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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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[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-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-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-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-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-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-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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[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-05739099] Specific and broad-spectrum antibacterial effectors of type VI secretion system drive competition of Stenotrophomonas rhizophila against bacteria from seed microbiota
ABSTRACT 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-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-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
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Ebrahim Osdaghi) 06 Sep 2024
https://hal.inrae.fr/hal-04690609v1
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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
[...]
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-03658569] Whole Genome Resources of 17 Curtobacterium flaccumfaciens Strains Including Pathotypes of C. flaccumfaciens pv. betae , C. flaccumfaciens pv. oortii , and C. flaccumfaciens pv. poinsettiae
RNA interference is a mechanism of suppressing gene expression in plants, animals and fungi. This regulation mechanism involves three main enzymes, Dicers (Dcr), Argonautes (Ago) and RNA Dependent RNA Polymerases (Rdrp) allowing to produce smallRNAs. RNA interference and smallRNAs have a role in the plant–microorganisms interaction, either in a pathogenic or in a symbiotic relationships. Alternaria brassicicola is a pathogenic fungus of the Brassicaceae plants. During plant infection, it is able to transmit itself vertically and horizontally, giving advantages for new infection and dissemination. To investigate RNA interference and the presence of smallRNAs in A. brassicicola, an in silico analysis was achieved. Two DCR, 4 AGO and 3 RDRP genes were identified comforting the presence of smallRNAs in A. brassicicola. SmallRNA sequencing from wild-type strain and DCR deleted mutants allowed the identifcation of 17 miRNAs in A. brassicicola. The synthesis of these miRNAs is only weakly influenced by the inactivation of DCR genes suggesting the possible existence of an alternative Dicer-independent miRNA synthesis pathway. Target's prediction of A. brassicicola miRNAs identified genes in the fungus and in the plant model Arabidopsis thaliana. Some miRNAs were predicted to target A. thaliana genes involved in the methylation of histone and in the disease resistance
ano.nymous@ccsd.cnrs.fr.invalid (Ebrahim Osdaghi) 04 May 2022
https://hal.inrae.fr/hal-03658569v1
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[hal-04843293] Clonality and Diversity in the Soft Rot Dickeya solani Phytopathogen
Bacterial diversity analyses often suffer from a bias due to sampling only from a limited number of hosts or narrow geographic locations. This was the case for the phytopathogenic species Dickeya solani, whose members were mainly isolated from a few hosts–potato and ornamentals–and from the same geographical area–Europe and Israel, which are connected by seed trade. Most D. solani members were clonal with the notable exception of the potato isolate RNS05.1.2A and two related strains that are clearly distinct from other D. solani genomes. To investigate if D. solani genomic diversity might be broadened by analysis of strains isolated from other environments, we analysed new strains isolated from ornamentals and from river water as well as strain CFBP 5647 isolated from tomato in the Caribbean island Guadeloupe. While water strains were clonal to RNS05.1.2A, the Caribbean tomato strain formed a third clade. The genomes of the three clades are highly syntenic; they shared almost 3900 protein families, and clade-specific genes were mainly included in genomic islands of extrachromosomal origin. Our study thus revealed both broader D. solani diversity with the characterisation of a third clade isolated in Latin America and a very high genomic conservation between clade members.
ano.nymous@ccsd.cnrs.fr.invalid (Frédérique van Gijsegem) 20 Dec 2024
https://hal.inrae.fr/hal-04843293v1
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[hal-04843376] Clavibacter lycopersici sp. nov.: a peach-colored actinobacterium isolated from symptomless tomato plant
In 2015, Gram-positive peach-coloured actinobacterial strains were isolated from symptomless tomato phyllosphere in Iran. Biochemical and physiological characteristics, as well as 16S rRNA phylogeny showed that the strains belong to Clavibacter sp., while they were non-pathogenic on the host of isolation, and morphologically distinct from the tomato pathogen C. michiganensis and other plant-associated bacteria. Multilocus sequence analysis of five housekeeping genes showed that the two peach-coloured strains CFBP 8615 T (Tom532 T ) and CFBP 8616 (Tom495) were phylogenetically distinct from all validly described Clavibacter species. Whole genome sequence-based indices, i.e. average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH), showed that the two peach-colored strains share nearly 100 % orthoANI value with one another, while they differ from all validly described Clavibacter species with the orthoANI/dDDH values <93 % and <50 %, respectively. Thus, based on both phenotypic features and orthoANI/dDDH indices the peach-coloured strains could belong to a new species within Clavibacter . In this study, we provide a formal species description for the peach-coloured tomato-associated Clavibacter strains. Clavibacter lycopersici sp. nov. is proposed for the new species with Tom532 T = CFBP 8615 T = ICMP 22100 T as type strain.
