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Yvan Moënne-loccoz - One of the best experts on this subject based on the ideXlab platform.
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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, 2019Co-Authors: Vahid Keshavarz-tohid, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Audrey Dubost, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Daniel MullerAbstract:Abstract 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.
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Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani
Research in Microbiology, 2017Co-Authors: Vahid Keshavarz-tohid, Claire Prigent-combaret, Jordan Vacheron, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Daniel Muller, Yvan Moënne-loccozAbstract:Fluorescent pseudomonads from bean root and rhizosphere in Iran were investigated for biocontrol of the fungal pathogen Rhizoctonia solani. Phylogenetic analysis of concatenated 16S rRNA, gyrB and rpoD sequences for 33 Pseudomonas isolates showed that 15 belonged to four clusters within the \textquoteleftP. fluorescens' group, i.e. one corresponding to P. thivervalensis, two others including P. moraviensis or P. baetica, and the last one without closely-related established species. The 18 other isolates belonged to five clusters within the \textquoteleftP. putida' group, one including P. mosselii and P. entomophila, another including strains currently described as P. putida, and three without closely-related species described. Ten isolates were selected based on in vitro inhibition of R. solani. Cellulase activity was identified in three pseudomonads, chitinase activity in two pseudomonads, extracellular protease activity in nine pseudomonads and hydrogen cyanide production in two pseudomonads. Genes coding for production of phenazine, pyoluteorin, pyrrolnitrin and 2,4-diacetylphloroglucinol were not found, whereas the 1-aminocyclopropane-1-carboxylate deamination gene acdS was present in three pseudomonads. The antagonistic acdS+ strain VKh13 from the \textquoteleftP. putida' group effectively protected soil-grown bean from R. solani AG 4-HGI. Results show that pseudomonads from uncharacterized taxa were readily obtained from Iranian soils and displayed biocontrol potential against R. solani.
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Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism
Frontiers in Microbiology, 2017Co-Authors: Juliana Almario, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Maxime Bruto, Daniel MullerAbstract: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.
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Denaturing gradient gel electrophoretic analysis of dominant 2,4-diacetylphloroglucinol biosynthetic phlD alleles in fluorescent Pseudomonas from soils suppressive or conducive to black root rot of tobacco
Soil Biology and Biochemistry, 2010Co-Authors: Michele Frapolli, Geneviève Défago, Yvan Moënne-loccozAbstract:In Switzerland, similar types of rhizosphere pseudomonads producing the biocontrol compound 2,4- diacetylphloroglucinol (Phl) have been found in soils suppressive to Thielaviopsis basicola-mediated black root rot of tobacco as well as in conducive soils. However, most findings were based on the analysis of a limited number of Pseudomonas isolates, obtained from a single experiment and only from T. basicolainoculated plants. Here, an approach based on denaturing gradient gel electrophoresis (DGGE) of dominant phlD alleles from tobacco rhizosphere provided different phlD migration patterns. Sequencing of phlD-DGGE bands revealed a novel phylogenetic cluster of phlD sequences found in both suppressive and conducive soils in addition to previously-documented phlD alleles. phlD-DGGE bands and alleles differed little from one plant to the next but more extensively from one sampling to the next during the three-year study. Three of the 13 bands and 12 of the 31 alleles were only found in suppressive soil, whereas five bands and 13 alleles were found exclusively in conducive soil. The population structure of phlDþ pseudomonads depended more on the individual soil considered and its suppressiveness status than on inoculation of tobacco with T. basicola. In conclusion, phlD-DGGE revealed additional phlD diversity compared with earlier analyses of individual Pseudomonas isolates, and showed differences in phlDþ Pseudomonas population structure in relation to disease suppressiveness.
