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1. Inhibition of broomrape germination by 2,4‐diacetylphloroglucinol produced by environmental Pseudomonas

Author

Tristan Lurthy, Ségolène Perot, Florence Gerin‐Eveillard, Marjolaine Rey, Florence Wisniewski‐Dyé, Jordan Vacheron, and Claire Prigent‐Combaret

Subjects
Biotechnology, TP248.13-248.65
Abstract

Abstract Parasitic weeds such as broomrapes (Phelipanche ramosa and Orobanche cumana) cause severe damage to crops and their development must be controlled. Given that phloroglucinol compounds (PGCs) produced by environmental Pseudomonas could be toxic towards certain plants, we assessed the potential herbicidal effect of the bacterial model Pseudomonas ogarae F113, a PGCs‐producing bacterium, on parasitic weed. By combining the use of a mutagenesis approach and of pure PGCs, we evaluated the in vitro effect of PGC‐produced by P. ogarae F113 on broomrape germination and assessed the protective activity of a PGC‐producing bacteria on oilseed rape (Brassica napus) against P. ramosa in non‐sterile soils. We showed that the inhibition of the germination depends on the PGCs molecular structure and their concentrations as well as the broomrape species and pathovars. This inhibition caused by the PGCs is irreversible, causing a brown coloration of the broomrape seeds. The inoculation of PGCs‐producing bacteria limited the broomrape infection of P. ramosa, without affecting the host growth. Moreover, elemental profiling analysis of oilseed rape revealed that neither F113 nor applied PGCs affected the nutrition capacity of the oilseed rape host. Our study expands the knowledge on plant‐beneficial Pseudomonas as weed biocontrol agents and opens new avenues for the development of natural bioherbicides to enhance crop yield.

Published
2023
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2. Dimethylpolysulfides production as the major mechanism behind wheat fungal pathogen biocontrol, by Arthrobacter and Microbacterium actinomycetes

Author

Aline Ballot, Jeanne Dore, Marjolaine Rey, Guillaume Meiffren, Thierry Langin, Pierre Joly, Assia Dreux-Zigha, Ahmed Taibi, and Claire Prigent-Combaret

Subjects
Bacteria-fungus interactions, wheat fungal pathogens, Microbacterium, Arthrobacter, volatile organic compounds (VOCs), biocontrol, Microbiology, QR1-502
Abstract

ABSTRACT Volatile organic compounds (VOCs) produced by plant-associated microorganisms could serve as natural biocontrol compounds. In this work, we investigate the potential of wheat rhizosphere Microbacterium and Arthrobacter actinomycetes to inhibit the growth of major wheat phytopathogenic fungi, Fusarium graminearum and Zymoseptoria tritici via production of antifungal VOCs. A correlative analysis between fungal-growth inhibition versus bacterial volatilomic profiles identified four dimethylpolysulfide (DMPS) VOCs as the main active compounds behind their biocontrol potential. Subsequent inhibition assays reveal that DMTriS (dimethyltrisulfide) exhibits the strongest inhibition effects, then dimethyldisulfide (DMDiS). Further investigation focuses on the mechanisms behind F. graminearum-growth inhibition by the most active strain Microbacterium JM188 in dual culture. Surprisingly, nine interaction-induced VOCs, including two fungal sesquiterpenes, were exclusively detected in dual cultures, suggesting a complex interplay between microbial VOC production and sensing. More importantly, all JM188 VOCs, including antifungal DMPS, were less abundant in dual cultures, suggesting an uptake of bacterial VOCs by the fungus. Quantification of pure DMPS after confrontation with F. graminearum confirmed complete and partial uptake by the fungus of DMTriS and DMDiS VOCs, respectively, suggesting a potential link between the fungal uptake level of bacterial VOCs and their toxicity. Finally, we demonstrated that F. graminearum growth inhibition leads to a complete depletion of DON (deoxynivalenol) carcinogenic mycotoxins, highlighting a significant modulation of fungal metabolism. Collectively, these results pinpoint DMPS as broad-range fungal-inhibiting VOCs produced by rhizosphere Microbacterium and Arthrobacter, and emphasize the extensive VOC-mediated interplay between bacterial biocontrol agents and fungal pathogens. IMPORTANCE As the management of wheat fungal diseases becomes increasingly challenging, the use of bacterial agents with biocontrol potential against the two major wheat phytopathogens, Fusarium graminearum and Zymoseptoria tritici, may prove to be an interesting alternative to conventional pest management. Here, we have shown that dimethylpolysulfide volatiles are ubiquitously and predominantly produced by wheat-associated Microbacterium and Arthrobacter actinomycetes, displaying antifungal activity against both pathogens. By limiting pathogen growth and DON virulence factor production, the use of such DMPS-producing strains as soil biocontrol inoculants could limit the supply of pathogen inocula in soil and plant residues, providing an attractive alternative to dimethyldisulfide fumigant, which has many non-targeted toxicities. Notably, this study demonstrates the importance of bacterial volatile organic compound uptake by inhibited F. graminearum, providing new insights for the study of volatiles-mediated toxicity mechanisms within bacteria-fungus signaling crosstalk.

Published
2023
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3. Dark-zone alterations expand throughout Paleolithic Lascaux Cave despite spatial heterogeneity of the cave microbiome

Author

Zélia Bontemps, Claire Prigent-Combaret, Alice Guillmot, Mylène Hugoni, and Yvan Moënne-Loccoz

Subjects
Lascaux Cave, Cave alteration, Decisional matrix, Anthropization, Unbalanced microbiota, Dark zones, Environmental sciences, GE1-350, Microbiology, QR1-502
Abstract

Abstract Background Cave anthropization related to rock art tourism can lead to cave microbiota imbalance and microbial alterations threatening Paleolithic artwork, but the underpinning microbial changes are poorly understood. Caves can be microbiologically heterogeneous and certain rock wall alterations may develop in different rooms despite probable spatial heterogeneity of the cave microbiome, suggesting that a same surface alteration might involve a subset of cosmopolitan taxa widespread in each cave room. We tested this hypothesis in Lascaux, by comparing recent alterations (dark zones) and nearby unmarked surfaces in nine locations within the cave. Results Illumina MiSeq metabarcoding of unmarked surfaces confirmed microbiome heterogeneity of the cave. Against this background, the microbial communities of unmarked and altered surfaces differed at each location. The use of a decision matrix showed that microbiota changes in relation to dark zone formation could differ according to location, but dark zones from different locations displayed microbial similarities. Thus, dark zones harbor bacterial and fungal taxa that are cosmopolitan at the scale of Lascaux, as well as dark zone-specific taxa present (i) at all locations in the cave (i.e. the six bacterial genera Microbacterium, Actinophytocola, Lactobacillus, Bosea, Neochlamydia and Tsukamurella) or (ii) only at particular locations within Lascaux. Scanning electron microscopy observations and most qPCR data evidenced microbial proliferation in dark zones. Conclusion Findings point to the proliferation of different types of taxa in dark zones, i.e. Lascaux-cosmopolitan bacteria and fungi, dark zone-specific bacteria present at all locations, and dark zone-specific bacteria and fungi present at certain locations only. This probably explains why dark zones could form in various areas of the cave and suggests that the spread of these alterations might continue according to the area of distribution of key widespread taxa.

Published
2023
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4. Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-Producing Azospirillum PGPR

Author

Jordan Valente, Florence Gerin, Agathe Mini, Rohan Richard, Jacques Le Gouis, Claire Prigent-Combaret, and Yvan Moënne-Loccoz

Subjects
Azospirillum, GWAS, IAA, PGPR, QTL, root, Biology (General), QH301-705.5
Abstract

Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the seedling colonization by the PGPR and the expression of the phenylpyruvate decarboxylase gene ppdC (for synthesis of the auxin indole-3-acetic acid), using gusA fusions. Then, the effects of the PGPR on the selected accessions stimulating Sp245 (or not) were compared in soil under stress. Finally, a genome-wide association approach was implemented to identify the quantitative trait loci (QTL) associated with PGPR interaction. Overall, the ancient genotypes were more effective than the modern genotypes for Azospirillum root colonization and ppdC expression. In non-sterile soil, A. baldaniorum Sp245 improved wheat performance for three of the four PGPR-stimulating genotypes and none of the four non-PGPR-stimulating genotypes. The genome-wide association did not identify any region for root colonization but revealed 22 regions spread on 11 wheat chromosomes for ppdC expression and/or ppdC induction rate. This is the first QTL study focusing on molecular interaction with PGPR bacteria. The molecular markers identified provide the possibility to improve the capacity of modern wheat genotypes to interact with Sp245, as well as, potentially, other Azospirillum strains.

Published
2023
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5. The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review

Author

Afeez Adesina Adedayo, Olubukola Oluranti Babalola, Claire Prigent-Combaret, Cristina Cruz, Marius Stefan, Funso Kutu, and Bernard R. Glick

Subjects
Biocontrol, Biofertilizer, Environmental health, Food safety, Plant health, Tomato, Medicine, Biology (General), QH301-705.5
Abstract

Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria’s structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere soil. These bacteria also help tomato plants acquire essential nutrients like potassium (K), magnesium (Mg), phosphorus (P), and nitrogen (N). Some rhizobacteria may offer a solution to low tomato production and help tackle food insecurity and farming problems. In this review, an overview of soil-inhabiting rhizobacteria focused on improving the sustainable production of Solanum lycopersicum.

Published
2022
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6. Secondary metabolites from plant‐associated Pseudomonas are overproduced in biofilm

Author

Laura Rieusset, Marjolaine Rey, Daniel Muller, Jordan Vacheron, Florence Gerin, Audrey Dubost, Gilles Comte, and Claire Prigent‐Combaret

Subjects
Biotechnology, TP248.13-248.65
Abstract

Summary Plant rhizosphere soil houses complex microbial communities in which microorganisms are often involved in intraspecies as well as interspecies and inter‐kingdom signalling networks. Some members of these networks can improve plant health thanks to an important diversity of bioactive secondary metabolites. In this competitive environment, the ability to form biofilms may provide major advantages to microorganisms. With the aim of highlighting the impact of bacterial lifestyle on secondary metabolites production, we performed a metabolomic analysis on four fluorescent Pseudomonas strains cultivated in planktonic and biofilm colony conditions. The untargeted metabolomic analysis led to the detection of hundreds of secondary metabolites in culture extracts. Comparison between biofilm and planktonic conditions showed that bacterial lifestyle is a key factor influencing Pseudomonas metabolome. More than 50% of the detected metabolites were differentially produced according to planktonic or biofilm lifestyles, with the four Pseudomonas strains overproducing several secondary metabolites in biofilm conditions. In parallel, metabolomic analysis associated with genomic prediction and a molecular networking approach enabled us to evaluate the impact of bacterial lifestyle on chemically identified secondary metabolites, more precisely involved in microbial interactions and plant‐growth promotion. Notably, this work highlights the major effect of biofilm lifestyle on acyl‐homoserine lactone and phenazine production in P. chlororaphis strains.

