Résumé
Micro-organisms associated with plants provide essential functions to their hosts, and therefore affect ecosystem productivity. Agricultural intensification has modified microbial diversity in the soil reservoir and may affect plant–microbial recruitment. Weeds develop spontaneously in crop fields, and could influence micro-organisms associated with crop plants through a neighbourhood effect. We explore the effect of weed species on crop plant microbiota as potentially auxiliary plants that affect agricultural productivity. We combined field and controlled laboratory studies to analyse the neighbourhood effect of weeds on wheat root endospheric mycobiota (i.e. fungi within roots) and growth. First, we analysed the effect of weed species diversity and identity recorded in the neighbourhood of individual wheat plants on soil and wheat root mycobiota in the field. Second, we used a plant-matrix design in laboratory conditions to test the effect of weed identity (nine weed treatments) and their ability to transmit root mycobiota to wheat roots, and the resulting impact on wheat growth. In contrast to soil mycobiota, we demonstrated that wheat root endospheric mycobiota was influenced by the diversity and identity of weeds developing in their 1 m2 neighbourhood. Wheat root endospheric microbiota strongly differs in terms of richness and composition depending on the neighbouring weed plant species. Weed species transmitted from 13% to 74% of their root microbiota to wheat roots depending on weed identity in controlled conditions. Synthesis. Weed neighbours modified wheat plant performance, possibly as a result of competitive interactions and changes in microbiota. Our findings suggest that crop root mycobiota was variable and was modulated by their weed neighbourhood. Synergistic effects between mycobiota of crops and weeds could therefore contribute to soil biodiversity and sustainable agriculture.
Auteurs, date et publication :
Auteurs Jie Hu , Claire Ricono , Paola Fournier , Samuel Mondy , Philippe Vandenkoornhuyse , Cendrine Mony
Publication : Journal of Ecology
Date : 2025
Volume : 111
Issue : 5
Pages : 994-1008
Catégorie(s)
#ANR-Citation #CNRS #EcoGenO #Université de RennesRésumé
Nitrogen loads in natural waters remain elevated in populated and agricultural areas with serious impact on estuarine and coastal ecosystems. Intertidal sediments can play a significant role in attenuating the high nitrogen levels in water via microbial nitrate reduction, in general dominated by denitrification. These heterotrophic processes are heavily mediated by both the quantity and quality of organic matter available. Benthic microalgae were experimentally investigated as organic carbon source for denitrifying microbes in intertidal mudflat sediments from the Seine Estuary (France). Dry microphytobenthos (including algae and their extracellular polymeric substances) were added to sediments and nitrate reduction rates were monitored over a two-week period using anoxic controlled flow-through reactor approach. Our results show that microphytobenthos addition resulted in significantly higher nitrate reduction (67–332% increase), highly related to the added amount of microphytobenthos. Moreover, increase of the low molecular weight carbohydrates consumption (11–39%) highlight the measurable contribution of extracellular polymeric substances to the carbon consumption during nitrate reduction. The addition of microphytobenthos increased the abundance of nitrite reductase genes, especially those encoding the nirS gene (43–152% increase) while nitrous oxide reductase genes (nosZ gene) remained constant. Microphytobenthos appeared to favor complete denitrification as suggested by an increase in nirS and a decrease in clade II nosZ gene copy numbers. This study confirms experimentally the assumption that microbes use microalgae and particularly labile extracellular polymeric substances as a carbon substrate for nitrate reduction. These results reinforce the impact played by microphytobenthos in intertidal mudflats by highlighting their role on denitrifying microbes and nitrate removal from water.
Auteurs, date et publication :
Auteurs Jérôme Morelle , Céline Roose-Amsaleg , Anniet M. Laverman
Publication : Estuarine, Coastal and Shelf Science
Date : 2022
Volume : 275
Pages : 108006
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering.
Auteurs, date et publication :
Auteurs Victor Mataigne , Nathan Vannier , Philippe Vandenkoornhuyse , Stéphane Hacquard
Publication : Frontiers in Microbiology
Date : 2021
Volume : 12
Pages : 780469
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Introduction
Microbial generalists and specialists are thought to have distinct impacts on community dynamics, while there have been limited efforts to estimate their contribution to microbial diversity.
Objectives
We aimed to resolve this research gap in microbial ecology to strengthen our understanding of the biogeography of microbial diversity, with implications for global-scale biodiversity mapping.
Methods
Herein, we identified the ecological characteristics of microbial generalists and specialists across over 3,000 farmland soil samples from eleven countries that encompassed seven climate types.
