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Complete genome sequence of Pseudomonas sp. HNIBRBA3361 isolated from a halophyte
Korean J. Microbiol. 2023;59(4):359-361
Published online December 31, 2023
© 2023 The Microbiological Society of Korea.

Seung Yeol Shin1,2, Heeyoung Kang1, Song-Ih Han2, and Jaeho Song1*

1Division of Microbiology, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
2Department of Microbial Biotechnology of Science & Technology, Mokwon University, Daejeon 35349, Republic of Korea
Correspondence to: *E-mail: songjh21@hnibr.re.kr; Tel.: +82-61-288-7960; Fax: +82-61-288-7974
Received November 28, 2023; Revised December 4, 2023; Accepted December 6, 2023.
Abstract
Pseudomonas sp. HNIBRBA3361 was isolated from the root of Zoysia sinica Hance and we reported the complete genome sequence for this strain. The genome of strain HNIBRBA3361 consisted of a single circular chromosome with the overall length of 4.5 Mb and the DNA G + C content of 66.0%. The genome showed the highest taxonomic relatedness with P. lalucatii R1b-54T and P. benzenivorans DSM 8628T on the base of the 16S rRNA gene similarity (98.6%) and the average nucleotide identity (85.3%), respectively. The HNIBRBA3361 genome contained a total of 4,045 protein-coding genes, 15 rRNAs and 65 tRNAs, and genes involved in the biosynthesis of compounds promoting plant growth and the degradation of xenobiotics.
Keywords : Pseudomonas, complete genome, halophyte, plant growth promoting, xenobiotics degrading
Body

The genus Pseudomonas is known as Gram-negative, aerobic, non-endosporic, motile, and rod shaped bacteria containing one or many flagella (Palleroni, 2015). Pseudomonas species have been isolated from diverse environments and at the time of writing, 332 ones have been validly published (https://lpsn.dsmz.de). Pseudomonas represents one of the most abundant bacterial groups in plant-associated environments, versatile metabolims of which are well kown as promoting plant growth such as producing plant hormones, siderophore, and antibiotics against pathogens, regulating root-structure, degrading xenobitics, and solublizing phosphate (Oteino et al., 2015; Chu et al., 2020; Chu et al., 2020, 2021; Zhang et al., 2020). For further study and potential utilization of the genus Pseudomonas, we present here the complete genome sequence of Pseudomonas sp. HNIBRBA3361 isolated from the root of a halophyte.

Pseudomonas sp. HNIBRBA3361 was isolated from a root sample of the halophyte Zoysia sinica Hance collected off Wando, Jeollanam-do, South Korea (34°23′47.92″ N, 126°40′18.91″ E) during the survey of indigenous species in Korean islands. The root sample was gently cleansed with sterilized phosphate buffered saline solution prior to homogenization. The homogenized sample was inoculated on Reasoner’s 2A medium (R2A; Difco) and strain HNIBRBA3361 was isolated after incubating at 20°C for four days. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (Qiagen) according to the manufacturer’s protocols. The complete genome of HNIBRBA3361 was sequenced using the PacBio Sequel System with a 20 kb SMRTbell library and the Illumina HiSeq 2500 sequencing platform (Macrogen). The PacBio Sequel platform generated a total of 229,895 long reads (2,026,822,094 bp) with a depth of 100×. Subsequent de novo assembly was carried out using SMRT Link version 1.8 with PacBio reads only, followed by error correction of contig bases with 18,524,624 Illumina short reads (2,764,527,503 bp) using Pilon (v1.21) (Walker et al., 2014).

