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Equipe de Recherche Rhizosphère

Daniel Muller

Maître de conférences en Ecologie Microbienne


  • Thèmes de recherches :
    1. Ecologie de la Rhizosphère
    2. Analyse de l’expression des communautés fonctionnelles

Parcours scientifique

  • Thèse en biologie moléculaire et cellulaire. 2004. Université Strasbourg1.
  • Chercheurs en microbiologie (2005 - 2007) Université de Tokyo, Institut des sciences médicales.
  • Postdoctorat ( 2007 - 2008) Ecologie Microbienne, Université Lyon 1.


  • Co-directeur de la thèse de Marie-Lara BOUFFAUD. 2008-2011. Diversité génétique et capacité du maïs à recruter des populations bactériennes rhizosphériques phytobénéfiques.
  • Directeur de la thèse de Juliana ALMARIO. 2009- 2012. Relation entre la propriété phytoprotectrice de synthèse de 2,4 diacétylphloroglucinol par les Pseudomonas fluorescents dans la rhizosphère, et la résistance des sols à la maladie de la pourriture noire des racines de tabac.



  • Keshavarz-Tohid, V., Vacheron, J., Dubost, A., Prigent-Combaret, C., Taheri, P., Tarighi, S., Taghavi, S.M., Moënne-Loccoz, Y., Muller, D., 2019. 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. Systematic and Applied Microbiology.
    Résumé : 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.
    Mots-clés : #3, #ibio, GGDC, group, Pseudomonads genomes.


  • Bouffaud, M.-L., Renoud, S., Dubost, A., Moënne-Loccoz, Y., Muller, D., 2018. 1-Aminocyclopropane-1-carboxylate deaminase producers associated to maize and other Poaceae species. Microbiome 6.
    Mots-clés : #3, #ibio.

  • Ibrahim, N.A.G.A.A., Omar, M.N.A.M., El Heba, G.A.A., Moënne-Loccoz, Y., Prigent-Combaret, C., Muller, D., 2018. Draft Genome Sequence of Plant Growth-Promoting <i>Bacillus altitudinis</i> Strain PAE4. Microbiology Resource Announcements 7.
    Mots-clés : #3.

  • Jacquemond, I., Muggeo, A., Lamblin, G., Tristan, A., Gillet, Y., Bolze, P.A., Bes, M., Gustave, C.A., Rasigade, J.-P., Golfier, F., Ferry, T., Dubost, A., Abrouk, D., Barreto, S., Prigent-Combaret, C., Thioulouse, J., Lina, G., Muller, D., 2018. Complex ecological interactions of Staphylococcus aureus in tampons during menstruation. Scientific Reports 8, 9942.
    Résumé : 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.
    Mots-clés : #3, #ibio.

  • Nonfoux, L., Chiaruzzi, M., Badiou, C., Baude, J., Tristan, A., Thioulouse, J., Muller, D., Prigent-Combaret, C., Lina, G., 2018. Impact of Currently Marketed Tampons and Menstrual Cups on Staphylococcus aureus Growth and Toxic Shock Syndrome Toxin 1 Production In Vitro. Applied and Environmental Microbiology 84, e00351-18.
    Résumé : 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.
    Mots-clés : #3, biofilm, elastomer, fiber, menstrual cup, Staphylococcus aureus, tampon, toxic shock syndrome toxin 1.


  • Almario, J., Bruto, M., Vacheron, J., Prigent-Combaret, C., Moënne-Loccoz, Y., Muller, D., 2017. Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism. Frontiers in Microbiology 8, 1218.
    Résumé : 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.
    Mots-clés : #3, biocontrol agent, DAPG, Diacetylphloroglucinol, phl Operon, phlACBD genes.

  • Lemanceau, P., Blouin, M., Muller, D., Moënne-Loccoz, Y., 2017. Let the Core Microbiota Be Functional. Trends in Plant Science 22, 583-595.
    Résumé : The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness., Recent advances in next-generation sequencing technology have boosted the field of plant–microorganism interactions, especially in rhizosphere ecology., The principle of a core microbiota has been proposed to describe the microbial community that is systematically associated with a given plant genotype., So far, this core microbiota was mostly defined on the basis of DNA sequences with taxonomic value, and not on their functional relevance., However, biogeography studies suggest that microbial reservoirs may differ depending upon soil types, thus questioning the universal distribution of the taxonomic core microbiota under various environmental conditions., The microbiota recruited by a given plant genotype in different environments seems to share greater functional similarity than taxonomic similarity.
    Mots-clés : #3, agroecology, coevolution, core microbiota, holobiont, rhizosphere.

  • Vacheron, J., Desbrosses, G., Renoud, S., Padilla-Aguilar, R.-M., Walker, V., Muller, D., Prigent-Combaret, C., 2017. Differential contribution of plant-beneficial functions from Pseudomonas kilonensis F113 to root system architecture alterations in Arabidopsis thaliana and Zea mays. Molecular Plant-Microbe Interactions MPMI–07.
    Résumé : 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 PGPR 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 [ACC] deaminase activity), Δgcd (glucose dehydrogenase deficient, impaired in phosphate solubilization), and ΔnirS (nitrite reductase deficient) and a quadruple mutant (deficient in the 4 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, whether in in vitro and in vivo conditions. The current work underlined 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.
    Mots-clés : #3, #4.

  • Vacheron, J., Dubost, A., Chapulliot, D., Prigent-Combaret, C., Muller, D., 2017. Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere. Genome Announcements 5, e00122-17.
    Résumé : We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated from the rhizosphere of maize during a greenhouse experiment. JV274 harbors genes involved in flexirubin production (darA and darB genes), bacterial competition (type VI secretion system), and gliding (bacterial motility; type IX secretion system).
    Mots-clés : #3, #4, #ibio.


  • Bouffaud, M.-L., Renoud, S., Moënne-Loccoz, Y., Muller, D., 2016. Is plant evolutionary history impacting recruitment of diazotrophs and nifH expression in the rhizosphere? Scientific Reports 6, 21690.
    Résumé : Is plant evolutionary history impacting recruitment of diazotrophs and <i>nifH</i> expression in the rhizosphere?
    Mots-clés : #3.

