Author Archives: eric

Article: Plos one

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The GSTome Reflects the Chemical Environment of White-Rot Fungi. A Deroy, F Saiag, Z Kebbi-Benkeder, N Touahri, A Hecker, … PloS one 10 (10), e0137083

Abstract

White-rot fungi possess the unique ability to degrade and mineralize all the different components of wood. In other respects, wood durability, among other factors, is due to the presence of extractives that are potential antimicrobial molecules. To cope with these molecules, wood decay fungi have developed a complex detoxification network including glutathione transferases (GST). The interactions between GSTs from two white-rot fungi, Trametes versicolor and Phanerochaete chrysosporium, and an environmental library of wood extracts have been studied. The results demonstrate that the specificity of these interactions is closely related to the chemical composition of the extracts in accordance with the tree species and their localization inside the wood (sapwood vs heartwood vs knotwood). These data suggest that the fungal GSTome could reflect the chemical environment encountered by these fungi during wood degradation and could be a way to study their adaptation to their way of life

Article: Forest Ecology and Management

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Pre-existing forests as sources of pathogens? The emergence of Armillaria ostoyae in a recently planted pine forest F Labbé, B Marcais, JL Dupouey, T Bélouard, X Capdevielle, D Piou, …. Forest Ecology and Management 357, 248-258

Abstract

Fungi are among the principal causal agents of emerging plant diseases, which are a matter of worldwide concern. Changes in land use, such as the expansion of cultivated areas, are implicated in the emergence of fungal diseases, but have been less often reported for native species plantations. In the maritime pine (Pinus pinaster) forest of the Landes de Gascogne (south-western France), pine mortality due to the root rot fungus Armillaria ostoyae (Basidiomycete) has been increasing over the last 30 years. The first cases of this disease occurred in 1920 only few years after a period of rapid major change to the landscape. During the second half of the 19th century the landscape was transformed from marshes to the largest monospecific maritime pine plantation forest in Europe. We carried out two surveys (0.24 and 1 million hectares) of Armillaria root rot disease in the Landes area, to investigate the spatial distribution of pathogen damage and to determine the role of historical factors in the establishment of this pattern. For the two surveys, spatial analyses and generalised linear models revealed a significant effect on the current geographical distribution of A. ostoyae disease of the proportion of pre-existing forest in the vicinity of afforested areas and a significant effect of the proximity of the first forests planted in the coastal dunes. These results suggest that A. ostoyae was commonly distributed in pre-existing forest areas, and that most of these fragments acted as source for the colonisation of newly planted forests. Better predictions on the risk of establishment of new disease foci in this forest area can be achieved from these results.

Eole

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Appel à candidatures – Bourses Eole 2015 session automne

Le Réseau Franco-Néerlandais accorde des bourses de mobilité destinées à des étudiants en master et à des doctorants, toutes disciplines confondues, pour un séjour d’études, de recherche ou un stage aux Pays-Bas. Ces bourses sont attribuées sur la base d’une sélection stricte des meilleurs projets.

Les bourses d’excellence « Eole » s’adressent en particulier à des doctorants devant faire un court séjour de recherche aux Pays-Bas dans le cadre de leur formation doctorale. Elles peuvent favoriser le bon fonctionnement de thèses en cotutelle. Les étudiants en Master qui effectuent un séjour de recherche, de formation ou de stage sont également éligibles. Ces bourses d’un montant forfaitaire de 500 à 1000€ ne sont pas renouvelables.

La demande portera sur des séjours prévus de novembre 2015 à juin 2016.
Date limite de réception des candidatures: le 1er octobre

Pour les modalités de candidature et critères d’admission :

Les pièces du dossier de candidature peuvent être en français ou en anglais.

Article: Microbial Ecology

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Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences. M Jeanbille, M Buée, C Bach, A Cébron, P Frey-Klett, MP Turpault, S Uroz. Microbial Ecology, 1-12.

Abstract

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Article: Annals of Forest Science

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Total phenolic and lignin contents, phytochemical screening, antioxidant and fungal inhibition properties of the heartwood extractives of ten Congo Basin tree species. S Mounguengui, JBS Tchinda, MK Ndikontar, S Dumarçay, C Attéké, … Annals of Forest Science, 1-10

Abstract

Content and type of extractives vary considerably among woody species in the Congo Basin tropical forest. They influence the natural durability of wood with respect to fungal and insect degradation. Species containing higher amounts of extractives and Klason lignin were generally less susceptible to fungal colonization. Phenolic extractives with large anti-fungal and high antioxidant activities were the main chemical family of compounds extracted from the tested species, which suggests a potential chemical valorization of these extractives.

