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Accueil > Pages Perso > Juliana Almario

Equipe Rhizosphère

Juliana Almario

Chercheuse

Je suis chargée de recherches au CNRS (section 30). Je m’intéresse au rôle du microbiote racinaire dans la nutrition des plantes.

Activité

  • Thèmes de recherches :
    1. Microbiote végètal
    2. Champignons endophytes pseudo-mycorhiziens
    3. Transfer de Phosphore (P) champignon->plante

Projets en cours
Stay tuned !

Parcours scientifique

  • Formation supérieure

2009 – 2012 Doctorat Écologie Microbienne.
Université Lyon 1, Villeurbanne, France
2007 – 2009 Master recherche (M2R) Écologie Microbienne.
Université Lyon 1, Villeurbanne, France
2004 – 2007 Licence Biologie (Microbiologie).
Université Lyon 1, Villeurbanne, France

  • Activité de recherche

2019–
Chargée de Recherche, Centre National de la Recherche Scientifique • UMR CNRS 5557 Écologie Microbienne, Université Lyon 1, Villeurbanne, France.

2017–2019
Prof. Assistant • Dept. Interactions microbiennes dans les écosystèmes végétaux, Université de Tübingen, Allemagne. Responsable projet : E. Kemen.
Profil temporel des réseaux microbiens établis sur les feuilles de Arabidopsis thaliana.

2016–2017
Post Doc • Institut Max Planck de la plante, Cologne, Allemagne.
Profil temporel des réseaux microbiens établis sur les feuilles de Arabidopsis thaliana. Responsable projet : E. Kemen.

2013–2016
Post Doc • Cluster of Excellence in Plant Sciences (CEPLAS) - Université de Cologne, Cologne, Allemagne. Responsable projet : M. Bucher.
Caractérisation structurelle et fonctionnelle du microbiote de Arabis alpina

2009 – 2012
Doctorat en Ecologie Microbienne • UMR CNRS 5557 Écologie Microbienne, Université Lyon 1, Villeurbanne, France. Responsables projet : D. Muller et Y. Moënne-Loccoz.
Relation entre la propriété phytoprotectrice de synthèse de 2,4-diacétylphloroglucinol par les bactéries Pseudomonas dans la rhizosphère, et la résistance des sols à la maladie de la pourriture noire des racines de tabac

Enseignement/Encadrement

  • Co-encadrement de thèse :
    2019 – 2022 • K. Lutap. Héritabilité du microbiote chez Lotus corniculatus (Co-responsable : E. Kemen).
    2014 – 2018 • I. Fabianska. Impact de la biodisponibilité du phosphore dans le sol sur la formation du microbiote racinaire chez Arabidopsis (Co-responsable : M. Bucher).

Publications

2019



  • Fabiańska I, Gerlach N, Almario J, Bucher M. 2019. Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in <i>Arabidopsis thaliana</i>. New Phytologist. 221:2123-2137. doi: 10.1111/nph.15538.


  • Xue L, Almario J, Fabiańska I, Saridis G, Bucher M. 2019. Dysfunction in the arbuscular mycorrhizal symbiosis has consistent but small effects on the establishment of the fungal microbiota in <i>Lotus japonicus</i>. New Phytologist. 224:409-420. doi: 10.1111/nph.15958.

2018



  • Karasov TL, et al. 2018. Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe. 24:168-179.e4. doi: 10.1016/j.chom.2018.06.011.
    Résumé : Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.
    Mots-clés : clonal expansion, microbial population genomics, pathogenicity, pseudomonas.

2017



  • Almario J, et al. 2017. Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism. Frontiers in Microbiology. 8:1218. doi: 10.3389/fmicb.2017.01218.
    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.