ano.nymous@ccsd.cnrs.fr.invalid (Ebrahim Osdaghi) 17 Dec 2024
https://hal.inrae.fr/hal-04843376v1
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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-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-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-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-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
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[hal-03700789] The Broad Host Range Plant Pathogen Dickeya dianthicola Shows a High Genetic Diversity
The wide host range phytopathogen D. dianthicola, first described in ornamentals in the 1950s, rapidly became a threat for potato production in Europe and, more recently, worldwide. Previous genomic analyses, mainly of strains isolated from potato, revealed little sequence diversity. To further analyse D. dianthicola genomic diversity, we used a larger genome panel of 41 isolates encompassing more strains isolated from potato over a wide time scale and more strains isolated from other hosts. The phylogenetic and pan-genomic trees revealed a large cluster of highly related genomes but also the divergence of two more distant strains, IPO 256 and 67.19, isolated from potato and impatiens, respectively, and the clustering of the three strains isolated from Kalanchoe with one more distinct potato strain. An SNP-based minimal spanning tree highlighted both diverse clusters of (nearly) clonal strains and several strains scattered in the MST, irrespective of country or date of isolation, that differ by several thousand SNPs. This study reveals a higher diversity in D. dianthicola than previously described. It indicates the clonal spread of this pathogen over long distances, as suspected from worldwide seed trading, and possible multiple introductions of D. dianthicola from alternative sources of contaminations.
ano.nymous@ccsd.cnrs.fr.invalid (Jacques Pédron) 21 Jun 2022
https://hal.inrae.fr/hal-03700789v1
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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-03686615] Building More Resilient Culture Collections: A Call for Increased Deposits of Plant-Associated Bacteria
Biological collections preserve our past, while helping protect our future and increase future knowledge. Plant bacterial culture collections are our security for domestic and global biosecurity. This feature article will provide an introduction to the global position of plant bacterial collections. The role of collections in monitoring plant pathogenic bacteria will be explored through the presentation of five cases studies. These case studies demonstrate why culture collections were imperative for the outcome in each situation. We discuss what we believe should be the best practices to improve microbial preservation and accessioning rates, and why plant bacterial culture collections must increase deposits to be prepared for future emerging pathogens. This is not only the case for global culture collections, but on a much bigger scale, our future scientific successes, our biosecurity decisions and responses, and our knowledge are contingent upon preserving our valuable bacterial strains. It is hoped that once you read this article, you will see the need to deposit your strains in registered public collections and make a concerted effort to build better bacterial culture collections with us.
ano.nymous@ccsd.cnrs.fr.invalid (Kirk Broders) 05 May 2025
https://hal.inrae.fr/hal-03686615v1
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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-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-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-03345026] Improving common bacterial blight phenotyping by using rub-inoculation and machine learning: cheaper, better, faster, stronger
Accurate assessment of plant symptoms plays a key role for measuring the impact of pathogens during plant-pathogen interaction. Common bacterial blight caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans (Xpp-Xcf) is a major threat to common bean. The pathogenicity of these bacteria is variable among strains, and depends mainly on a type III secretion system and associated type III effectors such as transcription activator-like effectors (TALEs). Because the impact of a single gene is often small and difficult to detect, a discriminating methodology is required to distinguish the slight phenotype changes induced during the progression of the disease. Here, we compared two different inoculation and symptom assessment methods for their ability to distinguish two tal mutants from their corresponding wild-type strains. Interestingly, rub-inoculation of the first leaves combined with symptom assessment by machine learning-based imaging allowed significant distinction between wild-type and mutant strains. By contrast, dip-inoculation of first trifoliate leaves combined with chlorophyll fluorescence imaging did not differentiate the strains. Furthermore, the new method developed here led to the miniaturization of pathogenicity tests and significant time savings.
ano.nymous@ccsd.cnrs.fr.invalid (Justine Foucher) 15 Sep 2021
https://hal.inrae.fr/hal-03345026v1
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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-03953038] Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa
Bacterial leaf streak disease caused by Xanthomonas translucens pv. undulosa is an economically important disease threatening wheat and barley crops around the globe. So far, specific PCR-based detection and identification tests for X. translucens pathovars are not available. In this study, we used comparative genomics approach to design a pathovar-specific primer pair for detection of X. translucens pv. undulosa in naturally infected seeds and its differentiation from other pathovars of the species. For this aim, complete genome sequences of strains of different X. translucens pathovars were compared and the specific PCR primer pair XtuF/XtuR was designed. These primers were strictly specific to X. translucens pv. undulosa as the expected 229 bp DNA fragment was not amplified in the closely-related pathovars nor in other xanthomonads, wheat pathogenic bacteria, and other plant pathogenic bacteria. High sensitivity of the primer pair XtuF/XtuR allowed detection of pure DNA of the pathogen in a concentration as low as 4.5 pg/µl. The pathogen was also detected in water suspension at a concentration of 8.6 × 102 cfu/ml. The PCR test was capable of detecting the pathogen in extracts of naturally infected wheat seeds at a concentration of 3.5 × 104 cfu/g while culture plate method was able to detect the pathogen at a concentration of 50 × 105 cfu/g of the same seeds. The PCR test developed in this study is a step forward for precise detection and identification of X. translucens pv. undulosa to prevent outbreaks of the bacterial leaf streak disease.
