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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-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-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 <94% and <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-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) 04 Oct 2026
https://univ-angers.hal.science/hal-05777029v1
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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-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-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-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-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-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
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[hal-02624826] Zucchini vein clearing disease is caused by several lineages within Pseudomonas syringae species complex.
Zucchini (Cucurbita pepo) is worldwide affected by Pseudomonas syringae inducing vein clearing, stunting and necroses during plantlet development. A collection of 58 P. syringae strains isolated from diseased zucchini plantlets was characterized by multilocus sequence analysis (MLSA). A subset of 23 strains responsible for vein clearing of zucchini (VCZ) was evaluated for pathogenicity on zucchini and their genomes were sequenced. Host range of six VCZ strains was evaluated on 11 cucurbit species. Most VCZ strains belong to clades 2a and 2b-a within phylogroup 2 of P. syringae species complex and are closely related to other strains previously isolated from cucurbits. Genome analyses revealed diversity among VCZ strains within each clade. One main cluster, once referred to by the invalid pathovar name [peponis], gathers VCZ strains presenting a narrow host range including zucchini and squashes. Other VCZ strains present a large host range including zucchini, squashes, cucumber, melons and in some cases watermelon. The VCZ strain pathogenic features are strongly associated with type III effector repertoires. Presence of avrRpt2 and absence of hopZ5 are associated with a narrow host range, while presence of hopZ5 and absence of avrRpt2 are most generally associated with a large host range. In order to better detect the different clusters identified with whole genome sequence and pathogenicity analyses, we used a specific-k-mers approach to refine the MLSA scheme. Using this novel MLSA scheme to type P. syringae isolates from diseased cucurbits would give insight into distribution of worldwide strains and origin of epidemics.
ano.nymous@ccsd.cnrs.fr.invalid (Caroline Lacault) 26 May 2020
https://hal.inrae.fr/hal-02624826v1
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[hal-05056253] Draft genome sequences of five Pseudomonas syringae pv. actinidifoliorum strains isolated in France
Pseudomonas syringae pv. actinidifoliorum causes necrotic spots on the leaves of Actinidia deliciosa and Actinidia chinensis. P. syringae pv. actinidifoliorum has been detected in New Zealand, Australia, France and Spain. Four lineages were previously identified within the P. syringae pv. actinidifoliorum species group. Here, we report the draft genome sequences of five strains of P. syringae pv. actinidifoliorum representative of lineages 1, 2 and 4, isolated in France. The whole genomes of strains isolated in New Zealand, representative of P. syringae pv. actinidifoliorum lineages 1 and 3, were previously sequenced. The availability of supplementary P. syringae pv. actinidifoliorum genome sequences will be useful for developing molecular tools for pathogen detection and for performing comparative genomic analyses to study the relationship between P. syringae pv. actinidifoliorum and other kiwifruit pathogens, such as P. syringae pv. actinidiae. (C) 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. This is an open access article under the CC BY-NC-ND license
ano.nymous@ccsd.cnrs.fr.invalid (Amandine Cunty) 09 May 2025
https://hal.science/hal-05056253v1
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[hal-05194267] Author Correction: Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome
Abstract The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species’ native range can provide valuable insights about habitat loss and the species’ adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole‐genome sequencing revealed 165 candidate SNPs associated with climatic adaptation in C. canephora , which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species.
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Thérèse Mofini) 31 Jul 2025
https://hal.science/hal-05194267v1
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[hal-04097465] Density declines, richness increases, and composition shifts in stream macroinvertebrates
Documenting trends of stream macroinvertebrate biodiversity is challenging because biomonitoring often has limited spatial, temporal, and taxonomic scopes. We analyzed biodiversity and composition of assemblages of >500 genera, spanning 27 years, and 6131 stream sites across forested, grassland, urban, and agricultural land uses throughout the United States. In this dataset, macroinvertebrate density declined by 11% and richness increased by 12.2%, and insect density and richness declined by 23.3 and 6.8%, respectively, over 27 years. In addition, differences in richness and composition between urban and agricultural versus forested and grassland streams have increased over time. Urban and agricultural streams lost the few disturbance-sensitive taxa they once had and gained disturbance-tolerant taxa. These results suggest that current efforts to protect and restore streams are not sufficient to mitigate anthropogenic effects.
