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[inserm-05384736] The contribution of comparative genomics to health geography research: A case study on the identification of sites at which M. ulcerans contamination occurs in Benin
We report here a significant advance in research into Buruli ulcer, a skin disease caused by an environmental bacterium (Mycobacterium ulcerans). We demonstrate the utility of crossed analyses of comparative genomics and geographic data to improve our understanding of the spatial dynamics of this disease and to identify potential sites of contamination with greater precision. An analysis of patient isolates from the endemic region Ouémé-Plateau (Benin) led to the detection, of a spatial clustering of three specific genotypes. It suggests the existence of different ecological reservoirs or particular environmental conditions favoring the restriction of the bacterium to particular areas with very tight geographic boundaries. A health geography survey was performed on patients infected with these genotypes, based on a method developed by our team: a detailed interview concerning the patient's place of residence, followed by a commented tour on foot of the sites mentioned, with the patient. All the sites visited were geolocalized by GPS. A cross-analysis of spatial and comparative genomics data led to identify zones frequented by multiple patients potentially linked to exposure to the bacterium. This mixed dynamic research approach, pave the way for a better understanding of M. ulcerans transmission and for improving preventive strategies.
ano.nymous@ccsd.cnrs.fr.invalid (Alexandra Boccarossa) 28 Jan 2026
https://inserm.hal.science/inserm-05384736v1
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[hal-05293171] Lactuchelins: New lipopeptide siderophores from Pseudomonas lactucae inhibit Xanthomonas campestris pv. campestris 8004
Seeds harbor diverse microbial communities, including beneficial microbes that play a vital role in protecting plants from seed-borne pathogens. Despite their critical importance, the molecular mechanisms driving intermicrobial competition within the seed microbiome remain poorly understood, limiting the potential to optimize seed inoculation strategies. In this study, we evaluated the inhibitory potential of 30 seed-borne bacterial strains against the phytopathogen Xanthomonas campestris pv. campestris 8004 (Xcc8004). We identified Pseudomonas lactucae CFBP13502 as a potent inhibitor of Xcc8004, mediated by exometabolites specifically induced in the presence of Lysobacterales (formerly Xanthomonadales). Transcriptomic analysis of CFBP13502 revealed upregulation of a gene cluster involved in the biosynthesis of a lipopeptide siderophore biosynthesis. Gene deletion confirmed that this cluster is essential for the growth inhibition of Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, providing strong evidence for the role of iron chelation. Through comparative metabolomics, we elucidated the structure of a novel family of lipopeptide siderophores, which we named lactuchelins, produced by CFBP13502. Our findings provide the first molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 01 Oct 2025
https://hal.science/hal-05293171v1
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[hal-05529897] Lactuchelins represent lipopeptide siderophores produced by <i>Pseudomonas lactucae</i> that inhibit <i>Xanthomonas campestris</i>
The seed is a habitat with limited resources and space. Although it is widely accepted that microbial competition is a key driver of the assembly of seed-associated microbial communities, the underlying mechanisms of this competition are not well understood. The initial objective of this work was to assess the importance of contact-independent microbial competition between the phytopathogenic bacterium Xanthomonas campestris pv. campestris 8004 (Xcc8004) and 30 strains representative of the bacterial populations most commonly associated with radish (Raphanus sativus) seeds. We identified Pseudomonas lactucae CFBP 13502 as a potent inhibitor of Xcc8004, mediated by exometabolites, specifically induced by certain seed-borne strains. Transcriptomic analysis linked this inducible activity to the upregulation of a gene cluster encoding a lipopeptide siderophore. Targeted gene deletion in P. lactucae CFBP 13502 confirmed that this cluster is essential for antagonism against Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, strongly supporting iron chelation as the underlying mechanism. Through comparative metabolomics, we elucidated the structure of a family of lipopeptide siderophores, produced by P. lactucae CFBP 13502, which we named lactuchelins. Our findings provide molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seedbased biocontrol strategies against seed-borne phytopathogens.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 27 Feb 2026
https://hal.inrae.fr/hal-05529897v1
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[hal-05618323] Seed-associated yeasts: diversity and beneficial effects on plants
A meta-analysis of seed microbiota defined 16 core taxa present in more than 20 plant species (Simonin et al., 2022). Among them, six seed core taxa were yeasts, belonging to the genera Vishniacozyma, Filobasidium, Sporobolomyces, and Aureobasidium, which are commonly detected in various environments (soil, root, shoot, air, litter from croplands, forest, deserts). However, within the seeds, yeast diversity and their functional roles remain poorly described. To fill this gap, we aimed to characterize the diversity of seed-associated yeasts across nine plant species (crops and non-cultivated species) using culturomics and microscopy and we evaluated 10 isolates for their antifungal activity and capacity to enhance plant growth. Our results showed that seed-associated yeasts predominantly belong to the Basidiomycota phylum, particularly the Tremellomycetes class. Our collection of 229 isolates covers 15 genera (2 of Ascomycota and 13 of Basidiomycota), with Holtermanniella, Vishniacozyma, Filobasidium, Naganishia and Sporobolomyces being the most frequently isolated. These dominant yeasts were isolated from multiple plant species (4 to 8), except for Naganishia only isolated from Solanum lycopersicum L. In vitro antifungal assays revealed that eight out of ten isolates significantly inhibited the growth at least one of six plant pathogens (Fusarium graminearum, F. culmorum, F. oxysporum sp. phaseoli, F. oxysporum sp. lycopersici, Alternaria brassicicola, Globisporangium ultimum). Both Aureobasidium isolates inhibited all plant pathogens growth, while other strains showed variable inhibition depending on the pathogen. In greenhouse experiments, most isolates slightly reduced bean seedling emergence and vigor under non-infected conditions, but Filobasidium and Hannaella improved seedling establishment when subjected to pathogen stress caused by G. ultimum. These results suggest that seeds represent a specific habitat that diverse Basidiomycota yeasts can colonize. Seed-associated yeast can compete with some plant pathogens and influence plant growth. To conclude, while yeasts are widely recognized as biotechnological resources, their potential in agriculture, particularly for plant growth promotion and protection remains underexplored and needs to be delved.
ano.nymous@ccsd.cnrs.fr.invalid (Muriel Marchi) 23 Oct 2026
https://univ-angers.hal.science/hal-05618323v1
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[hal-03695954] Extended Biocontrol
This book presents an exhaustive overview of the theoretical foundations and practical applications of biocontrol in agriculture. It encompasses all kinds of nature-based approaches for crop protection: introduction and conservation of natural enemies, release of sterile insects, enhancement of plant defenses, use of microorganisms, biopesticides, and semiochemicals. Cutting-edge knowledge in population biology, microbial ecology, epidemiology and chemical ecology is presented in accessible terms. The potential of field application is discussed with regard to practical aspects but also socioeconomic constraints. The 62 authors are researchers from a large panel of disciplines, from theoretical biology to social sciences.