  • Vacheron, J., Combes-Meynet, E., Walker, V., Gouesnard, B., Muller, D., Moënne-Loccoz, Y., Prigent-Combaret, C., 2016. Expression on roots and contribution to maize phytostimulation of 1-aminocyclopropane-1-decarboxylate deaminase gene acdS in Pseudomonas fluorescens F113. Plant and Soil 407, 187-202.
    Résumé : 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.
    Mots-clés : #3, #cesn, 1-aminocyclopropane-1-decarboxylate deaminase, acdS expression, ecology, Maize genotypes, Plant growth promotion, Plant Physiology, Plant Sciences, Soil Science & Conservation, Water deficit.

  • Vacheron, J., Moënne-Loccoz, Y., Dubost, A., Gonçalves-Martins, M., Muller, D., Prigent-Combaret, C., 2016. Fluorescent Pseudomonas Strains with only Few Plant-Beneficial Properties Are Favored in the Maize Rhizosphere. Plant Biotic Interactions 7, 1212.
    Résumé : 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.
    Mots-clés : #3, #cesn, #ibio, fluorescent Pseudomonas, Functional groups, Maize, PGPR, plant-beneficial properties.
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  • Lassalle, F., Muller, D., Nesme, X., 2015. Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis. Research in Microbiology.
    Mots-clés : #3, #4.

  • Youenou, B., Favre-Bonté, S., Bodilis, J., Brothier, E., Dubost, A., Muller, D., Nazaret, S., 2015. Comparative genomics of environmental and clinical <i>Stenotrophomonas maltophilia</i> strains with different antibiotic resistance profiles. Genome Biology and Evolution evv161.
    Mots-clés : #3, #8, #ibio.


  • Almario, J., Muller, D., Défago, G., Moënne-Loccoz, Y., 2014. Rhizosphere ecology and phytoprotection in soils naturally suppressive to Thielaviopsis black root rot of tobacco. Environmental Microbiology n/a-n/a.
    Résumé : Soil suppressiveness to disease is an intriguing emerging property in agroecosystems, with important implications since it enables significant protection of susceptible plants from soil-borne pathogens. Unlike many soils where disease suppressiveness requires crop monoculture to establish, certain soils are naturally suppressive to disease, and this type of specific disease suppressiveness is maintained despite crop rotation. Soils naturally suppressive to Thielaviopsis basicola-mediated black root rot of tobacco and other crops occur in Morens region (Switzerland) and have been studied for over 30 years. In Morens, vermiculite-rich suppressive soils formed on morainic deposits while illite-rich conducive soils developed on sandstone, but suppressiveness is of microbial origin. Antagonistic pseudomonads play a role in black root rot suppressiveness, including Pseudomonas protegens (formerly P. fluorescens) CHA0, a major model strain for research. However, other types of rhizobacterial taxa may differ in prevalence between suppressive and conducive soils, suggesting that the microbial basis of black root rot suppressiveness could be far more complex than solely a Pseudomonas property. This first review on black root rot suppressive soils covers early findings on these soils, the significance of recent results, and compares them with other types of suppressive soils in terms of rhizosphere ecology and plant protection mechanisms.
    Mots-clés : #3.

  • Bouffaud, M.-L., Poirier, M.A., Muller, D., Moënne-Loccoz, Y., 2014. Root microbiome relates to plant host evolution in maize and other Poaceae. Environmental Microbiology n/a–n/a.
    Résumé : Prokaryote-eukaryote interactions are primordial, but host selection of its bacterial community remains poorly understood. Since eukaryote evolution affects numerous traits shaping the ecology of their microbiome, we can expect that many evolutionary changes in the former will have the potential to impact on the composition of the latter. Consequently, the more phylogenetically distant the eukaryotic hosts, the more distinct their associated bacterial communities should be. We tested this with plants, by comparing the bacterial communities associated to maize genotypes or other Poaceae. 16S rRNA taxonomic microarray analysis showed that the genetic distance between rhizobacterial communities correlated significantly with the phylogenetic distance (derived from chloroplastic sequences) between Poaceae genotypes. This correlation was also significant when considering specific bacterial populations from all main bacterial divisions, instead of the whole rhizobacterial community. These results indicate that eukaryotic host's evolutionary history can be a significant factor shaping directly the assembly and composition of its associated bacterial compartment.
    Mots-clés : #3.

  • Bruto, M., Prigent-Combaret, C., Luis, P., Moënne-Loccoz, Y., Muller, D., 2014. Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes. Proceedings of the Royal Society B: Biological Sciences 281, 20140848.
    Résumé : Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.
    Mots-clés : #2, #3, adaptive horizontal transfer, inter-domain transfer, lateral gene transfer.

  • Bruto, M., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2014. Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Scientific Reports 4, 6261.
    Mots-clés : #3, #ibio.

  • Donn, S., Almario, J., Muller, D., Moënne-Loccoz, Y., Gupta, V.V.S.R., Kirkegaard, J.A., Richardson, A.E., 2014. Rhizosphere microbial communities associated with Rhizoctonia damage at the field and disease patch scale. Applied Soil Ecology 78, 37-47.
    Résumé : Rhizoctonia solani AG-8 is a major root pathogen in wheat (Triticum aestivum L.) systems worldwide and while natural disease suppression can develop under continuous cropping, this is not always the case. The main aim of our work was to elucidate the rhizosphere microbial community underlying a Rhizoctonia suppressive soil (Avon, South Australia) and to investigate how this community may develop in agricultural soils conducive to disease and of different soil type (Galong and Harden, New South Wales). The Avon suppressive soil community included Asaia spp. and Paenibacillus borealis, which were absent from a paired non-suppressive site. At Galong, soil taken from inside and outside disease patches showed no evidence of suppression, and disease suppression could not be transferred from the suppressive soil to the conducive soil from a different soil type and climatic area. 16S rRNA microarray analysis revealed Pseudomonas spp. were significantly more abundant inside than outside three disease patches at Galong. However, a survey of 32 patches across a range of stubble and tillage treatments at a nearby site showed no correlation between Pseudomonas and disease incidence. R. solani levels were significantly lower when stubble was retained rather than burnt or when nutrients (N, P and S) were incorporated with stubble during the non-crop period. Our results suggest soil type is an important factor for suppressive capability and that where specific disease suppression is absent, agronomic practice to increase soil carbon can encourage a non-specific microbial response that limits disease severity.
    Mots-clés : #3, Disease suppression, qPCR, R. solani AG-8, Rhizosphere microbiome, taxonomic microarray.