Article: Fungal Genetics and Biology

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Evolutionary divergence of Ure2pA glutathione transferases in wood degrading fungiT Roret, A Thuillier, F Favier, E Gelhaye, C Didierjean, M Morel-Rouhier Fungal Genetics and Biology

Abstract

The intracellular systems of detoxification are crucial for the survival of wood degrading fungi. Within these systems, glutathione transferases could play a major role since this family of enzymes is specifically extended in lignolytic fungi. In particular the Ure2p class represents one third of the total GST number in Phanerochaete chrysosporium. These proteins have been phylogenetically split into two subclasses called Ure2pA and Ure2pB. Ure2pB can be classified as Nu GSTs because of shared structural and functional features with previously characterized bacterial isoforms. Ure2pA can rather be qualified as Nu-like GSTs since they exhibit a number of differences. Ure2pA possess a classical transferase activity, a more divergent catalytic site and a higher structural flexibility for some of them, compared to Nu GSTs. The characterization of four members of this Ure2pA subclass (PcUre2pA4, PcUre2pA5, PcUre2pA6 and PcUre2pA8) revealed specific functional and structural features, suggesting that these enzymes have rapidly evolved and differentiated, probably to adapt to the complex chemical environment associated with wood decomposition.

Article: Applied Soil Ecology

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Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe. RE Creamer, SE Hannula, JP Van Leeuwen, D Stone, M Rutgers, …

Applied Soil Ecology

Abstract

Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, grass, forestry). Samples collected from across these sites ranged in soil properties; soil organic carbon (SOC), pH and texture. To assess the range in biodiversity and ecosystem function across the sites, fourteen biological methods were applied as proxy indicators for these functions. These methods measured the following: microbial diversity: DNA yields (molecular biomass), archaea, bacteria, total fungi and arbuscular mycorrhizal fungi; micro fauna diversity: nematode trophic groups; meso fauna diversity: enchytraeids and Collembola species; microbial function: nitrification, extracellular enzymes, multiple substrate induced respiration, community level physiological profiling and ammonia oxidiser/nitrification functional genes. Network analysis was used to identify the key connections between organisms under the different land use scenarios. Highest network density was found in forest soils and lowest density occurred in arable soils. Key taxomonic units (TUs) were identified in each land-use type and in relation to SOC and pH categorisations. Top-connected taxonomic units (i.e. displaying the most co-occurrence to other TUs) were identified for each land use type. In arable sites this was dominated by bacteria and fungi, while in grassland sites bacteria and fungi were most connected. In forest soils archaeal, enchytraeid and fungal TUs displayed the largest number of neighbours, reflecting the greatest connectivity. Multiple regression models were applied to assess the potential contribution of soil organisms to carbon cycling and storage and nutrient cycling of specifically nitrogen and phosphorus. Key drivers of carbon cycling were microbial biomass, basal respiration and fungal richness; these three measures have often been associated with carbon cycling in soils. Regression models of nutrient cycling were dependent on the model applied, showing variation in biological indicators.

Article: Genome announcements

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Draft Genome Sequence of Burkholderia sp. Strain PML1 (12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering Ability. S Uroz, P Oger Genome announcements 3 (4), e00798-15

ABSTRACT

We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated from the Oak-Scleroderma citrinum ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France).

Article: New Phytologist

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Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis J Doré, M Perraud, C Dieryckx, A Kohler, E Morin, B Henrissat, …New Phytologist

Summary

  • Extracellular proteins play crucial roles in the interaction between mycorrhizal fungi and their environment. Computational prediction and experimental detection allowed identification of 869 proteins constituting the exoproteome of Hebeloma cylindrosporum. Small secreted proteins (SSPs) and carbohydrate-active enzymes (CAZymes) were the two major classes of extracellular proteins.
  • Twenty-eight per cent of the SSPs were secreted by free-living mycelia and five of the 10 most abundant extracellular proteins were SSPs. By contrast, 63–75% of enzymes involved in nutrient acquisition were secreted.
  • A total of 150 extracellular protein-coding genes were differentially expressed between mycorrhizas and free-living mycelia. SSPs were the most affected. External environmental conditions also affected expression of 199 exoproteome genes in mycorrhizas. SSPs displayed different patterns of regulation in response to presence of a host plant or other environmental signals. Several of the genes most overexpressed in the presence of organic matter encoded oxidoreductases.
  • Hebeloma cylindrosporum has not fully lost its ancestral saprotrophic capacities but rather adapted them not to harm its hosts and to use soil organic nitrogen. The complex and divergent patterns of regulation of SSPs in response to a symbiotic partner and/or organic matter suggest various roles in the biology of mycorrhizal fungi.