ano.nymous@ccsd.cnrs.fr.invalid (Xavier Fauvergue) 15 Jun 2022
https://hal.inrae.fr/hal-03695954v1
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[hal-04037895] The terrestrial isopod symbiont ‘Candidatus Hepatincola porcellionum’ is a potential nutrient scavenger related to Holosporales symbionts of protists
The order Holosporales (Alphaproteobacteria) encompasses obligate intracellular bacterial symbionts of diverse Eukaryotes. These bacteria have highly streamlined genomes and can have negative fitness effects on the host. Herein, we present a comparative analysis of the first genome sequences of 'Ca. Hepatincola porcellionum', a facultative symbiont occurring extracellularly in the midgut glands of terrestrial isopods. Using a combination of long-read and short-read sequencing, we obtained the complete circular genomes of two Hepatincola strains and an additional metagenome-assembled draft genome. Phylogenomic analysis validated its phylogenetic position as an early-branching family-level clade relative to all other established Holosporales families associated with protists. A 16S rRNA gene survey revealed that this new family encompasses diverse bacteria associated with both marine and terrestrial host species, which expands the host range of Holosporales bacteria from protists to several phyla of the Ecdysozoa (Arthropoda and Priapulida). Hepatincola has a highly streamlined genome with reduced metabolic and biosynthetic capacities as well as a large repertoire of transmembrane transporters. This suggests that this symbiont is rather a nutrient scavenger than a nutrient provider for the host, likely benefitting from a nutrient-rich environment to import all necessary metabolites and precursors. Hepatincola further possesses a different set of bacterial secretion systems compared to protistassociated Holosporales, suggesting different host-symbiont interactions depending on the host organism.
ano.nymous@ccsd.cnrs.fr.invalid (Jessica Dittmer) 20 Mar 2023
https://hal.science/hal-04037895v1
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[hal-03607685] Enrichment in biodiversity and maturation of the soil food web under conservation agriculture is associated with suppression of rice-parasitic nematodes
Meloidogyne spp. and Hirschmanniella spp. are among the most damaging plant-parasitic nematodes (PPNs). They threaten rice production, the main staple food in Asia. Cropping systems that promote natural biocontrol and plant tolerance to diseases are put forward as sustainable solutions to protect rice from these pests. In particular, cropping systems managed under conservation agriculture (CA) are promising because they improve soil health and functioning. We investigated the effects of two cropping system components in a Cambodian field, (i) CA practices, i.e., no-tillage with a cover crop Stylosanthes guianensis (cv. Nina), versus conventional plow-based tillage with no cover crop, and (ii) using IR504, IR64, Azucena and Zhonghua 11 rice varieties, on PPNs in roots and on communities (bacteria, fungi and nematodes) in the rhizosphere. We used a sequencing approach via amplicon barcoding to target microbial marker genes (16 S and ITS rRNA gene) and a microscopic approach to identify and quantify nematodes in the rhizosphere compartment. The variety had less effect than agricultural practices on the infection by PPNs and on the assembly of the three rhizosphere communities. Under CA, the abundance of PPNs extracted from the roots was reduced by 88%. Soil quality was substantially improved (+83% of total Kjeldahl nitrogen, +34% of available phosphorus, +10% of exchangeable potassium, +110% of soil organic carbon, +30% for the cation exchange capacity), thus providing more basal resources for microbial decomposers, especially fungi (+164% putative saprotrophs). Characterization of the three rhizosphere communities revealed a shift in the structure associated with soil enrichment. Both microbial richness (+3% for bacteria and +38% for fungi) and diversity (Shannon index, +11% for fungi and +5% for nematodes) increased. The relative abundance of taxa was modified by CA with notably more mycorrhizal fungi (+329% Glomeromycota spp.) and fewer Pratylenchidae nematodes (−92% Hirschmanniella spp.) in the rhizosphere. The reassembly of the communities using CA was associated with regulation of PPN populations. The reduction in Meloidogyne spp. abundance in roots (−64%) was correlated with the maturity of the food web (maturity index, +10% under CA) and with the increase in the relative abundance of omnivorous nematodes in the rhizosphere (+68% under CA). Seven years of CA in this field enabled the whole soil food web to mature thus creating a favorable niche for potentially predatory nematodes and microbes antagonistic against PPNs. This study confirms that CA is an alternative to nematicides to limit infection by PPNs in rice cropping systems.
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Masson) 05 Mar 2024
https://hal.inrae.fr/hal-03607685v1
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[hal-03773237] The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso
Due to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabarcoding approach of the 16S rRNA gene (prokaryotes, three plant samples per field) and ITS (fungi, one sample per field). In addition to the expected structure by root compartments (root vs rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. In irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications.
ano.nymous@ccsd.cnrs.fr.invalid (Mariam Barro) 23 Nov 2023
https://hal.inrae.fr/hal-03773237v1
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[hal-05777029] A Seed-Derived Multi-Kingdom Synthetic Community Enhances Radish Seedling Protection Against Alternaria brassicicola Abra43
Seed-associated microorganisms represent a promising resource for developing microbiome-based strategies against seed-borne pathogens. Here, we assembled synthetic microbial communities (SynComs) from cultivable members of the natural radish seed microbiota and evaluated their capacity to protect seedlings against the seed-transmitted fungal pathogen Alternaria brassicicola Abra43. Seven SynComs representing single- or multi-kingdom combinations of bacteria (B), filamentous fungi (F), and yeasts (Y) (B, F, Y, BF, BY, FY, and BFY) were inoculated onto radish seeds. We assessed their effects on disease incidence, seedling growth, microbial community assembly (ITS1 and gyrB gene metabarcoding) and pathogen colonization (metabarcoding and specific qPCR on dhn1 gene for A. brassicicola Abra43). Protection of radish seedlings against A. brassicicola Abra43 strongly depended on SynCom composition. The yeast fraction alone provided little protection, whereas the bacterial fraction partially reduced symptoms and maintained seedling growth despite substantial pathogen colonization, suggesting increased plant tolerance. SynComs containing filamentous fungi markedly reduced A. brassicicola Abra43 abundance, and the full multi-kingdom BFY SynCom provided the most consistent protection, combining reduced disease incidence, restored seedling growth, and low pathogen relative and absolute abundance. Inoculated strains, Alternaria alternata ABAI001 and Plectosphaerella sp. FL19 were enriched in protective SynComs and displayed antagonistic activity against A. brassicicola Abra43 in vitro. Together, these results show that seed-derived multi-kingdom communities can reshape early plant microbiota and that combining bacterial and fungal strains with complementary ecological functions can improve protection against a seed-borne fungal pathogen.