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Effect of long-term vineyard monoculture on rhizosphere populations of pseudomonads carrying the antimicrobial biosynthetic genes phlD and/or hcnAB
FEMS Microbiology Ecology, 2009Co-Authors: Miroslav Svercel, Danilo Christen, Yvan Moënne-loccoz, Brion Duffy, Geneviève DéfagoAbstract:The impact of repeated culture of perennial plants (i.e. in long-term monoculture) on the ecology of plant-beneficial bacteria is unknown. Here, the influence of extremely long-term monocultures of grapevine (up to 1603 years) on rhizosphere populations of fluorescent pseudomonads carrying the biosynthetic genes phlD for 2,4-diacetylphloroglucinol and/or hcnAB for hydrogen cyanide was determined. Soils from long-term and adjacent short-term monoculture vineyards (or brushland) in four regions of Switzerland were baited with grapevine or tobacco plantlets, and rhizosphere pseudomonads were studied by most probable number (MPN)-PCR. Higher numbers and percentages of phlD1 and of hcnAB1 rhizosphere pseudomonads were detected on using soil from long-term vineyards. On focusing on phlD, restriction fragment length polymorphism profiling of the last phlD-positive MPN wells revealed seven phlD alleles (three exclusively on tobacco, thereof two new ones). Higher numbers of phlD alleles coincided with a lower prevalence of the allele displayed by the well-studied biocontrol strain Pseudomonas fluorescens F113. The prevalence of this allele was 35% for tobacco in long-term monoculture soils vs. 460% in the other three cases.We conclude that soils from long-term grapevine monocultures represent an untapped resource for isolating novel biocontrol Pseudomonas strains when tobacco is used as bait.
Jeanmarie Meyer - One of the best experts on this subject based on the ideXlab platform.
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Taxonomic heterogeneity, as shown by siderotyping, of strains primarily identified as Pseudomonas putida.
International Journal of Systematic and Evolutionary Microbiology, 2007Co-Authors: Jeanmarie Meyer, Christelle Gruffaz, Topi Tulkki, Daniel IzardAbstract:One hundred and forty-four fluorescent pseudomonad strains isolated from various environments (soil, water, plant rhizosphere, hospital) and received as Pseudomonas putida (83 strains), P. putida biovar A (49 strains), P. putida biovar B (10 strains) and P. putida biovar C (2 strains), were analysed by the pyoverdine-isoelectrofocusing and pyoverdine-mediated iron uptake methods of siderotyping. Both methods demonstrated a great diversity among these strains, which could be subdivided into 35 siderovars. Some siderovars specifically included strains that have subsequently been transferred to well-defined Pseudomonas species, e.g. Pseudomonas monteilii or Pseudomonas mosselii, or which could be related by their siderotype to Pseudomonas jessenii or Pseudomonas mandelii. Other siderovars included strains sharing a high level of DNA-DNA relatedness (>70 %), thus demonstrating that siderotyping could easily circumscribe strains at the species level. However, a group of seven strains, including the type strain, P. putida ATCC 12633(T), were allocated into four siderovars, despite sharing DNA-DNA relatedness values of higher than 70 %. Interestingly, the strong genomic relationships between these seven strains were supported by the structural relationships among their pyoverdines, thus reflecting their phylogenetic affinities. These results strongly support the view that pyoverdine-based siderotyping could be used as a powerful tool in Pseudomonas taxonomy.
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Pseudomonas lurida sp. nov., a fluorescent species associated with the phyllosphere of grasses.
