Author Archives: eric

Article: Annals of Forest Science

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Forest tree genomics: 10 achievements from the past 10 years and future prospects. C Plomion, C Bastien, MB Bogeat-Triboulot, L Bouffier, A Déjardin, … Annals of Forest Science, 1-27

Abstract

Key message

This review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology.

Context

A decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving genomics and bioinformatics toolbox has advanced our understanding of the structure, functioning, and evolution of forest tree genomes.

Aims and methods

This review highlights some of the discoveries and applications that “omics” technologies have made possible for forest trees over the past 10 years.

Results

In this review, we start by our current understanding of genome evolution and intricacies of gene regulation for reproduction, development, and responses to biotic and abiotic stresses. We then skim over advances in interactome analysis and epigenomics, the knowledge of the extent of genetic variation within and between species, revealing micro- and macro-evolutionary processes and species history, together with the complex architecture of quantitative traits. We finally end with applications in genetic resource conservation and breeding.

Conclusion

The knowledge gained through the use of these technologies has a huge potential impact for adapting forests to the main challenges they will have to face: changing demand from ecosystem services with potentially conflicting strategies in terms of conservation and use, as well as climate changes and associated threats. Genomics will undoubtedly play a major role over the next decade and beyond, not only to further understand the mechanisms underlying adaptation and evolution but also to develop and implement innovative management and policy actions to preserve the adaptability of natural forests and intensively managed plantations.

Article: Mycorrhiza

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SSR-based identification of genetic groups within European populations of Tuber aestivum Vittad. V Molinier, C Murat, M Peter, A Golotte, H De la Varga,… Mycorrhiza

Abstract

Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuberspecies, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivumto (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups.

Seminar: A. Deveau

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Aurélie Deveau présentera en salle de conférences (site Inra de Champenoux) un séminaire sur ses travaux  réalisés ces trois derniers mois dans le laboratoire de Pieter Dorrestein à San Diego. La présentation décrira la technique d’imagerie par spectrométrie de masse et ses applications aux analyses des mécanismes d’interactions entre micro-organismes des sols forestiers et racines de plantes.

Aurélie Devenu will present her recent work performed in the lab of Pieter Dorrestein dealing with imaging methods coupled to mass spectrometry in the goal to understand the   interactions between organisms in forest soils. The seminar will be held in the conference room friday 12h june at 1.30 pm.

Article: Plant Pathology

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Assessment of inoculation methods for screening black alder resistance to Phytophthora× alni. A Chandelier, C Husson, P Druart, B Marçais. Plant Pathology

Abstract

Identification of resistance to Phytophthora ×alni could provide the basis for a management strategy against alder decline in riparian ecosystems in Europe. Our objectives were to test methods to evaluate the resistance of riparian alders to the disease, and to screen alder genotypes for resistance. P. ×alni isolates were compared for their aggressiveness (lesion length on stem) and sporulation capacity (sporangia). While no difference of lesion lengths was found between isolates, sporangia production was dependent on isolate, highlighting the need to select carefully isolates for inoculation methods dealing with zoospores suspension. Inoculation tests carried out at different periods of the year revealed a seasonal change in susceptibility to the disease, with the period from June to September being the most efficient for inoculation tests. Stem-wounded inoculations tests carried out on excised shoots were unreliable for evaluating the level of resistance of alder genotypes to P. ×alni infection, with divergent results between two successive years or between two inoculation periods during the same year. In contrast, a method which mimics the natural conditions of infection based on flooding of rooted cuttings in artificially infected river water was found promising. Another method based on the inoculation of foliated terminal shoots with zoospore suspensions was found to be repeatable and could be used for high throughput analyses. Altogether, the results show a continuous resistance response from highly susceptible to moderately resistant genotypes. This suggests that breeding might be a useful strategy to manage alder decline caused by P. ×alni.

