Auteurs, date et publication :

Auteurs Paul Skelley , H Gasca-Álvarez

Publication : Insecta mundi

Date : 2025

Volume : 836

Pages : 1-8

Catégorie(s)

#⛔ No DOI found #CNRS #FORET Nouragues

Résumé

Plants affect the spatial distribution of soil microorganisms, but the influence of the local abiotic context is poorly documented. We investigated the effect of a single plant species, the cushion plant Silene acaulis, on habitat conditions and microbial community. We collected soil from inside (In) and outside (Out) of the cushions on calcareous and siliceous cliffs in the French Alps along an elevation gradient (2,000-3,000 m.a.s.l.). The composition of the microbial communities was assessed by Capillary-Electrophoresis Single Strand Conformation Polymorphism (CE-SSCP). Univariate and multivariate analyses were conducted to characterise the response of the microbial beta-diversity to soil parameters (total C, total N, soil water content, N-NH4+, N-NO3- and pH). Cushions affected the microbial communities, modifying soil properties. The fungal and bacterial communities did not respond to the same abiotic factors. Outside the cushions, the bacterial communities were strongly influenced by bedrock. Inside the cushions, the bacterial communities from both types of bedrock were highly similar, due to the smaller pH differences than in open areas. By contrast, the fungal communities were equally variable inside and outside of the cushions. Outside the cushions, the fungal communities responded weakly to soil pH. Inside the cushions, the fungal communities varied strongly with bedrock and elevation as well as increases in soil nutrients and water content. Furthermore, the dissimilarities in the microbial communities between the In and Out habitats increased with increasing habitat modification and environmental stress. Our results indicate that cushions act as a selective force that counteracts the influence of the bedrock and the resource limitations on the bacterial and fungal communities by buffering soil pH and enhancing soil nutrients. Cushion plants structure microbial communities, and this effect increases in stressful, acidic and nutrient-limited environments.

Auteurs, date et publication :

Auteurs Julien Roy , Cécile Hélène Albert , Philippe Choler , Jean-Christophe Clément , Sébastien Ibanez , Sébastien Lavergne , Patrick Saccone , Lucie Zinger , Roberto Alejandro Geremia

Publication : Frontiers in Microbiology

Date : 2025

Volume : 4

Catégorie(s)

#CNRS #Lautaret #UGA

Résumé

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 Rennes

Auteurs, 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 Rennes

Résumé

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 Rennes

Auteurs, date et publication :

Auteurs Laura García de Jalón , Jean-Marc Limousin , Franck Richard , Arthur Gessler , Martina Peter , Stephan Hättenschwiler , Alexandru Milcu , Ines Ibáñez

Publication : PLOS ONE

Date : 2020

Volume : 15

Issue : 6

Pages : e0229807

Catégorie(s)

#ANR-Citation #CNRS #FORET Puechabon

Résumé

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 Rennes

Résumé

Leaf area index (LAI) is a key ecological indicator for describing the structure of canopies and for modelling energy exchange between atmosphere and biosphere. While LAI of the forest overstory can be accurately assessed over large spatial scales via remote sensing, LAI of the forest understory (LAIu) is still largely ignored in ecological studies and ecosystem modelling due to the fact that it is often too complex to be destructively sampled or approximated by other site parameters. Additionally, so far only few attempts have been made to retrieve understory LAI via remote sensing, because dense canopies with high LAI are often hindering retrieval algorithms to produce meaningful estimates for understory LAI. Consequently, the forest understory still constitutes a poorly investigated research realm impeding ecological studies to properly account for its contribution to the energy absorption capacity of forest stands. This study aims to compare three conceptually different indirect retrieval methodologies for LAIu over a diverse panel of forest understory types distributed across Europe. For this we carried out near-to-surface measurements of understory reflectance spectra as well as digital surface photography over the extended network of Integrated Carbon Observation System (ICOS) forest ecosystem sites. LAIu was assessed by exploiting the empirical relationship between vegetation cover and light absorption (Beer-Lambert- Bouguer law) as well as by utilizing proposed relationships with two prominent vegetation indices: normalized difference vegetation index (NDVI) and simple ratio (SR). Retrievals from the three methods were significantly correlated with each other (r = 0.63–0.99, RMSE = 0.53–0.72), but exhibited also significant bias depending on the LAI scale. The NDVI based retrieval approach most likely overestimates LAI at productive sites when LAIu > 2, while the simple ratio algorithm overestimates LAIu at sites with sparse understory vegetation and presence of litter or bare soil. The purely empirical method based on the Beer-Lambert law of light absorption seems to offer a good compromise, since it provides reasonable LAIu values at both low and higher LAI ranges. Surprisingly, LAIu variation among sites seems to be largely decoupled from differences in climate and light permeability of the overstory, but significantly increased with vegetation diversity (expressed as species richness) and hence proposes new applications of LAIu in ecological modelling.

