Résumé
Agricultural intensification reduces not only biodiversity in agroecosystems but also key ecosystem functions such as soil fertility. By reintroducing biological diversity in fields, weeds may enhance soil biological fertility through their influence on crop microbiota. However, letting weeds grow in crop fields will depend on weed competitiveness, farmers’ perception and acceptance, and on crop management, which influences the occurrence and the abundance of weeds in the field. This study assessed the use of eight weed species to modify wheat plant root endospheric mycobiota, and the applicability of using these plants for mycobiota enrichment in the field. By combining controlled lab experiments and field studies, we demonstrated that weeds act either as a refuge for a high diversity of fungi or as a vector for transferring fungi to the crop, particularly symbionts. Weeds differed in their competitive effect on wheat growth and only three species significantly reduced wheat growth. Interviews with farmers’ revealed that weed species were better known and more appreciated in crop fields by organic farmers than by conventional farmers. Floristic surveys confirmed that both weed occurrence and cover were higher in organic fields than in conventional fields. A multicriteria analysis showed that Trifolium repens and V. persica had the highest potential for promoting wheat plant mycobiota. Among the weed species tested, these two are worth considering as auxiliaries to improve soil biological fertility in crop fields. Their use with the goal of selecting appropriate crop mycobiota should be relatively easier in organic farms where weeds are better accepted, whereas their use in conventional farms would require raising farmers’ awareness of the benefits of weeds for soil fertility.
Auteurs, date et publication :
Auteurs Claire Ricono , Jie Hu , Philippe Vandenkoornhuyse , Audrey Alignier , Cendrine Mony
Publication : Agriculture, Ecosystems & Environment
Date : 2025
Volume : 379
Pages : 109357
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Slow-growing bacteria, referred as tolerant or persistent, emerge as a major health issue since they are associated with antibiotic treatment failures and relapsing infections. Among others, type I toxin-antitoxin (TA) systems have been linked to slow-growing bacteria formation. They are composed of a peptide toxin whose overexpression confers growth stasis or cell death, and of an RNA antitoxin that base-pairs with the cognate toxin mRNA to inhibit its translation. In the human pathogen Staphylococcus aureus, it was recently shown that the SprF1 antitoxin is able to bind ribosomes to inhibit global translation and promote persister cell formation. Here, we used in silico analysis and MS2-affinity purification coupled with RNA sequencing (MAPS) to expand the RNA targetome of SprF1 and better understand its role in S. aureus antibiotic adaptation. We experimentally uncovered 12 mRNAs targets interacting with SprF1 and demonstrated that SprF1 directly interacts with yidC, encoding a protein insertase, and rpmE2, encoding the ribosomal protein L31, to either decrease or increase their protein expression. Finally, we showed that rpmE2 overexpression is associated with antibiotic tolerance which could contribute to the persister phenotype mediated by SprF1. Altogether, these findings highlight that some type I RNA antitoxins behave like typical regulatory RNAs, by interacting with several targets through various regulatory motifs to participate in bacterial adaptation.
Auteurs, date et publication :
Auteurs Emeline Ostyn , Marc Hallier , Stéphane Dreano , Yoann Augagneur , Marie-Laure Pinel-Marie
Date : 2024
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Earthworms contribute to a wide range of ecosystem services provided by the soil. Nevertheless, synecology of these organisms is still not properly elucidated especially in terms of species interactions. The aim of the present study was to determine the effects of anecic earthworm species interactions on their individual biomass. These effects were measured using three epi-anecic species, Lumbricus rubellus rubellus (Hoffmeister, 1843), Lumbricus centralis (Bouché, 1972), Lumbricus terrestris (Linné 1758), and three strict-anecic species, Aporrectodea caliginosa meridionalis (Bouché, 1972), Aporrectodea nocturna (Evans, 1946), Aporrectodea giardi (Savigny, 1826). Twenty-one pairs of individuals were established following five assemblages: monospecific pairwise assemblages of epi- and strict-anecic earthworms (2 × 3 treatments), bispecific pairwise assemblages within epi- and within strict-anecic earthworms (2 × 3 treatments) and bispecific pairwise assemblages with one epi- and one strict-anecic earthworm (3 × 3 treatments). Treatments were maintained in mesocosms for 30 days under controlled conditions (food provided at the soil surface at the beginning of the experiment) and changes in the earthworm individual biomass were measured. Strict-anecic earthworms in monospecific or bispecific assemblages maintained their initial biomass. In contrast, epi-anecic earthworms exhibited an increase of 12.4% and 23.7% of their biomass in monospecific and bispecific assemblages, respectively. In bispecific assemblages combining one epi- and one strict-anecic earthworm, epi-anecic earthworms solely gained biomass leading to a total increase of a 6.9%. Surprisingly, the biomass' changes were not homogenous within the two sub-categories as the six earthworm species exhibited species-specific responses. The greatest increases in individual biomass were recorded for epi-anecic earthworms in the bispecific assemblages. This study provides further evidence for the distinction between the two anecic sub-categories, as it indicates that species interactions is positive only for epi-anecic earthworm biomass.