  • Almario J, et al. 2017. Root-associated fungal microbiota of nonmycorrhizal <i>Arabis alpina</i> and its contribution to plant phosphorus nutrition. Proceedings of the National Academy of Sciences. 114:E9403-E9412. doi: 10.1073/pnas.1710455114.
    Résumé : Most land plants live in association with arbuscular mycorrhizal (AM) fungi and rely on this symbiosis to scavenge phosphorus (P) from soil. The ability to establish this partnership has been lost in some plant lineages like the Brassicaceae, which raises the question of what alternative nutrition strategies such plants have to grow in P-impoverished soils. To understand the contribution of plant–microbiota interactions, we studied the root-associated fungal microbiome of Arabis alpina (Brassicaceae) with the hypothesis that some of its components can promote plant P acquisition. Using amplicon sequencing of the fungal internal transcribed spacer 2, we studied the root and rhizosphere fungal communities of A. alpina growing under natural and controlled conditions including low-P soils and identified a set of 15 fungal taxa consistently detected in its roots. This cohort included a Helotiales taxon exhibiting high abundance in roots of wild A. alpina growing in an extremely P-limited soil. Consequently, we isolated and subsequently reintroduced a specimen from this taxon into its native P-poor soil in which it improved plant growth and P uptake. The fungus exhibited mycorrhiza-like traits including colonization of the root endosphere and P transfer to the plant. Genome analysis revealed a link between its endophytic lifestyle and the expansion of its repertoire of carbohydrate-active enzymes. We report the discovery of a plant–fungus interaction facilitating the growth of a nonmycorrhizal plant under native P-limited conditions, thus uncovering a previously underestimated role of root fungal microbiota in P cycling.

2014



  • Almario J, Gobbin D, Défago G, Moënne-Loccoz Y, Rezzonico F. 2014. Prevalence of type III secretion system in effective biocontrol pseudomonads. Research in Microbiology. doi: 10.1016/j.resmic.2014.03.008.
    Résumé : Functional type III secretion system (T3SS) genes are needed for effective biocontrol of Pythium damping-off of cucumber by Pseudomonas fluorescens KD, but whether biocontrol Pseudomonas strains with T3SS genes display overall a higher plant-protecting activity is unknown. The assessment of 198 biocontrol fluorescent pseudomonads originating from 60 soils worldwide indicated that 32% harbour the ATPase-encoding T3SS gene hrcN, which was most often found in tomato isolates. The hrcN+ biocontrol strains (and especially those also producing 2,4-diacetylphloroglucinol and displaying 1-aminocyclopropane-1-carboxylate deaminase activity) displayed higher plant-protecting ability in comparison with hrcN− biocontrol strains, both in the Pythium/cucumber and Fusarium/cucumber pathosystems.
    Mots-clés : #3, 2, 2,4-Diacetylphloroglucinol, 4-Diacetylphloroglucinol, ACC deaminase, Biocontrol, Pseudomonas, Type III secretion system.


  • 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. doi: 10.1111/1462-2920.12459.
    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.


  • Donn S, et al. 2014. Rhizosphere microbial communities associated with Rhizoctonia damage at the field and disease patch scale. Applied Soil Ecology. 78:37-47. doi: 10.1016/j.apsoil.2014.02.001.
    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, et al. 2014. Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers′ fields. Environmental Microbiology Reports. n/a–n/a. doi: 10.1111/1758-2229.12131.
    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.

2013



  • Almario J, et al. 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. doi: 10.1007/s11104-013-1677-1.
    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. doi: 10.1094/MPMI-11-12-0274-R.
    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.

2012



  • 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. doi: 10.1016/j.soilbio.2012.09.003.
    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.

Chapitre d’ouvrages

Vulgarisation

Communications Orales

2012

  • 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. In: Aussois, France p. .
    Mots-clés : #colloque.
    Note Note
    <p>00000</p>
  • 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. In: p. .
    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. Effect of clay mineralogy on the plant-protecting activity of Pseudomonas in the rhizosphere. In: Villeurbanne, France, p. .
    Mots-clés : #colloque.
    Note Note
    <p>00000</p>
  • 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. In: Copenhagen, Denmark p. .
    Mots-clés : #colloque.

Posters

2019

Article de revue


  • Fabiańska I, Gerlach N, Almario J, Bucher M. 2019. Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in <i>Arabidopsis thaliana</i>. New Phytologist. 221:2123-2137. doi: 10.1111/nph.15538.


  • Xue L, Almario J, Fabiańska I, Saridis G, Bucher M. 2019. Dysfunction in the arbuscular mycorrhizal symbiosis has consistent but small effects on the establishment of the fungal microbiota in <i>Lotus japonicus</i>. New Phytologist. 224:409-420. doi: 10.1111/nph.15958.

2018

Article de revue


  • Karasov TL, et al. 2018. Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe. 24:168-179.e4. doi: 10.1016/j.chom.2018.06.011.
    Résumé : Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.
    Mots-clés : clonal expansion, microbial population genomics, pathogenicity, pseudomonas.

