Auteurs, date et publication :
Auteurs
Date : 1970
Catégorie(s)
#Genosol #INRAERésumé
Fin de vie des résidus de polymères (bio)dégradables - BIOMALEG
Auteurs, date et publication :
Auteurs
Date : 1970
Catégorie(s)
#Genosol #INRAEAuteurs, date et publication :
Auteurs S. Dequiedt , N. P. A. Saby , M. Lelievre , C. Jolivet , J. Thioulouse , B. Toutain , D. Arrouays , A. Bispo , P. Lemanceau , L. Ranjard
Publication : Global Ecology and Biogeography
Date : 2025
Volume : 20
Issue : 4
Pages : 641-652
Catégorie(s)
#Genosol #INRAERésumé
Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1 / FF390. This in silico analysis of the specificity of FR1 / FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1 / FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.
Auteurs, date et publication :
Auteurs Nicolas Chemidlin Prévost-Bouré , Richard Christen , Samuel Dequiedt , Christophe Mougel , Mélanie Lelièvre , Claudy Jolivet , Hamid Reza Shahbazkia , Laure Guillou , Dominique Arrouays , Lionel Ranjard
Publication : Plos One
Date : 2011
Volume : 6
Issue : 9
Pages : e24166
Catégorie(s)
#Genosol #INRAERésumé
Spatial scaling and determinism of the wide-scale distribution of macroorganism diversity has been largely demonstrated over a century. For microorganisms, and especially for soil bacteria, this fundamental question requires more thorough investigation, as little information has been reported to date. Here by applying the taxa–area relationship to the largest spatially explicit soil sampling available in France (2,085 soils, area covered ~5.3 × 105 km2) and developing an innovative evaluation of the habitat–area relationship, we show that the turnover rate of bacterial diversity in soils on a wide scale is highly significant and strongly correlated with the turnover rate of soil habitat. As the diversity of micro- and macroorganisms appears to be driven by similar processes (dispersal and selection), maintaining diverse and spatially structured habitats is essential for soil biological patrimony and the resulting ecosystem services.
Auteurs, date et publication :
Auteurs L. Ranjard , S. Dequiedt , N. Chemidlin Prévost-Bouré , J. Thioulouse , N. P. A. Saby , M. Lelievre , P. A. Maron , F. E. R. Morin , A. Bispo , C. Jolivet , D. Arrouays , P. Lemanceau
Publication : Nature Communications
Date : 2013
Volume : 4
Pages : 1434
Catégorie(s)
#Genosol #INRAERésumé
The turnover of organic matter in soil depends on the activity of microbial decomposers. However, little is known about how modifications of the diversity of soil microbial communities induced by fresh organic matter (FOM) inputs can regulate carbon cycling. Here, we investigated the decomposition of two 13C labeled crop residues (wheat and alfalfa) and the dynamics of the genetic structure and taxonomic composition of the soil bacterial communities decomposing 13C labeled FOM and native unlabeled soil organic matter (SOM), respectively. It was achieved by combining the stable isotope probing method with molecular tools (DNA genotyping and pyrosequencing of 16S rDNA). Although a priming effect (PE) was always induced by residue addition, its intensity increased with the degradability of the plant residue. The input of both wheat and alfalfa residues induced a rapid dynamics of FOM-degrading communities, corresponding to the stimulation of bacterial phyla which have been previously described as copiotrophic organisms. However, the dynamics and the identity of the bacterial groups stimulated depended on the residue added, with Firmicutes dominating in the wheat treatment and Proteobacteria dominating in the alfalfa treatment after 3 days of incubation. In both treatments, SOM-degrading communities were dominated by Acidobacteria, Verrucomicrobia, and Gemmatimonadetes phyla which have been previously described as oligotrophic organisms. An early stimulation of SOM-degrading populations mainly belonging to Firmicutes and Bacteroidetes groups was observed in the alfalfa treatment whereas no change occurred in the wheat treatment. Our findings support the hypothesis that the succession of bacterial taxonomic groups occurring in SOM- and FOM-degrading communities during the degradation process may be an important driver of the PE, and consequently of carbon dynamics in soil.