Published
2020
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7. Field Site-Specific Effects of an Azospirillum Seed Inoculant on Key Microbial Functional Groups in the Rhizosphere

Author

Sébastien Renoud, Jordan Vacheron, Danis Abrouk, Claire Prigent-Combaret, Laurent Legendre, Daniel Muller, and Yvan Moënne-Loccoz

Subjects
microbial functional group, PGPR, inoculation, nitrogen fixers, ACC deaminase producers, 4-diacetylphloroglucinol producers, Microbiology, QR1-502
Abstract

The beneficial effects of plant growth–promoting Rhizobacteria (PGPR) entail several interaction mechanisms with the plant or with other root-associated microorganisms. These microbial functions are carried out by multiple taxa within functional groups and contribute to rhizosphere functioning. It is likely that the inoculation of additional PGPR cells will modify the ecology of these functional groups. We also hypothesized that the inoculation effects on functional groups are site specific, similarly as the PGPR phytostimulation effects themselves. To test this, we assessed in the rhizosphere of field-grown maize the effect of seed inoculation with the phytostimulatory PGPR Azospirillum lipoferum CRT1 on the size and/or diversity of selected microbial functional groups important for plant growth, using quantitative polymerase chain reaction and/or Illumina MiSeq metabarcoding. The functional groups included bacteria able to fix nitrogen (a key nutrient for plant growth), producers of 1-aminocyclopropane-1-carboxylate (ACC) deaminase (which modulate ethylene metabolism in plant and stimulate root growth), and producers of 2,4-diacetylphloroglucinol (an auxinic signal enhancing root branching). To test the hypothesis that such ecological effects were site-specific, the functional groups were monitored at three different field sites, with four sampling times over two consecutive years. Despite poor inoculant survival, inoculation enhanced maize growth. It also increased the size of functional groups in the three field sites, at the maize six-leaf and flowering stages for diazotrophs and only at flowering stage for ACC deaminase and 2,4-diacetylphloroglucinol producers. Sequencing done in the second year revealed that inoculation modified the composition of diazotrophs (and of the total bacterial community) and to a lesser extent of ACC deaminase producers. This study revealed an ecological impact that was field specific (even though a few taxa were impacted in all fields) and of unexpected magnitude with the phytostimulatory Azospirillum inoculant, when considering microbial functional groups. Further methodological developments are needed to monitor additional functional groups important for soil functioning and plant growth under optimal or stress conditions.

Published
2022
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8. Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads

Author

Sofija Andrić, Thibault Meyer, Augustin Rigolet, Claire Prigent-Combaret, Monica Höfte, Guillaume Balleux, Sébastien Steels, Grégory Hoff, René De Mot, Andrea McCann, Edwin De Pauw, Anthony Argüelles Arias, and Marc Ongena

Subjects
Bacillus velezensis, molecular cross-talk, Pseudomonas, bioactive secondary metabolites, cyclic lipopeptides, microbial ecology, Microbiology, QR1-502
Abstract

ABSTRACT Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera. IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.

Published
2021
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9. Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities

Author

Beatriz Manriquez, Daniel Muller, and Claire Prigent-Combaret

Subjects
experimental evolution, synthetic community, interaction network, microbiota, holobiont, evolutionary adaptation, Microbiology, QR1-502
Abstract

In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of microbial communities to new (and often complex) environments can be tackled with a combination of experimental evolution and next generation sequencing. This combination allows to analyse the real-time evolution of microbial populations in response to imposed environmental factors or during the interaction with a host, by screening for phenotypic and genotypic changes over a multitude of identical experimental cycles. Experimental evolution (EE) coupled with comparative genomics has indeed facilitated the monitoring of bacterial genetic evolution and the understanding of adaptive evolution processes. Basically, EE studies had long been done on single strains, allowing to reveal the dynamics and genetic targets of natural selection and to uncover the correlation between genetic and phenotypic adaptive changes. However, species are always evolving in relation with other species and have to adapt not only to the environment itself but also to the biotic environment dynamically shaped by the other species. Nowadays, there is a growing interest to apply EE on microbial communities evolving under natural environments. In this paper, we provide a non-exhaustive review of microbial EE studies done with systems of increasing complexity (from single species, to synthetic communities and natural communities) and with a particular focus on studies between plants and plant-associated microorganisms. We highlight some of the mechanisms controlling the functioning of microbial species and their adaptive responses to environment changes and emphasize the importance of considering bacterial communities and complex environments in EE studies.

Published
2021
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10. Wheat Metabolite Interferences on Fluorescent Pseudomonas Physiology Modify Wheat Metabolome through an Ecological Feedback

Author

Laura Rieusset, Marjolaine Rey, Florence Wisniewski-Dyé, Claire Prigent-Combaret, and Gilles Comte

Subjects
Pseudomonas, wheat, secondary metabolites, plant–bacteria interaction, metabolomics, ecological feedback, Microbiology, QR1-502
Abstract

Plant roots exude a wide variety of secondary metabolites able to attract and/or control a large diversity of microbial species. In return, among the root microbiota, some bacteria can promote plant development. Among these, Pseudomonas are known to produce a wide diversity of secondary metabolites that could have biological activity on the host plant and other soil microorganisms. We previously showed that wheat can interfere with Pseudomonas secondary metabolism production through its root metabolites. Interestingly, production of Pseudomonas bioactive metabolites, such as phloroglucinol, phenazines, pyrrolnitrin, or acyl homoserine lactones, are modified in the presence of wheat root extracts. A new cross metabolomic approach was then performed to evaluate if wheat metabolic interferences on Pseudomonas secondary metabolites production have consequences on wheat metabolome itself. Two different Pseudomonas strains were conditioned by wheat root extracts from two genotypes, leading to modification of bacterial secondary metabolites production. Bacterial cells were then inoculated on each wheat genotypes. Then, wheat root metabolomes were analyzed by untargeted metabolomic, and metabolites from the Adular genotype were characterized by molecular network. This allows us to evaluate if wheat differently recognizes the bacterial cells that have already been into contact with plants and highlights bioactive metabolites involved in wheat—Pseudomonas interaction.

Published
2022
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11. Effect of Inoculation Level on the Impact of the PGPR Azospirillum lipoferum CRT1 on Selected Microbial Functional Groups in the Rhizosphere of Field Maize

Author

Sébastien Renoud, Danis Abrouk, Claire Prigent-Combaret, Florence Wisniewski-Dyé, Laurent Legendre, Yvan Moënne-Loccoz, and Daniel Muller

Subjects
functional community, diazotrophs, nitrogen fixers, ACC deaminase producers, Biology (General), QH301-705.5
Abstract

The impact of inoculated plant growth-promoting rhizobacteria (PGPR) on its host physiology and nutrition depends on inoculum level. Whether the impact of the inoculated PGPR on the indigenous rhizosphere microbiota also varies with the PGPR inoculum level is unclear. Here, we tested this issue using the PGPR Azospirillum lipoferum CRT1—maize model system, where the initial seed inoculation is known to enhance maize growth and germination, and impacts the maize rhizomicrobiota, including microbial functional groups modulating plant growth. A. lipoferum CRT1 was added to the seeds at standard (105–6 cells.seed−1) or reduced (104–5 cells.seed−1) inoculation levels, in three fields. The effect of the two PGPR formulations was assessed on maize growth and on the nifH (nitrogen fixation), acdS (ACC deaminase activity) and phlD (2,4-diacetylphloroglucinol production) microbial functional groups. The size of the three functional groups was monitored by qPCR at the six-leaf stage and the flowering stage, and the diversity of the nifH and acdS functional groups (as well as the bacterial community) were estimated by MiSeq metabarcoding at the six-leaf stage. The results showed that the benefits of the reduced inoculant formulation were significant in two out of three fields, but different (often lower) than those of the standard formulation. The effects of formulations on the size of the three functional groups differed, and depended on field site and functional group. The reduced formulation had an impact on the diversity of nifH and acdS groups at one site, whereas the standard formulation had an impact at the two other sites. Inoculation significantly impacted the total bacterial community in the three fields, but only with the reduced formulation. In conclusion, the reduced inoculant formulation impacted the indigenous rhizosphere microbiota differently, but not less efficiently, than the standard formulation.

Published
2022
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12. Differential Contribution of Plant-Beneficial Functions from Pseudomonas kilonensis F113 to Root System Architecture Alterations in Arabidopsis thaliana and Zea mays

Author

Jordan Vacheron, Guilhem Desbrosses, Sébastien Renoud, Rosa Padilla, Vincent Walker, Daniel Muller, and Claire Prigent-Combaret

Subjects
Microbiology, QR1-502, Botany, QK1-989
Abstract

Fluorescent pseudomonads are playing key roles in plant-bacteria symbiotic interactions due to the multiple plant-beneficial functions (PBFs) they are harboring. The relative contributions of PBFs to plant-stimulatory effects of the well-known plant growth-promoting rhizobacteria Pseudomonas kilonensis F113 (formerly P. fluorescens F113) were investigated using a genetic approach. To this end, several deletion mutants were constructed, simple mutants ΔphlD (impaired in the biosynthesis of 2,4-diacetylphloroglucinol [DAPG]), ΔacdS (deficient in 1-aminocyclopropane-1-carboxylate deaminase activity), Δgcd (glucose dehydrogenase deficient, impaired in phosphate solubilization), and ΔnirS (nitrite reductase deficient), and a quadruple mutant (deficient in the four PBFs mentioned above). Every PBF activity was quantified in the wild-type strain and the five deletion mutants. This approach revealed few functional interactions between PBFs in vitro. In particular, biosynthesis of glucose dehydrogenase severely reduced the production of DAPG. Contrariwise, the DAPG production impacted positively, but to a lesser extent, phosphate solubilization. Inoculation of the F113 wild-type strain on Arabidopsis thaliana Col-0 and maize seedlings modified the root architecture of both plants. Mutant strain inoculations revealed that the relative contribution of each PBF differed according to the measured plant traits and that F113 plant-stimulatory effects did not correspond to the sum of each PBF relative contribution. Indeed, two PBF genes (ΔacdS and ΔnirS) had a significant impact on root-system architecture from both model plants, in in vitro and in vivo conditions. The current work underscored that few F113 PBFs seem to interact between each other in the free-living bacterial cells, whereas they control in concert Arabidopsis thaliana and maize growth and development.

Published
2018
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13. Does in vitro selection of biocontrol agents guarantee success in planta? A study case of wheat protection against Fusarium seedling blight by soil bacteria.

