Résumé
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
Catégorie(s)
#Genosol #INRAERésumé
Intensive land use practices necessary for providing food and raw materials are known to have a deleterious effect on soil. However, the effects that such practices have on soil microbes are less well understood. To investigate the effects of land use intensification on soil microbial communities we used a combined T-RFLP and pyrosequencing approach to study bacteria, archaea and fungi in spring and autumn at five long term observatories (LTOs) in Europe; each with a particular land use type and contrasting levels of intensification (low and high). Generally, due to large gradients in soil variables, both molecular methods revealed that soil microbial communities were structured according to differences in soil conditions between the LTOs, more so than land use intensity. Moreover, variance partitioning analysis also showed that soil properties better explained the differences in microbial communities than land use intensity effects. Predictable responses in dominant bacterial, archaeal and fungal taxa to edaphic conditions (e.g. soil pH and resource availability) were apparent between the LTOs. Some effects of land use intensification at individual field sites were observed. However, these effects were manifest when land use change affected soil conditions. Uniquely, this study details the responses of different microbial groups to soil type and land use intensification, and their relative importance across a range of European field sites. These findings reinforce our understanding of drivers impacting soil microbial community structure at both field and larger geographic scales.
Auteurs, date et publication :
Auteurs Bruce C. Thomson , Emilie Tisserant , Pierre Plassart , Stéphane Uroz , Rob I. Griffiths , S. Emilia Hannula , Marc Buée , Christophe Mougel , Lionel Ranjard , Johannes A. Van Veen , Francis Martin , Mark J. Bailey , Philippe Lemanceau
Publication : Soil Biology and Biochemistry
Date : 2015
Volume : 88
Pages : 403-413
Catégorie(s)
#Genosol #INRAERésumé
Soil is a primary resource used by mankind to ensure its needs mainly through agriculture. Its sustainability is regulated by the indigenous organisms it contains such as microorganisms. Current agricultural practices employ mixtures of pesticides to ensure the crops yield and can potentially impair these non-target organisms. However despite this environmental reality, studies dealing the susceptibility of microorganisms to pesticide mixtures are scarce. In this context, we designed a 3-month microcosm study to assess the ecotoxicity of realistic herbicide mixtures of formulated S-metolachlor (Dual Gold Safeneur®), mesotrione (Callisto®), and nicosulfuron (Milagro®) on the abundance, the diversity, and the activities of microorganisms from a “clay/organic matter-rich” soil, with a particular attention given to N-cycle communities. These communities appeared to be quite resistant to realistic mixtures even if transient effects occurred on the N-cycle-related communities with an increase of ammonification and an inhibition of nitrification as a short-term effect, followed by an increase of denitrification and an accumulation of nitrates. As nitrates are known to be highly leachable with a strong pollution potential, intensive studies should be carried out at field level to conclude on this potential accumulation and its consequences. Moreover, these data now need to be compared with other agricultural soils receiving these herbicide mixtures in order to bring general conclusion on such practices.
Auteurs, date et publication :
Auteurs Pierre Joly , Frédérique Bonnemoy , Pascale Besse-Hoggan , Fanny Perrière , Olivier Crouzet , Nathalie Cheviron , Clarisse Mallet
Publication : Water, air and soil pollution
Date : 2015
Volume : 226
Issue : 12
Pages : 413
Catégorie(s)
#BiochemEnv #Genosol #INRAERésumé
Land use practices alter the biomass and structure Of soil microbial communities. However, the impact of land management intensity on soil microbial diversity (i.e. richness and evenness) and consequences for functioning is still poorly understood. Here, we addressed this question by coupling molecular characterization of microbial diversity with measurements of carbon (C) mineralization in soils obtained from three locations across Europe, each representing a gradient of land management intensity under different soil and environmental conditions. Bacterial and fungal diversity were characterized by high throughput sequencing of ribosomal genes. Carbon cycling activities (i.e., mineralization of autochthonous soil organic matter, mineralization of allochthonous plant residues) were measured by quantifying C-12- and C-13-CO2 release after soils had been amended, or not, with C-13-labelled wheat residues. Variation partitioning analysis was used to rank biological and physicochemical soil parameters according to their relative contribution to these activities. Across all three locations, microbial diversity was greatest at intermediate levels of land use intensity, indicating that optimal management of soil microbial diversity might not be achieved under the least intensive agriculture. Microbial richness was the best predictor of the C-cycling activities, with bacterial and fungal richness explaining 32.2 and 17% of the intensity of autochthonous soil organic matter mineralization; and fungal richness explaining 77% of the intensity of wheat residues mineralization. Altogether, our results provide evidence that there is scope for improvement in soil management to enhance microbial biodiversity and optimize C transformations mediated by microbial communities in soil. (C) 2015 Elsevier Ltd. All rights reserved.
