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Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils
by
LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE) ; Institut de Recherche pour le Développement (IRD)
, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [Occitanie])
, Institut de Recherche Agricole pour le Développement [Yaoundé] (IRAD)
, Université Cheikh Anta Diop de Dakar [Sénégal] (UCAD)
, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda (PC)
, Simonin, Marie
, IRHS - Équipe EmerSys (Emergence, Systématique et Ecologie des Bactéries associées aux Plantes) (IRHS-EMERSYS) ; 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 Rennes Angers ; Institut national d'enseignement supérieur pour l'agriculture, l'ali
in
Agricultural management
/ Agricultural practices
/ Analysis
/ Archaea
/ Bacteria
/ Community structure
/ Ecology
/ Ecology, environment
/ Environmental aspects
/ Fungi
/ Genetic aspects
/ Genetics
/ Genotype
/ Genotype & phenotype
/ Genotypes
/ Life Sciences
/ Metagenomics
/ Microbiology
/ Microbiology and Parasitology
/ Microbiomes
/ Microorganisms
/ Plants genetics
/ Rhizosphere
/ Soil microbiology
/ Soil types
/ Soils
/ Symbiosis
/ Wheat
2020
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Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils
by
LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE) ; Institut de Recherche pour le Développement (IRD)
, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [Occitanie])
, Institut de Recherche Agricole pour le Développement [Yaoundé] (IRAD)
, Université Cheikh Anta Diop de Dakar [Sénégal] (UCAD)
, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda (PC)
, Simonin, Marie
, IRHS - Équipe EmerSys (Emergence, Systématique et Ecologie des Bactéries associées aux Plantes) (IRHS-EMERSYS) ; 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 Rennes Angers ; Institut national d'enseignement supérieur pour l'agriculture, l'ali
in
Agricultural management
/ Agricultural practices
/ Analysis
/ Archaea
/ Bacteria
/ Community structure
/ Ecology
/ Ecology, environment
/ Environmental aspects
/ Fungi
/ Genetic aspects
/ Genetics
/ Genotype
/ Genotype & phenotype
/ Genotypes
/ Life Sciences
/ Metagenomics
/ Microbiology
/ Microbiology and Parasitology
/ Microbiomes
/ Microorganisms
/ Plants genetics
/ Rhizosphere
/ Soil microbiology
/ Soil types
/ Soils
/ Symbiosis
/ Wheat
2020
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Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils
by
LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE) ; Institut de Recherche pour le Développement (IRD)
, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [Occitanie])
, Institut de Recherche Agricole pour le Développement [Yaoundé] (IRAD)
, Université Cheikh Anta Diop de Dakar [Sénégal] (UCAD)
, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda (PC)
, Simonin, Marie
, IRHS - Équipe EmerSys (Emergence, Systématique et Ecologie des Bactéries associées aux Plantes) (IRHS-EMERSYS) ; 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 Rennes Angers ; Institut national d'enseignement supérieur pour l'agriculture, l'ali
in
Agricultural management
/ Agricultural practices
/ Analysis
/ Archaea
/ Bacteria
/ Community structure
/ Ecology
/ Ecology, environment
/ Environmental aspects
/ Fungi
/ Genetic aspects
/ Genetics
/ Genotype
/ Genotype & phenotype
/ Genotypes
/ Life Sciences
/ Metagenomics
/ Microbiology
/ Microbiology and Parasitology
/ Microbiomes
/ Microorganisms
/ Plants genetics
/ Rhizosphere
/ Soil microbiology
/ Soil types
/ Soils
/ Symbiosis
/ Wheat
2020
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Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils
Journal Article
Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils
2020
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Overview
Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.
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