Author

Yoann Besset-Manzoni, Pierre Joly, Aline Brutel, Florence Gerin, Olivier Soudière, Thierry Langin, and Claire Prigent-Combaret

Subjects
Medicine, Science
Abstract

Biological control is a great hope for reducing the overutilization of pesticides in agricultural soils. It often involves microorganisms or molecules produced by microorganisms that will be able to interact with either a plant or pathogens of this plant to reduce the growth of the pathogen and limit its negative impact on the host plant. When new biocontrol products are developed, strains were mostly selected based on their ability to inhibit a pathogen of interest under in vitro conditions via antagonistic effects. Strains with no in vitro effect are often discarded and not tested in planta. But is the in vitro selection of bacterial agents according to their antagonism activities towards a plant pathogen the best way to get effective biocontrol products? To answer this question, we used wheat and the fungal pathogen Fusarium graminearum as a study pathosystem model. A library of 205 soil bacteria was screened in 2 types of in vitro growth inhibition tests against F. graminearum, and in an in planta experiment. We find strains which do not have inhibition phenotypes in vitro but good efficacy in planta. Interestingly, some strains belong to species (Microbacterium, Arthrobacter, Variovorax) that are not known in the literature for their ability to protect plants against fungal pathogens. Thus, developing a biocontrol product against F. graminearum must be preferentially based on the direct screening of strains for their protective activity on wheat plants against fungal diseases, rather than on their in vitro antagonistic effects on fungal growth.

Published
2019
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14. A Cross-Metabolomic Approach Shows that Wheat Interferes with Fluorescent Pseudomonas Physiology through Its Root Metabolites

Author

Laura Rieusset, Marjolaine Rey, Florence Gerin, Florence Wisniewski-Dyé, Claire Prigent-Combaret, and Gilles Comte

Subjects
Pseudomonas, wheat, secondary metabolites, plant-bacteria interaction, metabolomic, signaling, Microbiology, QR1-502
Abstract

Roots contain a wide variety of secondary metabolites. Some of them are exudated in the rhizosphere, where they are able to attract and/or control a large diversity of microbial species. In return, the rhizomicrobiota can promote plant health and development. Some rhizobacteria belonging to the Pseudomonas genus are known to produce a wide diversity of secondary metabolites that can exert a biological activity on the host plant and on other soil microorganisms. Nevertheless, the impact of the host plant on the production of bioactive metabolites by Pseudomonas is still poorly understood. To characterize the impact of plants on the secondary metabolism of Pseudomonas, a cross-metabolomic approach has been developed. Five different fluorescent Pseudomonas strains were thus cultivated in the presence of a low concentration of wheat root extracts recovered from three wheat genotypes. Analysis of our metabolomic workflow revealed that the production of several Pseudomonas secondary metabolites was significantly modulated when bacteria were cultivated with root extracts, including metabolites involved in plant-beneficial properties.

Published
2021
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15. Distribution of 2,4-Diacetylphloroglucinol Biosynthetic Genes among the Pseudomonas spp. Reveals Unexpected Polyphyletism

Author

Juliana Almario, Maxime Bruto, Jordan Vacheron, Claire Prigent-Combaret, Yvan Moënne-Loccoz, and Daniel Muller

Subjects
DAPG, 2,4-diacetylphloroglucinol, phl Operon, biocontrol agent, phlACBD genes, Microbiology, QR1-502
Abstract

Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG+Pseudomonas strains in the “P. corrugata” and “P. protegens” subgroups of the “Pseudomonas fluorescens” group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG+Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp. was investigated in sequenced genomes and type strains. Results showed that the DAPG+Pseudomonas include species of the “P. fluorescens” group, i.e., P. protegens, P. brassicacearum, P. kilonensis, and P. thivervalensis, as expected, as well as P. gingeri in which it had not been documented. Surprisingly, they also include bacteria outside the “P. fluorescens” group, as exemplified by Pseudomonas sp. OT69, and even two Betaproteobacteria genera. The phl operon-based phylogenetic tree was substantially congruent with the one inferred from concatenated housekeeping genes rpoB, gyrB, and rrs. Contrariwise to current supposition, ancestral character reconstructions favored multiple independent acquisitions rather that one ancestral event followed by vertical inheritance. Indeed, based on synteny analyses, these acquisitions appeared to vary according to the Pseudomonas subgroup and even the phylogenetic groups within the subgroups. In conclusion, our study shows that the phl+Pseudomonas populations form a polyphyletic group and suggests that DAPG biosynthesis might not be restricted to this genus. This is important to consider when assessing the ecological significance of phl+ bacterial populations in rhizosphere ecosystems.

Published
2017
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16. Unexpected Phytostimulatory Behavior for Escherichia coli and Agrobacterium tumefaciens Model Strains

Author

Vincent Walker, Maxime Bruto, Floriant Bellvert, René Bally, Daniel Muller, Claire Prigent-Combaret, Yvan Moënne-Loccoz, and Gilles Comte

Subjects
Microbiology, QR1-502, Botany, QK1-989
Abstract

Plant-beneficial effects of bacteria are often underestimated, especially for well-studied strains associated with pathogenicity or originating from other environments. We assessed the impact of seed inoculation with the emblematic bacterial models Agrobacterium tumefaciens C58 (plasmid-cured) or Escherichia coli K-12 on maize seedlings in nonsterile soil. Compared with the noninoculated control, root biomass (with A. tumefaciens or E. coli) and shoot biomass (with A. tumefaciens) were enhanced at 10 days for ‘PR37Y15’ but not ‘DK315’, as found with the phytostimulator Azospirillum brasilense UAP-154 (positive control). In roots as well as in shoots, Agrobacterium tumefaciens and E. coli triggered similar (in PR37Y15) or different (in DK315) changes in the high-performance liquid chromatography profiles of secondary metabolites (especially benzoxazinoids), distinct from those of Azospirillum brasilense UAP-154. Genome sequence analysis revealed homologs of nitrite reductase genes nirK and nirBD and siderophore synthesis genes for Agrobacterium tumefaciens, as well as homologs of nitrite reductase genes nirBD and phosphatase genes phoA and appA in E. coli, whose contribution to phytostimulation will require experimental assessment. In conclusion, the two emblematic bacterial models had a systemic impact on maize secondary metabolism and resulted in unexpected phytostimulation of seedlings in the Azospirillum sp.-responsive cultivar.

Published
2013
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17. Effect of Clay Mineralogy on Iron Bioavailability and Rhizosphere Transcription of 2,4-Diacetylphloroglucinol Biosynthetic Genes in Biocontrol Pseudomonas protegens

Author

Juliana Almario, Claire Prigent-Combaret, Daniel Muller, and Yvan Moënne-Loccoz

Subjects
Microbiology, QR1-502, Botany, QK1-989
Abstract

Pseudomonas strains producing 2,4-diacetylphloroglucinol (DAPG) can protect plants from soilborne phytopathogens and are considered the primary reason for suppressiveness of morainic Swiss soils to Thielaviopsis basicola-mediated black root-rot disease of tobacco, even though they also occur nearby in conducive sandstone soils. The underlying molecular mechanisms accounting for this discrepancy are not understood. In this study, we assessed the hypothesis that the presence of iron-rich vermiculite clay (dominant in suppressive soils) instead of illite (dominant in neighboring conducive soils) translates into higher levels of iron bioavailability and transcription of Pseudomonas DAPG synthetic genes in the tobacco rhizosphere. Rhizosphere monitoring of reporter gene systems pvd-inaZ and phlA-gfp in Pseudomonas protegens indicated that the level of iron bioavailability and the number of cells expressing phl genes (DAPG synthesis), respectively, were higher in vermiculitic than in illitic artificial soils. This was in accordance with the effect of iron on phlA-gfp expression in vitro and, indeed, iron addition to the illitic soil increased the number of cells expressing phlA-gfp. Similar findings were made in the presence of the pathogen T. basicola. Altogether, results substantiate the hypothesis that iron-releasing minerals may confer disease suppressiveness by modulating iron bioavailability in the rhizosphere and expression of biocontrol-relevant genes in antagonistic P. protegens.

Published
2013
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18. Fluorescent Pseudomonas strains with only few plant-beneficial properties are favored in the maize rhizosphere

Author

Jordan VACHERON, Yvan Moënne-Loccoz, Audrey DUBOST, Maximilien Gonçalves-Martins, Daniel Muller, and Claire Prigent-Combaret

Subjects
Maize, PGPR, functional groups, Fluorescent pseudomonas, plant-beneficial properties, Plant culture, SB1-1110
Abstract

Plant Growth-Promoting Rhizobacteria (PGPR) enhance plant health and growth using a variety of traits. Effective PGPR strains typically exhibit multiple plant-beneficial properties, but whether they are better adapted to the rhizosphere than PGPR strains with fewer plant-beneficial properties is unknown. Here, we tested the hypothesis that strains with higher numbers of plant-beneficial properties would be preferentially selected by plant roots. To this end, the co-occurrence of 18 properties involved in enhanced plant nutrition, plant hormone modulation, or pathogen inhibition was analyzed by molecular and biochemical methods in a collection of maize rhizosphere and bulk soil isolates of fluorescent Pseudomonas. Twelve plant-beneficial properties were found among the 698 isolates. Contrarily to expectation, maize preferentially selected pseudomonads with low numbers of plant-beneficial properties (up to five). This selection was not due to the predominance of strains with specific assortments of these properties, or with specific taxonomic status. Therefore, the occurrence of only few plant-beneficial properties appeared favorable for root colonization by pseudomonads.

Published
2016
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19. The Pseudomonas Secondary Metabolite 2,4-Diacetylphloroglucinol Is a Signal Inducing Rhizoplane Expression of Azospirillum Genes Involved in Plant-Growth Promotion

Author

Emeline Combes-Meynet, Joël F. Pothier, Yvan Moënne-Loccoz, and Claire Prigent-Combaret

Subjects
Microbiology, QR1-502, Botany, QK1-989
Abstract

During evolution, plants have become associated with guilds of plant-growth-promoting rhizobacteria (PGPR), which raises the possibility that individual PGPR populations may have developed mechanisms to cointeract with one another on plant roots. We hypothesize that this has resulted in signaling phenomena between different types of PGPR colonizing the same roots. Here, the objective was to determine whether the Pseudomonas secondary metabolite 2,4-diacetylphloroglucinol (DAPG) can act as a signal on Azospirillum PGPR and enhance the phytostimulation effects of the latter. On roots, the DAPG-producing Pseudomonas fluorescens F113 strain but not its phl-negative mutant enhanced the phytostimulatory effect of Azospirillum brasilense Sp245-Rif on wheat. Accordingly, DAPG enhanced Sp245-Rif traits involved in root colonization (cell motility, biofilm formation, and poly-β-hydroxybutyrate production) and phytostimulation (auxin production). A differential fluorescence induction promoter-trapping approach based on flow cytometry was then used to identify Sp245-Rif genes upregulated by DAPG. DAPG enhanced expression of a wide range of Sp245-Rif genes, including genes involved in phytostimulation. Four of them (i.e., ppdC, flgE, nirK, and nifX-nifB) tended to be upregulated on roots in the presence of P. fluorescens F113 compared with its phl-negative mutant. Our results indicate that DAPG can act as a signal by which some beneficial pseudomonads may stimulate plant-beneficial activities of Azospirillum PGPR.

