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Complete genome sequence of Vibrio sp. HNIBRBA4764 isolated from a halophyte
Korean J. Microbiol. 2023;59(4):356-358
Published online December 31, 2023
© 2023 The Microbiological Society of Korea.

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

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: kangh@hnibr.re.kr; Tel.: +82-61-288-7965; Fax: +82-61-288-7974
Received November 9, 2023; Revised December 1, 2023; Accepted December 2, 2023.
Abstract
Vibrio sp. HNIBRBA4764 was isolated from the root of halophyte Artemisia fukudo Makino and we report the complete genome sequence of the strain. The HNIBRBA4764 genome was consisted of two chromosomes with total length of 3.5 and 1.0 Mb, and the DNA G + C content of 46.0 and 45.0%, respectively. A total of 3,952 protein-coding genes, 25 rRNAs, and 90 tRNAs were identified in the HNIBRBA4764 genome. The HNIBRBA4764 genome shared more than 98.2% of the average nucleotide identity with the genome of Vibrio ruber LMG 23124T and contained genes for the biosynthesis of two antibiotics, prodigiosin and carbapenem.
Keywords : Vibrio, antibiotics, complete genome, halophyte
Body

Members of the genus Vibrio are commonly found in natural marine and estuarine environments and on the surfaces and in the intestinal parts of marine animals (Mok et al., 2019; Sampaio et al., 2022). They are known as Gram-negative, facultatively aerobic, curved rod-shaped, salt-requiring, and motile bacteria. Genomes of Vibrio spp. normally have two chromosomes, each unique and independent, with the large chromosome being approximately 3 Mb and the small chromosome varying from 0.8 to 2.4 Mb (Thompson et al., 2009). At the time of writing, the genus comprised of 149 recognized species and showed diverse physiological characteristics such as reducing nitrate to nitrite, degrading macromolecules, free-living or symbiosis, and producing pathogens (Sampaio et al., 2022). Among them, several species of the genus are known as producing antibiotic substates (Mansson et al., 2011; Buijs et al., 2020). Prodigiosin is one of the antibiotics derived from the genus Vibrio and characterized as an anticancer agent and a fungicide (Shieh et al., 2003; Morgan et al., 2017). Here, we report the complete genome sequence of a marine bacterium affiliated to strain V. ruber LMG 23124T, a prodigiosin producer.

Vibrio sp. HNIBRBA4764 was isolated from the root of halophyte (Artemisia fukudo Makino) collected off tidal flat in Goha-do, Mokpo, South Korea (34°46′24.9″ N, 126°21′33.5″ E) in August, 2022 during on the survey of plant growth-promoting bacteria. A piece of the root was gently washed with sterilized seawater and crushed in a 1.5 ml tube with 1 ml of sterilized seawater using a homogenizer. The strain HNIBRBA4764 was obtained by a dilution-plating method on Marine agar 2216 (MA; Difco) after incubating at 20°C for 7 days.

Genomic DNA was extracted from the HNIBRBA4764 cells cultured on MA for four days using the DNeasy Blood & Tissue kit (Qiagen) according to the manufacturer’s protocols. Strain HNIBRBA4764 was affiliated to the V. ruber LMG 23124T (99.9%) on the basis of the 16S rRNA gene sequence similarity. The complete genome sequence of the HNIBRBA4764 strain was obtained using the PacBio Sequel System with a 20 kb SMRTbell library and Illumina HiSeq 2500 sequencing platform (Macrogen). In total, 127,067 long reads (1,238,450,050 bp) were sequenced using the PacBio Sequel platform with 100× in depth. Likewise, 19,674,556 short reads (2,969,196,198 bp) were sequenced using the Illumina 151 bp pair-end library. De novo assembly was performed using the SMRT Link version 1.8 with PacBio reads only, followed by error correction of contig bases with Illumina reads using Pilon (v1.21) (Walker et al., 2014).

After assembly and mapping, the resultant whole-genome of strain HNIBRBA4764 was determined to two circular contigs. The genomes were annotated by NCBI Prokaryotic Genome Annotation Pipeline (PGAP) revision 6.5 (Tatusova et al., 2016). As the result, chromosome 1 is of 3,503,344 bp in size with the DNA G+C content of 46% and depth of 100×. The genome encodes 3,003 coding DNA sequences (CDSs), 25 rRNAs (5S, 16S, and 23S), and 86 tRNAs. Chromosome 2 encodes 949 coding DNA sequences (CDSs) and 4 tRNAs. Genomic relatedness between bacterial strains was estimated based on the average nucleotide identity (ANI) using OrthoANI algorithm in the EzBioCloud web service (Yoon et al., 2017). For genomic comparisons, the genome of V. ruber LMG 23124T (Accession No. AP024905, AP024906), the type strain of the species, was obtained from NCBI database. Genome features of the HNIBRBA4764 and LMG 23124T are presented in Table 1. The HNIBRBA4764 genome shared 98.2% of ANI with the LMG 23124T genome. Metabolic reconstruction based on KEGG was pathways and orthology assignments were obtained using BlastKOALA (Kanehisa et al., 2016). Assimilatory sulfate reduction (locus tag: RND59_04220, 04225, 04210, 08065, 08055), dissimilatory nitrate reduction (RND59_000270, 00285), prodigiosin (RND59_04460, 13750, 13745, 13755, 13730, 13765, 13775, 13770, 13780, 13785) were encoded on the HNIBRBA4764 and LMG 23124T genomes, but genes for the biosynthesis of carbapenem (RND59_08410) were only found on the HNIBRBA4764 genome. The genes involved in the production of prodigiosin and carbapenem in strain HNIBRBA4764 were identified and predicted by antiSMASH 6.1.1 (Blin et al., 2021) (Fig. 1). These genomic features may play a role in promoting the growth of a halophyte.

