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Article ; Online: The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings.

Garin, Tiffany / Brin, Chrystelle / Préveaux, Anne / Brault, Agathe / Briand, Martial / Simonin, Marie / Barret, Matthieu / Journet, Laure / Sarniguet, Alain

Molecular plant pathology

2024 Volume 25, Issue 1, Page(s) e13412

Abstract: Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system ( ...

Abstract	Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact-dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed-to-seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB, abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild-type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison with T6SS-deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomonas genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris.
MeSH term(s)	Seedlings/microbiology ; Xanthomonas campestris/genetics ; Type VI Secretion Systems ; Raphanus ; Seeds/microbiology ; Stenotrophomonas/genetics ; Bacterial Proteins/genetics
Chemical Substances	Type VI Secretion Systems ; Bacterial Proteins
Language	English
Publishing date	2024-01-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2020755-4
ISSN	1364-3703 ; 1364-3703
ISSN (online)	1364-3703
ISSN	1364-3703
DOI	10.1111/mpp.13412
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Seedling microbiota engineering using bacterial synthetic community inoculation on seeds.

Arnault, Gontran / Marais, Coralie / Préveaux, Anne / Briand, Martial / Poisson, Anne-Sophie / Sarniguet, Alain / Barret, Matthieu / Simonin, Marie

FEMS microbiology ecology

2024 Volume 100, Issue 4

Abstract: Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and ... ...

Abstract	Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple and effective seedling microbiota engineering method using SynCom inoculation on seeds. The method was successful using a wide diversity of SynCom compositions and bacterial strains that are representative of the common bean seed microbiota. First, this method enables the modulation of seed microbiota composition and community size. Then, SynComs strongly outcompeted native seed and potting soil microbiota and contributed on average to 80% of the seedling microbiota. We showed that strain abundance on seed was a main driver of an effective seedling microbiota colonization. Also, selection was partly involved in seed and seedling colonization capacities since strains affiliated to Enterobacteriaceae and Erwiniaceae were good colonizers while Bacillaceae and Microbacteriaceae were poor colonizers. Additionally, the engineered seed microbiota modified the recruitment and assembly of seedling and rhizosphere microbiota through priority effects. This study shows that SynCom inoculation on seeds represents a promising approach to study plant microbiota assembly and its consequence on plant fitness.
MeSH term(s)	Seedlings/microbiology ; Seeds ; Plants/microbiology ; Soil ; Microbiota
Chemical Substances	Soil
Language	English
Publishing date	2024-03-19
Publishing country	England
Document type	Journal Article
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiae027
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Article ; Online: Emergence and spread of

Briand, Martial / Boccarossa, Alexandra / Rieux, Adrien / Jacques, Marie-Agnès / Ganlanon, Line / Johnson, Christian / Eveillard, Matthieu / Marsollier, Laurent / Marion, Estelle

Microbiology spectrum

2024 Volume 12, Issue 4, Page(s) e0382723

Abstract: The classical lineage of : Importance: Mycobacterium ... ...

Abstract	The classical lineage of Importance: Mycobacterium ulcerans
MeSH term(s)	Humans ; Mycobacterium ulcerans/genetics ; Buruli Ulcer/epidemiology ; Buruli Ulcer/microbiology ; Phylogeny ; Genomics ; Biological Evolution
Language	English
Publishing date	2024-03-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03827-23
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Article: First report of

Cesbron, Sophie / Briand, Martial / Dittmer, Jessica / Bousset-Vaslin, Lydia / Jacques, Marie-Agnès / Sarniguet, Alain

Plant disease

2023

Abstract: In October 2022, v-shaped necrotic lesions were observed on the leaf margins of field-grown winter oilseed rape (WOSR), Brassica napus L., in western France (Ille-et-Vilaine (35) and Maine-et-Loire (49) departments). Disease incidence on volunteers and ... ...