Auteurs, date et publication :
Auteurs Noémie Pascault , Lionel Ranjard , Aurore Kaisermann , Dipankar Bachar , Richard Christen , Sébastien Terrat , Olivier Mathieu , Jean Lévêque , Christophe Mougel , Catherine Henault , Philippe Lemanceau , Michel Péan , Séverine Boiry , Sébastien Fontaine , Pierre-Alain Maron
Publication : Ecosystems
Date : 2013
Volume : 16
Issue : 5
Pages : 810-822
Catégorie(s)
#Genosol #INRAERésumé
Agricultural practices should modify the diversity of soil microbes. However, the precise relationships between soil properties and microbial diversity are poorly known. Here, we study the effect of agricultural management on soil microbial diversity and C turnover in tropical grassland of north-eastern Laos. Three years after native grassland conversion into agricultural land, we compared soils from five land use management systems: one till versus two no-till rotational cropping systems, one no-till improved pasture and the natural grassland. Soils were incubated in microcosms during 64 days at optimum temperature and humidity. Bacterial and fungal diversity were evaluated by metagenomic 454-pyrosequencing of 16S and 18SrRNA genes, respectively. Changes in soil respiration patterns were evaluated by monitoring 12C- and 13C-CO2 release after soil amendment with 13C-labelled wheat residues. Results show that residue mineralization increased with bacterial richness and diversity in the tilled treatment 7 days after soil amendment. Native soil organic C mineralization and priming effect increased with fungal richness and diversity in improved pasture and natural grassland. No-till cropping systems represented intermediate situations between tillage and pasture systems. Our findings evidence the potential of controlling soil microbial diversity by agricultural practices to improve soil biological properties. We suggest the promotion of no-till systems as a fair compromise between the need for agriculture intensification and soil ecological processes preservation.
Auteurs, date et publication :
Auteurs Pascal Lienhard , Sébastien Terrat , Olivier Mathieu , Jean Levêque , Nicolas Chemidlin Prévost-Bouré , Virginie Nowak , Tiffanie Régnier , Céline Faivre , Sengphanh Sayphoummie , Khamkéo Panyasiri , Florent Tivet , Lionel Ranjard , Pierre-Alain Maron
Publication : Environmental Chemistry Letters
Date : 2013
Volume : 11
Issue : 4
Pages : 391-398
Catégorie(s)
#Genosol #INRAERésumé
Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current ‘global changes’ context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.
Auteurs, date et publication :
Auteurs Vincent Tardy , Olivier Mathieu , Jean Lévêque , Sébastien Terrat , Abad Chabbi , Philippe Lemanceau , Lionel Ranjard , Pierre-Alain Maron
Publication : Environmental Microbiology Reports
Date : 2025
Volume : 6
Issue : 2
Pages : 173-183
Catégorie(s)
#ACBB #ACBB Lusignan #ANR-Citation #GenosolRésumé
Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes<Burgundy≤Brittany<<South-East) using the systematic grid of French Soil Quality Monitoring Network to evaluate the communities’ composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to 120 km radius) and/or medium (40 to 65 km radius) spatial scales, suggesting dispersal limitations at these scales.
Auteurs, date et publication :
Auteurs Nicolas Chemidlin Prévost-Bouré , Samuel Dequiedt , Jean Thioulouse , Mélanie Lelièvre , Nicolas P. A. Saby , Claudy Jolivet , Dominique Arrouays , Pierre Plassart , Philippe Lemanceau , Lionel Ranjard
Publication : Plos One
Date : 2014
Volume : 9
Issue : 11
Pages : e111667
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs Sylvie Nazaret , Rustam Aminov
Publication : Frontiers in Microbiology
Date : 2014
Volume : 5