Auteurs, date et publication :
Auteurs Kevin Hoeffner , Cécile Monard , Daniel Cluzeau , Mathieu Santonja
Publication : Applied Soil Ecology
Date : 2019
Volume : 144
Pages : 8-11
Catégorie(s)
#CNRS #EcoGenO #Université de RennesAuteurs, date et publication :
Auteurs Solenn Stoeckel , Ronan Becheler , Luis Portillo-Lemus , Marilyne Harang , Anne-Laure Besnard , Gilles Lassalle , Romain Causse-Védrines , Sophie Michon-Coudouel , Daniel J. Park , Bernard J. Pope , Eric J. Petit , Dominique Barloy
Publication : Peer Community Journal
Date : 2025
Volume : 4
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Environmental contamination by xenobiotics represents a major threat for natural ecosystems and public health. In response, xenobiotic detoxification is a fundamental trait of organisms for developmental plasticity and stress tolerance, but the underlying molecular mechanisms remain poorly understood in plants. To decipher this process, we explored the consequences of allopolyploidy on xenobiotic tolerance in the genus Spartina Schreb. Specifically, we focused on microRNAs (miRNAs) owing to their central function in the regulation of gene expression patterns, including responses to stress. Small RNA-Seq was conducted on the parents S. alterniflora and S. maritima, their F1 hybrid S. x townsendii and the allopolyploid S. anglica under phenanthrene-induced stress (phe), a model Polycyclic Aromatic Hydrocarbon (PAH) compound. Differentially expressed miRNAs in response to phe were specifically identified within species. In complement, the respective impacts of hybridization and genome doubling were detected, through changes in miRNA expression patterns between S. x townsendii, S. anglica and the parents. The results support the impact of allopolyploidy in miRNA-guided regulation of plant response to phe. In total, we identified 17 phe-responsive miRNAs in Spartina among up-regulated MIR156 and down-regulated MIR159. We also describe novel phe-responsive miRNAs as putative Spartina-specific gene expression regulators in response to stress. Functional validation using Arabidopsis (L.) Heynh. T-DNA lines inserted in homologous MIR genes was performed, and the divergence of phe-responsive miRNA regulatory networks between Arabidopsis and Spartina was discussed.
Auteurs, date et publication :
Auteurs Armand Cavé-Radet , Armel Salmon , Loup Tran Van Canh , Richard L. Moyle , Lara-Simone Pretorius , Oscar Lima , Malika L. Ainouche , Abdelhak El Amrani
Publication : Plant Molecular Biology
Date : 2023
Volume : 111
Issue : 3
Pages : 309-328
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Treatment with antibiotics leads to the selection of isolates with increased resistance. We investigated if evolution towards resistance was associated with virulence changes, in the context of P. aeruginosa ventilator-associated pneumonia (VAP). Four patients were selected because they had multiple VAP episodes during short periods (12 days to 5 weeks), with emergence of resistance. We performed whole-genome sequencing of 12 P. aeruginosa from bronchoalveolar lavages or blood culture (3 isolates per patient). Production of quorum sensing-dependent virulence factors, serum resistance, cytotoxicity against A549 cells, biofilm production, and twitching motility were studied. Each patient was infected with a unique strain. For all patients, resistance development was explained by genetic events in ampD, mexR or oprD. Additional variations were detected in virulence- and/or fitness-associated genes (algB, gacA, groEL, lasR, mpl, pilE, pilM, rhlR) depending on the strain. We noticed a convergence towards quorum sensing deficiency, correlated with a decrease of pyocyanin and protease production, survival in serum, twitching motility and cytotoxicity. In one patient, changes in pilM and pilE were related to enhanced twitching. We show that the emergence of resistance in P. aeruginosa is associated with virulence modification, even in acute infections. The consequences of this short-term pathoadaptation need to be explored.
Auteurs, date et publication :
Auteurs Elise Persyn , Mohamed Sassi , Marc Aubry , Martin Broly , Sandie Delanou , Karim Asehnoune , Nathalie Caroff , Lise Crémet
Publication : Scientific Reports
Date : 2019
Volume : 9
Issue : 1
Pages : 4720
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.