Abstract	In October 2022, v-shaped necrotic lesions were observed on the leaf margins of field-grown winter oilseed rape (WOSR), Brassica napus L., in western France (Ille-et-Vilaine (35) and Maine-et-Loire (49) departments). Disease incidence on volunteers and cultivated WOSR was generally low (5-10 %) but occasionally up to 80% on some fields. Leaf sections sampled from the margin of necrotic leaf tissue were dilacerated in sterile deionized water and the extract was spread onto tryptone soya agar (TSA) with cycloheximide (100 mg.L
Language	English
Publishing date	2023-11-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS-11-23-2326-PDN
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Article: Seed microbiota revealed by a large‐scale meta‐analysis including 50 plant species

Simonin, Marie / Briand, Martial / Chesneau, Guillaume / Rochefort, Aude / Marais, Coralie / Sarniguet, Alain / Barret, Matthieu

The new phytologist. 2022 May, v. 234, no. 4

2022

Abstract: Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing 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 ...

Abstract	Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing 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 richness varying from one to thousands of taxa. Hence, seed microbiota presents a variable (i.e. flexible) microbial fraction but we also identified a stable (i.e. core) fraction across samples. Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea agglomerans, Pseudomonas viridiflava, P. fluorescens, Cladosporium perangustum and Alternaria sp., are dominant seed taxa. The characterization of the core and flexible seed microbiota provided here will help uncover seed microbiota roles for plant health and design effective microbiome engineering.
Keywords	Alternaria ; Cladosporium ; Pantoea agglomerans ; Pseudomonas viridiflava ; fungi ; habitats ; inoculum ; meta-analysis ; microbiome ; plant health
Language	English
Dates of publication	2022-05
Size	p. 1448-1463.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18037
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Seed microbiota revealed by a large-scale meta-analysis including 50 plant species.

Simonin, Marie / Briand, Martial / Chesneau, Guillaume / Rochefort, Aude / Marais, Coralie / Sarniguet, Alain / Barret, Matthieu

The New phytologist

2022 Volume 234, Issue 4, Page(s) 1448–1463

Abstract: Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing 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 ...

Abstract	Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing 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 richness varying from one to thousands of taxa. Hence, seed microbiota presents a variable (i.e. flexible) microbial fraction but we also identified a stable (i.e. core) fraction across samples. Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea agglomerans, Pseudomonas viridiflava, P. fluorescens, Cladosporium perangustum and Alternaria sp., are dominant seed taxa. The characterization of the core and flexible seed microbiota provided here will help uncover seed microbiota roles for plant health and design effective microbiome engineering.
MeSH term(s)	Bacteria ; Microbiota ; Plants ; Seeds/microbiology
Language	English
Publishing date	2022-03-18
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18037
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Whole Genome Sequences of Nine

Gaudin, Charlotte / Gihaut, Christopher / Briand, Martial / Marques, Abi S A / Ferreira, Marisa A S V / Jacques, Marie-Agnès / Chen, Nicolas W G

Microbiology resource announcements

2023 Volume 12, Issue 3, Page(s) e0125922

Abstract: We report the complete and circularized genome sequences of nine strains of Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans, which cause common bacterial blight of bean. These assemblies provide high-quality material for functional ... ...

Abstract	We report the complete and circularized genome sequences of nine strains of Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans, which cause common bacterial blight of bean. These assemblies provide high-quality material for functional and evolutionary studies of these legume pathogens.
Language	English
Publishing date	2023-02-13
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/mra.01259-22
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Article: Analysis of the Diversity of Xylophilus ampelinus Strains Held in CIRM-CFBP Reveals a Strongly Homogenous Species

Portier, Perrine / Taghouti, Géraldine / Bertrand, Paul-Emile / Briand, Martial / Dutrieux, Cécile / Lathus, Audrey / Fischer-Le Saux, Marion

Microorganisms. 2022 July 28, v. 10, no. 8

2022

Abstract: Xylophilus ampelinus is the causal agent of blight and canker on grapevine. Only a few data are available on this species implying that the occurrence of this pathogen may be underestimated, and its actual ecological niche may not be understood. Moreover, ...

