispersion inference tool) but also in the field of propagation fronts, a field that is currently very active but has remained mainly confined to theoretical demonstrations.

Send CV, cover letter and contact details of two referees to Fabien Halkett ( before September 1, 2019.

Required skills
The candidate should have good skills in population genetics, modeling, ecology and evolutionary biology. A strong taste for teamwork is essential. Knowledge of French will be an asset.


Titre du sujet de thèse :
Etude et inférence de la dispersion lors de vagues de colonisation clonales chez un champignon phytopathogène responsable de la rouille du peuplier

Encadrants :
Pascal FREY (DR2, HDR), directeur de la thèse
Fabien HALKETT (CRCN), 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 : INRA (Département EFPA) et ANR. Durée 3 ans. Salaire mensuel net environ 1400€.

Résumé de la thèse
L’objectif majeur de cette thèse est d’étudier les conditions d’émergence de structures génétiques spatiales lors de vagues de propagation clonale. La thèse se propose d’explorer cette question à la fois sous l’angle théorique, à l’aide de simulations, mais également sous l’angle empirique, à l’aide de jeux de données collectées dans un système écologique particulier. Celui-ci présente l’avantage de pouvoir étudier des dynamiques invasives récurrentes. Dans la vallée de la Durance, qui forme un véritable corridor écologique, se développent chaque année des épidémies clonales de rouille du peuplier qui se propagent d’amont en aval le long de la ripisylve. Ce système écologique a déjà été bien décrit par l’équipe d’accueil et de nombreuses données sont disponibles pour la réalisation de la thèse. Ce projet a pour ambition de former une contribution originale et significative, non seulement à l’étude de génétique des populations clonales (avec pour but ultime de développer un outil d’inférence de la dispersion) mais également dans le domaine d’étude des fronts de propagation, domaine actuellement très actif mais qui est resté cantonné principalement à des démonstrations théoriques.

Candidature :
Envoyer un CV, une lettre de motivation et les coordonnées de 2 personnes de référence à Fabien Halkett ( avant le 1er septembre 2019.

Compétences recherchées
Le(la) candidat(e) devra avoir de bonnes compétences en génétique des populations, modélisation, écologie et biologie évolutive. Un goût prononcé pour le travail en équipe est indispensable.

PhD Defense : J. Legeay

Jean Legeay soutiendra sa thèse intitulée:

“Ecologie des Oomycètes et champignons phytopathogènes dans les sols des forêts de Guyane Française : éclairages sur les relations spécifiques entre les communautés de Phytophthora et d’arbres”

dans la salle de conférence du bâtiment des SDAR le vendredi 21 juin à 9h00.


Les mécanismes expliquant le maintien de la diversité végétale dans les forêts tropicales sont mal connus. Une hypothèse particulièrement étudiée est l’hypothèse Janzen-Connell qui postule que ces mécanismes sont essentiellement causés par les interactions entre les plantes et leurs ennemis naturels, en particulier les organismes pathogènes. Dans cette thèse, nous nous sommes donc intéressés aux agents pathogènes présents dans les sols d’une forêt néotropicale guyanaise et à leur lien de spécificité avec les plantes. Dans le cas où l’hypothèse Janzen-Connell serait vérifiée, on peut s’attendre à ce que les plantes structurent les communautés de micro-organismes pathogènes. Nos travaux se sont focalisés sur les Oomycètes et en particulier les Phytophthora, pathogènes des arbres très importants, mais nous nous sommes aussi intéressés aux champignons pathogènes.
Ainsi, nous avons développé et comparé des jeux d’amorces PCR spécifiques des Phytophthora et des Péronosporomycètes afin d’étudier ces organismes par metabarcoding. Ces amorces ont ensuite servi à étudier la diversité des communautés de Phytophthora dans des échantillons de sols de deux sites forestiers de Guyane Française prélevés au pied d’arbres appartenant à 10 familles végétales. Une faible diversité a été retrouvée, avec seulement 8 espèces ou taxons en tout, et la très large dominance d’un complexe d’espèces Phytophthora heveae. La structuration par la plante-hôte de ces communautés est plutôt faible. Dans une étude complémentaire, nous avons analysé la diversité des Oomycètes (dont le genre Phytophthora) et des champignons pathogènes dans les sols et les litières de six plantations monospécifiques et au sein d’une forêt naturelle de Guyane Française. La structuration par l’hôte s’est avérée nulle pour les Oomycètes et faible, bien que significative, pour les champignons pathogènes. Enfin, nous n’avons pas réussi à déclencher expérimentalement des mortalités ou dépérissements par des Oomycètes sur le wacapou, une espèce d’arbre guyanaise, via des inoculations de sols de forêt.
Au final, les résultats de cette thèse ne supportent pas l’hypothèse selon laquelle les Oomycètes seraient d’importants acteurs du maintien de la diversité végétale dans les forêts tropicales. Par ailleurs, ils nous interrogent sur la faible diversité de ce groupe de microorganismes dans les sols et litières dans un hotspot de diversité végétale.