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[hal-03762192] Investigating the microbial community of Cacopsylla spp. as potential factor in vector competence of phytoplasma
Phytoplasmas are obligatory intracellular bacteria that colonize the phloem of many plant species and cause hundreds of plant diseases worldwide. In nature, phytoplasmas are primarily transmitted by hemipteran vectors. While all phloem-feeding insects could in principle transmit phytoplasmas, only a limited number of species have been confirmed as vectors. Knowledge about factors that might determine the vector capacity is currently scarce. Here, we characterized the microbiomes of vector and non-vector species of apple proliferation (AP) phytoplasma 'Candidatus Phytoplasma mali' to investigate their potential role in the vector capacity of the host. We performed high-throughput 16S rRNA metabarcoding of the two principal AP-vectors Cacopsylla picta and Cacopsylla melanoneura and eight Cacopsylla species, which are not AP-vectors but co-occur in apple orchards. The microbiomes of all species are dominated by Carsonella, the primary endosymbiont of psyllids and a second uncharacterized Enterobacteriaceae endosymbiont. Each Cacopsylla species harboured a species-specific phylotype of both symbionts. Moreover, we investigated differences between the microbiomes of AP-vector versus non-vector species and identified the predominant endosymbionts but also Wolbachia and several minor taxa as potential indicator species. Our study highlights the importance of considering the microbiome in future investigations of potential factors influencing host vector competence. We investigated the potential role of symbiotic bacteria in the acquisition and transmission of phytoplasma. By comparing the two main psyillid vector species of Apple proliferation (AP) phytoplasma and eight co-occurring species, which are not able to vector AP-phytoplasma, we found differences in the microbial communities of AP-vector and non-vector species, which appear to be driven by the predominant symbionts in both vector species and Wolbachia and several minor taxa in the non-vector species. In contrast, infection with AP-phytoplasma did not affect microbiome composition in both vector species. Our study provides new insights into the endosymbiont diversity of Cacopsylla spp. and highlights the importance of considering the microbiome when investigating potential factors influencing host vector competence.
ano.nymous@ccsd.cnrs.fr.invalid (Hannes Schuler) 19 Mar 2024
https://hal.inrae.fr/hal-03762192v1
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[hal-03777977] Microbiome of pear psyllids: A tale about closely related species sharing their endosymbionts
Psyllids are phloem-feeding insects that can transmit plant pathogens such as phytoplasmas, intracellular bacteria causing numerous plant diseases worldwide. Their microbiomes are essential for insect physiology and may also influence the capacity of vectors to transmit pathogens. Using 16S rRNA gene metabarcoding, we compared the microbiomes of three sympatric psyllid species associated with pear trees in Central Europe. All three species are able to transmit ‘Candidatus Phytoplasma pyri’, albeit with different efficiencies. Our results revealed potential relationships between insect biology and microbiome composition that varied during psyllid ontogeny and between generations in Cacopsylla pyri and C. pyricola, as well as between localities in C. pyri. In contrast, no variations related to psyllid life cycle and geography were detected in C. pyrisuga. In addition to the primary endosymbiont Carsonella ruddii, we detected another highly abundant endosymbiont (unclassified Enterobacteriaceae). C. pyri and C. pyricola shared the same taxon of Enterobacteriaceae which is related to endosymbionts harboured by other psyllid species from various families. In contrast, C. pyrisuga carried a different Enterobacteriaceae taxon related to the genus Sodalis. Our study provides new insights into host–symbiont interactions in psyllids and highlights the importance of host biology and geography in shaping microbiome structure.
ano.nymous@ccsd.cnrs.fr.invalid (Liliya Štarhová Serbina) 15 Sep 2022
https://hal.inrae.fr/hal-03777977v1
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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-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-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-04709706] Division of labor within psyllids: metagenomics reveals an ancient dual endosymbiosis with metabolic complementarity in the genus <i>Cacopsylla</i>
<div><p>Hemipteran insects are well-known for their ancient associations with beneficial bacterial endosymbionts, particularly nutritional symbionts that provide the host with essential nutrients such as amino acids or vitamins lacking in the host's diet. Therefore, these primary endosymbionts enable the exploitation of nutrient-poor food sources such as plant sap or vertebrate blood. In turn, the strictly host-associ ated lifestyle strongly impacts the genome evolution of the endosymbionts, resulting in small and degraded genomes. Over time, even the essential nutritional functions can be compromised, leading to the complementation or replacement of an ancient endosymbiont by another, more functionally versatile bacterium. Herein, we provide evidence for a dual primary endosymbiosis in several psyllid species. Using metage nome sequencing, we produced the complete genome sequences of both the primary endosymbiont "Candidatus Carsonella ruddii" and an as yet uncharacterized Enterobac teriaceae bacterium from four species of the genus Cacopsylla. The latter represents a new psyllid-associated endosymbiont clade for which we propose the name "Candidatus Psyllophila symbiotica. " Fluorescent in situ hybridization confirmed the