Published
2011
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20. Duplication of Plasmid-Borne Nitrite Reductase Gene nirK in the Wheat-Associated Plant Growth–Promoting Rhizobacterium Azospirillum brasilense Sp245

Author

Joël F. Pothier, Claire Prigent-Combaret, Jacqueline Haurat, Yvan Moënne-Loccoz, and Florence Wisniewski-Dyé

Subjects
genome plasticity, nitrite reduction, PGPR, Microbiology, QR1-502, Botany, QK1-989
Abstract

In the plant growth–promoting rhizobacterium Azospirillum brasilense Sp245, nitric oxide produced by denitrification could be a signal involved in stimulation of root branching, and the dissimilatory nitrite reductase gene nirK is upregulated on wheat roots. Here, it was found that Sp245 did not contain one copy of nirK but two (named nirK1 and nirK2), localized on two different plasmids, including one plasmid prone to rearrangements. Their deduced protein sequences displayed 99.2% identity but their promoter regions and upstream genetic environment differed. Phylogenetic studies revealed that nirK1 and nirK2 clustered next to most β-proteobacterial sequences rather than in the vicinity of other Azospirillum spp. and most α-proteobacterial sequences, regardless of whether DNA or deduced protein sequences were used. This points to past horizontal gene transfers. Analysis of the number of nonsynonymous and synonymous substitutions per site indicated that nirK has been subjected to neutral selection in bacteria. The use of transcriptional fusions with egfp, encoding an enhanced green fluorescent protein variant, revealed that both nirK1 and nirK2 promoter regions were upregulated in vitro under microaerobiosis or the presence of nitrite as well as on wheat roots. The analysis of nirK1 and nirK2 mutants revealed that the two genes were functional. Overall, results suggest that nirK has been acquired horizontally by A. brasilense Sp245 from a distant relative and underwent subsequent duplication; however, both paralogs remained functional and retained their upregulation by the plant partner.

Published
2008
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21. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.

Author

Florence Wisniewski-Dyé, Kirill Borziak, Gurusahai Khalsa-Moyers, Gladys Alexandre, Leonid O Sukharnikov, Kristin Wuichet, Gregory B Hurst, W Hayes McDonald, Jon S Robertson, Valérie Barbe, Alexandra Calteau, Zoé Rouy, Sophie Mangenot, Claire Prigent-Combaret, Philippe Normand, Mickaël Boyer, Patricia Siguier, Yves Dessaux, Claudine Elmerich, Guy Condemine, Ganisan Krishnen, Ivan Kennedy, Andrew H Paterson, Victor González, Patrick Mavingui, and Igor B Zhulin

Subjects
Genetics, QH426-470
Abstract

Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land.

Published
2011
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23. Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-Producing Azospirillum PGPR

Author

Moënne-Loccoz, Jordan Valente, Florence Gerin, Agathe Mini, Rohan Richard, Jacques Le Gouis, Claire Prigent-Combaret, and Yvan

Subjects
Azospirillum, GWAS, IAA, PGPR, QTL, root, wheat
Abstract

Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the seedling colonization by the PGPR and the expression of the phenylpyruvate decarboxylase gene ppdC (for synthesis of the auxin indole-3-acetic acid), using gusA fusions. Then, the effects of the PGPR on the selected accessions stimulating Sp245 (or not) were compared in soil under stress. Finally, a genome-wide association approach was implemented to identify the quantitative trait loci (QTL) associated with PGPR interaction. Overall, the ancient genotypes were more effective than the modern genotypes for Azospirillum root colonization and ppdC expression. In non-sterile soil, A. baldaniorum Sp245 improved wheat performance for three of the four PGPR-stimulating genotypes and none of the four non-PGPR-stimulating genotypes. The genome-wide association did not identify any region for root colonization but revealed 22 regions spread on 11 wheat chromosomes for ppdC expression and/or ppdC induction rate. This is the first QTL study focusing on molecular interaction with PGPR bacteria. The molecular markers identified provide the possibility to improve the capacity of modern wheat genotypes to interact with Sp245, as well as, potentially, other Azospirillum strains.

Published
2023
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24. Biological Controls in Horticulture

Author

Nicolas GUIBERT, Maïder SAINT JEAN, Claire PRIGENT‐COMBARET, Jean‐Marc DEOGRATIAS, Cécile CABASSON, Pierre PÉTRIACQ, PRIGENT-COMBARET, Claire, and DUMAS, Bernard

Published
2022

25. Plant metabolomics to the benefit of crop protection and growth stimulation

Author

Cédric Bertrand, Claire Prigent-Combaret, Azucena González-Coloma, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon

Subjects
0106 biological sciences, Plant metabolomics, Biology, Rhizobacteria, 01 natural sciences, 03 medical and health sciences, Metabolomics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, Abiotic component, 0303 health sciences, business.industry, Crop yield, fungi, food and beverages, Biocontrol, Crop protection, Elicitor, Biotechnology, Metabolic pathway, Biomarker, Biostimulation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany, Volatilomics
Abstract

Biotic and abiotic stresses strongly affect plant growth, quality of production and crop yield. Respectively biocontrol products and biostimulants have been proposed as agronomic tools to counteract those stresses. Research and development on biocontrol and biostimulant products require the study and characterization of the biotic and abiotic interactions involved in these processes. Plant metabolomics approach plays a key role in the identification of chemical mediators involved in these two types of interactions. Metabolomics is a useful tool for the characterization of volatile organic compounds (VOCs) involved in plant-insect interactions, or for the bioguided identification of active compounds from new raw materials. On the other hand, metabolomics approach can be used for the characterization of metabolic pathways affected by plant priming, biostimulant or elicitor application and/or for mechanistic study of Plant-PGPR (Plant Growth Promoting Rhizobacteria) interaction through biomarker specific metabolic fingerprint study.

Published
2021

26. Small-Scale Variability in Bacterial Community Structure in Different Soil Types

Author

Jean Thioulouse, Claire Prigent-Combaret, Naoise Nunan, Geneviève L. Grundmann, Deborah Goffner, Jean M.F. Martins, Mylène Hugoni, Audrey Dubost, Danis Abrouk, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swedish University of Agricultural Sciences (SLU), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut des Géosciences de l’Environnement (IGE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Environnement, Santé, Sociétés (ESS), Centre National de la Recherche Scientifique (CNRS), EC2CO MicrobiEn AO2012779949French National Research Agency (ANR) ANR-11LABX-0010, Unité Mixte Internationale 'Environnement Santé Sociétés' (ESS), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Ecology and Environmental sciences, IEES-Paris, Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Unité de Neurobiologie des canaux Ioniques et de la Synapse (UNIS - Inserm U1072), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and EC2CO MicrobiEn AO2012779949French National Research Agency (ANR)ANR-11LABX-0010

Subjects
0301 basic medicine, 030106 microbiology, Soil Science, Biology, Spatial distribution, Generalist and specialist species, Ecological strategies, 03 medical and health sciences, Soil, Microbial ecology, RNA, Ribosomal, 16S, Ecosystem, Ecology, Evolution, Behavior and Systematics, Spatial organization, Soil Microbiology, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Ecology, Community, Microbiota, Spatial scale, Community structure, Biodiversity, 15. Life on land, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Bacterial diversity, Spatial ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.

Published
2021

27. Author Correction: Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

Author

Samuel Barreto, Michèle Bes, Gery Lamblin, Jean-Philippe Rasigade, Anne Tristan, Daniel Muller, Tristan Ferry, Y. Gillet, François Golfier, Claire Prigent-Combaret, Jean Thioulouse, Danis Abrouk, Gerard Lina, Isaline Jacquemond, Audrey Dubost, Anaëlle Muggeo, Pierre Adrien Bolze, and Claude Alexandre Gustave

Subjects
Adult, Staphylococcus aureus, lcsh:Medicine, medicine.disease_cause, Microbiology, Young Adult, RNA, Ribosomal, 16S, Medicine, DNA Barcoding, Taxonomic, Humans, lcsh:Science, Author Correction, Menstrual Hygiene Products, Multidisciplinary, Bacteria, business.industry, Microbiota, lcsh:R, Staphylococcal Infections, During menstruation, Shock, Septic, Menstruation, Vagina, lcsh:Q, Female, business, Tampon
Abstract

Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons' microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.

Published
2020

28. Vaginal Tampon Colonization by Staphylococcus aureus in Healthy Women

Author

Dorian Bosquet, Alexia Barbry, Claire Prigent-Combaret, Myriam Chiaruzzi, Thibaut Durand, Anne Tristan, Sabine Bourdeau, Gerard Lina, Laurence Cluzeau, Anaëlle Muggeo, Cédric Badiou, Michèle Bes, Isaline Jacquemond, Astrid Engelmann, Daniel Muller, Jean Thioulouse, Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), FINOVI foundation, ANR-11-LABX-0048,ECOFECT,Dynamiques eco-évolutives des maladies infectieuses(2011), ANR-11-IDEX-0007,Avenir L.S.E.,PROJET AVENIR LYON SAINT-ETIENNE(2011), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), THIOULOUSE, Jean, Dynamiques eco-évolutives des maladies infectieuses - - ECOFECT2011 - ANR-11-LABX-0048 - LABX - VALID, and PROJET AVENIR LYON SAINT-ETIENNE - - Avenir L.S.E.2011 - ANR-11-IDEX-0007 - IDEX - VALID

Subjects
medicine.disease_cause, Applied Microbiology and Biotechnology, healthy women, Menstruation, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Prevalence, 0303 health sciences, Ecology, Public and Environmental Health Microbiology, Middle Aged, Staphylococcal Infections, 3. Good health, medicine.anatomical_structure, vagina, Staphylococcus aureus, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Vagina, Female, France, menstruation, Biotechnology, Tampon, Adult, medicine.medical_specialty, Adolescent, Bacterial Toxins, [SDV.MHEP.GEO]Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, Intrauterine device, 03 medical and health sciences, Young Adult, medicine, Humans, Sex organ, Menstrual Hygiene Products, 030304 developmental biology, Gynecology, 030306 microbiology, business.industry, Toxic shock syndrome, Odds ratio, medicine.disease, equipment and supplies, colonization, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.GEO] Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, business, Food Science
Abstract

International audience; Tampons recovered from a cohort of 737 healthy women (median age, 32 years) were analyzed for the presence of Staphylococcus aureus. A total of 198 tampons (27%) were colonized by S. aureus, 28 (4%) by a strain producing toxic shock syndrome toxin 1 (TSST-1). S. aureus was detected more frequently in tampons that did not require an applicator for their insertion (74/233 [32%] versus 90/381 [24%]; odds ratio [OR] = 1.51 [95% confidence interval, 1.04 to 2.17]) and in women who used an intrauterine device for contraception (53/155 [34%] versus 145/572 [27%]; OR = 1.53 [95% confidence interval, 1.05 to 2.24]). The S. aureus strains isolated from tampons belonged to 22 different clonal complexes (CCs). The most prevalent CC was CC398 agr1 (n = 57 [27%]), a clone that does not produce superantigenic toxins, followed by CC30 agr3 (n = 27, 13%), producing TSST-1 (24/27 [89%]), the principal clone of S. aureus involved in menstrual toxic shock syndrome (MTSS).IMPORTANCE Menstrual toxic shock syndrome (MTSS) is an uncommon severe acute disease that occurs in healthy menstruating women colonized by TSST-1producing S. aureus who use intravaginal protection, such as tampons and menstrual cups. The catamenial product collected by the protection serves as a growth medium for S. aureus and allows TSST-1 production. Previous studies evaluated the prevalence of genital colonization by S. aureus by vaginal swabbing, but they did not examine tampon colonization. This study demonstrated a high prevalence of tampon colonization by S. aureus and the presence of the CC30 TSST-1 S. aureus clone responsible for MTSS in tampons from healthy women. The results support the vaginal carriage of this lineage in healthy women. In addition, the higher prevalence of S. aureus within tampons that do not require an applicator indicates a crucial role for handwashing before tampon handling to decrease the risk of tampon contamination.

