Auteurs, date et publication :
Auteurs Sebastien Terrat , Pierre Plassart , Emilie Bourgeois , Stéphanie Ferreira , Samuel Dequiedt , Nathalie Adele-Dit-De-Renseville , Philippe Lemanceau , Antonio Bispo , Abad Chabbi , Pierre-Alain Maron , others
Publication : Microbial biotechnology
Date : 2025
Volume : 8
Issue : 1
Pages : 131–142
Catégorie(s)
#ACBB #ACBB Lusignan #Genosol #INRAERésumé
Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across France, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i. e. OTU number) was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance), the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively), and the land use (1.4%). Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R-adj(2) of 0.56) and provides a reference value for a given pedoclimatic condition.
Auteurs, date et publication :
Auteurs Sebastien Terrat , Walid Horrigue , Samuel Dequietd , Nicolas P. A. Saby , Melanie Lelievre , Virginie Nowak , Julie Tripied , Tiffanie Regnier , Claudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Battle Karimi , Antonio Bispo , Pierre Alain Maron , Nicolas Chemidlin Prevost-Boure , Lionel Ranjard
Publication : PloS One
Date : 2017
Volume : 12
Issue : 10
Catégorie(s)
#ANR-Citation #Genosol #INRAEAuteurs, date et publication :
Auteurs Robert I. Griffiths , Bruce C. Thomson , Pierre Plassart , Hyun S. Gweon , Dorothy Stone , Rachael E. Creamer , Philippe Lemanceau , Mark J. Bailey
Publication : Applied Soil Ecology
Date : 2025
Volume : 97
Pages : 61-68
Catégorie(s)
#Genosol #INRAERésumé
Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity.
Auteurs, date et publication :
Auteurs Florentin Constancias , Sébastien Terrat , Nicolas P. A. Saby , Walid Horrigue , Jean Villerd , Jean-Philippe Guillemin , Luc Biju-Duval , Virginie Nowak , Samuel Dequiedt , Lionel Ranjard , Nicolas Chemidlin Prévost-Bouré
Publication : MicrobiologyOpen
Date : 2025
Volume : 4
Issue : 3
Pages : 505-517
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
The occurrence of Pseudomonas aeruginosa was monitored at a broad spatial scale in French agricultural soils, from various soil types and under various land uses to evaluate the ability of soil to be a natural habitat for that species. To appreciate the impact of agricultural practices on the potential dispersion of P. aeruginosa, we further investigated the impact of organic amendment at experimental sites in France and Burkina Faso. A real-time quantitative PCR (qPCR) approach was used to analyze a set of 380 samples selected within the French RMQS (“Réseau de Mesures de la Qualité des Sols”) soil library. In parallel, a culture-dependent approach was tested on a subset of samples. The results showed that P. aeruginosa was very rarely detected suggesting a sporadic presence of this bacterium in soils from France and Burkina Faso, whatever the structural and physico-chemical characteristics or climate. When we analyzed the impact of organic amendment on the prevalence of P. aeruginosa, we found that even if it was detectable in various manures (at levels from 103 to 105 CFU or DNA targets (g drywt)−1 of sample), it was hardly ever detected in the corresponding soils, which raises questions about its survival. The only case reports were from a vineyard soil amended with a compost of mushroom manure in Burgundy, and a few samples from two fields amended with raw urban wastes in the sub-urban area of Ouagadougou, Burkina Faso. In these soils the levels of culturable cells were below 10 CFU (g drywt)−1.
