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1. Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes

Author

Stéphanie Daval, Kévin Gazengel, Arnaud Belcour, Juliette Linglin, Anne‐Yvonne Guillerm‐Erckelboudt, Alain Sarniguet, Maria J. Manzanares‐Dauleux, Lionel Lebreton, and Christophe Mougel

Subjects
Biotechnology, TP248.13-248.65
Abstract

Summary The contribution of surrounding plant microbiota to disease development has led to the ‘pathobiome’ concept, which represents the interaction between the pathogen, the host plant and the associated biotic microbial community, resulting or not in plant disease. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, and the molecular response of the plant to the infection, with a dual‐RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time‐course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes and three soils harbouring high, medium or low microbiota diversities and levels of richness. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, these modulations being dependent on the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant host functions potentially involved in the change of plant disease level, such as pathogenicity‐related genes (NUDIX effector) in P. brassicae and plant defence‐related genes (glucosinolate metabolism) in B. napus.

Published
2020
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2. Fast computation of genome-metagenome interaction effects

Author

Florent Guinot, Marie Szafranski, Julien Chiquet, Anouk Zancarini, Christine Le Signor, Christophe Mougel, and Christophe Ambroise

Subjects
Statistical machine learning, Variable selection, Dimensionality reduction, Gene-environement interactions, GWAS, Genetic and metagenomic markers, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Motivation Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be examined jointly when estimating phenotypic variance. In this work we consider two types of biological markers: genotypic markers, which characterize an observation in terms of inherited genetic information, and metagenomic marker which are related to the environment. Both types of markers are available in their millions and can be used to characterize any observation uniquely. Objective Our focus is on detecting interactions between groups of genetic and metagenomic markers in order to gain a better understanding of the complex relationship between environment and genome in the expression of a given phenotype. Contributions We propose a novel approach for efficiently detecting interactions between complementary datasets in a high-dimensional setting with a reduced computational cost. The method, named SICOMORE, reduces the dimension of the search space by selecting a subset of supervariables in the two complementary datasets. These supervariables are given by a weighted group structure defined on sets of variables at different scales. A Lasso selection is then applied on each type of supervariable to obtain a subset of potential interactions that will be explored via linear model testing. Results We compare SICOMORE with other approaches in simulations, with varying sample sizes, noise, and numbers of true interactions. SICOMORE exhibits convincing results in terms of recall, as well as competitive performances with respect to running time. The method is also used to detect interaction between genomic markers in Medicago truncatula and metagenomic markers in its rhizosphere bacterial community. Software availability An R package is available [4], along with its documentation and associated scripts, allowing the reader to reproduce the results presented in the paper.

Published
2020
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3. Host-microbiota interactions: from holobiont theory to analysis

Author

Jean-Christophe Simon, Julian R. Marchesi, Christophe Mougel, and Marc-André Selosse

Subjects
Host-microbiota interactions, Holobiont, Hologenome, Metagenomics, Symbiosis, Microbial ecology, QR100-130
Abstract

Abstract In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series “Host-microbiota interactions: from holobiont theory to analysis,” we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.

Published
2019
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4. Hatching of Globodera pallida Induced by Root Exudates Is Not Influenced by Soil Microbiota Composition

Author

Camille Gautier, Lisa Martinez, Sylvain Fournet, Josselin Montarry, Jean-Claude Yvin, Eric Nguema-Ona, Anne-Yvonne Guillerm-Erckelboudt, Christophe Piriou, Juliette Linglin, Christophe Mougel, and Lionel Lebreton

Subjects
microbial composition, plant-parasitic nematodes, suicide hatching, potato, metabarcoding, Microbiology, QR1-502
Abstract

Plant-parasitic nematodes are among the most harmful pests of cultivated crops causing important economic losses. The ban of chemical nematicides requires the development of alternative agroecological approaches to protect crops against nematodes. For cyst nematodes, egg hatching is stimulated by host plant root exudates. Inducing “suicide hatching” of nematode second-stage juveniles (J2), using root exudates in the absence of the host plant, may constitute an effective and innovative biocontrol method to control cyst nematodes. However, before considering the development of this approach, understanding the effect of soil biotic component on cyst nematode hatching by root exudates is a major issue. The effectiveness of this approach could be modulated by other soil organisms consuming root exudates for growth as soil microbiota, and this must be evaluated. To do that, four different native agricultural soils were selected based on their physicochemical properties and their microbiota composition were characterized by rDNA metabarcoding. To disentangle the effect of microbiota from that of soil on hatching, four recolonized artificial soils were obtained by inoculating a common sterile soil matrix with the microbiota proceeding from each agricultural soil. Each soil was then inoculated with cysts of the potato cyst nematode, Globodera pallida, and low or high doses of potato root exudates (PREs) were applied. After 40 days, viable J2 remaining in cysts were counted to determine the efficiency of root exudates to stimulate hatching in different soils. Results showed that (i) when physicochemical and microbiota compositions varied among native soils, the hatching rates remained very high albeit small differences were measured and no dose effect was detected and (ii) when only microbiota composition varied among recolonized soils, the hatching rates were also high at the highest dose of PREs, but a strong dose effect was highlighted. This study shows that abiotic and biotic factors may not compromise the development of methods based on suicide hatching of cyst nematodes, using root exudates, molecules inducing J2 hatch, or trap crops.

Published
2020
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5. Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Author

Cervin Guyomar, Fabrice Legeai, Emmanuelle Jousselin, Christophe Mougel, Claire Lemaitre, and Jean-Christophe Simon

Subjects
Host-microbiota interactions, Aphids, Metagenomics, Symbiosis, Phylogeny, Microbial ecology, QR100-130
Abstract

Abstract Background Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact. Results We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host. Conclusions We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.

Published
2018
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6. Influential Insider: Wolbachia, an Intracellular Symbiont, Manipulates Bacterial Diversity in Its Insect Host

Author

Morgane Ourry, Agathe Crosland, Valérie Lopez, Stéphane A. P. Derocles, Christophe Mougel, Anne-Marie Cortesero, and Denis Poinsot

Subjects
cabbage root fly, Delia radicum, Wolbachia, endosymbiont, Erwinia, bacterial communities, Biology (General), QH301-705.5
Abstract

Facultative intracellular symbionts like the α-proteobacteria Wolbachia influence their insect host phenotype but little is known about how much they affect their host microbiota. Here, we quantified the impact of Wolbachia infection on the bacterial community of the cabbage root fly Delia radicum by comparing the microbiota of Wolbachia-free and infected adult flies of both sexes. We used high-throughput DNA sequencing (Illumina MiSeq, 16S rRNA, V5-V7 region) and performed a community and a network analysis. In both sexes, Wolbachia infection significantly decreased the diversity of D. radicum bacterial communities and modified their structure and composition by reducing abundance in some taxa but increasing it in others. Infection by Wolbachia was negatively correlated to 8 bacteria genera (Erwinia was the most impacted), and positively correlated to Providencia and Serratia. We suggest that Wolbachia might antagonize Erwinia for being entomopathogenic (and potentially intracellular), but would favor Providencia and Serratia because they might protect the host against chemical plant defenses. Although they might seem prisoners in a cell, endocellular symbionts can impact the whole microbiota of their host, hence its extended phenotype, which provides them with a way to interact with the outside world.

Published
2021
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7. Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae.

Author

Lionel Lebreton, Anne-Yvonne Guillerm-Erckelboudt, Kévin Gazengel, Juliette Linglin, Morgane Ourry, Pascal Glory, Alain Sarniguet, Stéphanie Daval, Maria J Manzanares-Dauleux, and Christophe Mougel

Subjects
Medicine, Science
Abstract

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.

Published
2019
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8. Influence of Belowground Herbivory on the Dynamics of Root and Rhizosphere Microbial Communities

Author

Morgane Ourry, Lionel Lebreton, Valérie Chaminade, Anne-Yvonne Guillerm-Erckelboudt, Maxime Hervé, Juliette Linglin, Nathalie Marnet, Alain Ourry, Chrystelle Paty, Denis Poinsot, Anne-Marie Cortesero, and Christophe Mougel

Subjects
Delia radicum, Brassica napus, soil microbial diversity, rhizosphere and root microbial communities, herbivory, metabolites, Evolution, QH359-425, Ecology, QH540-549.5
Abstract

Recent studies are unraveling the impact of microorganisms from the roots and rhizosphere on interactions between plants and herbivorous insects and are gradually changing our perception of the microorganisms' capacity to affect plant defenses, but the reverse effect has seldom been investigated. Our study aimed at determining how plant herbivory influences the dynamics of root and rhizosphere microbial community assemblages and whether potential changes in root metabolites and chemical elements produced during herbivory can be related to microbial community diversity. We conducted our study on oilseed rape (Brassica napus) and its major belowground herbivore, the cabbage root fly (Delia radicum). We further assessed the influence of initial soil microbial diversity on these interactions. Different microbial diversities based on a common soil matrix were obtained through a removal-recolonization method. Root and rhizosphere sampling targeted different stages of the herbivore development corresponding to different perturbation intensities. Root bacterial communities were more affected by herbivory than some rhizosphere bacterial phyla and fungal communities, which seemed more resistant to this perturbation. Root herbivory enhanced the phylum of γ-Proteobacteria in the roots and rhizosphere, as well as the phylum of Firmicutes in the rhizosphere. Herbivory tended to decrease most root amino acids and sugars, and it increased trehalose, indolyl glucosinolates, and sulfur. Higher abundances of four bacterial genera (Bacillus, Paenibacillus, Pseudomonas, and Stenotrophomonas) were associated following herbivory to the increase of trehalose and some sulfur-containing compounds. Further research would help to identify the biological functions of the microbial genera impacted by plant infestation and their potential implications in plant defense.

Published
2018
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9. Bacterial Community Diversity Harboured by Interacting Species.

Author

Mikaël Bili, Anne Marie Cortesero, Christophe Mougel, Jean Pierre Gauthier, Gwennola Ermel, Jean Christophe Simon, Yannick Outreman, Sébastien Terrat, Frédérique Mahéo, and Denis Poinsot

Subjects
Medicine, Science
Abstract

All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.

Published
2016
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10. Interaction between Medicago truncatula and Pseudomonas fluorescens: evaluation of costs and benefits across an elevated atmospheric CO(2).

