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Complete genome sequence of Cytobacillus firmus JBRS159, a biocontrol agent against bacterial panicle blight of rice plants
Korean J. Microbiol. 2023;59(1):55-57
Published online March 31, 2023
© 2023 The Microbiological Society of Korea.

Swarnalee Dutta1, Jun An Kang1, Nguyen Van Khanh1, Soo Yeon Choi2, and Yong Hoon Lee1,3*

1Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea
2Crop Foundation Division, National Institute of Crop Science, Wanju 55365, Republic of Korea
3Advanced Institute of Environment and Bioscience, Plant Medical Research Center, and Institute of Bio-industry, Jeonbuk National University, Iksan 54596, Republic of Korea
Correspondence to: *E-mail:; Tel.: +82-63-850-0841; Fax: +82-63-850-0834
Received March 6, 2023; Revised March 29, 2023; Accepted March 29, 2023.
Cytobacillus firmus JBRS159 (JBRS159) isolated from rice grain suppressed bacterial seedling rot caused by Burkholderia glumae and promoted growth of Arabidopsis and rice. Here, we present the complete genome sequence of JBRS159 to reveal underlying characteristics for biocontrol and growth promotion activities. The genome comprises of two contigs of 4,867,753 bp and 96,746 bp (total 4,964,499 bp) with GC content 41.9% and 36.6%, respectively. Contig 1 includes 4,703 protein CDSs, 107 tRNAs, and 36 rRNAs while contig 2 contains 111 protein CDSs. The analysis revealed gene clusters for siderophore, hydrogen cyanide, and acetoin production, and phosphate solubilization, which are important for plant growth promotion and biocontrol of diseases.
Keywords : Bacillus, biocontrol, growth promotion, PGPR

Cytobacillus firmus (formerly known as Bacillus firmus), a Gram-positive bacterium, has been reported to promote plant growth and have antagonistic activity against nematodes (Ghahremani et al., 2020; Patel and Gupta, 2020; Huang et al., 2021). Cytobacillus firmus produced indole-3-acetic acid (IAA) and biosynthesized silver nanoparticles that showing antimicrobial activities, which made the strain to be scientific interest (Gunasekaran et al., 2022; Saied et al., 2022). The C. firmus JBRS159 that was isolated from rice grain using 1/10 tryptic soy agar media supplemented with 1% rice seed extracts showed biocontrol efficacy against bacterial seedling rot caused by Burkholderia glumae and promoted the growth of Arabidopsis and rice. In this study, we analyzed the whole genome of the strain JBRS159 to understand the underlying mechanism in biocontrol and growth promotion activities. The strain JBRS159 was deposited in the Korean Agricultural Culture Collection (KACC) with accession number of KACC 92494P.

Total genomic DNA was extracted using the Wizard Genomic DNA purification kit (Promega) according to the manufacturer’s instructions and whole genome was sequenced by Macrogen Inc. with high-throughput sequencing approaches using PacBio Sequel System and Illumina HiSeqXten. The sequencing libraries were prepared using PacBio Sequel Microbial Library Construction (Pacific Biosciences) and a TruSeq Nano DNA kit for Illumina following manufacturer’s protocols. Annotation of the genome was performed using the National Center for Biotechnology Information (NCBI)’s Prokaryotic Genome Annotation Pipeline 2.0 (PGAP) (Tatusova et al., 2016). The PacBio platform produced a total of 235,105 subreads (total 2,744,936,018) with N50 of 14,097 and average length of 11,675. Illumina generated 13,181,626 reads with 100% coverage. Corrected reads were assembled de novo, circularized using the SMRT analysis pipeline and corrected by Pilon to produce two contigs with 4,867,753 bp and 96,746 bp (total 4,964,499 bp) and an N50 value of 4,867,753. The GC content of contig 1 and contig 2 were 41.9% and 36.6%, respectively. Each contig has 4,865 and 115 total coding sequences (CDSs) and 4,703 and 111 protein CDSs. There are 107 tRNAs and 36 rRNAs (12, 12, 12 of 5S, 16S, and 23S, respectively) in contig 1 and none in contig 2 (Table 1).