Auteurs, date et publication :
Auteurs Amélie Deredjian , Céline Colinon , Edmond Hien , Elisabeth Brothier , Benjamin Youenou , Benoit Cournoyer , Samuel Dequiedt , Alain Hartmann , Claudy Jolivet , Sabine Houot , Lionel Ranjard , Nicolas P. A. Saby , Sylvie Nazaret
Publication : Frontiers in Cellular and Infection Microbiology
Date : 2014
Volume : 4
Catégorie(s)
#Genosol #INRAE #PRO #PRO ColmarRésumé
Using organic waste products (OWP) in agriculture makes it possible to increase productivity with less use of mineral fertilizers. However, the lasting effect on soil microbial communities of an OWP application repeated over several years needs further investigation. In the present study, soils were sampled from two long-term field experiments: QualiAgro and Colmar (France), where different types of OWP characterized by more or less stable organic matter had been applied for more than 10 years, and were compared to a control treatment. At QualiAgro, the carbon inputs due to OWP application were greater (∼4 t C ha−1 every two years) than at Colmar (∼1.7 t C ha−1 every two years). On both sites, soil samples were taken more than six months after the last OWP input. At QualiAgro, soil organic carbon, N and P2O5 concentrations, pH, and CEC were increased by repeated OWP inputs, as compared to the control. Soil microbial community parameters were also lastingly affected by OWP application. A 50% increase in microbial biomass was observed with OWP with the most stable organic matter contents. The prokaryotic community structure was influenced: directly by the OWP applied, and indirectly by soil properties changes. Soil pH appeared as a major driver for structure of the soil prokaryotic community. Fungal community structure was only directly influenced by the OWP applied. Contrastingly, at Colmar, OWP application had no impact on soil chemical characteristics or microbial communities’ parameters. This was probably due to the smaller amount of OWP applied than at QualiAgro, and/or a longer delay between the OWP application and soil sampling. Altogether, our results show that, depending on its type, the applied OWP could produce a lasting increase in soil microbial biomass and shape microbial community structure.
Auteurs, date et publication :
Auteurs S. Sadet-Bourgeteau , S. Houot , S. Dequiedt , V. Nowak , V. Tardy , S. Terrat , D. Montenach , V. Mercier , B. Karimi , N. Chemidlin Prévost-Bouré , P. A. Maron
Publication : Applied Soil Ecology
Date : 2018
Volume : 125
Pages : 278-287
Catégorie(s)
#ANR-Citation #Genosol #INRAE #PRORésumé
Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.
Auteurs, date et publication :
Auteurs Vincent Tardy , Abad Chabbi , Xavier Charrier , Christophe de Berranger , Tiffanie Reignier , Samuel Dequiedt , Celine Faivre-Primot , Sebastien Terrat , Lionel Ranjard , Pierre-Alain Maron
Publication : Plos One
Date : 2015
Volume : 10
Issue : 6
Catégorie(s)
#ACBB #ACBB Lusignan #ANR-Citation #GenosolRésumé
Finding more sustainable ways to produce food is a major challenge for humanity in the face of biodiversity extinction and climate change. Consequently, research on the ability of agroecosystems to provide multiple functions is growing. In this regard, the relative importance of organic farming and landscape-scale measures for improving multifunctionality has recently been debated. We investigated the effects of farming system (conventional vs. organic) at field scale, total length of hedgerows in the landscape and their interaction on the multifunctionality of 40 winter cereal fields in Brittany (France). Our multifunctionality assessment integrated 21 indicators of five agroecosystem goods: biodiversity conservation, nutrient cycling and soil structure, pest and disease regulation, food production and socio-economic performance. Many indicators of biodiversity conservation, pest and disease regulation, and socio-economic performance were higher in organic than in conventional systems. However, indicators of nutrient cycling and soil structure did not improve and food production was much lower in organic systems. Total hedgerow length in the landscape had less influence than organic farming on indicators, although we observed positive interactions. Granivorous carabid abundance and semi-net margin were highest in organic fields located in well-preserved hedgerow landscapes. Synthesis and applications. Our study suggests that field-scale organic farming is necessary to promote biodiversity conservation and associated ecological functioning in crop fields, whereas landscape-scale preservation of semi-natural habitats alone is likely insufficient. Preservation of hedgerows in the landscape brings additional ecological and socio-economic benefits for organic systems without compromising agricultural production. More broadly, our results call for more ambitious research into the myriad possible combinations of farming practices and agri-environmental measures at both field and landscape scales, to improve both below-ground and above-ground functioning.