ano.nymous@ccsd.cnrs.fr.invalid (Samantha Rumschlag) 15 May 2023
https://hal.inrae.fr/hal-04097465v1
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[hal-03844050] Wolbachia infection dynamics in a natural population of the pear psyllid Cacopsylla pyri (Hemiptera: Psylloidea) across its seasonal generations
Abstract Wolbachia is one of the most abundant intracellular symbionts of arthropods and has profound effects on host biology. Wolbachia transmission and host phenotypes often depend on its density within the host, which can be affected by multiple biotic and abiotic factors. However, very few studies measured Wolbachia density in natural host populations. Here, we describe Wolbachia in the pear psyllid Cacopsylla pyri from three populations in the Czech Republic. Using phylogenetic analyses based on wsp and multilocus sequence typing genes, we demonstrate that C. pyri harbours three new Wolbachia strains from supergroup B. A fourth Wolbachia strain from supergroup A was also detected in parasitised immatures of C. pyri , but likely came from a hymenopteran parasitoid. To obtain insights into natural Wolbachia infection dynamics, we quantified Wolbachia in psyllid individuals from the locality with the highest prevalence across an entire year, spanning several seasonal generations of the host. All tested females were infected and Wolbachia density remained stable across the entire period, suggesting a highly efficient vertical transmission and little influence from the environment and different host generations. In contrast, we observed a tendency towards reduced Wolbachia density in males which may suggest sex-related differences in Wolbachia -psyllid interactions.
ano.nymous@ccsd.cnrs.fr.invalid (Liliya Štarhová Serbina) 19 Mar 2024
https://hal.inrae.fr/hal-03844050v1
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[hal-04709702] Seasonal wild dance of dual endosymbionts in the pear psyllid Cacopsylla pyricola (Hemiptera: Psylloidea)
<div><p>Most sap-feeding insects maintain obligate relationships with endosymbiotic bacteria that provide their hosts with essential nutrients. However, knowledge about the dynamics of endosymbiont titers across seasons in natural host populations is scarce. Here, we used quantitative PCR to investigate the seasonal dynamics of the dual endosymbionts "Candidatus Carsonella ruddii" and "Ca. Psyllophila symbiotica" in a natural population of the pear psyllid Cacopsylla pyricola (Hemiptera: Psylloidea: Psyllidae). Psyllid individuals were collected across an entire year, covering both summer and overwintering generations. Immatures harboured the highest titers of both endosymbionts, while the lowest endosymbiont density was observed in males. The density of Carsonella remained high and relatively stable across the vegetative period of the pear trees, but significantly dropped during the non-vegetative period, overlapping with C. pyricola's reproductive diapause. In contrast, the titer of Psyllophila was consistently higher than Carsonella's and exhibited fluctuations throughout the sampling year, which might be related to host age. Despite a tightly integrated metabolic complementarity between Carsonella and Psyllophila, our findings highlight differences in their density dynamics throughout the year, that might be linked to their metabolic roles at different life stages of the host.</p><p>Symbiotic associations between Eukaryotic and Prokaryotic organisms have had a tremendous impact on the diversification of multicellular organisms, contributing to a great proportion of the planet's biodiversity 1,2 . For instance, endosymbiotic bacteria played a central role in shaping the ecological niches of phytophagous insects by enabling them to feed on a nutritionally unbalanced plant sap diet 3-5 . Bacterial endosymbionts of phytophagous insects are often housed within specialized cells (bacteriocytes) aggregated within special organs (bacteriomes) and provide their hosts with essential nutrients lacking in the plant sap 4,6 . This resulted in the establishment of obligate co-diverging host-symbiont associations, accompanied by drastic reductions in the genome size of the symbiotic bacteria until only core housekeeping genes and biosynthetic pathways for the nutrients required by the insect hosts are retained 7-9 . Many sap-feeding hemipteran lineages, such as sternorrhynchans (aphids, adelgids, psyllids, scales, mealybugs) and auchenorrhynchans (planthoppers, spittlebugs, cicadas), are associated with more than one obligate endosymbiont 9 . In most dual endosymbiotic systems studied to date, the primary endosymbiont supplies the host with the majority of essential amino acids (EAAs), whereas the co-primary endosymbiont complements the genes or pathways that are no longer present in the primary endosymbiont 10-13 .