Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato
© Deng et al. 2015
Received: 19 June 2015
Accepted: 29 September 2015
Published: 1 December 2015
Strain UFB2 was isolated from a soybean field soil in Mississippi and identified as a member of Pseudomonas chlororaphis. Strain UFB2 has a broad-spectrum antimicrobial activity against common soil-borne pathogens. Plate assays showed that strain UFB2 was especially efficient in inhibiting the growth of Clavibacter michiganensis 1–07, the causal agent of the devastating bacterial canker of tomato. Here, the complete genome sequence of P. chlororaphis strain UFB2 is reported and described. The strain UFB2 genome consists of a circular chromosome of 6,360,256 bp of which 87.86 % are protein-coding bases. Genome analysis revealed multiple gene islands encoding various secondary metabolites such as 2,4-diacetylphloroglucinol. Further genome analysis will provide more details about strain UFB2 antibacterial activities mechanisms and the use of this strain as a potential biocontrol agent.
KeywordsPseudomonas chlororaphis strain UFB2 Complete genome Biocontrol Bacterial canker of tomato Secondary metabolites
Bacterial strains of Pseudomonas chlororaphis are aerobic Gram-positive bacteria and many of the strains possess a wide-spectrum antifungal activity against soil-borne plant pathogens [1–5]. P. chlororaphis strains have been reported to be efficient plant-growth-promoting bacteria, which can be used as inoculants for biofertilization, phytostimulation and biocontrol . The use of P. chlororaphis strains as biocontrol agents is promising because they are capable of producing a variety of antimicrobial secondary metabolites including phenazine-1-carboxamide, 2-hydroxyphenazine, pyrrolnitrin, hydrogen cyanide, chitinases and proteases [6–8]. Moreover, P. chlororaphis is considered to be nonpathogenic to humans, wildlife, or the environment according to U.S. environmental protection agency (EPA) . Antimicrobial activities and low risks to animals and the environments have made the bacterium P. chlororaphis highly potential biocontrol agents in agriculture [8, 10]. A genome-wide research and analysis could provide useful information about the mechanisms of how P. chlororaphis protects plants against soil-borne phytopathogens. Currently, the whole genomes of a few P. chlororaphis strains that exhibit antifungal activity have been sequenced. These include P. chlororaphis strain PA23 that can protect canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum [2, 11], and P. chlororaphis PCL1606 that was isolated from avocado rhizosphere and exhibited biocontrol activity against soil-borne phytopathogenic fungi . In addition, another functionally-uncharacterized strain, P. chlororaphis subsp. aurantiaca JD37, was recently sequenced (NCBI reference sequence: NZ_CP009290.1). Genome sequences of P. chlororaphis strains with significant antibacterial activity have not been reported previously.
Strain UFB2 was isolated from a soybean field soil in Mississippi. Preliminary analysis of the 16S rRNA gene indicated that it is a member of P. chlororaphis . Plate assays indicated P. chlororaphis strain UFB2 has a broad spectrum of antimicrobial activities, especially against bacterial canker pathogen of tomato: Clavibacter michiganensis [12, 13]. Greenhouse trials demonstrated both living cells and culture extract of strain UFB2 can be used for disease management of bacterial canker of tomato. In this study, the P. chlororaphis strain UFB2 complete genome sequence and annotation are reported. The gene islands within strain UFB2 genome that encode various secondary metabolites, including antimicrobial compounds, are also described. The detailed description of the strain UFB2 genome will shed light into further studies of biocontrol effectiveness and applications of Pseudomonas species.
Classification and features
Classification and general features of Pseudomonas chlororaphis UFB2 according to the MIGS recommendations 
Species Pseudomonas chlororaphis
pH range; Optimum
D-glucose, D-galactose, L-rhamnose, D-mannitol, D-raffinose, D-fructose, D-arabinose, 2D-ribose, L-arabinose, L-xylose, D-xylose.
Fatty acid analysis was performed by gas chromatography (gas chromatograph, model 6890 N, Agilent Technologies) and analyzed by the Microbial Identification System (MIDI, Sherlock Version 6.1; database, TSBA40). The analysis of total cells showed the major fatty acids are C 16:1 ω7c (32 %), C 16:0 (28 %), C 18:1 ω7c (19 %). Fatty acid 3-hydroxy C 12:0 (5 %), C 12:0 (4 %), 2-hydroxy C 12:0 (4 %) and 3-hydroxy C 10:0 (3 %) were found in minor amount.
Genome sequencing information
Genome project history
P. chlororaphis strain UFB2 was selected for sequencing because of its significant antimicrobial activities and its potential as a biocontrol agent for agricultural use. Genomes of three P chlororaphis strains have been sequenced as of May 2015. Sequencing of the whole genome of strain UFB2 makes more data available for genome comparison and analysis within P. chlororaphis species.
libraries of 400 bp, mate pair library of 2,000, 5,000 and 8,000 bp
DNAStar Seqman NGen v12
Gene calling method
NCBI Prokaryotic Genome Annotation Pipeline
GenBank Date of Release
Jun 9th, 2015
Source Material Identifier
Growth conditions and genomic DNA preparation
P. chlororaphis strain UFB2 was cultured in liquid NBY medium overnight at 28 °C in a shaker at 220 rpm. The genomic DNA was extracted from 50 mL of the culture using the Wizard Genomic DNA Purification Kit (Promega Corporation, Madison, WI, USA). Totally approximately 900 μg of DNA were obtained with an OD260/280 of 1.9. The DNA sample was used for library construction with Illumina Genomic DNA Sample Preparation Kit (Illumina, CA, USA).