ano.nymous@ccsd.cnrs.fr.invalid (Natalia Guschinskaya) 23 Oct 2026
https://univ-angers.hal.science/hal-05777029v1
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[hal-05290191] Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations
Drought is a critical risk in developing countries for staple crops like common bean ( Phaseolus vulgaris L.). We conducted an experiment to understand the legacy effects of repeated drought exposure across plant generations on the root and rhizosphere microbiome of the common bean, hypothesizing that a legacy of exposure improves overall plant microbiome resilience. We profiled the bacterial microbiome using marker gene amplicon sequencing over two plant generations in a complete factorial design for two common bean genotypes, Red Hawk and Flavert. We performed parallel experiments for Red Hawk in two different countries using soils of Pays de la Loire, France, and Michigan, USA. Despite the clear and relatively consistent drought effects on the plant phenotypes, there was neither response of the Red Hawk microbiomes to drought, nor a notable legacy of drought exposure. For Flavert, there was a minor legacy drought effect for the second generation in the rhizosphere microbiome beta diversity. This study demonstrates that rhizosphere microbiomes can be resistant to drought stress and that cross-generational legacy depends on soil origin and host genotype. Such parallel experiments across countries, while difficult to implement, are useful to inform generalities and build theory towards prediction on microbiome responses to global change.
ano.nymous@ccsd.cnrs.fr.invalid (A. Fina Bintarti) 21 Oct 2026
https://hal.science/hal-05290191v2
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[hal-05101924] Modifications of the bacterial community of rice roots infected by a plant parasitic nematode in infested fields
Meloidogyne graminicola, also known as the rice root-knot nematode, is the most damaging plant parasitic nematode, especially on rice in Asia. This obligate soilborne parasite creates galls that disturb the root morphology and physiology, making plants more susceptible to other diseases (e.g. blast) and / or abiotic stress (e.g. water stress). Since the root microbiome is important for plant health, we assessed the impact of M. graminicola on the root microbiome of rice plants. In this study, we present results obtained from a survey conducted in Northern Vietnam in 2017. We collected infected (with galls) and non-infected roots from three naturally infested rice fields. Using an amplicon barcoding approach, we observed different microbiome composition, diversity and network structures. Interestingly, we observed a higher species richness (24%) and diversity in infected roots but fewer enriched metabolic pathways based on the predicted functional profiling of these microbial communities. Some of these enriched pathways were related to pyruvate fermentation and TCA cycle. Differential abundance testing analyses highlighted that species such as Flavobacterium succinicans and Ensifer adhaerens were respectively enriched in non-infected and infected roots. Additionally, the infected community network was denser and more connected, and we identified specific hub taxa that could be keystones in these infected microbiomes. These findings show deep modifications of the rice root microbiome composition and functions when exposed to the parasitic pressure of M. graminicola. The identified indicator taxa and pathways could be used in future studies as markers of rice root infection.
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Masson) 06 Jun 2025
https://hal.science/hal-05101924v1
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[hal-04973215] Fungal Oligopeptide Transporters have different substrate specificities despite their high sequence identity.
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ano.nymous@ccsd.cnrs.fr.invalid (Carmen Becerra-Rodríguez) 02 Mar 2025
https://hal.inrae.fr/hal-04973215v1
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[hal-04670942] Comparative transcriptomics reveals a highly polymorphic Xanthomonas HrpG virulence regulon
Background: Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. Results: In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. Conclusions: The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS.
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Quiroz Monnens) 13 Aug 2024
https://hal.inrae.fr/hal-04670942v1
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[hal-03576592] Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains
In summer 2019, widespread occurrence of crown gall disease caused byAgrobacterium spp. was observed on commercially grown ornamental plants in south-ern Iran. Beside agrobacteria, pale yellow-pigmented Gram-negative strains resemblingthe members of Xanthomonas were also associated with crown gall tissues on weep-ing fig (Ficus benjamina) and Amaranthus sp. plants. The purpose of the present studywas to characterize the crown gall-associated Xanthomonas strains using plant inocula-tion assays, molecular-phylogenetic analyses, and comparative genomics approaches.Pathogenicity tests showed that the Xanthomonas strains did not induce diseasesymptoms on their host of isolation. However, the strains induced hypersensitive reac-tion on tobacco, geranium, melon, squash, and tomato leaves via leaf infiltration.Multilocus sequence analysis suggested that the strains belong to clade IA ofXanthomonas, phylogenetically close to Xanthomonas translucens, X. theicola, and X.hyacinthi. Average nucleotide identity and digital DNA-DNA hybridization valuesbetween the whole-genome sequences of the strains isolated in this study and refer-ence Xanthomonas strains are far below the accepted thresholds for the definition ofprokaryotic species, signifying that these strains could be defined as two new specieswithin clade IA of Xanthomonas. Comparative genomics showed that the strains iso-lated from crown gall tissues are genetically distinct from X. translucens, as almost allthe type III secretion system genes and type III effectors are lacking in the formergroup. The data obtained in this study provide novel insight into the breadth ofgenetic diversity of crown gall-associated bacteria and pave the way for research ongall-associated Xanthomonas-plant interactions.
ano.nymous@ccsd.cnrs.fr.invalid (Hamzeh Mafakheri) 10 Jun 2022
https://hal.inrae.fr/hal-03576592v1
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[hal-04932122] Celebrating the 20th Anniversary of the First Xanthomonas Genome Sequences – How Genomics Revolutionized Taxonomy, Provided Insight into the Emergence of Pathogenic Bacteria, Enabled New Fundamental Discoveries and Helped Developing Novel Control Measures – A Perspective from the French Network on Xanthomonads
In this Opinion paper, members of the French Network on Xanthomonads give their personal view on what they consider to be some of the groundbreaking discoveries in the field of molecular plant pathology over the past 20 years. By celebrating the 20th anniversary of the first Xanthomonas genome sequences, they explain how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and contributed to the development of novel control measures. Collectively, such new, genomics-enabled perspective will help to ensure sustainable agriculture and conservation of our environment in the future.
ano.nymous@ccsd.cnrs.fr.invalid (Ralf Koebnik) 06 Feb 2025
https://hal.inrae.fr/hal-04932122v1
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[ird-04483657] Celebrating the 20th anniversary of the first Xanthomonas genome sequences – how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and helped developing novel control measures – a perspective from the French network on Xanthomonads
In this Opinion paper, members of the French Network on Xanthomonads give their personal view on what they consider to be some of the groundbreaking discoveries in the field of molecular plant pathology over the past 20 years. By celebrating the 20th anniversary of the first Xanthomonas genome sequences, they explain how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and contributed to the development of novel control measures. Collectively, such new, genomics-enabled perspective will help to ensure sustainable agriculture and conservation of our environment in the future.