co-localization of both endosymbionts in the bacteriome. The metabolic repertoire of Psyllophila is highly conserved across host species and complements the tryptophan biosynthesis pathway that is incomplete in the co-occurring Carsonella. Unlike co-primary endosymbionts in other insects, the genome of Psyllophila is almost as small as the one of Carsonella, indicating an ancient co-obligate endosymbiosis rather than a recent association to rescue a degrading primary endosymbiont. IMPORTANCE Heritable beneficial bacterial endosymbionts have been crucial for the evolutionary success of numerous insects by enabling the exploitation of nutri tionally limited food sources. Herein, we describe a previously unknown dual endo symbiosis in the psyllid genus Cacopsylla, consisting of the primary endosymbiont "Candidatus Carsonella ruddii" and a co-occurring Enterobacteriaceae bacterium for which we propose the name "Candidatus Psyllophila symbiotica. " Its localization within the bacteriome and its small genome size confirm that Psyllophila is a co-primary endosymbiont widespread within the genus Cacopsylla. Despite its highly eroded genome, Psyllophila perfectly complements the tryptophan biosynthesis pathway that is incomplete in the co-occurring Carsonella. Moreover, the genome of Psyllophila is almost as small as Carsonella's, suggesting an ancient dual endosymbiosis that has now reached a precarious stage where any additional gene loss would make the system collapse. Hence, our results shed light on the dynamic interactions of psyllids and their endosymbionts over evolutionary time.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Jessica Dittmer) 25 Sep 2024
https://hal.inrae.fr/hal-04709706v1
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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-04690679] The bacterial community of the European spruce bark beetle in space and time
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ano.nymous@ccsd.cnrs.fr.invalid (Abdelhameed Moussa) 02 Jun 2025
https://hal.inrae.fr/hal-04690679v1
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[hal-04494530] Multiple factors driving the acquisition efficiency of apple proliferation phytoplasma in Cacopsylla melanoneura
Abstract Phytoplasmas are bacterial pathogens located in the plant’s phloem that are responsible for several plant diseases and are mainly transmitted by phloem-sucking insects. Apple proliferation (AP) is an economically important disease associated with the presence of ‘ Candidatus Phytoplasma mali’ which is transmitted by two psyllid species. While Cacopsylla picta is a vector in different regions, the vector efficiency of C. melanoneura varies between different populations. This species is considered the main AP vector in Northwestern Italy but plays a minor role in Northeastern Italy and other European regions. To investigate whether the psyllid and/or the phytoplasma subtype drive the phytoplasma acquisition in C. melanoneura , a phytoplasma acquisition experiment was set up using single mating couples of overwintered individuals from different psyllid populations and phytoplasma subtypes. All analyzed insect populations acquired phytoplasma, but with different efficiencies and concentrations. The main factors driving the acquisition were the phytoplasma subtype and its concentration in the leaves of the infected trees together with the psyllid lineage. The phytoplasma concentration in the psyllids was again influenced by the phytoplasma subtype, the psyllid lineage and the region of origin, whereas the phytoplasma concentration in the leaves and the psyllid haplotype defined with the cytochrome oxidase I gene had only a minor impact on the phytoplasma concentration. This is the first study evaluating the roles of both the psyllid haplotype and the phytoplasma subtype on the acquisition process and highlights the importance of C. melanoneura as an additional AP vector.
ano.nymous@ccsd.cnrs.fr.invalid (Erika Corretto) 07 Mar 2024
https://hal.inrae.fr/hal-04494530v1
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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
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[hal-05304991] The Endosymbiont Consortia of Two Cixiidae Planthoppers Reveal an Ancient Symbiosis With ‘<i>Candidatus</i> Mirabilia Symbiotica’
Insects of the suborder Auchenorrhyncha harbour multiple ancient endosymbionts that jointly produce essential nutrients lacking from the host's diet. Compared to cicadas, leafhoppers, and spittlebugs, our understanding of the multipartite symbioses among planthoppers, an extremely diverse insect group, is still very limited. Herein, we assembled the genomes of the primary endosymbionts of two planthopper species from the Cixiidae family, Cixius wagneri and Pentastiridius leporinus, both vectors of phytopathogenic Arsenophonus in Europe. Each species harboured a different tripartite endosymbiont consortium: while P. leporinus carried the well-known combination 'Candidatus Karelsulcia muelleri', 'Ca. Vidania fulgoroideae', and 'Ca. Purcelliella pentastirinorum', C. wagneri harboured a yet unknown Gammaproteobacterium in addition to Karelsulcia and Vidania. This new endosymbiont 'Ca. Mirabilia symbiotica' is likely much older than Purcelliella, considering its extremely reduced genome. In both species, Karelsulcia and Vidania jointly produce the 10 essential amino acids, whereas Purcelliella and Mirabilia provide the non-essential amino acid cysteine and slightly different gene sets encoding B vitamins. Our findings confirm the functional stability of multipartite planthopper endosymbiont consortia despite changing partners over evolutionary time. In addition, we describe a new Rickettsia strain from the Meloidae group colonising P. leporinus, highlighting the diversity of bacterial endosymbionts associated with planthoppers.