International Journal of Systematic and Evolutionary Microbiology, 2007Co-Authors: Undine Behrendt, Peter Schumann, Andreas Ulrich, Cathrin Spröer, Jeanmarie MeyerAbstract:The taxonomic position of a group of fluorescent pseudomonad strains isolated from the phyllosphere of grasses was investigated through a polyphasic approach. Riboprinting analysis revealed highly similar patterns for the investigated strains which supported, together with the agreement of many phenotypic characteristics, their affiliation to the same species. A comparison of 16S rRNA gene sequences of strain P 513/18(T), a representative strain from the grass isolates, revealed that it was affiliated to the cluster of the 'Pseudomonas fluorescens group', with Pseudomonas costantinii as the closest phylogenetic neighbour. However, DNA-DNA hybridization showed a clear demarcation at the species level between strain P 513/18(T) and P. costantinii. Furthermore, a comparison of riboprint patterns with Pseudomonas species clustering next to the novel grass isolates on the basis of 16S rRNA gene sequences supported their separate species status at the phylogenetic level. Based on phenotypic features, the novel isolates could also be differentiated from the other fluorescent Pseudomonas species that share positive arginine dihydrolase and oxidase reactions. As a consequence of these phenotypic and phylogenetic analyses, the isolates from the grass pyllosphere represent a novel species for which the name Pseudomonas lurida sp. nov. is proposed. The type strain is P 513/18(T) (=DSM 15835(T)=LMG 21995(T)).
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siderotyping and bacterial taxonomy a siderophore bank for a rapid identification at the species level of fluorescent and non fluorescent Pseudomonas
2007Co-Authors: Jeanmarie MeyerAbstract:Bacteria belonging to the genus Pseudomonas are largely distributed in nature and can be isolated from most environments including soil, plant rhizosphere and phylosphere, or water. A few species are pathogens for animals, e.g., Pseudomonas plecoglossicida (Nishimori et al. 2000) or are, like the genus type-species Pseudomonas aeruginosa, opportunist human pathogens implicated in severe illnesses like cystic fibrosis. A greater number are plant pathogens, mainly found on the surfaces of plant leaves and stems such as Pseudomonas syringae and the related species Pseudomonas amygdali, Pseudomonas avellanae, Pseudomonas cannabina, Pseudomonas ficuserectae, Pseudomonas meliae, Pseudomonas savastanoi, Pseudomonas tremae and Pseudomonas viridiflava (Gardan et al. 1999). Others, e.g., Pseudomonas palleroniana and Pseudomonas salomonii (Gardan et al. 2002), or Pseudomonas tolaasii and Pseudomonas costantinii (Munsch et al. 2002), have been associated with serious crop damages affecting rice, garlic or mushrooms, respectively. However, most of the Pseudomonas spp. remain to be considered as non-pathogenic saprophytic bacteria, harboring for many of them behaviours of biotechnological interests such as chemical bioremediation, crop protection or plant growth promotion. In soil, pseudomonads represent one of the most important Gram-negative genera among culturable aerobic bacteria usually found. According to student lab courses done on soil samples over many years in our laboratory, 1–10% of soil isolates correspond to bacteria easily recognized as fluorescent Pseudomonas thanks to the yellow-green, highly fluorescent halo existing around such colonies growing on the iron-poor Casamino acid (CAA)-agar medium. Some 2 Siderotyping and Bacterial Taxonomy: A Siderophore Bank for a Rapid Identification at the Species Level of Fluorescent and Non-Fluorescent Pseudomonas
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environmental fluorescent Pseudomonas and pyoverdine diversity how siderophores could help microbiologists in bacterial identification and taxonomy
2004Co-Authors: Jeanmarie Meyer, Valerie GeoffroyAbstract:Siderophore-based methods could be successfully used for bacterial identification. Preliminary data for other bacteria (nonfluorescent Pseudomonas species, Burkholderia species, rhizobia, and bradyrhizobia, as well as enterobacteria, mycobacteria, and Aeromonas species) strongly indicate that any siderophore could be used as a taxonomic marker for its producing bacteria, which means that the emerging concept of siderotyping as a taxonomic tool could be applied to a large part of the microbial world. Nonfluorescent siderophores produced by fluorescent pseudomonads, together with pyoverdines, e.g., pyochelin, salicylic acid, or quinolobactin, and other compounds such as those produced by nonfluorescent pseudomonads, e.g., ornibactins, cepabactin, or desferriferrioxamines, are revealed by an overlay of 1% melted agarose in CAS reagent, which reveals siderophores as yellow to pink spots appearing at the surface of the gel. It is clear that siderotyping could be very useful for bacterial identification and Pseudomonas taxonomy: following the recognition of the type of pyoverdine it produces, a taxonomically undefined fluorescent pseudomonad is classified in a corresponding siderovar. The methods of siderotyping are very fast and easy to perform. The method has already proved its efficiency in the bacterial identification of fluorescent Pseudomonas species and in the detection of new species. Depending on the specificity level expressed by the pyoverdine, it should thus be possible to achieve, during a single experimental step, both isolation and identification of a fluorescent Pseudomonas strain.