Author

Clémentine Lepinay, Thierry Rigaud, Christophe Salon, Philippe Lemanceau, and Christophe Mougel

Subjects
Medicine, Science
Abstract

Soil microorganisms play a key role in both plants nutrition and health. Their relation with plant varies from mutualism to parasitism, according to the balance of costs and benefits for the two partners of the interaction. These interactions involved the liberation of plant organic compounds via rhizodeposition. Modification of atmospheric CO(2) concentration may affect rhizodeposition and as a consequence trophic interactions that bind plants and microorganisms. Positive effect of elevated CO(2) on plants are rather well known but consequences for micoorganisms and their interactions with plants are still poorly understood. A gnotobiotic system has been developed to study the interaction between Medicago truncatula Jemalong J5 and the mutualistic bacteria Pseudomonas fluorescens strain C7R12 under two atmospheric CO(2) concentrations: ambient (365 ppm) versus enriched (750 ppm). Costs and benefits for each partner have been determined over time by measuring plant development and growth, the C and N contents of the various plant parts and the density of the bacteria in rhizosphere compartments. Following the increase in CO(2), there was a beneficial effect of P. fluorescens C7R12 on development, vegetative growth, and C/N content of M. truncatula. Concerning plant reproduction, an early seed production was noticed in presence of the bacterial strain combined with increased atmospheric CO(2) conditions. Paradoxically, this transient increase in seed production was correlated with a decrease in bacterial density in the rhizosphere soil, revealing a cost of increased CO(2) for the bacterial strain. This shift of costs-benefits ratio disappeared later during the plant growth. In conclusion, the increase in CO(2) concentration modifies transiently the cost-benefit balance in favor of the plant. These results may be explained either by a competition between the two partners or a change in bacterial physiology. The ecosystem functioning depends on the stability of many plant-microbe associations that abiotic factors can disrupt.

Published
2012
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11. Soil nitrogen availability and plant genotype modify the nutrition strategies of M. truncatula and the associated rhizosphere microbial communities.

Author

Anouk Zancarini, Christophe Mougel, Anne-Sophie Voisin, Marion Prudent, Christophe Salon, and Nathalie Munier-Jolain

Subjects
Medicine, Science
Abstract

Plant and soil types are usually considered as the two main drivers of the rhizosphere microbial communities. The aim of this work was to study the effect of both N availability and plant genotype on the plant associated rhizosphere microbial communities, in relation to the nutritional strategies of the plant-microbe interactions, for six contrasted Medicago truncatula genotypes. The plants were provided with two different nutrient solutions varying in their nitrate concentrations (0 mM and 10 mM). First, the influence of both nitrogen availability and Medicago truncatula genotype on the genetic structure of the soil bacterial and fungal communities was determined by DNA fingerprint using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Secondly, the different nutritional strategies of the plant-microbe interactions were evaluated using an ecophysiological framework. We observed that nitrogen availability affected rhizosphere bacterial communities only in presence of the plant. Furthermore, we showed that the influence of nitrogen availability on rhizosphere bacterial communities was dependent on the different genotypes of Medicago truncatula. Finally, the nutritional strategies of the plant varied greatly in response to a modification of nitrogen availability. A new conceptual framework was thus developed to study plant-microbe interactions. This framework led to the identification of three contrasted structural and functional adaptive responses of plant-microbe interactions to nitrogen availability.

Published
2012
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12. Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure.

Author

Pierre Plassart, Sébastien Terrat, Bruce Thomson, Robert Griffiths, Samuel Dequiedt, Mélanie Lelievre, Tiffanie Regnier, Virginie Nowak, Mark Bailey, Philippe Lemanceau, Antonio Bispo, Abad Chabbi, Pierre-Alain Maron, Christophe Mougel, and Lionel Ranjard

Subjects
Medicine, Science
Abstract

Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.

Published
2012
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13. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR.

Author

Nicolas Chemidlin Prévost-Bouré, Richard Christen, Samuel Dequiedt, Christophe Mougel, Mélanie Lelièvre, Claudy Jolivet, Hamid Reza Shahbazkia, Laure Guillou, Dominique Arrouays, and Lionel Ranjard

Subjects
Medicine, Science
Abstract

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1/FF390. This in silico analysis of the specificity of FR1/FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1/FF390 for Fungi was validated in vitro by cloning--sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.

Published
2011
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14. A field indicator for rhizosphere effect monitoring in arable soils

Author

Sébastian Mira, Mathieu Emily, Christophe Mougel, Morgane Ourry, Edith Le Cadre, Sol Agro et hydrosystème Spatialisation (SAS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut Agro Rennes Angers, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (UCPH), and ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Plant soil feedback, Intercropping, Plant diversity, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Microbiota, Soil Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Science, Holobiont
Abstract

International audience; For the agroecological transition, the rhizosphere is a critical interface for plants to acquire resources and to enhance plant health with limited inputs. In the present study, we developed a new indicator to estimate and monitor the intensity of plant-soil-microbiota interactions under field conditions.A Rhizosphere Effect Indicator (REI) was calculated by comparing individual and aggregated variables of bulk soil to those of the rhizosphere (i.e. soil enzyme activities and nutrient fluxes) every 2 weeks in the fields of three farms along a crop-diversification gradient. The diversity and structure of microbial communities in bulk soil and the rhizosphere in each field were assessed at flowering.The REI revealed statistically distinct dynamics and intensities of rhizosphere functioning among the three farms. Soil enzyme activities contributed more to the rhizosphere effect than nitrate and phosphate fluxes. Molecular analysis distinguished the two soil compartments and all crop-diversification levels. An integrated REI that provided a single value monitored the rhizosphere effect reliably.Methodological limits due to sampling of the rhizosphere under field conditions must be overcome to develop the REI, but the REI can serve as a complementary tool to traditional soil analysis for agroecological cropping system design and evaluation.

Published
2022

17. MinYS: mine your symbiont by targeted genome assembly in symbiotic communities

Author

Christophe Mougel, Wesley Delage, Fabrice Legeai, Claire Lemaitre, Jean-Christophe Simon, Cervin Guyomar, German Centre for Integrative Biodiversity Research (iDiv), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut national de recherche en informatique et en automatique (INRIA), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)

Subjects
Whole genome sequencing, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Contig, 030302 biochemistry & molecular biology, Sequence assembly, food and beverages, Standard Article, Computational biology, biochemical phenomena, metabolism, and nutrition, Biology, biology.organism_classification, Genome, 03 medical and health sciences, Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Buchnera, 030304 developmental biology, Reference genome
Abstract

Most metazoans are associated with symbionts. Characterizing the effect of a particular symbiont often requires to get access to its genome, which is usually done by sequencing the whole community. We present MinYS, a targeted assembly approach to assemble one particular genome of interest from such metagenomic data. First, taking advantage of a reference genome, a subset of the reads is assembled into a set of backbone contigs. Then, this draft assembly is completed using the whole metagenomic readset in a de novo manner. The resulting assembly is output as a genome graph, allowing to distinguish different strains with potential structural variants coexisting in the sample. MinYS was applied to 50 pea aphid re-sequencing samples, with low and high diversity, in order to recover the genome sequence of its obligatory bacterial symbiont, Buchnera aphidicola. It was able to return high quality assemblies (one contig assembly in 90% of the samples), even when using increasingly distant reference genomes, and to retrieve large structural variations in the samples. Due to its targeted essence, it outperformed standard metagenomic assemblers in terms of both time and assembly quality.

Published
2020

18. A core microbiota of the plant-earthworm interaction conserved across soils

Author

Arnaud Mounier, Christophe Mougel, Cécile Monard, Manuel Blouin, Ruben Puga-Freitas, Samuel Jacquiod, Aymé Spor, Laurent Philippot, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), RA19028.AEC.ISEC2CO-Biohefect-MicrobiEn-AuxAzote, Samuel Jacquiod was funded by the University of Bourgogne Franche-Comté via the ISITE-BFC International Junior Fellowship award (AAP3:RA19028.AEC.IS)., Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest

Subjects
Biogeochemical cycle, Microorganism, Soil Science, Context (language use), [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Microbiology, 03 medical and health sciences, Abundance (ecology), Soil functions, Archeae, 030304 developmental biology, 2. Zero hunger, Abiotic component, 0303 health sciences, Rhizosphere, biology, Bacteria, Host (biology), Ecology, Earthworm, Fungi, 04 agricultural and veterinary sciences, Plant, 15. Life on land, biology.organism_classification, Soil type, Loam, Soil water, 040103 agronomy & agriculture, Core microbiota, 0401 agriculture, forestry, and fisheries, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microcosm
Abstract

Microorganisms participate in most crucial soil functions and services benefiting human activities, such as biogeochemical cycles, bioremediation and food production. Their activity happens essentially in hotspots created by major soil macroorganisms, like rhizosphere and cast shaped by plants and earthworms respectively1. While effects of individual macroorganism on soil microbes are documented, no studies attempted to decipher how the mosaic of microhabitats built by multiple macroorganisms and their interaction determine the structure of microbial communities. Here we show a joint shaping of soil bacterial communities by these two macroorganisms, with a prevalent role of plants over earthworms. In a controlled microcosm experiment with three contrasted soils and meticulous microhabitat sampling, we found that the simultaneous presence of barley and endogeic earthworms resulted in non-additive effects on cast and rhizosphere bacterial communities. Using a source-sink approach derived from the meta-community theory2,3, we found specific cast and rhizospherecore microbiota4,5of the plant-eartworm interaction, detected in all soils only when both macroorganisms are present. We also evidenced acore networkof the plant-earthworm interaction, with cosmopolitan OTUs correlated both in cast and rhizosphere of all soils. Our study provides a new framework to explore aboveground-belowground interactions through the prism of microbial communities. This multiple-macroorganisms shaping of bacterial communities also affects fungi and archaea, while being strongly influenced by soil type. Further functional investigations are needed to understand how thesecore microbiotaandcore networkcontribute to the modulation of plant adaptive response to local abiotic and biotic conditions.

