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Complete genome sequence of Salinicola endophyticus HNIBRBA4755, a halophyte-associated bacterium§
Korean J. Microbiol. 2024;60(4):298-301
Published online December 31, 2024
© 2024 The Microbiological Society of Korea.

Seung Yeol Shin1,3, Heeyoung Kang1, Nakyeong Lee2, Hyomin Seo1, Song-Ih Han3, and Jaeho Song1*

1Division of Microbiology, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
2Division of Environmental Materials, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
3Department 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

§Supplemental material for this article may be found at http://www.kjom.org/main.html
Received November 8, 2024; Revised December 4, 2024; Accepted December 4, 2024.
Abstract
Salinicola endophyticus HNIBRBA4755 was isolated from the root of halophyte Salicornia europaea (L.) Dumort. The complete genome of strain HNIBRBA4755 consists of 4,319,187 bp with a DNA G + C content of 66.0%. The genome contains 3,782 protein-coding genes, 72 tRNAs, and 5 rRNA operons as 16S-5S-23S rRNAs. Genome analysis revealed the presence of biosynthetic pathways for two siderophores, pyochelin and aerobactin. The siderophore activity of the strain was confirmed using the chrome azurol S assay. The genome sequence of strain HNIBRBA4755 provides insights into the potential and underlying genomic basis of interaction between bacteria and halophytes.
Keywords : Salincola, complete genome, halophyte, siderophore
Body

The genus Salinicola, belonging to the family Halomonadaceae, was first proposed by Anan’ina et al. (2007) with S. socius as the type species. Salinicola genomes normally showed range in size from 3.6 to 4.4 Mb and contained diverse metabolic pathways (Olsson et al., 2017; Fidalgo et al., 2019; Nguyen et al., 2023). Members of the genus have showed various physiological characteristics such as nitrate to nitrite reducing, macromolecules degrading, polyhydroxybutyrate (PHB) accumulating and H2S producing, and halotolerance (de la Haba et al., 2010; Fidalgo et al., 2019). Among them, several ones are known as bacteria promoting plant-growth with functions such as producing siderosphore, degrading aromatic compouns, and solubilizing phosphate (Szymańska et al., 2016; Nguyen et al., 2023; Duarte et al., 2024). Here, we report the complete genome sequence of a siderosphore-producing bacterium affiliated to S. endophyticus.

Strain HNIBRBA4755 was isolated from the roots of Salicornia europaea, a halophyte collected from tidal flat (37°15'31.1'' N, 126°29'6.16'' E) in July, 2022 during on the survey of halophyte-associated bacteria. A piece of the roots was gently washed with sterilized seawater and crushed using a homogenizer (IKA) with 1 ml of sterilized seawater. A pale-yellow colony, designated HNIBRBA4755, 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 HNIBRBA4755 cells cultured on MA for three days using the DNeasy Blood & Tissue kit (Qiagen) according to the manufacturer’s protocols. The complete genome sequence of the HNIBRBA4755 strain was obtained using the PacBio Sequel System with a 20 kb SMRTbell library and Illumina HiSeq 2500 sequencing platform (Macrogen). The PacBio Sequel platform generated a total of 101,270 HiFi reads (824,776,663 bp). De novo assembly was performed using the SMRT Link version 13.0 with PacBio reads only, followed by error correction of contig bases with 38,821,588 Illumina reads (5,854,368,443 bp) using Pilon (v1.21) (Walker et al., 2014). Genomic map of NIBRBA4755 was created with Proksee software (Supplementary data Fig. S1) (Grant et al., 2023). Strain HNIBRBA4755 contains a single circular chromosome of 4,319,187 bp with the DNA G + C content of 66.0%.

The genome sequence was annotated by NCBI Prokaryotic Genome Annotation Pipeline (PGAP) revision 6.5 (Tatusova et al., 2016). The genome encodes 3,782 coding DNA sequences (CDSs), 15 rRNAs (5S, 16S, and 23S), and 72 tRNAs (Table 1). 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). The HNIBRBA4755 genome shared 99.7% of the 16S rRNA gene similarity and 91.0% of ANI with the S. endophyticus CPA92T genome. The genes involved in the production of siderophores in strain HNIBRBA4755 were identified and predicted by antiSMAH 6.1.1 (Blin et al., 2021). Metabolic reconstruction based on Kyoto Encyclopedia of Genes and Genomes (KEGG) was pathways and orthology assignments were obtained using BlastKOALA (Kanehisa et al., 2016). Genes for the synthesis of pyochelin (pchABDEFG) and aerobactin (iucABCD) were encoded on the HNIBRBA4755 genome (Fig. 1). Pyochelin and aerobactin are highly bacterial iron chelating siderophores belonging to phenolates and hydroxymates groups, respectively, and contribute to trigger immunity in plants (Aznar and Dellagi, 2015). Genes related to degradation of benzoate (benAD, catABC, pcaIJL, and fadAI) were encoded on the HNIBRBA4755 genome. Benzoate is a common plant component and some soil bacteria that exhibit benzoate degradation have been proven to be antagonists of fungal and bacterial phytopathogens (Esikova et al., 2021). Genomic features of strains HNIBRBA4755 and CPA92T, a closely related strain, are listed in Table 1.

General genomic features of strains Salinicola endophyticus HNIBRBA4755 and CPA92T

Genomic features HNIBRBA4755 CPA92T
Accession No. CP159578 PZJO00000000
No. of Contigs 1 23
Genome length (Mb) 4,319,187 4,355,527
G + C content (%) 66.0 65.8
Coding genes 3,782 3,823
tRNA 72 62
rRNA 15 3
Genes coding for
benzoate degradation + -
pyochelin biosynthesis + -
aerobactin biosynthesis + +

Fig. 1. Genome region and gene organization for pyochelin (A) and aerobactin (B) clusters in strain HNIBRBA4755, predicted by antiSMASH.

Production of siderophore was confirmed using chrome azurol S (CAS) agar (Schwyn and Neilands, 1987). The strain was inoculated on CAS agar plates and incubated for 14 days at 20°C. Orange color circles around the colonies of strain HNIBRBA4755 were confirmed (Supplementary data Fig. S2), indicating that siderophore and resultant chelate were produced. These data suggest that the genomic features of strain HNIBRBA4755 are relevant to plant growth in halophyte.

Strain and nucleotide sequence accession numbers

Strain HNIBRBA4755 has been deposited at the Bank of Bioresources from Island and Coast (BOBIC) under the accession number HNIBR-BC5355. The GenBank/EMBL/DDBJ accession number for the complete genome sequence of strain HNIBRBA4755 is CP159578.

적 요

Salinicola endophyticus HNIBRBA4755 균주는 염생식물 퉁퉁마디 뿌리에서 분리되었고, 본 연구에서 전장 유전체 염기서열을 분석하였다. 해당 균주의 게놈은 4,319,187 bp 염기로 구성되어 있는데 GC 함량은 66.0%였고, 3,782개의 단백질을 코딩하는 유전자와 5개의 rRNA 오페론 및 72개의 tRNA 유전자를 보유하고 있었다. 게놈 분석 결과, 두 가지 siderophore, pyochelin과 aerobactin의 생합성 경로가 존재함이 밝혀졌다. 이 균주의 siderophore 활성은 chrome azurol S 검정을 사용하여 확인되었다. HNIBRBA4755 균주의 게놈 서열은 박테리아와 염생식물 간의 상호작용의 잠재적이고 근본적인 게놈 분석에 통찰력을 제공한다.

Acknowledgments

This study was supported by the research grant “Survey of Indigenous Species in Korean Islands” (HNIBR202401102) 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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