ano.nymous@ccsd.cnrs.fr.invalid (Ralf Koebnik) 29 Feb 2024
https://ird.hal.science/ird-04483657v1
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[hal-05667119] MIRRI-FRANCE at a glance
Microbial Resource Centres (mBRCs) or microbial biobanks play a central role in advancing research and innovation but remain insufficiently acknowledged within the scientific landscape. The European initiative MIRRI has laid the foundation for greater visibility, yet this recognition must also be consolidated at the national level, where their operational activities take place. National funding of mBRCs is therefore essential to enhance their standing, ensure long-term sustainability, and maximise their scientific and societal impact. In France, a first step forward was the integration of mBRCs into the national infrastructure RARe (Resources for research in Biology, Agronomy and Environment) and its microbial pillar, which positioned the network on the national roadmap of research infrastructures. The 10 French mBRCs currently involved cover a wide range of fields, including human and veterinary health, plant health, food fermentation and biotechnology. Together, they conserve more than 62,000 pure strains of bacteria, cyanobacteriota, yeasts, filamentous fungi and microbiota of human, animal, plant, environmental, and food origins. The network brings together around 60 staff members across 8 sites in France. All mBRCs operate under a quality management system and are ISO 9001:2015 certified for the acquisition, preservation, characterisation, and distribution of microbial resources. They also implement Data Management Plans (DMPs) and comply with FAIR principles as well as GDPR requirements. A key challenge is to bring together mBRCs belonging to different institutions, each with its own strategy and objectives. To achieve this, the network has been established as a contractual vehicle under the status of a Scientific Interest Group (Groupement d’Intérêt Scientifique, GIS), providing flexible yet robust governance. The GIS has no legal status but serves as a contractual framework between three founding institutions — INRAE, Institut Pasteur, and Université de Bretagne Occidentale — which assume binding legal commitments. The objective of this national organisation is to strengthen cooperation between mBRCs, while ensuring alignment between the national MIRRI node and the microbial pillar of RARe. The GIS MIRRI-France is designed to remain open to all public collections meeting service quality requirements and wishing to join. This collaborative approach aims to provide mBRCs with the means to act in a coordinated manner, to better communicate the value of their microbial resources and to raise funds to enhance their characterisation and to develop innovative services — ultimately fostering scientific excellence, supporting innovation, and maximising the benefits of microbial resources for research and society. reference RARe Microbial pillar: https://www.agrobrc-rare.org/eng/rare-members/microorganism-pillar
ano.nymous@ccsd.cnrs.fr.invalid (Michel-Yves Mistou) 23 Jun 2026
https://hal.science/hal-05667119v1
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[hal-03978256] Complete genome sequencing of three clade-1 xanthomonads reveals genetic determinants for a lateral flagellin and the biosynthesis of coronatine-like molecules in Xanthomonas
Evolutionarily early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, and Xanthomonas translucens, which infects small-grain cereals, diverse grasses, but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches indicated that this clade likely contains more, yet undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. In addition, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
ano.nymous@ccsd.cnrs.fr.invalid (Chloé Peduzzi) 13 Apr 2023
https://hal.inrae.fr/hal-03978256v1
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[hal-03623139] Taxonomic Refinement of Xanthomonas arboricola
Xanthomonas arboricola comprises a number of economically important fruit tree pathogens classified within different pathovars. Dozens of non-pathogenic and taxonomically un-validated strains are also designated as X. arboricola leading to a complicated taxonomic status in the species. In this study, we have evaluated the whole genome resources of all available Xanthomonas spp. strains designated as X. arboricola in the public databases to refine the members of the species based on DNA similarity indexes and core genome-based phylogeny. Our results show that out of the nine validly described pathovars within X. arboricola, pathotype strains of seven pathovars are taxonomically genuine belonging to the core clade of the species regardless of the argue of their pathogenicity on the host of isolation (thus the validity of pathovar status). However, strains of X. arboricola pv. guizotiae and X. arboricola pv. populi do not belong to X. arboricola due to the low DNA similarities between the type strain of the species and the pathotype strains of these two pathovars. Thus, we propose to elevate the two pathovars to the rank of a species as X. guizotiae sp. nov. with the type strain CFBP 7408T, and X. populina sp. nov. with the type strain CFBP 3123T. In addition, other mislabeled strains of X. arboricola were scattered within Xanthomonas spp. either belonging to previously described species or representing novel species which await formal description.
ano.nymous@ccsd.cnrs.fr.invalid (Sadegh Zarei) 11 Dec 2023
https://hal.inrae.fr/hal-03623139v1
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[hal-05101901] A view on the soil food web to understand parasitic nematodes reduction in rice
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ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Masson) 06 Jun 2025
https://hal.science/hal-05101901v1
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[hal-05782339] Seed-associated yeasts: diversity and antagonistic traits against fungal pathogens
Seeds host diverse microbial communities including yeasts that may play a crucial ecological role in plant health and development. Yeasts were isolated from seeds of four crop species (wheat, bean, tomato, and rapeseed) and identified by sequencing the ITS and D1/D2 rDNA regions. This previous work revealed a rich community spanning multiple genera such as Aureobasidium, Naganishia, VIshniacozyma, Sporobolomyces and Filobasidium. Some genera exhibited broad host ranges while others appeared to be specific to seed environment, suggesting niche adaptation among seed microbiota. These results provided the basis to explore seed-associated yeasts as potential biocontrol or plant growth promoting solutions. To assess their functional traits, particularly their antifungal activity and capacity to enhance plant growth, we first conducted in vitro antagonistic assays against five fungal pathogens (Fusarium graminearum, Fusarium culmorun, Fusarium oxysporum sp. phaseoli, Fusarium oxysporum sp. lycopersici, Alternaria brassicicola) and the oomycete Globisporagium ultimum, using both diffusible and volatile organic compound tests. Eight out of ten yeast isolates significantly inhibited at least one pathogen. Isolates particularly from the genera Aureobasidium, Naganishia and Vishniacozyma, showed strong inhibitory 2 effects, reaching up to 28% across both tests, suggesting the production of antifungal metabolites or nutrient competition as possible mechanisms. To validate these observations in planta, yeast isolates were tested on bean (Phaseolus vulgaris) under controlled greenhouse condition (22 ± 2 °C, 8h dark/16h light, 7 days). Non-infected and infected with oomycete Globisporagium utimum soils were compared. While most isolates slightly reduced emergence and seedling vigor under non-infected condition, bean derived yeasts such as Filobasidium and Hannaella improved seedling establisment under pathogen stress. These results highlight a context-dependent protective effect, suggesting that some seed-borne yeasts promote early growth under stress by favoring rapid germination and establishment before pathogen infection Overall, this work provides new insights into the ecological functions of seed associated yeasts showing that they can support plant health through multiple ecological interactions, either by directly antagonizing pathogens or by promoting plant growth. Future work will integrate genomic and metabolomic approaches to elucidate the molecular mechanisms underlying these beneficial interactions.
