Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.


:The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.


Appl Environ Microbiol


Jun SR,Wassenaar TM,Nookaew I,Hauser L,Wanchai V,Land M,Timm CM,Lu TY,Schadt CW,Doktycz MJ,Pelletier DA,Ussery DW




Has Abstract


2015-10-30 00:00:00














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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Parker MA

    更新日期:2002-04-01 00:00:00

  • Quantification of nitrogen reductase and nitrite reductase genes in soil of thinned and clear-cut Douglas-fir stands by using real-time PCR.

    abstract::The abundance of nifH, nirS, and nirK gene fragments involved in nitrogen (N) fixation and denitrification in thinned second-growth Douglas-fir (Pseudotsuga menziesii subsp. menziesii [Mirb.] Franco) forest soil was investigated by using quantitative real-time PCR. Prokaryotic N cycling is an important aspect of N ava...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Levy-Booth DJ,Winder RS

    更新日期:2010-11-01 00:00:00

  • Detection of botulinum neurotoxin serotype A, B, and F proteolytic activity in complex matrices with picomolar to femtomolar sensitivity.

    abstract::Rapid, high-throughput assays that detect and quantify botulinum neurotoxin (BoNT) activity in diverse matrices are required for environmental, clinical, pharmaceutical, and food testing. The current standard, the mouse bioassay, is sensitive but is low in throughput and precision. In this study, we present three bioc...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Dunning FM,Ruge DR,Piazza TM,Stanker LH,Zeytin FN,Tucker WC

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  • Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction.

    abstract::Production of unconventional oil and gas continues to rise, but the effects of high-density hydraulic fracturing (HF) activity near aquatic ecosystems are not fully understood. A commonly used biocide in HF, 2,2-dibromo-3-nitrilopropionamide (DBNPA), was studied in microcosms of HF-impacted (HF+) versus HF-unimpacted ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Campa MF,Techtmann SM,Ladd MP,Yan J,Patterson M,Garcia de Matos Amaral A,Carter KE,Ulrich N,Grant CJ,Hettich RL,Lamendella R,Hazen TC

    更新日期:2019-10-16 00:00:00

  • Identification of a Novel Elastin-Degrading Enzyme from the Fish Pathogen Flavobacterium psychrophilum.

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    authors: Rochat T,Pérez-Pascual D,Nilsen H,Carpentier M,Bridel S,Bernardet JF,Duchaud E

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  • Determination of thermal inactivation kinetics of hepatitis A virus in blue mussel (Mytilus edulis) homogenate.

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Bozkurt H,D'Souza DH,Davidson PM

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    pub_type: 杂志文章


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    pub_type: 杂志文章


    authors: Denolf P,Jansens S,Peferoen M,Degheele D,Van Rie J

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Timms P

    更新日期:1981-01-01 00:00:00

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    abstract::A defined medium for Aquaspirillum serpens VHL allows the replacement of the complex media now in use. It was developed by batch culture methods but supports growth in continuous culture. A basal salts medium supplemented with L-aspartic acid, L-alanine, and L-glutamic acid provided the best growth (turbidity), as lon...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Whitby GE,Murray RG

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    authors: Saito K,Drgon T,Robledo JA,Krupatkina DN,Vasta GR

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    authors: Bonnet C,Diarrassouba F,Brousseau R,Masson L,Topp E,Diarra MS

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    authors: Korthals ET,Winfrey MR

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    authors: Berg G,Sullivan G

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    authors: Schoenborn L,Yates PS,Grinton BE,Hugenholtz P,Janssen PH

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    authors: Posno M,Heuvelmans PT,van Giezen MJ,Lokman BC,Leer RJ,Pouwels PH

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    abstract::Cold shock at 0 to 15 degrees C for 1 to 3 h increased the thermal sensitivity of Listeria monocytogenes. In a model broth system, thermal death time at 60 degrees C was reduced by up to 45% after L. monocytogenes Scott A was cold shocked for 3 h. The duration of the cold shock affected thermal tolerance more than did...

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    authors: Hiessl S,Böse D,Oetermann S,Eggers J,Pietruszka J,Steinbüchel A

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    authors: Ishimori Y,Karube I,Suzuki S

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    authors: Blackburn M,Golubeva E,Bowen D,Ffrench-Constant RH

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    authors: Rapala J,Sivonen K,Lyra C,Niemelä SI

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    authors: Coquet L,Cosette P,Quillet L,Petit F,Junter GA,Jouenne T

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    pub_type: 杂志文章


    authors: Chen F,Suttle CA,Short SM

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    authors: Brown DR,Holt JG,Pattee PA

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Tortoso AC,Hutchinson GL

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    authors: Siragusa S,Di Cagno R,Ercolini D,Minervini F,Gobbetti M,De Angelis M

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