Published
2020

29. Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

Author

Michèle Bes, Gery Lamblin, Jean Thioulouse, Audrey Dubost, François Golfier, Isaline Jacquemond, Daniel Muller, Anne Tristan, Samuel Barreto, Yves Gillet, Danis Abrouk, Claude Alexandre Gustave, Tristan Ferry, Jean-Philippe Rasigade, Anaëlle Muggeo, Gerard Lina, Pierre Adrien Bolze, Claire Prigent-Combaret, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Hospices Civils de Lyon (HCL), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Centre National de Reference des Staphylocoques, Université de Lyon, Hôpital de la Croix-Rousse [CHU - HCL], Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de Chirurgie Gynécologique Oncologique et Obstétrique [CHU Lyon Sud], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], LABEX ECOFECT of Universite de Lyon within the programme 'Investissements d'Avenir' ANR-11-LABX-0048, ANR-11-IDEX-0007, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Davoine, Laure-Hélène, Service de Chirurgie Gynécologique et Oncologique – Obstétrique [CHU Lyon Sud], Service des Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse, CHU-HCL], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
staphylococcus aureus, 0301 basic medicine, [SDV.IMM] Life Sciences [q-bio]/Immunology, [SDV]Life Sciences [q-bio], femme, 030106 microbiology, microbiome, Virulence, Severe disease, lcsh:Medicine, Biology, [SDV.MHEP.GEO]Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, medicine.disease_cause, Article, Microbiology, 03 medical and health sciences, microbiote, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Microbiome, lcsh:Science, ComputingMilieux_MISCELLANEOUS, cycle menstruel, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, communauté microbienne, Multidisciplinary, lcsh:R, Toxic shock syndrome, santé humaine, medicine.disease, During menstruation, equipment and supplies, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, medicine.anatomical_structure, Staphylococcus aureus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Vagina, [SDV.IMM]Life Sciences [q-bio]/Immunology, lcsh:Q, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Tampon
Abstract

Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons’ microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.

Published
2018

30. Ancient wheat varieties have a higher ability to interact with plant growth‐promoting rhizobacteria

Author

Claire Prigent Combaret, Jordan Valente, Florence Gerin, Jacques Le Gouis, Yvan Moënne-Loccoz, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French National Research Agency (ANR) ANR-14-CE19-0017, and ANR-14-CE19-0017,BacterBlé,Effets phytobénéfiques des rhizobactéries pour l'adaptation du blé à la limitation en azote et au stress hydrique(2014)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Genotype, Physiology, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Plant Science, Rhizobacteria, DAPG, Poaceae, 01 natural sciences, Plant Roots, Crop, 03 medical and health sciences, Soil, genotypes, Rhizobiaceae, wheat, Pseudomonas, Colonization, Plant breeding, Soil Microbiology, Triticum, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 2. Zero hunger, biology, Inoculation, Strain (biology), food and beverages, Nuclear Proteins, biology.organism_classification, phytostimulation, Horticulture, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, breeding, PGPR, fluorescence, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Plant interactions with plant growth-promoting rhizobacteria (PGPR) are highly dependent on plant genotype. Modern plant breeding has largely sought to improve crop performance but with little focus on the optimization of plant x PGPR interactions. The interactions of the model PGPR strain Pseudomonas kilonensis F113 were therefore compared in 199 ancient and modern wheat genotypes. A reporter system, in which F113 colonization and expression of 2,4-diacetylphloroglucinol biosynthetic genes (phl) were measured on roots was used to quantify F113 x wheat interactions under gnotobiotic conditions. Thereafter, eight wheat accessions that differed in their ability to interact with F113 were inoculated with F113 and grown in greenhouse in the absence or presence of stress. F113 colonization was linked to improved stress tolerance. Moreover, F113 colonization and phl expression were higher overall on ancient genotypes than modern genotypes. F113 colonization improved wheat performance in the four genotypes that showed the highest level of phl expression compared with the four genotypes in which phl expression was lowest. Taken together, these data suggest that recent wheat breeding strategies have had a negative impact on the ability of the plants to interact with PGPR.

Published
2019

31. Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov

Author

Daniel Muller, S. M. Taghavi, Vahid Keshavarz-Tohid, Yvan Moënne-Loccoz, Saeed Tarighi, Audrey Dubost, Claire Prigent-Combaret, Parissa Taheri, Jordan Vacheron, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Academic Research cluster 3 of Region Rhone-Alpes, Centre National de la Recherche Scientifique (CNRS), and Vice-Chancellor's office for Research and Technology in Agricultural Science and Environmental Research of Khuzestan, Iran

Subjects
DNA, Bacterial, Sequence analysis, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, Species Specificity, Pseudomonads genomes, Phylogenetics, GGDC, Gene, Ecology, Evolution, Behavior and Systematics, Phylogeny, Soil Microbiology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Genes, Essential, Phylogenetic tree, biology, 030306 microbiology, Pseudomonas putida, Pseudomonas, Nucleic Acid Hybridization, Sequence Analysis, DNA, biology.organism_classification, 16S ribosomal RNA, Phenotype, Genes, Bacterial, Pseudomonas putida group, Bacteria, Genome, Bacterial
Abstract

International audience; Bacteria of the Pseudomonas putida group are studied for a large panel of properties ranging from plant growth promotion and bioremediation to pathogenicity. To date, most of the classification of individual pseudomonads from this group relies on 16S RNA gene analysis, which is insufficient for accurate taxonomic characterization within bacterial species complexes of the Pseudomonas putida group. Here, a collection of 20 of these bacteria, isolated from various soils, was assessed via multi-locus sequence analysis of rpoD, gyrB and rrs genes. The 20 strains clustered in 7 different clades of the P. putida group. One strain per cluster was sequenced and results were compared to complete genome sequences of type strains of the P. putida group. Phylogenetic analyses, average nucleotide identity data and digital DNA hybridizations, combined to phenotypic characteristics, resulted in the proposition and description of four new species i.e. Pseudomonas alloputida Kh7 T (= LMG 29756 T = CFBP 8484 T) sp. nov., Pseudomonas inefficax JV551A3 T (= DSM108619 T = CFBP 8493 T) sp. nov., Pseudomonas persica RUB6 T (= LMG 29757 T = CFBP 8486 T) sp. nov. and Pseudomonas shirazica VM14 T (= LMG 29953 T = CFBP 8487 T) sp. nov.

Published
2019

32. Impacts of Microbial Inoculants on the Growth and Yield of Maize Plant

Author

Elizabeth Temitope Alori, Olubukola Oluranti Babalola, Claire Prigent-Combaret, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
0106 biological sciences, Aflatoxin, Biofertilizer, Soil Science, Biofertilizers, 01 natural sciences, 03 medical and health sciences, Pseudomonas protegens, Soil, Pseudomonas kilonensis, Microbial inoculants, Microbial inoculant, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, Crop yield, Pseudomonas, 15. Life on land, biology.organism_classification, Horticulture, Shoot, Pseudomonas spp, Maize gynotype, Animal Science and Zoology, Agronomy and Crop Science, 010606 plant biology & botany, Biotechnology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Background:The use of microbial inoculants holds a great promise to improve crop yield without the negative environmental and health hazard associated with chemical fertilizer.Aim:To investigate ifPseudomonasspp. (Pseudomonas kilonensisF113 andPseudomonas protegensCHA0 strains) have promoting effects on vegetative growth and yield of different maize genotypes (viz. AFLATOXIN SYN 4W, TZB-SR, AFLATOXIN R SYN 2Y, AFLATOXIN SYN 3W and AFLATOXIN SYN-2Y) under different soil types.Methods:Both pot and field experiments were employed. Bacterialized seeds were sown (2 seeds/pot/stand).Results:Pot experiment showed that both the bacterial species significantly stimulated the growth of maize shoot length, stem girth, leaf length, root length and root weight. The effect of genotypes AFLATOXIN SYN 4W, TZB-SR, AFLATOXIN R SYN 2Y and AFLATOXIN SYN 3W are not significantly different from one another but AFLATOXIN SYN-2Y showed a significantly lower increase in the measured parameters. No significant difference was observed according to soil types. AFLATOXIN SYN 4W showed a significantly higher root weight while AFLATOXIN R SYN 2Y showed a significantly higher root length compared to the other maize genotypes. Moreover,Pseudomonassignificantly increased maize growth and yield under field experiment. AFLATOXIN R SYN 2Y and AFLATOXIN SYN 4W showed a significantly higher yield than the other maize genotypes studied.Conclusion:We concluded thatPseudomonas kilogenensisF113 andPseudomonas protegensCHA0 are potential biofertilizers.

Published
2019

33. Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies

Author

Laura Rieusset, Claire Prigent-Combaret, Pierre Joly, Yoann Besset-Manzoni, Gilles Comte, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire d'Ecologie des Hydrosystèmes Fluviaux (EHF), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), and BIOVITIS (FRANCE)

Subjects
Crops, Agricultural, 0301 basic medicine, genetic structures, Health, Toxicology and Mutagenesis, 030106 microbiology, Biology, Rhizobacteria, microbial cooperation, 03 medical and health sciences, microbial consortium, Sustainable agriculture, Microbial cooperation, Environmental Chemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, biocontrol, Microbial inoculant, Soil Microbiology, ComputingMilieux_MISCELLANEOUS, microbial metabolite, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Rhizosphere, Bacteria, business.industry, Microbiota, fungi, quorum sensing, food and beverages, Agriculture, General Medicine, 15. Life on land, Microbial consortium, Pollution, cell–cell communication, Crop protection, Biotechnology, sustainable agriculture, Microbial population biology, rhizosphere, business, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

National audience; The rhizosphere hosts a considerable microbial community. Among that community, bacteria called plant growth-promoting rhizobacteria (PGPR) can promote plant growth and defense against diseases using diverse distinct plant-beneficial functions. Crop inoculation with PGPR could allow to reduce the use of pesticides and fertilizers in agrosystems. However, microbial crop protection and growth stimulation would be more efficient if cooperation between rhizosphere bacterial populations was taken into account when developing biocontrol agents and biostimulants. Rhizospheric bacteria live in multi-species biofilms formed all along the root surface or sometimes inside the plants (i.e., endophyte). PGPR cooperate with their host plants and also with other microbial populations inside biofilms. These interactions are mediated by a large diversity of microbial metabolites and physical signals that trigger cell–cell communication and appropriate responses. A better understanding of bacterial behavior and microbial cooperation in the rhizosphere could allow for a more successful use of bacteria in sustainable agriculture. This review presents an ecological view of microbial cooperation in agrosystems and lays the emphasis on the main microbial metabolites involved in microbial cooperation, plant health protection, and plant growth stimulation. Eco-friendly inoculant consortia that will foster microbe–microbe and microbe–plant cooperation can be developed to promote crop growth and restore biodiversity and functions lost in agrosystems.