ano.nymous@ccsd.cnrs.fr.invalid (Hosna Alvandi) 24 Jan 2023
https://hal.inrae.fr/hal-03953038v1
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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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[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-05717688] Monitoring the Occurrence and Distribution of Stewart’s Wilt of Maize in Iran
Stewart’s wilt of maize, caused by the gram-negative bacterium Pantoea stewartii subsp. stewartii, is one of the economically important diseases of the crop around the globe. The disease has not yet been reported in Iran. Following preliminary observation of suspected symptoms on maize plants in Southeastern Iran in 2019, a 4-year comprehensive field survey and sampling program was initiated across maize-growing areas in the country to monitor the occurrence and distribution of the disease. During 2019 to 2022, 180 maize fields were surveyed, from which 400 symptomatic and asymptomatic maize samples were collected. Among dozens of bacterial strains isolated from leaves and stems of maize plants, 22 strains phenotypically resembled those of Pantoea spp. Species-specific PCR and multilocus phylogenetic analyses using the sequences of atpD, gyrB, infB, and rpoB genes showed that P. stewartii subsp. stewartii is the causal agent of Stewart’s wilt in Iran. All strains induced leaf chlorosis and plant stunting on maize plants under greenhouse conditions 7 to 15 days postinoculation, confirmed with accomplishment of Koch’s postulates. These 22 strains were isolated in Bushehr, Fars, Hormozgan, Kermanshah, Khuzestan, Kohgiluyeh-Boyer Ahmad, and Sistan-Baluchistan provinces. Results of the present study confirmed the occurrence of P. stewartii subsp. stewartii causing Stewart’s wilt of maize in Iran. The occurrence of Stewart’s wilt on maize in Iran can lead to yield reduction, trade restrictions, increased control costs, and threats to food security. Considering the quarantine status of the pathogen in Iran, strict inspections are warranted to combat potential threats due to Stewart’s wilt epidemics in the country.
ano.nymous@ccsd.cnrs.fr.invalid (Hosna Alvandi) 14 Aug 2026
https://hal.inrae.fr/hal-05717688v1
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[hal-05717668] Contribution of Floral Transmission to the Assembly and Health Impact of Bacterial Communities in Watermelon Seeds
<div><p>Flower-sourced assembly of seed microbiota remains an understudied ecological process. Here, we investigated the floral transmission pathway for bacterial acquisition by developing seeds of watermelon (Citrullus lanatus). Comparison of stigmaand seed-associated bacterial communities from field-grown C. lanatus revealed significant overlap: up to 40% of the bacterial diversity that was detected in seed was also found on stigmas. In a field pollinator exclusion experiment, honeybee visitation to flower stigmas had no significant effect on bacterial community composition in seeds. Among a collection of bacterial isolates from stigmas and seeds collected in the field, more than half (57%) were able to transmit to seeds after inoculation onto stigmas under laboratory conditions. Interestingly, for most bacterial strains, fruit set rates increased after floral inoculation, and in some cases even in the absence of transmission to the seed. We also found that bacterial isolates from watermelon stigmas and seeds had variable (i.e., positive or negative) effects on seed germination and seedling emergence. Our findings highlight the contribution of floral transmission to seed microbiota assembly and its consequences for seedling fitness.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Gillian E Bergmann) 14 Aug 2026
https://hal.inrae.fr/hal-05717668v1
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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-03834661] Single seed microbiota: assembly and transmission from parent plant to seedling
The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collected throughout seed developments of beans and radishes. Seeds were associated with a dominant bacterial taxon that represented more than 75% of all reads. The identity of this taxon was highly variable between the plants and within the seeds of the same plant. We identified selection as the main ecological process governing the succession of dominant taxa during seed filling and maturation. In a second step, we evaluated the seedling transmission of seed-borne taxa in 160 individual plants. While the initial bacterial abundance on seeds was not a good predictor of seedling transmission, the identities of the seed-borne taxa modified the phenotypes of seedlings. Overall, this work revealed that individual seeds are colonized by a few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 05 Sep 2024
https://hal.inrae.fr/hal-03834661v1
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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-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-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-04470041] A 2000-Year-Old Bacillus stercoris Strain Sheds Light on the Evolution of Cyclic Antimicrobial Lipopeptide Synthesis