Daniel Muller - One of the best experts on this subject based on the ideXlab platform.
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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, 2019Co-Authors: Vahid Keshavarz-tohid, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Audrey Dubost, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Daniel MullerAbstract:Abstract 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.
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Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani
Research in Microbiology, 2017Co-Authors: Vahid Keshavarz-tohid, Claire Prigent-combaret, Jordan Vacheron, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Daniel Muller, Yvan Moënne-loccozAbstract:Fluorescent pseudomonads from bean root and rhizosphere in Iran were investigated for biocontrol of the fungal pathogen Rhizoctonia solani. Phylogenetic analysis of concatenated 16S rRNA, gyrB and rpoD sequences for 33 Pseudomonas isolates showed that 15 belonged to four clusters within the \textquoteleftP. fluorescens' group, i.e. one corresponding to P. thivervalensis, two others including P. moraviensis or P. baetica, and the last one without closely-related established species. The 18 other isolates belonged to five clusters within the \textquoteleftP. putida' group, one including P. mosselii and P. entomophila, another including strains currently described as P. putida, and three without closely-related species described. Ten isolates were selected based on in vitro inhibition of R. solani. Cellulase activity was identified in three pseudomonads, chitinase activity in two pseudomonads, extracellular protease activity in nine pseudomonads and hydrogen cyanide production in two pseudomonads. Genes coding for production of phenazine, pyoluteorin, pyrrolnitrin and 2,4-diacetylphloroglucinol were not found, whereas the 1-aminocyclopropane-1-carboxylate deamination gene acdS was present in three pseudomonads. The antagonistic acdS+ strain VKh13 from the \textquoteleftP. putida' group effectively protected soil-grown bean from R. solani AG 4-HGI. Results show that pseudomonads from uncharacterized taxa were readily obtained from Iranian soils and displayed biocontrol potential against R. solani.
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Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism
Frontiers in Microbiology, 2017Co-Authors: Juliana Almario, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Maxime Bruto, Daniel MullerAbstract: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.
Claire Prigent-combaret - One of the best experts on this subject based on the ideXlab platform.
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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, 2019Co-Authors: Vahid Keshavarz-tohid, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Audrey Dubost, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Daniel MullerAbstract:Abstract 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.
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Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani
Research in Microbiology, 2017Co-Authors: Vahid Keshavarz-tohid, Claire Prigent-combaret, Jordan Vacheron, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Daniel Muller, Yvan Moënne-loccozAbstract:Fluorescent pseudomonads from bean root and rhizosphere in Iran were investigated for biocontrol of the fungal pathogen Rhizoctonia solani. Phylogenetic analysis of concatenated 16S rRNA, gyrB and rpoD sequences for 33 Pseudomonas isolates showed that 15 belonged to four clusters within the \textquoteleftP. fluorescens' group, i.e. one corresponding to P. thivervalensis, two others including P. moraviensis or P. baetica, and the last one without closely-related established species. The 18 other isolates belonged to five clusters within the \textquoteleftP. putida' group, one including P. mosselii and P. entomophila, another including strains currently described as P. putida, and three without closely-related species described. Ten isolates were selected based on in vitro inhibition of R. solani. Cellulase activity was identified in three pseudomonads, chitinase activity in two pseudomonads, extracellular protease activity in nine pseudomonads and hydrogen cyanide production in two pseudomonads. Genes coding for production of phenazine, pyoluteorin, pyrrolnitrin and 2,4-diacetylphloroglucinol were not found, whereas the 1-aminocyclopropane-1-carboxylate deamination gene acdS was present in three pseudomonads. The antagonistic acdS+ strain VKh13 from the \textquoteleftP. putida' group effectively protected soil-grown bean from R. solani AG 4-HGI. Results show that pseudomonads from uncharacterized taxa were readily obtained from Iranian soils and displayed biocontrol potential against R. solani.