Published
2018

34. Impact of Currently Marketed Tampons and Menstrual Cups on Staphylococcus aureus Growth and Toxic Shock Syndrome Toxin 1 Production In Vitro

Author

Louis Nonfoux, Jean Thioulouse, Jessica Baude, Daniel Muller, Cédric Badiou, Myriam Chiaruzzi, Anne Tristan, Claire Prigent-Combaret, Gerard Lina, Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Physiology, medicine.disease_cause, Applied Microbiology and Biotechnology, law.invention, Enterotoxins, 0302 clinical medicine, law, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS, [STAT.AP]Statistics [stat]/Applications [stat.AP], Superantigens, Ecology, Public and Environmental Health Microbiology, Staphylococcal Infections, Shock, Septic, Staphylococcus aureus, Shock (circulatory), Vagina, Toxic shock syndrome toxin-1, Female, medicine.symptom, [STAT.ME]Statistics [stat]/Methodology [stat.ME], [PHYS.PHYS.PHYS-DATA-AN]Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an], Biotechnology, Tampon, 030106 microbiology, Bacterial Toxins, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, medicine, Humans, Cotton Fiber, Menstrual Hygiene Products, business.industry, Toxin, Toxic shock syndrome, medicine.disease, equipment and supplies, In vitro, Culture Media, Oxygen, Menstrual cup, Biofilms, business, Food Science, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Fifteen currently marketed intravaginal protection products (11 types of tampon and 4 types of menstrual cup) were tested by the modified tampon sac method to determine their effect on Staphylococcus aureus growth and toxic shock syndrome toxin 1 (TSST-1) production. Most tampons reduced S. aureus growth and TSST-1 production, with differences based on brand and composition, and the level of S. aureus growth was higher in destructured than in unaltered tampons. We observed higher levels of S. aureus growth and toxin production in menstrual cups than in tampons, potentially due to the additional air introduced into the bag by cups, with differences based on cup composition and size. IMPORTANCE Menstrual toxic shock syndrome is a rare but severe disease. It occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock syndrome toxin 1 using intravaginal protection, such as tampons or menstrual cups. Intravaginal protection induces TSS by the collection of catamenial products, which act as a growth medium for S. aureus . Previous studies evaluated the impact of tampon composition on S. aureus producing toxic shock syndrome toxin 1, but they are not recent and did not include menstrual cups. This study demonstrates that highly reproducible results for S. aureus growth and TSST-1 production can be obtained by using a simple protocol that reproduces the physiological conditions of tampon and cup usage as closely as possible, providing recommendations for tampon or cup use to both manufacturers and consumers. Notably, our results do not show that menstrual cups are safer than tampons and suggest that they require similar precautions.

Published
2018

35. Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani

Author

Jordan Vacheron, Saeed Tarighi, Yvan Moënne-Loccoz, Seyed Mohsen Taghavi, Parissa Taheri, Daniel Muller, Vahid Keshavarz-Tohid, Claire Prigent-Combaret, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Ferdowsi University of Mashhad (Iran) 3/33365, and CNRS (France)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Iran, Microbiology, Plant Roots, Rhizoctonia, Rhizoctonia solani, 03 medical and health sciences, chemistry.chemical_compound, Pseudomonas, Botany, Antibiosis, Molecular Biology, Phylogeny, Soil Microbiology, Plant Diseases, Rhizosphere, biology, Biocontrol, Fabaceae, General Medicine, Ribosomal RNA, biology.organism_classification, 16S ribosomal RNA, Pyrrolnitrin, Phylogenetic diversity, 030104 developmental biology, chemistry, Chitinase, biology.protein
Abstract

International audience; Fluorescent pseudomonads from bean root and rhizosphere in Iran were investigated for biocontrol of the fungal pathogen Rhizoctonia solani. Phylogenetic analysis of concatenated 16S rRNA, gyrB and rpoD sequences for 33 Pseudomonas isolates showed that 15 belonged to four clusters within the \textquoteleftP. fluorescens' group, i.e. one corresponding to P. thivervalensis, two others including P. moraviensis or P. baetica, and the last one without closely-related established species. The 18 other isolates belonged to five clusters within the \textquoteleftP. putida' group, one including P. mosselii and P. entomophila, another including strains currently described as P. putida, and three without closely-related species described. Ten isolates were selected based on in vitro inhibition of R. solani. Cellulase activity was identified in three pseudomonads, chitinase activity in two pseudomonads, extracellular protease activity in nine pseudomonads and hydrogen cyanide production in two pseudomonads. Genes coding for production of phenazine, pyoluteorin, pyrrolnitrin and 2,4-diacetylphloroglucinol were not found, whereas the 1-aminocyclopropane-1-carboxylate deamination gene acdS was present in three pseudomonads. The antagonistic acdS+ strain VKh13 from the \textquoteleftP. putida' group effectively protected soil-grown bean from R. solani AG 4-HGI. Results show that pseudomonads from uncharacterized taxa were readily obtained from Iranian soils and displayed biocontrol potential against R. solani.

Published
2017

36. Advances in the rhizosphere: stretching the interface of life

Author

Eric J. W. Visser, Philippe Hinsinger, Claire Prigent-Combaret, Liesje Mommer, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), University of Medical Center, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
0106 biological sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Rhizosphere, Ecology, Interface (Java), Ecology (disciplines), Plant Ecology, Soil Science, Plant physiology, Plant Ecology and Nature Conservation, 04 agricultural and veterinary sciences, Plant Science, Biology, PE&RC, 01 natural sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Plantenecologie en Natuurbeheer, Life Science, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany
Abstract

Contains fulltext : 161853.pdf (Publisher’s version ) (Closed access)

Published
2016

37. Expression on roots and contribution to maize phytostimulation of 1-aminocyclopropane-1-decarboxylate deaminase gene acdS in Pseudomonas fluorescens F113

Author

Claire Prigent-Combaret, Daniel Muller, Brigitte Gouesnard, Emeline Combes-Meynet, Jordan Vacheron, Yvan Moënne-Loccoz, Vincent Walker, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Ministere de l'Enseignement Superieur et de la Recherche (Paris), Academic Research Cluster 3 of Rhone-Alpes Region, ANR project SymbioMaize : ANR-12-JSV7-0014-0, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
0301 basic medicine, Soil Science & Conservation, [SDV]Life Sciences [q-bio], 030106 microbiology, Mutant, Soil Science, Maize genotypes, Pseudomonas fluorescens, Plant Science, 03 medical and health sciences, Botany, Gene, Water deficit, 2. Zero hunger, biology, Strain (chemistry), Inoculation, Plant Sciences, Plant physiology, biology.organism_classification, acdS expression, Germination, Plant Physiology, Plant growth promotion, ecology, 1-aminocyclopropane-1-decarboxylate deaminase, Bacteria
Abstract

AGAP : équipe GE2pop; International audience; Aims The plant-beneficial bacterium Pseudomonas fluorescens F113 harbours an acdS gene, which enables deamination of 1-aminocyclopropane-1-carboxylate. The impact of abiotic and biotic factors on the expression of this gene was assessed, as well as the plant-beneficial properties of F113 under different soil moistures. Methods An acdS-egfp biosensor was constructed in F113, validated in vitro and used to analyse, by microscopy, its expression on roots of Zea mays comparatively to Beta vulgaris. An acdS mutant was constructed and compared with the wild-type to characterize plant-beneficial effects of F113 on maize lines EP1 and FV2, under well-watered and water deficit conditions. Results Different patterns of root colonization and acdS expression were observed according to plant genotype. acdS rhizoplane expression was higher on Beta vulgaris, and on maize line FV2 and hybrid PR37Y15 than on maize line EP1 and teosinte. Strain F113 but not its acdS mutant promoted root growth of EP1 under well-watered conditions and germination of FV2 under water deficit conditions. Conclusions Maize lines differed in their ability to induce acdS expression and to respond to P. fluorescens F113. The maize line leading to higher acdS expression, FV2, was the one benefiting from inoculation under water deficit.

Published
2016

38. Bacterial hybrid histidine kinases in plant-bacteria interactions

Author

Claire Prigent-Combaret, Florence Wisniewski-Dyé, Stéphanie Borland, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre National de la Recherche Scientifique (CNRS), Université de Lyon, Université Claude Bernard Lyon 1 (UCBL), Ministere de l'Enseignement Superieur et de la Recherche, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre National de la Recherche Scientifique ( CNRS ), Université de Lyon (COMUE), Université Claude Bernard Lyon 1 ( UCBL ), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
0301 basic medicine, biology, Bacteria, Histidine Kinase, [ SDV ] Life Sciences [q-bio], Kinase, [SDV]Life Sciences [q-bio], 030106 microbiology, Histidine kinase, Gene Expression Regulation, Bacterial, Plants, biology.organism_classification, Microbiology, Two-component regulatory system, Cell biology, 03 medical and health sciences, Response regulator, 030104 developmental biology, Signalling, Biochemistry, Bacterial Proteins, Signal transduction, Histidine
Abstract

Two-component signal transduction systems are essential for many bacteria to maintain homeostasis and adapt to environmental changes. Two-component signal transduction systems typically involve a membrane-bound histidine kinase that senses stimuli, autophosphorylates in the transmitter region and then transfers the phosphoryl group to the receiver domain of a cytoplasmic response regulator that mediates appropriate changes in bacterial physiology. Although usually found on distinct proteins, the transmitter and receiver modules are sometimes fused into a so-called hybrid histidine kinase (HyHK). Such structure results in multiple phosphate transfers that are believed to provide extra-fine-tuning mechanisms and more regulatory checkpoints than classical phosphotransfers. HyHK-based regulation may be crucial for finely tuning gene expression in a heterogeneous environment such as the rhizosphere, where intricate plant–bacteria interactions occur. In this review, we focus on roles fulfilled by bacterial HyHKs in plant-associated bacteria, providing recent findings on the mechanistic of their signalling properties. Recent insights into understanding additive regulatory properties fulfilled by the tethered receiver domain of HyHKs are also addressed.