2017

Article de revue


  • Almario J, et al. 2017. Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism. Frontiers in Microbiology. 8:1218. doi: 10.3389/fmicb.2017.01218.
    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.


  • Almario J, et al. 2017. Root-associated fungal microbiota of nonmycorrhizal <i>Arabis alpina</i> and its contribution to plant phosphorus nutrition. Proceedings of the National Academy of Sciences. 114:E9403-E9412. doi: 10.1073/pnas.1710455114.
    Résumé : Most land plants live in association with arbuscular mycorrhizal (AM) fungi and rely on this symbiosis to scavenge phosphorus (P) from soil. The ability to establish this partnership has been lost in some plant lineages like the Brassicaceae, which raises the question of what alternative nutrition strategies such plants have to grow in P-impoverished soils. To understand the contribution of plant–microbiota interactions, we studied the root-associated fungal microbiome of Arabis alpina (Brassicaceae) with the hypothesis that some of its components can promote plant P acquisition. Using amplicon sequencing of the fungal internal transcribed spacer 2, we studied the root and rhizosphere fungal communities of A. alpina growing under natural and controlled conditions including low-P soils and identified a set of 15 fungal taxa consistently detected in its roots. This cohort included a Helotiales taxon exhibiting high abundance in roots of wild A. alpina growing in an extremely P-limited soil. Consequently, we isolated and subsequently reintroduced a specimen from this taxon into its native P-poor soil in which it improved plant growth and P uptake. The fungus exhibited mycorrhiza-like traits including colonization of the root endosphere and P transfer to the plant. Genome analysis revealed a link between its endophytic lifestyle and the expansion of its repertoire of carbohydrate-active enzymes. We report the discovery of a plant–fungus interaction facilitating the growth of a nonmycorrhizal plant under native P-limited conditions, thus uncovering a previously underestimated role of root fungal microbiota in P cycling.

2014

Article de revue


  • Almario J, Gobbin D, Défago G, Moënne-Loccoz Y, Rezzonico F. 2014. Prevalence of type III secretion system in effective biocontrol pseudomonads. Research in Microbiology. doi: 10.1016/j.resmic.2014.03.008.
    Résumé : Functional type III secretion system (T3SS) genes are needed for effective biocontrol of Pythium damping-off of cucumber by Pseudomonas fluorescens KD, but whether biocontrol Pseudomonas strains with T3SS genes display overall a higher plant-protecting activity is unknown. The assessment of 198 biocontrol fluorescent pseudomonads originating from 60 soils worldwide indicated that 32% harbour the ATPase-encoding T3SS gene hrcN, which was most often found in tomato isolates. The hrcN+ biocontrol strains (and especially those also producing 2,4-diacetylphloroglucinol and displaying 1-aminocyclopropane-1-carboxylate deaminase activity) displayed higher plant-protecting ability in comparison with hrcN− biocontrol strains, both in the Pythium/cucumber and Fusarium/cucumber pathosystems.
    Mots-clés : #3, 2, 2,4-Diacetylphloroglucinol, 4-Diacetylphloroglucinol, ACC deaminase, Biocontrol, Pseudomonas, Type III secretion system.


  • 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. doi: 10.1111/1462-2920.12459.
    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.


  • Donn S, et al. 2014. Rhizosphere microbial communities associated with Rhizoctonia damage at the field and disease patch scale. Applied Soil Ecology. 78:37-47. doi: 10.1016/j.apsoil.2014.02.001.
    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, et al. 2014. Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers′ fields. Environmental Microbiology Reports. n/a–n/a. doi: 10.1111/1758-2229.12131.
    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.

2013

Article de revue


  • Almario J, et al. 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. doi: 10.1007/s11104-013-1677-1.
    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. doi: 10.1094/MPMI-11-12-0274-R.
    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.

2012

Article de revue


  • 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. doi: 10.1016/j.soilbio.2012.09.003.
    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.
Article de 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. In: Aussois, France p. .
    Mots-clés : #colloque.
    Note Note
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  • 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. In: p. .
    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. Effect of clay mineralogy on the plant-protecting activity of Pseudomonas in the rhizosphere. In: Villeurbanne, France, p. .
    Mots-clés : #colloque.
    Note Note
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  • 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. In: Copenhagen, Denmark p. .
    Mots-clés : #colloque.
Thèse

  • Almario J. 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. http://www.theses.fr/2012LYO10337/document (Consulté sans date).
    Mots-clés : #3.