</p><p>Although endosymbionts provide important benefits, maintaining them also entails fitness costs for the host. For instance, in aphids the titer of the primary endosymbiont Buchnera is negatively correlated with the overall host reproductive rate 14 . This is likely due to metabolic costs involved in endosymbiont maintenance 15 . Hence, optimal regulation of endosymbiont titers by the host is crucial to maintain a delicate balance: endosymbiont titers should be as low as possible to reduce the associated costs for the host but as high as necessary to produce sufficient amounts of nutrients and to ensure vertical transmission to the next generation 16-18 . Furthermore, due to different investments in reproduction, the host's nutritional requirements may vary across the host's life cycle OPEN</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Liliya Štarhová Serbina) 25 Sep 2024
https://hal.inrae.fr/hal-04709702v1
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[hal-03576717] Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome
Fungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [ Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Thérèse Mofini) 12 Jul 2022
https://hal.inrae.fr/hal-03576717v1
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[pasteur-05668730] Policy Briefing: from access to use—untangling the international legal frameworks that govern microbial resources
The wide geographic distribution of microorganisms, combined with their vast taxonomic and functional diversity, make them indispensable reservoirs of genetic variation that sustain ecosystem resilience and fuel biotechnological innovation. However, to use this diversity, microbiologists must navigate a complex legal and regulatory landscape governed by multiple United Nations treaties and their respective access and benefit-sharing frameworks as well as regulatory frameworks specific to particular ecosystems, biosecurity, pathogens, and intellectual property. This complex regulatory web is also actively growing and changing, which makes it immensely challenging for a “regular” microbiologist to navigate. For policymakers and negotiators, it is also difficult to appreciate the full complexity that practitioners experience. This policy briefing provides a concise regulatory guide for practitioners and policymakers alike, summarized in a graphical overview, to provide more clarity and understanding for those at the edge of decision-making and practice.
ano.nymous@ccsd.cnrs.fr.invalid (Davide Faggionato) 24 Jun 2026
https://pasteur.hal.science/pasteur-05668730v1
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[hal-05668729] Policy in Practice: How to do the Nagoya Protocol: common misconceptions, challenges and best practices for access and benefit-sharing compliance
The Nagoya Protocol establishes an international framework for access and benefit-sharing including for microbial research. Yet many microbiologists have only a vague understanding of what the Nagoya Protocol requires and are unsure how to navigate its complexities, despite the fact that non-compliance can have significant legal consequences and far-reaching reputational and legal impacts. This paper discusses common misconceptions and practical challenges that microbiologists may encounter when complying with the Nagoya Protocol and a step-by-step guide on how to “do” the Nagoya Protocol. We present three case studies to showcase real-life experiences and provide best practice principles for access and benefit-sharing while fostering biodiversity conservation, equitable collaboration, and sustainable innovation.
ano.nymous@ccsd.cnrs.fr.invalid (Davide Faggionato) 25 Jun 2026
https://hal.science/hal-05668729v1
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[hal-04451939] Biological inhibition of denitrification (BDI): an early plant strategy for Fallopia x bohemica seedling development.