Published
2020

19. Hatching of

Author

Camille, Gautier, Lisa, Martinez, Sylvain, Fournet, Josselin, Montarry, Jean-Claude, Yvin, Eric, Nguema-Ona, Anne-Yvonne, Guillerm-Erckelboudt, Christophe, Piriou, Juliette, Linglin, Christophe, Mougel, and Lionel, Lebreton

Subjects
suicide hatching, microbial composition, metabarcoding, food and beverages, potato, plant-parasitic nematodes, Microbiology, Original Research
Abstract

Plant-parasitic nematodes are among the most harmful pests of cultivated crops causing important economic losses. The ban of chemical nematicides requires the development of alternative agroecological approaches to protect crops against nematodes. For cyst nematodes, egg hatching is stimulated by host plant root exudates. Inducing “suicide hatching” of nematode second-stage juveniles (J2), using root exudates in the absence of the host plant, may constitute an effective and innovative biocontrol method to control cyst nematodes. However, before considering the development of this approach, understanding the effect of soil biotic component on cyst nematode hatching by root exudates is a major issue. The effectiveness of this approach could be modulated by other soil organisms consuming root exudates for growth as soil microbiota, and this must be evaluated. To do that, four different native agricultural soils were selected based on their physicochemical properties and their microbiota composition were characterized by rDNA metabarcoding. To disentangle the effect of microbiota from that of soil on hatching, four recolonized artificial soils were obtained by inoculating a common sterile soil matrix with the microbiota proceeding from each agricultural soil. Each soil was then inoculated with cysts of the potato cyst nematode, Globodera pallida, and low or high doses of potato root exudates (PREs) were applied. After 40 days, viable J2 remaining in cysts were counted to determine the efficiency of root exudates to stimulate hatching in different soils. Results showed that (i) when physicochemical and microbiota compositions varied among native soils, the hatching rates remained very high albeit small differences were measured and no dose effect was detected and (ii) when only microbiota composition varied among recolonized soils, the hatching rates were also high at the highest dose of PREs, but a strong dose effect was highlighted. This study shows that abiotic and biotic factors may not compromise the development of methods based on suicide hatching of cyst nematodes, using root exudates, molecules inducing J2 hatch, or trap crops.

Published
2020

20. Long-lasting effects of antibiotics on bacterial communities of adult flies

Author

Christophe Mougel, Maxime R. Hervé, Lionel Lebreton, Anne-Marie Cortesero, Yannick Outreman, Denis Poinsot, Valérie Lopez, Morgane Ourry, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique, INRARégion BretagneMP-P10026 EB06, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
antibiotic resistance, medicine.drug_class, Tetracycline, media_common.quotation_subject, Antibiotics, Population, Zoology, Insect, Biology, Applied Microbiology and Biotechnology, Microbiology, Delia radicum, 03 medical and health sciences, Antibiotic resistance, RNA, Ribosomal, 16S, medicine, Journal Article, Animals, Microbiome, education, cabbage root fly, 030304 developmental biology, media_common, tetracycline, generations, 0303 health sciences, education.field_of_study, Bacteria, Ecology, 030306 microbiology, Host (biology), Microbiota, Research Support, Non-U.S. Gov't, fungi, biology.organism_classification, bacterial communities, Anti-Bacterial Agents, [SDE]Environmental Sciences, medicine.drug
Abstract

Insect symbionts benefit their host and their study requires large spectrum antibiotic use like tetracycline to weaken or suppress symbiotic communities. While antibiotics have a negative impact on insect fitness, little is known about antibiotic effects on insect microbial communities and how long they last. We characterized the bacterial communities of adult cabbage root fly Delia radicum in a Wolbachia-free population and evaluated the effect of tetracycline treatment on these communities over several generations. Three D. radicum generations were used: the first- and second-generation flies either ingested tetracycline or not, while the third-generation flies were untreated but differed with their parents and/or grandparents that had or had not been treated. Fly bacterial communities were sequenced using a 16S rRNA gene. Tetracycline decreased fly bacterial diversity and induced modifications in both bacterial abundance and relative frequencies, still visible on untreated offspring whose parents and/or grandparents had been treated, therefore demonstrating long-lasting transgenerational effects on animal microbiomes after antibiotic treatment. Flies with an antibiotic history shared bacterial genera, potentially tetracycline resistant and heritable. Next, the transmission should be investigated by comparing several insect development stages and plant compartments to assess vertical and horizontal transmissions of D. radicum bacterial communities.

Published
2020

21. Protection agroécologique pour le maintien de la santé des plantes

Author

Claudia Bartoli, Jean-Noel Aubertot, Isabelle Litrico-Chiarelli, Christophe Mougel, Grenier, Anne-Sophie, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

International audience; La production agricole et la gestion des bioagresseurs.De nouveaux leviers à explorer : les interactions plante-microbiote et leur place dans les écosystèmes agricoles.Vers un couplage entre microbiote et pratiques agroécologiques.

Published
2020

22. Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes

Author

Lionel Lebreton, Kévin Gazengel, Christophe Mougel, Alain Sarniguet, Anne-Yvonne Guillerm-Erckelboudt, Juliette Linglin, Arnaud Belcour, Stéphanie Daval, Maria J. Manzanares-Dauleux, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université d'Angers (UA)-AGROCAMPUS OUEST, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Université de Rennes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université d'Angers (UA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health and Environment division and the Plant Biology and Breeding division of the French National Research Institute for Agriculture, Food and the Environment (INRAE)., Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, bactérie pathogène du sol, plasmodiophora brassicae, Brassica, Plasmodiophorida, Applied Microbiology and Biotechnology, Biochemistry, 01 natural sciences, Soil, association mycorhizienne, Genotype, Plant-Microbe interactions, interaction microorganisme sol, Pathogen, Research Articles, 2. Zero hunger, Genetics, 0303 health sciences, Rhizosphere, Vegetal Biology, système racinaire, Effector, Microbiota, Microbiology and Parasitology, food and beverages, NUDIX effector, Microbiologie et Parasitologie, Plant disease, Agricultural sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Pathobiome, Biotechnology, Research Article, Microbiome, Dual-RNAseq, Phytopathology and phytopharmacy, lcsh:Biotechnology, Bioengineering, Biology, complex mixtures, brassica napus, Clubroot, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, lcsh:TP248.13-248.65, protection des plantes, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Diseases, 030304 developmental biology, 030306 microbiology, Host (biology), fungi, medicine.disease, biology.organism_classification, Phytopathologie et phytopharmacie, maladie des plantes, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Microbial population biology, Transcriptome, Biologie végétale, Sciences agricoles, 010606 plant biology & botany
Abstract

The objective was to further the understanding of the complex interaction between the soil microbiota, a plant pathogen and the host plant. The effect of different soil microbial diversities on the level of disease and on the transcriptomes of the interacting pathogen and host plant was studied., Summary The contribution of surrounding plant microbiota to disease development has led to the ‘pathobiome’ concept, which represents the interaction between the pathogen, the host plant and the associated biotic microbial community, resulting or not in plant disease. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, and the molecular response of the plant to the infection, with a dual‐RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time‐course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes and three soils harbouring high, medium or low microbiota diversities and levels of richness. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, these modulations being dependent on the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant host functions potentially involved in the change of plant disease level, such as pathogenicity‐related genes (NUDIX effector) in P. brassicae and plant defence‐related genes (glucosinolate metabolism) in B. napus.

Published
2020

23. Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design

Author

Lionel Lebreton, Ludovic Legrand, Yoann Aigu, Ludovic Cottret, Jérôme Gouzy, Stéphanie Daval, Christophe Mougel, Arnaud Belcour, Maria J. Manzanares-Dauleux, Kévin Gazengel, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0106 biological sciences, Mitochondrial DNA, Clubroot, Spermidine, Genomics, Plasmodiophorida, 01 natural sciences, Genome, DNA, Mitochondrial, Transcriptome, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Mitochondrial genome, Databases, Genetic, Genetics, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Phylogeny, 030304 developmental biology, 0303 health sciences, Obligate, biology, 030306 microbiology, ClubrootCyc, fungi, food and beverages, Brassicaceae, DNA, Protozoan, medicine.disease, biology.organism_classification, Metabolic pathway, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Genome, Mitochondrial, Genome, Protozoan, Metabolic Networks and Pathways, 010606 plant biology & botany, Reference genome
Abstract

Plasmodiophora brassicae is an obligate biotrophic pathogenic protist responsible for clubroot, a root gall disease of Brassicaceae species. In addition to the reference genome of the P. brassicae European e3 isolate and the draft genomes of Canadian or Chinese isolates, we present the genome of eH, a second European isolate. Refinement of the annotation of the eH genome led to the identification of the mitochondrial genome sequence, which was found to be bigger than that of Spongospora subterranea, another plant parasitic Plasmodiophorid phylogenetically related to P. brassicae. New pathways were also predicted, such as those for the synthesis of spermidine, a polyamine up-regulated in clubbed regions of roots. A P. brassicae pathway genome database was created to facilitate the functional study of metabolic pathways in transcriptomics approaches. These available tools can help in our understanding of the regulation of P. brassicae metabolism during infection and in response to diverse constraints.

Published
2019

24. Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect? A demonstration in oilseed rape

Author

Valérie Chaminade, Anne-Marie Cortesero, Chrystelle Paty, Christophe Mougel, Juliette Linglin, Anne-Yvonne Guillerm-Erckelboudt, Julie Aubert, Tom Lachaise, Morgane Ourry, Nathalie Marnet, Lionel Lebreton, and Denis Poinsot

Subjects
0106 biological sciences, 0301 basic medicine, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Life history theory, 03 medical and health sciences, Botany, Plant defense against herbivory, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Rhizosphere, Herbivore, Larva, Biotic component, biology, Ecology, fungi, food and beverages, 15. Life on land, biology.organism_classification, 030104 developmental biology, Insect Science, Adaptation, Agronomy and Crop Science, Delia radicum, 010606 plant biology & botany
Abstract

Interactions between plants and phytophagous insects play an important part in shaping the biochemical composition of plants. Reciprocally plant metabolites can influence major life history traits in these insects and largely contribute to their fitness. Plant rhizospheric microorganisms are an important biotic factor modulating plant metabolites and adaptation to stress. While plant-insects or plant-microorganisms interactions and their consequences on the plant metabolite signature are well-documented, the impact of soil microbial communities on plant defenses against phytophagous insects remains poorly known. In this study, we used oilseed rape (Brassica napus) and the cabbage root fly (Delia radicum) as biological models to tackle this question. Even though D. radicum is a belowground herbivore as a larva, its adult life history traits depend on aboveground signals. We therefore tested whether soil microbial diversity influenced emergence rate and fitness but also fly oviposition behavior, and tried to link possible effects to modifications in leaf and root metabolites. Through a removal-recolonization experiment, 3 soil microbial modalities ("high," "medium," "low") were established and assessed through amplicon sequencing of 16S and 18S ribosomal RNA genes. The "medium" modality in the rhizosphere significantly improved insect development traits. Plant-microorganism interactions were marginally associated to modulations of root metabolites profiles, which could partly explain these results. We highlighted the potential role of plant-microbial interaction in plant defenses against Delia radicum. Rhizospheric microbial communities must be taken into account when analyzing plant defenses against herbivores, being either below or aboveground.

