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Complete genome sequence of Pseudomonas moraviensis EFBE32, a biocontrol bacterium against pepper bacterial wilt
Korean J. Microbiol. 2022;58(4):308-310
Published online December 31, 2022
© 2022 The Microbiological Society of Korea.

Ju Hee An1,2, Songhwa Kim1, Mee Kyung Sang1, Yong Ju Jin1, Dayeon Kim1, Sang Yoon Kim2, and Jaekyeong Song1*

1Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju 55365, Republic of Korea
2Agricultural Life Science, Sunchon National University, Suncheon 57922, Republic of Korea
Correspondence to: *E-mail: mgjksong@korea.kr; Tel.: +82-63-238-3041; Fax: +82-63-238-3834
Received November 3, 2022; Revised December 3, 2022; Accepted December 5, 2022.
Abstract
Pseudomonas moraviensis strain EFBE32 is a biocontrol bacterium against bacterial wilt which is known as most destructive disease caused by Ralstonia solanacearum. Here, we report the whole genome sequence of P. moraviensis strain EFBE32. The sequence analysis revealed that P. moraviensis strain EFBE32 has a single 6,030,129 bps circular chromosome with a DNA G + C-content of 60.1%. This chromosome contains 5,239 coding sequences and 16 rRNA and 69 tRNA genes. In the result of sequence analysis, it is revealed that strain EFBE32 possessed genes coding the disease suppression related enzymes, acyl-homoserine lactone acylase (QuiP and PvdQ) which is known as quorum quenching enzyme, and hydrogen cyanide synthase (HcnA, B, and C).
Keywords : Pseudomonas moraviensis, bacterial wilt, biocontrol, EFBE32, genome
Body

Bacterial wilt (BW) caused by Ralstonia solanacearum is known as one of the most destructive diseases of plant, especially affecting serious loss on yield of diverse solanaceous crops including potatoes, tomatoes, pepper and eggplant worldwide (Garcia et al., 2019). To date, multifaceted approaches based on physical, chemical, cultural, and biological methods have been applied to manage BW. Among them, biological control of BW has emerged as a promising method for eco-friendly and sustainable agricultural practice and alternatives to use of chemical pesticides that raise problems such as soil environmental pollution, residual toxicity, and occurrence of pesticide-resistance strains (Garcia et al., 2019; Lahlali et al., 2022).

Pseudomonas moraviensis strain EFBE32 was isolated from the branch of apple in Eumseong, Chungcheongbuk-do, Korea and grown in tryptic soy broth (TSB) at 28℃ for 48 h under aerobic condition. Pseudomonas moraviensis strain EFBE32 showed the antagonistic activity against Ralstonia solanacearum on TSA medium and the control effect against development of BW in pepper seedling. The strain EFBE32 was deposited to the Korean Agricultural Culture Collection (KACC) (accession number KACC 81246BP).

Genomic DNA was extracted from the cultured P. moraviensis strain EFBE32 cells using a QIAamp DNA mini kit (Qiagen), according to the manufacturer’s protocols. The whole genome of P. moraviensis strain EFBE32 was sequenced with a 20-kb SMRTbell™ template library using the Pacific Biosciences (PacBio) RSII Single Molecule Real Time sequencing platform, and Illumina NovaSeq6000 platform at Macrogen. The genome was assembled using Microbial Assembly Application by Macrogen, and annotated using NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016). The complete genome sequence of P. moraviensis strain EFBE32 was found to comprise 6,030,129 bp, with an average DNA GC-content of 60.1%. The P. moraviensis strain EFBE32 chromosome contains 5,239 protein-coding sequences (CDSs), 16 rRNA and 69 tRNA genes with no plasmids (Table 1). The OrthoANI values, which are calculated using the OrthoANI algorithm version v0.93.1 (Lee et al., 2016), showed that the strain EFBE32 shared an average nucleotide identity (ANI) of 98.75–98.78 (99.65% of 16S rRNA gene) with Pseudomonas moraviensis strains (Fig. 1). The strain EFBE32 genome showed to possess genes coding the disease suppression related enzymes, such as hydrogen cyanide synthase (HcnA, B, and C) (Pacheco-Moreno et al., 2021), and acyl-homoserine lactone acylase (QuiP and PvdQ) which is known as quorum quenching enzyme (Rodríguez et al., 2020). Further antiSMASH analysis (Blin et al., 2021) revealed that the strain EFBE32 genome contains a secondary metabolite biosynthetic gene cluster of the lipopeptide surfactant, putisolvin, which is found to inhibit biofilm formation and degrading existing biofilms and associate with the antimicrobial activity (Kuiper et al., 2004; Ye et al., 2014).

Genome features of <italic>Pseudomonas moraviensis</italic> EFBE32
Genome features Chromosome
Genome size (bp) 6,030,129
G + C content (%) 60.1
Protein-coding genes (CDSs) 5,239
Number of rRNAs 6, 5, 5 (5S, 16S, 23S)
Number of tRNAs 69
ncRNAs 4
Number of pseudogenes 52
Plasmids 0
Accession number (GenBank) CP107544


Fig. 1. UPGMA and Heatmap generated with OrthoANI values calculated from the OAT software. The letter (T) means type strain of the species. The scale bar means 1% sequence divergence.

Overall, the sequence analysis of the P. moraviensis strain EFBE32 genome revealed that it possesses several genes that are potential for use in biocontrol against plant pathogenic microbes. We expect that this strain would be used for constructing the eco-friendly strategy for biocontrol against BW disease.

Nucleotide sequence accession number

The whole genome sequence of P. moraviensis strain EFBE32 described in this study was deposited to the National Center for Biotechnology Information (NCBI) with the accession number CP107544.

적 요

풋마름병은 Ralstonia solanacearum에 의해 발생하는 가장 파괴적인 식물병으로 알려져 있다. 풋마름병을 억제하는 활성을 가진 Pseudomonas moraviensis EFBE32 균주의 전장 유전체 염기서열 분석은 EFBE32 균주가 6,030,129 bp를 가진 단일 환형 염색체로서 G + C 함량은 60.1%로 구성되었다는 것을 보여준다. 이 유전체는 5,239개의 단백질을 암호하는 염기서열을 가졌으며 16개의 rRNA와 69개의 tRNA 유전자를 포함한다. 염기서열 분석을 통해 EFBE32 균주가 병 억제와 관련된 정족수 소거 효소, acyl-homoserinelactone acylase (QuiP and PvdQ)와 시안화수소를 합성하는 효소, hydrogen cyanide synthase (HcnA, B, and C)를 암호화하는 유전자를 가졌음을 밝혔다.

Acknowledgments

This study was carried out with the financial support for the project “Research Program for Agricultural Science & Technology Development (Project No. PJ015051)” provided by the National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea.

Conflict of Interest

The authors have no conflict of interest to report.

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