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. 2016 Jun 10;227:25–26. doi: 10.1016/j.jbiotec.2016.04.020

Complete genome sequence of Pseudomonas azotoformans S4, a potential biocontrol bacterium

Yang Fang a,b,1, Lijuan Wu a,1, Guoqing Chen a, Guozhong Feng a,⁎
PMCID: PMC4869038  PMID: 27080451

Highlights

  • •

    Pseudomonas azotoformans S4 shows strong inhibitory activities against Fusarium fujikurio, a serious rice fungal pathogen.

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    The first complete genome of Pseudomonas azotoformans was sequenced in this study.

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    The genome consists of 6,859,618 bp with 5991 coding DNA sequences.

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    The genome contains 9 candidate gene clusters for the biosynthesis of secondary metabolites.

Keywords: Pseudomonas azotoformans, Genome sequence, Gene cluster, Secondary metabolism

Abstract

Pseudomonas azotoformans is a Gram-negative bacterium and infects cereal grains, especially rice. P. azotoformans S4 from soil sample derived from Lijiang, Yunnan Province, China, appeared to be strong inhibitory activity against Fusarium fujikurio, a serious rice fungal pathogen. Here, we present the complete genome of P. azotoformans S4, which consists of 6,859,618 bp with a circle chromosome, 5991 coding DNA sequences, 70 tRNA and 19 rRNA. The genomic analysis revealed that 9 candidate gene clusters are involved in the biosynthesis of secondary metabolites.

Pseudomonas azotoformans is a Gram-negative bacterium of the group Pseudomonas fluorescens, the genus Pseudomonas (Anzai et al., 2000). P. azotoformans is characterized to infect cereal grains, especially rice (Iizuka and Komogata, 1963). It is reported that P. azotoformans was used as effective biocontrol bacterium against cucumber Colletotrichum orbiculare (Sang et al., 2014). Recently we isolated P. azotoformans S4 from soil sample derived from Lijiang, Yunnan Province, China. This strain appeared to be strong inhibitory activity against Fusarium fujikurio (unpublished data), indicating that it is a potential biocontrol agent to protect rice against Bakanae disease (Wulff et al., 2010), an important rice disease caused by F. fujikurio (Wiemann et al., 2013). To further understand and explore the potential application of P. azotoformans S4, here we present the complete genome sequence of this strain.

The genome of S4 strain was sequenced using Single Molecular, Real-Time (SMRT) technology with the PacBio RS II sequencer (Berlin et al., 2015). The genomic DNA was isolated from P. azotoformans S4. 493,537,679 bases were acquired at 71.95 fold coverage. The yielded sequence reads were filtered and assembled using SMRT Analysis 2.3.0 (Koren and Phillippy, 2015). The resulting genome sequence revealed the presence of a single, circle chromosome with a size of 6,859,618 bp and an overall G + C content of 60.31% (Table 1). The circle chromosome was predicted with NCBI Prokaryotic Genome Automatic Annotation Pipeline (NCBI, 2013), resulting in the annotation of 5991 coding DNA sequences (CDSs). Furthermore, 94 RNA were identified, including 70 tRNA, and 19 rRNA, respectively. All the genomic information is shown in Table 1.

Table 1.

General genome feature of Pseudomonas sp. strain S4.

Features Values
Genome size (bp) 6,859,618
Contig numbers 1
Total number of genes 6324
G + C% numbers 60.31%
Protein coding genes 5991
RNA genes 94
tRNAs 70
rRNAs 19
ncRNAs 5
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Bacteria often use the strategy of antibiotic secondary metabolism in biocontrol (Rokem et al., 2007, van Wezel and McDowall, 2011). We analyzed the potential of the S4 strain to produce secondary metabolites using antiSMASH (Weber et al., 2015). 9 candidate gene clusters involved in secondary metabolism were found, including 4 NRPS gene clusters, 3 bacteriocin gene clusters, 1 terpene gene cluster and 1 unspecified gene cluster, suggesting that S4 strain has a wide range antibiotic activity. These candidate genes or gene clusters will be further analyzed to identify which one is responsible for inhibiting F. fujikurio.