Published
2017

25. Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Author

Christophe Mougel, Fabrice Legeai, Emmanuelle Jousselin, Cervin Guyomar, Claire Lemaitre, Jean-Christophe Simon, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universite of Rennes 1, Plant Health and Environment division of INRA, ANR Speciaphid : ANR-11-BSV7-005-01, ANR-11-BSV7-0005,SPECIAPHID,Génétique de l'adaptation trophique et mécanismes d'isolement reproducteur chez les pucerons(2011), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)

Subjects
0106 biological sciences, 0301 basic medicine, Microbiology (medical), Biology, 010603 evolutionary biology, 01 natural sciences, Microbiology, lcsh:Microbial ecology, 03 medical and health sciences, Buchnera, Microbial ecology, Host-microbiota interactions, Aphids, Metagenomics, Symbiosis, Phylogeny, Phylogenetics, RNA, Ribosomal, 16S, Animals, Rickettsia, Evolutionary dynamics, 2. Zero hunger, Mutualism (biology), Facultative, Aphid, Research, Microbiota, food and beverages, 15. Life on land, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Holobiont, 030104 developmental biology, Evolutionary biology, lcsh:QR100-130, Metagenome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial
Abstract

Background Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact. Results We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host. Conclusions We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take. Electronic supplementary material The online version of this article (10.1186/s40168-018-0562-9) contains supplementary material, which is available to authorized users.

Published
2018

26. FAST COMPUTATION OF GENOME-METAGENOME INTERACTION EFFECTS

Author

Florent Guinot, Marie Szafranski, Christophe Mougel, Christophe Ambroise, Christine Le Signor, Julien Chiquet, Anouk Zancarini, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), AgroParisTech, ENSIIE, Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Univ Paris Saclay, Univ Evry, Lab Math & Modelisat Evry, CNRS, F-91037 Evry, France, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Univ Amsterdam, Swammerdam Inst Life Sci, Biosyst Data Anal Grp, Plant Hormone Biol Grp, Sci Pk 904, NL-1098 XH Amsterdam, Netherlands, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Centre National de la Recherche Scientifique (CNRS)-ENSIIE-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and SILS Other Research (FNWI)

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, Computer science, [SDV]Life Sciences [q-bio], Gene-environment interactions, Genome-wide association study, 01 natural sciences, Genome, Machine Learning (cs.LG), 010104 statistics & probability, Lasso (statistics), [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Structural Biology, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], GWAS, lcsh:QH301-705.5, dimensionality reduction, 0303 health sciences, Applied Mathematics, Linear model, Computational Theory and Mathematics, hierarchical clustering, [STAT.ME]Statistics [stat]/Methodology [stat.ME], variable selection, lcsh:QH426-470, dimension reduction, Mathematics - Statistics Theory, Feature selection, Computational biology, Statistics Theory (math.ST), Statistics - Applications, Methodology (stat.ME), 03 medical and health sciences, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Statistical machine learning, FOS: Mathematics, Applications (stat.AP), 0101 mathematics, Molecular Biology, Statistics - Methodology, 030304 developmental biology, Genetic association, Genetic and metagenomic markers, gGenetic and metagenomic markers, Dimensionality reduction, Research, interactions, lcsh:Genetics, gene-environement interactions, statistical learning, lcsh:Biology (General), [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Metagenomics
Abstract

Motivation Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be examined jointly when estimating phenotypic variance. In this work we consider two types of biological markers: genotypic markers, which characterize an observation in terms of inherited genetic information, and metagenomic marker which are related to the environment. Both types of markers are available in their millions and can be used to characterize any observation uniquely. Objective Our focus is on detecting interactions between groups of genetic and metagenomic markers in order to gain a better understanding of the complex relationship between environment and genome in the expression of a given phenotype. Contributions We propose a novel approach for efficiently detecting interactions between complementary datasets in a high-dimensional setting with a reduced computational cost. The method, named SICOMORE, reduces the dimension of the search space by selecting a subset of supervariables in the two complementary datasets. These supervariables are given by a weighted group structure defined on sets of variables at different scales. A Lasso selection is then applied on each type of supervariable to obtain a subset of potential interactions that will be explored via linear model testing. Results We compare SICOMORE with other approaches in simulations, with varying sample sizes, noise, and numbers of true interactions. SICOMORE exhibits convincing results in terms of recall, as well as competitive performances with respect to running time. The method is also used to detect interaction between genomic markers in Medicago truncatula and metagenomic markers in its rhizosphere bacterial community. Software availability An package is available [4], along with its documentation and associated scripts, allowing the reader to reproduce the results presented in the paper.

Published
2018

27. Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae: The impact of a pathogen on the plant root and rhizosphere microbiota

Author

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

Subjects
Chytridiomycota, Rhizosphere, biology, Firmicutes, fungi, food and beverages, Fungus, Root hair, biology.organism_classification, medicine.disease, Actinobacteria, Clubroot, Botany, medicine, Proteobacteria
Abstract

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.

Published
2018
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28. A core microbiota of plant and earthworm interaction? Phylogenetic and functional aspects

Author

Manuel Blouin, Samuel Jacquiod, Arnaud Mounier, Aymé Spor, Ruben Puga Freitas, Christophe Mougel, Cécile Monard, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), EL Mjiyad, Noureddine, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), and Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV] Life Sciences [q-bio], core microbiota, Archae, soil fertility, [SDV]Life Sciences [q-bio], nitrogen cycle, fungi, bacteria, plant – earthworm interaction
Abstract

International audience; The core microbiota concept has been proposed to describe the subset of a microbiota (e.g. the rhizosphere microbial community) associated with a given host (e.g. a plant) going beyond macroenvironment differences (e.g. soil type), and characterized by taxonomic markers (e.g. 16S rRNA gene sequences). Its existence has been questioned by geographical studies, showing the overruling soil type effect in shaping microbial communities. As far as biotic determinants are concerned, several “hosts” or macroorganisms are impacting a given habitat and its specific microbial community. In soils, there is an overlap between the so-called rhizosphere and the drilosphere, defined as the functional domains under the influence of plant roots and earthworms respectively. Plants and earthworms have been sharing the same soils over geological times, thus microbial communities living at the congruence of rhizosphere and drilosphere could be specific of plant-earthworm interaction, as a consequence of their coevolution. Here we tested the hypothesis of a specific core microbiota at the interface of two interacting macroorganisms, in three different soils. We grew barley in microcosms in the presence/absence of the endogeic earthworm Aporrectodea caliginosa. We investigated the structure of microbial communities and quantified their abundance. Because interactions between earthworms and plants have been proposed tobe mediated through the mineralization of organic matter and the release of nutrients, we also studied the abundance of genes involved in nitrogen cycling in different micro environments (bulk soil, rhizosphere and earthworm casts). 16S rRNA gene amplicon sequencing revealed the presence of microsites core microbiota over the three soil types. Despite an expected strong influence of soil type on microbial community composition (59% of explained variance), significant effects of both microsites (13%) and macro-organisms presence (7%) were observed. Many genes of the nitrogen cycle were influenced by soil type, whereas earthworms were only responsible for an increase in the abundance of the ureC gene. The interaction between plant and soil type was modifying the abundance of nosZ, nifH and narG, in the rhizosphere suggesting a strong control of the nitrogen cycle by the plant dependent on soil fertility. A refined analysis on each soil separately revealed a significant interaction between plant and earthworm presence on the structure of the rhizosphere and drilosphere microbiota. This suggests that assembly of microbial community in plant rhizospheres and earthworm casts was dependent on the mutual presence of earthworm and plant respectively. Several bacterial species were significantly enriched at the interface of plant rhizosphere and earthworm casts, suggesting that direct/indirect relationships between macroorganisms associated microbiota resulted in recruiting and promoting specific members.

Published
2017

29. Microbial metacommunity: a METABAR coding approach

Author

Marc Buee, Matthieu Barret, Maria Bernard, Didier Debroas, Isabelle Domaizon, Laure Fauchery, Claude Husson, Valerie Laval, Géraldine Pascal, Charlie Pauvert, Christophe Mougel, Thomas Pommier, Dirk Redecker, Aymé Spor, Sébastien Terrat, Veronique Edel-Hermann, Corinne Vacher, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), BIOlogie et GEstion des Risques en agriculture (BIOGER), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne ( LMGE ), Université Clermont Auvergne ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques ( CARRTEL ), Institut National de la Recherche Agronomique ( INRA ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ), BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes ( BIOGER-CPP ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Institut National de la Recherche Agronomique ( INRA ), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), ProdInra, Archive Ouverte, AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)

Subjects
[SDV] Life Sciences [q-bio], communauté microbienne, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], microbial community
Abstract

Microbial metacommunity: a METABAR coding approach. 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens)

Published
2017

30. Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities

Author

Jean Claude Cleyet-Marel, Christophe Mougel, Philippe Lemanceau, Sylvie Mazurier, Amandine Viollet, Barbara Pivato, Cécile Gubry-Rangin, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institute of Biological and Environmental Sciences, (SFIRC), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Laboratoire des symbioses tropicales et méditerranéennes ( LSTM ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université Montpellier 1 ( UM1 ) -Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), and ( SFIRC )

