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Jos M. Raaijmakers - One of the best experts on this subject based on the ideXlab platform.
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microbial and volatile profiling of Soils Suppressive to fusarium culmorum of wheat
Proceedings of The Royal Society B: Biological Sciences, 2020Co-Authors: Adam Ossowicki, Jos M. Raaijmakers, Marnix H. Medema, Vittorio Tracanna, Marloes L. C. Petrus, Gilles P Van Wezel, Paolina GarbevaAbstract:In disease-Suppressive Soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date...
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Microbial and volatile profiling of Soils Suppressive to Fusarium culmorum of wheat
Proceedings of the Royal Society B: Biological Sciences, 2020Co-Authors: Adam Ossowicki, Jos M. Raaijmakers, Marnix H. Medema, Vittorio Tracanna, Marloes L. C. Petrus, Gilles P. Van Wezel, Paolina GarbevaAbstract:In disease-Suppressive Soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual Suppressive Soils and the degree of natural variability of soil Suppressiveness remains unclear. Here, we screened a large collection of field Soils for Suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease Suppressiveness was observed, with 14% showing a clear Suppressive phenotype. The microbiological basis of Suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all Suppressive Soils. Nonetheless, co-occurrence network analysis revealed that two Suppressive Soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all Suppressive Soils. Our study raises new questions regarding the possible mechanistic variability of disease-Suppressive phenotypes across physico-chemically different Soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-Suppressive microbiomes.
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Involvement of Burkholderiaceae and sulfurous volatiles in disease-Suppressive Soils.
The ISME Journal, 2018Co-Authors: Víctor J. Carrión, Irene De Bruijn, Viviane Cordovez, Olaf Tyc, Desalegn W. Etalo, Victor De Jager, Marnix H. Medema, Leo Eberl, Jos M. RaaijmakersAbstract:Disease-Suppressive Soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of Soils Suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392–3, 2016), but the mechanisms and microbial species involved in the soil Suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil Suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in Suppressive than in non-Suppressive Soils. Here, isolation, phylogeny, and soil bioassays revealed a significant disease-Suppressive activity for representative isolates of Burkholderia pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P. terricola. In vitro antifungal activity was only observed for P. graminis. Comparative genomics and metabolite profiling further showed that the antifungal activity of P. graminis PHS1 was associated with the production of sulfurous volatile compounds encoded by genes not found in the other four genera. Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide reductase and a cysteine desulfurase, resulted in a loss of antifungal activity both in vitro and in situ. These results indicate that specific members of the Burkholderiaceae family contribute to soil Suppressiveness via the production of sulfurous volatile compounds.
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Comparative microbiome analysis of a Fusarium wilt Suppressive soil and a Fusarium wilt conducive soil from the Châteaurenard region
Frontiers in Microbiology, 2018Co-Authors: Katarzyna Siegel Hertz, Jos M. Raaijmakers, Veronique Edel-hermann, Emilie Chapelle, Sébastien Terrat, Christian SteinbergAbstract:Disease-Suppressive Soils are Soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from Suppressive and non-Suppressive (conducive) Soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the Suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-Suppressiveness to the conducive soil by mixing 10% (w/w) of the Suppressive soil into the conducive soil. Fungal diversity differed significantly between the Suppressive and conducive Soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the Suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the Suppressive and mixed Soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-Suppressive Soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-Suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt Suppressive Soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt Suppressiveness.
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DataSheet1.docx
2018Co-Authors: Katarzyna Siegel Hertz, Jos M. Raaijmakers, Veronique Edel-hermann, Emilie Chapelle, Sébastien Terrat, Christian SteinbergAbstract:Disease-Suppressive Soils are Soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from Suppressive and non-Suppressive (conducive) Soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the Suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-Suppressiveness to the conducive soil by mixing 10% (w/w) of the Suppressive soil into the conducive soil. Fungal diversity differed significantly between the Suppressive and conducive Soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the Suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the Suppressive and mixed Soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-Suppressive Soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-Suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt Suppressive Soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt Suppressiveness.
Yvan Moënne-loccoz - One of the best experts on this subject based on the ideXlab platform.
