The genus Pseudarthrobacter comprises aerobic, motile, and Gram-positive bacteria. The members of this genus are found in soil containing heavy metals such as copper and arsenic (Fekih et al., 2018). In this study, Pseudarthrobacter sp. strain NIBRBAC000502772 was isolated from the soil of a shooting range in Hongcheon, Republic of Korea. Luria-Bertani (LB) medium containing 370 ppm of arsenate was used to isolate metal-resistant bacteria (Abbas et al., 2014). A single colony of the isolated strain was incubated at 30°C in LB medium on a rotary shaker at 200 rpm. After 24 h of incubation, bacterial cells were collected and its genomic DNA was extracted using a Qiagen MagAttract high molecular weight DNA isolation kit following the manufacturer’s protocol (Qiagen). Genome sequencing was performed using a previously described third-generation, long-read sequencer (Jung et al., 2019). The quantity and quality of the genomic DNA were assessed using an Agilent 2100 Bioanalyzer. More than 10 µg of high-quality, RNA-free genomic DNA was used to construct a 20 kb library using the SMRTbell^TM Template Prep Kit 1.0 (PacBio Biosciences). Whole genome sequencing was carried out using a PacBio RSII machine at DNA Link, Inc.

Pseudarthrobacter sp. NIBRBAC000502772 comprised a circular single chromosome of 4,803,563 bp with 273 fold average coverage. SMRT portal ver. 2.3 was used for de novo assembly of sequence reads with the HGAP protocol ver. 3.0. Whole genome sequence of strain NIBRBAC000502772 was deposited in GenBank (accession numbers: CP041188). A circular map representing the genome of the strain (Fig. 1) was generated using the CGview server (Stothard and Wishart, 2005). Pseudarthrobacter sp. NIBRBAC000502772 genome contains 4,450 total genes, 4,173 protein-coding genes, 52 tRNA, 12 rRNA and 65.01% G + C content (Table 1).

Table 1

Genome features of Pseudarthrobacter sp. NIBRBAC000502772

Genome features	Value
GenBank accession	CP041188
Genome size (bp)	4,803,563
G + C content (%)	65.01
No. of contig	1
Total genes	4,450
Protein-coding genes	4,173
tRNA	52
rRNA	12

Fig. 1. Graphical circular maps of the chromosome of Pseudarthrobacter sp. NIBRBAC000502772. From the center to the outside: genome size label, G + C content (black), GC skew (green and purple), CDS (blue), ORF (green), Blast results (yellow-green).

Genome annotation was performed by means of the Rapid Annotation using Subsystem Technology (RAST) server (Aziz et al., 2008) and the NCBI Prokaryotic Genome annotation pipeline (PGAP) (Tatusova et al., 2016). Functional genes related to plant growth promoting activity were identified. We have also investigated various genes that are putatively involved in auxin biosynthesis and resistance to heavy metals, particularly arsenate. The heavy metal resistome included several ars gene clusters containing one copy of an arsR encoding arsenical resistance operon repressor. There were also two copies of arsC genes encoding arsenate reductase, along with genes encoding copper resistance (copC and copD), and seven copies of copper oxidase related genes. This finding suggests that strain NIBRBAC000502772 also has a copper resistance system. We found indole-3-glycerol phosphate synthase, which can catalyze 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate into 1-C-(indol-3-yl)-glycerol 3-phosphate for synthesizing tryptophan, a precursor of auxin. Furthermore, tryptophan synthase alpha and beta subunits, which are essential for catalyzing the final two steps of tryptophan synthesis were identified (Table 2). The ability to synthesize plant hormones suggests the agricultural potentiality of this strain (Ibal et al., 2018). The PGAP analysis showed that the genome of the strain contains genes encoding nitrite/nitrate transporter, nitrate reductase, nitrate reductase small/large subunits, and nitrite reductase. Moreover, we also found genes involved in the molybdenum cofactor assembly, which is required for nitrate reductase activity (Lee et al., 2017).

Table 2

Auxin, denitrification, and heavy metal resistance related genes of Pseudarthrobacter sp. NIBRBAC000502772

Gene	Size (bp)	Product	Locus-tag
Auxin
ami	1,455	Amidase	NIBR502772_03500
trpA	1,266	Tryptophan synthase subunit alpha	NIBR502772_10900
trpB	1,266	Tryptophan synthase subunit alpha	NIBR502772_10895
trpC	822	Tryptophan biosynthesis protein TrpC	NIBR502772_10890
Denitrification
narT	1,220	Nitrate transporter	NIBR502772_12630
nar	1,352	Nitrate reductase	NIBR502772_03465
narG	3,710	Nitrate reductase alpha chain	NIBR502772_12650
narH	1,712	Nitrate reductase beta chain	NIBR502772_12645
narI	800	Nitrate reductase gamma chain	NIBR502772_12635
narJ	620	Nitrate reductase chaperone	NIBR502772_12640
nirC	851	Nitrite transporter	NIBR502772_20735
nirB	2,630	Nitrite reductase large subunit	NIBR502772_08815
nirD	362	Nitrite reductase small subunit	NIBR502772_08820
nirK	1,745	Nitrite reductase	NIBR502772_18940
Heavy Metals
arsR	755	Arsenical resistance operon repressor	NIBR502772_07390
arsC	710	Arsenate reductase	NIBR502772_18480
	422		NIBR502772_18490
copC	629	Copper resistance protein	NIBR502772_04590
copD	2,150		NIBR502772_01160
cueO	461	Blue copper oxidase	NIBR502772_00065
	461		NIBR502772_00155
	578		NIBR502772_13885
	1,082		NIBR502772_21375
mco	1,463	Multicopper oxidase	NIBR502772_14080
	1,448		NIBR502772_17550
	1.499		NIBR502772_19270

In this study, we fully sequenced the whole genome of Pseudarthrobacter sp. NIBRBAC000502772 and partially analyzed it for either heavy metal resistance or plant growth promoting abilities. This findings signify that Pseudarthrobacter sp. NIBRBAC000502772 has potential as a plant growth promoting bacterium.

Nucleotide sequence accession number

The whole genome sequence have been deposited in GenBank under the accession number CP041188.

한국 강원도 홍천 지역에 위치한 사격장 토양에서 식물 생장 호르몬 옥신을 생성하는 그람 양성의 호기성 간균인 Pseudarthrobacter sp. NIBRBAC000502772 균주를 분리하였다. 이 균주의 유전체는 65.01%의 G + C 비율을 가지고 있으며, 총 4,450개의 유전자를 갖는 4,803,563 bp의 길이로 구성되었다. 이 균주는 옥신 생합성 및 중금속에 대한 내성과 관련된 유전자를 가지고 있다. 또한, 아질산염 및 질산염 탈질과 관련한 유전자도 발견되어 농업 유용미생물로의 개발가능성을 보여주었다.

This research was supported by a grant from the National Institute of Biological Resources (NIBR202012103, NIBR 202013103), funded by the Ministry of Environment of the Republic of Korea; and the Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ013383), Rural Development Administration, Republic of Korea. The authors acknowledge the National Institute of Biological Resources (NIBR) for providing DNA samples of Pseudarthrobacter sp. NIBRBAC000502772 (DNA no. NIBR GR0000604032).