Results
Considering the distinct distributions of generalists and specialists in degree of connexions, betweenness and as key species in network topology, both generalists and specialists contributed to species interactions, though through different modalities. A stronger signature of deterministic processes in specialists indicated their lower tolerance to environment fluctuations. Generalists, in contrast, were more characterized by stochastic processes with higher diversification and transition rates that suggested more important roles in maintaining community stability when exposed to environmental disturbances. The relationship between latitude and diversity combining with distance-decay effects showed that generalists dampened microbial biogeographical patterns, with contrasting impacts by specialists.
Conclusion
By demonstrating the ecological characteristics of microbial generalists and specialists, this study deepens our understanding of microbial diversity and highlights the need to impart systematic distinctions among different categories of species when modelling and predicting the fate of ecosystems in the face of global climate change, rather than assuming that species are functionally equivalent.
Auteurs, date et publication :
Auteurs Qicheng Xu , Philippe Vandenkoornhuyse , Ling Li , Junjie Guo , Chen Zhu , Shiwei Guo , Ning Ling , Qirong Shen
Publication : Journal of Advanced Research
Date : 2025
Catégorie(s)
#CNRS #EcoGenO #Université de RennesAuteurs, date et publication :
Auteurs Cendrine Mony , Brendan J. M. Bohannan , Kabir Peay , Philippe Vandenkoornhuyse , Mathew A. Leibold
Date : 2021
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Abstract
Background
Long-term responders (LTRs) are defined by at least 18 months of response to sunitinib in metastatic clear-cell renal cell carcinoma (ccRCC). Well-described by clinical studies, the phenotype of these tumors has never been explored.
Patients and Methods
In a retrospective and multicenter study, 90 ccRCCs of patients with metastatic disease were analyzed. Immunohistochemistry (carbonic anhydrase IX, vascular endothelial growth factor, c-MET, programmed death-ligand 1 [PD-L1], and PD-1) and VHL status were performed. Progression-free survival and overall survival were calculated from sunitinib introduction and from progression. LTRs and their corresponding tumors were compared with others using univariate and multivariate analysis.
Results
Twenty-eight patients were LTRs. They had a median progression-free survival of 28 months versus 4 months for other patients (P < .001). Similarly, LTRs had a median overall survival of 49 months versus 14 months (P < .001), even from progression (median, 21 vs. 7 months; P = .029). They were associated with a favorable or intermediate risk (International Metastatic Renal Cell Carcinoma Database Consortium model) (P = .007) and less liver metastasis (P = .036). They experienced more frequent complete or partial responses at the first radiologic evaluation (P = .035). The corresponding ccRCCs were associated with less nucleolar International Society for Urological Pathology grade 4 (P = .037) and hilar fat infiltration (P = .006). They were also associated with low PD-L1 expression (P = .02). Only the International Metastatic Renal Cell Carcinoma Database Consortium model and PD-L1 expression remained significant after multivariate analysis (P = .014 and P = .029, respectively).
Conclusion
Primary tumor characteristics of LTRs were studied for the first time and demonstrated a different phenotype. Interestingly, they were characterized by low expression of PD-L1, suggesting a potentially lower impact of targeted immunotherapy in these patients.
Auteurs, date et publication :
Auteurs Solène-Florence Kammerer-Jacquet , Angelique Brunot , Mathilde Lefort , Sahar Bayat , Benoit Peyronnet , Gregory Verhoest , Romain Mathieu , Alexandra Lespagnol , Jean Mosser , Brigitte Laguerre , Alain Ravaud , Jean-Christophe Bernhard , Frantz Dupuis , Mokrane Yacoub , Marc-Antoine Belaud-Rotureau , Karim Bensalah , Nathalie Rioux-Leclercq
Publication : Clinical Genitourinary Cancer
Date : 2019
Volume : 17
Issue : 3
Pages : 169-176.e1
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Milk production is highly dependent on the optimal development of the mammary epithelium. It is therefore essential to better understand mammary epithelial cell growth and maintenance from the related epithelial lineage during the animal life. Here, we characterized the epithelial lineage at puberty, lactation and dry-off in bovine using the cell surface markers CD49f, CD24, and CD10. The pubertal period was characterized by a high proportion of CD49fpos cells corresponding to various epithelial subpopulations, notably the CD24pos subpopulations. The proportion of CD49fpos cells was weaker during lactation and dry-off, and CD24pos cells were relatively few. Of note, the (sub)population profile at dry-off appeared close to that during lactation. Using a targeted gene approach, we associated specific genes with epithelial subpopulations, their expression level varying, or not, according to physiological stages. Caseins were only expressed in the CD49fmedCD24neg subpopulation. Basal marker genes (keratin(KRT)5, KRT14 and αSMA) were found in the CD49fhighCD24neg subpopulations. Luminal gene markers (KRT7, KRT8 and KRT19, CDH1 and the PRLR) were expressed in the CD49flowCD24neg subpopulation. The CD49flowCD24pos subpopulation, only abundant at puberty, expressed luminal gene markers and KI67 at high level. In contrast to others, the CD49fhighCD24pos cells accounted for a small proportion of total cells, decreasing from puberty to dry-off. They were characterized by expression of luminal and basal gene markers and low KI67 level. Interestingly, this subpopulation showed a remarkable stability of gene expression profile throughout physiological stages and bear the hallmark of quiescence that designate them as the potential bovine mammary stem cells.
