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Yvan Moënne-loccoz – One of the best experts on this subject based on the ideXlab platform.

  • 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, 2019
    Co-Authors: Vahid Keshavarz-tohid, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Audrey Dubost, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Daniel Muller
    Abstract:

    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.

  • Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani
    Research in Microbiology, 2017
    Co-Authors: Vahid Keshavarz-tohid, Claire Prigent-combaret, Daniel Muller, Jordan Vacheron, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Yvan Moënne-loccoz
    Abstract:

    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.

  • Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism
    Frontiers in Microbiology, 2017
    Co-Authors: Juliana Almario, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Maxime Bruto, Daniel Muller
    Abstract:

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

Jeanmarie Meyer – One of the best experts on this subject based on the ideXlab platform.

  • Taxonomic heterogeneity, as shown by siderotyping, of strains primarily identified as Pseudomonas putida.
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Jeanmarie Meyer, Christelle Gruffaz, Topi Tulkki, Daniel Izard
    Abstract:

    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.

  • Pseudomonas lurida sp. nov., a fluorescent species associated with the phyllosphere of grasses.
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Undine Behrendt, Peter Schumann, Andreas Ulrich, Cathrin Spröer, Jeanmarie Meyer
    Abstract:

    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 DNA hybrhybridization 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)).

  • siderotyping and bacterial taxonomy a siderophore bank for a rapid identification at the species level of fluorescent and non fluorescent Pseudomonas
    , 2007
    Co-Authors: Jeanmarie Meyer
    Abstract:

    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

Daniel Muller – One of the best experts on this subject based on the ideXlab platform.

  • 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, 2019
    Co-Authors: Vahid Keshavarz-tohid, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Audrey Dubost, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Daniel Muller
    Abstract:

    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.

  • Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani
    Research in Microbiology, 2017
    Co-Authors: Vahid Keshavarz-tohid, Claire Prigent-combaret, Daniel Muller, Jordan Vacheron, Parissa Taheri, Saeed Tarighi, Seyed Mohsen Taghavi, Yvan Moënne-loccoz
    Abstract:

    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.

  • Distribution of 2,4-diacetylphloroglucinol biosynthetic genes among the Pseudomonas spp. reveals unexpected polyphyletism
    Frontiers in Microbiology, 2017
    Co-Authors: Juliana Almario, Yvan Moënne-loccoz, Claire Prigent-combaret, Jordan Vacheron, Maxime Bruto, Daniel Muller
    Abstract:

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