Complete genome sequence of the plant growth-promoting endophytic bacterium Rhodanobacter glycinis T01E-68 isolated from tomato (Solanum lycopersicum L.) plant roots

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Korean Journal of Microbiology (2019) Vol. 55, No. 4, pp. 422-424 pISSN 0440-2413

DOI https://doi.org/10.7845/kjm.2019.9115 eISSN 2383-9902

Complete genome sequence of the plant growth-promoting endophytic bacterium Rhodanobacter glycinis T01E-68 isolated from tomato

(Solanum lycopersicum L.) plant roots

Shin Ae Lee, Bashistha Kumar Kanth, Hyeon Su Kim, Tae-Wan Kim, Mee Kyung Sang, Jaekyeong Song, and Hang-Yeon Weon*

Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju 55365, Republic of Korea

토마토 뿌리에서 분리한 식물생육 촉진 내생 세균

Rhodanobacter glycinis T01E-68 균주의 유전체 염기서열

이신애 ･ 바시스타 쿠마르 캔스 ･ 김현수 ･ 김태완 ･ 상미경 ･ 송재경 ･ 원항연*

국립농업과학원 농업생물부 농업미생물과

(Received September 25, 2019; Revised November 1, 2019; Accepted November 4, 2019)

*For correspondence. E-mail: [email protected];

Tel.: +82-63-238-3042; Fax: +82-63-238-3834

Rhodanobacter glycinis strain T01E-68 was isolated from tomato plant roots. The bacteria confer tolerance to plant against osmotic stress induced by salt and resistance against bacterial wilt disease caused by Ralstonia solanacearum. The genome of the strain T01E-68 consists of a circular chromo- some of 4,172,240 bp with a G + C content of 64.57%. The genome includes 3,471 coding genes, 6 rRNAs, and 49 tRNAs.

Genes identified in the genome are related to antioxidant activity, proline biosynthesis, and secondary metabolites bio- synthesis including aryl polyene, lasso peptide, and beta- lactone, which may play roles in plant growth-promoting and biocontrol activities.

Keywords: Rhodanobacter, biocontrol, genome sequence, plant growth-promoting bacteria

Plant associated microorganisms inhabit not only surrounding plant tissues but also inner tissues and they play beneficial roles in plant growth and health (Turner et al., 2013). The agri-

cultural application of beneficial bacteria is getting more attention for environment-friendly agricultural managements.

The bacteria showing beneficial effects, such as plant growth

promotion, biocontrol, and nitrogen fixation activities, have

been commercialized as biostimulants, biofertilizers, and bio-

control agents (Backer et al., 2018). Strain T01E-68 was

isolated from the tomato plant roots cultivated in a greenhouse

in Jeju, Republic of Korea (33.459765 N 126.363764 E). The

strain exhibited plant growth-promoting activity under osmotic

stress conditions (-500 and -1,000 kPa) with high-salt solutions

and biocontrol activity against soil-borne pathogen, Ralstonia

solanacearum (Weon et al., 2019). As it was closely related to

Rhodanobacter glycinis MO64

^T

with 99.73% 16S rRNA gene

sequence similarity, strain T01E-68 was identified into Rho-

danobacter glycinis. The genus Rhodanobater was dominant

in the ginger cultivated soil with low disease incidence (Liu et

al., 2017). Strains of Rhodanobacter isolated from the roots of

peace lily (Spathiphyllum alpha) and beach morning glory

(Calystegia soldanella) plants exhibited biocontrol activities

(De Clercq et al., 2006; Shin et al., 2007). However, its bene-

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Complete genome sequence of R. glycinis T01E-68∙

423 Korean Journal of Microbiology, Vol. 55, No. 4

Table 1. Genome features of Rhodanobacter glycinis strain T01E-68

Genome feature Value

Genome size (bp) 4,172,240

Number of contigs 1

G + C content (%) 64.57

Protein-coding genes 3,471

tRNAs 49

rRNAs (5S, 16S, 23S) 6 (2, 2, 2)

Pseudogenes 131

ficial functions for plant growth and the underlying molecular mechanisms are largely unknown. In this study, we conducted whole genome sequencing to provide genetic information of strain T01E-68 and identify genes related to tomato growth and health.