Subjects
0106 biological sciences, 0301 basic medicine, plant, Plant Science, 01 natural sciences, Plant Roots, rhizobium, Mycorrhizae, gram negative bacteria, Type III Secretion Systems, Mycorrhiza, Arbuscular mycorrhiza, genes, Soil Microbiology, Rhizosphere, biology, Pseudomonas, bacterial-populations, General Medicine, medicago truncatula, Medicago truncatula, Rhizobium, pseudomonas fluorescens, rhizosphère, roots, root nodulation, Pseudomonas fluorescens, Microbial communities, Fungus, Mycology, system, diversity, soil, 03 medical and health sciences, Botany, Genetics, Molecular Biology, formation de nodosités, Ecology, Evolution, Behavior and Systematics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, fungi, Gene Expression Regulation, Bacterial, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, bacterial infections and mycoses, 030104 developmental biology, écologie mycorhizienne, bactérie gram négatif, Mutation, Type III secretion, bacteria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany, nonpathogenic fusarium, helper bacteria
Abstract

International audience; Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads harboring T3SS (T3SS+) would be beneficial to arbuscular mycorrhizal symbiosis because non-pathogenic fluorescent pseudomonads have been previously shown to be much more abundant in mycorrhizal than in non-mycorrhizal roots. We tested this hypothesis by comparing mycorrhization and the associated rhizosphere microbial communities of Medicago truncatula grown in a non-sterile soil inoculated with either the T3SS+ mycorrhiza helper bacterium Pseudomonas fluorescens (C7R12) or a T3SS- mutant of the strain. Results showed that the bacterial secretion system was responsible for the promotion of mycorrhization because root colonization by arbuscular mycorrhizal fungi was not promoted by the T3SS- mutant. The observed T3SS-mediated promotion of mycorrhization was associated with changes in the rhizosphere bacterial communities and the increased occurrence of Claroidoglomeraceae within the intraradical arbuscular mycorrhizal fungi. Furthermore, both pseudomonad strains promoted the host-free growth of a model arbuscular mycorrhizal fungus in vitro, suggesting that T3SS-mediated promotion of mycorrhization occurs during plant-fungal interactions rather than during the pre-symbiotic phase of fungal growth. Taken together, these data provide evidence for the involvement of T3SS in promoting arbuscular mycorrhization by a model fluorescent pseudomonad and suggest the implication of interactions between the bacterium and mycorrhizas.

Published
2017

31. Bacterial community diversity harboured by interacting species

Author

Christophe Mougel, Jean-Pierre Gauthier, Frédérique Mahéo, Sébastien Terrat, Yannick Outreman, Jean Simon, Mikaël Bili, Anne Marie Cortesero, Denis Poinsot, Gwennola Ermel, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Microbiologie : Risques Infectieux, Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -CHU Pontchaillou [Rennes]-Faculté de Chirurgie Dentaire de Rennes-Faculté d'Odontologie-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes]-Faculté de Chirurgie Dentaire de Rennes-Faculté d'Odontologie-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université de Rennes (UNIV-RENNES)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], lcsh:Medicine, species, Artificial Gene Amplification and Extension, Pathogenesis, Pathology and Laboratory Medicine, phylogeny, cabbage, genus, Polymerase Chain Reaction, geography, Parasitoid, Abundance (ecology), [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Medicine and Health Sciences, Rickettsia, lcsh:Science, Trophic level, Multidisciplinary, biology, Ecology, Microbiota, beetle, Genomics, Biodiversity, Bacterial Pathogens, Insects, Coleoptera, symbiont, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, pyrosequencing, Medical Microbiology, Host-Pathogen Interactions, [SDE]Environmental Sciences, Wolbachia, France, Pathogens, microbial community, Research Article, Arthropoda, Spiroplasma, Mollicutes, Microbial Genomics, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Phylogenetics, Genetics, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology Techniques, Molecular Biology, Microbial Pathogens, parasitoid, Bacteria, Host (biology), Diptera, lcsh:R, fungi, Organisms, Biology and Life Sciences, biology.organism_classification, Invertebrates, Hymenoptera, 030104 developmental biology, lcsh:Q, Microbiome, Delia radicum
Abstract

International audience; All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts. © 2016 Bili et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Published
2016

32. Combining ecophysiological and microbial ecological approaches to study the relationship between Medicago truncatula genotypes and their associated rhizosphere bacterial communities

Author

Christophe Mougel, Sébastien Terrat, Nathalie G. Munier-Jolain, Anouk Zancarini, Christophe Salon, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, INRA [089201PPO24S00901], Regional Council of Burgundy (France), and Regional Council of Burgundy [AIB 29000427, 29000594]

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Soil Science, Plant Science, 01 natural sciences, 03 medical and health sciences, Medicago truncatula, Genotype, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Nutrition, 030304 developmental biology, 2. Zero hunger, Diversity, 0303 health sciences, Rhizosphere, biology, Ecology, fungi, food and beverages, Plant physiology, 15. Life on land, biology.organism_classification, Plant level, Bacterial communities, [SDE]Environmental Sciences, Genetic structure, 010606 plant biology & botany
Abstract

International audience; To assess how plant genotype and rhizosphere bacterial communities may interact, the genetic structure and diversity of bacterial communities in the rhizosphere soil of different Medicago truncatula genotypes were studied in relation to the plant carbon and nitrogen nutrition at the whole plant level. The genetic structure and diversity of plant-associated rhizosphere bacterial communities was analysed by Automated Ribosomal Intergenic Spacer Analysis and 454-pyrosequencing. In parallel, the carbon and nitrogen nutrition of the plants was estimated by a phenotypic description at both structural level (growth) and functional level (using carbon and nitrogen isotope labeling and an ecophysiological framework). An early effect of the plant genotype was observed on the rhizosphere bacterial communities, while few significant differences were detected at the plant structural phenotypic level. However, at a functional level, the different Medicago truncatula genotypes could be distinguished by their different nutritional strategies. Moreover, a comparison analysis showed that ecophysiological profiles of the different Medicago truncatula genotypes were correlated to the genetic structure and the diversity of the rhizosphere bacterial communities. The exploration of the genetic structure and diversity of rhizosphere bacterial communities combined with an ecophysiological approach is an innovative way to progress in our knowledge of plant-microbe interactions in the rhizosphere.

Published
2012

33. Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

Author

Mélanie Lelievre, Patrick Wincker, Christophe Mougel, Claudy Jolivet, Sébastien Terrat, Richard Christen, Dipankar Bachar, Pierre-Alain Maron, Pierre Plassart, Antonio Bispo, Philippe Lemanceau, Samuel Dequiedt, Tiffanie Regnier, Lionel Ranjard, and Virginie Nowak

Subjects
2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, Firmicutes, Soil chemistry, Bioengineering, 15. Life on land, biology.organism_classification, complex mixtures, Applied Microbiology and Biotechnology, Biochemistry, Actinobacteria, 03 medical and health sciences, Crenarchaeota, Metagenomics, Soil water, Botany, Pyrosequencing, Soil microbiology, 030304 developmental biology, Biotechnology
Abstract

Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.

Published
2011

34. Fluorescent pseudomonads harboring type III secretion genes are enriched in the mycorrhizosphere of Medicago truncatula

Author

Christophe Mougel, Sylvie Mazurier, Amandine Viollet, Agnès Robin, Philippe Lemanceau, and Thérèse Corberand

Subjects
0303 health sciences, Rhizosphere, Ecology, 030306 microbiology, Pseudomonas, Bulk soil, Mycorrhizosphere, Pseudomonas fluorescens, biochemical phenomena, metabolism, and nutrition, Biology, bacterial infections and mycoses, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, Medicago truncatula, 03 medical and health sciences, Botany, bacteria, Mycorrhiza, Soil microbiology, 030304 developmental biology
Abstract

Type III secretion systems (T3SSs) of Gram-negative bacteria mediate direct interactions with eukaryotic cells. Pseudomonas spp. harboring T3SS genes (T3SS+) were previously shown to be more abundant in the rhizosphere than in bulk soil. To discriminate the contribution of roots and associated arbuscular mycorrhizal fungi (AMF) on the enrichment of T3SS+ fluorescent pseudomonads in the rhizosphere of Medicago truncatula, their frequency was assessed among pseudomonads isolated from mycorrhizal and nonmycorrhizal roots and from bulk soil. T3SS genes were identified by PCR targeting a conserved hrcRST DNA fragment. Polymorphism of hrcRST in T3SS+ isolates was assessed by PCR-restriction fragment length polymorphism and sequencing. Genotypic diversity of all pseudomonads isolated, whether or not harboring T3SS, was described by BOX-PCR. T3SS+ pseudomonads were significantly more abundant in mycorrhizal than in nonmycorrhizal roots and in bulk soil, and all were shown to belong to the phylogenetic group of Pseudomonas fluorescens on the basis of 16S rRNA gene identity. Four hrcRST genotypes were described; two only included isolates from mycorrhizal roots. T3SS+ and T3SS- pseudomonads showed different genetic backgrounds as indicated by their different BOX-PCR types. Taken together, these data suggest that T3SSs are implicated in interactions between fluorescent pseudomonads and AM in medic rhizosphere.

Published
2011

35. Microdiversity of Burkholderiales associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula

Author

Pierre Offre, Philippe Lemanceau, Séverine Siblot, Barbara Pivato, Christophe Mougel, Sylvie Mazurier, and Graziella Berta

Subjects
2. Zero hunger, 0303 health sciences, Rhizosphere, Medicago, Ecology, biology, 030306 microbiology, Context (language use), 15. Life on land, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, Medicago truncatula, Comamonadaceae, 03 medical and health sciences, Burkholderiales, Botany, Mycorrhiza, 030304 developmental biology, Oxalobacteraceae
Abstract

The genetic diversity of bacterial communities associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula was characterized by two approaches. Firstly, phylogenetic analysis was performed on 164 partial 16S rRNA gene-intergenic spacer (IGS) sequences from operational taxonomic units previously shown to be preferentially associated with mycorrhizal roots. These sequences were distributed into three branches corresponding to Comamonadaceae, Oxalobacteraceae and Rubrivivax subgroups. Most sequences were obtained from mycorrhizal roots, indicating the preferential association of the corresponding families with mycorrhizal roots. A second phylogenetic analysis was performed on the partial 16S rRNA gene-IGS sequences of 173 isolates among a large collection of isolates, from mycorrhizal and nonmycorrhizal roots, belonging to Comamonadaceae and Oxalobacteraceae on the basis of their positive hybridization with a partial 16S rRNA gene-IGS probe obtained in this study. Sequence analysis confirmed the affiliation of 166 isolates to Comamonadaceae and seven to Oxalobacteraceae. Oxalobacteraceae isolates were more abundant in mycorrhizal (five) than in nonmycorrhizal (two) roots, whereas Comamonadaceae isolates were more abundant in nonmycorrhizal (109) than mycorrhizal roots (57). Further analysis of Comamonadaceae isolates by BOX-PCR showed that the genetic structure of culturable populations belonging to this family differed significantly in mycorrhizal and nonmycorrhizal roots, as indicated by distributions in different BOX types, differences being significantly explained by BOX types only including isolates from mycorrhizal roots. These data are discussed in an ecological context.

