Abstract
Delftia tsuruhatensis MTQ3 is a plant growth-promoting rhizobacterium (PGPR) isolated from tobacco rhizosphere. Here, we report the draft genome sequence of D. tsuruhatensis MTQ3. Several functional genes related to antimicrobial activity and environment adaption have been found in the genome. This is the first genome sequence of D. tsuruhatensis related to PGPR.
GENOME ANNOUNCEMENT
Delftia tsuruhatensis, the type species of Delftia, is considered a plant growth-promoting rhizobacterium (PGPR) (1–3), an organic pollutant degradation strain (4, 5), and an opportunistic pathogenic bacterium to the human body (6, 7). D. tsuruhatensis is widespread in rhizosphere soil, activated sludge, and polluted environments. Although some researchers have reported the antimicrobial activity of D. tsuruhatensis, its antimicrobial substance and relevant synthesis mechanisms are still unclear. D. tsuruhatensis MTQ3 was isolated from the soil of tobacco rhizosphere in Guizhou, China, and it has shown antimicrobial activity against pathogens of soilborne plant diseases such as Ralstonia solanacearum and Phytophthora nicotianae.
Here, we report the draft genome sequence of D. tsuruhatensis MTQ3. Genomic DNA was extracted and sequenced using the Illumina HiSeq 2500 platform. The whole shotgun sequencing produced 8,206,833 paired-end reads with an average insert size of 580 bp (over 780-fold coverage). Another mate-paired (MP) library containing 3- to 5-kb inserts was constructed, and 13,462,994 paired-end reads were produced. All these raw data were then filtered by Trimmomatic v 0.30 (8). Filtered reads were assembled, scaffolded, and gap filled with Velvet v. 1/2/08 (9), SSPACE v. 2.0 (10), and GapFiller v. 1.11 (11). Final assembly consisted of 12 scaffolds (length ≥500 bp) with an N50 length of 742,938 bp, an average length of 522,672 bp, and the largest length of 1,608,022 bp. The genome sequence was annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/).
The genome consists of 6.27 Mb, with a G+C content of 66.79%. A total of 5,005 coding sequences (CDS), 13 pseudogenes, 72 tRNA genes, 1 noncoding RNA (ncRNA), and 10 rRNA genes were identified. Average nucleotide identity (ANI) analysis (12) revealed that D. tsuruhatensis MTQ3 is phylogenetically related to D. tsuruhatensis 391 (98.34%) (GenBank accession no. JNWH00000000), D. acidovorans CCUG 274B (97.96%) (AGYX00000000), D. acidovorans SPH-1 (94.94%) (NC_010002), Delftia sp. 670 (94.30%) (JNWI00000000), D. acidovorans CCUG 15835 (92.70%) (AGYY00000000), and Delftia sp. Cs1-4 (91.37%) (NC_015563).
Many genes involved in the antimicrobial activity of D. tsuruhatensis MTQ3 were identified in the genome, such as the bacteriocin gene (AA671_02705), polyketide synthase (PKS) gene (AA671_12420), nonribosomal peptide synthetase (NRPS) gene (AA671_12430), balhimycin synthesis gene (AA671_12395), quinolinate synthesis gene (AA671_01765), and phenazine synthesis gene (AA671_00865). Some genes responsible for the processing and transport of antibiotics were identified in the genome, including antibiotic biosynthesis monooxygenase gene (AA671_01400, AA671_17345), macrolide transporter gene (AA671_00980), and antibiotic ABC transporter substrate-binding gene (AA671_25335).
In addition, D. tsuruhatensis MTQ3 possesses genes with likely relevance to rhizosphere competence and adaptation in polluted environments. Specifically, quercetin dioxygenase (AA671_16710, AA671_18600) is likely a plant microbe-signaling bacterium involved in degrading plant-produced antimicrobial root exudates (13, 14). Protocatechuate dioxygenase (AA671_06970, AA671_06975, AA671_20040, AA671_20045, AA671_25085, AA671_25090) may be related to the degradation of aromatic acid (15). Genes related to the degradation of phenylacetic acid (AA671_06085, AA671_20955, AA671_23770, AA671_24525, AA671_24535) and hydroxyatrazine (AA671_03765) were also identified.
Nucleotide sequence accession numbers.
The whole-genome shotgun project of D. tsuruhatensis MTQ3 has been deposited in DDBJ/ENA/GenBank under the accession number LCZH00000000. The version described in this paper is the first version, LCZH01000000.
ACKNOWLEDGMENTS
We thank all people for their contributions to the accomplishment of this task. This work was supported by the Research Project of Zunyi Tobacco Company (2008zyyckj-01), Guizhou, China.