ano.nymous@ccsd.cnrs.fr.invalid (Nathan Kavunu) 07 Oct 2026
https://hal.science/hal-05782339v1
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[hal-04599898] Terroir, baker’s practices, wheat varieties and their influence on sourdough microbial diversity
The microbial diversity of many ecosystems has recently been described but the question remains of the extent to which species and varieties develop and evolve within their particular environments. Altenatively, are they essentially ubiquitous, being more frequent in certain localities as a result of the conditions encountered? Is the distribution geographically structured, and/or influenced by other factors ? Using sourdough breadmaking ecosystems as a model and participatory research approach, we are analysing human influence on the dispersion and selection of lactic acid bacteria and yeasts. In France, microbial diversity associated with bread-making has not been well-documented. Bread can be made by two kind of artisans, farmer-bakers and artisan-bakers. Both use sourdough to leaven the bread. Sourdough is a dough composed of wheat and rye flour, or only one of these two ingredients, water, possibly supplemented with salt and subjected to an acidifying natural fermentation, whose function is to ensure the dough raising Décret No. 93- 1074, 13 sept. 1993). This aim of this study was to describe diversity of microbial species in baker's sourdough (yeasts and lactic acid bacteria) and to understand the evolutionary process (dispersion, selection) that shape this diversity.
ano.nymous@ccsd.cnrs.fr.invalid (Elisa Michel) 04 Jun 2024
https://hal.inrae.fr/hal-04599898v1
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[hal-03560813] A rapid and simple method for assessing and representing genome sequence relatedness
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 rela- tively computationally intensive and therefore precludes analyses of large datasets com- posed of thousands of genome sequences.In this work we proposed a workflow to com- pute and visualize relationships between genomic sequences. A dataset containing more than 3,500 Pseudomonas genome sequences was successfully classified with an alter- native OGRI based on k-mer counts in few hours with the same precision as ANI. A new visualization method based on zoomable circle packing was employed for assess- ing relationships among the 350 groups generated. Amendment of databases with these Pseudomonas groups greatly improved the classification of metagenomic read sets with k-mer-based classifier.
ano.nymous@ccsd.cnrs.fr.invalid (Martial Briand) 19 Feb 2025
https://hal.inrae.fr/hal-03560813v1
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[hal-05766312] Compost microbiota enhance susceptibility to thermoinhibition in lettuce seeds
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Olivier Leprince) 27 Sep 2026
https://hal.science/hal-05766312v1
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[hal-04494294] Mean species responses predict effects of environmental change on coexistence
Abstract Environmental change research is plagued by the curse of dimensionality: the number of communities at risk and the number of environmental drivers are both large. This raises the pressing question if a general understanding of ecological effects is achievable. Here, we show evidence that this is indeed possible. Using theoretical and simulation‐based evidence for bi‐ and tritrophic communities, we show that environmental change effects on coexistence are proportional to mean species responses and depend on how trophic levels on average interact prior to environmental change. We then benchmark our findings using relevant cases of environmental change, showing that means of temperature optima and of species sensitivities to pollution predict concomitant effects on coexistence. Finally, we demonstrate how to apply our theory to the analysis of field data, finding support for effects of land use change on coexistence in natural invertebrate communities.
ano.nymous@ccsd.cnrs.fr.invalid (Frederik de Laender) 07 Mar 2024
https://hal.inrae.fr/hal-04494294v1
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[hal-04749383] Activation of plant immunity by galbonolides promotes rhizosphere colonisation by Streptomyces sp. AgN23
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Clément Nicolle) 23 Oct 2024
https://hal.science/hal-04749383v1
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[hal-05739099] Specific and broad-spectrum antibacterial effectors of type VI secretion system drive competition of Stenotrophomonas rhizophila against bacteria from seed microbiota
The type VI secretion system (T6SS) is a bacterial weapon that injects deadly effectors (T6Es) directly into a target competitor encountered in a microbial community. Stenotrophomonas rhizophila CFBP13503 ( Sr ), a seed-borne bacterium, uses its T6SS to target a wide range of other bacterial species, impacting seed microbiota assembly, and controlling phytopathogen transmission from seed to seedling. How the large T6E repertoire and other features contribute to S. rhizophila ’s impact was investigated. Using transcriptional and translational reporters combined with fluorescence microscopy and proteomic approaches, we confirmed the expression and production of nine effectors secreted by a highly dynamic T6SS. This resulted in killing target cells through four major cell death phenotypes, with different frequencies depending on the target species. The systematic deletion of single effectors revealed a general synergy in killing a wide range and diverse seed-borne bacteria, but also a target-specific killing. Comparative genomics suggests that Sr -T6Es are commonly shared in the Stenotrophomonas genus diversity but are also highly plastic and acquired from diverse bacterial families. Inversely, T6SS-resistance markers, such as capsule and orthologous immunities, are weakly distributed in seed microbiota, and do not explain resistance to Sr -T6SS. Importantly, two amidases explained the major T6SS antibacterial activity, and only the Rhs-fused effector targeted a Gram-positive bacterium. Our work depicts the generalist or specific role of each effector in the S. rhizophila T6SS activity targeting either aggressive, closely related, broad, or Gram-positive bacteria from seed microbiota. IMPORTANCE The type VI secretion system (T6SS) is largely distributed among seed-borne bacteria. However, it remains important to understand how this interbacterial competition weapon could provide a competitive advantage for some strains and influence microbiome assembly during seed-to-seedling transmission. The Stenotrophomonas rhizophila CFBP 13503 strain, a seed-associated bacterium, cumulated several T6SS features like a constitutive and highly dynamic T6SS associated with 12 putative antibacterial T6Es that shape microbiota assembly through broad and strain-specific targeting within seed microbiota. Hence, genomic analysis suggests that S. rhizophila T6E repertoire is adaptive thanks to genetic gain and loss or through gene regulation. In the context of microbiome engineering, the relevance of this study is to highlight the need to associate broad-effective and competitive S. rhizophila strains, as well as T6SS-resistant strains, in bacterial synthetic communities as seed inoculum against phytopathogens.