Auteurs, date et publication :
Auteurs Sébastien Boinot , Audrey Alignier , Stéphanie Aviron , Colette Bertrand , Nathalie Cheviron , Gwendoline Comment , Emma Jeavons , Cécile Le Lann , Samuel Mondy , Christian Mougin , Pierre-Antoine Précigout , Claire Ricono , Corinne Robert , Grégoire Saias , Philippe Vandenkoornhuyse , Cendrine Mony
Publication : Journal of Applied Ecology
Date : 2025
Volume : 62
Issue : 1
Pages : 53-63
Catégorie(s)
#BiochemEnv #CNRS #EcoGenO #GenosolRésumé
A better understanding of the links between dissolved organic matter and biogeochemical processes in soil could help in evaluating global soil dynamics. To assess the effects of land cover and parental material on soil biogeochemistry, we studied 120 soil samples collected from various ecosystems in Burgundy, France. The potential solubility and aromaticity of dissolved organic matter was characterised by pressurised hot-water extraction of organic carbon (PH-WEOC). Soil physico-chemical characteristics (pH, texture, soil carbon and nitrogen) were measured, as was the δ13C signature both in soils and in PH-WEOC. We also determined bacterial and fungal abundance and the genetic structure of bacterial communities. Our results show that the potential solubility of soil organic carbon is correlated to carbon and clay content in the soil. The aromaticity of PH-WEOC and its δ13C signature reflect differences in the decomposition pathways of soil organic matter and in the production of water-extractable organic compounds, in relation to land cover. The genetic structure of bacterial communities is related to soil texture and pH, and to PH-WEOC, revealing that water-extractable organic matter is closely related to the dynamics of bacterial communities. This comprehensive study, at the regional scale, thus provides better definition of the relationships between water-extractable organic matter and soil biogeochemical properties.
Auteurs, date et publication :
Auteurs J. Guigue , J. Lévêque , O. Mathieu , P. Schmitt-Kopplin , M. Lucio , D. Arrouays , C. Jolivet , S. Dequiedt , N. Chemidlin Prévost-Bouré , L. Ranjard
Publication : Soil Biology and Biochemistry
Date : 2025
Volume : 84
Pages : 158-167
Catégorie(s)
#ANR-Citation #Genosol #INRAERésumé
The use of herbicides for weed control is very common, but some of them represent a threat to human health, are environmentally detrimental and stimulate herbicide resistance. Therefore, using microorganisms as natural herbicides appears as a promising alternative. The mycoflorae colonizing different species of symptomatic and asymptomatic weeds were compared to characterize the possible mycoherbicidal candidates associated with symptomatic weeds. A collection of 475 symptomatic and asymptomatic plants belonging to 23 weed species was established. A metabarcoding approach based on amplification of the internal transcribed spacer (ITS) region combined with high-throughput amplicon sequencing revealed the diversity of fungal communities hosted by these weeds: 542 fungal genera were identified. The variability of the composition of fungal communities revealed a dispersed distribution of taxa governed neither by geographical location nor by the botanical species, suggesting a common core displaying non-specific interactions with host plants. Beyond this core, specific taxa were more particularly associated with symptomatic plants. Some of these, such as Alternaria, Blumeria, Cercospora, Puccinia, are known pathogens, while others such as Sphaerellopsis, Vishniacozyma and Filobasidium are not, at least on crops, and constitute new tracks to be followed in the search for mycoherbicidal candidates. IMPORTANCE: This approach is original because the diversity of weed-colonizing fungi has rarely been studied before. Furthermore, targeting both the ITS1 and ITS2 regions to characterize the fungal communities i) highlighted the complementarity of these two regions, ii) revealed a great diversity of weed-colonizing fungi, and iii) allowed for the identification of potential mycoherbicides, among which unexpected genera.
Auteurs, date et publication :
Auteurs Marion Triolet , Véronique Edel-Hermann , Nadine Gautheron , Samuel Mondy , Carole Reibel , Olivier André , Jean-Philippe Guillemin , Christian Steinberg
Publication : Applied and Environmental Microbiology
Date : 2022
Pages : aem0217721