Résumé

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 #Genosol

Auteurs, date et publication :

Auteurs B. Karimi , Chemidlin Prévost-Bouré , Samuel Dequiedt , Sébastien Terrat , Lionel Ranjard

Date : 2025

Volume : 41

Catégorie(s)

#Genosol #INRAE

Résumé

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 #INRAE

Résumé

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 #INRAE

Auteurs, date et publication :

Auteurs Naoise Nunan , Julie Leloup , Léo S. Ruamps , Valérie Pouteau , Claire Chenu

Publication : Scientific Reports

Date : 2025

Volume : 8

Issue : 1

Catégorie(s)

#Genosol #INRAE

Résumé

The priming effect in soil is proposed to be generated by two distinct mechanisms: ‘stoichiometric decomposition’ and/or ‘nutrient mining’ theories. Each mechanism has its own dynamics, involves its own microbial actors, and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each priming effect generation mechanism via the modification of soil microbial and physicochemical properties. Soils were sampled in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects. Abiotic and biotic soil descriptors were characterized including bacterial and fungal phylogenetic composition. Potential organic matter mineralization and PE were assessed 7 and 42 days after the beginning of incubation with 13C-enriched wheat straw. Both priming mechanisms were mainly driven by the mean annual temperature but in opposite directions. The priming effect generated by stoichiometric decomposition was fostered under colder climates, because of soil enrichment in less developed organic matter, as well as in fast-growing populations. Conversely, the priming effect generated by nutrient mining was enhanced under warmer climates, probably because of the lack of competition between slow-growing populations mining SOM and fast-growing populations for the energy-rich residue entering the soil. Our study leads to hypotheses about the consequences of climate change on both PE generation mechanisms and associated consequences on soil carbon sequestration.

Auteurs, date et publication :

Auteurs Kanto Razanamalala , Tantely Razafimbelo , Pierre-Alain Maron , Lionel Ranjard , Nicolas Chemidlin , Mélanie Lelièvre , Samuel Dequiedt , Volaniaina H. Ramaroson , Claire Marsden , Thierry Becquer , Jean Trap , Eric Blanchart , Laetitia Bernard

Publication : The ISME Journal

Date : 2018

Volume : 12

Issue : 2

Pages : 451-462

Catégorie(s)

#Genosol #INRAE

Résumé

To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.

Auteurs, date et publication :

Auteurs Pierre Plassart , Nicolas Chemidlin Prevost-Boure , Stephane Uroz , Samuel Dequiedt , Dorothy Stone , Rachel Creamer , Robert I. Griffiths , Mark J. Bailey , Lionel Ranjard , Philippe Lemanceau

Publication : Scientific Reports

Date : 2019

Volume : 9

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

Although land use drives soil bacterial diversity and community structure, little information about the bacterial interaction networks is available. Here, we investigated bacterial co-occurrence networks in soils under different types of land use (forests, grasslands, crops and vineyards) by sampling 1798 sites in the French Soil Quality Monitoring Network covering all of France. An increase in bacterial richness was observed from forests to vineyards, whereas network complexity respectively decreased from 16,430 links to 2,046. However, the ratio of positive to negative links within the bacterial networks ranged from 2.9 in forests to 5.5 in vineyards. Networks structure was centered on the most connected genera (called hub), which belonged to Bacteroidetes in forest and grassland soils, but to Actinobacteria in vineyard soils. Overall, our study revealed that soil perturbation due to intensive cropping reduces strongly the complexity of bacterial network although the richness is increased. Moreover, the hub genera within the bacterial community shifted from copiotrophic taxa in forest soils to more oligotrophic taxa in agricultural soils.

Auteurs, date et publication :

Auteurs Battle Karimi , Samuel Dequiedt , Sebastien Terrat , Cloudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Antonio Bispo , Nicolas Chemidlin Prevost-Boure , Lionel Ranjard

Publication : SCIENTIFIC REPORTS

Date : 2019

Volume : 9

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

The temporal dynamics of rhizosphere and root microbiota composition was compared between healthy and infected Chinese cabbage plants by the pathogen Plasmodiophora brassicae. When inoculated with P. brassicae, disease was measured at five sampling dates from early root hair infection to late gall development. The first symptoms of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root from healthy and inoculated plants was characterized through high-throughput DNA sequencing of bacterial (16S) and fungal (18S) molecular markers and compared at each sampling date. In healthy plants, Proteobacteria and Bacteroidetes bacterial phyla dominated the rhizosphere and root microbiota of Chinese cabbage. Rhizosphere bacterial communities contained higher abundances of Actinobacteria and Firmicutes compared to the roots. Moreover, a drastic shift of fungal communities of healthy plants occurred between the two last sampling dates, especially in plant roots, where most of Ascomycota fungi dominated until they were replaced by a fungus assigned to the Chytridiomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly at a late step during the root secondary cortical infection stage of clubroot disease. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytridiomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.

Auteurs, date et publication :

Auteurs Lionel Lebreton , Anne-Yvonne Guillerm-Erckelboudt , Kevin Gazengel , Juliette Linglin , Morgane Ourry , Pascal Glory , Alain Sarniguet , Stephanie Daval , Maria J. Manzanares-Dauleux , Christophe Mougel

Publication : PLOS ONE

Date : 2019

Volume : 14

Issue : 2

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

Aim Intensive studies since the beginning of the 21st century have provided vast amounts of knowledge about soil microbial diversity at local and global scales. However, microbial habitats have been poorly investigated at large scale. This study aims to characterize soil bacterial habitats across France for the first time by integrating the description of numerous environmental factors and human activities. Location We focus on the large spatial scale of mainland France using the largest spatially explicit soil sampling set available across France (2,173 soils, area = 5.5 × 105 km2). Major taxa studied Soil bacteria and archaea were studied by a high throughput sequencing approach targeting the V3-V4 region of the 16S ribosomal ribonucleic acid (rRNA) gene directly amplified from soil DNA. Methods We applied decision tree learning and geostatistical approaches combining the abundant data on soil microbes and large-scale environmental description in order to conduct a comprehensive analysis of soil bacterial and archaeal communities. Results We identified a complex mosaic of 16 distinct terrestrial habitats, based on soil type and management (pH, C : N ratio, land use). As for plants and animals, each habitat hosted generalist and specialist taxa and a specific interaction network directly or indirectly impacted by human activities. Main conclusions In a context of global change, our results emphasize that the policies for biodiversity and habitat conservation should now integrate soil microorganisms conceptually and technically.

Auteurs, date et publication :

Auteurs Battle Karimi , Jean Villerd , Samuel Dequiedt , Sébastien Terrat , Nicolas Chemidlin-Prévost Bouré , Christophe Djemiel , Mélanie Lelièvre , Julie Tripied , Virginie Nowak , Nicolas P. A. Saby , Antonio Bispo , Claudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Lionel Ranjard

Publication : Global Ecology and Biogeography

Date : 2025

Volume : 29

Issue : 8

Pages : 1399-1411

Catégorie(s)

#ANR-Citation #Genosol #INRAE