Published
2008

36. Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination

Author

Virginie Nowak, Noémie Pascault, Lionel Ranjard, Jean M.F. Martins, Sabrina Bouko, Christophe Mougel, and David P. H. Lejon

Subjects
Genetics, 0303 health sciences, Genetic diversity, Ecology, biology, 030306 microbiology, Soil organic matter, Pseudomonas fluorescens, Soil classification, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, DNA profiling, Genetic variation, Gene cluster, Soil microbiology, 030304 developmental biology
Abstract

A molecular fingerprinting assay was developed to assess the diversity of copA genes, one of the genetic determinants involved in bacterial resistance to copper. Consensus primers of the copA genes were deduced from an alignment of sequences from proteobacterial strains. A PCR detection procedure was optimized for bacterial strains and allowed the description of a novel copA genetic determinant in Pseudomonas fluorescens. The copA DNA fingerprinting procedure was optimized for DNA directly extracted from soils differing in their physico-chemical characteristics and in their organic status (SOS). Particular copA genetic structures were obtained for each studied soil and a coinertia analysis with soil physico-chemical characteristics revealed the strong influence of pH, soil texture and the quality of soil organic matter. The molecular phylogeny of copA gene confirmed that specific copA genes clusters are specific for each SOS. Furthermore, this study demonstrates that this approach was sensitive to short-term responses of copA gene diversity to copper additions to soil samples, suggesting that community adaptation is preferentially controlled by the diversity of the innate copA genes rather than by the bioavailability of the metal.

Published
2007

37. Diversity of root-associated fluorescent pseudomonads as affected by ferritin overexpression in tobacco

Author

Christophe Mougel, Agnès Robin, Thérèse Corberand, Philippe Lemanceau, Jean-Marie Meyer, Gérard Vansuyt, and Sylvie Mazurier

Subjects
0303 health sciences, Rhizosphere, Siderophore, Pyoverdine, biology, 030306 microbiology, Wild type, biology.organism_classification, Microbiology, Ferritin, 03 medical and health sciences, chemistry.chemical_compound, chemistry, biology.protein, Pythium aphanidermatum, Antagonism, Pathogen, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

A transgenic tobacco overexpressing ferritin (P6) was recently shown to accumulate more iron than the wild type (WT), leading to a reduced availability of iron in the rhizosphere and shifts in the pseudomonad community. The impact of the transgenic line on the community of fluorescent pseudomonads was assessed. The diversity of 635 isolates from rhizosphere soils, rhizoplane + root tissues, and root tissues of WT and P6, and that of 98 isolates from uncultivated soil was characterized. Their ability to grow under iron stress conditions was assessed by identifying their minimal inhibitory concentrations of 8-hydroxyquinoline for each isolate, pyoverdine diversity by isoelectrofocusing and genotypic diversity by random amplified polymorphism DNA. The antagonistic activity of representative isolates and of some purified pyoverdines against a plant pathogen (Pythium aphanidermatum Op4) was tested in vitro. In overall, isolates taken from P6 tobacco showed a greater ability to grow in iron stress conditions than WT isolates. The antagonism by some of the representative isolates was only expressed under iron stress conditions promoting siderophore synthesis and their pyoverdines appeared to have a specific structure as assessed by mass spectrometry. For other isolates, antagonism was still expressed in the presence of iron, suggesting the involvement of metabolites other than siderophores. Altogether, these data indicate that the transgenic tobacco that over-accumulates iron selected fluorescent pseudomonads, less susceptible to iron depletion and more antagonistic to the tested plant pathogen than those selected by the tobacco WT.

Published
2007

38. Plant traits related to nitrogen uptake influence plant-microbe competition

Author

Christophe Mougel, Florence Deau, Delphine Moreau, Céline Faivre, Barbara Pivato, Laurent Philippot, David Bru, Annick Matejicek, Hugues Busset, Florence Strbik, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Plant Health and Environment division of the French National Institute for Agricultural Research (INRA), and Philippot, Laurent

Subjects
0106 biological sciences, Microorganism, [SDV]Life Sciences [q-bio], RNA, Archaeal, 01 natural sciences, chemistry.chemical_compound, Soil, Nitrate, RNA, Ribosomal, 16S, Soil Microbiology, media_common, 2. Zero hunger, Biomass (ecology), Rhizosphere, Ecology, food and beverages, 04 agricultural and veterinary sciences, Plants, greenhouse experiment, RNA, Bacterial, [SDE]Environmental Sciences, rhizosphère, Soil microbiology, competition, Nitrogen, media_common.quotation_subject, plant-microbe interactions, Biology, Competition (biology), Denitrifying bacteria, nitrate, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, functional trait, Nitrogen cycle, Ecology, Evolution, Behavior and Systematics, Bacteria, nitrogène, fungi, Crenarchaeota, 15. Life on land, oligotrophic-nitrophilic gradient, Agronomy, chemistry, 040103 agronomy & agriculture, compétition, 0401 agriculture, forestry, and fisheries, nitrogen, rhizosphere, 010606 plant biology & botany
Abstract

International audience; Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more relevant for understanding plant-microbe interactions than composite traits, such as nitrophily, which are related to a number of ecophysiological processes.

Published
2015

39. Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites

Author

Mark J. Bailey, S. Emilia Hannula, Lionel Ranjard, Marc Buée, Bruce C. Thomson, Pierre Plassart, Emilie Tisserant, Johannes A. van Veen, Christophe Mougel, Francis Martin, Robert I. Griffiths, Stéphane Uroz, Philippe Lemanceau, Centre for Ecology and Hydrology, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Natural Environment Research Council (NERC), Netherland Institute for Ecology (NIOO), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nerderlands Instituut voor Ecologie (NIOO), Royal Netherlands Academy of Arts and Sciences (KNAW), NERC Natural Environment Research Councilceh020009ceh020008, Region Bourgogne-Franche-Comte, ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), European Project: 264465,EC:FP7:ENV,FP7-ENV-2010,ECOFINDERS(2011), Regional Council of Burgundy, ANR(ANR-11-LABX-0002-01), European Project: 264465, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and Microbial Ecology (ME)

Subjects
2. Zero hunger, Land use, Ecology, Soil biodiversity, [SDV]Life Sciences [q-bio], Archaeal communities, Soil Science, Edaphic, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 15. Life on land, Soil type, Microbiology, Bacterial communities, Fungal communities, Microbial population biology, 13. Climate action, T-RFLP, international, Soil pH, Environmental science, Soil ecology, Land use, land-use change and forestry, 454 pyrosequencing
Abstract

International audience; 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.

Published
2015

40. Understanding and managing soil biodiversity: a major challenge in agroecology

Author

Lionel Ranjard, Daniel Wipf, Barbara Pivato, Philippe Lemanceau, Pierre Plassart, Christophe Mougel, Pierre-Alain Maron, Sylvie Mazurier, Vincent Tardy, Cécile Revellin, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Lemanceau, Philippe, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), and Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST

Subjects
sol, Environmental Engineering, fertilité des sols, croissance végétale, Soil biodiversity, Biodiversité et Ecologie, Soil biology, Microbial communities, Biology, Soil fertility, biodiversité, Ecosystem services, Biodiversity and Ecology, biologie du sol, Soil functions, santé des plantes, 2. Zero hunger, Soil health, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, communauté microbienne, Plant growth and heath, Land use, business.industry, Ecology, Environmental resource management, Biodiversity, Agroécologie, 15. Life on land, Soil type, 13. Climate action, Agroecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Agronomy and Crop Science
Abstract

International audience; Soils are living environments in which particularly abundant and diverse microbiome and fauna are evolving. The resulting biological functioning has a direct impact not only on soil fertility but also on a series of ecosystems services. Thus, microbial communities are involved in geochemical cycles in which microbial enzymes catalyse the different steps. Modulation of the corresponding activities is essential as these affect plant growth and environmental quality. In general, biodiversity affects both the productivity and stability of agroecosystems. It is therefore of paramount importance to take soil biodiversity and biological functioning into account when designing cropping systems and evaluating their impacts. The progress achieved in soil microbiology in recent years now makes it possible to propose analyses of soil biology, as has been feasible for many years for soil physicochemistry. These analyses obviously require the use of standardized procedures for soil sampling, measuring the abundance and diversity of the microbial communities, as well as the identification of bioindicators. Similarly, referential systems need to be established to interpret these analyses and diagnose the biological status of soils, and, more especially, to determine whether the obtained values are within the range of variations normal for a given soil type and land use. Great progress to standardize such procedures and establish referential systems has been achieved during large-scale research programmes carried out to characterize biodiversity on national and European scales. These diagnostic elements need to be accompanied by recommendations. The aim of ongoing research is thus to propose aids for decision-making, based on the results of biological analyses, so attempts can be made to monitor and manage biodiversity to satisfy soil fertility requirements and ensure the ecosystem services expected of soils.

Published
2015

41. Effect of ferritin overexpression in tobacco on the structure of bacterial and pseudomonad communities associated with the roots

Author

Gérard Vansuyt, Philippe Lemanceau, Agnès Robin, Sylvie Mazurier, Christophe Mougel, and Séverine Siblot

Subjects
2. Zero hunger, 0303 health sciences, Rhizosphere, Ecology, biology, Ribosomal Intergenic Spacer analysis, Nicotiana tabacum, 04 agricultural and veterinary sciences, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, Ferritin, 03 medical and health sciences, Genotype, Botany, 040103 agronomy & agriculture, biology.protein, 0401 agriculture, forestry, and fisheries, Restriction fragment length polymorphism, Solanaceae, Bacteria, 030304 developmental biology
Abstract

The genetic structures of total bacterial and pseudomonad communities were characterized in rhizosphere soil and rhizoplane+root tissues of tobacco wild type and a ferritin overexpressor transgenic line (P6) by a cultivation-independent method using directly extracted DNA at the end of three consecutive plant cultures. The structure of total bacterial communities was characterized by automated ribosomal intergenic spacer analysis (A-RISA), and that of pseudomonad communities was characterized by PCR-restriction fragment length polymorphism (PCR-RFLP) from DNA amplified with specific primers. The structure of total bacterial communities was significantly modified in the rhizosphere soil by the overaccumulation of iron in the tobacco transgenic P6 line at the first culture, to a lesser extent at the second culture, and not at all at the third culture. No significant difference was recorded between the total communities associated with the roots (rhizoplane+root tissues) of the two plant genotypes in any of the cultures. In contrast, the difference in pseudomonad structure between the two plant genotypes increased with successive culture at the root level, but was not detected at a significant level in the rhizosphere soil. The impact of iron overaccumulation by the tobacco transgenic P6 line on pseudomonads supports previous findings on the importance of iron competition among fluorescent pseudomonads.

