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Complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502771 isolated from shooting range soil in Republic of Korea
Korean J. Microbiol. 2019;55(4):419-421
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

Min-Kyu Park1,2, Yeong-Jun Park1, Min-Chul Kim1, Gi-Ung Kang1, MinJi Kim1, YoungJae Jo1, Hyuk-Joon Kwon2, Myung-Suk Kang2, Min-Ha Kim2, Soo-Young Kim2, and Jae-Ho Shin1*

1School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
2National Institute of Biological Resources, Incheon 22689, Republic of Korea
Correspondence to: *E-mail: jhshin@knu.ac.kr;
Tel.: +82-53-950-5716; Fax: +82-53-953-7233
Received August 16, 2019; Revised September 18, 2019; Accepted October 30, 2019.
Abstract

Pseudarthrobater sp. NIBRBAC000502771 is a Gram-positive, aerobic, rod-shaped and auxin producing bacterium which was isolated from shooting range soil in Hongcheon, Republic of Korea. We report the complete genome sequence of the strain. A whole genome contig was composed of 4,495,979 bp length with 66.1% of G + C contents and 4,295 genes. The complete genome contains genes to produce auxin and genes resist to heavy metals.

Keywords : Pseudarthrobacter sp., auxin, heavy metal resistance
Body

The genus of Pseudarthrobacter is an aerobic, motile, Gram- positive bacterium. The member of genus Pseudarthrobacter has been found in metal habitats (Fekih et al., 2018) such as copper and arsenic conditions. In this study, we report the isolation and taxonomic characterization of Pseudarthrobacter sp. strain NIBRBAC000502771 from shooting range soil at Hongcheon, Republic of Korea. The strain NIBRBAC000502771 was grown in tenfold diluted Luria-Bertani (LB + Arc) medium, that comprises 370 ppm of arsenate, and used to grow heavy metal resistant bacteria (Abbas et al., 2014). The systematic analysis of 16S rRNA gene sequence revealed that strain NIBRBAC000502771 has the highest identity to Pseudarthrobacter phenanthrenivorans Sphe3 (98.9%) hence, belongs to the genus Pseudarthrobacter. A colony of the isolated strain was grown in of LB at 30°C with 200 RPM and the genomic DNA was isolated by Qiagen MagAttract high molecular weight DNA isolation kit as described by the manufacturer (Qiagen). Genome sequencing was performed using a third-generation, long-read sequencer PacBio RSII as described by Jung et al. (2019). Approximately, 10 µg of high-quality, RNA-free genomic DNA was used to construct 20-kb SMRTbell library using the DNA Templated Prep kit 1.0 (PacBio). Later on, used PacBio RSII machine at DNA Link, Inc..

The HGAP protocol 3.0 software was considered for the genome annotation and assembly. The resulting whole genome sequence of the strain NIBRBAC000502771 has been deposited in the GenBank with the accession numbers of CP041187. A circular map of the genome of strain NIBRBAC000502771 (Fig. 1) was created by using the CGview software (Stothard and Wishart, 2004).

The Rapid Annotations using subsystem technology (RAST) server (Aziz et al., 2008) and NCBI Prokaryotic Genome annotation pipeline (PGAP) (Tatusova et al., 2016) were used for the functional annotation of predicted genes. The Pseudarthrobacter sp. NIBRBAC000502771 genome size was 4,495,979 bp with 66.1% of G + C contents (Table 1). Several genes were reported that are putatively involved in auxin producing and heavy metal tolerance, especially arsenate. The heavy metal resistome containing several ars clusters such as 15 of arsR, and 3 copies of arsC genes encoding arsenate reductases were found. Two copies of acr3 genes that encode arsenate permease were also found. Along with it, two copies of copC and copD were also found and are implied in copper efflux system. Above all, several other copper metabolism related genes that play a significant role in copper resistance such as multicopper oxidase, copper metallochaperone PCu(A)C, and copper chaperone were found. The other agriculturally most required secondary metabolite synthesizing genes such as Indol-3-glycerol phosphate synthase which makes catalytic action 1-(2-carboxyphenylamino)-1- deoxy-D-ribulose 5-phosphate into 1-C-(indol-3-yl)-glycerol 3-phosphate to synthesize the tryptophan as a precursor for auxin were also found. The most essential enzymes that play a significant part in the tryptophan synthesis such as tryptophan synthase alpha and beta subunit were also observed. The power to synthesize plant hormones suggests the agricultural availability of this strain (Ibal et al., 2018).

Genome features of Pseudarthrobacter sp. NIBRBAC000502771

Genomic featuresValue
GenBank accessionCP041187
Genome size (bp)4,495,979
G + C contents (%)66.1
No. of contig1
Total genes4,295
Protein-coding genes4,228
tRNA52

Fig. 1.

Graphical circular maps of the chromosome of Pseudarthrobacter sp. NIBRBAC000502771. From the center to the outside: genome size label, GC skew (green and purple), G + C contents (Black), Blast results (Pink), ORF (Red).


Nucleotide sequence accession numbers

The whole genome sequence was deposited in GenBank under accession number CP041187. As well, the strain was deposited in the National Institute of Biological Resources (NIBR) under accession number NIBRBAC000502771.

적 요

한국 홍천의 사격장 토양에서 분리된 Pseudarthrobacter sp. NIBRBAC000502771 균주는 그람양성의 호기성 간균이다. 이 균주의 유전체는 4,495,979 bp의 길이와 66.1%의 G + C 비율을 가지고 있으며, 총 4,295개의 유전자가 발견되었다. 또한 옥신과 중금속 내성 관련 유전자도 완전 해독한 유전체에 존재하였다.

Acknowledgements

This research was supported by a grant from the National Institute of Biological Resources (NIBR201913102), funded by the Ministry of Environment (MOE) of the Republic of Korea. The authors thank the National Institute of Biological Resources (NIBR) for providing DNA samples of Pseudarthrobacter sp. NIBRBAC000502771 (DNA no. NIBRGR0000604031).

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December 2019, 55 (4)