ano.nymous@ccsd.cnrs.fr.invalid (Jessica Dittmer) 08 Dec 2025
https://hal.science/hal-05304991v1
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[hal-05364527] The hidden life of Xylella : mining the NCBI Sequence Read Archive reveals potential new species, host plants, and infected areas for this elusive bacterial plant pathogen
ABSTRACT New crop disease outbreaks can occur when phytopathogenic bacterial pathogens acquire new traits, switch to a new host plant, or are introduced into new geographic areas. Therefore, the rapid detection of a pathogen in a new environment and/or in a new host plant is essential to mitigate disease outbreaks. However, bacteria with a wide plant host range, many asymptomatic hosts, and slow symptom development can sometimes remain unnoticed for years. This is the case for the vector-borne xylem-inhabiting bacterium Xylella fastidiosa known to infect hundreds of plant species worldwide and its sister species X. taiwanensis , currently thought to be restricted to Taiwan. To investigate whether the two Xylella species are already present in other parts of the world, potentially in unrecognized host species, we performed an in-depth data mining of raw sequence data available in the NCBI Sequence Read Archive. This led to the identification of 62 datasets from diverse plant and insect samples from around the world. Furthermore, nine draft and one circular Xylella genome could be assembled from these datasets. Our results reveal several potential new host plants and previously unrecognized infected areas in the Americas, Africa, and Southeast Asia. Moreover, the newly assembled genomes represent several new strains of both X. fastidiosa and X. taiwanensis as well as an additional Xylella species infecting wild rice. Taken together, our work extends our knowledge on the genetic diversity, host range, and global distribution of the genus Xylella and can orient surveillance programs towards new regions and host plants. IMPORTANCE The rapid detection of a pathogen in a new environment and/or in a new host plant is essential to mitigate disease outbreaks. However, bacteria with a wide plant host range, many asymptomatic hosts, and slow symptom development can sometimes remain unnoticed for years. In this work, we used an in-depth screening of publicly available raw sequencing data as an alternative approach to investigate the distribution of the xylem-inhabiting bacteria Xylella fastidiosa and X. taiwanensis across the world. Our results reveal several potential new host plants and previously unrecognized infected areas in the Americas, Africa, and Southeast Asia. Moreover, we provide evidence, including a complete genome sequence, for a third Xylella species infecting wild rice. This work extends our knowledge of the genetic diversity, plant host range, and global distribution of the genus Xylella in natural environments and motivates surveillance programs in so-far-neglected biomes, regions, and host plants.
ano.nymous@ccsd.cnrs.fr.invalid (Martial Briand) 21 Nov 2025
https://univ-angers.hal.science/hal-05364527v1
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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-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-05585962] Etiology of Bacterial Soft Rot and Corm Decay in Saffron
Saffron ( Crocus sativus) is the world's most expensive spice. The plant is propagated vegetatively through corms. Infection of saffron corms with soil-dwelling pathogens would impact reproduction of the plant, resulting in significant yield losses. The etiology of soft rot and corm decay-inducing bacterial infections in saffron has rarely been investigated. This study aimed to isolate, identify, and characterize bacterial agents associated with saffron corm decay and soft rot in Iran. Symptomatic saffron corms were collected across the eastern, western, and central provinces of the country. Seventeen bacterial strains possessing pectinolytic activity were isolated in this study. Molecular-phylogenetic analysis using 16S rRNA and gyrA/ gyrB sequences accomplished with whole-genome sequencing of the representative strains led to the identification of gram-positive species Bacillus halotolerans, Bacillus subtilis, and a Paenibacillus sp., as well as gram-negative bacteria Acinetobacter johnsonii, a Chryseobacterium sp., and a Serratia sp. Pathogenicity assays confirmed that these bacterial strains not only infected saffron plants but also had pectinolytic activity on a range of monocotyledonous and dicotyledonous plants including beetroot, carrot, cucumber, garlic, onion, potato, and turnip. Further, the Bacillus sp. and Paenibacillus sp. strains could suppress the growth of other strains isolated in this study, indicating their potential competition on the same host. Whole-genome sequence-based analyses showed that the Paenibacillus sp. and Chryseobacterium sp. strains could potentially belong to novel species. The results of the present study shed light on the etiology of soft rot, inducing bacterial infections in the hub of saffron production in the Middle East.
ano.nymous@ccsd.cnrs.fr.invalid (Hamid Abachi) 09 Apr 2026
https://hal.inrae.fr/hal-05585962v1
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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-05015613] CIRM-CFBP : Plan de Gestion des Données
Plan de Gestion des Données du CIRM-CFBP. Le CIRM est un Groupement d'Intérêt Scientifique (GIS) créé en 2004 par INRAE autour de ses collections de micro-organismes (bactéries, levures et champignons filamenteux). Il est Coordonné par INRAE et est constitué de cinq centres de ressources biologique (CRB), tous certifiés ISO 9001. Ces CRB conservent plus de 22 000 souches de bactéries associées aux plantes, bactéries pathogènes, bactéries d'intérêt alimentaire, levures et champignons filamenteux. Le CIRM est labellisé « ISC », Infrastructure Scientifique de Recherche par l’IR RARe. Le CIRM-CFBP est le CRB dédié aux bactéries associées aux plantes. Il est accueilli à l'UMR 1345 IRHS. INRAE.
ano.nymous@ccsd.cnrs.fr.invalid (Perrine Portier) 01 Apr 2025
https://hal.inrae.fr/hal-05015613v1
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[hal-04973215] Fungal Oligopeptide Transporters have different substrate specificities despite their high sequence identity.
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ano.nymous@ccsd.cnrs.fr.invalid (Carmen Becerra-Rodríguez) 02 Mar 2025
https://hal.inrae.fr/hal-04973215v1
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[hal-05667267] Guardians or Gateways? The Intricate Relationship Between Plant Cell Walls and Pathogenic Xanthomonas
Plants have evolved a complex cell wall (CW) providing support and protection against environmental constraints, including constant attacks from pests and pathogens. Indeed, the plant CW serves as both a physical barrier and a sophisticated monitoring and signalling system, making it a central component of plant immunity. The Xanthomonas genus encompasses a large diversity of plant-pathogenic bacteria that, together, can infect a wide range of more than 400 plant species including monocots and dicots. Remarkably, Xanthomonas species are subdivided into highly specialized pathovars infecting a narrow range of plant species and/or tissues, each possessing a distinct CW structure and composition. This diversity makes Xanthomonas a perfect case for studying the interactions between bacterial pathogens and the plant CW. In this review, we provide an overview of the intricate interactions between Xanthomonas and the plant CW during the infection process. During infection, Xanthomonas degrades the plant CW both directly by using CW degrading enzymes and indirectly by reprogramming the plant transcriptome to enhance the expression of plant CW modifying enzymes. This degradation of the plant CW plays a central role during infection. On the plant side, it triggers immune responses, while on the Xanthomonas side, it facilitates bacterial invasion and access to nutrients, and activates a signalling hub that primes the pathogen for host colonization.