Published
2016

39. Fluorescent Pseudomonas Strains with only Few Plant-Beneficial Properties Are Favored in the Maize Rhizosphere

Author

Maximilien Gonçalves-Martins, Daniel Muller, Audrey Dubost, Jordan Vacheron, Yvan Moënne-Loccoz, Claire Prigent-Combaret, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), and Academic Research Cluster 3 of Rhone-Alpes Region, ANR project SyinbioMaize ANR-12-JSV7-0014-01

Subjects
0301 basic medicine, Botanics, maïs, [SDV]Life Sciences [q-bio], Bulk soil, Plant Science, lcsh:Plant culture, Rhizobacteria, plant-beneficial properties, 03 medical and health sciences, fluorescent pseudomonas, PGPR, maize, functional groups, Botany, fluorescent Pseudomonas, lcsh:SB1-1110, Colonization, rhizobactérie, pathologie végétale, Pathogen, Original Research, 2. Zero hunger, Rhizosphere, biology, Pseudomonas, fungi, food and beverages, biodégradation, biology.organism_classification, communauté bactérienne, Maize, Botanique, 030104 developmental biology, plante, Functional groups, Plant hormone, pseudomonas fluorescens, Plant nutrition
Abstract

International audience; Plant Growth-Promoting Rhizobacteria (PGPR) enhance plant health and growth using a variety of traits. Effective PGPR strains typically exhibit multiple plant-beneficial properties, but whether they are better adapted to the rhizosphere than PGPR strains with fewer plant-beneficial properties is unknown. Here, we tested the hypothesis that strains with higher numbers of plant-beneficial properties would be preferentially selected by plant roots. To this end, the co-occurrence of 18 properties involved in enhanced plant nutrition, plant hormone modulation, or pathogen inhibition was analyzed by molecular and biochemical methods in a collection of maize rhizosphere and bulk soil isolates of fluorescent Pseudomonas. Twelve plant-beneficial properties were found among the 698 isolates. Contrarily to expectation, maize preferentially selected pseudomonads with low numbers of plant-beneficial properties (up to five). This selection was not due to the predominance of strains with specific assortments of these properties, or with specific taxonomic status. Therefore, the occurrence of only few plant-beneficial properties appeared favorable for root colonization by pseudomonads.

Published
2016

40. Core and Accessory Genomes of the Diazotroph Azospirillum

Author

Florence Wisniewski-Dye, Benoît Drogue, Stéphanie Borland, Claire Prigent-Combaret, Kirill Borziak, Luis Lozano, Patrick Mavingui, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), BioEnergy Science Center, The University of Tennessee [Knoxville], Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Frans J. de Bruijn, Pillet, Lauriane, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

41. Differential responses of Oryza sativa secondary metabolism to biotic interactions with cooperative, commensal and phytopathogenic bacteria

Author

Florence Wisniewski-Dyé, Cédric Bertrand, Claire Prigent-Combaret, Gilles Comte, Amel Chamam, Unité de Recherche Clinique, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Lariboisière, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique, ANR project AZORIZ ANR-08-BLAN-0098, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Lariboisière, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre de recherches insulaires et observatoire de l'environnement ( CRIOBE ), and Université de Perpignan Via Domitia ( UPVD ) -École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Azospirillum lipoferum, Burkholderia, Secondary Metabolism, Plant Science, Secondary metabolite, Rhizobacteria, Oryza, Bacterial Physiological Phenomena, Plant Roots, [ CHIM.ORGA ] Chemical Sciences/Organic chemistry, Gene Expression Regulation, Plant, Botany, Genetics, medicine, Escherichia coli, Secondary metabolism, Plant secondary metabolism, 2. Zero hunger, Flavonoids, Oryza sativa, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, fungi, Hydroxycinnamic acid, food and beverages, 15. Life on land, biology.organism_classification, Rice secondary, Commensalism, Cooperation, Parasitism, metabolite profiling, Bacteria, medicine.drug
Abstract

International audience; Main conclusionProfiling of plant secondary metabolite allows to differentiate the different types of ecological interactions established between rice and bacteria. Rice responds to ecologically distinct bacteria by altering its content of flavonoids and hydroxycinnamic acid derivatives.Plants’ growth and physiology are strongly influenced by the biotic interactions that plants establish with soil bacterial populations. Plants are able to sense and to respond accordingly to ecologically distinct bacteria, by inducing defense pathways against pathogens to prevent parasitic interactions, and by stimulating the growth of root-associated beneficial or commensal bacteria through root exudation. Plant secondary metabolism is expected to play a major role in this control. However, secondary metabolite responses of a same plant to cooperative, commensal and deleterious bacteria have so far never been compared. The impact of the plant growth-promoting rhizobacteria (PGPR) Azospirillum lipoferum 4B on the secondary metabolite profiles of two Oryza sativa L. cultivars (Cigalon and Nipponbare) was compared to that of a rice pathogen Burkholderia glumae AU6208, the causing agent of bacterial panicle blight and of a commensal environmental bacteria Escherichia coli B6. Root and shoot rice extracts were analyzed by reversed-phase high-performance liquid chromatography (RP-HPLC). Principal component analyses (PCAs) pinpointed discriminant secondary metabolites, which were characterized by mass spectrometry. Direct comparison of metabolic profiles evidenced that each bacterial ecological interaction induced distinct qualitative and quantitative modifications of rice secondary metabolism, by altering the content of numerous flavonoid compounds and hydroxycinnamic acid (HCA) derivatives. Secondary metabolism varied according to the cultivars and the interaction types, demonstrating the relevance of secondary metabolic profiling for studying plant–bacteria biotic interactions.

Published
2015

42. Alleviation of Abiotic and Biotic Stresses in Plants by Azospirillum

Author

Claire Prigent-Combaret, Daniel Muller, Jordan Vacheron, Olubukola Oluranti Babalola, Sébastien Renoud, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Fabricio Dario Cassán, Yaacov Okon, Cecilia M. Creus, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
0106 biological sciences, 2. Zero hunger, Abiotic component, 0303 health sciences, 030306 microbiology, Abiotic stress, business.industry, Biofertilizer, [SDV]Life Sciences [q-bio], fungi, food and beverages, 15. Life on land, Biology, Rhizobacteria, 01 natural sciences, Biotechnology, 03 medical and health sciences, 13. Climate action, Sustainable agriculture, Plant defense against herbivory, Soil fertility, business, Microbial inoculant, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany
Abstract

In the face of global changes, plants must adapt to a wide range and often combined biotic and abiotic stresses that seriously impaired plant growth and development. Plants develop complex strategies to deal with water stress conditions, soil fertility losses, soil pollutions, pests, and disease. Emerging evidence suggest the involvement of common hormonal players in plant defense signaling pathways triggered in response to biotic and abiotic stresses. Besides plant strategies, plant growth-promoting rhizobacteria (PGPR), which colonize the root system and establish cooperative interactions with plants can improve their growth and help them to adapt to and cope with multiple stresses including drought, salinity, heavy metal pollutions, and parasites. Accordingly, PGPR supply added values to the plant defense strategies by expressing many relevant functions for modulating the plant hormonal balance, increasing nutrients supply to the plant, improving the functional and physical properties of protective barriers against plant parasites. Among PGPR, Azospirillum strains were long viewed as biofertilizers and less as biocontrol agents. It is becoming evident that Azospirillum is able to protect plants against a myriad of detrimental conditions. This review provides an update of works regarding the ability of Azospirillum strains to alleviate plant stress and brings out the relevant involved plant-beneficial functions. Developing PGPR-based bio-inoculants is a promising strategy to improve the growth and health of crops and develop sustainable agriculture.

Published
2015

43. Plant growth-promoting properties of Pseudomonas biocontrol agent producing 2,4 diacetylphloroglucinol

Author

Jordan Vacheron, Emeline Combes-Meynet, Yvan Moënne-Loccoz, Daniel Muller, Claire Prigent-Combaret, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Cédric Bertrand, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Pillet, Lauriane

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

44. Horizontal Acquisition of Prokaryotic Genes for Eukaryote Functioning and Niche Adaptation

Author

Maxime Bruto, Grégory Hoff, Daniel Muller, Claire Prigent-Combaret, Yvan Moënne-Loccoz, Patricia Luis, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
Ecological niche, Genetics, 0303 health sciences, Lateral gene transfer (LGT), Mechanism (biology), [SDV]Life Sciences [q-bio], Interdomain gene transfer, Biology, biology.organism_classification, HGT dynamic, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, Horizontal gene transfer, Eukaryote, Adaptation, Niche adaptation, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

International audience; Horizontal gene transfer (HGT) is a major mechanism of evolution, in that it is pervasive and can dramatically affect lifestyle by allowing adaptation to specialized niches. Although research has mostly focused on HGT within prokaryotes, examples of inter-domain transfers from prokaryotes to eukaryotes are increasing, and such inter-domain HGT is emerging as a very significant component in ecological and evolutionary terms. Here, different cases of intra- and inter-domain HGT conferring an adaptive advantage to eukaryotes are reviewed to examine novel trends and HGT paradigms. Thus, HGT appears to play an important role in eukaryotic adaptation to specific environmental conditions, including in the ecological evolution toward parasitic lifestyles and pathogenesis. The diversity of prokaryotes and their genetic potential are emerging as a vast reservoir to foster rapid eukaryote evolution.

Published
2013

45. Unexpected phytostimulatory behavior for Escherichia coli and Agrobacterium tumefaciens model strains

Author

Maxime Bruto, René Bally, Gilles Comte, Vincent Walker, Floriant Bellvert, Daniel Muller, Claire Prigent-Combaret, Yvan Moënne-Loccoz, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Département de chimie organique, Université de Genève (UNIGE), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), and Université de Genève ( UNIGE )

Subjects
MESH : Escherichia coli, MESH : Seedling, MESH : Zea mays, MESH : Nitrite Reductases, Physiology, MESH: Zea mays, MESH: Plant Shoots, [SDV]Life Sciences [q-bio], MESH : Plant Roots, MESH: Plant Roots, medicine.disease_cause, Plant Roots, MESH: Biomass, Biomass, 2. Zero hunger, 0303 health sciences, MESH : Biomass, biology, MESH: Escherichia coli, MESH: Agrobacterium tumefaciens, General Medicine, Agrobacterium tumefaciens, MESH : Plant Shoots, MESH : Agrobacterium tumefaciens, Seeds, Shoot, Plant Shoots, Nitrite Reductases, Zea mays, Microbiology, 03 medical and health sciences, Botany, Escherichia coli, medicine, Secondary metabolism, Gene, 030304 developmental biology, [ SDV ] Life Sciences [q-bio], 030306 microbiology, MESH: Nitrite Reductases, Azospirillum brasilense, biology.organism_classification, Nitrite reductase, MESH : Seeds, MESH: Seeds, Seedlings, MESH: Seedling, Agronomy and Crop Science, Bacteria
Abstract

International audience; Plant-beneficial effects of bacteria are often underestimated, especially for well-studied strains associated with pathogenicity or originating from other environments. We assessed the impact of seed inoculation with the emblematic bacterial models Agrobacterium tumefaciens C58 (plasmid-cured) or Escherichia coli K-12 on maize seedlings in nonsterile soil. Compared with the noninoculated control, root biomass (with A. tumefaciens or E. coli) and shoot biomass (with A. tumefaciens) were enhanced at 10 days for 'PR37Y15' but not 'DK315', as found with the phytostimulator Azospirillum brasilense UAP-154 (positive control). In roots as well as in shoots, Agrobacterium tumefaciens and E. coli triggered similar (in PR37Y15) or different (in DK315) changes in the high-performance liquid chromatography profiles of secondary metabolites (especially benzoxazinoids), distinct from those of Azospirillum brasilense UAP-154. Genome sequence analysis revealed homologs of nitrite reductase genes nirK and nirBD and siderophore synthesis genes for Agrobacterium tumefaciens, as well as homologs of nitrite reductase genes nirBD and phosphatase genes phoA and appA in E. coli, whose contribution to phytostimulation will require experimental assessment. In conclusion, the two emblematic bacterial models had a systemic impact on maize secondary metabolism and resulted in unexpected phytostimulation of seedlings in the Azospirillum sp.-responsive cultivar.