ano.nymous@ccsd.cnrs.fr.invalid (Boris Taillefer) 04 Sep 2026
https://hal.inrae.fr/hal-05739099v1
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[hal-05695137] Seed-applied multi-kingdom synthetic communities selectively reshape bacterial communities and highlight key criteria for strain selection
Defined microbial communities (also known as synthetic communities) are showing promising results for plant health but are lacking an efficient lab to field transition. This is the due to limited knowledge on how to efficiently modulate plant microbiota by considering complex environments and multikingdom interactions. In this study, we aimed to better understand the transmission and impact of multi-kingdom synthetic communities (SynComs) from the seed to seedling stage. We constructed 20 different SynComs using both a priori and random approaches, from pool of diverse strains including 24 bacteria, 11 yeasts and 10 filamentous fungi. SynComs were inoculated on Brassica napus seeds and we monitored both transmission and impact on the microbiota of 15-day-old seedlings grown in non-sterile soil. Optimization of the inoculation protocol showed that alginate coating improved
ano.nymous@ccsd.cnrs.fr.invalid (Logan Suteau) 16 Jul 2026
https://univ-angers.hal.science/hal-05695137v1
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[hal-05694740] Unexplored Yeast diversity in Seed Microbiota
Yeasts isolated from seeds and seedlings of diverse plant species • Most isolates are Basidiomycota yeasts, especially of the Tremellomycetes class • The most frequently isolated yeasts belong to Holtermanniella, Vishniacozyma, Filobasidium and Sporobolomyces genera • The collection is representative of taxa found in seed microbiota of multiple plant species, including core members
ano.nymous@ccsd.cnrs.fr.invalid (Muriel Marchi) 16 Jul 2026
https://univ-angers.hal.science/hal-05694740v1
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[hal-02627510] Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean
Background: Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some cases, pathological convergence is observed for individuals belonging to distant phylogenetic clades. This is the case for Xanthomonas strains responsible for common bacterial blight of bean, spread across four genetic lineages. All the strains from these four lineages converged for pathogenicity on common bean, implying possible gene convergences and/or sharing of a common arsenal of genes conferring the ability to infect common bean. Results: To search for genes involved in common bean specificity, we used a combination of whole-genome analyses without a priori, including a genome scan based on k-mer search. Analysis of 72 genomes from a collection of Xanthomonas pathovars unveiled 115 genes bearing DNA sequences specific to strains responsible for common bacterial blight, including 20 genes located on a plasmid. Of these 115 genes, 88 were involved in successive events of horizontal gene transfers among the four genetic lineages, and 44 contained nonsynonymous polymorphisms unique to the causal agents of common bacterial blight. Conclusions: Our study revealed that host specificity of common bacterial blight agents is associated with a combination of horizontal transfers of genes, and highlights the role of plasmids in these horizontal transfers.
ano.nymous@ccsd.cnrs.fr.invalid (Nicolas Chen) 26 May 2020
https://hal.inrae.fr/hal-02627510v1
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[hal-05620671] Clavibacter vidaverae sp. nov., Clavibacter rahimiani sp. nov. and Clavibacter davisi sp. nov.: corynebacterial plant pathogens isolated from small-grain cereals
During 2020–2024, 25 Gram-positive actinobacterial strains were isolated from small-grain cereals in Iran. Colony morphology, phenotypic characteristics and multilocus sequence analyses showed that the strains belonged to the coryneform genus Clavibacter (family Microbacteriaceae ). The Clavibacter strains isolated from small-grain cereals in Iran were distributed within five distinct phylogenetic clades. Two of those clades included Clavibacter tessellarius and Clavibacter zhangzhiyongii , while the other three groups of Clavibacter strains were taxonomically undetermined and phylogenetically distinct from all validly described species in the genus. Whole-genome sequence-based indices, i.e. average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), showed that the latter three phylogenetic clades differed from all validly described Clavibacter species, with ANI/dDDH values &lt;94% and &lt;70%, respectively. Analyses of KEGG pathways and pathogenicity-associated genes revealed substantial differences among the five Clavibacter groups associated with small-grain cereals. All Clavibacter strains were capable of infecting their hosts of isolation, i.e. wheat, barley and oat. Thus, based on both phenotypic features, i.e. differences in colony morphology, biolog microbial identification microplate data and polar lipid repertoires, as well as DNA similarity indices, the three clades could represent three new species within Clavibacter . In this study, we provide formal species descriptions for three Clavibacter clades isolated from small-grain cereals. These three species include Clavibacter vidaverae sp. nov. (type strain Sh2088ᵀ=CFBP 9070ᵀ=ICMP 24732ᵀ), Clavibacter rahimiani sp. nov. (type strain Sh2141ᵀ=CFBP 9069ᵀ=ICMP 24735ᵀ) and Clavibacter davisi sp. nov. (type strain Sh2036ᵀ=CFBP 9071ᵀ=ICMP 24729ᵀ).
ano.nymous@ccsd.cnrs.fr.invalid (Asma Rahmanzadeh) 12 May 2026
https://hal.science/hal-05620671v1
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[hal-04665509] A stage‐dependent seed defense response to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean
Although seed represents an important means of plant pathogen dispersion, the seed–pathogen dialogue remains largely unexplored. A multiomic approach was performed at different seed developmental stages of common bean ( Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans ( Xcf ), At the early seed developmental stages, we observed high transcriptional changes both in seeds with bacterial recognition and defense signal transduction genes, and in bacteria with up‐regulation of the bacterial type 3 secretion system. This high transcriptional activity of defense genes in Xcf ‐colonized seeds during maturation refutes the widely diffused assumption considering seeds as passive carriers of microbes. At later seed maturation stages, few transcriptome changes indicated a less intense molecular dialogue between the host and the pathogen, but marked by changes in DNA methylation of plant defense genes, in response to Xcf colonization. We showed examples of pathogen‐specific DNA methylations in colonized seeds acting as plant defense silencing to repress plant immune response during the germination process. Finally, we propose a novel plant–pathogen interaction model, specific to the seed tissues, highlighting the existence of distinct phases during seed–pathogen interaction with seeds being actively interacting with colonizing pathogens, then both belligerents switching to more passive mode at later stages.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 31 Jul 2024
https://hal.inrae.fr/hal-04665509v1
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[hal-01134880] Draft Genome Sequence of the Flagellated Xanthomonas fuscans subsp. fuscans Strain CFBP 4884
<p>We report the draft genome sequence of the flagellated strain CFBP 4884 of Xanthomonas fuscans subsp. fuscans, which was isolated in an outbreak of common bacterial blight of beans along with non-flagellated strains. Comparative genomics will allow one to decipher the genomic diversity of strains cohabiting in epidemics.</p>
ano.nymous@ccsd.cnrs.fr.invalid (A. Indiana) 24 Mar 2015
https://hal.science/hal-01134880v1
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[hal-05772577] Seed Microbiota Diversity and Culture Collection of Four Major Crops Covering Different Genotypes and Production Modes
Seed microbiota play a crucial role in plant health and development, yet remain understudied compared to other plant-associated microbial communities. This study aimed to characterize seed microbiota diversity across four major crops (common bean, rapeseed, tomato, and wheat) and establish a comprehensive strain collection of seed-borne microorganisms (bacteria and fungi). We employed a combination of culture-dependent and culture-independent approaches to analyze 68 seed samples representing diverse genotypes and production modes. Our results revealed highly variable seed microbiota, with bacterial colonization ranging from 10 to 100 million bacterial CFUs per gram of seeds, and microbial richness varying from 4 to 351 bacterial and 16 to 138 fungal amplicon sequence variants (ASVs) per sample. Both plant genotype and production mode significantly influenced microbiota composition, with each seed sample produced harboring a distinct microbial assemblage. Interestingly, seeds produced in confined environments exhibited lower bacterial colonization but higher microbial richness compared to field-produced seeds. We observed divergent ecological drivers shaping bacterial and fungal communities. Bacterial assemblages were more host-specific and variable, while fungal communities showed greater stability and a substantial core microbiome shared across plant species. Our culturomics approach yielded a collection of 2,510 bacterial and 837 fungal isolates, representing 10-21% of the seed microbiota diversity detected by metabarcoding and the majority of the prevalent and abundant taxa. Notably, 44-60% of cultured bacterial isolates were not detected by metabarcoding, highlighting the complementary nature of these approaches to detect rare or under amplified taxa in PCR. This study provides insights into the complexity and variability of seed microbiota across different crops and production conditions. Our findings emphasize the importance of combining culturomics and sequencing methods for comprehensive characterization of seed microbiota to uncover the potential of seed-borne microorganisms as bioinoculants for sustainable agriculture.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 30 Sep 2026
