Article: Journal of soil science

Tree genotype and seasonal effects on soil properties and biogeochemical functioning in Mediterranean pine forests. L Pérez‐Izquierdo, L Saint‐André, P Santenoise… – European Journal of Soil Science


In forests, intraspecific genetic variation in trees can affect the entire ecosystem, which in turn, depends on the different processes occurring through space and time in soil. We hypothesized that, in addition to the effect of the local site, tree genotype and season would have an effect on the properties and functions of the edaphic environment. We studied soils beneath different genotypes of Pinus pinaster Ait. (Atlantic, Mediterranean and African) in 45‐year old common gardens in spring and autumn. The pH, organic matter, nutrients and infrared spectroscopy together with enzyme activities were determined and used to evaluate the soil properties and biogeochemical functioning. In addition to strong site effects, tree genotype and seasonal effects were detected on soil properties and functions. Both were major controlling factors of microbially mediated functioning, especially processes related to the carbon (C) and nitrogen (N) cycles. In general, the soil environment beneath the Atlantic trees was different from that under the Mediterranean and African genotypes, with differences in raw infrared spectra and increased activities of enzymes involved in hemicellulose degradation and N mobilization. Regarding the season, the largest soil humidity (RH), electric conductivity (EC), and N and potassium (K) concentrations, coupled with the smallest phosphorus (P) concentration and C:N ratios were detected in autumn. Degradation of C peaked in autumn, while P and N mobilization usually peaked in spring. Our results showed that, beyond local site effects, there were detectable effects of tree genotype and season in Mediterranean forest soils, which governed microbially mediated processes that might have relevant functional consequences at the ecosystem level.

Seminars of the week

Thursday 5th, 12h30 (FST 3rd floor): Thomas Bacchetta(IAM redox)

” Diversité des protéines SSP1-like fongiques: approches fonctionnelle et biochimique “

Friday 6th, 1.30pm (INRA, LEGF): Shingo Miyauchi(IAM ecogeno)

“Comparative genomics of 112 fungi (+ development of visual omics tools)”

Article: Genome Announcements

Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle C Murat, A Kuo, KW Barry, A Clum, RB Dockter, L Fauchery, M Iotti, … Genome Announcements 6 (25), e00537-18


The ascomycete Tuber borchii (Pezizomycetes) is a whitish edible truffle that establishes ectomycorrhizal symbiosis with trees and shrubs. This fungus is ubiqui- tous in Europe and is also cultivated outside Europe. Here, we present the draft genome sequence of T. borchii strain Tbo3840 (97.18 Mb in 969 scaffolds, with 12,346 predicted protein-coding genes).

Article: Nature Plants

Oak genome reveals facets of long lifespan C Plomion, JM Aury, J Amselem, T Leroy, F Murat, S Duplessis, S Faye, …Nature Plants, 1


Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Article: Biochimica et Biophysica Acta

Conserved functions of Arabidopsis mitochondrial late-acting maturation factors in the trafficking of iron‑sulfur clusters MA Uzarska, J Przybyla-Toscano, F Spangar, F Zannini, R Lill, …Biochimica et Biophysica Acta (BBA)-Molecular Cell Research


Numerous proteins require iron‑sulfur (Fe-S) clusters as cofactors for their function. Their biogenesis is a multi-step process occurring in the cytosol and mitochondria of all eukaryotes and additionally in plastids of photosynthetic eukaryotes. A basic model of Fe-S protein maturation in mitochondria has been obtained based on studies achieved in mammals and yeast, yet some molecular details, especially of the late steps, still require investigation. In particular, the late-acting biogenesis factors in plant mitochondria are poorly understood. In this study, we expressed the factors belonging to NFU, BOLA, SUFA/ISCA and IBA57 families in the respective yeast mutant strains. Expression of the Arabidopsis mitochondrial orthologs was usually sufficient to rescue the growth defects observed on specific media and/or to restore the abundance or activity of the defective Fe-S or lipoic acid-dependent enzymes. These data demonstrate that the plant mitochondrial counterparts, including duplicated isoforms, likely retained their ancestral functions. In contrast, the SUFA1 and IBA57.2 plastidial isoforms cannot rescue the lysine and glutamate auxotrophies of the respective isa1-isa2Δ and iba57Δ strains or of the isa1-isa2-iba57Δ triple mutant when expressed in combination. This suggests a specialization of the yeast mitochondrial and plant plastidial factors in these late steps of Fe-S protein biogenesis, possibly reflecting substrate-specific interactions in these different compartments.

Article: Fungal Genomics

Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples. L Fauchery, S Uroz, M Buée, A Kohler. Fungal Genomics, 21-35


Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS). The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material. However, environmental-derived samples from soil, wood, or litter often contain phenolic compounds, pigments, and other molecules that can be inhibitors for reactions during sequencing library construction. In this chapter, we propose an optimized protocol allowing the preparation of high quality and long fragment DNA from different samples (mycelium, fruiting body, soil) compatible with the current sequencing requirements.

Seminars of the week

Thursday 14th of June, 12.30 (FST, 3rd floor):Vuong N’Guyen(IAM -redox)

“Functional characterization of detoxification systems of wood decaying fungi: genetic approach”

Friday 15th of June, 12.30 (FST, 3rd floor):Florine Gérard (IAM -redox)

Contribution à l’étude sur les variants protéiques responsables du clivage phénotypique virulent/avirulent chez la rouille du peuplier 

Friday 15th of June, 1.30 pm (INRA LEGF):Feng Zhang (IAM -ecogenomic)

Investigation of interaction between Laccaria bicolor and populus.

Brunch champignons

Le Brunch “Champignons forestiers, opportunités et risques pour l’homme, l’arbre et le bois” a été construit en collaboration avec le Centre Inra Grand Est-Nancy. La table ronde a permis de mettre en lumière les ressources insoupçonnées des champignons dont on ne perçoit que le chapeau à l’image de leur biologie souterraine ! Les champignons jouent un rôle capital en forêt puisqu’ils nouent des interactions et interdépendances intimes et durables avec la flore de l’écosystème forestier. Aujourd’hui, l’enjeu est de consolider nos connaissances sur la multitude d’espèces de champignons, de faire reconnaître leur valeur environnementale et leurs propriétés afin de mieux les exploiter. Ce Brunch passionnant a été l’occasion pour le public de débattre des aspects parfois inattendus des champignons et d’imaginer le champ des possibles. Animé par Francis MARTIN, directeur du Laboratoire d’excellence ARBRE porté par l’Inra, ce rendez-vous gourmand a été l’occasion pour les étudiants, institutionnels, professionnels, enseignants-chercheurs et usagers présents de débattre des aspects méconnus des champignons qui peuvent se révéler utiles pour les acteurs économiques et les citoyens.

Capture d’écran 2018-06-05 à 16.19.50

Capture d’écran 2018-06-05 à 16.15.46

Seminar: Z. Chen

Mercredi 6 juin, 9h30 INRA (salle de conférence INRA): Zhixiao Chen (IAM ecogeno)

“Persistance de Tuber magnatumdans le sol après plantation d’arbres mycorhizés”