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

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

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

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

Résumé

Theory surrounding landscape ecology has been built on the species distribution of birds and plants, but increasing evidence now exists for below-ground organisms, whose dispersal may also be affected by above-ground landscape structures. Uncertainties remain for how communities of microorganisms respond to landscape structure over time, and whether some groups of microorganisms react more than others. Here, we investigated if fungal or bacterial diversity is driven by the amount of forest cover in the current or the past landscape. We tested the habitat amount hypothesis (HAH) on ancient forests of the Cevennes national park, that experienced increased fragmentation 150 years ago, and are today surrounded by recent forests. As ancient forests are often more diverse in plant species, we hypothesized that the higher quantity of ancient forests in the landscape, the richer local fungal and bacterial communities would be. More precisely, we expected that ectomycorrhizal fungi, and pathotrophic fungi, often indicators of mature forests, would be also more sensitive to forest history and therefore to the quantity of ancient forests than bacteria and saprotrophic fungi. We sampled 40 soil cores per 0.5 ha, pooled in 8 composite samples per plot in 27 landscapes and sequenced ITS1 and 16S markers by Illumina-Mi seq. To identify functional groups of fungi, we relied on their taxonomy and the use of public databases. Our results partly follow the HAH, as fungal richness was positively related with the quantity of ancient forests in the landscape and not by the focal patch size. Ectomycorrhizal and pathotrophic fungi were positively affected by the ancient forest cover, and so were saprotrophic ones, but not bacteria. Local factors also shaped the communities such as soil composition and elevation, confirming classical patterns in soil microbial ecology. Interestingly, past landscape structure was better at explaining fungal community richness than contemporary landscape, suggesting a time lag in the response of communities to landscape modification and a potential extinction debt. Our results reveal the importance of below-ground communities in studies of landscape and historical ecology, with their structure and functions likely to be intimately linked with soil and landscape history.

Auteurs, date et publication :

Auteurs Sophie Mennicken , Floriane Kondratow , Florian Buralli , Sophie Manzi , Emilie Andrieu , Melanie Roy , Antoine Brin

Publication : FRONTIERS IN ECOLOGY AND EVOLUTION

Date : 2020

Volume : 8

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

BACKGROUND: The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.
RESULTS: BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.
CONCLUSIONS: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.

Auteurs, date et publication :

Auteurs Christophe Djemiel , Samuel Dequiedt , Battle Karimi , Aurélien Cottin , Thibault Girier , Yassin El Djoudi , Patrick Wincker , Mélanie Lelièvre , Samuel Mondy , Nicolas Chemidlin Prévost-Bouré , Pierre-Alain Maron , Lionel Ranjard , Sébastien Terrat

Publication : BMC bioinformatics

Date : 2020

Volume : 21

Issue : 1

Pages : 492

Catégorie(s)

#ANR-Citation #Genosol #INRAE

Résumé

According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.

Auteurs, date et publication :

Auteurs Laurie Dunn , Christophe Lang , Nicolas Marilleau , Sébastien Terrat , Luc Biju-Duval , Mélanie Lelièvre , Solène Perrin , Nicolas Chemidlin Prévost-Bouré

Publication : PLOS ONE

Date : 2025

Volume : 16

Issue : 6

Pages : e0252216

Catégorie(s)

#Genosol #INRAE

Résumé

Aphanomyces euteiches Drechs is a pathogenic soil-borne oomycete that causes root rot of legumes, one of the most serious diseases affecting legume production worldwide. There is currently no registered pesticide and no available resistant pea cultivar. Avoidance of infested fields based on disease risk assessment prior to pea sowing remains the main method available to manage the disease, but time-consuming bioassays are required to assess disease severity on susceptible plants grown in field soil samples. Direct quantification of A. euteiches inoculum in the soil by targeting multicopy genomic sequences of the internal transcribed spacer 1 with a qPCR-based method has been proposed as a rapid alternative for disease prediction. However, the method lacks sensitivity to accurately quantify low inoculum levels from naturally infested fields. We developed a suitable methodology based on droplet digital PCR (ddPCR) to quantify low A. euteiches inoculum levels in naturally infested soils. The methodology was validated on 200 soil samples taken from four naturally infested fields in the main pea cropping area in the north of France. The comparative analysis of inoculum density and disease severity of the 50 samples within each of the four fields revealed a non-homogeneous distribution of the A. euteiches population; this explains why the disease is visible in the form of foci. A significant relationship between pea root rot disease severity determined by bioassays and A. euteiches inoculum density was highlighted, and a linear mixed model is proposed to predict disease severity from inoculum density.

Auteurs, date et publication :

Auteurs Simon Gibert , Véronique Edel-Hermann , Rayanti Moussa Mcolo , Elodie Gautheron , Joël Michel , Eric Bernaud , Nadine Gautheron , Jean-Marie Sol , Gery Capelle , Rachel Galland , Arnaud Bardon-Debats , Claudine Lambert , Christian Steinberg

Publication : European Journal of Plant Pathology

Date : 2021

Volume : 161

Issue : 3

Pages : 503-528

Catégorie(s)

#Genosol #INRAE

Résumé

Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered – public leisure, traffic, and urban agriculture – sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.

Auteurs, date et publication :

Auteurs Amélie Christel , Samuel Dequiedt , Nicolas Chemidlin-Prevost-Bouré , Florian Mercier , Julie Tripied , Gwendoline Comment , Christophe Djemiel , Lionel Bargeot , Eric Matagne , Agnès Fougeron , Jean-Bertrand Mina Passi , Lionel Ranjard , Pierre-Alain Maron

Publication : Science of The Total Environment

Date : 2023

Pages : 163455

Catégorie(s)

#Genosol #INRAE