ABSTRACT
Pseudomonas chlororaphis Lzh-T5 is a plant growth-promoting rhizobacterium (PGPR) with antimicrobial activity isolated from tomato rhizosphere in the city of Dezhou, Shandong Province, China. Here, the draft genome sequence of P. chlororaphis Lzh-T5 is reported, and several functional genes related to antifungal antibiotics and siderophore biosynthesis have been found in the genome.
GENOME ANNOUNCEMENT
Rhizobacteria referred to as plant growth-promoting rhizobacteria (PGPRs) (1, 2), which have antimicrobial activity and could influence plant growth, have the potential for use as bioagents in controlling plant diseases and improving crop production. Pseudomonas chlororaphis is a widespread bacterium in the rhizosphere soil which can produce phenazine antibiotics that exhibit antifungal activity (3–6).
Strain P. chlororaphis Lzh-T5 was isolated from tomato rhizosphere in an area affected by root rot, a fungal disease caused by Fusarium moniliforme. Here, we report the draft genome sequence of P. chlororaphis Lzh-T5. Genomic DNA of P. chlororaphis Lzh-T5 was extracted and then sequenced using the PacBio and Illumina MiSeq systems, respectively.
The raw data were filtered and assembled by SPAdes software version 3.9.0 (7) and A5-MiSeq version 20150522 (8) to generate 1,224 Mb of total clean data, and the genome coverage was 164.0×. The assembled genome of P. chlororaphis Lzh-T5 comprises a single circular chromosome of 6,826,693 bp in length, with a GC content of 63.06%. Its genome comprises 6,282 genes, 6,116 open reading frames (ORFs), 67 tRNA genes, and 16 rRNA genes, which is similar to P. chlororaphis PA23 (99%) (GenBank accession number CP008696), P. chlororaphis ATCC 13985 (99%) (GenBank accession number LT629738), and P. chlororaphis LMG 21630 (98%) (GenBank accession number LT629747).
Like most Pseudomonas spp., P. chlororaphis Lzh-T5 possessed several gene clusters to generate siderophores, such as pyoverdine (PVD) and achromobactin. There were two nonadjacent clusters involved in PVD synthesis, including 4 nonribosomal peptide synthetase (NRPS) genes (GenBank accession numbers CXP47_RS20395, CXP47_RS20400, CXP47_RS20405, and CXP47_RS20875) (9). Clusters to synthesize achromobactin consisted of the synthesis genes acsA-F (CXP47_RS15760, CXP47_RS15765, CXP47_RS15770, CXP47_RS15780, CXP47_RS15785 and CXP47_RS15790) and achromobactin transporter genes cbrA through cbrD (CXP47_RS15755, CXP47_RS15750, CXP47_RS15745, and CXP47_RS15740) (10).
P. chlororaphis Lzh-T5 can also synthesize antifungal antibiotics, and gene clusters for antibiotics synthesis were found. For example, prnA through prnD (CXP47_RS17640, CXP47_RS17635, CXP47_RS17630, and CXP47_RS17625) coding for pyrrolnitrin (11), hcnA through hcnC (CXP47_RS12080, CXP47_RS12085, and CXP47_RS12090) coding for volatile compound hydrogen cyanide (12), and phzI, phzR, phzA through phzG, and phzO (CXP47_RS25500, CXP47_RS25505, CXP47_RS25510, CXP47_RS25515, CXP47_RS25520, CXP47_RS25525, CXP47_RS25530, CXP47_RS25535, CXP47_RS25540, and CXP47_RS25545) coding for phenazine, were found (3). Meanwhile, as nitrogen-containing pigments, phenazine and its derivatives also have many biotechnological applications, such as colorimetric redox indicators (13).
In conclusion, the genome sequence and annotation of P. chlororaphis Lzh-T5 contributed to revealing the molecular mechanism of its antimicrobial activity, which suggests that P. chlororaphis Lzh-T5 could be used as a biocontrol agent of various soilborne diseases.
Accession number(s).
The whole-genome shotgun project of Pseudomonas chlororaphis Lzh-T5 has been deposited at GenBank under the accession number CP025309.