Auteurs, date et publication :
Auteurs Laurence Finot , Eric Chanat , Frederic Dessauge
Publication : Journal of Mammary Gland Biology and Neoplasia
Date : 2019
Volume : 24
Issue : 2
Pages : 185-197
Catégorie(s)
#CNRS #EcoGenO #Université de RennesAuteurs, date et publication :
Auteurs Luc Burté , Charles A. Cravotta , Lorine Bethencourt , Julien Farasin , Mathieu Pédrot , Alexis Dufresne , Marie-Françoise Gérard , Catherine Baranger , Tanguy Le Borgne , Luc Aquilina
Publication : Environmental Science & Technology
Date : 2019
Volume : 53
Issue : 10
Pages : 5848-5857
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Agricultural intensification has been demonstrated to induce a loss of biodiversity. Despite the key role of symbiotic microorganisms in plant nutrition and protection, the impact of agricultural intensification on these microorganisms is not fully understood. Organic farming and field edges (as semi-natural elements) may promote a higher microbial diversity thanks to lower anthropic disturbance and higher plant diversity. We sampled wheat individuals in pairs of wheat fields (one organic and one conventional) along a distance gradient to the edges (hedgerow vs. grassy), in 20 landscape windows selected along an uncorrelated gradient of organic farming and hedgerow density. We demonstrated that organic farming shaped microbial composition and increased fungal and bacterial richness, while hedgerows had a neutral or negative effect on richness depending on the microbial phyla considered. In contrast to bacteria, fungal communities were heterogeneously distributed within fields, having a higher diversity for some phyla close to field edges. Overall we highlighted that fungi responded more to the field scale while bacteria were more affected by landscape scale. The effect of agricultural intensification on plant microbiota and therefore on the functions provided by microorganisms to the plants has to be considered at a multiple spatial scale—from field to landscape.
Auteurs, date et publication :
Auteurs Claire Ricono , Philippe Vandenkoornhuyse , Stéphanie Aviron , Olivier Jambon , Sophie Michon-Coudouel , Romain Causse-Vedrines , Solène Mauger , Cendrine Mony
Publication : FEMS Microbiology Ecology
Date : 2022
Volume : 98
Issue : 3
Pages : fiac027
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Due to the importance of arbuscular mycorrhizal fungi (AMF) in ecosystem productivity, a key ecological question is how do their communities assemble? As plant spatial patterns constitute a mosaic of AM fungi habitats, we hypothesized that AM fungal community assembly is determined by plant community structure, both in space and time. We tested our hypothesis by sampling individuals of two host-plant species, Brachypodium pinnatum and Elytrigia repens, from experimental communities cultivated in mesocosms, and assessed their AM fungal root colonizers by mass sequencing. We related AM fungal community structure to the distribution of neighbouring plant species at different spatio-temporal scales. We demonstrated that AM fungal community assembly depends mostly on past plant spatial patterns at a small spatial scale (5 cm), indicating that plants growing at given locations leave a footprint on the AM fungi community. This spatial scale of response was also influenced by the host-plant species, probably by its clonal propagation. Synthesis. Overall, we highlighted that processes involved in Arbuscular mycorrhizal (AM) fungal community assembly do not operate at the rough scale of the overall plant community mosaic but are instead locally determined, delineating the AM fungal ‘eye-view’ of the host-plant community.
Auteurs, date et publication :
Auteurs Anne-Kristel Bittebiere , Philippe Vandenkoornhuyse , Elodie Maluenda , Agnès Gareil , Alexandra Dheilly , Sophie Coudouel , Mathieu Bahin , Cendrine Mony
Publication : Journal of Ecology
Date : 2025
Volume : 108
Issue : 2
Pages : 546-560