Peribacillus butanolivorans strain KJ40, a soil bacterium isolated

from the rhizosphere soil of pepper, ameliorates drought stress

in the host plant. Here, we report the whole genome sequence

of strain KJ40. The sequence analysis revealed that strain KJ40

possesses a single 5,451,105 bp circular chromosome with an

DNA G + C-content of 38.13%. This chromosome contains

4,945 protein-coding sequences and 39 rRNA and 84 tRNA

genes. Thereafter using the sequencing data, the major genes

related to stress tolerance and plant growth processes, such as

proline and spermidine synthesis, and butanediol production,

were identified.

Keywords: Peribacillus butanolivorans, drought stress, genome,

KJ40, plant tolerance

Plants are constantly exposed to various biotic and abiotic

stresses, such as plant pathogens, pests, temperature, salinity,

and water, which affect plant growth and crop productivity

(Pandey et al., 2017). Drought stress is considered as one of

major abiotic stresses that negatively affect plant growth and

crop productivity (Jaleel et al., 2009). Many chemical fertilizers

and biofertilizers are used to ameliorate biotic and abiotic

stresses. Moreover, beneficial microorganisms are used as

biostimulants to improve the growth and yield of crops. Bacillus

strains are known as the most useful bacteria for plant and have

been investigated and used for the promotion of plant growth,

control of plant pathogens, and alleviation of stress tolerance

(Kim et al., 2017; Yoo et al., 2019; Saxena et al., 2020).

Previously, we reported that the Peribacillus butanolivorans

(reclassified from the genus Bacillus, Patel and Gupta, 2020)

strain KJ40 could be used as a potential biostimulant for the

alleviation of drought stress tolerance in chili pepper and that

the plants inoculated with this bacterial strain had increased

shoot fresh weight, chlorophyll, and stomatal conductance and

decreased malondialdehyde levels under natural drought

conditions (Kim et al., 2019). To better understand the

molecular mechanisms of abiotic stress tolerance induced by

this strain in plants, we analyzed the whole genome sequence of

strain KJ40.

Strain KJ40 was isolated from the pepper rhizosphere soil

and grown in tryptic soy broth at 28°C for 40 h under aerobic

condition. Genomic DNA was extracted from the cultured

strain KJ40 cells using a QIAamp DNA mini kit (Qiagen),

Korean Journal of Microbiology (2020) Vol. 56, No. 4, pp. 407-409 pISSN 0440-2413DOI https://doi.org/10.7845/kjm.2020.0103 eISSN 2383-9902Copyright ⓒ 2020, The Microbiological Society of Korea

Complete genome sequence of Peribacillus butanolivorans KJ40,

a soil bacterium alleviating drought stress in plants

Jaekyeong Song* , Songwha Kim, Ju Hee An, Mee Kyung Sang, and Hang-Yeon Weon

Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA),

Wanju 55365, Republic of Korea

식물의 가뭄 스트레스를 저감하는 토양 세균, Peribacillus butanolivorans

KJ40의 전체 게놈 서열

송재경* ･ 김송화 ･ 안주희 ･ 상미경 ･ 원항연

국립농업과학원 농업미생물과

(Received October 12, 2020; Revised November 10, 2020; Accepted November 10, 2020)

*For correspondence. E-mail: mgjksong@korea.kr;

Tel.: +82-63-238-3041; Fax: +82-63-238-3834

https://orcid.org/0000-0002-3553-6660https://orcid.org/0000-0002-3553-6660

408 ∙ Song et al.

미생물학회지 제56권 제4호

according to the manufacturer’s protocols. The whole genome

of strain KJ40 was sequenced with a 20-kb SMRTbell™

template library using the Pacific Biosciences (PacBio) RSII

Single Molecule Real Time (SMRT) sequencing platform at

Chunlab. The genome was assembled and annotated using

previously described analytical procedures (van Heel et al.,

2013; Weber et al., 2015; Kim et al., 2017). The complete genome

sequence of strain KJ40 was found to comprise 5,541,105 bp,

with an average DNA GC-content of 38.13%; no plasmids were

detected (Fig. 1). Strain KJ40 chromosome contains 4,945

protein-coding sequences (CDSs), and 39 rRNA and 84 tRNA

genes (Table 1). The sequencing analysis revealed that strain

KJ40 possesses a large number of genes associated with plant

abiotic stress tolerance and growth promotion. It also contains

genes related to proline and spermidine biosynthesis (proA, B,

and C, speA, B, D, and E), which encode organic osmolytes,

thereby inducing plant stress tolerance, and a gene (fabG)

involved in the biosynthesis of abscisic acid. The genome of

strain KJ40 also contains other genes related to osmotic stress

Fig. 1. Circular genome maps of the Peribacillus butanolivorans KJ40 complete genome. The circular map consists of five circles. From the outermost circle

to the inner, each circle contains information about (1) rRNA/ tRNA, (2) Reverse CDS, (3) Forward CDS, (4) GC Ratio, and (5) GC Skew.

Table 1. Genome features of Peribacillus butanolivorans KJ40

Genomic features Chromosome

Genome size (bp) 5,451,105

Number of contigs 1

G + C content (%) 38.13

Protein-coding genes (CDSs) 4,945

rRNA genes 39

tRNA genes 84

ncRNA genes 6

Pseudogenes 180

Plasmids 0

Accession number (GenBank) CP050509

Complete genome sequence of Peribacillus butanolivorans KJ40 ∙ 409

Korean Journal of Microbiology, Vol. 56, No. 4

and heat shock tolerance and genes for acetoin utilization (acuA,

B, and C) and acetolactate synthase (ilvB and ilvH), which are

involved in butanediol biosynthesis and are known to promote

plant growth. Strain KJ40 genome has genes associated with

the synthesis of siderophores (iucA, B, C, and D), which are

known to stimulate plant health. It also possesses genes related

to exopolysaccharide production (capB and D, epsC and exoO).

Overall, the genome analysis of strain KJ40 genome revealed

that it possesses several genes that are essential for alleviating

drought stress in plants and thus is a promising biostimulant for

improving crop productivity.

Nucleotide sequence accession number

The whole genome sequence of strain KJ40 described in this

study was deposited to the National Center for Biotechnology

Information (NCBI) with the accession number CP050509.

Additionally, the strain was deposited to the Korean Agricultural

Culture Collection (KACC) under the accession number KACC

92262P.

적 요

식물의 가뭄 스트레스에 대한 내성을 강화시키는 Peribacillus

butanolivorans KJ40 균주는 고추 근권 토양에서 분리되었다.

본 연구에서 KJ40 균주의 전체 염기서열을 분석한 결과, KJ40

균주는 5,451,105 bp를 가진 단일 환형 염색체로서 G + C 함량

은 38.13%로 구성되었다. 이 유전체는 4,945개의 단백질 암호

화 염기서열을 가졌으며, 39개의 rRNA와 84개의 tRNA 유전

자를 포함하였다. 유전체로부터 스트레스 내성과 생육 증진에

관련된 프롤린과 스퍼미딘의 합성과 부탄디올의 생성관련 유

전자를 확인하였다.

Acknowledgments

This study was carried out with the support of “Research

Program for Agricultural Science & Technology Development

(Project No PJ01351903)” from the National Institute of

Agricultural Sciences, Rural Development Administration,

Republic of Korea.

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