https://univ-angers.hal.science/hal-05772577v1
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[hal-05535812] Transient microbial architects: tracing the legacy effects of ephemeral taxa during plant microbiome assembly
Plant microbiota assembly is a dynamic process shaped by a succession of microbial dispersal events, interactions, and environmental fluctuations. While most research emphasizes the roles of resident and core taxa in driving microbiome structure and plant health, the ecological significance of transient microbial members (taxa temporarily present in plant tissue and then disappearing from microbiota) remains underexplored. In this opinion article, we propose that these ephemeral microorganisms may act as 'transient microbial architects', capable of generating legacy effects that influence the trajectory of microbiota assembly and long-term plant fitness. By reviewing the available temporal studies, we show that transient taxa often collectively represent the most diverse and abundant plant microbiota members compared to core taxa. We highlight how priority effects, niche modification, and microbe-microbe interactions mediated by transient taxa, can alter community composition, modulate the recruitment of symbionts, and shape plant responses to biotic and abiotic stressors. We identify outstanding questions and propose methodological advances to address them, including high-resolution longitudinal sampling and integrative omics approaches, that will enable the detection and functional characterization of these elusive taxa. Finally, we discuss the potential for harnessing transient microbial architects in microbiome engineering strategies for sustainable agriculture, emphasizing the need for targeted interventions during critical plant developmental windows. By recognizing and harnessing the legacy effects of these transient members, we gain access to previously overlooked ecological levers for shaping plant-microbe interactions.
ano.nymous@ccsd.cnrs.fr.invalid (Logan Suteau) 08 Apr 2026
https://hal.inrae.fr/hal-05535812v1
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[hal-03299428] Transmission of Seed and Soil Microbiota to Seedling
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 by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa.
ano.nymous@ccsd.cnrs.fr.invalid (Aude Rochefort) 25 Oct 2021
https://hal.inrae.fr/hal-03299428v1
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[hal-04379301] First report of Xanthomonas campestris pv. campestris causing black rot on oilseed rape (Brassica napus L.) in France
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% in 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-1) and Polyflor (Syngenta,
ano.nymous@ccsd.cnrs.fr.invalid (Sophie Cesbron) 01 Feb 2024
https://hal.inrae.fr/hal-04379301v1
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[hal-05739227] The efficiency of different transmission routes of Xanthomonas citri pv. fuscans and other seed-borne bacteria to bean seeds
Seed transmission is a critical pathway for the dispersal of phytopathogenic bacteria. This transmission can occur through three main routes: floral, internal, and external. Yet the relative contribution of individual transmission routes remains poorly characterized. Using a pathosystem based on Xanthomonas citri pv. fuscans ( Xcf ) and common bean ( Phaseolus vulgaris cv. Flavert), we quantified the efficiency of each route. Under our experimental conditions, the vascular route was the most efficient with 25% of contaminated seeds and population sizes averaging 10 7 CFU per contaminated seed. Deploying this experimental framework to ten seed-borne bacterial strains isolated from bean revealed that almost none transmitted to seeds through any route, or at best at low efficiency. However, most of the strains were capable of surviving and disseminating within the vascular system. A major bottleneck for seed transmission was identified for pod vascular organs colonization and the similar behavior of an Xcf mutant, deficient in the T3SS, suggested that plant immunity could be involved at this step. Co-inoculation of a consortium composed of the seed-borne strains with Xcf reduced the number of seeds contaminated by Xcf at the highest inoculum concentration, although other consortia members were never recovered from seeds. This suggests that the strains are recognized by the plant and trigger defense responses. These findings also raise questions about the mechanisms used by seed-associated bacteria to colonize seeds in situ.
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Chadelaud) 04 Sep 2026
https://hal.inrae.fr/hal-05739227v1
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[hal-05739215] Insights into the transmission of seedborne Pseudomonas syringae strains that cause zucchini diseases
Vein clearing of zucchini (VCZ) and bacterial leaf spot (BLS) are caused by various strains of the Pseudomonas syringae species complex that infect zucchini ( Cucurbita pepo ) seeds. VCZ strains have a narrow host range of cucurbits and affect only seedlings, whereas BLS strains have a broader host range and cause symptoms on adult plants. A multiplex qPCR test showed that VCZ strains predominated in infected seed lots produced in different countries. We surveyed hybrid seed crops grown in parallel in two French regions to address inoculum sources. According to DNA-based approach, parental seed lots were positive to BLS strains, although no culturable bacteria were recovered. Hybrid seed lots produced in the Rhone Valley (southeastern France) showed higher infection rates than those produced in Limagne (central France), and VCZ strains were recovered only from the Rhone Valley. Two representative strains of VCZ and BLS colonized seeds through the vascular and floral pathways, whereas only the BLS strain was transmitted through the pericarp. These findings suggest that floral transmission, potentially mediated by pollinators, could explain the predominance of VCZ strains under favorable regional conditions, and that pericarp transmission in BLS strains could be linked to their capacity to cause disease on adult plants. Furthermore, some infections undetected in seeds became apparent after germination, indicating that testing germinated seeds rather than seeds could help seed industry to take in account only bacterial infections transmitted to the seedling. Together, these results provide valuable insights into the epidemiology of P. syringae transmission to zucchini seeds.
ano.nymous@ccsd.cnrs.fr.invalid (Caroline Lacault) 04 Sep 2026
https://hal.inrae.fr/hal-05739215v1
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[hal-04338621] A novel “ceasefire” model to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean
Summary Although seed represents an important means of plant pathogen dispersion, the seed-pathogen dialogue remains largely unexplored. A multi-omic approach ( i.e. dual RNAseq, plant small RNAs and methylome) was performed at different seed developmental stages of common bean ( Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans ( Xcf ). In this condition, Xcf did not produce disease symptoms, neither affect seed development. Although, an intense molecular dialogue, via important transcriptional changes, was observed at the early seed developmental stages with down-regulation of plant defense signal transduction, via action of plant miR, and upregulation of the bacterial Type 3 Secretion System. At later seed maturation stages, molecular dialogue between host and pathogen was reduced to few transcriptome changes, but marked by changes in DNA methylation of plant defense and germination genes, in response to Xcf colonization, potentially acting as defense priming to prepare the host for the post-germination battle. This distinct response of infected seeds during maturation, with a more active role at early stages refutes the widely diffused assumption considering seeds as passive carriers of microbes. Finally, our data support a novel plant-pathogen interaction model, specific to the seed tissues, which differs from others by the existence of distinct phases during seed-pathogen interaction with seeds first actively interacting with colonizing pathogens, then both belligerents switch to more passive mode at later stages. We contextualized this observed scenario in a novel hypothetical model that we called “ceasefire”, where both the pathogen and the host benefit from temporarily laying down their weapons until the moment of germination.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 14 Jan 2025
https://hal.inrae.fr/hal-04338621v1
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[hal-03299446] Seed microbiota revealed by a large-scale meta-analysis including 50 plant species
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.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 05 Sep 2026
https://hal.inrae.fr/hal-03299446v1
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[hal-05515835] SeqDetectVeg: a major project to develop a NGS tool for multi-target detection of bacterial and fungal pathogens transmitted by vegetable seeds.