Published
2013

46. Comparison of prominent Azospirillum strains in Azospirillum–Pseudomonas–Glomus consortia for promotion of maize growth

Author

Monika Maurhofer, Augusto Ramírez-Trujillo, Gilles Comte, Geneviève Défago, Jesús Caballero-Mellado, Jan Jansa, Yvan Moënne-Loccoz, Andreas von Felten, Olivier Couillerot, Vincent Walker, Claire Prigent-Combaret, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Universidad Autónoma del Estado de México (UAEM), Universidad Nacional Autónoma de México (UNAM), Institute for Integrative Biology [Zürich] (IBZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), and European Union (EU) MicroMaize 036314

Subjects
0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Pseudomonas fluorescens, Rhizobacteria, Real-Time Polymerase Chain Reaction, 01 natural sciences, Applied Microbiology and Biotechnology, Zea mays, Pseudomonas, Botany, Colonization, Glomeromycota, Microbial inoculant, Glomus, 2. Zero hunger, Chemistry and Materials Science, biology, Inoculation, fungi, food and beverages, 04 agricultural and veterinary sciences, General Medicine, biology.organism_classification, Environmental biotechnology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Azospirillum, 010606 plant biology & botany, Biotechnology
Abstract

Azospirillum are prominent plant growth-promoting rhizobacteria (PGPR) extensively used as phytostimulatory crop inoculants, but only few studies are dealing with Azospirillum -containing mixed inocula involving more than two microorganisms. We compared here three prominent Azospirillum strains as part of three-component consortia including also the PGPR Pseudomonas fluorescens F113 and a mycorrhizal inoculant mix composed of three Glomus strains. Inoculant colonization of maize was assessed by quantitative PCR, transcription of auxin synthesis gene ipdC (involved in phytostimulation) in Azospirillum by RT-PCR, and effects on maize by secondary metabolic profiling and shoot biomass measurements. Results showed that phytostimulation by all the three-component consortia was comparable, despite contrasted survival of the Azospirillum strains and different secondary metabolic responses of maize to inoculation. Unexpectedly, the presence of Azospirillum in the inoculum resulted in lower phytostimulation in comparison with the Pseudomonas Glomus two-component consortium, but this effect was transient. Azospirillum 's ipdC gene was transcribed in all treatments, especially with three-component consortia, but not with all plants and samplings. Inoculation had no negative impact on the prevalence of mycorrhizal taxa in roots. In conclusion, this study brought new insights in the functioning of microbial consortia and showed that Azospirillum Pseudomonas Glomus three-component inoculants may be useful in environmental biotechnology for maize growth promotion.

Published
2013

47. Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum-Oryza sativa association

Author

Florence Wisniewski-Dyé, Gilles Comte, Claire Prigent-Combaret, Floriant Bellvert, Hervé Sanguin, Guillaume Meiffren, Amel Chamam, Cédric Bertrand, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], F62 - Physiologie végétale - Croissance et développement, Plant Science, 01 natural sciences, Biochemistry, Root colonization, F01 - Culture des plantes, Cultivar, 2. Zero hunger, 0303 health sciences, Rhizosphere, food and beverages, General Medicine, Phenolic metabolites, Métabolite secondaire, Rendement des cultures, PGPR, Shoot, Azospirillum lipoferum, Host-Pathogen Interactions, medicine.drug, Oryza sativa, Horticulture, Biology, Secondary metabolite, 03 medical and health sciences, Symbiosis, Phenols, Botany, medicine, Croissance, Rhizobactérie, Molecular Biology, Microbial inoculant, 030304 developmental biology, fungi, Secondary metabolite profiling, Oryza, Rhizosphère, Composé phénolique, Aptitude à coloniser, Azospirillum, 010606 plant biology & botany, Racine
Abstract

International audience; Azospirillum is a plant growth-promoting rhizobacterium (PGPR) able to enhance growth and yield of cereals such as rice, maize and wheat. The growth-promoting ability of some Azospirillum strains appears to be highly specific to certain plant species and cultivars. In order to ascertain the specificity of the associative symbiosis between rice and Azospirillum, the physiological response of two rice cultivars, Nipponbare and Cigalon, inoculated with two rice-associated Azospirillum was analyzed at two levels: plant growth response and plant secondary metabolic response. Each strain of Azospirillum (Azospirillum lipoferum 4B isolated from Cigalon and Azospirillum sp. B510 isolated from Nipponbare) preferentially increased growth of the cultivar from which it was isolated. This specific effect is not related to a defect in colonization of host cultivar as each strain colonizes effectively both rice cultivars, either at the rhizoplane (for 4B and B510) and inside the roots (for B510). The metabolic profiling approach showed that, in response to PGPR inoculation, profiles of rice secondary metabolites were modified, with phenolic compounds such as flavonoids and hydroxycinnamic derivatives being the main metabolites affected. Moreover, plant metabolic changes differed according to Azospirillum strain \texttimes cultivar combinations; indeed, 4B induced major secondary metabolic profile modifications only on Cigalon roots, while B510, probably due to its endophytic feature, induced metabolic variations on shoots and roots of both cultivars, triggering a systemic response. Plant secondary metabolite profiling thereby evidences the specific interaction between an Azospirillum strain and its original host cultivar.

Published
2013

48. Control of the Cooperation Between Plant Growth-Promoting Rhizobacteria and Crops by Rhizosphere Signals

Author

Benoît Drogue, Emeline Combes-Meynet, Yvan Moënne-Loccoz, Florence Wisniewski-Dye, Claire Prigent-Combaret, Chautard, Marie-Gabrielle, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
phytohormones, [SDV] Life Sciences [q-bio], antimicrobial compounds, primary and secondary metabolites, [SDV]Life Sciences [q-bio], rhizosphere signals, PGPR, plant‐beneficial genes, spatial population distribution, quorum sensing
Abstract

International audience; Molecular Microbial Ecology of the Rhizosphere covers current knowledge on the molecular basis of plant-microbe interactions in the rhizosphere. Also included in the book are both reviews and research-based chapters describing experimental materials and methods. Edited by a leader in the field, with contributions from authors around the world, Molecular Microbial Ecology of the Rhizosphere brings together the most up-to-date research in this expanding area, and will be a valuable resource for molecular microbiologists and plant soil scientists, as well as upper level students in microbiology, ecology, and agriculture.

Published
2013

49. The nucleoid-associated protein Fis directly modulates the synthesis of cellulose, an essential component of pellicle-biofilms in the phytopathogenic bacterium Dickeya dadantii

Author

Claire Prigent-Combaret, Ouafa Zghidi-Abouzid, Géraldine Effantin, Philippe Lejeune, Sylvie Reverchon, William Nasser, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Trafic et signalisation membranaires chez les bactéries (MTSB), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Microbiologie, adaptation et pathogénie ( MAP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), and Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
MESH : Operator Regions, Genetic, Operator Regions, Genetic, MESH : Molecular Sequence Data, MESH : Operon, MESH : Solanum tuberosum, MESH: Base Sequence, MESH: Virulence, Chicory, MESH: Plant Diseases, Genes, Reporter, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, MESH: Cellulose, MESH: Gene Expression Regulation, Bacterial, Virulence, MESH : Plant Diseases, MESH : Virulence, MESH : beta-Galactosidase, MESH : Enterobacteriaceae, MESH : Genes, Reporter, MESH: beta-Galactosidase, MESH : Biofilms, MESH: Repressor Proteins, MESH: Transcription Initiation Site, Transcription Initiation Site, MESH : Repressor Proteins, MESH : Gene Expression Regulation, Bacterial, MESH: Operon, Molecular Sequence Data, MESH: Biofilms, MESH: Solanum tuberosum, MESH: Artificial Gene Fusion, MESH: Enterobacteriaceae, Enterobacteriaceae, Operon, Cellulose, Plant Diseases, Solanum tuberosum, MESH: Molecular Sequence Data, Base Sequence, MESH : Cellulose, MESH: Genes, Reporter, Gene Expression Regulation, Bacterial, beta-Galactosidase, Artificial Gene Fusion, MESH : Chicory, Repressor Proteins, MESH : Artificial Gene Fusion, MESH : Transcription Initiation Site, MESH: Operator Regions, Genetic, Biofilms, MESH: Chicory, MESH : Base Sequence, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Bacteria use biofilm structures to colonize surfaces and to survive in hostile conditions, and numerous bacteria produce cellulose as a biofilm matrix polymer. Hence, expression of the bcs operon, responsible for cellulose biosynthesis, must be finely regulated in order to allow bacteria to adopt the proper surface-associated behaviours. Here we show that in the phytopathogenic bacterium, Dickeya dadantii, production of cellulose is required for pellicle-biofilm formation and resistance to chlorine treatments. Expression of the bcs operon is growth phase-regulated and is stimulated in biofilms. Furthermore, we unexpectedly found that the nucleoid-associated protein and global regulator of virulence functions, Fis, directly represses bcs operon expression by interacting with an operator that is absent from the bcs operon of animal pathogenic bacteria and the plant pathogenic bacterium Pectobacterium. Moreover, production of cellulose enhances plant surface colonization by D. dadantii. Overall, these data suggest that cellulose production and biofilm formation may be important factors for surface colonization by D. dadantii and its subsequent survival in hostile environments. This report also presents a new example of how bacteria can modulate the action of a global regulator to co-ordinate basic metabolism, virulence and modifications of lifestyle.

Published
2012

50. Which specificity in cooperation between phytostimulating rhizobacteria and plants?

Author

Benoît Drogue, Stéphanie Borland, Hugo Doré, Florence Wisniewski-Dyé, Claire Prigent-Combaret, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
[SDV]Life Sciences [q-bio], Plant Development, Large range, Biology, Rhizobacteria, Bacterial Physiological Phenomena, Microbiology, Plant genotype, 03 medical and health sciences, Bacterial colonization, Symbiosis, Botany, Plant growth-promoting rhizobacteria, Molecular Biology, Soil Microbiology, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Host (biology), Chemotaxis, fungi, food and beverages, General Medicine, Plants, Attraction, Cooperation, Adherence, Host specificity
Abstract

Plant growth-promoting rhizobacteria (PGPR) are found in association with a large range of host plants. Although the subject of plant host specificity has been well studied in parasitic and mutualistic interactions, the question of whether phytostimulating rhizobacteria efficiently interact only with a specific host remains poorly discussed. This review presents elements suggesting the existence of specificity in three-step establishment of associative symbiosis between phytostimulating rhizobacteria and plants: bacterial attraction by the host plant, bacterial colonization of roots, and functioning of associative symbiosis.

Published
2012

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