  • Kyselková, M., Almario, J., Kopecký, J., Ságová-Marečková, M., Haurat, J., Muller, D., Grundmann, G., Moënne-Loccoz, Y., 2014. Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers′ fields. Environmental Microbiology Reports n/a–n/a.
    Résumé : Very few soil quality indicators include disease suppressiveness criteria. We assessed whether 64 16S rRNA microarray probes whose signals correlated with tobacco black-root-rot suppressiveness in greenhouse analysis, could also discriminate suppressive from conducive soils under field conditions. Rhizobacterial communities of tobacco and wheat sampled in two years from four farmers’ fields of contrasted suppressiveness status were compared. The 64 previously-identified indicator probes correctly classified 72% of 29 field samples, with 9 probes for Azospirillum, Gluconacetobacter, Sphingomonadaceae, Planctomycetes, Mycoplasma, Lactobacillus crispatus and Thermodesulforhabdus providing the best prediction. The whole probe set (1033 probes) revealed strong effects of plant, field location and year on rhizobacterial community composition, and a smaller (7% variance) but significant effect of soil suppressiveness status. 17 additional probes correlating with suppressiveness status in the field (noticeably for Agrobacterium, Methylobacterium, Ochrobactrum) were selected, and combined with the 9 others they improved correct sample classification from 72% to 79% (100% tobacco and 63% wheat samples). Pseudomonas probes were not informative in the field, even those targeting biocontrol pseudomonads producing 2,4-diacetylphloroglucinol, nor was quantitative PCR for 2,4-diacetylphloroglucinol-synthesis gene phlD. This study shows that a subset of 16S rRNA probes targeting diverse rhizobacteria can be useful as suppressiveness indicators under field conditions.
    Mots-clés : #3.

  • Ramírez-Bahena, M.H., Vial, L., Lassalle, F., Diel, B., Chapulliot, D., Daubin, V., Nesme, X., Muller, D., 2014. Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Molecular Phylogenetics and Evolution.
    Résumé : Linear chromosomes are atypical in bacteria and likely a secondary trait derived from ancestral circular molecules. Within the Rhizobiaceae family, whose genome contains at least two chromosomes, a particularity of Agrobacterium fabrum (formerly A. tumefaciens) secondary chromosome (chromid) is to be linear and hairpin-ended thanks to the TelA protelomerase. Linear topology and telA distributions within this bacterial family was screened by pulse field gel electrophoresis and PCR. In A. rubi, A. larrymoorei, Rhizobium skierniewicense, A. viscosum, Agrobacterium sp. NCPPB 1650, and every genomospecies of the biovar 1/A. tumefaciens species complex (including R. pusense, A. radiobacter, A. fabrum, R. nepotum plus seven other unnamed genomospecies), linear chromid topologies were retrieved concomitantly with telA presence, whereas the remote species A. vitis, Allorhizobium undicola, Rhizobium rhizogenes and Ensifer meliloti harbored a circular chromid as well as no telA gene. Moreover, the telA phylogeny is congruent with that of recA used as a marker gene of the Agrobacterium phylogeny. Collectively, these findings strongly suggest that single acquisition of telA by an ancestor was the founding event of a large and diverse clade characterized by the presence of a linear chromid. This clade, characterized by unusual genome architecture, appears to be a relevant candidate to serve as a basis for a possible redefinition of the controversial Agrobacterium genus. In this respect, investigating telA in sequenced genomes allows to both ascertain the place of concerned strains into Agrobacterium spp. and their actual assignation to species/genomospecies in this genus.
    Mots-clés : #3, #4, Bacterial speciation, Genome architecture, Protelomerase, Species complex, TelA.


  • Almario, J., Kyselková, M., Kopecký, J., Ságová-Marečková, M., Muller, D., Grundmann, G., Moënne-Loccoz, Y., 2013. Assessment of the relationship between geologic origin of soil, rhizobacterial community composition and soil receptivity to tobacco black root rot in Savoie region (France). Plant and Soil 1-12.
    Résumé : Background and aims In Morens (Switzerland), soils formed on morainic deposits (which contain vermiculite clay and display particular tobacco rhizobacterial community) are naturally suppressive to Thielaviopsis basicola-mediated tobacco black root rot, but this paradigm was never assessed elsewhere. Here, we tested the relation between geology and disease suppressiveness in neighboring Savoie (France). Methods Two morainic and two sandstone soils from Savoie were compared based on disease receptivity (T. basicola inoculation tests on tobacco), clay mineralogy (X-ray diffraction), tobacco rhizobacterial community composition (16S rRNA gene-based taxonomic microarray) and phlD + Pseudomonas populations involved in 2,4-diacetylphloroglucinol production (real-time PCR and tRFLP). Results Unlike in Morens, in Savoie the morainic soils were receptive to disease whereas T. basicola inoculation did not increase disease level in the sandstone soils. Vermiculite was not present in Savoie soils. The difference in rhizobacterial community composition between Savoie morainic and sandstone soils was significant but modest, and there was little agreement in bacterial taxa discriminating soils of different disease receptivity levels when comparing Morens versus Savoie soils. Finally, phlD + rhizosphere pseudomonads were present at levels comparable to those in Morens soils, but with different diversity patterns. Conclusions The morainic model of black root rot suppressiveness might be restricted to the particular type of moraine occurring in the Morens region, and the low disease receptivity of sandstone soils in neighboring Savoie might be related to other plant-protection mechanisms.
    Mots-clés : #3, 16S microarray, 2,4-Diacetylphloroglucinol, bacterial community, Black root rot, ecology, Moraine, Plant Physiology, Plant Sciences, Real-time PCR, rhizosphere, Soil Science & Conservation, Suppressive soil, Thielaviopsis basicola.

  • Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2013. Effect of Clay Mineralogy on Iron Bioavailability and Rhizosphere Transcription of 2,4-Diacetylphloroglucinol Biosynthetic Genes in Biocontrol <i>Pseudomonas protegens</i>. Molecular Plant-Microbe Interactions 130213113028008.
    Résumé : Pseudomonas strains producing 2,4-diacetylphloroglucinol (DAPG) can protect plants from soil-borne phytopathogens and are considered the primarily 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 mechanism(s) 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 respectively indicated that the level of iron bioavailability and the number of cells expressing phl genes (DAPG synthesis) 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 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.
    Mots-clés : #3.

  • Andres, J., Arsène-Ploetze, F., Barbe, V., Brochier-Armanet, C., Cleiss-Arnold, J., Coppée, J.-Y., Dillies, M.A., Geist, L., Joublin, A., Koechler, S., Lassalle, F., Marchal, M., Médigue, C., Muller, D., Nesme, X., Plewniak, F., Proux, C., Ramirez-Bahena, M.-H., Schenowitz, C., Sismeiro, O., Vallenet, D., Santini, J.-M., Bertin, P.N., 2013. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium Rhizobium sp. NT-26. Genome Biology and Evolution.
    Résumé : Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolise the compound. Here we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonising capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes which enable it to metabolise arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions.
    Mots-clés : #3, #4, arsenic metabolism, motility/biofilm, Rhizobium/Agrobacterium, rhizosphere, transcriptomics/proteomics.