Auteurs, date et publication :
Auteurs Vincent Tardy , Ayme Spor , Olivier Mathieu , Jean Leveque , Sebastien Terrat , Pierre Plassart , Tiffanie Regnier , Richard D. Bardgett , Wim H. van der Putten , Pier Paolo Roggero , Giovanna Seddaiu , Simonetta Bagella , Philippe Lemanceau , Lionel Ranjard , Pierre-Alain Maron
Publication : Soil Biology and Biochemistry
Date : 2015
Volume : 90
Pages : 204-213
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Dissolved organic matter in soil is a highly reactive pool of organic matter and is of great importance for biogeochemical cycles in soil. A better understanding of its dynamics relies on its molecular characterisation. Here, the molecular composition of water-extracted organic matter at elevated pressure and temperature (PH-WEOM) obtained from 120 Burgundy soils was investigated using high-field Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR MS). Unsupervised multivariate statistical analysis (UMSA) was used to retrieve classes of samples with specific molecular characteristics. Accordingly, van Krevelen diagram, Kendrick mass defect (KMD), as well as aromaticity index (AI) and aromaticity equivalent (Xc), were applied to present a pool of ubiquitous molecular formulas and to evaluate the PH-WEOM molecular heterogeneity in the sample set. Based on UMSA, the PH-WEOM from forest soils revealed a clearly distinct molecular composition, with major contributions from lignin- and tannin-like compounds, and with its aromaticity related to soil characteristics, especially the soil pH. No clear evidence of land-cover influence on the PH-WEOM molecular composition was found for cropland and grassland soils, but the role of pH was also identified for these samples, and agrees with molecular patterns attributed to microbial activity, with the presence of compounds with high H/C ratio. A group of samples from cropland soils developed on residual formations is characterised by a very specific molecular composition, rich in aliphatic organosulfur-like compounds, highlighting the importance of specific soil processes in the molecular composition of PH-WEOM. This work demonstrates the potential of FT-ICR MS to resolve the high chemical complexity of PH-WEOM in soils and the intricate influences of both biotic and abiotic environmental factors on the molecular composition of PH-WEOM in soils.
Auteurs, date et publication :
Auteurs Julien Guigue , Mourad Harir , Olivier Mathieu , Marianna Lucio , Lionel Ranjard , Jean Leveque , Philippe Schmitt-Kopplin
Publication : Biogeochemistry
Date : 2025
Volume : 128
Issue : 3
Pages : 307-326
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Promoting diverse and functioning biological communities is an important objective of agroecology, with increasing attention given to the important role of soil biodiversity. In an experimental study conducted under field conditions, we followed over four years the dynamic of soil organisms from various sizes and trophic niches in four variants of a cropping system which are differentiated by soil tillage, residue management and N fertilization rate. Differentiation in overall family diversity, as well as in the abundance and diversity of the multiple trophic groups was evaluated every two years. Our study demonstrated a delayed but effective differentiation in soil biota diversity following implementation of the agricultural practices. Soil biodiversity varied throughout time with some groups responding more readily than others, thereby highlighting differences related to trophic position and body size. The visualization of diversity profiles revealed an increasing impact of agricultural practices on group diversity towards higher trophic levels. While tillage appeared a main factor of influence, surprisingly little impact of residue management and nitrogen fertilization could be observed. Predicting the response of the soil biota to anthropogenic influence calls for an understanding of complex interactions between soil organisms in heterogeneous soil microhabitats. Through its multi-taxonomic approach, the present study increases our understanding of the dynamic of soil communities in agricultural cropping systems and helps identify possible consequences for soil functioning.
Auteurs, date et publication :
Auteurs Valérie Coudrain , Mickaël Hedde , Matthieu Chauvat , Pierre-Alain Maron , Emilie Bourgeois , Bruno Mary , Joël Léonard , Flemming Ekelund , Cécile Villenave , Sylvie Recous
Publication : Agriculture, Ecosystems & Environment
Date : 2016
Volume : 225
Pages : 12-21