Published
2006

42. Temporal variability of airborne bacterial community structure in an urban area

Author

Karine Bizet, Lionel Ranjard, Esmeralda Carvalho, Pierre Alain Maron, Géraldine Marck, Philippe Lemanceau, Christophe Mougel, David P. H. Lejon, Nadège Cubito, Microbiologie, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Bertin Technologies, and CRITT 2ABI, Bourgogne Technologies

Subjects
Atmospheric Science, Hierarchy, bactérie aérienne, geography.geographical_feature_category, 010504 meteorology & atmospheric sciences, air, Ecology, [SDE.MCG]Environmental Sciences/Global Changes, Ribosomal Intergenic Spacer analysis, Population structure, Community structure, Sampling (statistics), 010501 environmental sciences, Urban area, bacterial community, temporal varibility, 01 natural sciences, diversity, Geography, diversité génétique, Principal component analysis, GENETIQUE DES POPULATIONS, 0105 earth and related environmental sciences, General Environmental Science
Abstract

International audience; Temporal airborne bacterial genetic community structure and meteorological factors were analysed above an urban area in the northwest of France from December 2003 to April 2004 with a sampling strategy considering different time intervals (from an hour to a month). Principal component analysis (PCA) of B-ARISA (Bacterial-Automated Ribosomal Intergenic Spacer Analysis) profiles revealed a hierarchy in the temporal variability of bacterial community: daily

Published
2006

43. Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodological Variability

Author

Jean-Christophe Lata, Sylvie Nazaret, Franck Poly, Jean Thioulouse, L. Ranjard, Christophe Mougel, Microbiologie, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), INRA, Institut National de la Recherche Agronomique (INRA), Microbiologie du Sol et de l'Environnement (MSE), Microbiology Laborarory, Université de Neuchâtel (UNINE), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Ecologie Systématique et Evolution (ESE), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Supported by the C.N.R.S., the Ministe`re de l'Ame´- nagement du Territoire et de l'Environnement, and the E.U. as part of the 'Mercure en Guyane' project, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Institut National de la Recherche Agronomique ( INRA ), Microbiologie du Sol et de l'Environnement ( MSE ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Université de Neuchâtel, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Biogéochimie et écologie des milieux continentaux ( Bioemco ), École normale supérieure - Paris ( ENS Paris ) -Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -AgroParisTech-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie Systématique et Evolution ( ESE ), Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Ecole Nationale du Génie Rural, des Eaux et des Forêts ( ENGREF ), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie ( PMEBBCE ), Etablissement National d'Enseignement Supérieur Agronomique de Dijon ( ENESAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), ProdInra, Migration, Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, Ribosomal Intergenic Spacer analysis, Biology, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, 03 medical and health sciences, Intergenic region, RNA, Ribosomal, 16S, DNA, Ribosomal Spacer, Methods, DNA, Fungal, ComputingMilieux_MISCELLANEOUS, Ecosystem, Soil Microbiology, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Genetics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Bacteria, Ecology, 030306 microbiology, Fungi, Reproducibility of Results, Genes, rRNA, Spacer DNA, BIOLOGIE MOLECULAIRE, Ribosomal RNA, DNA Fingerprinting, DNA extraction, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, RNA, Ribosomal, 23S, DNA profiling, RRNA Operon, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Soil microbiology, Food Science, Biotechnology
Abstract

Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extraction and PCR amplification) and biological (inter- and intrasite) variations were evaluated by comparing the number and intensity of peaks (bands) between electrophoregrams (profiles) and by multivariate analysis. Our results showed that ARISA is a high-resolution, highly reproducible technique and is a robust method for discriminating between microbial communities. To evaluate the potential biases in community description provided by ARISA, we also examined databases on length distribution of ribosomal intergenic spacers among bacteria (L. Ranjard, E. Brothier, and S. Nazaret, Appl. Environ. Microbiol. 66:5334–5339, 2000) and fungi.

Published
2001

44. Stimulation of different functional groups of bacteria by various plant residues as a driver of soil priming effect

Author

Séverine Boiry, Lionel Ranjard, Christophe Mougel, Sébastien Terrat, Noémie Pascault, Pierre-Alain Maron, Jean Lévêque, Richard Christen, Michel Pean, Aurore Kaisermann, Olivier Mathieu, Dipankar Bachar, Catherine Hénault, Sébastien Fontaine, Philippe Lemanceau, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut de signalisation, biologie du développement et cancer (ISBDC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Groupe de Recherches Appliquées en Phytotechnologie (GRAP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de recherche sur l'Ecosystème Prairial (UREP), Institut National de la Recherche Agronomique (INRA), Study financially supported by the Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME) and the Burgundy region., European Project: 264465,EC:FP7:ENV,FP7-ENV-2010,ECOFINDERS(2011), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UR 0874 Unité de recherche sur l'Ecosystème Prairial, Institut National de la Recherche Agronomique (INRA)-Unité de recherche sur l'Ecosystème Prairial (UREP)-Ecologie des Forêts, Prairies et milieux Aquatiques (EFPA), Université Côte d'Azur (UCA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
Firmicutes, [SDE.MCG]Environmental Sciences/Global Changes, Stable-isotope probing, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Decomposer, soil, 03 medical and health sciences, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, soil organic matter, Botany, carbon cycle, Environmental Chemistry, Gemmatimonadetes, Organic matter, stable isotope probing, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, Ecology, biology, Soil organic matter, Verrucomicrobia, bacterial diversity, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, pyrosequencing, Agronomy, chemistry, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Acidobacteria
Abstract

13 pages; International audience; 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, SOMdegrading 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 FOMdegrading communities during the degradation process may be an important driver of the PE, and consequently of carbon dynamics in soil.

Published
2013

45. Combining molecular microbial ecology with ecophysiology and plant genetics for a better understanding of plant-microbial communities' interactions in the rhizosphere

Author

Nathalie G. Munier-Jolain, Delphine Moreau, Thierry Rigaud, Christophe Mougel, Judith Burstin, Barbara Pivato, Philippe Lemanceau, Christophe Salon, Anouk Zancarini, Clémentine Lepinay, Gérard Duc, Agroécologie [Dijon], Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), F.J. de Bruijn, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biogéosciences [UMR 6282] [Dijon] (BGS), and Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Ecophysiology, quantitative genetics, ecophysiology, Plant genetics, [ SDV.SA.SDS ] Life Sciences [q-bio]/Agricultural sciences/Soil study, Biology, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 01 natural sciences, 03 medical and health sciences, plant–microbes interactions, Microbial ecology, Botany, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Rhizosphere, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Ecology, modeling, Quantitative genetics, Microbial population biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, microbial community, rhizosphere, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

18 pages; International audience

Published
2013

46. Legumes for feed, food, biomaterials and bioenergy in Europe : a review

Author

Christophe Mougel, Christian Huyghe, Marie-Hélène Jeuffroy, Anne-Sophie Voisin, Marie-Benoît Magrini, Sylvain Pellerin, Elise Pelzer, Jean-Marc Meynard, Jacques Guéguen, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Communication de centre, Agronomie, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Agrosystèmes Cultivés et Herbagers (ARCHE), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Département Sciences pour l'Action et le Développement (DEPT SAD), Transfert Sol-Plante et Cycle des Eléments Minéraux dans les Ecosystèmes Cultivés (TCEM), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Département Sciences pour l'Action et le Développement, École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut National de la Recherche Agronomique (INRA), Voisin, Anne-Sophie, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité de recherche sur les Biopolymères, Interactions Assemblages ( BIA ), Institut National de la Recherche Agronomique ( INRA ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Agrosystèmes Cultivés et Herbagers ( ARCHE ), Institut National Polytechnique [Toulouse] ( INP ) -Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Supérieure Agronomique de Toulouse, Institut National de Recherche Agronomique, Transfert Sol-Plante et Cycle des Eléments Minéraux dans les Ecosystèmes Cultivés ( TCEM ), and Institut National de la Recherche Agronomique ( INRA ) -École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux ( ENITAB )

Subjects
agroecology, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Environmental Engineering, legumes, bioenergy, Ecosystem services, agri-food system, Sustainable agriculture, Cropping system, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Agroecology, Legume, 2. Zero hunger, Sustainable development, business.industry, Agroforestry, 15. Life on land, outlets, biomaterials, intercropping, france, europe, ecosystem services, 13. Climate action, Agriculture, Sustainability, ecosystemservices, business, Agronomy and Crop Science
Abstract

Legume growing has many benefits. Indeed legumes provide plant proteins for animal feed and human food. Legumes fix atmospheric N2 and, in turn, provide cheap and green N fertilisers. Additionally, legumes are used as diversification crops in rotations based on oilseed rape and cereals. Despite those benefits, legume crops in Europe represent less than 4 % of arable lands, and European legume seeds are underused for animal and human nutrition. Nonetheless, European authorities are now fostering the development of legume crops for sustainable agriculture. Here, we analyse forage and grain legume-producing systems since 1950 in order to identify the actual constraints of legume development. We show that legumes can contribute to the agroecological transition for sustainable agriculture, food and energy and for sustainable agri-food systems. Then, we point out that high added-value niche markets are required for supporting legume production. The major research needs identified are (1) analysing the constraints of the current systems and identifying ways of moving towards systems that include more legumes, (2) identifying new and diversified uses for legumes in a sustainable food chain, (3) assessing and improving the ecosystem services provided by legumes at cropping system and territory scales and (4) promoting agroecology through and for legume crop management.

