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Whole-genome sequence of Bacillus aryabhattai strain GW320, a potential plant growth-promoting rhizobacterium from Cucumis sativus L. rhizospheric soil
Korean J. Microbiol. 2021;57(1):62-65
Published online March 31, 2021
© 2021 The Microbiological Society of Korea.

Tae-Kyung Hwang1,2, Yeong-Jun Park3, Min-Ji Kim3, Gyu-Dae Lee3, Ryeong-Hui Kim4, Tae-Il Lee5, Soon-Ki Park1*, and Jae-Ho Shin3,4*

1Major in Plant Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
3Gunwi Agricultural Technology Center, Gunwi-gun, Gyeongsangbuk-do 39026, Republic of Korea
4Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
4Department of Integrative Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
5Seongju Agricultural Technology Center, Seongju-gun, Gyeongsangbuk-do 40056, Republic of Korea
Correspondence to: (S.K. Park) E-mail: psk@knu.ac.kr;
Tel.: +82-53-950-7751; Fax: +82-53-958-6880 /
(J.H. Shin) E-mail: jhshin@knu.ac.kr;
Tel.: +82-53-950-5716; Fax: +82-53-953-7233
Received December 31, 2020; Revised February 10, 2021; Accepted February 21, 2021.
Abstract
Bacillus aryabhattai GW320 (= KACC 22234) was isolated from the rhizosphere of Cucumis sativus L. in Gunwi-gun, Republic of Korea, and its whole-genome sequence was analyzed in this study. Its whole genome consists of circular chromosomes and plasmids, with genome sizes of 6,036,752 bp and 152,341 bp, respectively. The G + C content of its chromosome is 61.5%. The chromosome and plasmid contain 5,599 protein- coding genes. Besides, genes related to auxin biosynthesis, urea degradation, and nitrogen assimilation were identified in the chromosome. Thus, Bacillus aryabhattai GW320 has the potential to be an agriculturally useful strain.
Keywords : Bacillus aryabhattai, auxin biosynthesis, nitrogen assimilation, urea degradation, whole-genome sequencing
Body

Plant growth-promoting rhizobacteria (PGPR), including Bacillus, are commonly found in the rhizosphere and can stimulate plant growth through direct or indirect mechanisms (Backer et al., 2018). Bacillus aryabhattai is a Gram-positive, rod-shaped, and spore-forming bacterium and the plant growth-promoting (PGP) activity of this species was reported in 2012 (Lee et al., 2012). Recently, B. aryabhattai MDSR7 and MDSR11 showed improved soybean and wheat plant growth (Ramesh et al., 2014). Here, B. aryabhattai GW320 isolated from Cucumis sativus L. rhizospheric soil in Gunwi-gun, Republic of Korea (36°14'41.7" N 128°33'15.6" E) was investigated to identify the genome characteristics.

A single colony of strain GW320 was incubated at 30°C for 24 h at 200 rpm in LB medium. Subsequently, manual extraction of genomic DNA was performed. The quantity and quality of the extracted DNA were analyzed using a Qubit 3.0 fluorometer and a NanoDrop One Spectrophotometer (Thermo Fisher Scientific), respectively. Whole-genome sequencing was conducted using the PacBio Sequel system (Pacific Biosciences) at Macrogen Inc. De novo assembly using subreads proceeded through HGAP4 protocol using the SMRT link software v.7.0, and the default parameter was applied. The sequencing depth was calculated as 150 × average genome coverage. Then, genome annotation was proceeded through the rapid annotations using subsystem technology server and the NCBI prokaryotic genome annotation pipeline (Aziz et al., 2008; Tatusova et al., 2016). After this, the circular genome map of strain GW320 was visualized by CGview software (Stothard and Wishart, 2005).