In summary, the first complete genome of P. azotoformans S4 strain was sequenced, which will facilitate the biosynthetic studies of some important secondary metabolites and provides a possible application for controlling rice bakanae disease.

Strain and nucleotide sequence accession numbers

This strain has been deposited in China Centre for Type Culture Collection (CCTCC) with deposit number as CCTCC AB 2016041. The complete genome sequence has been deposited at GenBank under the Accession No. CP014546.

Acknowledgments

This research was supported by Incremental project of Chinese Academy of Agricultural Sciences (No. 2015ZL058), Innovation project of Chinese Academy of Agricultural Sciences. We thank Beijing Novogene Bioinformatics Technology Co., Ltd. for help in sequencing and bioinformatics.

References

  1. Anzai Y., Kim H., Park J.Y., Wakabayashi H., Oyaizu H. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int. J. Syst. Evol. Microbiol. 2000;50(Pt. 4):1563–1589. doi: 10.1099/00207713-50-4-1563. [DOI] [PubMed] [Google Scholar]
  2. Berlin K., Koren S., Chin C.S., Drake J.P., Landolin J.M., Phillippy A.M. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 2015;33:623–630. doi: 10.1038/nbt.3238. [DOI] [PubMed] [Google Scholar]
  3. Iizuka H., Komogata K. New species of Pseudomonas belonged to fluorescent group (Studies on the microorganisms of cereal grains. Part V) J. Agric. Chem. Soc. Jpn. 1963;37:137–141. [Google Scholar]
  4. Koren S., Phillippy A.M. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 2015;23:110–120. doi: 10.1016/j.mib.2014.11.014. [DOI] [PubMed] [Google Scholar]
  5. NCBI . 2013. NCBI Prokaryotic Genome Annotation Pipeline.https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Rokem J.S., Lantz A.E., Nielsen J. Systems biology of antibiotic production by microorganisms. Nat. Prod. Rep. 2007;24:1262–1287. doi: 10.1039/b617765b. [DOI] [PubMed] [Google Scholar]
  7. Sang M.K., Kim E.N., Han G.D., Kwack M.S., Jeun Y.C., Kim K.D. Priming-mediated systemic resistance in cucumber induced by Pseudomonas azotoformans GC-B19 and Paenibacillus elgii MM-B22 against Colletotrichum orbiculare. Phytopathology. 2014;104:834––842. doi: 10.1094/PHYTO-11-13-0305-R. [DOI] [PubMed] [Google Scholar]
  8. van Wezel G.P., McDowall K.J. The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat. Prod. Rep. 2011;28:1311–1333. doi: 10.1039/c1np00003a. [DOI] [PubMed] [Google Scholar]
  9. Weber T., Blin K., Duddela S., Krug D., Kim H.U., Bruccoleri R., Lee S.Y., Fischbach M.A., Muller R., Wohlleben W., Breitling R., Takano E., Medema M.H. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43:W237–W243. doi: 10.1093/nar/gkv437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Wiemann P., Sieber C.M., von Bargen K.W., Studt L., Niehaus E.M., Espino J.J., Huss K., Michielse C.B., Albermann S., Wagner D., Bergner S.V., Connolly L.R., Fischer A., Reuter G., Kleigrewe K., Bald T., Wingfield B.D., Ophir R., Freeman S., Hippler M., Smith K.M., Brown D.W., Proctor R.H., Munsterkotter M., Freitag M., Humpf H.U., Guldener U., Tudzynski B. Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog. 2013;9:e1003475. doi: 10.1371/journal.ppat.1003475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Wulff E.G., Sorensen J.L., Lubeck M., Nielsen K.F., Thrane U., Torp J. Fusarium spp. associated with rice Bakanae: ecology, genetic diversity, pathogenicity and toxigenicity. Environ. Microbiol. 2010;12:649––657. doi: 10.1111/j.1462-2920.2009.02105.x. [DOI] [PubMed] [Google Scholar]

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