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Bacterial, archaeal and micro-eukaryotic communities characterize a disease-Suppressive or conducive soil and a cultivar resistant or susceptible to common scab
Scientific Reports, 2019Co-Authors: Jan Kopecky, Yvan Moënne-loccoz, Zuzana Samkova, Ensyeh Sarikhani, Martina Kyselková, Marek Omelka, Vaclav Kristufek, Jiri Divis, Geneviève Grundmann, Marketa Sagova-mareckovaAbstract:Control of common scab disease can be reached by resistant cultivars or Suppressive Soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a Suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both Soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the Suppressive and conducive soil. The effect of soil Suppressiveness x cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.
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Rhizosphere ecology and phytoprotection in Soils naturally Suppressive to Thielaviopsis black root rot of tobacco
Environmental Microbiology, 2014Co-Authors: Juliana Almario, Daniel Muller, Geneviève Défago, Yvan Moënne-loccozAbstract:Soil Suppressiveness to disease is an intriguing emerging property in agroecosystems, with important implications because 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.
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Effect of Clay Mineralogy on Iron Bioavailability and Rhizosphere Transcription of 2,4-Diacetylphloroglucinol Biosynthetic Genes in Biocontrol Pseudomonas protegens
Molecular Plant-Microbe Interactions, 2013Co-Authors: Juliana Almario, Daniel Muller, Claire Prigent-combaret, Yvan Moënne-loccozAbstract: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.
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Pseudomonas and other Microbes in Disease-Suppressive Soils
Organic Fertilisation Soil Quality and Human Health, 2012Co-Authors: M. Kyselková, Yvan Moënne-loccozAbstract:Soil-borne phytopathogens cause extensive damage to cultivated plants worldwide, resulting in yield loss worth billions of Euros each year. Soil fumigation is the most effective chemical treatment but is too expensive for many crops, and fumigants like methyl bromide are being phased out for environmental reasons. In this context, much is to be learned from disease-Suppressive Soils, where susceptible plants are protected from soil-borne pathogens by the indigenous microbiota, because these microbial interactions may be exploited to design sustainable crop protection strategies for ordinary farm Soils. However, our knowledge of plant-protecting microorganisms and biocontrol mechanisms involved in soil Suppressiveness remain very fragmented, as most knowledge on disease Suppressive Soils comes from studies restricted to individual plant-protecting microbial populations, mostly fluorescent Pseudomonas species. The phenomenon of disease Suppressiveness remains therefore poorly understood, even in the most studied cases such as Suppressiveness to wheat take-all.
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Monitoring of the relation between 2,4-diacetylphloroglucinol-producing Pseudomonas and Thielaviopsis basicola populations by real-time PCR in tobacco black root-rot Suppressive and conducive Soils
Soil Biology and Biochemistry, 2012Co-Authors: Juliana Almario, Yvan Moënne-loccoz, Daniel MullerAbstract: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 >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.
Brian R. Kerry - One of the best experts on this subject based on the ideXlab platform.