Background and Aims: The successful plant Fallopia x bohemica presents interesting capacities for the control of soil nitrogen cycle at the adult stage, named the biological denitrification inhibition (BDI). BDI strategy allows the plant, through the production of secondary metabolites (procyanidins), to compete with denitrifying microbial community and to divert, to its benefit, the nitrate from soil. This study aims to analyze whether seedlings of F. x bohemica, can implement BDI at the seedling stage. We also determined whether soil nitrogen availability influence the implementation of BDI and seedling growth. Methods: We sowed achenes of F. x bohemica in soils representing a nitrogen gradient (6 treatments) and harvested seedlings after twenty and forty days of growth. The denitrification and related microbial communities (i.e., functional gene abundances of nirK and nirS), soil parameters (nitrate content and Accepted Manuscript humidity) and plant performances (biomass, growth and root morphology) were determined. Key Results: On soil without nitrogen addition, BDI was observed after twenty days of growth, whereas a stimulation of denitrification was found after forty days. The increase of soil N content had few effects on activity and structure of soil denitrifying community and on the plant biomasses or the relative growth rates. Correlations between plant and microbial parameters were observed after 20 days of growth reflecting early and strong chemical interactions between plants and denitrifying community, which decreased with plant growth after 40 days. Conclusions: This study shows that an early in the first weeks of growth, and then to a change to a root conservative strategy after 40 days. This switch to a conservative strategies involved resource storage, an altered allocation to aboveground and belowground parts and an investment in fine roots. It now seems clear that this storage strategy starts very young with an early BDI establishment, allowing this clonal plant exceptional storage and multiplication capacities.
ano.nymous@ccsd.cnrs.fr.invalid (Amélie Cantarel) 12 Feb 2024
https://hal.science/hal-04451939v1
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[hal-03701557] Protist Predation Influences the Temperature Response of Bacterial Communities
Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these microbiomes under future climates is still poorly understood. Here, we assess whether predation by a key global bacterial consumer—protists—influences the temperature response of the community structure and function of a freshwater microbiome. To do so, we exposed microbial communities to two cosmopolitan protist species— Tetrahymena thermophila and Colpidium sp.—at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to community shifts, these responses changed over time and in the presence of protists. Protists influenced microbial biomass and respiration rate through direct and indirect effects on bacterial community structure, and predator presence actually reduced microbial respiration at elevated temperature. Indicator species analyses showed that these predator effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities but also demonstrates that the presence of a large predator can mediate these responses to warming.
ano.nymous@ccsd.cnrs.fr.invalid (Jennifer D.. Rocca) 22 Jun 2022
https://hal.inrae.fr/hal-03701557v1
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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-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-05081398] A cross-systems primer for synthetic microbial communities
The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research.Here the authors outline best practices for the development, implementation and evaluation of synthetic microbial communities (or SynComs) across different systems.
ano.nymous@ccsd.cnrs.fr.invalid (Elijah Mehlferber) 23 May 2025
https://hal.inrae.fr/hal-05081398v1
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[hal-04688338] Alkaline mine drainage drives stream sediment microbial community structure and function
With advances in eDNA metabarcoding, environmental microbiomes are increasingly used as cost-effective tools for monitoring ecosystem health. Stream ecosystems in Central Appalachia, heavily impacted by alkaline drainage from mountaintop coal mining, present ideal opportunities for biomonitoring using stream microbiomes, but the structural and functional responses of microbial communities in different environmental compartments are not well understood. We investigated sediment microbiomes in mining impacted streams to determine how community composition and function respond to mining and to look for potential microbial bioindicators. Using 16s rRNA gene amplicon sequencing, we found that mining leads to shifts in microbial community structure, with the phylum Planctomycetes enriched by 1-6% at mined sites. We observed ~51% increase in species richness in bulk sediments. In contrast, of the 31 predicted metabolic pathways that changed significantly with mining, 23 responded negatively. Mining explained 15-18% of the variance in community structure and S, Se, %C and %N were the main drivers of community and functional pathway composition. We identified 12 microbial indicators prevalent in the ecosystem and sensitive to mining. Overall, alkaline mountaintop mining drainage causes a restructuration of the sediment microbiome, and our study identified promising microbial indicators for the long-term monitoring of these impacted streams.
