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Draft genome sequence of the carbofuran-degrading Bacillus amyloliquefaciens DYC2-1 isolated from a farmland soil
Korean J. Microbiol. 2023;59(1):49-51
Published online March 31, 2023
© 2023 The Microbiological Society of Korea.

Haeseong Park, Ji-Hwan Lim, Sun Il Seo, Kang-hyun Choi, and Pyoung Il Kim*

Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Republic of Korea
Correspondence to: *E-mail: pikim30@cialm.or.kr; Tel.: +82-63-536-6001; Fax: +82-63-536-6003
Received February 20, 2023; Revised March 20, 2023; Accepted March 22, 2023.
Abstract
Bacillus amyloliquefaciens DYC2-1 was isolated from a cabbage agricultural field and has demonstrated the ability to degrade carbofuran. We have sequenced and assembled a draft genome of DYC2-1, which consists of 3,875,891 bp and has a G + C content of 45.9%. The draft genome contains 3,962 coding sequences, 28 rRNAs and 97 tRNAs. We also identified gene clusters responsible for producing secondary metabolites with antimicrobial activity, as well as genes involved in the production of indole-3-acetic acid. These compounds have been shown to promote plant growth through various mechanisms. Collectively, our findings suggest that the genomic features of B. amyloliquefaciens DYC2-1 may account for its potential role as a plant growth-promoting bacterium.
Keywords : Bacillus amyloliquefaciens, biocontrol strain, draft genome, plant growth-promoting microorganism
Body

Bacillus strains are frequently used as commercialized plant growth‐promoting rhizobacteria (PGPRs) due to their robust spore forming-ability and production of several secondary metabolites (Meng et al., 2019; Kim et al., 2022). Among these, Bacillus amyloliquefaciens is known to produce compounds that promote plant growth and control plant diseases through various mechanisms (Gowtham et al., 2018; Kazerooni et al., 2021). In this study, we report the draft genome sequences of B. amyloliquefaciens DYC2-1, a recently discovered carbofuran-degrading bacterium (Lim et al., 2021). We isolated bacterial strains from pesticide-contaminated soil sampled from farmland in Damyang-gun, Korea, where cabbage is a major crop (N 35°20'29.9'' and E 126°57'22.4''). To prepare fine-grained soil, the soil sample was sifted 3 times by using a sieve with a 2 mm pore size (2.0 mm Test Sieve; ChungGye sieve co., Ltd.). For enrichment culture, minimal salt media (MSM) was prepared, and contained the following compounds: 2 g/L KH2PO4, 7.5 g/L K2HPO4, 0.1 g/L MgCl2, 0.5 g/L NaCl, and 1 ml/L trace element solution. The trace element solution was composed of the following components (mg/L): (CH3COO)2Cu·H2O, 10; CoCl2·6H2O, 3; EDTA, 500; FeCl2·6H2O, 20; (NH4)6Mo7O24· 4H2O, 20; ZnCl2, 30. The entire process of bacterial strain isolation was described in our previous research article (Lim et al., 2021). To perform whole-genome sequencing, the DYC2-1 strain was grown in 400 ml of tryptic soy broth at 30°C and 100 rpm for 16 h. The cells were harvested by centrifugation at 4000 rpm and 4°C. After centrifugation, supernatant of the cell was completely discarded, and the cell pellet was stored in refrigerator at 4°C before genome-analysis. Whole-genome sequencing was performed by CJ bioscience, Inc., using a PacBio Sequel system (Illumina). The draft genome of B. amyloliquefaciens DYC2-1 is circular and comprises 3,875,891 bp with a G + C content of 45.9%. The draft genome also includes 3,962 coding sequences, 28 rRNAs, 97 tRNAs (Table 1). The antiSMASH analysis (https://antismash.secondarymetabolites.org/, accessed on 15 February 2023) was used to identify secondary metabolite biosynthesis gene clusters in strain DYC2-1 including the iturin gene cluster (Blin et al., 2021). In addition to iturin, the genome analyzed by antiSMASH contained several other gene clusters that are predicted to encode antifungal compounds such as bacillaene, bacillibactin, bacilysin, fengycins, surfactin, and subtilin (Sansinenea and Ortiz, 2011). With the exception of surfactin, the genomic sequences of six antimicrobial compounds were found to be consistent with those identified in the Bacillus genus. The sequence for surfactin, on the other hand, exhibited 86% similarity with that of Bacillus. We also investigated genes associated with compounds that support plant growth and development, such as the putative nitrogen fixation gene YutI (Li et al., 2021). In addition, we identified several genes involved in the biosynthesis of indole-3-acetic acid and various volatile compounds (Xu et al., 2020). Based on our observations, the DYC2-1 strain has significant potential as a biocontrol rhizobacteria and for promoting plant growth.

General features of the <italic>Bacillus amyloliquefaciens</italic> DYC2-1 genome
Characteristic Genome
Genome size (bp) 3,875,891
GC content (%) 45.9
Number of contigs 5
Number of CDSs 3,962
N50 (bp) 2,597,289
Mean of CDS length (bp) 863.8
Median of CDS length (bp) 732
Mean length of intergenic region 117.4
Number of rRNA genes 28
Number of tRNA genes 97


Nucleotide sequence accession number

Genome information of B. amlyloliquefaciens DYC2-1 is available in the GenBank database under the accession number: JAPWDN000000000. Also, the strain was deposited in the Korean Agricultural Culture Collection (KACC) under the accession number KACC 92464P.

적 요

카보퓨란을 분해하는 미생물인 Bacillus amyloliquefaciens DYC2-1 균주의 전장유전체 염기서열을 PacBio Sequel 플랫폼 기술을 활용하여 해독 및 분석하였다. 유전체 분석 결과 전체 유전체 크기는 3,875,891 bp로 G + C 함량 45.9%, 생성된 컨티그 5개, 단백질 코딩 유전자 3,962개를 포함하고 있었다. 유전체로부터 분석을 통하여 항균활성을 가지는 효소 관련 유전자 및 유전자군을 DYC2-1 균주의 유전체에서 확인하였다. 본 연구에서 얻어진 유전체 분석 결과를 종합해 보았을 때, DYC2-1 균주는 농업 및 산업 현장에서 유용하게 활용될 수 있을 것이다.

Acknowledgments

This work was carried out with the support of the “Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ014800)” Rural Development Administration, Republic of Korea.

Conflict of Interest

The authors declare no notable conflict of interest

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