Category Archives: Academic productions
Article: Planta
Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray. F Sillo, JU Fangel, B Henrissat, A Faccio, P Bonfante… – Planta
Abstract
Main conclusion
A combined approach, using a carbohydrate microarray as a support for genomic data, has revealed subtle plant cell-wall remodelling during Tuber melanosporum and Corylus avellanainteraction.
Cell walls are involved, to a great extent, in mediating plant–microbe interactions. An important feature of these interactions concerns changes in the cell-wall composition during interaction with other organisms. In ectomycorrhizae, plant and fungal cell walls come into direct contact, and represent the interface between the two partners. However, very little information is available on the re-arrangement that could occur within the plant and fungal cell walls during ectomycorrhizal symbiosis. Taking advantage of the Comprehensive Microarray Polymer Profiling (CoMPP) technology, the current study has had the aim of monitoring the changes that take place in the plant cell wall in Corylus avellana roots during colonization by the ascomycetous ectomycorrhizal fungus T. melanosporum. Additionally, genes encoding putative plant cell-wall degrading enzymes (PCWDEs) have been identified in the T. melanosporum genome, and RT-qPCRs have been performed to verify the expression of selected genes in fully developed C. avellana/T. melanosporum ectomycorrhizae. A localized degradation of pectin seems to occur during fungal colonization, in agreement with the growth of the ectomycorrhizal fungus through the middle lamella and with the fungal gene expression of genes acting on these polysaccharides.
Article: Bulletin of Mathematical Biology
Mate Finding, Sexual Spore Production, and the Spread of Fungal Plant Parasites FM Hamelin, F Castella, V Doli, B Marçais, V Ravigné, MA Lewis. Bulletin of Mathematical Biology, 1-18
Abstract
Sexual reproduction and dispersal are often coupled in organisms mixing sexual and asexual reproduction, such as fungi. The aim of this study is to evaluate the impact of mate limitation on the spreading speed of fungal plant parasites. Starting from a simple model with two coupled partial differential equations, we take advantage of the fact that we are interested in the dynamics over large spatial and temporal scales to reduce the model to a single equation. We obtain a simple expression for speed of spread, accounting for both sexual and asexual reproduction. Taking Black Sigatoka disease of banana plants as a case study, the model prediction is in close agreement with the actual spreading speed (100 km per year), whereas a similar model without mate limitation predicts a wave speed one order of magnitude greater. We discuss the implications of these results to control parasites in which sexual reproduction and dispersal are intrinsically coupled.
Article: Forest Pathology
Phytophthora× alni and Phytophthora lacustris associated with common alder decline in Central Portugal M Kanoun‐Boulé, T Vasconcelos, J Gaspar, S Vieira, C Dias‐Ferreira, …Forest Pathology
Summary
Since the early 1990s, an emerging disease induced by the highly aggressive oomycete Phytophthora ×alni has caused widespread alder decline across Europe. In parallel, P. lacustris, a recently described species associated with riparian habitats, has been subject of increasing interest. A field survey conducted in 2014 showed high mortality rates in alder stands located in the riparian gallery along two rivers in Central Portugal. The pathogens isolated from necrotic alder stem base during this study were identified as P. ×alni and P. lacustris. This paper is the first to report the occurrence of P. lacustris in Portugal and presents the first finding of P. ×alni affecting mature trees in natural ecosystems located in Central Portugal.
Article: Mycorrhiza
Reconstructing the evolutionary history of gypsy retrotransposons in the Périgord black truffle (Tuber melanosporum Vittad.) T Payen, C Murat, F Martin. Mycorrhiza, 1-11
Abstract
Truffles are ascomycete fungi belonging to genus Tuber, and they form ectomycorrhizal associations with trees and shrubs. Transposable elements constitute more than 50 % of the black Périgord truffle (Tuber melanosporum) genome, which are mainly class 1 gypsy retrotransposons, but their impact on its genome is unknown. The aims of this study are to investigate the diversity of gypsy retrotransposons in this species and their evolutionary history by analysing the reference genome and six resequenced genomes of different geographic accessions. Using the reverse transcriptase sequences, six different gypsy retrotransposon clades were identified. Tmt1 and Tmt6are the most abundant transposable elements, representing 14 and 13 % of the T. melanosporumgenome, respectively. Tmt6 showed a major burst of proliferation between 1 and 4 million years ago, but evidence of more recent transposition was observed. Except for Tmt2, the other clades tend to aggregate, and their mode of transposition excluded the master copy model. This suggests that each new copy has the same probability of transposing as other copies. This study provides a better view of the diversity and dynamic nature of gypsy retrotransposons in T. melanosporum. Even if the major gypsy retrotransposon bursts are old, some elements seem to have transposed recently, suggesting that they may continue to model the truffle genomes.
