Auteurs, date et publication :
Auteurs Clément Lermyte , Pierre-Michel Forget
Publication : Tropical Conservation Science
Date : 2025
Volume : 2
Issue : 4
Pages : 374-387
Catégorie(s)
#CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs Olivier Boissier , Axelle Bouiges , Irene Mendoza , François Feer , Pierre‐Michel Forget
Publication : Biotropica
Date : 2025
Volume : 46
Issue : 5
Pages : 633-641
Catégorie(s)
#CNRS #FORET NouraguesRésumé
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 RennesAuteurs, date et publication :
Auteurs Christopher Baraloto , Quentin Molto , Suzanne Rabaud , Bruno Hérault , Renato Valencia , Lilian Blanc , Paul V. A. Fine , Jill Thompson
Publication : Biotropica
Date : 2013
Volume : 45
Issue : 3
Pages : 288–298
Catégorie(s)
#CIRAD #CNRS #FORET Nouragues #FORET ParacouRésumé
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
The most unusual, and thus irreplaceable, functions performed by species in three different species-rich ecosystems are fulfilled by only the rare species in these ecosystems.
Auteurs, date et publication :
Auteurs David Mouillot , David R. Bellwood , Christopher Baraloto , Jerome Chave , Rene Galzin , Mireille Harmelin-Vivien , Michel Kulbicki , Sebastien Lavergne , Sandra Lavorel , Nicolas Mouquet , C. E. Timothy Paine , Julien Renaud , Wilfried Thuiller , Georgina M. Mace
Publication : PLoS Biology
Date : 2013
Volume : 11
Issue : 5
Pages : e1001569
Catégorie(s)
#CIRAD #CNRS #FORET Nouragues #FORET ParacouRésumé
A central challenge in ecology is understanding the emergence of patterns as the result of interactions among individuals. Dynamic forest models can provide a fine-scale description of the ecological, physiological and environmental processes that explain the demography of coexisting tree species. This in turn helps predict changes under future scenarios. However, model accessibility is a major obstacle to a wide use and communication across scientific disciplines and for educational purposes. Here, we present the R package rcontroll, which provides access to the TROLL forest simulator in the R environment. TROLL is individual-based and spatially explicit and leverages knowledge of ecology, biogeochemistry and tree ecophysiology through a trait-based parameterisation. TROLL has been used to simulate carbon fluxes and tree diversity in tropical and subtropical forests and to explore forest resilience to disturbance and environmental changes more generally. rcontroll provides a user-friendly environment to set up and analyse TROLL simulations with varying community compositions, ecological parameters and climate conditions. We show how to test parameter sensitivity in TROLL using the rcontroll R package. We also demonstrate the flexibility and ease of use of rcontroll by replicating a previously published study based on the TROLL simulator. Both examples are included with reproducible code documents. Complex forest simulators are important scientific tools for science and education, and wide access to these tools is an important condition for their adoption. TROLL is designed to address a wide range of ecological and environmental questions, and the new R package rcontroll is designed to be an entry point for TROLL model users.
Auteurs, date et publication :
Auteurs Sylvain Schmitt , Guillaume Salzet , Fabian Jörg Fischer , Isabelle Maréchaux , Jerome Chave
Publication : Methods in Ecology and Evolution
Date : 2025
Volume : 14
Issue : 11
Pages : 2749-2757
Catégorie(s)
#ANR-Citation #CNRS #FORET NouraguesRésumé
The breakdown of plant material fuels soil functioning and biodiversity. Currently, process understanding of global decomposition patterns and the drivers of such patterns are hampered by the lack of coherent large-scale datasets. We buried 36,000 individual litterbags (tea bags) worldwide and found an overall negative correlation between initial mass-loss rates and stabilization factors of plantderived carbon, using the Tea Bag Index (TBI). The stabilization factor quantifies the degree to which easy-to-degrade components accumulate during early-stage decomposition (e.g. by environmental limitations). However, agriculture and an interaction between moisture and temperature led to a decoupling between initial mass-loss rates and stabilization, notably in colder locations. Using TBI improved mass-loss estimates of natural litter compared to models that ignored stabilization. Ignoring the transformation of dead plant material to more recalcitrant substances during early-stage decomposition, and the environmental control of this transformation, could overestimate carbon losses during early decomposition in carbon cycle models.
Auteurs, date et publication :
Auteurs Judith M. Sarneel , Mariet M. Hefting , Taru Sandén , Johan Van Den Hoogen , Devin Routh , Bhupendra S. Adhikari , Juha M. Alatalo , Alla Aleksanyan , Inge H. J. Althuizen , Mohammed H. S. A. Alsafran , Jeff W. Atkins , Laurent Augusto , Mika Aurela , Aleksej V. Azarov , Isabel C. Barrio , Claus Beier , María D. Bejarano , Sue E. Benham , Björn Berg , Nadezhda V. Bezler
Publication : Ecology Letters
Date : 2025
Volume : 27
Issue : 5
Pages : e14415
Catégorie(s)
#CNRS #FORET PuechabonRésumé
Changes in rainfall amounts and patterns have been observed and are expected to continue in the near future with potentially significant ecological and societal consequences. Modelling vegetation responses to changes in rainfall is thus crucial to project water and carbon cycles in the future. In this study, we present the results of a new model-data intercomparison project, where we tested the ability of 10 terrestrial biosphere models to reproduce the observed sensitivity of ecosystem productivity to rainfall changes at 10 sites across the globe, in nine of which, rainfall exclusion and/or irrigation experiments had been performed. The key results are as follows: (a) Intermodel variation is generally large and model agreement varies with timescales. In severely water-limited sites, models only agree on the interannual variability of evapotranspiration and to a smaller extent on gross primary productivity. In more mesic sites, model agreement for both water and carbon fluxes is typically higher on fine (daily–monthly) timescales and reduces on longer (seasonal–annual) scales. (b) Models on average overestimate the relationship between ecosystem productivity and mean rainfall amounts across sites (in space) and have a low capacity in reproducing the temporal (interannual) sensitivity of vegetation productivity to annual rainfall at a given site, even though observation uncertainty is comparable to inter-model variability. (c) Most models reproduced the sign of the observed patterns in productivity changes in rainfall manipulation experiments but had a low capacity in reproducing the observed magnitude of productivity changes. Models better reproduced the observed productivity responses due to rainfall exclusion than addition. (d) All models attribute ecosystem productivity changes to the intensity of vegetation stress and peak leaf area, whereas the impact of the change in growing season length is negligible. The relative contribution of the peak leaf area and vegetation stress intensity was highly variable among models.
Auteurs, date et publication :
Auteurs Athanasios Paschalis , Simone Fatichi , Jakob Zscheischler , Philippe Ciais , Michael Bahn , Lena Boysen , Jinfeng Chang , Martin De Kauwe , Marc Estiarte , Daniel Goll , Paul J Hanson , Anna B Harper , Enqing Hou , Jaime Kigel , Alan K Knapp , Klaus S Larsen , Wei Li , Sebastian Lienert , Yiqi Luo , Patrick Meir
Publication : Global Change Biology
Date : 2025
Volume : 26
Pages : 3336-3355
Catégorie(s)
#CNRS #FORET PuechabonAuteurs, date et publication :
Auteurs Terry L Erwin
Publication : ZooKeys
Date : 2025
Issue : 145
Pages : 79