Article: Environmental Microbiology

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Fine-scale spatial genetic structure analysis of the black truffle Tuber aestivum and its link to aroma variability. V Molinier, C Murat, H Crochet, D Wipf, R Splivallo. Environmental Microbiology

Abstract

Truffles are symbiotic fungi in high demand by food connoisseurs. Improving yield and product quality requires a better understanding of truffle genetics and aroma biosynthesis. One aim here was to investigate the diversity and fine-scale spatial genetic structure of the Burgundy truffle Tuber aestivum. The second aim was to assess how genetic structuring along with fruiting body maturation and geographical origin influenced single constituents of truffle aroma.

A total of thirty-nine Burgundy truffles collected in two orchards were characterized in terms of aroma profile (SPME-GC/MS) and genotype (microsatellites). A moderate genetic differentiation was observed between the populations of the two orchards. An important seasonal and spatial genetic structuring was detected. Within one orchard individuals belonging to the same genet were generally collected during a single season and in the close vicinity from each other. Maximum genet size nevertheless ranged from 46-92 m. Geographical origin or maturity only had minor effects on aroma profiles but genetic structuring, specifically clonal identity, had a pronounced influence on the concentrations of C8– and C4-VOCs.

Our results highlight a high seasonal genetic turnover and indicate that the aroma of Burgundy truffle is influenced by the identity of single clones/genets.

Seminar: P. Silar

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Pr Philippe Silar from “Université Paris Diderot will give a talk entitled:

“Podospora anserina, a model to study the degradation of plant biomass”

The seminar will be held Friday 5th June at 2pm (salle ESA Fac de sciences).

It will be possible to follow it (visioconference) in LEGF room at INRA.

Article: Soil Biology and Biochemistry

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Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry JM Talbot, F Martin, A Kohler, B Henrissat, KG Peay. Soil Biology and Biochemistry

Abstract

Linking community composition to ecosystem function is a challenge in complex microbial communities. We tested the hypothesis that key biological features of fungi – evolutionary history, functional guild, and abundance of functional genes – can predict the biogeochemical activity of fungal species during decay. We measured the activity of 10 different enzymes produced by 48 model fungal species on leaf litter in laboratory microcosms. Taxa included closely related species with different ecologies (i.e. species in different “functional guilds”) and species with publicly available genomes. Decomposition capabilities differed less among phylogenetic lineages of fungi than among different functional guilds. Activity of carbohydrases and acid phosphatase was significantly higher in litter colonized by saprotrophs compared to ectomycorrhizal species. By contrast, oxidoreductase activities per unit fungal biomass were statistically similar across functional guilds, with white rot fungi having highest polyphenol oxidase activity and ectomycorrhizal fungi having highest peroxidase activity. On the ecosystem level, polyphenol oxidase activity in soil correlated with the abundance of white rot fungi, while soil peroxidase activity correlated with the abundance of ectomycorrhizal fungi in soil. Copy numbers of genes coding for different enzymes explained the activity of some carbohydrases and polyphenol oxidase produced by fungi in culture, but were not significantly better predictors of activity than specific functional guild. Collectively, our data suggest that quantifying the specific functional guilds of fungi in soil, potentially through environmental sequencing approaches, allows us to predict activity of enzymes that drive soil biogeochemical cycles.

Article: Annals of Forest Science

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An evolutionary ecology perspective to address forest pathology challenges of today and tomorrow. ML Desprez-Loustau, J Aguayo, C Dutech, KJ Hayden, C Husson, … Annals of Forest Science, 1-23

Abstract

Key message

Increasing human impacts on forests, including unintentional movement of pathogens, climate change, and large-scale intensive plantations, are associated with an unprecedented rate of new diseases. An evolutionary ecology perspective can help address these challenges and provide direction for sustainable forest management.

Context

Forest pathology has historically relied on an ecological approach to understand and address the practical management of forest diseases. A widening of this perspective to include evolutionary considerations has been increasingly developed in response to the rising rates of genetic change in both pathogen populations and tree populations due to human activities.