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Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism
Frontiers in Microbiology, 2017Co-Authors: Juliana Almario, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Maxime Bruto, Daniel MullerAbstract: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.
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Development of a 16S rRNA microarray approach for the monitoring of rhizosphere Pseudomonas populations associated with the decline of take-all disease of wheat.
Soil Biology and Biochemistry, 2008Co-Authors: Hervé Sanguin, L. Kroneisen, Kevin Gazengel, M. Kyselková, Benoit Remenant, Claire Prigent-combaret, G.l. Grundmann, Alain Sarniguet, Yvan Moënne-loccozAbstract:So far, the analysis of microbial populations associated with wheat monocropping-induced decline of take-all disease (Gaeumannomyces graminis var. tritici) has focused mainly on culturable biocontrol pseudomonads. The objective of this study was to develop a taxonomic rrs (16S rRNA gene) microarray to assess the changes in Pseudomonas populations taking place during take-all decline. The microarray contains 12 probes for five Pseudomonas phylogenetic clusters chosen because they include well-known plant-beneficial pseudomonads. Four of the clusters are within the ‘Pseudomonas fluorescens’ species complex. PCR primers were selected to target these five clusters, and they were validated using 53 pseudomonads belonging or not to these clusters. Microarray analysis of the pseudomonads enabled discrimination between strains from several Pseudomonas clusters. Rhizosphere samples were collected from field plots grown with wheat for 1 (low level of take-all disease), 5 (high level of disease) or 10 years (low level of disease, suppressiveness reached). Microarray data could distinguish Pseudomonas populations from some of the wheat plants grown in the same plot. When comparing treatments, there was a difference between years 1 and 10. Cloning–sequencing of rrs enabled to define more precisely this difference by identifying two major Pseudomonas populations, one associated with year 1 and the other with year 10 (disease suppressiveness), which represent new clades within the ‘P. fluorescens’ complex. These populations may be useful as soil quality indicators. In conclusion, the combination of microarray and cloning–sequencing approaches highlighted changes in the prevalence of two major Pseudomonas populations, giving new insights on the dynamics of root-associated pseudomonads during take-all decline
Samuel W Cartinhour - One of the best experts on this subject based on the ideXlab platform.
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recombineering using recte from Pseudomonas syringae
Applied and Environmental Microbiology, 2010Co-Authors: Bryan Swingle, Eric Markel, Alan H Chambers, Samuel W CartinhourAbstract:In this report, we describe the identification of functions that promote genomic recombination of linear DNA introduced into Pseudomonas cells by electroporation. The genes encoding these functions were identified in Pseudomonas syringae pv. syringae B728a based on similarity to the lambda Red Exo/Beta and RecET proteins encoded by the lambda and Rac bacteriophages of Escherichia coli. The ability of the pseudomonad-encoded proteins to promote recombination was tested in P. syringae pv. tomato DC3000 using a quantitative assay based on recombination frequency. The results show that the Pseudomonas RecT homolog is sufficient to promote recombination of single-stranded DNA oligonucleotides and that efficient recombination of double-stranded DNA requires the expression of both the RecT and RecE homologs. Additionally, we illustrate the utility of this recombineering system to make targeted gene disruptions in the P. syringae chromosome.
