Résumé
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 #INRAEAuteurs, date et publication :
Auteurs Mikaël Bili , Anne Marie Cortesero , Christophe Mougel , Jean Pierre Gauthier , Gwennola Ermel , Jean Christophe Simon , Yannick Outreman , Sébastien Terrat , Frédérique Mahéo , Denis Poinsot , Kostas Bourtzis
Publication : Plos One
Date : 2016
Volume : 11
Issue : 6
Pages : e0155392
Catégorie(s)
#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
Catégorie(s)
#ACBB #ACBB Mons #ANR-Citation #GenosolAuteurs, date et publication :
Auteurs B. Karimi , Chemidlin Prévost-Bouré , Samuel Dequiedt , Sébastien Terrat , Lionel Ranjard
Date : 2025
Volume : 41
Catégorie(s)
#Genosol #INRAERésumé
Soil microorganisms are essential to agroecosystem functioning and services. Yet, we still lack information on which farming practices can effectively shape the soil microbial communities. The aim of this study was to identify the farming practices, which are most effective at positively or negatively modifying bacterial and fungal diversity while considering the soil environmental variation at a landscape scale. A long-term research study catchment (12 km2) representative of intensive mixed farming (livestock and crop) in Western Europe was investigated using a regular grid for soil sampling (n = 186). Farming systems on this landscape scale were described in terms of crop rotation, use of fertilizer, soil tillage, pesticides treatments, and liming. Molecular microbial biomass was estimated by soil DNA recovery. Bacterial and fungal communities were analyzed by 16S and 18S rRNA gene pyrosequencing. Microbial biomass was significantly stimulated by the presence of pasture during the crop rotation since temporary and permanent pastures, as compared to annual crops, increased the soil microbial biomass by +23% and +93% respectively. While soil properties (mainly pH) explained much of the variation in bacterial diversity, soil tillage seemed to be the most influential among the farming practices. A 2.4% increase in bacterial richness was observed along our gradient of soil tillage intensity. In contrast, farming practices were the predominant drivers of fungal diversity, which was mainly determined by the presence of pastures during the crop rotation. Compared to annual crops, temporary and permanent pastures increased soil fungal richness by +10% and +14.5%, respectively. Altogether, our landscape-scale investigation allows the identification of farming practices that can effectively shape the soil microbial abundance and diversity, with the goal to improve agricultural soil management and soil ecological integrity.
Auteurs, date et publication :
Auteurs Cédric Le Guillou , Nicolas Chemidlin Prévost‐Bouré , Battle Karimi , Nouraya Akkal‐Corfini , Samuel Dequiedt , Virginie Nowak , Sébastien Terrat , Safya Menasseri‐Aubry , Valérie Viaud , Pierre-Alain Maron , Lionel Ranjard
Publication : MicrobiologyOpen
Date : 2025
Pages : e00676
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 165 ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 165 rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism.
Auteurs, date et publication :
Auteurs Battle Karimi , Sebastien Terrat , Samuel Dequiedt , Nicolas P. A. Saby , Walid Horriguel , Melanie Lelievre , Virginie Nowak , Claudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Antonio Bispo , Pierre-Alain Maron , Nicolas Chemidlin Prevost-Boure , Lionel Ranjard
Publication : Science Advances
Date : 2025
Volume : 4
Issue : 7
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs Naoise Nunan , Julie Leloup , Léo S. Ruamps , Valérie Pouteau , Claire Chenu
Publication : Scientific Reports
Date : 2025
Volume : 8
Issue : 1