Published
2013

47. Interaction between Medicago truncatula and Pseudomonas fluorescens: evaluation of costs and benefits across an elevated atmospheric CO2

Author

Thierry Rigaud, Christophe Salon, Philippe Lemanceau, Clémentine Lepinay, Christophe Mougel, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Study funded by a doctoral grant from National Institute for Agricultural Research (INRA Plant Health and Environment division), by the Regional Council of Burgundy (project nu AIB29000359, grants AIB 29000427 & 29000594 for support to intregrated Agrale 6 projects)., Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biogéosciences [Dijon] ( BGS ), and Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS )

Subjects
0106 biological sciences, lcsh:Medicine, plant, Plant Science, 01 natural sciences, Plant Roots, Plant reproduction, nitrogen, Plant Microbiology, terrestrial ecosystem, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, lcsh:Science, Soil Microbiology, 2. Zero hunger, Mutualism (biology), Abiotic component, Plant Growth and Development, 0303 health sciences, Rhizosphere, dynamic, Multidisciplinary, response, biology, Ecology, food and beverages, Medicago truncatula, carbon-dioxide, development, soil, rhizosphere, Pseudomonas fluorescens, Seeds, Soil microbiology, Ecosystem Functioning, Research Article, [ SDV.SA.SDS ] Life Sciences [q-bio]/Agricultural sciences/Soil study, Flowers, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Microbiology, Ecosystems, Microbial Ecology, 03 medical and health sciences, Symbiosis, Plant-Environment Interactions, Botany, Biology, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Analysis of Variance, Atmosphere, Plant Ecology, lcsh:R, fungi, Computational Biology, 15. Life on land, Carbon Dioxide, biology.organism_classification, Plant Leaves, Agronomy, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem Modeling, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

10 pages; International audience; Soil microorganisms play a key role in both plants nutrition and health. Their relation with plant varies from mutualism to parasitism, according to the balance of costs and benefits for the two partners of the interaction. These interactions involved the liberation of plant organic compounds via rhizodeposition. Modification of atmospheric CO2 concentration may affect rhizodeposition and as a consequence trophic interactions that bind plants and microorganisms. Positive effect of elevated CO2 on plants are rather well known but consequences for micoorganisms and their interactions with plants are still poorly understood. A gnotobiotic system has been developed to study the interaction between Medicago truncatula Jemalong J5 and the mutualistic bacteria Pseudomonas fluorescens strain C7R12 under two atmospheric CO2 concentrations: ambient (365 ppm) versus enriched (750 ppm). Costs and benefits for each partner have been determined over time by measuring plant development and growth, the C and N contents of the various plant parts and the density of the bacteria in rhizosphere compartments. Following the increase in CO2, there was a beneficial effect of P. fluorescens C7R12 on development, vegetative growth, and C/N content of M. truncatula. Concerning plant reproduction, an early seed production was noticed in presence of the bacterial strain combined with increased atmospheric CO2 conditions. Paradoxically, this transient increase in seed production was correlated with a decrease in bacterial density in the rhizosphere soil, revealing a cost of increased CO2 for the bacterial strain. This shift of costs-benefits ratio disappeared later during the plant growth. In conclusion, the increase in CO2 concentration modifies transiently the cost-benefit balance in favor of the plant. These results may be explained either by a competition between the two partners or a change in bacterial physiology. The ecosystem functioning depends on the stability of many plant-microbe associations that abiotic factors can disrupt.

Published
2012

48. Soil nitrogen availability and plant genotype modify the nutrition strategies of M. truncatula and the associated rhizosphere microbial communities

Author

Christophe Salon, Marion Prudent, Anne-Sophie Voisin, Anouk Zancarini, Christophe Mougel, Nathalie G. Munier-Jolain, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, INRA, and Regional Council of Burgundy (France) [089201PPO24S00901]

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Ecophysiology, lcsh:Medicine, plant, Plant Science, 01 natural sciences, Soil, Nutrient, Plant Microbiology, Edaphology, lcsh:Science, 2. Zero hunger, Plant Growth and Development, 0303 health sciences, Rhizosphere, Multidisciplinary, biology, Ecology, Fungal genetics, food and beverages, Soil classification, Soil Ecology, Medicago truncatula, nutrition, associated rhizosphere microbial communities, Plant Physiology, [SDE]Environmental Sciences, Research Article, DNA, Plant, Genotype, Nitrogen, Ribosomal Intergenic Spacer analysis, Microbiology, Microbial Ecology, 03 medical and health sciences, Plant-Environment Interactions, Botany, Biology, 030304 developmental biology, Plant Ecology, lcsh:R, fungi, Plant community, 15. Life on land, biology.organism_classification, soil, nitrogen, medicago truncatula, genotype, Agronomy, lcsh:Q, Agronomic Ecology, Agroecology, 010606 plant biology & botany
Abstract

International audience; Plant and soil types are usually considered as the two main drivers of the rhizosphere microbial communities. The aim of this work was to study the effect of both N availability and plant genotype on the plant associated rhizosphere microbial communities, in relation to the nutritional strategies of the plant-microbe interactions, for six contrasted Medicago truncatula genotypes. The plants were provided with two different nutrient solutions varying in their nitrate concentrations (0 mM and 10 mM). First, the influence of both nitrogen availability and Medicago truncatula genotype on the genetic structure of the soil bacterial and fungal communities was determined by DNA fingerprint using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Secondly, the different nutritional strategies of the plant-microbe interactions were evaluated using an ecophysiological framework. We observed that nitrogen availability affected rhizosphere bacterial communities only in presence of the plant. Furthermore, we showed that the influence of nitrogen availability on rhizosphere bacterial communities was dependent on the different genotypes of Medicago truncatula. Finally, the nutritional strategies of the plant varied greatly in response to a modification of nitrogen availability. A new conceptual framework was thus developed to study plant-microbe interactions. This framework led to the identification of three contrasted structural and functional adaptive responses of plant-microbe interactions to nitrogen availability.

Published
2012

49. Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

Author

Sébastien, Terrat, Richard, Christen, Samuel, Dequiedt, Mélanie, Lelièvre, Virginie, Nowak, Tiffanie, Regnier, Dipankar, Bachar, Pierre, Plassart, Patrick, Wincker, Claudy, Jolivet, Antonio, Bispo, Philippe, Lemanceau, Pierre-Alain, Maron, Christophe, Mougel, and Lionel, Ranjard

Subjects
DNA, Bacterial, Soil, Bacteria, Molecular Sequence Data, Brief Reports, Biodiversity, Biomass, Metagenomics, complex mixtures, Phylogeny, Soil Microbiology
Abstract

Summary Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15 000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.

Published
2011

50. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR

Author

Samuel Dequiedt, Mélanie Lelievre, Laure Guillou, Claudy Jolivet, Nicolas Chemidlin Prévost-Bouré, Richard Christen, Hamid Reza Shahbazkia, Lionel Ranjard, Christophe Mougel, Dominique Arrouays, AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Institute of Developmental Biology and Cancer (IBDC), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), GenoSol (plateforme de l'université de Bourgogne), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité INFOSOL (ORLEANS INFOSOL), Institut National de la Recherche Agronomique (INRA), Universidade do Algarve (UAlg), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ADEME (French Agency for Energy and Environment), French National Research Agency (ANR), French Ministry for Ecology and Sustainable Development (MEEDDM), French Ministry of Agriculture (MAP), French Institute for Environment (IFEN), French Institute for Research and Development (IRD), National Forest Inventory (IFN), National Institute for Agronomic Research (INRA), FLAveur, VIsion et Comportement du consommateur (FLAVIC), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), InfoSol (InfoSol), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Microbiologie, Institut de signalisation, biologie du développement et cancer (ISBDC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Université de Bourgogne (UB), Microbiologie du Sol et de l'Environnement ( MSE ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Institute of Developmental Biology and Cancer ( IBDC ), Centre National de la Recherche Scientifique ( CNRS ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité INFOSOL ( ORLEANS INFOSOL ), Institut National de la Recherche Agronomique ( INRA ), Universidade do Algarve, Faro, Diversité et Interactions au sein du Plancton Océanique ( DIPO ), Adaptation et diversité en milieu marin ( ADMM ), and Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
fungal abundance, organic carbon content, real-time Q-PCR, length polymorphism, SYBRGreen method, type de sol, [SDV]Life Sciences [q-bio], lcsh:Medicine, Plant Science, Plant Roots, 18S ribosomal RNA, SYBRGreen method, type de sol, [ SDE ] Environmental Sciences, Soil, Fungal Reproduction, lcsh:Science, DNA, Fungal, Phylogeny, organic carbon content, 2. Zero hunger, 0303 health sciences, Diversity, Multidisciplinary, fungal abundance, Ecology, Reveals, Fungal genetics, Polymerase-chain-reaction, Agriculture, Biodiversity, Amplicon, Soil Ecology, soil texture, amplification enzymatique de l'adn, Bacterial communities, Samples, real-time Q-PCR, Community Ecology, [SDE]Environmental Sciences, Rhizosphere, Research Article, Soil texture, In silico, Molecular Sequence Data, Soil Science, Computational biology, Mycology, Biology, Real-Time Polymerase Chain Reaction, Microbiology, Microbial Ecology, 03 medical and health sciences, Species Specificity, Medicago truncatula, Microbial community, RNA, Ribosomal, 18S, Soil ecology, 030304 developmental biology, DNA Primers, Ribosomal-Rna genes, [ SDV ] Life Sciences [q-bio], 030306 microbiology, lcsh:R, Fungi, Botany, Reproducibility of Results, length polymorphism, soil texture, Sequence Analysis, DNA, Dna, 15. Life on land, amplification enzymatique de l'adn, DNA extraction, lcsh:Q, Primer (molecular biology)
Abstract

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen (R) method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1/FF390. This in silico analysis of the specificity of FR1/FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1/FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C:N ratio and land use in determining fungal abundance in soils. ADEME (French Agency for Energy and Environment); French National Research Agency (ANR); French Ministry for Ecology and Sustainable Development (MEEDDM); French Ministry of Agriculture (MAP); French Institute for Environment (IFEN); French Institute for Research and Development (IRD); National Forest Inventory (IFN); National Institute for Agronomic Research (INRA)

Published
2011

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