Genomic features of <italic>Cytobacillus firmus</italic> JBRS159 genome
Genome features Contig 1 Contig 2 Total
Genome size (bp) 4,867,753 96,746 4,964,499
GC % 41.9 36.6 41.8
CDS (total) 4,865 115 4,980
CDS (with protein) 4,703 111 4,814
tRNAs 107 0 107
rRNAs (5S, 16S, 23S) 12, 12, 12 0 36
GenBank accession No. JAQZDS010000002.1 JAQZDS010000001.1

The genome contains genes or gene clusters for the production of siderophore (petrobactin) and hydrogen cyanide; and phosphate solubilization such as Pi-specific transporter (pst), alkaline phosphatase (phoA), and glycerophosphoryldiester phosphodiesterase (glpQ), which are important for plant growth promotion and competition with other microbes. Genes related to biosynthesis of acetoin, IAA, and tryptophan were also identified. Genes, swrC_1 (gene locus tag PUS82_ 17525), swrC_2 (PUS82_21695), and swrC_3 (PUS82_24345) putatively encoding proteins for swarming motility and bacF gene (PUS82_17340) for bactofilin filament, which might help in plant root colonization were also detected. Analysis through ‘antibiotics & Secondary Metabolite Analysis Shell’ (antiSMASH) v. 6 (Blin et al., 2021) predicted contig 1 to contain clusters for Class I and Class II lanthipeptide, chalcone synthase (T3PKS), and terpene. Contig 2 did not have any secondary metabolite encoding cluster.

In view of the beneficial traits and functional roles for disease suppression and growth promotion of the strain JBRS159, the genome sequence will contribute to understand the mechanisms and in planta associated characteristics, and consequently to use the strain as biocontrol agent in fields.

Nucleotide sequence accession number

The genome of Cytobacillus firmus JBRS159 was made publicly available at NCBI GenBank (Acc. No. JAQZD S000000000). The strain has been deposited in the Korean Agricultural Culture Collection with the accession number KACC 92494P.

적 요

벼 종자에서 분리한 Cytobacillus firmus JBRS159 (JBRS159) 균주는 세균벼알마름병의 발생을 억제하였고, 벼와 애기장대의 생육을 촉진하였다. 이러한 특성을 이해하기 위하여 본 연구에서는 JBRS159균주의 전체 염기서열을 해독하고 분석하였다. 게놈은 4,867,753 bp 및 96,746 bp의 염기서열을 가진 2개의 contig로 구성되어 있는데, 각각의 GC 함량은 41.9% 및 36.6%였다. 첫번째 contig는 4,865개의 단백질을 코딩하는 유전자와 107개의 tRNA 및 36개의 rRNA로 구성되어 있었고, 두번째 contig는 115개의 유전자로 구성되어 있었다. 유전체의 분석을 통해 2차 대사산물인 siderophore, hydrogen cyanide 및 acetoin을 생산하고, 인산을 가용화하는 능력이 있는 것을 확인하였는데, 이러한 특성들은 JBRS159균주의 병 방제 및 식물 생육 촉진 효과와 관련이 있을 것으로 판단된다.


This research was supported by the Cooperative Research Program for Agriculture Science & Technology Development (PJ015566), Rural Development Administration, Republic of Korea.

Conflict of Interest

The authors declare that there is no conflict of interest.

  1. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, and Weber T. 2021. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49, W29-W35.
    Pubmed KoreaMed CrossRef
  2. Ghahremani Z, Escudero N, Beltrán-Anadón D, Saus E, Cunquero M, Andilla J, Loza-Alvarez P, Gabaldón T, and Sorribas F. 2020. Bacillus firmus strain I-1582, a nematode antagonist by itself and through the plant. Front. Plant Sci. 11, 796.
    Pubmed KoreaMed CrossRef
  3. Gunasekaran Y, Thiyageshwari S, Ariyan M, Roy Choudhury A, Park JH, Selvi D, Chithra L, and Anandham R. 2022. Alleviation of sodic stress in rice by exploring the exopolysaccharide-producing sodic-tolerant bacteria. Agriculture 12, 1451.
  4. Huang M, Bulut A, Shrestha B, Matera C, Grundler FMW, and Schleker ASS. 2021. Bacillus firmus I-1582 promotes plant growth and impairs infection and development of the cyst nematode Heterodera schachtii over two generations. Sci. Rep. 11, 14114.
    Pubmed KoreaMed CrossRef
  5. Patel S and Gupta RS. 2020. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int. J. Syst. Evol. Microbiol. 70, 406-438.
    Pubmed CrossRef
  6. Saied E, Hashem AH, Ali OM, Selim S, Almuhayawi MS, and Elbahnasawy MA. 2022. Photocatalytic and antimicrobial activities of biosynthesized silver nanoparticles using Cytobacillus firmus. Life 12, 1331.
    Pubmed KoreaMed CrossRef
  7. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.
    Pubmed KoreaMed CrossRef

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