Auteurs, date et publication :

Auteurs Jan-Peter George , Wei Yang , Hideki Kobayashi , Tobias Biermann , Arnaud Carrara , Edoardo Cremonese , Matthias Cuntz , Silvano Fares , Giacomo Gerosa , Thomas Grünwald , Niklas Hase , Michael Heliasz , Andreas Ibrom , Alexander Knohl , Bart Kruijt , Holger Lange , Jean-Marc Limousin , Denis Loustau , Petr Lukeš , Riccardo Marzuoli

Publication : Ecological Indicators

Date : 2021

Volume : 128

Pages : 107841

Catégorie(s)

#CNRS #FORET Puechabon

Résumé

Abstract DNA metabarcoding is becoming the tool of choice for biodiversity assessment across taxa and environments. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines to remove experimental noise exist. However, these often only partially target produced artefacts, or are marker specific. In addition, assessments of data curation quality and chosen filtering thresholds are seldom available in existing pipelines, partly due to the lack of appropriate visualisation tools. Here, we present metabaR, an r package that provides a comprehensive suite of tools to effectively curate DNA metabarcoding data after basic bioinformatic analyses. In particular, metabaR uses experimental negative or positive controls to identify different types of artefactual sequences, that is, contaminants and tag-jumps. It also flags potentially dysfunctional PCRs based on PCR replicate similarities when those are available. Finally, metabaR provides tools to visualise DNA metabarcoding data characteristics in their experimental context as well as their distribution, and facilitates assessment of the appropriateness of data curation filtering thresholds. metabaR is applicable to any DNA metabarcoding experimental design but is most powerful when the design includes experimental controls and replicates. More generally, the simplicity and flexibility of the package makes it applicable any DNA marker, and data generated with any sequencing platform, and pre-analysed with any bioinformatic pipeline. Its outputs are easily usable for downstream analyses with any ecological r package. metabaR complements existing bioinformatics pipelines by providing scientists with a variety of functions to effectively clean DNA metabarcoding data and avoid serious misinterpretations. It thus offers a promising platform for automatised data quality assessments of DNA metabarcoding data for environmental research and biomonitoring.

Auteurs, date et publication :

Auteurs Lucie Zinger , Clément Lionnet , Anne-Sophie Benoiston , Julian Donald , Céline Mercier , Frédéric Boyer

Publication : Methods in Ecology and Evolution

Date : 2025

Volume : 12

Issue : 4

Pages : 586–592

Catégorie(s)

#CNRS #eDNA

Auteurs, date et publication :

Auteurs Benoît Sotton , Alain Paris , Séverine Le Manach , Alain Blond , Gérard Lacroix , Alexis Millot , Charlotte Duval , Hélène Huet , Qin Qiao , Sophie Labrut , Giovanni Chiapetta , Joelle Vinh , Arnaud Catherine , Benjamin Marie

Publication : Scientific Reports

Date : 2025

Volume : 7

Issue : 1

Catégorie(s)

#ANR-Citation #CNRS #ENS #PLANAQUA