The resulting whole genome of HNIBRBA3361 was determined after assembly and mapping to be a circular chromosome of 4,500,624 bp with a DNA G + C content of 66.0%. The genome contains 4,045 coding DNA sequences (CDSs), 15 rRNAs (5S, 16S, and 23S) and 65 tRNAs on the basis of the NCBI Prokaryotic Genome Annotation Pipeline (Tatusova et al., 2016). The genomic relatedness between HNIBRBA3361 and related bacterial strain was estimated based on the average nucleotide identity (ANI) using the OrthoANI algorithm on the EzBioCloud web service (Yoon et al., 2017). The HNIBRBA3361 genome shared 98.6% of the 16S rRNA gene similarity with P. lalucatii R1b-54T and 85.3% of ANI with the P. benzenivorans DSM 8628T genome. Genome features of the HNIBRBA3361 and DSM 8628T are presented in Table 1.

General genomic features of Pseudomonas sp. HNIBRBA3361 and Pseudomonas benzenivorans DSM 8628T
Genomic features HNIBRBA3361 DSM 8628T
Accession No. CP137892 FNCT00000000
No. of Contigs 1 44
Genome length (Mb) 4,500,624 5,743,144
G + C content (%) 66.0 65.2
Coding sequences 4,032 5,382
tRNA 65 60
rRNA 15 6
Genes for biosynthesis
Toxoflavin + -
Indole-3-acetic acid + -


Metabolic reconstruction was conducted using BlastKOALA based on KEGG database (Kanehisa et al., 2016). Assimilatory sulfate reduction (locus tag: SBP02_16265, 11345, 16560), assimilatory nitrate reduction (SBP02_06260, 11215), benzoate degradation (SBP02_11675, 11660, 11640, 11650, 11645, 11580), and pyrroloquinoline for phosphate solubilization (SBP02_06660, 07355, 07350, 07345, 07340, 07335, 07210, 00605, 00610, 00615) were encoded on the HNIBRBA3361 and DSM 8628T genomes, but genes for the biosynthesis of indole-3-acetic acid (IAA) (SBP02_20515, 20510, 18195, 18200) and toxoflavin (SBP02_01345, 17655, 01360, 01350, 01365) were found on the HNIBRBA3361 genome. Toxoflavin derived from Pesudomonas spp. is known as causing inhibition of several plant-pathogenic bacteria (Philmus et al., 2015). The presence of genes related to the synthesis of IAA, toxoflavin, and pyrroloquinoline and the degradation of benzoate on the HNIBRBA3361 genome may play an important role in the growth of halophyte.

Strain and nucleotide sequence accession numbers

Strain HNIBRBA3361 has been deposited at the Bank of Bioresources from Island and Coast (BOBIC). The GenBank/EMBL/DDBJ accession number for the complete genome sequence of HNIBRBA3361 is CP137892. The associated BioProject and BioSample accession numbers are PRJNA 1035956 and SAMN38107891, respectively.

적 요

본 연구에서는 갯잔디(Zoysia sinica Hance)의 뿌리에서 분리된 Pseudomonas sp. HNIBRBA3361의 전장 유전체 염기서열을 분석하였다. HNIBRBA3361 균주의 유전체는 4.5 Mb 크기의 66.0%의 DNA G + C함량을 갖는 원형의 유전체로 나타났다. 이 유전체는 16S rRNA 유전자 상동성과 평균 염기서열 유사도를 기준으로 각각 P. lalucatii R1b-54T (98.6 %) 및 P. benzenivorans DSM 8628T (85.3%)와 가장 높은 유전적 관련성을 보였다. HNIBRBA3361 유전체는 4,045개의 protein-coding, 15개의 rRNA 및 65개의 tRNA 유전자를 포함하고 식물의 생장을 촉진하는 물질의 생합성과 생체이물 분해에 관련된 유전자를 포함하였다.

Acknowledgments

This study was supported by the research grant “Survey of Indigenous Species in Korean Islands” (HNIBR202101111) from the Honam National Institute of Biological Resources of the Ministry of Environment in Korea.

Conflict of Interest

Jaeho Song is Editor of KJM. He was not involved in the review process of this article. The authors have declared that no competing interest exists.

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  • Honam National Institute of Biological Resources
     
      HNIBR202101111