Footnotes
Citation Hou Q, Wang C, Guo H, Xia Z, Ye J, Liu K, Yang Y, Hou X, Liu H, Wang J, Du B, Ding Y. 2015. Draft genome sequence of Delftia tsuruhatensis MTQ3, a strain of plant growth-promoting rhizobacterium with antimicrobial activity. Genome Announc 3(4):e00822-15. doi:10.1128/genomeA.00822-15.
REFERENCES
- 1.Validov S, Kamilova F, Qi S, Stephan D, Wang JJ, Makarova N, Lugtenberg B. 2007. Selection of bacteria able to control Fusarium oxysporum f. sp. radicis-lycopersici in stonewool substrate. J Appl Microbiol 102:461–471. doi: 10.1111/j.1365-2672.2006.03083.x. [DOI] [PubMed] [Google Scholar]
- 2.Han J, Sun L, Dong X, Cai Z, Sun X, Yang H, Wang Y, Song W. 2005. Characterization of a novel plant growth-promoting bacteria strain Delftia tsuruhatensis HR4 both as a diazotroph and a potential biocontrol agent against various plant pathogens. Syst Appl Microbiol 28:66–76. doi: 10.1016/j.syapm.2004.09.003. [DOI] [PubMed] [Google Scholar]
- 3.Jin F, Ding Y, Ding W, Reddy MS, Fernando WG, Du B. 2011. Genetic diversity and phylogeny of antagonistic bacteria against Phytophthora nicotianae isolated from tobacco rhizosphere. Int J Mol Sci 12:3055–3071. doi: 10.3390/ijms12053055. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Zhang LL, He D, Chen JM, Liu Y. 2010. Biodegradation of 2-chloroaniline, 3-chloroaniline, and 4-chloroaniline by a novel strain Delftia tsuruhatensis H1. J Hazard Mater 179:875–882. doi: 10.1016/j.jhazmat.2010.03.086. [DOI] [PubMed] [Google Scholar]
- 5.De Gusseme B, Vanhaecke L, Verstraete W, Boon N. 2011. Degradation of acetaminophen by Delftia tsuruhatensis and Pseudomonas aeruginosa in a membrane bioreactor. Water Res 45:1829–1837. doi: 10.1016/j.watres.2010.11.040. [DOI] [PubMed] [Google Scholar]
- 6.Preiswerk B, Ullrich S, Speich R, Bloemberg GV, Hombach M. 2011. Human infection with Delftia tsuruhatensis isolated from a central venous catheter. J Med Microbiol 60:246–248. doi: 10.1099/jmm.0.021238-0. [DOI] [PubMed] [Google Scholar]
- 7.Keusch S, Speich R, Treder U, Ulrich Somaini S. 2013. Central venous catheter infections in outpatients with pulmonary hypertension treated with continuous iloprost. Respiration 86:402–406. doi: 10.1159/000350441. [DOI] [PubMed] [Google Scholar]
- 8.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Zerbino DR. 2010. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics Chapter 11:Unit 11.5. doi: 10.1002/0471250953.bi1105s31. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding preassembled contigs using SSPACE. Bioinformatics 27:78–79. doi: 10.1093/bioinformatics/btq683. [DOI] [PubMed] [Google Scholar]
- 11.Boetzer M, Pirovano W. 2012. Toward almost closed genomes with GapFiller. Genome Biol 13:R56. doi: 10.1186/gb-2012-13-6-r56. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. doi: 10.1073/pnas.0906412106. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R. 2007. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25:1007–1014. doi: 10.1038/nbt1325. [DOI] [PubMed] [Google Scholar]
- 14.Ramos FA, Takaishi Y, Shirotori M, Kawaguchi Y, Tsuchiya K, Shibata H, Higuti T, Tadokoro T, Takeuchi M. 2006. Antibacterial and antioxidant activities of quercetin oxidation products from yellow onion (Allium cepa) skin. J Agr Foods Chem 54:3551–3557. doi: 10.1021/jf060251c. [DOI] [PubMed] [Google Scholar]
- 15.Guzik U, Hupert-Kocurek K, Sitnik M, Wojcieszyńska D. 2014. Protocatechuate 3,4-dioxygenase: a wide substrate specificity enzyme isolated from Stenotrophomonas maltophilia KB2 as a useful tool in aromatic acid biodegradation. J Mol Microbiol Biotechnol 24:150–160. doi: 10.1159/000362791. [DOI] [PubMed] [Google Scholar]