Résumé
Polar regions are characterized by rocky terrains with sparse vegetation and oligotrophic soils, i.e. “fellfields”. In such ecosystems, microbial communities should be essential for soil-plant functioning but their diversity is poorly explored. The sub-Antarctic Kerguelen Islands fellfields are characterized by an endemic long-lived cushion plant, Lyallia kerguelensis which rhizosphere may be a shelter for microbes in this harsh environment. Cushions are affected by necrosis and we expect the rhizomicrobiome composition to be related to plant necrosis. We analysed bacterial and fungal communities in bulk- and rhizospheric soils from L. kerguelensis in five different fellfields across the Kerguelen Islands using 16S rRNA and ITS1 metabarcoding. We found that soil microbial communities were composed of both restricted and cosmopolitan taxa. While all sites were dominated by the same bacterial taxa (Chloroflexi, Actinobacteria, α-Proteobacteria and Acidobacteria), the relative abundance of the main fungal phyla (Ascomycota, Basidiomycota, Mortierellomycota and Rozellomycota) highly differed between sites. L. kerguelensis rhizomicrobiome was at least as diverse as the bulk soil, making the rhizosphere a possible reservoir of microbial diversity. It was composed of the same main bacterial phyla than detected in the bulk soil while the composition of the rhizosphere fungal communities was specific to each plant. No common microorganisms were identified regarding cushion necrosis extent across plants and sites, but several microbial putative functions were shared, suggesting a possible shift in soil functioning with cushion necrosis increase. Our study brings new information on the diversity and composition of the microbial communities of fellfield soils in a sub-Antarctic Island and the rhizomicrobiome of a characteristic endemic cushion plant.
Auteurs, date et publication :
Auteurs Lorène Julia Marchand , Françoise Hennion , Michèle Tarayre , Marie-Claire Martin , Benoit Renaud Martins , Cécile Monard
Publication : Frontiers in Soil Science
Date : 2025
Volume : 2
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
The role of Epigenetics in Epithelial Mesenchymal Transition (EMT) has recently emerged. Two epigenetic enzymes with paradoxical roles have previously been associated to EMT, EZH2 (Enhancer of Zeste 2 Polycomb Repressive Complex 2 (PRC2) Subunit), a lysine methyltranserase able to add the H3K27me3 mark, and the histone demethylase KDM6B (Lysine Demethylase 6B), which can remove the H3K27me3 mark. Nevertheless, it still remains unclear how these enzymes, with apparent opposite activities, could both promote EMT. In this study, we evaluated the function of these two enzymes using an EMT-inducible model, the lung cancer A549 cell line. ChIP-seq coupled with transcriptomic analysis showed that EZH2 and KDM6B were able to target and modulate the expression of different genes during EMT. Based on this analysis, we described INHBB, WTN5B, and ADAMTS6 as new EMT markers regulated by epigenetic modifications and directly implicated in EMT induction.
Auteurs, date et publication :
Auteurs Camille Lachat , Diane Bruyère , Amandine Etcheverry , Marc Aubry , Jean Mosser , Walid Warda , Michaël Herfs , Elodie Hendrick , Christophe Ferrand , Christophe Borg , Régis Delage-Mourroux , Jean-Paul Feugeas , Michaël Guittaut , Eric Hervouet , Paul Peixoto
Publication : Cancers
Date : 2020
Volume : 12
Issue : 12
Pages : 3649
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to evaluate the hologenome concept. If deterministic forces shape plant holobionts, then grafted plants will exhibit a particular signature in the root microbiota community, the holobiont composition. Reciprocally, if the microbiota of these chimeric plants is randomly assembled, the hologenome concept would be of limited importance for plants. We analyzed the root-endosphere microbiota of two independent model plant systems including ungrafted and reciprocal-grafting treatments. Consistent with the idea that co-evolution shapes at least in part host-microbiota combinations, grafted and ungrafted hosts harbor markedly different microbiota compositions. The results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with a stronger effect of the rootstock than scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.