Article: Tree Genetics and Genomes
Genetic diversity and genetic structure of black alder (Alnus glutinosa [L.] Gaertn) in the Belgium-Luxembourg-France cross-border area
Dominique Mingeot , Claude Husson, Patrick Mertens, Bernard Watillon, Pierre Bertin, Philippe Druart. Tree Genomics and Genomes
Abstract
Due to its beneficial effects on river ecosystems, black alder (Alnus glutinosa) is one of the tree species selected for planting on riverbanks in the cross-border area encompassing Wallonia in Belgium, Lorraine in France, and Luxembourg. The preservation of this species, however, is threatened by an invasive pathogen that particularly targets and kills young alder individuals. The objectives of this study were to characterize the genetic diversity and the genetic structure of A. glutinosa at this local level with the aim of assisting the conservation and replanting strategies and to determine if a germplasm collection comprising individuals from the same cross-border area captures the diversity present in the region. Nuclear simple sequence repeat (SSR) and chloroplastic DNA (cpDNA) markers were used to analyze four local wild populations and the germplasm collection which is representative of two river catchments and six legal provenance regions. Three populations distant from the studied area were also included. A panel of 14 nuclear SSR loci revealed high allelic diversity and very low differentiation among wild populations (mean FST = 0.014). The germplasm collection displayed a range of alleles that were representative of the different populations, and no significant differentiation between the germplasm collection and the local wild populations was observed, making this collection, as far as allelic diversity is concerned, suitable for providing trees for riverbank replanting programs. Using SSR markers, various statistical approaches consistently indicated the lack of a significant geographical structure at the level of the river catchments or provenance regions. In contrast, two cpDNA haplotypes were detected and displayed a cross-border geographically structured distribution that could be taken into account in defining new cross-border provenance regions.
Article: PLoS ONE
Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood Hervé Vincent, Ketter Elodie, Pierrat Jean-Claude, Gelhaye Eric, Frey-Klett Pascale. PLoS ONE 1 (11), e0147100
Abstract
Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.
Article: Frontiers in Plant Science
The poplar Rust-Induced Secreted Protein (RISP) inhibits the growth of the leaf rust pathogen Melampsora larici-populina and triggers cell culture alkalinisation B Petre, A Hecker, H Germain, P Tsan, J Sklenar, G Pelletier, A Séguin, … Frontiers in Plant Science 7, 97
Abstract
Plant cells secrete a wide range of proteins in extracellular spaces in response to pathogen attack. The poplar Rust-Induced Secreted Protein (RISP) is a small cationic protein of unknown function that was identified as the most induced gene in poplar leaves during immune responses to the leaf rust pathogen Melampsora larici-populina, an obligate biotrophic parasite. Here, we combined in planta and in vitro molecular biology approaches to tackle the function of RISP. Using a RISP-mCherry fusion transiently expressed in Nicotiana benthamiana leaves, we demonstrated that RISP is secreted into the apoplast. A recombinant RISP specifically binds to M. larici-populina urediniospores and inhibits their germination. It also arrests the growth of the fungus in vitro and on poplar leaves. Interestingly, RISP also triggers poplar cell culture alkalinisation and is cleaved at the C-terminus by a plant-encoded mechanism. Altogether our results indicate that RISP is an antifungal protein that has the ability to trigger cellular responses.
MetaMicrobial Environmental Genomics
A new book of the series: “Methods in Molecular Biology ” (Volume 1399 2016) entitled “MetaMicrobial Environmental Genomics” has been edited by F. Martin and S. Uroz
One chapter entitled :”Identification and in situ Distribution of a Fungal Gene Marker: The Mating Type Genes of the Black Truffle” has been written by H. De la Varga and C. Murat
Article: Mycorrhiza
Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development. A Deveau, S Antony-Babu, F Le Tacon, C Robin, P Frey-Klett, S Uroz. Mycorrhiza, 1-11
Abstract
Ectomycorrhizae create a multitrophic ecosystem formed by the association between tree roots, mycelium of the ectomycorrhizal fungus, and a complex microbiome. Despite their importance in the host tree’s physiology and in the functioning of the ectomycorrhizal symbiosis, detailed studies on ectomycorrhiza-associated bacterial community composition and their temporal dynamics are rare. Our objective was to investigate the composition and dynamics of Tuber melanosporumectomycorrhiza-associated bacterial communities from summer to winter seasons in a Corylus avellana tree plantation. We used 16S ribosomal RNA (rRNA)-based pyrosequencing to compare the bacterial community structure and the richness in T. melanosporum’s ectomycorrhizae with those of the bulk soil. The T. melanosporum ectomycorrhizae harbored distinct bacterial communities from those of the bulk soil, with an enrichment in Alpha- and Gamma-proteobacteria. In contrast to the bacterial communities of truffle ascocarps that vastly varies in composition and richness during the maturation of the fruiting body and to those from the bulk soil, T. melanosporum ectomycorrhiza-associated bacterial community composition stayed rather stable from September to January. Our results fit with a recent finding from the same experimental site at the same period that a continuous supply of carbohydrates and nitrogen occurs from ectomycorrhizae to the fruiting bodies during the maturation of the ascocarps. We propose that this creates a stable niche in the ectomycorrhizosphere although the phenology of the tree changes.