  • Nesme, X., Costechareyre, D., Bahena, M.H.R., Muller, D., Nesme, J., Chapulliot, D., Bertolla, F., Willems, A., Lassalle, F., Vial, L., Lavire, C., 2013. Investigating the species and strain diversity of agrobacteria by MLSA: toward a phylogenetically relevant redefinition of the genus Agrobacterium. Frontiers in Plant-Microbe Interaction.
    Résumé : Agrobacteria is the name usually given to bacteria inducing the crown gall disease to numerous crops. Agrobacteria belong to different species that appeared phylogenetically intermingled with species of rhizobia, the symbiotic bacteria that induce nitrogen fixing nodules to Fabaceae, leading authors to propose the inclusion of agrobacteria within the genus Rhizobium. This proposal was contested by other authors who suggested to keep the early division in Agrobacterium and Rhizobium up to a clarification of the phylogeny. In the present work, we applied the multi-locus sequence analysis method to construct a robust phylogeny of agrobacteria and close relatives in order to clarify their taxonomic positions. Results allowed the clear assignation of bacteria to clades that fit to bona fide species previously defined by genomic methods (i.e. genomospecies). As a consequence MLSA could be used as a proxy to delineate novel species that virtually fit with the genomic definition of a species. Plant pathogenic agrobacteria were found to belong to different genomospecies distributed into three clades. Two clades encompasses species that are either bona fide Rhizobium species such as R. tropici for R. rhizogenes or more different taxa such as R. taibainensis and Allorhizobium undicola for R. vitis. A third clade encompasses all other plant pathogenic agrobacteria as well as benign plant commensals, plant growth promoting rhizobacteria, industrial strains and human opportunists. We propose to consider this large clade for a novel delineation of the genus Agrobacterium. As such, Agrobacterium spp. would include A. rubi, A. larrymooreii, A. skierniewicense (formerly R. skierniewicense), A. viscosum, A. radiobacter (i.e. the genomospecies G4 of Agrobacterium), A. fabrum, A. nepotum (formerly R. nepotum), A. pusense (formerly R. pusense) as well as bona fide genomospecies that have not yet received Latin binominals. An unifying trait of Agrobacterium members is their unique genome architecture characterized by the presence of a linear chromid (e.g. secondary chromosome) and the consequential occurrence in their genome of telA, the gene that encodes the protelomerase required to process the replication of the linear chromid. These particular traits strongly support the present proposal for a renewed definition of the genus Agrobacterium.
    Mots-clés : #4.

  • Vacheron, J., Desbrosses, G., Bouffaud, M.-L., Touraine, B., Moënne-Loccoz, Y., Muller, D., Legendre, L., Wisniewski-Dyé, F., Prigent-Combaret, C., 2013. Plant growth-promoting rhizobacteria and root system functioning. Frontiers in Plant Science - Functional plant Ecology 4, 356.
    Résumé : The rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. Among the latter, plant growth-promoting rhizobacteria (PGPR) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. Modification of root system architecture by PGPR implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development of root hairs. PGPR also modify root functioning, improve plant nutrition and influence the physiology of the whole plant. Recent results provided first clues as to how PGPR signals could trigger these plant responses. Whether local and/or systemic, the plant molecular pathways involved remain often unknown. From an ecological point of view, it emerged that PGPR form coherent functional groups, whose rhizosphere ecology is influenced by a myriad of abiotic and biotic factors in natural and agricultural soils, and these factors can in turn modulate PGPR effects on roots. In this paper, we address novel knowledge and gaps on PGPR modes of action and signals, and highlight recent progress on the links between plant morphological and physiological effects induced by PGPR. We also show the importance of taking into account the size, diversity, and gene expression patterns of PGPR assemblages in the rhizosphere to better understand their impact on plant growth and functioning. Integrating mechanistic and ecological knowledge on PGPR populations in soil will be a prerequisite to develop novel management strategies for sustainable agriculture.
    Mots-clés : #3, #cesn, functional group, ISR, phytohormone, plant nutrition, plant-PGPR cooperation, rhizo-microbiome, rhizosphere.
    Note Note

  • Walker, V., Bruto, M., Bellvert, F., Bally, R., Muller, D., Prigent-Combaret, C., Moënne-Loccoz, Y., Comte, G., 2013. Unexpected Phytostimulatory Behavior for Escherichia coli and Agrobacterium tumefaciens Model Strains. Molecular Plant-Microbe Interactions 26, 495-502.
    Mots-clés : #3, #cesn.


  • Almario, J., Moënne-Loccoz, Y., Muller, D., 2012. Monitoring of the relation between 2,4-diacetylphloroglucinol-producing <i>Pseudomonas</i> and <i>Thielaviopsis basicola</i> populations by real-time PCR in tobacco black root-rot suppressive and conducive soils. Soil Biology and Biochemistry.
    Résumé : Natural suppressiveness of Swiss soils to Thielaviopsis basicola-mediated tobacco black root rot is thought to depend mainly on fluorescent pseudomonads producing the antimicrobial compound 2,4-diacetylphloroglucinol. However, the relation between these phl+ Pseudomonas populations and both the T. basicola population and disease suppressiveness in these soils is unknown, and real-time PCR tools were used to address this issue. Significant rhizosphere levels of phl+ pseudomonads had been evidenced before in suppressive as well as conducive soils, but this was done using culture-based approaches only. Here, a phlD-based real-time PCR method targeting all phlD+ genotypes, unlike the strain-specific real-time PCR methods available so far, was developed and validated (detection limit around 4 log cells g−1 soil and amplification efficiency &gt;80%). When implemented on Swiss soils suppressive or conducive to black root rot, it clarified the hypothesis that suppressiveness does not require higher levels of phlD+ pseudomonads. The parallel assessment of T. basicola population by real-time PCR (method of Huang and Kang, 2010) suggested that suppressiveness was not due to the inability of the pathogen to colonize the rhizosphere and tobacco roots in suppressive soils, but rather that phl+ pseudomonads might act by limiting root penetration by the pathogen in suppressive soils. In conclusion, an effective real-time PCR method was achieved for phlD+ pseudomonads and can be used to monitor this key functional group in various environmental conditions, including here to better understand the ecology of suppressive soils.
    Mots-clés : #3, 2,4-Diacetylphloroglucinol, Biocontrol, Morens, phlD, Pseudomonas, rhizosphere, Suppressive soil, Thielaviopsis basicola.