Aims

Here, five topics for which the evolutionary perspective is especially relevant are highlighted.

Results

The first relates to the evolutionary diversity of fungi and fungal-like organisms, with issues linked to the identification of species and their ecological niches. The second theme deals with the evolutionary processes that allow forest pathogens to adapt to new hosts after introductions or to become more virulent in homogeneous plantations. The third theme presents issues linked to disease resistance in tree breeding programs (e.g., growth-defense trade-offs) and proposes new criteria and methods for more durable resistance. The last two themes are dedicated to the biotic environment of the tree–pathogen system, namely, hyperparasites and tree microbiota, as possible solutions for health management.

Conclusion

We conclude by highlighting three major conceptual advances brought by evolutionary biology, i.e., that (i) “not everything is everywhere”, (ii) evolution of pathogen populations can occur on short time scales, and (iii) the tree is a multitrophic community. We further translate these into a framework for immediate policy recommendations and future directions for research.

PROFAS B+

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Le deuxième appel à candidatures du programme de bourses algéro-français PROFAS B+ est ouvert du 1er au 31 mai 2015 au titre de l’année universitaire 2015-2016. Campus France, opérateur national pour la promotion de l’enseignement supérieur, l’accueil et la mobilité internationale, a été choisi par l’Ambassade de France en Algérie et le Ministère algérien de l’Enseignement supérieur et de la Recherche scientifique pour le suivi et la gestion du PROFAS B+.

Ce programme s’adresse aux doctorants en co-encadrement ou en cotutelle de thèse, dans le cadre de partenariats entre laboratoires français et algériens existants de qualité. Ce programme financé à parité entre l’Algérie et la France a pour objectif de répondre tant quantitativement que qualitativement, par la formation d’enseignants-chercheurs qualifiés, au besoin urgent d’encadrement des étudiants dans les établissements d’enseignement supérieur algériens. En 2014, il a permis à 87 boursiers algériens de rejoindre des laboratoires d’excellence en France pour une durée de 7 à 12 mois.

La refonte du programme en 2014 permet maintenant aux boursiers PROFAS B+ de bénéficier de prestations assurées par Campus France en plus du versement mensuel d’une bourse comprise entre 1 280 et 1 420 euros (montants 2014). Ces prestations garantissent un accueil et un suivi des doctorants pendant leur mobilité dans les meilleures conditions et consistent en :
- La recherche et la réservation d’un logement
- La prise en charge des billets de train et des nuitées d’hôtel à l’arrivée en France
- Une assurance santé et responsabilité civil e
- La prise en charge des frais de recherche dans les laboratoires d’accueil jusqu’à 1 000 euros par doctorant

– Le suivi régulier du séjour et de l’avancée des recherches

En outre, d’autres prestations, comme la prise en charge des billets d’avion des boursiers entre l’Algérie et la France, sont assurées.

Les établissements universitaires français entretenant des relations dans les domaines de la recherche et de l’enseignement supérieur avec l’Algérie sont invités à diffuser l’appel à candidatures auprès des laboratoires, des équipes de recherche ou des enseignants-chercheurs concernés afin qu’ils prennent contact avec leurs partenaires algériens. Cette prise de contact pourrait permettre l’identification de doctorants algériens les plus brillants et dont le sujet de thèse présente un caractère innovant.

Retrouvez ici l’appel à candidatures en cours : http://www.if-algerie.com/actualites/appels-a-projet/profas-b-lancement-du-2eme-appel-a-candidatures

Mme Sonia Jedidi, Attachée de coopération universitaire et de recherche à l’Ambassade de France en Algérie (sonia.jedidi@diplomatie.gouv.fr) et M. Yoann Le Bonhomme, Responsable du service Afrique du Nord et Moyen-Orient à Campus France (yoann.lebonhomme@campusfrance.org) se tiennent à votre disposition pour toute question.