ano.nymous@ccsd.cnrs.fr.invalid (Charlotte Gaudin) 23 Jun 2026
https://hal.science/hal-05667267v1
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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-05481592] Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations
<div><p>Drought is a critical risk in developing countries for staple crops like common bean (Phaseolus vulgaris L.). We conducted an experiment to understand the legacy effects of repeated drought exposure across plant generations on the root and rhizosphere microbiome of the common bean, hypothesizing that a legacy of exposure improves overall plant microbiome resilience. We profiled the bacterial microbiome using marker gene amplicon sequencing over two plant generations in a complete factorial design for two common bean genotypes, Red Hawk and Flavert. We performed parallel experiments for Red Hawk in two different countries using soils of Pays de la Loire, France, and Michigan, USA. Despite the clear and relatively consistent drought effects on the plant phenotypes, there was neither response of the Red Hawk microbiomes to drought, nor a notable legacy of drought exposure. For Flavert, there was a minor legacy drought effect for the second generation in the rhizosphere microbiome beta diversity. This study demonstrates that rhizosphere microbiomes can be resistant to drought stress and that cross-generational legacy depends on soil origin and host genotype. Such parallel experiments across countries, while difficult to implement, are useful to inform generalities and build theory towards prediction on microbiome responses to global change.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (A Fina Bintarti) 28 Jan 2026
https://hal.inrae.fr/hal-05481592v1
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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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[inserm-04492349] Emergence and spread of Mycobacterium ulcerans at different geographic scales
ABSTRACT The classical lineage of Mycobacterium ulcerans is the most prevalent clonal group associated with Buruli ulcer in humans. Its reservoir is strongly associated with the environment. We analyzed together 1,045 isolates collected from 13 countries on two continents to define the evolutionary history and population dynamics of this lineage. We confirm that this lineage spread over 7,000 years from Australia to Africa with the emergence of outbreaks in distinct waves in the 18th and 19th centuries. In sharp contrast with its global spread over the last century, transmission chains are now mostly local, with little or no dissemination between endemic areas. This study provides new insights into the phylogeography and population dynamics of M. ulcerans, highlighting the importance of comparative genomic analyses to improve our understanding of pathogen transmission. IMPORTANCE Mycobacterium ulcerans is an environmental mycobacterial pathogen that can cause Buruli ulcer, a severe cutaneous infection, mostly spread in Africa and Australia. We conducted a large genomic study of M. ulcerans , combining genomic and evolutionary approaches to decipher its evolutionary history and pattern of spread at different geographic scales. At the scale of villages in an endemic area of Benin, the circulating genotypes have been introduced in recent decades and are not randomly distributed along the river. On a global scale, M. ulcerans has been spreading for much longer, resulting in distinct and compartmentalized endemic foci across Africa and Australia.
ano.nymous@ccsd.cnrs.fr.invalid (Martial Briand) 28 Mar 2024
https://inserm.hal.science/inserm-04492349v1
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[hal-05620671] Clavibacter vidaverae sp. nov., Clavibacter rahimiani sp. nov. and Clavibacter davisi sp. nov.: corynebacterial plant pathogens isolated from small-grain cereals
During 2020–2024, 25 Gram-positive actinobacterial strains were isolated from small-grain cereals in Iran. Colony morphology, phenotypic characteristics and multilocus sequence analyses showed that the strains belonged to the coryneform genus Clavibacter (family Microbacteriaceae ). The Clavibacter strains isolated from small-grain cereals in Iran were distributed within five distinct phylogenetic clades. Two of those clades included Clavibacter tessellarius and Clavibacter zhangzhiyongii , while the other three groups of Clavibacter strains were taxonomically undetermined and phylogenetically distinct from all validly described species in the genus. Whole-genome sequence-based indices, i.e. average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), showed that the latter three phylogenetic clades differed from all validly described Clavibacter species, with ANI/dDDH values &lt;94% and &lt;70%, respectively. Analyses of KEGG pathways and pathogenicity-associated genes revealed substantial differences among the five Clavibacter groups associated with small-grain cereals. All Clavibacter strains were capable of infecting their hosts of isolation, i.e. wheat, barley and oat. Thus, based on both phenotypic features, i.e. differences in colony morphology, biolog microbial identification microplate data and polar lipid repertoires, as well as DNA similarity indices, the three clades could represent three new species within Clavibacter . In this study, we provide formal species descriptions for three Clavibacter clades isolated from small-grain cereals. These three species include Clavibacter vidaverae sp. nov. (type strain Sh2088ᵀ=CFBP 9070ᵀ=ICMP 24732ᵀ), Clavibacter rahimiani sp. nov. (type strain Sh2141ᵀ=CFBP 9069ᵀ=ICMP 24735ᵀ) and Clavibacter davisi sp. nov. (type strain Sh2036ᵀ=CFBP 9071ᵀ=ICMP 24729ᵀ).
