search for




 

Complete genome sequence of a plant growth-promoting bacterium Pseudarthrobacter sp. NIBRBAC000502772, isolated from shooting range soil in the Republic of Korea
Korean J. Microbiol. 2020;56(4):390-393
Published online December 31, 2020
© 2020 The Microbiological Society of Korea.

Min-Kyu Park1, Yeong-Jun Park1, MinJi Kim1, Min-Chul Kim1, Jerald Conrad Ibal1, Gi-Ung Kang1, Gyu-Dae Lee1, Setu Bazie Tagele1, 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 July 14, 2020; Revised October 5, 2020; Accepted October 8, 2020.
Abstract
Pseudarthrobacter sp. NIBRBAC000502772 is a Gram-positive, aerobic, rod-shaped, auxin-producing bacterium that was isolated from the soil of a shooting range in Hongcheon, in the Republic of Korea. The whole genome of the strain is 4,803,563 bp in length, with 65.01% G + C content and 4,450 genes. The strain contains genes related to auxin biosynthesis and heavy metal resistance. In addition, it has been found to contain genes related to denitrification of nitrite and nitrate.
Keywords : Pseudarthrobacter sp., auxin biosynthesis, denitrification, heavy metal resistance
Body

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 SMRTbellTM 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).

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).

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.

적 요

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.

Acknowledgments

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).

References
  1. Abbas SZ, Riaz M, Ramzan N, Zahid MT, Shakoori FR, and Rafatullah M. 2014. Isolation and characterization of arsenic resistant bacteria from wastewater. Braz. J. Microbiol. 45, 1309-1315.
    Pubmed KoreaMed CrossRef
  2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, and Kubal MKubal M, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9, 75.
    Pubmed KoreaMed CrossRef
  3. Fekih IB, Zhang C, Li YP, Zhao Y, Alwathnani HA, Saquib Q, Rensing C, and Cervantes C. 2018. Distribution of arsenic resistance genes in prokaryotes. Front. Microbiol. 9, 2473.
    Pubmed KoreaMed CrossRef
  4. Ibal JC, Jung BK, Park CE, and Shin JH. 2018. Plant growth-promoting rhizobacteria used in South Korea. Appl. Biol. Chem. 61, 709-716.
    CrossRef
  5. Jung YG, Jung BK, Park CE, Ibal JC, Kim SJ, and Shin JH. 2019. Complete genome sequence of Microbacterium aurum strain KACC 15219T, a carbohydrate-degrading bacterium. Korean J. Microbiol. 55, 164-166.
  6. Lee YJ, Park MK, Park GS, Lee SJ, Lee SJ, Kim BS, Shin JH, and Lee DW. 2017. Complete genome sequence of the thermophilic bacterium Geobacillus subterraneus KCTC3922T as a potential denitrifier. J. Biotechnol. 251, 141-144.
    Pubmed CrossRef
  7. Stothard P and Wishart DS. 2005. Circular genome visualization and exploration using CGView. Bioinformatics 21, 537-539.
    Pubmed CrossRef
  8. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.
    Pubmed KoreaMed CrossRef


September 2021, 57 (3)
Full Text(PDF) Free

Social Network Service
Services

Author ORCID Information

Funding Information