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Complete genome sequence of the plant growth-promoting endophytic bacterium Rhodanobacter glycinis T01E-68 isolated from tomato (Solanum lycopersicum L.) plant roots
Korean J. Microbiol. 2019;55(4):422-424
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

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
Correspondence to: *E-mail: why@korea.kr;
Tel.: +82-63-238-3042; Fax: +82-63-238-3834
Received September 25, 2019; Revised November 1, 2019; Accepted November 4, 2019.
Abstract

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 chromosome 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 biosynthesis 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
Body

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 agricultural 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 biocontrol 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 MO64T with 99.73% 16S rRNA gene sequence similarity, strain T01E-68 was identified into Rhodanobacter 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 beneficial 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 Biosciences (PacBio) RSII single-molecule real-time (SMRT) sequencing platform with a 20 kb SMRTbellTM 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 Prokaryotic 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 identified 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 transporter 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 biosynthesis (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 detected in the genome using antiSMASH. The secondary metabolites 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.

Genome features of Rhodanobacter glycinis strain T01E-68

Genome featureValue
Genome size (bp)4,172,240
Number of contigs1
G + C content (%)64.57
Protein-coding genes3,471
tRNAs49
rRNAs (5S, 16S, 23S)6 (2, 2, 2)
Pseudogenes131

Nucleotide sequence accession numbers

Rhodanobacter glycinis T01E-68 has been deposited in the Korean Agricultural Culture Collection under accession number 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 토마토 생육을 촉진시키고, 토마토의 풋마름병을 억제하는 효과를 나타낸다. 이 균주는 4,172,240 bp 크기의 원형 염색체로 구성되어 있으며, G + C 함량은 64.57%이다. 유전체는 3,471개 단백질 암호화 유전자와 6개 rRNA, 49개 tRNA를 포함하고 있다. 해당 유전체에서 항산화 활성, 프롤린 생합성과 aryl polyene, lasso peptide, beta-lactone 등 이차대사산물 생합성에 관여하는 유전자를 발견하였다. 본 연구에서 해독한 유전체 정보는 식물생육촉진과 관련된 기작을 연구하기 위한 기초자료가 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.

References
  1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, and Kubal M, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 9, 75.
    Pubmed KoreaMed CrossRef
  2. Backer R, Rokem JS, Ilangumaran G, Lamont J, Praslickova D, Ricci E, Subramanian S, and Smith DL. 2018. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front. Plant Sci. 9, 1473.
    Pubmed KoreaMed CrossRef
  3. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, and Weber T. 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47, W81-W87.
    Pubmed KoreaMed CrossRef
  4. De Clercq D, Van Trappen S, Cleenwerck I, Ceustermans A, Swings J, Coosemans J, and Ryckeboer J. 2006. Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix. Int. J. Syst. Evol. Microbiol. 56, 1755-1759.
    Pubmed CrossRef
  5. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, and Kuhn M, et al. 2016. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286-293.
    Pubmed KoreaMed CrossRef
  6. Liu Y, Wu L, Wu X, Li H, Liao Q, Zhang X, Sun Z, and Li W. 2017. Analysis of microbial diversity in soil under ginger cultivation. Scientifica. 2017, 8256865.
    Pubmed KoreaMed CrossRef
  7. Shin DS, Park MS, Jung S, Lee MS, Lee KH, Bae KS, and Kim SB. 2007. Plant growth-promoting potential of endophytic bacteria isolated from roots of coastal sand dune plants. J. Microbiol. Biotechnol. 17, 1361-1368.
    Pubmed
  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
  9. Turner TR, James EK, and Poole PS. 2013. The plant microbiome. Genome Biol. 14, 209.
    Pubmed KoreaMed CrossRef
  10. Weon HY, Sang MK, Lee SA, Song J, Kwon SW, and Lee SY. 2019. Rhodanobacter glycinis T01E-68 promoting plant growth, inducing tolerance of plants to abiotic stress, and controlling plant diseases, and uses thereof. Korean Patent No. 10-1972068.


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