ano.nymous@ccsd.cnrs.fr.invalid (Asma Rahmanzadeh) 12 May 2026
https://hal.science/hal-05620671v1
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[inserm-05384736] The contribution of comparative genomics to health geography research: A case study on the identification of sites at which M. ulcerans contamination occurs in Benin
We report here a significant advance in research into Buruli ulcer, a skin disease caused by an environmental bacterium (Mycobacterium ulcerans). We demonstrate the utility of crossed analyses of comparative genomics and geographic data to improve our understanding of the spatial dynamics of this disease and to identify potential sites of contamination with greater precision. An analysis of patient isolates from the endemic region Ouémé-Plateau (Benin) led to the detection, of a spatial clustering of three specific genotypes. It suggests the existence of different ecological reservoirs or particular environmental conditions favoring the restriction of the bacterium to particular areas with very tight geographic boundaries. A health geography survey was performed on patients infected with these genotypes, based on a method developed by our team: a detailed interview concerning the patient's place of residence, followed by a commented tour on foot of the sites mentioned, with the patient. All the sites visited were geolocalized by GPS. A cross-analysis of spatial and comparative genomics data led to identify zones frequented by multiple patients potentially linked to exposure to the bacterium. This mixed dynamic research approach, pave the way for a better understanding of M. ulcerans transmission and for improving preventive strategies.
ano.nymous@ccsd.cnrs.fr.invalid (Alexandra Boccarossa) 28 Jan 2026
https://inserm.hal.science/inserm-05384736v1
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[hal-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-05056273] Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System
ABSTRACT Xanthomonas arboricola is conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. This study showed that X. arboricola also encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. The aim of this study was to assess the X. arboricola population structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. A multilocus sequence analysis (MLSA) was performed on a collection of 100 X. arboricola strains, including 27 nonpathogenic strains isolated from walnut. Nonpathogenic strains grouped outside clusters defined by pathovars and formed separate genetic lineages. A multilocus variable-number tandem-repeat analysis (MLVA) conducted on a collection of X. arboricola strains isolated from walnut showed that nonpathogenic strains clustered separately from clonal complexes containing Xanthomonas arboricola pv. juglandis strains. Some nonpathogenic strains of X. arboricola did not contain the canonical type III secretion system (T3SS) and harbored only one to three type III effector (T3E) genes. In the nonpathogenic strains CFBP 7640 and CFBP 7653, neither T3SS genes nor any of the analyzed T3E genes were detected. This finding raises a question about the origin of nonpathogenic strains and the evolution of plant pathogenicity in X. arboricola . T3E genes that were not detected in any nonpathogenic isolates studied represent excellent candidates to be those responsible for pathogenicity in X. arboricola .
ano.nymous@ccsd.cnrs.fr.invalid (Salwa Essakhi) 05 May 2025
https://hal.science/hal-05056273v1
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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-04670942] Comparative transcriptomics reveals a highly polymorphic Xanthomonas HrpG virulence regulon
Background: Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. Results: In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. Conclusions: The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS.
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Quiroz Monnens) 13 Aug 2024
https://hal.inrae.fr/hal-04670942v1
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[hal-05533608] Elucidating the interplay between metabolites and microorganisms in the spermosphere of common bean (Phaseolus vulgaris L.) seeds
The spermosphere, the dynamic interface surrounding germinating seeds, is shaped by the intricate interplay between seed-exuded natural compounds and seed-associated microbial communities. In this work, we provide the first comprehensive metabolomic and microbiome characterization of common bean ( Phaseolus vulgaris ) spermosphere of eight genotypes produced in two contrasted production regions. Through an integrated approach, we explored the metabolomic and microbiota composition in the spermosphere of germinating common bean seeds and elucidated their environmental and genotype regulation. We detected and analyzed 2,467 metabolite features (Mf) through untargeted metabolomics categorized into fourteen metabolic categories, highlighting the prevalence of amino acids, flavonoids, and terpenoids. Genotype was the key factor influencing the chemical composition of the spermosphere. Furthermore, we identified 19 bacterial families and 23 fungal families inhabiting the spermosphere, with both genotype and seed production location exerting varying degrees of influence on microbial community composition. Through a multiscale integrated approach, we revealed specific associations between metabolites and microorganisms, such as negative correlation between flavonoids and Bacillus spp., emphasizing the genotype-dependent nature of these interactions. This comprehensive investigation sheds light on the mechanisms underlying seed germination and the complex interactions between plant genotypes, seed exudates, environmental conditions, and microbial communities in the spermosphere. These findings provide a framework for developing innovative strategies to promote seed health and sustainable crop production. IMPORTANCE The spermosphere, the dynamic interface around germinating seeds, is shaped by the intricate interplay between seed-exuded compounds and microbial communities. Despite the importance of these interactions for eventual seedling emergence and health, little knowledge is available on the subject. We are the first to comprehensively analyze the chemical and microbial diversity of the spermosphere of Phaseolus vulgaris (common bean). We identified thousands of primary and specialized metabolites, highlighting their diversity but largely unknown roles in germinating seed-environment interactions. We revealed significant genotype-driven differences in the chemical composition as well as the influence of both genotype and seed production location on microbial community structure in the spermosphere. Our metabolome-microbiome integrative analysis suggests that common bean shapes the spermosphere microbiome through specific seed exudates. This research advances our understanding of the metabolic capabilities and ecological roles of seed microbiota within the spermosphere, contributing to our understanding of seed health and vigor.
ano.nymous@ccsd.cnrs.fr.invalid (Chandrodhay Saccaram) 02 Mar 2026
https://hal.science/hal-05533608v1
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[hal-05611383] Système de sécrétion de type 6, Quorum Quenching et Composés Organiques Volatiles: des stratégies de biocontrôle complémentaires?