  • Bouffaud, M.L., Kyselková, M., Gouesnard, B., Grundmann, G., Muller, D., Moënne-Loccoz, Y., 2012. Is diversification history of maize influencing selection of soil bacteria by roots? Molecular Ecology 21, 195–206.
    Résumé : A wide range of plant lines has been propagated by farmers during crop selection and dissemination, but consequences of this crop diversification on plant-microbe interactions have been neglected. Our hypothesis was that crop evolutionary history shaped the way the resulting lines interact with soil bacteria in their rhizospheres. Here, the significance of maize diversification as a factor influencing selection of soil bacteria by seedling roots was assessed by comparing rhizobacterial community composition of inbred lines representing the five main genetic groups of maize, cultivated in a same European soil. Rhizobacterial community composition of 21-day-old seedlings was analysed using a 16S rRNA taxonomic microarray targeting 19 bacterial phyla. Rhizobacterial community composition of inbred lines depended on the maize genetic group. Differences were largely due to the prevalence of certain Betaproteobacteria and especially Burkholderia, as confirmed by quantitative PCR and cloning/sequencing. However, these differences in bacterial root colonization did not correlate with plant microsatellite genetic distances between maize genetic groups or individual lines. Therefore, the genetic structure of maize that arose during crop diversification (resulting in five main groups), but not the extent of maize diversification itself (as determined by maize genetic distances), was a significant factor shaping rhizobacterial community composition of seedlings.
    Mots-clés : #3, bacterial community, plant diversity, rhizosphere, taxonomic microarray, Zea mays.

  • Lett, M.C., Muller, D., Lièvremont, D., Silver, S., Santini, J., 2012. Unified Nomenclature for Genes Involved in Prokaryotic Aerobic Arsenite Oxidation. Journal of Bacteriology 194, 207-208.
    Mots-clés : #3.

  • Ramírez-Bahena, M.H., Nesme, X., Muller, D., 2012. Rapid and simultaneous detection of linear chromosome and large plasmids in Proteobacteria. Journal of Basic Microbiology 736-739.
    Résumé : Bacterial genomic architectures are complex and play important roles in genome evolution. While most bacterial lineage genomes contain a single chromosome often accompanied by plasmids, more and more genomes are described as harboring a linear or a second chromosome. Thus, the development of bacterial genomics leads to the study of bacterial genome architectures. In order to avoid laborious techniques combining several methods, we developed an original plug-free pulsed field gel electrophoresis procedure, that enabled us to co-characterize reproducibly the presence of linear chromosomes and plasmids ranging between 30 kb and 2000 kb in various proteobacterial lineages. (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
    Mots-clés : #3, #4, Chromid, Genome architecture, Pulsed Field Gel Electrophoresis (PFGE).


  • Lassalle, F., Campillo, T., Vial, L., Baude, J., Costechareyre, D., Chapulliot, D., Shams, M., Abrouk, D., Lavire, C., Oger-Desfeux, C., Hommais, F., Gueguen, L., Daubin, V., Muller, D., Nesme, X., 2011. Genomic Species Are Ecological Species as Revealed by Comparative Genomics in <i>Agrobacterium tumefaciens</i>. Genome Biology and Evolution 3, 762-781.
    Résumé : The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species.
    Mots-clés : #3, #4, #cesn, #ibio, Agrobacterium, bacterial evolution, bacterial species, ecological niche, linear chromosome.


  • Arsène-Ploetze, F., Koechler, S., Marchal, M., Coppée, J.Y., Chandler, M., Bonnefoy, V., Brochier-Armanet, C., Barakat, M., Barbe, V., Battaglia-Brunet, F., Bruneel, O., Bryan, C.G., Cleiss-Arnold, J., Cruveiller, S., Erhardt, M., Heinrich-Salmeron, A., Hommais, F., Joulian, C., Krin, E., Lieutaud, A., Lièvremont, D., Michel, C., Muller, D., Ortet, P., Proux, C., Siguier, P., Roche, D., Rouy, Z., Salvignol, G., Slyemi, D., Talla, E., Weiss, S., Weissenbach, J., Médigue, C., Bertin, P.N., 2010. Structure, Function, and Evolution of the <i>Thiomonas</i> spp. Genome. PLoS Genet 6, e1000859.
    Résumé : Recent advances in the field of arsenic microbial metabolism have revealed that bacteria colonize a large panel of highly contaminated environments. Belonging to the order of Burkholderiales, Thiomonas strains are ubiquitous in arsenic-contaminated environments. The genome of one of them, i.e. Thiomonas sp. 3As, was deciphered and compared to the genome of several other Thiomonas strains. We found that their flexible gene pool evolved to allow both the surviving and growth in their peculiar environment. In particular, the acquisition by strains of the same species of different genomic islands conferred heavy metal resistance and metabolic idiosyncrasies. Our comparative genomic analyses suggest that the natural environment influences the genomic evolution of these bacteria. Importantly, these results highlight the genomic variability that may exist inside a taxonomic group, enlarging the concept of bacterial species.
    Mots-clés : #3, #5.

  • Couillerot, O., Bouffaud, M. L., Baudoin, E., Muller, D., Caballero-Mellado, J., Moënne-Loccoz, Y., 2010. Development of a real-time PCR method to quantify the PGPR strain <i>Azospirillum lipoferum</i> CRT1 on maize seedlings. Soil Biology and Biochemistry 42, 2298-2305.
    Résumé : Azospirillum lipoferum CRT1 is a promising phytostimulatory PGPR for maize, whose effect on the plant is cell density-dependent. A nested PCR method is available for detection of the strain but does not allow quantification. The objective was to develop a real-time PCR method for quantification of A. lipoferum CRT1 in the rhizosphere of maize seedlings. Primers were designed based on a strain-specific RFLP marker, and their specificity was verified under qualitative and quantitative PCR conditions based on successful CRT1 amplification and absence of cross-reaction with genomic DNA from various rhizosphere strains. Real-time PCR conditions were then optimized using DNA from inoculated or non-inoculated maize rhizosphere samples. The detection limit was 60 fg DNA (corresponding to 19 cells) with pure cultures and 4 × 104 CFU equivalents g−1 lyophilized sample consisting of mixture of rhizosphere soil and roots. Inoculant quantification was effective down to 104 CFU equivalents g−1. Assessment of CRT1 rhizosphere levels in a field trial was in accordance with estimates from semi-quantitative PCR targeting another locus. This real-time PCR method, which is now available for direct rhizosphere monitoring of A. lipoferum CRT1 in greenhouse and field experiments, could be used as a reference for developing quantification tools for other Azospirillum inoculants.
    Mots-clés : #3, Azospirillum, Inoculant quantification, PGPR, Real-time PCR, Root colonization.