Auteurs, date et publication :
Auteurs Marine Biget , Tingting Wang , Cendrine Mony , Qicheng Xu , Lucie Lecoq , Veronique Chable , Kevin R. Theis , Ning Ling , Philippe Vandenkoornhuyse
Date : 2022
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Earthworms in interaction with soil microorganisms play a key role in litter decomposition. Moreover, as soil engineers, earthworms modify microbial communities and their enzymatic activities. Most studies focusing on earthworms and soil enzymatic activities compare distinct ecological categories of earthworms whereas their contributions and interactions within a given ecological category remain largely unknown. In this context, the aims of the present study were to determine and compare the contribution of (1) three strict-anecic earthworm species, (2) three epi-anecic earthworm species and (3) the pairwise interactions between these different species on Lolium perenne leaf litter decomposition and soil microbial activity. After 30 days of incubation, the surface litter mass loss and five soil enzymatic activities (FDAse, β-D-glucosidase, cellobiohydrolase, leucine amino-peptidase and acid phosphatase) were measured in both earthworm burrows and middens. In mono-specific assemblages, leaf litter mass loss and enzymatic activities were significantly higher in the presence of epi-anecic compared to strict-anecic species, whatever the species identity. These differences were higher for the β-D-glucosidase, leucine amino-peptidase and FDAse (+78%, +57% and +34%, respectively). Earthworm species interactions at both intra- and inter-ecological sub-categories did not enhance either leaf litter mass loss or enzymatic activities. Interestingly, FDAse activity was higher in earthworm burrows whereas acid phosphatase activity was higher in earthworm middens. These results indicate that the two anecic ecological sub-categories have different impacts on soil functioning and each of them regroups earthworm species with similar behaviour. This functional distinction highlights the key role of epi-anecic earthworms in fresh surface litter burial and decomposition, featuring their importance on nutrient cycling in soil and for microbial activities stimulation through resource availability.
Auteurs, date et publication :
Auteurs Kevin Hoeffner , Mathieu Santonja , Daniel Cluzeau , Cécile Monard
Publication : Soil Biology and Biochemistry
Date : 2019
Volume : 132
Pages : 93-100
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Type III epithelial–mesenchymal transition (EMT) has been previously associated with increased cell migration, invasion, metastasis, and therefore cancer aggressiveness. This reversible process is associated with an important gene expression reprogramming mainly due to epigenetic plasticity. Nevertheless, most of the studies describing the central role of epigenetic modifications during EMT were performed in a single-cell model and using only one mode of EMT induction. In our study, we studied the overall modulations of gene expression and epigenetic modifications in four different EMT-induced cell models issued from different tissues and using different inducers of EMT. Pangenomic analysis (transcriptome and ChIP–sequencing) validated our hypothesis that gene expression reprogramming during EMT is largely regulated by epigenetic modifications of a wide range of genes. Indeed, our results confirmed that each EMT model is unique and can be associated with a specific transcriptome profile and epigenetic program. However, we could select some genes or pathways that are similarly regulated in the different models and that could therefore be used as a common signature of all EMT models and become new biomarkers of the EMT phenotype. As an example, we can cite the regulation of gene-coding proteins involved in the degradation of the extracellular matrix (ECM), which are highly induced in all EMT models. Based on our investigations and results, we identified ADAM19 as a new biomarker of in vitro and in vivo EMT and we validated this biological new marker in a cohort of non-small lung carcinomas.
Auteurs, date et publication :
Auteurs Paul Peixoto , Amandine Etcheverry , Marc Aubry , Anaïs Missey , Camille Lachat , Jérôme Perrard , Elodie Hendrick , Régis Delage-Mourroux , Jean Mosser , Christophe Borg , Jean-Paul Feugeas , Michaël Herfs , Michaël Boyer-Guittaut , Eric Hervouet
Publication : Cell Death & Disease
Date : 2019
Volume : 10
Issue : 3
Pages : 1-17
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are approved for second-line treatment of EGFR wild-type (EGFR-wt) nonsmall cell lung cancer (NSCLC). However, results from randomised trials performed to compare EGFR-TKIs with chemotherapy in this population did not show any survival benefit. In the era of immunotherapy, many drugs are approved for second-line treatment of EGFR-wt NSCLC and there is a need to reassess the role of EGFR-TKIs in this setting.The Biomarkers France study is a large nationwide cohort of NSCLC patients tested for EGFR mutations. We used this database to collect clinical, biological, treatment and outcome data on EGFR-wt patients who received second-line treatment with either EGFR-TKIs or chemotherapy.Among 1278 patients, 868 received chemotherapy and 410 received an EGFR-TKI. Median overall survival and progression-free survival were longer with chemotherapy than with an EGFR-TKI. Overall survival was 8.38 versus 4.99 months, respectively (hazard ratio 0.70, 95% CI 0.59-0.83; p<0.0001) and progression-free survival was 4.30 versus 2.83 months, respectively (hazard ratio 0.66, 95% CI 0.57-0.77; p<0.0001).This study is helpful to guide a multiline treatment strategy for EGFR-wt NSCLC patients. Immunotherapy is approved for second-line treatment. For third-line treatment, chemotherapy results in longer overall survival and progression-free survival, and should be preferred to EGFR-TKIs.
