Matthieu Barret

Matthieu Barret
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Institut de Recherche en Horticulture et Semences (IRHS)

Ph.D.

About

118
Publications
25,357
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Introduction
My research focuses on the biological and ecological processes involved in the assembly of the seed microbiota. More specifically I am interested in (i) the seed transmission pathways employed by microorganisms, (ii) seed-microbial and inter-microbial interactions occurring during seed development and (iii) the impact of community structure on seed vigor.
Additional affiliations
November 2012 - present
French National Institute for Agriculture, Food, and Environment (INRAE)
Position
  • Institut National de la Recherche Agronomique
June 2009 - October 2012
University College Cork

Publications

Publications (118)
Preprint
Full-text available
Pollen, as all other plant tissues, harbors different microorganisms. As honey bees (Apis mellifera) collect and pack pollen they add regurgitated nectar to moisten and glue the pollen grains, possibly changing the microbial composition. In this study, we compared the microbiota of clean Brassica napus pollen with that of bee-worked corbicular poll...
Article
Seed microbiota constitutes a primary inoculum for plants that is gaining attention due to its role for plant health and productivity. Here, we performed a meta‐analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa rich...
Article
Full-text available
Coherent genomic groups are frequently used as a proxy for bacterial species delineation through computation of overall genome relatedness indices (OGRI). Average nucleotide identity (ANI) is a widely employed method for estimating relatedness between genomic sequences. However, pairwise comparisons of genome sequences based on ANI is relatively co...
Article
Full-text available
This study combined culture-dependent (strain isolation plus molecular identification) and culture-independent (metabarcoding) approaches to characterize the diversity of microbiota on wheat and oilseed rape residues. The goal was to develop a methodology to culture microorganisms with the aim of being able to establish synthetic crop residue micro...
Article
Full-text available
The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities...
Preprint
Full-text available
Seed microbiota constitutes a primary inoculum for plants that is gaining attention due to its role for plant health and productivity. Here, we performed a meta-analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa rich...
Preprint
Full-text available
Gaining basic understanding of processes involved in seed microbiota assembly is a prerequisite for improving crop establishment. Investigation of microbiota structure during seed development revealed that individual seeds of bean and radish were associated with a dominant bacterial taxon representing more than 75% of all reads. The identity of thi...
Article
Full-text available
Background: The reconstruction of metagenome-assembled genomes (MAGs) has emerged as a powerful approach for combining the taxonomic and functional content of microbial populations. Aim: To use this new approach to highlight mechanisms linking gut microbiota to NAFLD severity METHODS: Stool samples were collected from 96 NAFLD patients on the da...
Article
The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of our study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and co...
Preprint
Full-text available
Seed microbial community constitutes a primary inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. Here, we characterized the interchange event or coalescence of seed and soil microbiota and how it structured seedling bacterial and...
Article
Full-text available
Oilseed rape residues are a crucial determinant of stem canker epidemiology as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterize the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify microorganisms interacting with th...
Article
Full-text available
Seed microbiota acts as a starting point for the assembly of the plant microbiota and contributes to successful plant establishment. To date, the order and timing of microbial taxa immigration during seed development and maturation remained unknown. We investigated the temporal dynamics of seed bacterial communities in bean and radish. A high phylo...
Article
Full-text available
The assembly of the seed microbiota involves some early microbial seed colonizers that are transmitted from the maternal plant through the vascular system, while other microbes enter through the stigma. Thus, the seed microbiota consists of microbes not only recruited from the plant vascular tissues, but also from the flower. Flowers are known to b...
Article
Full-text available
Background: Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues and to identify microorganisms inter...
Preprint
Full-text available
Background Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici . We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues, and to identify microorganisms inter...
Article
Full-text available
Seeds are involved in the transmission of microorganisms from one plant generation to the next and consequently act as reservoirs for the plant microbiota. The driving processes influencing seed microbiota assemblage have not been yet deciphered because of confounding factors related to environmental location, agricultural practices, and host genot...
Article
Full-text available
Background: Microbiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employe...
Preprint
Background Microbiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed....
Preprint
Full-text available
Trees, as foundation species, play a pivotal role in the species interaction networks that constitute forest ecosystems. From the seed stage, they interact with microbial communities that affect their growth, health and fitness. Despite their eco-evolutionary importance, the processes shaping seed microbial communities in natural forests have recei...
Poster
Full-text available
Zymoseptoria tritici is one of the most damaging pathogens of wheat, causing yield losses of up to 40%. Like many other cereal foliar pathogens, it remains on crop residues during the intercropping season, where it reproduces sexually, with ascospores infecting seedlings at the beginning of subsequent seasons. Despite the importance of residues as...
Preprint
Background Microbiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed....
Preprint
Full-text available
The assembly of the seed microbiota involves some early microbial seed colonizers that are transmitted from the maternal plant through the vascular system, while other microbes enter through the stigma. Thus, the seed microbiota consists of microbes not only recruited from the vascular tissues of the plant, but also from the flower. Flowers are kno...
Article
Full-text available
Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study, we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases...
Article
Full-text available
Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of tw...
Preprint
Full-text available
