Article: Mycorrhiza

N-Acetylglucosaminidase activity, a functional trait of chitin degradation, is regulated differentially within two orders of ectomycorrhizal fungi: Boletales and Agaricales F Maillard, M Didion, L Fauchery, C Bach, M Buée. Mycorrhiza, 1-7

Abstract

Chitin is one of the most abundant nitrogen-containing polymers in forest soil. Ability of ectomycorrhizal (EM) fungi to utilize chitin may play a key role in the EM symbiosis nutrition and soil carbon cycle. In forest, EM fungi exhibit high diversity, which could be based on function partitioning and trait complementarity. Although it has long been recognized that closely related species share functional characteristics, the phylogenetic conservatism of functional traits within microorganisms remains unclear. Because extracellular N-acetylglucosaminidase activity has been proposed as functional trait of chitin degradation, we screened this activity on 35 EM fungi species with or without chitin in the growth medium to (i) describe the functional diversity of EM fungi and (ii) identify potential links between this functional trait and EM fungal phylogeny. We observed large variations of the extracellular N-acetylglucosaminidase activities among the fungal strains. Furthermore, our results revealed two regulation patterns of extracellular N-acetylglucosaminidase activities. Indeed, these chitinolytic activities were stimulated or repressed in the presence of chitin, in comparison to the control treatment. These profiles of extracellular N-acetylglucosaminidase stimulation/repression might be conserved at a high phylogenetic level in the Basidiomycota phylum, as illustrated by the opposite patterns of regulation between Boletales and Agaricales. Finally, the downregulation of this activity by chitin, for some EM fungal groups, might suggest another chitin degradation pathway.

Article: The New Phytologist

The ectomycorrhizal basidiomycete Laccaria bicolor releases a secreted β-1, 4 endoglucanase that plays a key role in symbiosis development. F Zhang, GE Anasontzis, A Labourel, C Champion, M Haon, … The New phytologist

Abstract

In ectomycorrhiza, root ingress and colonization of the apoplast by colonizing hyphae is thought to rely mainly on the mechanical force that results from hyphal tip growth, but this could be enhanced by secretion of cell-wall-degrading enzymes, which have not yet been identified. The sole cellulose-binding module (CBM1) encoded in the genome of the ectomycorrhizal Laccaria bicolor is linked to a glycoside hydrolase family 5 (GH5) endoglucanase, LbGH5-CBM1. Here, we characterize LbGH5-CBM1 gene expression and the biochemical properties of its protein product. We also immunolocalized LbGH5-CBM1 by immunofluorescence confocal microscopy in poplar ectomycorrhiza. We show that LbGH5-CBM1 expression is substantially induced in ectomycorrhiza, and RNAi mutants with a decreased LbGH5-CBM1 expression have a lower ability to form ectomycorrhiza, suggesting a key role in symbiosis. Recombinant LbGH5-CBM1 displays its highest activity towards cellulose and galactomannans, but no activity toward L. bicolor cell walls. In situ localization of LbGH5-CBM1 in ectomycorrhiza reveals that the endoglucanase accumulates at the periphery of hyphae forming the Hartig net and the mantle. Our data suggest that the symbiosis-induced endoglucanase LbGH5-CBM1 is an enzymatic effector involved in cell wall remodeling during formation of the Hartig net and is an important determinant for successful symbiotic colonization.

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 : Melanie.Morel@univ-lorraine.fr

Site Web : http://mycor.nancy.inra.fr/IAM/

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 : Melanie.Morel@univ-lorraine.fr

Web site : http://mycor.nancy.inra.fr/IAM/

Posted in Job

Article: BMC Genomics

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors Z Zeng, H Sun, EJ Vainio, T Raffaello, A Kovalchuk, E Morin, S Duplessis, … BMC genomics 19 (1), 220

Abstract

Background

Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species.

Results

To better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates.

Conclusion

Our study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence

Article: Mycorrhiza

Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino PE Courty, M Buée, JJT Tech, D Brulé, Y Colin, JHJ Leveau, S Uroz Mycorrhiza, 1-1

Abstract

Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.

Article: New Phytologist

The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. C Strullu-Derrien, MA Selosse, P Kenrick, FM Martin The New phytologist

Abstract

 The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The occurrence of mycorrhizas is now well established in c. 85% of extant plants, yet the geological record of these associations is sparse. Fossils preserved under exceptional conditions provide tantalizing glimpses into the evolutionary history of mycorrhizas, showing the extent of their occurrence and aspects of their evolution in extinct plants. The fossil record has important roles to play in establishing a chronology of when key fungal associations evolved and in understanding their importance in ecosystems through time. Together with calibrated phylogenetic trees, these approaches extend our understanding of when and how groups evolved in the context of major environmental change on a global scale. Phylogenomics furthers this understanding into the evolution of different types of mycorrhizal associations, and genomic studies of both plants and fungi are shedding light on how the complex set of symbiotic traits evolved. Here we present a review of the main phases of the evolution of mycorrhizal interactions from palaeontological, phylogenetic and genomic perspectives, with the aim of highlighting the potential of fossil material and a geological perspective in a cross-disciplinary approach.