Auteurs, date et publication :
Auteurs Pascale Tomasini , Solenn Brosseau , Julien Mazières , Jean-Philippe Merlio , Michèle Beau-Faller , Jean Mosser , Marie Wislez , L'Houcine Ouafik , Benjamin Besse , Isabelle Rouquette , Didier Debieuvre , Fabienne Escande , Virginie Westeel , Clarisse Audigier-Valette , Pascale Missy , Alexandra Langlais , Frank Morin , Denis Moro-Sibilot , Gérard Zalcman , Fabrice Barlesi
Publication : The European Respiratory Journal
Date : 2017
Volume : 50
Issue : 2
Pages : 1700514
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Fungal communities in the root endosphere are heterogeneous at fine scale. The passenger hypothesis assumes that this heterogeneity is driven by host plant distribution. Plant composition and host plant configuration should then influence root fungal assemblages. We used a large-scale experimental design of 25 mixtures of grassland plants. We sampled Brachypodium pinnatum in each mesocosm, and used amplicon mass-sequencing to analyze the endospheric mycobiota. We used plant distribution maps to assess plant species richness and evenness (heterogeneity of composition), and patch size and the degree of isolation of B. pinnatum (heterogeneity of configuration) on fungal community assembly. The Glomeromycotina community in B. pinnatum roots was not related to either floristic heterogeneity or productivity. For Ascomycota, the composition of operational taxonomic units (OTUs) was driven by plant evenness while OTU richness decreased with plant richness. For Basidiomycota, richness increased with host plant aggregation and connectivity. Plant productivity influenced Ascomycota, inducing a shift in OTU composition and decreasing evenness. Plant heterogeneity modified root mycobiota, with potential direct (i.e. host preference) and indirect (i.e. adaptations to abiotic conditions driven by plant occurrence over time) effects. Plant communities can be envisioned as microlandscapes consisting of a variety of fungal niches.
Auteurs, date et publication :
Auteurs Cendrine Mony , Philomène Brunellière , Nathan Vannier , Anne-Kristel Bittebiere , Philippe Vandenkoornhuyse
Publication : New Phytologist
Date : 2025
Volume : 225
Issue : 4
Pages : 1777-1787
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
BACKGROUND: Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce.
METHODS: We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an Agrostis stolonifera population. The normalized RNA/DNA ratio, designated the 'mean expression ratio', was used as a functional trait proxy. The link between this trait and phylogenetic relatedness was measured using the Blomberg's K statistic.
RESULTS: Fungal communities were highly diverse. Only ∼1.5% of the 635 OTUs detected were shared by all individuals, however these accounted for 33% of the sequence number. The endophytic fungal communities in plant roots exhibit phylogenetic clustering that can be explained by a plant host effect acting as environmental filter. The 'mean expression ratio' displayed significant but divergent phylogenetic signals between fungal phyla.
DISCUSSION: These results suggest that environmental filtering by the host plant favours the co-existence of related and similar OTUs within the Basidiomycota community assembly, whereas the Ascomycota and Glomeromycota communities seem to be impacted by competitive interactions which promote the co-existence of phylogenetically related but ecologically dissimilar OTUs.
Auteurs, date et publication :
Auteurs Amandine Lê Van , Achim Quaiser , Marie Duhamel , Sophie Michon-Coudouel , Alexis Dufresne , Philippe Vandenkoornhuyse
Publication : PeerJ
Date : 2025
Volume : 5
Pages : e3454
Catégorie(s)
#CNRS #EcoGenO #Université de RennesAuteurs, date et publication :
Auteurs Xu Pan , Mathieu Santonja , Pierre Emmanuel Courty , Olaf Butensch n , Matty Berg , Phil Murray , Benjamin Yguel , Daphn e Brul , Andreas Prinzing
Publication : Authorea
Date : 2020
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind while microorganisms, the invisible majority of biodiversity, were disregarded. We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of one meter over two years (i.e. at five time points) by combining an experimental corridor-mesocosm with high-throughput amplicon sequencing. We show that the plant root endospheric mycobiota was sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta-diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants. Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions.
Auteurs, date et publication :
Auteurs Jie Hu , Philippe Vandenkoornhuyse , Fadwa Khalfallah , Romain Causse-Védrines , Cendrine Mony
Publication : New Phytologist
Date : 2025
Volume : n/a
Issue : n/a