Auteurs, date et publication :
Auteurs Qicheng Xu , Ning Ling , Achim Quaiser , Junjie Guo , Jianyun Ruan , Shiwei Guo , Qirong Shen , Philippe Vandenkoornhuyse
Publication : Microbial Ecology
Date : 2021
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Background and Aim Water is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptation. Here, we analyzed the endospheric fungal microbiota composition in rice and its relation to plant genotype and drought. Methods Fifteen rice genotypes (Oryza sativa ssp. indica) were grown in the field, under well-watered conditions or exposed to a drought period during flowering. The effect of genotype and treatment on the root fungal microbiota composition was analyzed by 18S ribosomal DNA high throughput sequencing. Grain yield was determined after plant maturation. Results There was a host genotype effect on the fungal community composition. Drought altered the composition of the root-associated fungal community and increased fungal biodiversity. The majority of OTUs identified belonged to the Pezizomycotina subphylum and 37 of these significantly correlated with a higher plant yield under drought, one of them being assigned to Arthrinium phaeospermum. Conclusion This study shows that both plant genotype and drought affect the root-associated fungal community in rice and that some fungi correlate with improved drought tolerance. This work opens new opportunities for basic research on the understanding of how the host affects microbiota recruitment as well as the possible use of specific fungi to improve drought tolerance in rice.
Auteurs, date et publication :
Auteurs Beatriz Andreo-Jimenez , Philippe Vandenkoornhuyse , Amandine Lê Van , Arvid Heutinck , Marie Duhamel , Niteen Kadam , Krishna Jagadish , Carolien Ruyter-Spira , Harro Bouwmeester
Publication : PeerJ
Date : 2019
Volume : 7
Pages : e7463
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Understanding the assembly rules of mycorrhizal fungi is crucial, given their tremendous importance in plant nutrition and health. Differentiation in plant-associated arbuscular mycorrhizal fungi (AMF) is likely driven by a host-preference effect. Coexisting plant species may then affect a focal plant microbiota through fungal dispersal among plants, and plant preferential recruitment of AMF. Both mechanisms are likely shaped by the plant's phylogenetic and functional strategies. We expected that (a) the structure of AMF assemblages associated with a focal plant depends on the identity of the neighbouring plant species; (b) this effect would be predicted by the phylogenetic and functional similarity between the focal and neighbouring plant species. These predictions were tested during the first stages of growth, by simulating the early development of plants within a community Using an experimental matrix-focal plant species design testing 15 neighbouring plants from five taxonomic families, we demonstrated that the neighbouring plants provided different species pools for the focal plant, Medicago truncatula, and influenced AMF communities associated with focal plant, especially in terms of richness but not relative evenness. Medicago truncatula grown with Brassicaceae or other Poaceae species displayed respectively no or low AMF richness compared to those grown with Rosaceae and Asteraceae species. These effects were weakly dependent on the phylogenetic distance from the neighbouring plant but were predicted by the functional proximity. AMF assemblages were enriched and bore more resemblance to the neighbouring plants when the neighbouring plants were functionally dissimilar from the focal one. Functional dissimilarity was only a significant predictor when based on traits characterizing the nutrient use and uptake strategy rather than on a more integrated growing strategy of the plant. Microbiota composition was shown to be dependent on the identity of the neighbouring plant, particularly on its functional below-ground niche. At the colonization stage, when the plant arrives in a community, plant mycobiota might be influenced by the spatial distribution of plants already present in the community. This work suggests a new view of the concept of niche partitioning in space for plants based on microorganism–plant interactions. A free Plain Language Summary can be found within the Supporting Information of this article.
Auteurs, date et publication :
Auteurs Cendrine Mony , Valentin Gaudu , Claire Ricono , Olivier Jambon , Philippe Vandenkoornhuyse
Publication : Functional Ecology
Date : 2025
Volume : 35
Issue : 8
Pages : 1768-1782
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
To identify novel epigenetic signatures that could provide predictive information that is complementary to promoter methylation status of the O-6-methylguanine-DNA methyltransferase (MGMT) gene for predicting temozolomide (TMZ) response, among glioblastomas (GBMs) without glioma-CpGs island methylator phenotype (G-CIMP)
Auteurs, date et publication :
Auteurs An-An Yin , Ya-Long He , Amandine Etcheverry , Yu-He Liu , Marc Aubry , Jill Barnholtz-Sloan , Bo-Lin Liu , Jean Mosser , Zi-Fan Lu , Xiang Zhang
Publication : Clinical Epigenetics
Date : 2019
Volume : 11
Issue : 1
Pages : 76