Background: Since the dawn of agriculture, human selection on plants has progressively differentiated input-demanding productive crops from their wild progenitors thriving in marginal areas. Barley (Hordeum vulgare), the fourth most cultivated cereal globally, is a prime example of this process. We previously demonstrated that wild and domesticated...
Preprint
Full-text available
A bstract Coherent genomic groups are frequently used as a proxy for bacterial species delineation through computation of overall genome relatedness indices (OGRI). Average nucleotide identity (ANI) is a widely employed method for estimating relatedness between genomic sequences. However, pairwise comparisons of genome sequences based on ANI is rel...
Preprint
Full-text available
Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of tw...
Article
Full-text available
A rapid and simple method for assessing and representing genome sequences relatedness
Article
Trees, as foundation species, play a pivotal role in the species interaction networks that constitute forest Ecosystems. From the seed stage, they interact with microbial communities that affect their growth, health and fitness. Despite their eco-evolutionary importance, the processes shaping seed microbial communities in natural forests have recei...
Chapter
This chapter discusses the rhizosphere effect. The rhizosphere represents a major area of exchanges between soil, roots and soil‐borne organisms, in particular the soil microbiota. It is remarkable to note that, despite its cost to the plant, the release of rhizodeposits has been maintained during plant evolution and is shared by all plant species....
Preprint
Full-text available
Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases...
Article
Full-text available
Microbial interactions occurring on and around seeds are especially important for plant fitness since seed-borne microorganisms are the initial source of inoculum for the plant microbiota. In this study, we analyze structural and functional changes occurring within the plant microbiota at these early stages of the plant cycle, namely germination an...
Article
A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interacti...
Article
Full-text available
The present work reports the discovery and complete genome sequencing of a virus from symptomless radish seedlings, classifiable as a novel member of the genus Alphapartitivirus, family Partitiviridae. Total RNA extracted from germinating seedlings was sequenced using Illumina technology. Bioinformatic analysis of the RNA-seq data revealed two cont...
Article
Full-text available
Alternaria brassicicola causes dark spot (or black spot) disease, which is one of the most common and destructive fungal diseases ofBrassicaceaespp. worldwide. Here, we report the draft genome sequence of strain Abra43. The assembly comprises 29 scaffolds, with anN50value of 2.1 Mb. The assembled genome was 31,036,461 bp in length, with a G+C conte...
Preprint
Full-text available
A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interacti...
Poster
Full-text available
In bacterial systematics, the use of average nucleotide identities (ANI) is now widely used to group bacterial genomes in phylogenetic groups or cliques. However, the computational time of this distance parameter which uses BLAST algorithm, could be long and could be a limiting factor to study large datasets. As an example, 56000 bacterial genomes...
Article
Full-text available
Aims Seeds are vectors of a diversified microbiota including plant pathogens. To better understand transmission of common bacterial blight (CBB) agents to bean seeds, we analyzed the role of non-pathogenic xanthomonads on seed transmission efficiency and investigated the location of Xanthomonas citri pv. fuscans (Xcf) into seeds and plantlets. Met...
Article
Full-text available
Background Seeds host bacterial inhabitants but only a limited knowledge is available on which taxa inhabit seed, which niches could be colonized, and what the routes of colonization are. Scope Within this commentary, a discussion is provided on seed bacterial inhabitants, their taxa, and from where derive the seed colonizers. Conclusions Seeds/a...
Article
Full-text available
Background and aimsSeeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations. Meth...
Article
Deciphering the evolutionary history and transmission patterns of virulence determinants is necessary to understand the emergence of novel pathogens. The main virulence determinant of most pathogenic proteobacteria is the type three secretion system (T3SS). The Xanthomonas genus includes bacteria responsible for numerous epidemics in agroecosystems...
Article
Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transm...
Poster
Full-text available
Despite the recognized contribution of crop debris as inoculum source of many plant pathogens, little is known about the structure and function of microbial entities associated to this plant habitat, and their interactions with residue-borne plant pathogens. The objective of this work is to characterize bacterial and fungal assemblages associated t...
Article
Biocontrol strategies using organic substrates such as wood fibers and biocontrol agents such as Trichoderma are currently developed to control soil pathogens such as Fusarium oxysporum. Nonetheless, such biocontrol methods give discording results, notably because microbial communities of organic substrates actually are not taken into account. Ther...
Book
Full-text available
Plants are surrounded with microorganisms whose abundance is promoted by the release of plant organic compounds and by the presence of niches favourable to microbial development and activities. These microorganisms thrive in three main plant compartments, i.e., spermosphere, rhizosphere and phyllosphere, which are interconnected. They are recruited...
Chapter
Full-text available
Plants are surrounded with microorganisms whose abundance is promoted by the release of plant organic compounds and by the presence of niches favourable to microbial development and activities. These microorganisms thrive in three main plant compartments, i.e., spermosphere, rhizosphere and phyllosphere, which are interconnected. They are recruited...
Conference Paper
Full-text available
SkIf is a comparative genomics tool that detect genomic regions (from SNPs to genomic islands) specifically associated to a group of organisms (defined by the user). SkIf identify specific sequences for a group of organisms sharing a common trait of interest. The user uploads a library of sequences (DNA, RNA, or AA) then choose one reference sequ...
Article
Full-text available
In order to contribute to the description of sourdough LAB composition, MiSeq sequencing and qPCR methods were performed in association with cultural methods. A panel of 16 French organic bakers and farmer-bakers were selected for this work. The lactic acid bacteria (LAB) diversity of their organic sourdoughs was investigated quantitatively and qua...
Article
Full-text available
Seeds are involved in the vertical transmission of microorganisms from one plant generation to another and consequently act as reservoirs for the plant microbiota. However, little is known about the structure of seed-associated microbial assemblages and the regulators of assemblage structure. In this work, we have assessed the response of seed-asso...
Data
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