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Annabelle Merieau) 04 May 2026
https://hal.science/hal-05611383v1
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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-05535196] Evolutionary dynamics of obligate endosymbiosis in the psyllid genus Cacopsylla
Phloem-sucking hemipterans maintain obligate, heritable symbiotic bacteria to overcome nutritional deficiencies caused by their unbalanced diet. While some groups retain ancient primary symbionts, others supplement or replace them with additional symbionts conferring adaptive benefits. Here, we explore the diversity and evolutionary dynamics of multiple endosymbionts in psyllids of the genus Cacopsylla. While the primary symbiont Carsonella is found in all analysed species, the ancient co-primary symbiont Psyllophila is absent in Cacopsylla pyrisuga, which instead harbours a Sodalis symbiont with a larger genome, located in the syncytium of the bacteriome. Phylogenomic analyses demonstrated co-divergence of Carsonella and Psyllophila with their hosts, whereas the occurrence of closely related Sodalis across different psyllid lineages indicates several independent acquisitions. The presence of additional facultative Sodalis and Serratia symbionts further highlights the dynamic host-symbiont relationships in psyllids and their essential roles in insect niche adaptation and evolution.
ano.nymous@ccsd.cnrs.fr.invalid (Erika Corretto) 02 Apr 2026
https://hal.inrae.fr/hal-05535196v1
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[hal-05556397] Dormancy and reactivation of the seed and its microbiome: a holobiont perspective
Desiccation-tolerant seeds provide an intriguing system for studying microbial dormancy, which includes reversible inactivation and reactivation in response to stress. Focusing on bacterial responses to desiccation and rehydration, we offer a holistic interpretation of dormancy and quiescence within the seed holobiont, highlighting both parallels and distinctions between microbes and their plant host. Based on pilot evidence, we propose that microbial dormancy supports persistence throughout the life cycle of desiccation-tolerant seeds. Transcriptomic analyses of seed-transmitted bacteria have identified genes implicated in inactivation and the viable-but-nonculturable state. Our analysis of Xanthomonas citri pv. fuscans illustrates this during seed maturation. However, the signals triggering microbial reactivation and the potential reciprocal interactions between seed dormancy and quiescence, and microbial dormancy, remain unknown. Elucidating this interplay within the seed holobiont could enhance plant growth and health either by promoting seed germination through microbial inoculation or by enabling early detection of seed-transmitted phytopathogens.
ano.nymous@ccsd.cnrs.fr.invalid (Davide Gerna) 03 Apr 2026
https://hal.inrae.fr/hal-05556397v1
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[hal-05293005] T6SS-mediated competition by Stenotrophomonas rhizophila shapes seed-borne bacterial communities and seed-to-seedling transmission dynamics
ABSTRACT Seeds harbor diverse microbial communities important for plant growth and health. During germination, seed exudation triggers intense microbial competition, shaping the communities transmitted to seedlings. This study explores the role of the bacterial type VI secretion system (T6SS)-mediated interference competition in seed microbiota transmission to seedlings. The analysis of T6SS distribution within 180 genome sequences of seed-borne bacterial strains enabled the construction of synthetic communities (SynCom) with different levels of phylogenetic diversity and T6SS richness. These SynComs were inoculated with Stenotrophomonas rhizophila CFBP13503, a bacterial strain possessing an active T6SS in vitro and in planta . The impact of T6SS on SynCom composition was assessed in vitro by comparing CFBP13503 wild-type strain or its isogenic T6SS-deficient mutant co-inoculation. Additionally, the effects of T6SS on bacterial community dynamics during seed-to-seedling transmission were examined following seed-inoculation. The T6SS of S. rhizophila CFBP13503 targets a broad range of bacteria belonging to 5 different orders. The susceptibility of competing bacteria was partly explained by their phylogenetic proximity and metabolic overlap with CFBP13503. Furthermore, the T6SS modulates the relative abundance of specific bacterial taxa during seed-to-seedling transmission, depending on the initial seed inoculum and plant developmental stage. Depending on the sensitivity of the co-inoculated competitors, the T6SS can provide a competitive advantage to CFBP13503, resulting in an increase in population size. Importance The high prevalence of T6SS in seed-borne bacteria supports the importance of T6SS-mediated competition for seed microbiota assembly. In vitro , S. rhizophila CFBP13503 T6SS exerts a strong impact on bacterial community dynamics. The susceptibility to T6SS increases with the phylogenetic and metabolic proximity of bacteria to CFBP13503, suggesting an influence of interspecies trophic patterns in T6SS-mediated competitions. In planta and in soil, CFBP13503 T6SS influences specific bacterial taxa, leading to shifts in bacterial interactions and distinct community dynamics. T6SS-mediated competition plays a pivotal role in shaping seed bacterial communities and the dynamics of seed-to-seedling transitions.
