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

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 6,859,618bp 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 This strain appeared to be strong inhibitory activity against Fusarium fujikurio (unpublished data), indicating that it is a potential biocontrol agent to protect rice against Bakanae disease (Wulff et al., 2010), an important rice disease caused by F.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

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.