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development of a new management strategy for the control of root knot nematodes meloidogyne spp in organic vegetable production
Pest Management Science, 2003Co-Authors: S D Atkins, L Hidalgodiaz, Helen Kalisz, Tim H Mauchline, P R Hirsch, Brian R. KerryAbstract:The nematophagous fungus, Pochonia chlamydosporia (Goddard) Zare & Gams, has been investigated as a potential biological control agent for use in integrated pest management strategies for Meloidogyne incognita (Kof & White) Chitwood in vegetable crops. The release of the fungus as a biological control agent requires a diagnostic method to monitor its spread in the environment and to gain knowledge of its ecology. Only molecular methods are sufficiently discriminating to enable the detection of specific isolates of fungi in soil. A method to extract DNA from soil was developed to increase the efficacy of PCR-based diagnostic tests that use specific primers. A selected isolate of P chlamydosporia var catenulata was applied at densities similar to those that occur naturally in nematode-Suppressive Soils. The fungus significantly reduced nematode infestations in soil following a tomato crop, in a strategy that combined the use of the fungus with crop rotation. The survival of the fungus in soil was also examined in controlled conditions in which it remained in soil in densities significantly greater than its original application rate for at least 5 months. Hence, it seems that populations of this fungus may be built up in soil and have significant effects on the regulation of root-knot nematode populations. © 2003 Society of Chemical Industry
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development of a new management strategy for the control of root knot nematodes meloidogyne spp in organic vegetable production
Pest Management Science, 2003Co-Authors: S D Atkins, L Hidalgodiaz, Helen Kalisz, Tim H Mauchline, P R Hirsch, Brian R. KerryAbstract:The nematophagous fungus, Pochonia chlamydosporia (Goddard) Zare & Gams, has been investigated as a potential biological control agent for use in integrated pest management strategies for Meloidogyne incognita (Kof & White) Chitwood in vegetable crops. The release of the fungus as a biological control agent requires a diagnostic method to monitor its spread in the environment and to gain knowledge of its ecology. Only molecular methods are sufficiently discriminating to enable the detection of specific isolates of fungi in soil. A method to extract DNA from soil was developed to increase the efficacy of PCR-based diagnostic tests that use specific primers. A selected isolate of P chlamydosporia var catenulata was applied at densities similar to those that occur naturally in nematode-Suppressive Soils. The fungus significantly reduced nematode infestations in soil following a tomato crop, in a strategy that combined the use of the fungus with crop rotation. The survival of the fungus in soil was also examined in controlled conditions in which it remained in soil in densities significantly greater than its original application rate for at least 5 months. Hence, it seems that populations of this fungus may be built up in soil and have significant effects on the regulation of root-knot nematode populations.
Juliana Almario - One of the best experts on this subject based on the ideXlab platform.
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Rhizosphere ecology and phytoprotection in Soils naturally Suppressive to Thielaviopsis black root rot of tobacco
Environmental Microbiology, 2014Co-Authors: Juliana Almario, Daniel Muller, Geneviève Défago, Yvan Moënne-loccozAbstract:Soil Suppressiveness to disease is an intriguing emerging property in agroecosystems, with important implications because 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.
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Effect of Clay Mineralogy on Iron Bioavailability and Rhizosphere Transcription of 2,4-Diacetylphloroglucinol Biosynthetic Genes in Biocontrol Pseudomonas protegens
Molecular Plant-Microbe Interactions, 2013Co-Authors: Juliana Almario, Daniel Muller, Claire Prigent-combaret, Yvan Moënne-loccozAbstract: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.
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Monitoring of the relation between 2,4-diacetylphloroglucinol-producing Pseudomonas and Thielaviopsis basicola populations by real-time PCR in tobacco black root-rot Suppressive and conducive Soils
Soil Biology and Biochemistry, 2012Co-Authors: Juliana Almario, Yvan Moënne-loccoz, Daniel MullerAbstract: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 >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.
Daniel Muller - One of the best experts on this subject based on the ideXlab platform.
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Rhizosphere ecology and phytoprotection in Soils naturally Suppressive to Thielaviopsis black root rot of tobacco
Environmental Microbiology, 2014Co-Authors: Juliana Almario, Daniel Muller, Geneviève Défago, Yvan Moënne-loccozAbstract:Soil Suppressiveness to disease is an intriguing emerging property in agroecosystems, with important implications because 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.
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Effect of Clay Mineralogy on Iron Bioavailability and Rhizosphere Transcription of 2,4-Diacetylphloroglucinol Biosynthetic Genes in Biocontrol Pseudomonas protegens
Molecular Plant-Microbe Interactions, 2013Co-Authors: Juliana Almario, Daniel Muller, Claire Prigent-combaret, Yvan Moënne-loccozAbstract: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.
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Monitoring of the relation between 2,4-diacetylphloroglucinol-producing Pseudomonas and Thielaviopsis basicola populations by real-time PCR in tobacco black root-rot Suppressive and conducive Soils
Soil Biology and Biochemistry, 2012Co-Authors: Juliana Almario, Yvan Moënne-loccoz, Daniel MullerAbstract: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 >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.