The whole-genome sequence of B. aryabhattai GW320 was composed of 6,063,752 bp of chromosome, and its G + C content was 61.5%. Also, strain GW320 had one plasmid, and its length was 152,341 bp (Fig. 1). Genome information of B. aryabhattai GW320 is summarized in Table 1. Functional genes of the B. aryabhattai GW320 was investigated based on the annotation result, and it was revealed that strain GW320 has genes related to PGP activities, such as auxin biosynthesis, urea degradation, and nitrogen assimilation (Table 2) (Barbosa et al., 2013; Goswami et al., 2015). Functional genes of B. aryabhattai GW320 suah as auxin biosynthesis, such as alpha and beta subunit of tryptophan synthase (trpA and trpB), indole-3-glycerol phosphate synthase (trpC), anthranilate phosphoribosyltransferase (trpD), and phosphoribosylanthranilate isomerase (trpF) were detected. Furthermore, three genes, including encoded aminotransferase class enzyme (I5S86_12580), FAD-dependent oxidoreductase (I5S86_03300), and aldehyde dehydrogenase family protein (I5S86_00525) were classified into the tryptophan-dependent auxin biosynthesis pathway (Zhang et al., 2019). In strain GW320, alpha, beta, and gamma subunits of urease, and its accessory proteins (ureA, ureB, ureC, ureD, ureE, ureF, and ureG) were detected. Furthermore, the strain GW320 possessed glutamine synthetase (glnA) related to stress resistance (De Andrade Santos et al., 2018). Therefore, this study’s results suggest the potential role of B. aryabhattai GW320 as a PGP rhizobacterium.

Genome features of Bacillus aryabhattai GW320

Genome features Chromosome Plasmid
Genome size (bp) 6,063,752 152,341
G + C contents (%) 61.5 58.0
Number of contigs 1 (CP065421.1) 1 (CP065422.1)
Protein-coding genes 5,442 157
rRNAs 22 -
tRNAs 74 -
ncRNA 4 -
Pseudogenes 73 5


Genes related to plant growth-promoting activity in Bacillus aryabhattai GW320 genome

Function Gene Size (bp) Protein Locus-tag
Urea decomposition ureA 302 Urease subunit gamma I5S86_13045
ureB 317 Urease subunit beta I5S86_13050
ureC 1,703 Urease subunit alpha I5S86_13055
ureD 833 Urease accessory protein UreD I5S86_13040
ureG 623 Urease accessory protein UreG I5S86_13075
ureE 491 Urease accessory protein UreE I5S86_13060
ureF 674 Urease accessory protein UreF I5S86_13070

Auxin biosynthesis trpA 809 Tryptophan synthase subunit alpha I5S86_01200
trpB 1,217 Tryptophan synthase subunit beta I5S86_01205
trpC 833 Indole-3-glycerol phosphate synthase I5S86_26690
trpD 1,049 Anthranilate phosphoribosyl transferase I5S86_26695
trpF 620 Phosphoribosylanthranilate isomerase I5S86_08665
- 1,412 Aminotransferase class V-fold I5S86_12580
PLP-dependent enzyme
- 1,691 FAD-dependent oxidoreductase I5S86_03300
- 1,478 Aldehyde dehydrogenase family protein I5S86_00525

Stress resistance glnA 1,407 Glutamine synthetase I5S86_21960


Fig. 1. Circular genome map of Bacillus aryabhattai GW320 chromosome and its plasmid. From inside to outside of the circular genome map, each circle in the genome map contains 1) G + C contents, 2) G + C Skew, 3) Forward CDS, and 4) Reverse CDS.

Nucleotide sequence data and strain accession number

The whole-genome sequences were deposited in GenBank under accession numbers CP065421.1 and CP065422.1. The strain is available in the National Institute of Agricultural Sciences under the accession number KACC 22234.

적 요

본 연구에 활용된 Bacillus aryabhattai GW320 (= KACC 22234) 균주는 군위군 오이 경작지 근권 토양에서 분리되었다. GW320 균주의 유전체를 분석한 결과, 6,063,752 bp및 152,341 bp의 유전체와 플라스미드 DNA 하나씩으로 이루어져 있었으며, 유전체의 GC비율은 61.5%였다. 유전체에는 총 5,599개의 유전자가 발견되었으며 22개의 rRNA 유전자, 74개의 tRNA 유전자 및 4개의 ncRNA 유전자가 포함되어 있었다. 또한 옥신 생합성, 요소 가용화 및 질소 동화 관련 유전자가 존재하므로 식물 생장 촉진 근권 미생물로서의 잠재력을 보였다.

Acknowledgments

This work was supported by a regional researcher program through the National Research Foundation (NRF), funded by the Ministry of Education (NRF-2020R1I1A3074522).

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