  • Lieutaud, A., Lis, R.V., Duval, S., Capowiez, L., Muller, D., Lebrun, R., Lignon, S., Fardeau, M.L., Lett, M.C., Nitschke, W., Schoepp-Cothenet, B., 2010. Arsenite Oxidase from <i>Ralstonia</i> sp. 22 Characterization of the enzyme and its interaction with soluble cytochromes. Journal of Biological Chemistry 285, 20433-20441.
    Résumé : We characterized the aro arsenite oxidation system in the novel strain Ralstonia sp. 22, a β-proteobacterium isolated from soil samples of the Salsigne mine in southern France. The inducible aro system consists of a heterodimeric membrane-associated enzyme reacting with a dedicated soluble cytochrome c554. Our biochemical results suggest that the weak association of the enzyme to the membrane probably arises from a still unknown interaction partner. Analysis of the phylogeny of the aro gene cluster revealed that it results from a lateral gene transfer from a species closely related to Achromobacter sp. SY8. This constitutes the first clear cut case of such a transfer in the Aro phylogeny. The biochemical study of the enzyme demonstrates that it can accommodate in vitro various cytochromes, two of which, c552 and c554, are from the parent species. Cytochrome c552 belongs to the sox and not the aro system. Kinetic studies furthermore established that sulfite and sulfide, substrates of the sox system, are both inhibitors of Aro activity. These results reinforce the idea that sulfur and arsenic metabolism are linked.
    Mots-clés : #3, Arsenite Oxidase, Bacterial Metabolism, Bioenergetics, Cytochrome c, Electron Transfer, Enzyme Kinetics, Enzyme Purification, Evolution.


  • Quéméneur, M., Heinrich-Salmeron, A., Muller, D., Lièvremont, D., Jauzein, M., Bertin, P.N., Garrido, F., Joulian, C., 2008. Diversity Surveys and Evolutionary Relationships of <i>aoxB</i> Genes in Aerobic Arsenite-Oxidizing Bacteria. Applied and Environmental Microbiology 74, 4567-4573.
    Résumé : A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.
    Mots-clés : #3.


  • Muller, D., Médigue, C., Koechler, S., Barbe, V., Barakat, M., Talla, E., Bonnefoy, V., Krin, E., Arsène-Ploetze, F., Carapito, C., Chandler, M., Cournoyer, B., Cruveiller, S., Dossat, C., Duval, S., Heymann, M., Leize, E., Lieutaud, A., Lièvremont, D., Makita, Y., Mangenot, S., Nitschke, W., Ortet, P., Perdrial, N., Schoepp, B., Siguier, P., Simeonova, D.D., Rouy, Z., Segurens, B., Turlin, E., Vallenet, D., Dorsselaer, A.V., Weiss, S., Weissenbach, J., Lett, M.C., Danchin, A., Bertin, P.N., 2007. A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments. PLoS Genet 3, e53.
    Résumé : Microorganisms play a crucial role in nutrient biogeochemical cycles. Arsenic is found throughout the environment from both natural and anthropogenic sources. Its inorganic forms are highly toxic and impair the physiology of most higher organisms. Arsenic contamination of groundwater supplies is giving rise to increasingly severe human health problems in both developing and industrial countries. In the present work, we investigated the metabolism of this metalloid in Herminiimonas arsenicoxydans, a representative organism of a novel bacterial genus widespread in aquatic environments. Examination of the genome sequence and experimental evidence revealed that it is remarkably capable of coping with arsenic. Our observations support the existence of multiple strategies allowing arsenic-metabolizing microbes to efficiently colonize toxic environments. In particular, arsenic oxidation and scavenging may have played a crucial role in the development of early stages of life on Earth. Such mechanisms may one day be exploited as part of a potential bioremediation strategy in toxic environments.
    Mots-clés : #3, #6.

Chapitre d’ouvrages


  • Vacheron, J., Combes-Meynet, E., Bellvert, F., Moënne-Loccoz, Y., Muller, D., Prigent-Combaret, C., 2015. Plant growth-promoting properties of Pseudomonas biocontrol agent producing 2,4 diacetylphloroglucinol, dans: Natural Products And Biocontrol.
    Mots-clés : #3, #cesn.

  • Vacheron, J., Renoud, S., Muller, D., Babalola, O.O., Prigent-Combaret, C., 2015. Alleviation of Abiotic and Biotic Stresses in Plants by Azospirillum, dans: Cassán, F.D., Okon, Y., Creus, C.M. (Éd.), Handbook For Azospirillum. Springer International Publishing, p. 333-365.
    Résumé : 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.
    Mots-clés : Eukaryotic Microbiology, Mycology.


  • Bruto, M., Prigent-Combaret, C., Luis, P., Hoff, G., Moënne-Loccoz, Y., Muller, D., 2013. Horizontal Acquisition of Prokaryotic Genes for Eukaryote Functioning and Niche Adaptation, dans: Pontarotti, P. (Éd.), Evolutionary Biology: Exobiology And Evolutionary Mechanisms. Springer Berlin Heidelberg, p. 165-179.
    Résumé : 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.
    Mots-clés : #2, #3, Animal Genetics and Genomics, Animal Systematics/Taxonomy/Biogeography, Biodiversity, evolutionary biology, HGT dynamic, Interdomain gene transfer, Lateral gene transfer (LGT), Plant Genetics & Genomics, Plant Systematics/Taxonomy/Biogeography.


  • Shams, M., Campillo, T., Lavire, C., Muller, D., Nesme, X., Vial, L., 2012. Rapid and efficient methods to isolate, type strains and determine species of <i>Agrobacterium</i> spp. in pure culture and complex environments, dans: Biochemical Testing. InTech, Purdue University, USA.
    Mots-clés : #3, #4, #cesn.



