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Complete genome sequence of Paenibacillus tritici PH55-1, a diazinon-degrading soil bacterium
Korean J. Microbiol. 2021;57(4):283-285
Published online December 31, 2021
© 2021 The Microbiological Society of Korea.

Songhwa Kim1,2, Ju Hee An1, Hang-Yeon Weon1, Ho-Jong Ju2, and Jaekyeong Song1*

1Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju 55365, Republic of Korea
2Department of Agricultural Biology, College of Agricultural Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
Correspondence to: E-mail: mgjksong@korea.kr;
Tel.: +82-63-238-3041; Fax: +82-63-238-3834
Received September 7, 2021; Revised October 13, 2021; Accepted October 18, 2021.
Abstract
Paenibacillus tritici strain PH55-1 is a diazinon-degrading soil bacterium isolated from the plastic house soil in Chungju-si. Here, we report the whole genome sequence of P. tritici strain PH55-1. Sequence analysis revealed that P. tritici strain PH55-1 possesses a single 7,708,938-bp circular chromosome with a DNA G + C-content of 51.8%. This chromosome contains 6,450 protein-coding sequences, 30 rRNA, and 84 tRNA genes. Sequence analysis revealed that strain PH55-1 possessed genes coding for organophosphorus pesticide degradation-related enzymes, such as phosphodiesterase and phosphatase, and genes for diazinon degradation-related enzymes such as metallo- ß-hydrolase.
Keywords : Paenibacillus tritici, degradation, diazinon, genome, PH55-1
Body

Organophosphorus pesticides (OPPs) have been extensively used in agricultural practice for more than 40 years (Cycoń et al., 2009). Residues of persistent pesticides remain in the environment without breaking down for long period (Khudhur and Ismaeel Sarmamy, 2019). One of the pesticides, diazinon, has been widely used in agriculture and horticulture to control insects in crops, ornamentals, lawns, fruits, and vegetables throughout the world (Garfitt et al., 2002). Diazinon negatively affects the nervous system of humans and animals by attaching to acetylcholinesterase (Cox, 2000). To eliminate OPPs or reduce their concentration from the environment, the development of sustainable microbial-based bioremediation strategies was initiated in the early 1970s, and the enzymatic degradation of OPPs by organophosphorus hydrolase enzymes has been well studied in this regard (Mahajan et al., 2019).

Paenibacillus tritici strain PH55-1 was isolated from the plastic house soil and grown in tryptic soy broth (TSB) at 20°C for 48 h under aerobic conditions at a pH range of pH 6.0–10.0 (optimum 8.0). Genomic DNA was extracted from cultured P. tritici strain PH55-1 cells using a QIAamp DNA mini kit (Qiagen), according to the manufacturer’s protocol. The whole genome of P. tritici strain PH55-1 was sequenced with a 20-kb SMRTbellTM template library using the Pacific Biosciences (PacBio) RSII Single Molecule Real Time 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 P. tritici strain PH55-1 was found to comprise 7,708,938-bp, with an average DNA G + C-content of 51.8%. No plasmids were detected (Fig. 1). The P. tritici strain PH55-1 contained 6,450 protein-coding sequences (CDSs), 30 rRNA, and 84 tRNA genes (Table 1). The genome of strain PH55-1 has genes associated with the synthesis of Metallo-ß-hydrolase (gloB and ahlD), which are known to be diazinon degradation-related enzymes, and genes which code for the organophosphorus pesticide degradation-related enzymes (bcrC, phnP, phoA, phoN, and ycsE), such as phosphodiesterase and phosphatases. It also possesses genes related to chemotaxis (cheW, cheY, ctpH, mcpA, mcpC, mcpS, tlpB, and tlpC).