Some bacteria (notably the genera Bacillus and Clostridium) have the capacity to form endospores that can survive for millions of years in isolated habitats. The genomes of such ancient bacteria provide unique opportunities to understand bacterial evolution and metabolic capabilities over longer time scales. Herein, we sequenced the genome of a 2000-year-old bacterial strain (Mal05) isolated from intact apple seeds recovered during archaeological excavations of a Roman villa in Italy. Phylogenomic analyses revealed that this strain belongs to the species Bacillus stercoris and that it is placed in an early-branching position compared to most other strains of this species. Similar to other Bacillus species, B. stercoris Mal05 had been previously shown to possess antifungal activity. Its genome encodes all the genes necessary for the biosynthesis of fengycin and surfactin, two cyclic lipopeptides known to play a role in the competition of Bacilli with other microorganisms due to their antimicrobial activity. Comparative genomics and analyses of selective pressure demonstrate that these genes are present in all sequenced B. stercoris strains, despite the fact that they are not under strong purifying selection. Hence, these genes may not be essential for the fitness of these bacteria, but they can still provide a competitive advantage against other microorganisms present in the same environment.
ano.nymous@ccsd.cnrs.fr.invalid (Bessem Chouaia) 21 Feb 2024
https://hal.science/hal-04470041v1
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[hal-04749383] Activation of plant immunity by galbonolides promotes rhizosphere colonisation by Streptomyces sp. AgN23
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ano.nymous@ccsd.cnrs.fr.invalid (Clément Nicolle) 23 Oct 2024
https://hal.science/hal-04749383v1
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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-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-05056275] Niches and routes of transmission of Xanthomonas citri pv. fuscans to bean seeds
Seeds are vectors of a diversified microbiota including plant pathogens. To better understand transmission of common bacterial blight (CBB) agents to bean seeds, we analyzed the role of non-pathogenic xanthomonads on seed transmission efficiency and investigated the location of Xanthomonas citri pv. fuscans (Xcf) into seeds and plantlets. Competition between CBB and NP strains was initially assessed in vitro and then extended in planta to monitor the impact of co-inoculation on Xcf seed transmission. Moreover, location of Xcf strains in seeds and seedlings was visualized using a combination of gfp-tagged strain and DOPE-FISH/CSLM. Whereas CBB agent growth was inhibited in vitro by some seed-borne non-pathogenic xanthomonads strains, these strains did not transmit efficiently to seed through floral pathway and did not affect Xcf seed transmission. Xcf cells were observed entering seed through vascular elements and parenchyma of funiculus, but also micropyle and testa. Xcf cells were observed, moreover, among other bacteria on radicle surfaces, especially tip, in cotyledons, and plumules. CBB agents are more efficient than non-pathogenic xanthomonads in using the floral route to colonize seeds. CBB agents are located within different niches in the seed tissues up to the embryonic axis.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 05 May 2025
https://univ-angers.hal.science/hal-05056275v1
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[anses-05418638] Complete genome sequence data of Xylella fastidiosa subspecies multiplex ST88 and ST89 indicate distinct introductions in France
Xylella fastidiosa is a Gram-negative bacterium native to the Americas and classified as a priority pest under EU regulations. This xylem-limited plant pathogenic bacterium has a wide host range and is transmitted by insect vectors. Since 2013, X. fastidiosa has been identified in several European countries including Italy, France, Spain and Portugal, with different subspecies and sequence types (ST) detected. Since 2015, most strains identified in France are of the subspecies multiplex, specifically ST6 and ST7. Two new STs of X. fastidiosa subsp. multiplex, ST88 and ST89, were recently detected in the region Provence-Alpes-Côte d'Azur (PACA), and one strain of each ST has been isolated from infected plants. To investigate the phylogenetic relationships between the four STs present in France, a complete circular genome and a single-contig genome were assembled for the ST89 and ST88 strains, respectively, by combining PacBio and Illumina sequencing data. A phylogenomic analysis was performed to investigate the phylogenetic position and potential origin of these new strains. This data article contributes to improve our knowledge of the diversity and origin of X. fastidiosa subsp. multiplex in France and Europe.
ano.nymous@ccsd.cnrs.fr.invalid (Amandine Cunty) 07 Jan 2026
https://anses.hal.science/anses-05418638v1