  • Vacheron, J., Muller, D., Prigent-Combaret, C., 2012. Journal de bord des ARCs 2012/2013.
    Résumé : Brève dans le journal des ARC 2012

Communications Orales



  • Renoud, S., Bouffaud, M.L., Moënne-Loccoz, Y., Muller, D., 2014. Influence de l’histoire évolutive des céréales sur deux groupes fonctionnels phytobénéfiques bactériens, dans: . Aussois, France.
    Résumé : Les plantes, par l’intermédiaire de leurs exsudats racinaires, influencent le fonctionnement du rhizo-microbiome de façon différente selon le génotype de plante rencontré, entre ou au sein d’une espèce de plante. Nous avons observé une relation entre la structure taxonomique de la communauté microbienne et l’histoire évolutive des Poacées, mais ceci nous donne peu d’information sur le fonctionnement des communautés rhizosphériques. Nous avons testé l’hypothèse d’une influence de l’histoire évolutive végétale sur deux groupes fonctionnels de bactéries phytobénéfiques. D’une part le groupe des fixateurs d’azote qui a un rôle dans la croissance de la plante en améliorant la nutrition azotée. D’autre part le groupe fonctionnel possédant le gène acdS codant pour l’ACC désaminase, une enzyme modulant la production de l’éthylène en dégradant le précurseur de cette hormone. L’abondance de ces deux groupes fonctionnels, analysée par (RT) PCR quantitative, était peu influencée par la lignée de plante (maïs, blé, sorgho et téosinte). De plus, le gène acdS n’est exprimé qu’en présence de la plante, alors que nifH est exprimé à des niveaux similaires dans le sol non-planté et en présence de la plante. La diversité des groupes fonctionnels, étudiée par T-RFLP, montre que les populations hébergeant le gène ne l’expriment pas toutes. En conclusion, la comparaison des distances phylogénétiques entre les céréales indique que l’histoire évolutive des Poacées ne semble pas être le facteur influençant les deux groupes fonctionnels.
    Mots-clés : #3, #colloque.
  • Vacheron, J., Muller, D., Prigent-Combaret, C., 2014. Impact of abiotic conditions on the distribution of plant-beneficial functions in fluorescent Pseudomonads, dans: . Présenté à 11ème Rencontre Plantes-bactéries, communication orale, Aussois, France.
    Résumé : La croissance des plantes est fortement influencée par les interactions qu’elles établissent avec les microorganismes du sol. Les plantes vont sélectionner via leurs exsudats racinaires, une communauté microbienne spécifique. En retour, certaines bactéries de cette communauté, qualifiées de PGPR (Plant Growth-Promoting Rhizobacteria) sont capables de stimuler la croissance de nombreuses céréales comme le maïs, grâce à l’expression d’une large variété de fonctions phytobénéfiques (Richardson et al. 2009 Plant Soil 321:305; Vacheron et al. 2013 Front. Plant Sci. 4:356). Aujourd’hui, la distribution de ces fonctions phytobénéfiques chez les bactéries est encore mal connue. Cependant, le séquençage récent de différents génomes de PGPR couplé à des approches de génomique comparative a montré qu’une même bactérie PGPR peut posséder plusieurs fonctions phytobénéfiques (i.e. fonctions co-occurentes). Des réseaux de régulation particuliers seraient impliqués dans le contrôle de l’expression de ces fonctions les unes par rapport aux autres, favorisant leur synergie et in fine leur efficacité sur le végétal (Bashan et de Bashan 2010 Adv. Agron. 108:77). Dans cette étude, la distribution de fonctions phytobénéfiques chez une collection d’isolats rhizosphériques, appartenant à un groupe bactérien bien connu dans la littérature pour comporter de nombreuses bactéries PGPR, le groupe des Pseudomonas fluorescents, a été considérée en prenant en compte le sol et la variété de maïs d’origine des isolats obtenus. Les premiers résultats montrent une influence d’au moins un des deux paramètres sur la répartition des fonctions phytobénéfiques chez ce groupe bactérien.
    Mots-clés : #colloque.