Rhodanobacter glycinis strain T01E-68 was cultured on Reasoner’s 2A (R2A) agar medium at 28°C for 2 days and the genomic DNA was extracted using a QIAamp DNA mini kit (Qiagen), according to the manufacturer’s protocols. Whole- genome sequencing was carried out using the Pacific Bio- sciences (PacBio) RSII single-molecule real-time (SMRT) sequencing platform with a 20 kb SMRTbell

^TM

template at ChunLab Inc. All generated reads were assembled de novo using RS HGAP assembly version 3.0. Gene prediction and functional annotations were carried out using the NCBI Pro- karyotic Genomes Annotation Pipeline (Tatusova et al., 2016), EggNOG 4.5 (Huerta-Cepas et al., 2016), and the Rapid Annotation Subsystem Technology (RAST server) (Aziz et al., 2008). Gene clusters encoding second metabolites were iden- tified using antiSMASH 5.0 (Blin et al., 2019).

The complete genome of the Rhodanobacter glycinis T01E- 68 consists of a 4,172,240 bp circular chromosome with 64.57%

G + C content. A total of 3,471 coding sequences, 6 rRNAs (two 5S rRNAs, two 16S rRNAs, and two 23S rRNAs), 49 tRNAs, 5 ncRNAs, and 131 pseudogenes were predicted (Table 1). The genome of Rhodanobacter glycinis T01E-68 possesses genes encoding sodium/proton antiporters and potassium trans- porter that are responsible for modulating homeostasis of Na

⁺

and K

⁺

, respectively, in the cell. We also found genes encoding antioxidant enzymes including superoxide dismutase, catalase, and glutathione peroxidase. The enzymes are produced under various stress conditions to reduce reactive oxygen species that

lead to cellular damage. Three genes involved in proline bio- synthesis (proA, proB, and proC) were detected in the T01E-68 genome, suggesting that the proline, an effective osmolyte, may protect plants from abiotic stresses such as drought, salinity, and extreme temperatures. The gene clusters encoding aryl polyene, lasso peptide, and β-lactone biosynthesis were de- tected in the genome using antiSMASH. The secondary meta- bolites might be related to anti-microbial and anti-oxidative activities. This complete genome sequence provides genetic information to understand molecular mechanisms of plant growth-promoting bacteria.

Nucleotide sequence accession numbers

Rhodanobacter glycinis T01E-68 has been deposited in the Korean Agricultural Culture Collection under accession num- ber KACC 92176P and the complete genome sequence has been deposited in NCBI under the GenBank accession number CP042807.

적 요

토마토 뿌리에서 분리한 Rhodanobacter glycinis T01E-68 균주는 높은 염류에 의해 유도된 삼투 스트레스 조건에서 토 마토 생육을 촉진시키고, 토마토의 풋마름병을 억제하는 효 과를 나타낸다. 이 균주는 4,172,240 bp 크기의 원형 염색체로 구성되어 있으며, G + C 함량은 64.57%이다. 유전체는 3,471 개 단백질 암호화 유전자와 6개 rRNA, 49개 tRNA를 포함하 고 있다. 해당 유전체에서 항산화 활성, 프롤린 생합성과 aryl polyene, lasso peptide, beta-lactone 등 이차대사산물 생합성 에 관여하는 유전자를 발견하였다. 본 연구에서 해독한 유전 체 정보는 식물생육촉진과 관련된 기작을 연구하기 위한 기초 자료가 될 것으로 기대한다.

Acknowledgements

This study was carried out with the support of “Research

Program for Agricultural Science & Technology Development

(Project No. PJ01424401)” from the National Institute of

Agricultural Sciences, Rural Development Administration,

Republic of Korea.

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미생물학회지 제55권 제4호

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