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. 2013;8(3):e58640.
doi: 10.1371/journal.pone.0058640. Epub 2013 Mar 13.

The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas Sp. UW4

Free PMC article

The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas Sp. UW4

Jin Duan et al. PLoS One. .
Free PMC article


The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated "housekeeping" genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Figure 1
Figure 1. Circular genome map of P. sp. UW4.
From the outside in, the outer black circle shows the scale line in Mbps; circles 2 and 3 represent the coding region with the colors of the COG categories; circle 4 and 5 show tRNA (green) and rRNA (red), respectively; circle 6 displays the IS elements (blue); circle 7 shows the genomic islands (orange); circle 8 represents mean centered G+C content (bars facing outside-above mean, bars facing inside-below mean); circle 9 shows GC skew (G−C)/(G+C). GC content and GC skew were calculated using a 10-kb window in steps of 200 bp.
Figure 2
Figure 2. Genomic islands of P. sp. UW4 predicted by IslandViewer.
The outer black circle shows the scale line in Mbps. Predicted genomic islands are colored based on the following methods: SIGI-HMM, orange; IslandPath-DIMOB, blue; Integrated detection, red. Black plot represents the GC content (%).
Figure 3
Figure 3. Schematic overview of metabolic pathways and transport systems in P. sp. UW4.
Individual pathways are denoted by single-headed arrows, while reversible pathways are denoted by double-headed arrows.
Figure 4
Figure 4. Phylogenetic tree of 21 different Pseudomonas species, base on 1,679 conserved genes.
Numbers on nodes represent percentages of individual trees containing that relationship. The scale bar corresponds to the number of substitutions per site.
Figure 5
Figure 5. Comparative synteny line plots of the complete six-frame translations of the whole genome sequences of P. sp. UW4 with other P. fluorescens.
P. protegens, and P. putida genomes. The analysis was carried out using Artemis Comparison Tool and computed using TBLASTX with a cutoff E value of 1 E-5. The red bars between the DNA lines indicate individual TBLASTX matches, and the blue lines exhibit inverted matches. The cutoff identities and alignments length are 75% and 30 amino acids, respectively.
Figure 6
Figure 6. ML phylogenetic tree of 16S rRNA sequences from completely sequenced Pseudomonas genomes.
Nodal support was evaluated by aLRT. Different species are shown in different colors. Only unique sequences from each genome were included for this analysis.
Figure 7
Figure 7. Phylogenetic tree of 128 Pseudomonas strains based on four concatenated genes including 16S rRNA, gyrB, rpoB and rpoD.
Dendrogram was generated by neighbor-joining and distance matrix was calculated by the Jukes-Cantor algorithm. The bar at the bottom indicates sequence divergence. Nodal support was evaluated with 1000 bootstrap pseudoreplications and values of greater than 50% are shown at the nodes.

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    1. Glick BR, Karaturovic DM, Newell PC (1995) A novel procedure for rapid isolation of plant growth promoting pseudomonads. Canadian Journal of Microbiology 41(6): 533–536.
    1. Shah S, Li J, Moffatt BA, Glick BR (1998) Isolation and Characterization of ACC deaminase genes from two different plant growth-promoting rhizobacteria. Canadian Journal of Microbiology 44(9): 833–843. - PubMed
    1. Hontzeas N, Richardson AO, Belimov A, Safronova V, Abu-Omar MM, et al. (2005) Evidence for horizontal transfer of 1-aminocyclopropane-1-carboxylate deaminase genes. Applied and Environmental Microbiology 71(11): 7556–7558. - PMC - PubMed
    1. Li J, Ovakim DH, Charles TC, Glick BR (2000) An ACC deaminase minus mutant of Enterobacter cloacae UW4 no longer promotes root elongation. Current Microbiology 41(2): 101–105. - PubMed
    1. Grichko VP, Glick BR (2000) Identification of DNA sequences that regulate the expression of the Enterobacter cloacae UW4 1-aminocyclopropane-1-carboxylate deaminase gene. Canadian Journal of Microbiology 46(12): 1159–1165. - PubMed

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Funding for this study was provided by the Natural Science and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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