  • Almario, J., Moënne-Loccoz, Y., Muller, D., 2012. Monitoring natural populations of 2,4-diacetylphloroglucinol-producing Pseudomonas spp. in tobacco black root-rot suppressive and conducive soils through a new real-time PCR method, dans: . Présenté à 10th Plant-Bacteria Interactions Meeting, Aussois, France.
    Mots-clés : #colloque.
    Note Note
  • Almario, J., Moënne-Loccoz, Y., Muller, D., 2012. Suivi par PCR quantitative des populations de Pseudomonas phyto-protectrices dans la rhizosphère de sols résistants ou sensibles à la maladie de la pourriture noire des racines de tabac, dans: .
    Résumé : Les bactéries Pseudomonas vivant en association avec les racines des plantes et produisant le composé antifongique 2,4-diacétylphloroglucinol (DAPG) jouent un rôle prépondérant dans la résistance de certains sols à des maladies causées par des pathogènes racinaires. Dans les sols résistants à la maladie de la pourriture noire des racines de tabac, ces bactéries antagonistes peuvent limiter les dégâts causés par le pathogène Thielaviopsis basicola sans qu'un lien entre leur densité et le niveau de protection (résistance des sols) n'ait pu être établi par des approches culturales. Dans cette étude, une méthode de PCR quantitative ciblant de manière globale les différentes espèces de Pseudomonas produisant du DAPG a été développée pour suivre ce groupe fonctionnel dans la rhizosphère. Cette méthode a été couplée à une analyse de t-RFLP pour suivre aussi la diversité de ces bactéries. Les effectifs et la diversité de ces Pseudomonas ainsi que la densité du pathogène ont été suivis en parallèle dans les racines et la rhizosphère de plants de tabac cultivés en serre dans quatre sols résistants ou sensibles. Contrairement aux approches culturales, cette méthode a permis de mettre en évidence des différences de densité des Pseudomonas producteurs de DAPG entre les sols, mais elles semblent indépendantes du statut résistant/sensible du sol dans la mesure où les plus hauts effectifs ont été rencontrés dans un sol sensible. Des variations dans les effectifs et la diversité de ces bactéries liées à la densité du pathogène ont pu aussi être observées. La méthode développée ici permet de suivre les populations de Pseudomonas producteurs de DAPG dans la rhizosphère, en alternative aux méthodes culturales traditionnellement utilisées, et avec des applications dépassant le cadre de l'étude des sols résistants.
    Mots-clés : #3, #colloque.
  • Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2012. Relation between landscape distribution of disease-suppressive soils, iron bioavailability for biocontrol Pseudomonas on roots, and rhizosphere expression of genes for 2,4-diacetylphloroglucinol synthesis, dans: . Présenté à 14th International Symposium on Microbial Ecology ISME14, Copenhagen, Denmark.
  • Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2012. Effect of clay mineralogy on the plant-protecting activity of Pseudomonas in the rhizosphere, dans: . Présenté à 2nd meeting of Ph.D. students in Ecology, Evolution, Microbiology and Modelization, Villeurbanne, France.
    Mots-clés : #colloque.
    Note Note
  • Bruto, M., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y., 2012. Etude génomique des déterminants codant les propriétés phytobénéfiques des Protéobactéries, dans: . Présenté à 10th Plant-Bacteria Interactions Meeting, Aussois, France.
    Résumé : Le développement et la croissance des plantes sont fortement influencés par les symbioses mutualistes ou associatives avec des bactéries du sol. Parmi elles, les symbioses associatives (coopérations) restent mal connues, car elles impliquent une grande diversité de taxons bactériens et de propriétés phytobénéfiques. Notre objectif est de comprendre, par des approches génomiques, la distribution et l'évolution des gènes codant des propriétés phytobénéfiques chez les Proteobactéries en symbiose associative avec la plante. Vingt de ces gènes parmi les plus emblématiques ont été recherchés dans les génomes séquencés de bactéries symbiotiques associatives, mais aussi de bactéries mutualistes ou parasites de plantes (BLAST). La majorité des gènes étudiés présente une distribution dépendante de la phylogénie, comme par exemple ph/D (synthèse de 2,4- diacétylphloroglucinol) chez les Pseudomonadaceae, le type d'interaction biotique étant d'importance moindre. Néanmoins, certains gènes sont davantage ubiquistes, comme acdS (désamination de l'l-aminocyclopropane-1- carboxylate) et pqqABCD (production de pyrroloquinoline). Une approche couplant génomique comparative et analyse phylogénétique est en cours pour estimer les transferts horizontaux, que nous avons mis en évidence dans le cas d' hcnB (synthèse d'acide cyanhydrique) et de ses orthologues putatifs. Ces résultats illustrent l'intérêt des approches de génomique pour mieux comprendre la diversité et l'évolution des bactéries favorisant la croissance des plantes
    Mots-clés : #3, #colloque.
  • Bruto, M., Prigent-Combaret, C., Moënne-Loccoz, Y., Muller, D., 2012. Extensive interkingdom horizontal transfers of 1-aminocyclopropane-1-carboxylate deaminase genes between bacteria and filamentous microeukaryotes, dans: . Présenté à 16th Evolutionary Biology Meeting at Marseille, Marseille France.
    Mots-clés : #colloque.
    Note Note
  • Campillo, T., Baude, J., Vial, L., Bellvert, F., Lassalle, F., Gaillard, V., Muller, D., Kerzaon, I., Hommais, F., Lavire, C., Nesme, X., 2012. Particularités génomiques et adaptations spécifiques des espèces bactériennes : cas d'Agrobacterium fabrum, dans: . Aussois, France.
    Résumé : Des groupes de souches distincts et génomiquement cohérents structurent la diversité bactérienne de manière discontinue permettant de caractériser des clades à partir desquels sont définis les espèces et les genres. L'existence de ces groupes très bien délimités résulte vraisemblablement de leurs adaptations à des niches écologiques spécifiques qui les isoleraient des espèces apparentées. Afin de tester cette hypothèse, les particularités génomiques "spécifiques" de l'une des espèces génomiques du complexe d'espèces Agrobacterium tumefaciens ont été recherchées afin d'en caractériser les adaptations écologiques "spécifiques". Sept régions de gènes "spécifiques" ont ainsi été mises en évidence chez A. fabrum (le nouveau nom du génomovar 08 d' A. tumefaciens dont la souche-type est C58). Par une approche d'écologie inverse, la caractérisation de ces régions génomiques a ensuite été entreprise afin de découvrir les adaptations écologiques spécifiques associées. Ceci a permis de mettre en évidence des phénotypes "spécifiques" d' A.fabrum parmis lesquelles nous avons plus particulièrement étudié l'aptitude à dégrader des composés phénoliques tels que l'acide férulique ou l'acide coumarique. Cette adaptation permettrait à A. fabrum de détoxiquer des molécules majoritairement retrouvées dans les parois des cellules végétales et à les utiliser en outre comme source de carbone. La dégradation spécifique de ce type de composé végétal toxique semble bien être une des composantes de la niche spécifique de cette espèce lui permettant de concurrencer les autres espèces d'A. tumefaciens lors de la colonisation des racines de certaines plantes.
    Mots-clés : #3, #4, #cesn, #colloque.
  • Muller, D., Bouffaud, M.L., Gouesnard, B., Moënne-Loccoz, Y., 2012. Significance of the evolution of Zea mays and other Poaceae for rhizobacterial community composition (conférence invitée), dans: . Présenté à 16th Evolutionary Biology Meeting at Marseille, Marseille France.
  • Muller, D., Bouffaud, M.L., Kyselkova, M., Gouesnard, B., Grundmann, G., Moënne-Loccoz, Y., 2012. Histoire évolutive des céréales et composition de la communauté bactérienne rhizosphérique, dans: . Présenté à 10th Plant-Bacteria Interactions Meeting, Aussois, France.
  • Vacheron, J., Bellvert, F., Moënne-Loccoz, Y., Muller, D., Prigent-Combaret, C., 2012. Evaluation of 2,4-diacetylphloroglucinol fluorescent Pseudomonas for plant growth promotion, dans: . Présenté à The World Congress On Biostimulants, communication orale, Strasbourg, France.
    Mots-clés : #3, #cesn, #colloque.



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  • Renoud, S., 2015. Effect of Azospirillum inoculation on the abundance and genetic diversity of key phytobeneficial microbial functional groups in the maize rhizosphere, dans: . Présenté à Rhizosphere4, communication orale, Maastricht , Pays-Bas.
    Mots-clés : #3, #cesn, #poster.


  • Walker, V., 2014. Symbiomaize Project: Effect of maize diversification on its associative symbiosis with P. fluorescens rhizobacteria, dans: . Présenté à 15ème Rencontre du Groupe Régional de Recherche en Microbiologie des Interactions, communication orale, Villeurbanne, France.
    Mots-clés : #3, #cesn, #poster.


  • Vacheron, J., 2012. Développement de nouveaux inoculants bactériens agricoles stimulateurs de la croissance des céréales, dans: . Présenté à Journée de rencontre des doctorants, E2M2, communication orale, Villeurbanne, France.
    Mots-clés : #3, #cesn, #poster.