Genome sequencing and assembly
One standard library with an average insert size of 400 bp and three mate pair libraries with an average insert size of 2,000 bp, 5,000 bp and 8,000 bp were prepared and sequenced on the Illumina MiSeq instrument according to the manufacturer’s instructions. The genome was de novo assembled using a method as described by Durfee et al.  using DNAStar Seqman NGen (Version 12, DNASTAR, Inc. Madison, WI U.S.). The standard library and 2,000 bp mate pair library were selected for the de novo assembly. A total of 30 million short reads were scanned and extracted from the raw data files as input data. The short reads were preprocessed by Seqman NGen to trim adaptors and filter low-quality reads. Automatic Mer size and a minimum match percentage of 98 % were selected. 29 million short reads were assembled into 29 contigs and SeqMan Pro (Version 12, DNASTAR, Inc. Madison, WI U.S.) was used to order the contigs in one scaffold according to the mate pair data. The first round assembled sequence was then used as a template for a complete reassembly. The 2,000 bp and 8,000 bp mate pair data were incorporated to proofread the first assembly and to maximize coverage and quality. Adjacent contigs, if possible, were merged. Remaining gaps were filled by PCR and Sanger sequencing. No contigs that might correspond to plasmids remained unassembled. IslandViewer  was used to predict and identify genomic islands.
Automatic annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline , which combines gene calling algorithm with similarity-based gene detection approach to predict protein-coding genes, structural RNAs (5S, 16S, 23S), tRNAs and small non-coding RNAs. Additional gene prediction analysis and functional annotation were performed by the Integrated Microbial Genomes platform .
% of Total
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, Cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
Blast research of P. chlororaphis strain UFB2 genome against P. syringae pv. syringae B728a (NC_007005), P. putida KT2440 (NC_002947), P. chlororaphis strain PA23 (NZ_CP008696), P. aeruginosa PAO1 (NC_002516), P. fluorescens Pf0-1 (NC_007492) and P. sp. UW4 (NC_019670) genome revealed multiple unique gene regions which were only found in the strain UFB2 genome (Fig. 3). The BLASTn atlas showed noticeable genome diversity of strain UFB2 when compared to other Pseudomonas species. Seventy genomic islands ranging from 4 kbp to 30 kbp were also identified throughout the strain UFB2 genome, indicating significant horizontal gene transfers occurred during the evolution of strain UFB2 to better adapt the environment it inhabited.
P. chlororaphis strain UFB2 harbors an intact phl gene cluster (VM99_23970-23995), which is responsible for biosynthesis of the antimicrobial compound 2,4-diacetylphloroglucinol [33, 34]. 2,4-diacetylphloroglucinol is an especially efficient agent against soil borne fungal plant pathogens . The phl gene cluster is involved in the Pseudomonas antifungal activity against Clavibacter michiganensis 1–07 . Hydrogen cyanide [37, 38] biosynthesis gene homologs were also identified in strain UFB2 genome. The production of hydrogen cyanide by Pseudomonas species helps protect plants from soil-borne fungal pathogens [39, 40]. Biosynthetic gene clusters of common Pseudomonas species-produced antibiotics such as phenazine , pyrrolnitrin  and pyoluteorin  were not identified in strain UFB2 genome. Biosynthetic gene clusters of common toxins that contribute to plant and animal pathogenicity and/or virulence of Pseudomonas species were also searched for within strain UFB2 genome. The toxin biosynthetic gene cluster that were not identified in strain UFB2 genome include the phytotoxin lipopeptide syringomycin , tobacco wildfire spotting causal agent tabtoxin , bacterial canker of kiwifruit causal agent phaseolotoxin , plant-hormone-mimic toxin coronatine , and cytotoxic agent pederin . Strain UFB2 genome harbors homolog genes to those in the bacterial apical necrosis causal agent mangotoxin  biosynthesis gene cluster. However, mboC gene homolog that is required for mangotoxin production  was not identified in strain UFB2 genome. Overall, the lack of the key pathogenicity/virulence genes in strain UFB2 further indicates that strain UFB2 has a great potential as a biocontrol agent.
The complete genome sequence of P. chlororaphis strain UFB2 is described in this report. The strain UFB2 was originally isolated from the rhizosphere of a healthy soybean plant growing in a group of plants exhibiting charcoal rot disease in Mississippi. This strain possesses significant antimicrobial activities against a wide range of plant pathogenic bacteria and fungi. It is evident that the genome of P. chlororaphis strain UFB2 harbors the complete gene set for production of the antimicrobial compounds 2,4-DAPG and HCN, which may largely contribute to its antimicrobial activities. However, gene homologs required for biosynthesis of all the known toxins to plants, such as syringomycin, tabtoxin, phaseolotoxin, tolaasin, coronatine, or pederin, were absent from the strain UFB2 genome. The genome sequence of P. chlororaphis strain UFB2 will help in understanding genetic mechanisms of the antimicrobial activity studies that are useful for development of biologically-based disease management in agriculture.
We thank Chuan-Yu Hsu and Kurt C. Showmaker for sequencing services and Richard Baird, Sead Sabanadzovic and Justin Thornton for helpful discussion. This research was funded by USDA NIFA to SL (MIS-401170).
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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