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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(4): 493-495

https://doi.org/10.48022/mbl.2401.10013

Received: October 28, 2024; Accepted: October 31, 2024

Complete Genome Sequence of Bacillus pumilus CIMT1, Isolated from the Rhizosphere of Soybean (Glycine max L.)

Da-Ryung Jung1†, Tino Bashizi1†, and Jae-Ho Shin1,2*

1Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
2NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of Korea

Correspondence to :
Jae-Ho Shin,       jhshin@knu.ac.kr

†These authors contributed equally to this work.

Abstract

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This study presents the complete genome sequence of Bacillus pumilus CIMT1, which was isolated from the rhizosphere of soybean (Glycine max L.). The genome of strain CIMT1 consists of a single chromosome and two plasmids, with a total size of 3,906,487 bp and a G + C content of 41.0%.

Keywords: Bacillus pumilus, complete genome, soybean

Body

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Bacillus pumilus is a Gram-positive, spore-forming bacterium that is commonly found in the soil environment. This species has been widely reported as a plant growth-promoting rhizobacterium, capable of enhancing plant growth and productivity through various mechanisms [1, 2]. Additionally, B. pumilus can directly promote plant growth by producing phytohormones such as auxin and cytokinin, which can stimulate root development and shoot growth [3, 4]. Furthermore, B. pumilus is known to facilitate nutrient availability by solubilizing phosphate and other essential minerals, thereby supporting nutrient uptake in plants [3].

In this study, B. pumilus CIMT1 was isolated from the rhizosphere of soybean (Glycine max L.), which was sampled from the greenhouse of Kyungpook National University (Daegu, Republic of Korea). To isolate the strain, 1 g of rhizosphere soil was serially diluted and plated on tryptic soy agar, which was then incubated at 30℃ for 5 days. A single colony of the strain was subsequently isolated and repeatedly subcultured to obtain a pure culture.

The genomic DNA of strain was extracted using Wizard® Genomic DNA Purification Kit (Promega, USA) following the manufacturer’s guidelines. The quality and quantity of the extracted DNA was evaluated using a Qubit Flex fluorometer (Thermo Fisher Scientific, USA) and a NanoDrop One microvolume UV-Vis spectrophotometer (Thermo Fisher Scientific).

Whole-genome sequencing was performed using Oxford Nanopore Technologies (ONT) to produce long reads. The library preparation was prepared following the manufacturer’s protocol, using the SQK-LSK109 ligation sequencing kit (ONT, UK) together with the NEBNext companion module (New England Biolabs, USA). Sequencing was carried out on the MinION platform (ONT) with a FLO-MIN111 R10.3 flow cell for a duration of 48 h at KNU NGS Core Facility (Daegu, Republic of Korea).

FASTQ files were generated by performing base calling with Guppy v4.4.1 software set to high accuracy mode (HAC). Initial quality control of the raw FASTQ reads was conducted using Filtlong v0.2.1 (https://github.com/rrwick/Filtlong). The lowest-quality 5% of the reads were filtered out with default parameters to ensure high-quality data for subsequent analysis. This entire procedure yielded a total of 299,012,786 bp, consisting of 78,290 reads, with the longest read being 114,158 bp. The raw genome coverage achieved was 76x.

The analytical methods followed those established in previous study [5]. The filtered reads were assembled de novo using Flye v2.9.1 (https://github.com/mikolmog-orov/Flye), optimized for high-quality ONT reads. Subsequently, the resulting assembly was polished with Medaka v1.7.2 (https://github.com/nanoporetech/medaka) to improve the base call accuracy, using the high-quality reads generated in the previous step. This process led to the assembly of the B. pumilus CIMT1 genome into three contigs: a chromosome with a length of 3,884,314 bp and two plasmids of 7,061 bp and 15,112 bp, respectively. Species identification and plasmid detection were conducted using Mash v2.3 (https://github.com/marbl/Mash) against RefSeq genomes and plasmids, and Sourmash v4.6.1 against GenBank. Furthermore, genome annotation was conducted using Bakta v1.6.1 [6], which facilitated the identification of coding sequences, rRNAs, tRNAs, and other genomic features (Table 1). Finally, the whole genome sequence was visualized using the CGview website (Fig. 1).

Table 1 . Genetic feature of B. pumilus CIMT1.

FeatureValue
Genome size (bp)3,906,487
Number of contigs3
G + C ratio (%)41.0
Number of protein-coding genes4,021
rRNA genes24
tRNA genes82
tmRNA genes1
ncRNA genes21
Pseudo genes31


Figure 1.Genome map of the circular chromosome sequence of B. pumilus CIMT1, generated through the visualization tool (CGView).

Data Availability

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The complete genome sequence data for B. pumilus CIMT1 have been submitted to the BioProject with the accession number PRJ-NA1153722.

Acknowledgments

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This research was supported by a project to train professional personnel in biological materials by the Ministry of Environment, by Korea Basic Science Institute (National research Facilities and Equipment center) grant funded by the Ministry of Education (2021R1A6C101A416) and by with the support of “Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ015697)” Rural Development Administration, Republic of Korea.

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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  1. Liu H, Wang Z, Xu W, Zeng J, Li L, Li S, et al. 2020. Bacillus pumilus LZP02 promotes rice root growth by improving carbohydrate metabolism and phenylpropanoid biosynthesis. Mol. Plant-Microbe Interact. 33: 1222-1231.
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  2. Kang Y, Shen M, Wang H, Zhao Q. 2015. Complete genome sequence of Bacillus pumilus strain WP8, an efficient plant growth-promoting rhizobacterium. Genome Announc. 3: e01452-01414.
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  3. Dobrzyński J, Jakubowska Z, Dybek B. 2022. Potential of Bacillus pumilus to directly promote plant growth. Front. Microbiol. 13: 1069053.
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  4. Nascimento FX, Hernández AG, Glick BR, Rossi MJ. 2020. Plant growth-promoting activities and genomic analysis of the stressresistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest. Biotechnol. Rep. 25: e00406.
    Pubmed KoreaMed CrossRef
  5. Park S, Lee G, Kim I, Jeong Y, Shin J. 2023. Complete genome sequence of the Enterobacter asburiae IK3 isolated from a Soybean (Glycine max) rhizosphere. Microbiol. Biotechnol. Lett. 51: 306-308.
    CrossRef
  6. Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. 2021. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb. Genom. 7: 000685.
    Pubmed KoreaMed CrossRef

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