Abstract	Xylophilus ampelinus is the causal agent of blight and canker on grapevine. Only a few data are available on this species implying that the occurrence of this pathogen may be underestimated, and its actual ecological niche may not be understood. Moreover, its genetic diversity is not well known. To improve our knowledge of this species, an analysis of the complete genome sequences available in NCBI was performed. It appeared that several sequences are misidentified. The complete genome sequence of the type strain was obtained and primers designed in order to sequence gyrB and rpoD genes for the strains held in CIRM-CFBP. The genetic barcoding data were obtained for 93 strains, isolated over 35 years and from several geographical origins. The species revealed to be strongly homogenous, displaying nearly identical sequences for all strains. However, the oldest strains of this collection were isolated in 2001 therefore, a new isolation campaign and epidemiological surveys are necessary, along with the obtention of new complete genome sequences for this species.
Keywords	Vitis ; Xylophilus ampelinus ; blight ; genetic barcoding ; genetic variation ; genome ; niches ; nucleotide sequences ; pathogens
Language	English
Dates of publication	2022-0728
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms10081531
Database	NAL-Catalogue (AGRICOLA)

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Article: Zucchini Vein Clearing Disease Is Caused by Several Lineages Within

Lacault, Caroline / Briand, Martial / Jacques, Marie-Agnès / Darrasse, Armelle

Phytopathology

2020 Volume 110, Issue 4, Page(s) 744–757

Abstract: Zucchini ( ...

Abstract	Zucchini (
MeSH term(s)	Multilocus Sequence Typing ; Phylogeny ; Plant Diseases ; Pseudomonas syringae ; Virulence
Language	English
Publishing date	2020-03-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-07-19-0266-R
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Article ; Online: Novel tetraplex qPCR assays for simultaneous detection and identification of Xylella fastidiosa subspecies in plant tissues

Dupas Enora / Briand Martial / Jacques Marie-Agnès / Cesbron Sophie

Abstract: AbstractXylella fastidiosa is an insect-borne bacterium confined to the xylem vessels of plants. This plant pathogen has a broad host range estimated to 560 plant species. Five subspecies of the pathogen with different but overlapping host ranges have ... ...

Abstract	AbstractXylella fastidiosa is an insect-borne bacterium confined to the xylem vessels of plants. This plant pathogen has a broad host range estimated to 560 plant species. Five subspecies of the pathogen with different but overlapping host ranges have been described, but only three subspecies are widely accepted, namely subspecies fastidiosa, multiplex and pauca. Initially limited to the Americas, Xf has been detected in Europe since 2013. As management of X. fastidiosa outbreaks in Europe depends on the identification of the subspecies, accurate determination of the subspecies in infected plants as early as possible is of major interest. Thus, we developed various tetraplex and triplex qPCR assays for Xylella fastidiosa detection and subspecies identification in planta in a single reaction. We designed primers and probes using SkIf, a bioinformatics tool based on k-mers, to detect specific signatures of the species and subspecies from a dataset of 58 genome sequences representative of X. fastidiosa diversity. We tested the qPCR assays on 39 target and 30 non-target strains, as well as on 13 different plant species spiked with strains of the different subspecies of X. fastidiosa, and on samples from various environmental and inoculated host plants. Sensitivity of simplex assays was equal or slightly better than the reference protocol on purified DNA. Tetraplex qPCR assays had the same sensitivity than the reference protocol and allowed X. fastidiosa detection in all spiked matrices up to 103 cells.mL−1. Moreover, mix infections of two to three subspecies could be detected in the same sample with tetraplex assays. In environmental plant samples, the tetraplex qPCR assays allowed subspecies identification when the current method based on multilocus sequence typing failed. The qPCR assays described here are robust and modular tools that are efficient for differentiating X. fastidiosa subspecies directly in plant samples.
Keywords	covid19
Publisher	biorxiv
Document type	Article ; Online
DOI	10.1101/699371
Database	COVID19

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