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Mylène Ruh) 17 Feb 2026
https://univ-angers.hal.science/hal-05515835v1
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[hal-05140475] Preservation of Seed Microbiota : a challenge to maintain viability and function
Plant-associated microbiota are complex heterogeneous communities, including non-cultivable strains. Preservation of heterogeneous community will lead to heterogenous survival, altering the taxonomic composition which in turn can alter the functionalities of the microbiota. The preservation processes mastered by Biological Resource Centers (BRC), like deep freezing at -80°C or at -196°C in liquid nitrogen, or lyophilisation, are well adapted to isolated strains and we lack insights to understand what happens to microbiota during preservation. To overcome these limitations, the MICORBE project (https://www.microbeproject.eu/) aims at developping protocols and a framework permitting BRCs to preserve viable microbiota, in order to have these available for the future. At CIRM-CFBP, the French Collection for Plant-associated Bacteria (https://cirm-cfbp.fr), as part of the MICROBE project, we focus on the use-case seed. What methodology will be the most efficient and suitable for preserving the micro-organisms of seed microbiota, over the long term? All this, of course, while minimising the effects of preservation and guaranteeing viability, metabolic functions and the less altered possible taxonomic composition after preservation. We chose to assess the taxonomic composition using metabarcoding, the metabolic profile with Biolog Ecoplates and the cultivable bacterial and fungal fraction independently of each other. All of this before and after 9 different preservation conditions in liquid nitrogen. The first results are encouraging showing that it’s possible to preserve a complex community. More analyses are necessary to finely determine how the microbiota are altered during preservation. These experiments will enable us to refine the process to ultimately propose the best suited option for long term plant-microbiota preservation, from seeds or other plant parts.
ano.nymous@ccsd.cnrs.fr.invalid (Céline Mirguet) 02 Jul 2025
https://hal.inrae.fr/hal-05140475v1
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[hal-03344454] Complete and Circularized Genome Sequences of 17 Xanthomonas Strains Responsible for Common Bacterial Blight of Bean
We report the complete and circularized genome sequences of 17 strains of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli, which cause common bacterial blight of bean. These new assemblies combining PacBio and short-read sequencing methods provide high-quality material for studying the evolution of these plant pathogens.
ano.nymous@ccsd.cnrs.fr.invalid (Martial Briand) 30 Aug 2024
https://hal.inrae.fr/hal-03344454v1
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[hal-03349711] Complete and Circularized Genome Sequences of Three Xanthomonas Strains Pathogenic on Soybean and Alfalfa
We report the complete and circularized genome sequences of two strains of Xanthomonas citri pv. glycines causing bacterial pustule on soybean and one strain of Xanthomonas euvesicatoria pv. alfalfae causing bacterial leaf and stem spot on alfalfa. These assemblies provide high-quality material for functional and evolutionary studies of these legume pathogens.
ano.nymous@ccsd.cnrs.fr.invalid (Mylène Ruh) 30 Aug 2024
https://hal.inrae.fr/hal-03349711v1
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[hal-02941967] Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils
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.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 30 Dec 2023
https://hal.inrae.fr/hal-02941967v1
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[hal-02516590] Assembly of seed-associated microbial communities within and across successive plant generations
<p>Background and aims</p> <p>Seeds 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.</p> <p>Methods</p> <p>Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model.</p> <p>Results</p> <p>Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota.</p> <p>Conclusions</p> <p>These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Samir Rezki) 13 Apr 2023
https://univ-angers.hal.science/hal-02516590v1
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[hal-02972234] Temporal dynamics of bacterial communities during seed development and maturation
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 phylogenetic turnover was observed for both plant species with few taxa associated with all seed developmental stages. Greater heterogeneity in community structure within each stage was observed for radish. While about one-third of radish seed bacterial taxa were detected in buds, flowers and fruits, very few taxa seem to be transmitted by the floral route in bean. In the latter species, bacterial populations belonging to the P. fluorescens species complex were found either in buds, flowers and fruits or in seeds. The relative phylogenetic proximity of these bacterial populations combined with their habitat specificity led us to explore the genetic determinants involved in successful seed transmission in bean. Comparative genomic analyses of representatives bacterial strains revealed dozens of coding sequences specifically associated with seed-transmitted strains. This study provided a first glimpse on processes involved in seed microbiota assembly, which could be used for designing plant-beneficial microbial consortia.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 20 Oct 2020
https://hal.inrae.fr/hal-02972234v1
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[hal-02770824] Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam
Meloidogyne graminicola, also known as the rice root-knot nematode, is one of the most damaging plant-parasitic nematode, especially on rice. This obligate soilbome parasite induces the formation of galls that disturb the root morphology and physiology. Its impact on the root microbiome is still not well described. Here, we conducted a survey in Northern Vietnam where we collected infected (with galls) and non-infected root tips from the same plants in three naturally infested fields. Using a metabarcoding approach, we discovered that M. graminicola infection caused modifications of the root bacterial community composition and network structure. Interestingly, we observed in infected roots a higher diversity and species richness (+24% observed ESVs) as well as a denser and more complex co-occurrence network (+44% nodes and +136% links). We identified enriched taxa that include several hubs, which could serve as potential indicators or biocontrol agents of the nematode infection. Moreover, the community of infected roots is more specific suggesting changes in the functional capabilities to survive in the gall environment. We thus describe the signature of the gall microbiome (the 'gallobiome, with shifting abundances and enrichments that lead to a strong restructuration of the root microbiome.
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Masson) 04 Jun 2020
https://hal.science/hal-02770824v1
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[hal-02624817] Novel Tetraplex Quantitative PCR Assays for Simultaneous Detection and Identification of Xylella fastidiosa Subspecies in Plant Tissues
Xylella fastidiosa (Xf) 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 quantitative PCR (qPCR) assays for X. 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 data set 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 10(3) 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
ano.nymous@ccsd.cnrs.fr.invalid (Enora Dupas) 26 May 2020
https://hal.inrae.fr/hal-02624817v1