ano.nymous@ccsd.cnrs.fr.invalid (Tiffany Garin) 01 Oct 2025
https://hal.inrae.fr/hal-05293005v1
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[hal-05535831] The center of wheat domestication drives diversity of Clavibacter pathogens
Microbial plant pathogens possess higher diversity in the center of domestication of their host plants than in the introduced geographic area of the corresponding crops. In this study, the center of wheat, barley, and oat domestication in the Iranian Plateau was surveyed to shed light on the population structure, taxonomic diversity, and biology of Clavibacter species associated with these crops. Comprehensive field surveys completed with pathological assays and molecular-phylogenetic analyses showed that phylogenetically diverse groups of Clavibacter strains were associated with bacterial mosaic symptoms on small grain cereals in this domestication center. Besides the two previously described species, Clavibacter tessellarius and Clavibacter zhangzhiyongii , three clades of atypical Clavibacter strains, phylogenetically distinct from all described Clavibacter species, were isolated from wheat, barley, and oat in this study. Thus, Clavibacter strains associated with small grain cereals in the center of domestication of these crops belong to at least five taxonomically distinct clades, whereas simultaneous occurrence of multitaxa Clavibacter strains on small grain cereals has never been reported outside the Iranian Plateau. All five phylogenetic Clavibacter clades were capable of inducing mosaic and chlorosis on their host of isolation. Whole genome sequence-based comparative investigations showed that most virulence-associated genomic contents of the five Clavibacter clades isolated in this study were somewhat similar. Data obtained in this study suggest a correlation between the center of wheat, barley, and oat domestication and the high taxonomic diversity of the accompanying Clavibacter pathogens. Additional phylogeographic investigations in the area would strengthen this co-evolutionary hypothesis. IMPORTANCE Members of the gram-positive corynebacterial genus Clavibacter sp. (family Microbacteriaceae ) are seed-borne plant pathogens causing economically important plant diseases on annual crops and vegetables. While comprehensive global-scale studies have been conducted to study the population structure of Clavibacter species infecting tomato, potato, and pepper, phylogenomics investigations have not yet been conducted to monitor the taxonomic diversity, pathogenicity, and origin of Clavibacter strains pathogenic to small grain cereals. Archaeobotanical investigations suggested that human agriculture was established ≈11,000 years ago in the foothills of the Zagros Mountains in Northwestern Iran, while wheat and barley were among the very first crops domesticated in these areas. Thus, the analyses of taxonomic diversity and population structure of Clavibacter strains in the Iranian Plateau would shed light on the correlation between the center of domestication of these crops and the center of diversity of accompanying bacterial pathogens. Our findings showed that most of the Clavibacter strains isolated from small grain cereals in Iran belonged to the two previously described species Clavibacter tessellarius and Clavibacter zhangzhiyongii , while several strains were grouped in three distinct clades, all representing hypothetical novel species in the genus.
ano.nymous@ccsd.cnrs.fr.invalid (Asma Rahmanzadeh) 02 Apr 2026
https://hal.inrae.fr/hal-05535831v1
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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-05576361] SeqDetectVeg: a major project to develop NGS tools for multi-target detection of bacterial and fungal pathogens transmitted by vegetable seeds
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Mylène Ruh) 01 Apr 2026
https://univ-angers.hal.science/hal-05576361v1
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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-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-04688341] The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings
Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact‐dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed‐to‐seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB , abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild‐type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison with T6SS‐deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomona s genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris .
ano.nymous@ccsd.cnrs.fr.invalid (Tiffany Garin) 05 Sep 2024
https://hal.inrae.fr/hal-04688341v1
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[hal-05462503] Evaluation of cowpea varietal response to bacterial blight in Burkina Faso: Implications for breeding and integrated disease management
Cowpea bacterial blight, caused by Xanthomonas citri pv. vignicola (Burkh.), is increasingly becoming a major constraint to cowpea productivity worldwide. The use of genotypes that are resistant and/or tolerant to the pathogen is an effective means of controlling the disease. In this study, we evaluated the response of 12 cowpea genotypes of Burkina Faso to three strains (CFBP 7111, CFBP 7112, and CFBP 7113) of X. citri pv. vignicola under greenhouse conditions. For each strain, an inoculum of 1 × 10⁸ CFU/mL⁻¹ was used to inoculate two-week-old trifoliate leaves. Parameters assessed included symptom percentage, bacterial population size, yield components, and leaf chlorophyll content. The results revealed that genotype Yiisyandé was the most affected by all strains, with approximately 50% leaf symptom coverage. In contrast, genotype KVx745-11P showed no symptoms for any of the strains. Strain CFBP 7113 generally reached the highest bacterial populations (7.17 log CFU/cm² for genotype Komcallé). KVx745-11P also exhibited the best yield, with an average per plant of 8.83 pods, 14.56 g pod weight, 90.92 seeds, and 13.37 g seed weight. These observations provide a solid basis for incorporating KVx745-11P into breeding programs aimed at developing broad-spectrum, durable resistant cowpea cultivars.
ano.nymous@ccsd.cnrs.fr.invalid (Nanwinyélé Euvaris Somé) 16 Jan 2026
https://hal.science/hal-05462503v1
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[ird-04483657] Celebrating the 20th anniversary of the first Xanthomonas genome sequences – how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and helped developing novel control measures – a perspective from the French network on Xanthomonads
In this Opinion paper, members of the French Network on Xanthomonads give their personal view on what they consider to be some of the groundbreaking discoveries in the field of molecular plant pathology over the past 20 years. By celebrating the 20th anniversary of the first Xanthomonas genome sequences, they explain how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and contributed to the development of novel control measures. Collectively, such new, genomics-enabled perspective will help to ensure sustainable agriculture and conservation of our environment in the future.
ano.nymous@ccsd.cnrs.fr.invalid (Ralf Koebnik) 29 Feb 2024
https://ird.hal.science/ird-04483657v1
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[hal-05263393] Transcriptomic dataset of Phaseolus vulgaris leaves in response to the inoculation of pathogenic Xanthomonas citri pv. fuscans and its type III secretion system-defective mutant hrcV
Xanthomonas citri pv. fuscans (Xcf) and Xanthomonas phaseoli pv. phaseoli (Xpp) are responsible for the Common Bacterial Blight (CBB), a major common bean (Phaseolus vulgaris) disease. The pathogenicity of Xcf and Xpp is known to be dependent upon a functional Type III Secretion System (T3SS) allowing the injection of numerous bacterial Type III Effectors (T3Es) into plant cells. T3Es have been described as able to disrupt plant defence and manipulate plant metabolism. In this work we described the transcriptomic response of one susceptible (Flavert) and one resistant (Vezer) cultivars of P. vulgaris to the inoculation of the virulent strain Xcf CFBP4885 or its avirulent T3SS-defective hrcV mutant (CFBP13802). Leaves of both bean cultivars were infiltrated with water or bacterial suspensions. Inoculated leaves were sampled at 24 or 48 h post inoculation (hpi). The experiment was independently repeated three times for total RNA extraction and sequencing analysis. Library construction and total RNA sequencing were performed with BGISEQ-500 at Beijing Genomics Institute (BGI, Hong-Kong), generating an average of 24M of paired-end reads of 100bp per sample. FastQC was used to check reads quality. Mapping analyses were made using a quasi-mapping alignment from Salmon (version 1.2.1) against the Phaseolus vulgaris reference genome (version 2.1), revealing the expression profiles of 36,978 transcripts in leaf tissues. Fastq raw data and count files from 36 samples are available in the Gene Expression Omnibus (GEO) repository of the National Center for Biotechnology Information (NCBI) under the accession number GSE271236. This dataset is a valuable resource to investigate the role of T3Es in subverting the cellular functions of bean.