ano.nymous@ccsd.cnrs.fr.invalid (Lingrong Jin) 05 Sep 2024
https://hal.inrae.fr/hal-04688338v1
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[hal-05698209] Genotype-specific root morphology and metabolic traits shape bacterial communities and tolerance to Fusarium root rot in wheat
Plant genotype plays a critical role in shaping root-associated microbiota and in modulating plant tolerance to soilborne diseases such as Fusarium root rot (FRR). In this study, we investigated how four wheat ( Triticum aestivum ) varieties, with differing tolerance to FRR, influence the composition and structure of bacterial communities in the rhizosphere and root endosphere. In the current study evaluated root traits that may contribute to the genotype-specific assembly of bacterial communities across the four wheat genotypes. The variety Concret exhibited the highest FRR tolerance, whereas Pilier was the most susceptible. Analyses of root morphology revealed significant genotype-dependent differences in root length and volume. Notably, traits associated with the tolerant genotype were positively correlated with the abundance of key beneficial bacterial genera in the rhizosphere, including Bacillus , Lysobacter , and Sphingomonas . Untargeted metabolomics identified 879 features, with 20 key metabolites distinguishing the wheat genotypes, including alkaloids, benzoate derivatives, and benzoxazinoid-derived compounds. Correlation analysis revealed significant relationships between these root metabolites and key bacterial taxa. This findings demonstrate that wheat genotypes influence the assembly of the root microbiota through genotype-based morphological and metabolic traits, providing valuable insights into the specific root traits that wheat genotypes can leverage to modulate the plant microbiome and enhance disease resistance.
ano.nymous@ccsd.cnrs.fr.invalid (Omar Hafidi) 20 Jul 2026
https://hal.inrae.fr/hal-05698209v1
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[hal-04684659] Clarification on the implementation of the Nagoya Protocol in France for the access and sharing of benefits arising from the utilization of microbial genetic resources
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ano.nymous@ccsd.cnrs.fr.invalid (Mariana Ferrari) 03 Sep 2024
https://hal.inrae.fr/hal-04684659v1
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[hal-04843937] Garlic Bulb Decay and Soft Rot Caused by the Cross-Kingdom Pathogen Burkholderia gladioli
In 2021, two gram-negative bacterial strains were isolated from garlic (Allium sativum) bulbs showing decay and soft rot symptoms in Central Iran. The bacterial strains were aggressively pathogenic on cactus, garlic, gladiolus, onion, potato, and saffron plants and induced soft rot symptoms on carrot, cucumber, potato, and radish discs. Furthermore, they were pathogenic on sporophores of cultivated and wild mushrooms. Phylogenetic analyses revealed that the bacterial strains belong to Burkholderia gladioli. Garlic bulb rot caused by B. gladioli has rarely been reported in the literature. Historically, B. gladioli strains had been assigned to four pathovars, namely, B. gladioli pv. alliicola, B. gladioli pv. gladioli, B. gladioli pv. agaricicola, and B. gladioli pv. cocovenenans, infecting onion, Gladiolus sp., and mushrooms and poisoning foods, respectively. Multilocus (i.e., 16S rRNA, atpD, gyrB, and lepA genes) sequence-based phylogenetic investigations including reference strains of B. gladioli pathovars showed that the two garlic strains belong to phylogenomic clade 2 of the species, which includes the pathotype strain of B. gladioli pv. alliicola. Although the garlic strains were phylogenetically closely related to the B. gladioli pv. alliicola reference strains, they possessed pathogenicity characteristics that overlapped with three of the four historical pathovars, including the ability to rot onion (pv. alliicola), gladiolus (pv. gladioli), and mushrooms (pv. agaricicola). Furthermore, the pathotype of each pathovar could infect the hosts of other pathovars, undermining the utility of the pathovar concept in this species. Overall, using phenotypic pathovar-oriented assays to classify B. gladioli strains should be replaced by phylogenetic or phylogenomic analysis.