ACKNOWLEDGMENTS
This work was supported by Natural Science Foundation of Shandong Province (grant ZR2015CQ002), the Taishan Young Scholars Program of Shandong Province of China (grant tsqn20161049), the Talent Introduction Project of Dezhou University of China (grant 2016kjrc10), Projects of Science and Technology for Colleges and Universities in Shandong Province (grants J17KA099 and J15LE09), the National Natural Science Foundation of China (grants 31500606 and 61671107), and the Shandong Provincial Key Laboratory of Agricultural Microbiology Open Fund (grant SDKL2017015).
Footnotes
Citation Li Z, Li X, Zeng Q, Chen M, Liu D, Wang J, Shen L, Song F. 2018. Genome sequence of Pseudomonas chlororaphis Lzh-T5, a plant growth-promoting rhizobacterium with antimicrobial activity. Genome Announc 6:e00328-18. https://doi.org/10.1128/genomeA.00328-18.
REFERENCES
- 1.Handelsman J, Stabb EV. 1996. Biocontrol of soilborne plant pathogens. Plant Cell 8:1855–1869. doi: 10.1105/tpc.8.10.1855. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Bhattacharyya PN, Jha DK. 2012. Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28:1327–1350. doi: 10.1007/s11274-011-0979-9. [DOI] [PubMed] [Google Scholar]
- 3.Calderón CE, Ramos C, de Vicente A, Cazorla FM. 2015. Comparative genomic analysis of Pseudomonas chlororaphis PCL1606 reveals new insight into antifungal compounds involved in biocontrol. Mol Plant Microbe Interact 28:249–260. doi: 10.1094/MPMI-10-14-0326-FI. [DOI] [PubMed] [Google Scholar]
- 4.Ranjbariyan A, Shams-Ghahfarokhi M, Razzaghi-Abyaneh M. 2014. Antifungal activity of a soil isolate of Pseudomonas chlororaphis against medically important dermatophytes and identification of a phenazine-like compound as its bioactive metabolite. J Mycol Med 24:e57–e64. doi: 10.1016/j.mycmed.2014.01.117. [DOI] [PubMed] [Google Scholar]
- 5.Morohoshi T, Wang WZ, Suto T, Saito Y, Ito S, Someya N, Ikeda T. 2013. Phenazine antibiotic production and antifungal activity are regulated by multiple quorum-sensing systems in Pseudomonas chlororaphis subsp. aurantiaca StFRB508. J Biosci Bioeng 116:580–584. doi: 10.1016/j.jbiosc.2013.04.022. [DOI] [PubMed] [Google Scholar]
- 6.Kiprianova EA, Shepelevich VV, Klochko VV, Ostapchuk AN, Varbanets LD, Skokliuk LB, Berezkina AE, Avdeeva LV. 2013. Antifungal and antiviral substances of Pseudomonas chlororaphis subsp. aureofaciens strains–components of gaupsin. Mikrobiol Z 75:28–35. (In Russian.) [PubMed] [Google Scholar]
- 7.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Coil D, Jospin G, Darling AE. 2015. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589. doi: 10.1093/bioinformatics/btu661. [DOI] [PubMed] [Google Scholar]
- 9.Ringel MT, Dräger G, Brüser T. 2016. PvdN enzyme catalyzes a periplasmic pyoverdine modification. J Biol Chem 291:23929–23938. doi: 10.1074/jbc.M116.755611. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Berti AD, Thomas MG. 2009. Analysis of achromobactin biosynthesis by Pseudomonas syringae pv. syringae B728a. J Bacteriol 191:4594–4604. doi: 10.1128/JB.00457-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Costa R, van Aarle IM, Mendes R, van Elsas JD. 2009. Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within Gram-negative bacteria. Environ Microbiol 11:159–175. doi: 10.1111/j.1462-2920.2008.01750.x. [DOI] [PubMed] [Google Scholar]
- 12.Michelsen CF, Stougaard P. 2012. Hydrogen cyanide synthesis and antifungal activity of the biocontrol strain Pseudomonas fluorescens In5 from Greenland is highly dependent on growth medium. Can J Microbiol 58:381–390. doi: 10.1139/w2012-004. [DOI] [PubMed] [Google Scholar]
- 13.Bilal M, Guo S, Iqbal HMN, Hu H, Wang W, Zhang X. 2017. Engineering Pseudomonas for phenazine biosynthesis, regulation, and biotechnological applications: a review. World J Microbiol Biotechnol 33:191. doi: 10.1007/s11274-017-2356-9. [DOI] [PubMed] [Google Scholar]