ano.nymous@ccsd.cnrs.fr.invalid (Christopher Gihaut) 22 Sep 2025
https://hal.inrae.fr/hal-05263393v1
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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-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-05515835] SeqDetectVeg: a major project to develop a NGS tool for multi-target detection of bacterial and fungal pathogens transmitted by vegetable seeds.
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ano.nymous@ccsd.cnrs.fr.invalid (Mylène Ruh) 17 Feb 2026
https://univ-angers.hal.science/hal-05515835v1
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[hal-05529897] Lactuchelins represent lipopeptide siderophores produced by <i>Pseudomonas lactucae</i> that inhibit <i>Xanthomonas campestris</i>
The seed is a habitat with limited resources and space. Although it is widely accepted that microbial competition is a key driver of the assembly of seed-associated microbial communities, the underlying mechanisms of this competition are not well understood. The initial objective of this work was to assess the importance of contact-independent microbial competition between the phytopathogenic bacterium Xanthomonas campestris pv. campestris 8004 (Xcc8004) and 30 strains representative of the bacterial populations most commonly associated with radish (Raphanus sativus) seeds. We identified Pseudomonas lactucae CFBP 13502 as a potent inhibitor of Xcc8004, mediated by exometabolites, specifically induced by certain seed-borne strains. Transcriptomic analysis linked this inducible activity to the upregulation of a gene cluster encoding a lipopeptide siderophore. Targeted gene deletion in P. lactucae CFBP 13502 confirmed that this cluster is essential for antagonism against Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, strongly supporting iron chelation as the underlying mechanism. Through comparative metabolomics, we elucidated the structure of a family of lipopeptide siderophores, produced by P. lactucae CFBP 13502, which we named lactuchelins. Our findings provide molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seedbased biocontrol strategies against seed-borne phytopathogens.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 27 Feb 2026
https://hal.inrae.fr/hal-05529897v1
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[hal-05101924] Modifications of the bacterial community of rice roots infected by a plant parasitic nematode in infested fields
Meloidogyne graminicola, also known as the rice root-knot nematode, is the most damaging plant parasitic nematode, especially on rice in Asia. This obligate soilborne parasite creates galls that disturb the root morphology and physiology, making plants more susceptible to other diseases (e.g. blast) and / or abiotic stress (e.g. water stress). Since the root microbiome is important for plant health, we assessed the impact of M. graminicola on the root microbiome of rice plants. In this study, we present results obtained from a survey conducted in Northern Vietnam in 2017. We collected infected (with galls) and non-infected roots from three naturally infested rice fields. Using an amplicon barcoding approach, we observed different microbiome composition, diversity and network structures. Interestingly, we observed a higher species richness (24%) and diversity in infected roots but fewer enriched metabolic pathways based on the predicted functional profiling of these microbial communities. Some of these enriched pathways were related to pyruvate fermentation and TCA cycle. Differential abundance testing analyses highlighted that species such as Flavobacterium succinicans and Ensifer adhaerens were respectively enriched in non-infected and infected roots. Additionally, the infected community network was denser and more connected, and we identified specific hub taxa that could be keystones in these infected microbiomes. These findings show deep modifications of the rice root microbiome composition and functions when exposed to the parasitic pressure of M. graminicola. The identified indicator taxa and pathways could be used in future studies as markers of rice root infection.
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Masson) 06 Jun 2025
https://hal.science/hal-05101924v1
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[hal-05290191] Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations
Drought is a critical risk in developing countries for staple crops like common bean ( Phaseolus vulgaris L.). We conducted an experiment to understand the legacy effects of repeated drought exposure across plant generations on the root and rhizosphere microbiome of the common bean, hypothesizing that a legacy of exposure improves overall plant microbiome resilience. We profiled the bacterial microbiome using marker gene amplicon sequencing over two plant generations in a complete factorial design for two common bean genotypes, Red Hawk and Flavert. We performed parallel experiments for Red Hawk in two different countries using soils of Pays de la Loire, France, and Michigan, USA. Despite the clear and relatively consistent drought effects on the plant phenotypes, there was neither response of the Red Hawk microbiomes to drought, nor a notable legacy of drought exposure. For Flavert, there was a minor legacy drought effect for the second generation in the rhizosphere microbiome beta diversity. This study demonstrates that rhizosphere microbiomes can be resistant to drought stress and that cross-generational legacy depends on soil origin and host genotype. Such parallel experiments across countries, while difficult to implement, are useful to inform generalities and build theory towards prediction on microbiome responses to global change.
ano.nymous@ccsd.cnrs.fr.invalid (A. Fina Bintarti) 30 Sep 2025
https://hal.science/hal-05290191v1