Genome features of Paenibacillus tritici PH55-1

Genome features Chromosome
Genome size (bp) 7,708,938
G + C content (%) 51.8
Protein-coding genes (CDSs) 6,450
Number of rRNAs 10, 10, 10 (5S, 16S, 23S)
Number of tRNAs 84
ncRNAs 4
Number of pseudogenes 78
Plasmids 0
Accession number (GenBank) CP073365


Fig. 1. Circular genome maps of the Paenibacillus tritici PH55-1 complete genome. From the outermost circle to the inner, each circle contains information about (1) Contig, (2) Forward CDS, (3) Reverse CDS, (4) rRNA and tRNA, (5) GC Skew, and (6) GC Ratio.

Overall, the sequencing and sequence analysis of the genome of P. tritici strain PH55-1 revealed several genes that have potential for use in the bioremediation of diazinon-contaminated soils. This strain could be used to construct OPPs-degrading microorganism consortium with another OPP-degrading strain for the bioremediation of OPP residues in agricultural soils.

Nucleotide sequence accession number

The whole genome sequence of P. tritici strain PH55-1 described in this study was deposited in the National Center for Biotechnology Information (NCBI) with the accession number CP073365. Additionally, the strain was deposited in the Korean Agricultural Culture Collection (KACC) (accession number KACC 92326P).

적 요

유기인계 살충제인 다이아지논을 분해할 수 있는 Paenibacillus tritici PH55-1 균주는 청주 지역의 비닐하우스 토양으로부터 분리하였다. PH55-1 균주의 전체 염기서열을 분석한 결과, PH55-1 균주는 7,708,938 bp를 가진 단일 환형 염색체로서 G + C 함량은 51.8%로 구성되었다. 이 유전체는 6,450개의 단백질을 암호하는 염기서열을 가졌으며 30개의 rRNA와 84개의 tRNA 유전자를 포함한다. 전장 유전체 분석을 통해 PH55-1 균주는 유기인계 농약 분해와 관련된 효소인 포스포다이에스터라제와 포스파타제를 암호화하는 유전자와 다이아지논 분해와 관련된 효소인 메탈로-베타-하이드로라제를 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 – PJ01480002)” provided by the National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea. We would like to thank Editage (www.editage.co.kr) for English language editing.

Conflict of Interest

The authors have no conflicts of interest to report.

References
  1. Cox C. 2000. Diazinon: Toxicology. J. Pestic. Reform. 20, 15-21.
  2. Cycoń M, Wójcik M, and Piotrowska-Seget Z. 2009. Biodegration of the organophosphorus insecticide diazinon by Serratia sp. and Pseudomonas sp. and their use in bioremediation of contaminated soil. Chemosphere 76, 494-501.
  3. Garfitt SJ, Jones K, Mason HJ, and Cocker J. 2002. Exposure to the organophosphate diazinon: data from a human volunteer study with oral and dermal doses. Toxicol. Lett. 134, 105-113.
    Pubmed CrossRef
  4. Kim SY, Song H, Sang MK, Weon HY, and Song J. 2017. The complete genome sequence of Bacillus velezensis strain GH1-13 reveals agriculturally beneficial properties and a unique plasmid. J. Biotechnol. 259, 221-227.
    Pubmed CrossRef
  5. Khudhur N and Ismaeel Sarmamy AO. 2019. Determination of diazinon residue in artificially polluted soils. Zanco J. Pure Appl. Sci. 31, 1-8.
  6. Mahajan R, Chandel S, and Chatterjee S. 2019. Environmental fate of organophosphate residues from agricultural soils to fresh farm produce: microbial interventions for sustainable bioremediation strategies. In Kumar A, Sharma S (eds.). Microbes and Enzymes in Soil Health and Bioremediation. Microorganisms for Sustainability, vol. 16. Springer, Singapore.
    CrossRef
  7. van Heel AJ, de Jong A, Montalbán-López M, Kok J, and Kuipers OP. 2013. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res. 41, W448-W453.
    Pubmed KoreaMed CrossRef
  8. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, and Wohlleben WWohlleben W, et al. 2015. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43, W237-W243.
    Pubmed KoreaMed CrossRef


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  • National Institute of Agricultural Sciences, Rural Development Administration
     
      PJ01480002