06/04/18 – 13h30- INRA (LGEF): Maira de Freitas Pereira (IAM – ecogeno )
“Role of effectors-like SSPs in the ectomycorrhiza formation and functioning of Cenococcum geophilum”
Author Archives: eric
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/
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.
The conversation : Ethics and Nutrition
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.
Article: Forest pathology
Do higher summer temperatures restrict the dissemination of Hymenoscyphus fraxineus in France? M Grosdidier, R Ioos, B Marçais. Forest Pathology
Summary
Hymenoscyphus fraxineus is an invasive pathogen that severely affects European ashes, jeopardizing the use of this species in forestry. However, even aggressive invasive pathogens require environmental conditions conducive to disease development. Hence, H. fraxineus survival at temperatures above 35°C is limited, which could reduce its impact in southern Europe. This study examined the effect of environmental conditions, mainly summer temperatures, on ash dieback development in southeast France between 2015 and 2016. Fourteen sites were selected according to altitudinal and longitudinal gradients covering a wide range of mean summer temperatures. Disease severity, density of infected and healthy rachises in the litter and quantity of apothecia produced on infected rachises were measured. Results point to limited disease severity in this area because of the occurrence of high summer temperatures that are unfavourable to the pathogen. In a context of global warming, increases in temperatures could have a positive impact on ashes by limiting ash dieback development.
Seminar: Thomas Kroj
Jeudi 29 mars 2018, 10h30 (salle de conférence INRA): Thomas Kroj (INRA Montpellier)
“Novel insight into plant immunity and fungal virulence from the study of effectors of the blast fungus Magnaporthe oryzae“
Article: Applied and Environmental Microbiology
Assessing airborne fungal communities by high-throughput sequencing using passive traps J Aguayo, C Fourrier-Jeandel, C Husson, R Ioos Applied and Environmental Microbiology, AEM. 02637-17
ABSTRACT
Techniques based on the high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols including different passive spore traps, spore recovery procedures, DNA extraction kits and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two sub loci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of trap are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.
Importance The advent of high throughput sequencing (HTS) methods such as those offered by next-generation sequencing (NGS) techniques has opened a new era in the study of fungal diversity in different environmental substrates. In this study we show that the assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, comparison of sample processing protocols showed that several methodological biases may impact results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.
Article: Annals of Forest Science
Comparison of teak wood properties according to forest management: short versus long rotation DE Rizanti, W Darmawan, B George, A Merlin, S Dumarcay, H Chapuis, … Annals of Forest Science 75 (2), 39
Context
In Indonesia, teak wood has been supplied from the state forests (Perhutani) for long rotation teak and from community teak plantations for short rotation teak. Short rotation teak has been harvested at 7–10 years and long rotation teak at 40–60 years.
Aims
This paper discusses the characterization of technical properties of short and long rotation teak wood based on the chemical, anatomical, physical, and mechanical properties.
Methods
The properties of short rotation and long rotation teak woods were characterized by measuring their density, extractive contents, chemical composition, swelling, wettability, water sorption isotherm, decay resistance, anatomical properties, bending strength (modulus of rupture (MOR), modulus of elasticity (MOE)), and hardness.
Results
The results indicate that short rotation teak was not particularly different in swelling, MOE and MOR, and Brinell hardness compared to long rotation teak, although it was less dense and less durable due to lower heartwood and extractive contents. Therefore, careful attention should be given to the use of short rotation teak in some wood-processing technologies.
Conclusion
Lower wood density and durability of the short rotation compared to the long rotation teak will restrict its utilization to some extent for both indoor and outdoor applications. Fast-growing teak from community cannot be used as usual heartwood teak from Perhutani because of the very low proportion of useful heartwood in the stem.