ano.nymous@ccsd.cnrs.fr.invalid (Hamid Abachi) 14 May 2025
https://hal.inrae.fr/hal-04843937v1
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[hal-04692305] Wild mushrooms as potential reservoirs of plant pathogenic bacteria: a case study on Burkholderia gladioli
ABSTRACT Fruit bodies (sporocarps) of wild mushrooms growing in natural environments play a substantial role in the preservation of microbial communities, for example, clinical and food-poisoning bacteria. However, the role of wild mushrooms as natural reservoirs of plant pathogenic bacteria remains almost entirely unknown. Furthermore, bacterial transmission from a mushroom species to agricultural plants has rarely been recorded in the literature. In September 2021, a creamy-white Gram-negative bacterial strain was isolated from the sporocarp of Suillus luteus (slippery jack) growing in Bermuda grass ( Cynodon dactylon ) lawn in Southern Iran. A similar strain was isolated from the same fungus in the same area in September 2022. Both strains were identified as Burkholderia gladioli based on phenotypic features as well as phylogeny of 16S rRNA and three housekeeping genes. The strains were not only pathogenic on white button mushrooms ( Agaricus bisporus ) but also induced hypersensitive reaction (HR) on tobacco and common bean leaves and caused soft rot on a set of diverse plant species, that is, chili pepper, common bean pod, cucumber, eggplant, garlic, gladiolus, narcissus, onion, potato, spring onion, okra, kohlrabi, mango, and watermelon. Isolation of plant pathogenic B. gladioli strains from sporocarp of S. luteus in two consecutive years in the same area could be indicative of the role of this fungus in the preservation of the bacterium in the natural environment. B. gladioli associated with naturally growing S. luteus could potentially invade neighboring agricultural crops, for example, vegetables and ornamentals. The potential role of wild mushrooms as natural reservoirs of phytopathogenic bacteria is further discussed. IMPORTANCE The bacterial genus Burkholderia contains biologically heterogeneous strains that can be isolated from diverse habitats, that is, soil, water, diseased plant material, and clinical specimens. In this study, two Gram-negative pectinolytic bacterial strains were isolated from the sporocarps of Suillus luteus in September 2021 and 2022. Molecular phylogenetic analyses revealed that both strains belonged to the complex species Burkholderia gladioli , while the pathovar status of the strains remained undetermined. Biological investigations accomplished with pathogenicity and host range assays showed that B. gladioli strains isolated from S. luteus in two consecutive years were pathogenic on a set of diverse plant species ranging from ornamentals to both monocotyledonous and dicotyledonous vegetables. Thus, B. gladioli could be considered an infectious pathogen capable of being transmitted from wild mushrooms to annual crops. Our results raise a hypothesis that wild mushrooms could be considered as potential reservoirs for phytopathogenic B. gladioli .
ano.nymous@ccsd.cnrs.fr.invalid (Mozhde Hamidizade) 12 Sep 2024
https://hal.inrae.fr/hal-04692305v1
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[hal-04690609] Multiphasic investigations imply transfer of orange-/red-pigmented strains of the bean pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens to a new species as C. aurantiacum sp. nov., elevation of the poinsettia pathogen C. flaccumfaciens pv. poinsettiae to the species level as C. Poinsettiae sp. nov., and synonymy of C. albidum with C. citreum
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ano.nymous@ccsd.cnrs.fr.invalid (Ebrahim Osdaghi) 06 Sep 2024
https://hal.inrae.fr/hal-04690609v1
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[hal-03794351] Analysis of the Diversity of Xylophilus ampelinus Strains Held in CIRM-CFBP Reveals a Strongly Homogenous Species
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.
ano.nymous@ccsd.cnrs.fr.invalid (Perrine Portier) 03 Oct 2022
https://hal.inrae.fr/hal-03794351v1