Fig. 1. Genome region and gene organization for prodigiosin and carbapenem clusters in strain HNIBRBA4764, predicted by antiSMASH.
(A) prodigiosin cluster, (B) carbapenem cluster. PigH, 4-hydroxy-2,2'-bipyrrole-5-methanol synthase; PigF, 4-hydroxy-2,2'-bipyrrole-5-carbaldehyde O-methyltransferase.

General genomic features of strains Vibrio sp. HNIBRBA4764 and Vibrio ruber LMG 23124T

All genomes have prodigiosin biosynthesis and show 45.5% G + C contents.

Genomic features HNIBRBA4764 LMG 23124T
Isolation source halophyte seawater
Accession No. CP134780, CP134781 AP024905, AP024906
No. of contigs 2 2
Genome length (Mb) 4,603,068 4,622,997
Chromosome 1 3,503,344 3,470,339
2 1,099,724 1,217,089
Coding sequences 3,952 3,896
tRNA 90 86
rRNA 25 30
Genes for biosynthesis
Carbapenem + -


Strain and nucleotide sequence accession numbers

Strain HNIBRBA4764 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 strain HNIBRBA4764 is CP134780-134781. The associated BioProject and BioSample accession numbers are PRJNA1018590 and SAMN37445943, respectively.

적 요

Vibrio sp. HNIBRBA4764 균주는 염생식물 큰비쑥 뿌리에서 분리되었고, 본 연구에서 전장 유전체 염기서열을 분석하였다. HNIBRBA4764 유전체는 총 2개의 원형 유전체가 확인되고 각각 3.5 Mb와 1.0 Mb의 크기를 보였다. 유전체의 G + C함량은 45.5% 였으며 3,952개의 protein-coding, 25개의 rRNA 및 90개의 tRNA 유전자를 보유하고 있었다. HNIBRBA4764 균주의 유전체는 Vibrio ruber LMG 23124T 균주와 98.2%의 평균 유전자 유사도 값을 보였고 항생물질인 prodigiosin과 carbapenem의 생합성 관련 유전자를 포함하였다.

Acknowledgments

This study was supported by the research grant “Survey of Indigenous Species in Korean Islands” (HNIBR202301108) 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.

References
  1. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, and Weber T. 2021. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49, W29-W35.
    Pubmed KoreaMed CrossRef
  2. Buijs Y, Isbrandt T, Zhang SD, Larsen TO, and Gram L. 2020. The antibiotic andrimid produced by Vibrio coralliilyticus increases expression of biosynthetic gene clusters and antibiotic production in Photobacterium galatheae. Front. Microbiol. 11, 622055.
    CrossRef
  3. Kanehisa M, Sato Y, and Morishima K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731.
    Pubmed CrossRef
  4. Mansson M, Gram L, and Larsen TO. 2011. Production of bioactive secondary metabolites by marine Vibrionaceae. Mar. Drugs 9, 1440-1468.
    Pubmed KoreaMed CrossRef
  5. Mok JS, Ryu A, Kwon JY, Park K, and Shim KB. 2019. Abundance, antimicrobial resistance, and virulence of pathogenic Vibrio strains from molluscan shellfish farms along the Korean coast. Mar. Pollut. Bull. 149, 110559.
    Pubmed CrossRef
  6. Morgan S, Thomas MJ, Walstrom KM, Warrick EC, and Gasper BJ. 2017. Characterization of prodiginine compounds produced by a Vibrio species isolated from salt flat sediment along the Florida Gulf Coast. Fine Focus. 3, 33-51.
    CrossRef
  7. Sampaio A, Silva V, Poeta P, and Aonofriesei F. 2022. Vibrio spp.: Life strategies, ecology, and risks in a changing environment. Diversity 14, 97.
    CrossRef
  8. Shieh WY, Chen YW, Chaw SM, and Chiu HH. 2003. Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. Int. J. Syst. Evol. Microbiol. 53, 479-484.
    CrossRef
  9. 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
  10. Thompson CC, Vicente ACP, Souza RC, Vasconcelos ATR, Vesth T, Alves N, Ussery DW, Iida T, and Thompson FL. 2009. Genomic taxonomy of vibrios. BMC Evol. Biol. 9, 258.
    Pubmed KoreaMed CrossRef
  11. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, and Young SK, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963.
    Pubmed KoreaMed CrossRef
  12. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, and Chun J. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613-1617.
    Pubmed KoreaMed CrossRef


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  • Honam National Institute of Biological Resources
     
      HNIBR202301108