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.

Table 1

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

Table 2

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.

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.

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