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Complete genome sequence of Algibacter luteus HNIBRBA226 isolated from coastal seawater
Korean J. Microbiol. 2023;59(3):227-229
Published online September 30, 2023
© 2023 The Microbiological Society of Korea.

Seung Yeol Shin, Heeyoung Kang, and Jaeho Song*

Division of Microbiology, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
Correspondence to: *E-mail: songjh21@hnibr.re.kr; Tel.: +82-61-288-7960; Fax: +82-61-288-7974
Received August 1, 2023; Revised August 31, 2023; Accepted September 4, 2023.
Abstract
Cells of the genus Algibacter belonging to the family Flavobacteriaceae are known as Gram-negative, facultatively anaerobic, rod-shaped, and gliding bacteria. Here, we report the complete genome sequence of A. luteus HNIBRBA226 isolated from coastal seawater. The strain showed the highest sequence similarity in 16S rRNA gene sequence with A. luteus P7-3-5T (99.9%). The HNIBRBA226 genome contained a circular chromosome of 3.7 Mb with the DNA G + C content of 33.5 mol%. A total of 3,208 protein coding genes, 7 rRNAs, and 39 tRNAs were identified in the HNIBRBA226 genome. The HNIBRBA226 genome shared more than 96.1% of the average nucleotide identity with the P7-3-5T genome, but uniquely contained cellulase.
Keywords : Algibacter luteus, Flavobacteriaceae, cellulase, complete genome
Body

Genus Arenitalea, a member of the family Flavobacteriaceae, was first proposed based on the description of a Gram-negative, facultatively anaerobic, rod-shaped, and gliding bacterium isolated from intertidal sand of the Yellow Sea (Zhang et al., 2013) and has been reported from diverse marine habitats including seawater (Cho et al., 2017), marine particle (Schultz et al., 2020), and seaweed (Wang et al., 2022). In 2022, Arenitalea lutea, the type species of the genus, was reclassified into the genus Algibacter (Li et al., 2021). The genome of the type strain of the species Algibacter luteus (Zhang et al., 2013; Li et al., 2021) was sequenced, which resulted in a size of 3.38 Mb in 51 contigs (> 500 bp) (Zhang et al., 2012; GenBank accession no. ALIH00000000). Here, we report the complete genome sequence of a marine bacterium affiliated to the species A. luteus and metabolic features based on the genome analyses.

Strain HNIBRBA226 was isolated from coastal seawater collected off Goheung-gun (34°31'56" N, 127°07'18" E), South Korea. The strain was isolated using a dilution-plating method on Marine agar 2216 (MA; Difco). Genomic DNA was obtained from cells cultivated for four days on MA using the DNeasy Blood & Tissue kit (Qiagen) following the manufacturer’s protocols. The 16S rRNA gene sequence obtained by Sanger sequencing indicates that the strain is a member of the genus Algibacter exhibiting the highest similarity to Algibacter luteus P7-3-5T (99.9%). Whole genome sequencing was performed using both of PacBio Sequel System with a 20kb SMRTbell library and Illumina HiSeq 2500 sequencing platform (Macrogen). In total, 52,228 long reads (487,409,283 bp) were sequenced using the PacBio Sequel platform with 317× in depth. Likewise, 6,572,514 short reads (991,372,862 bp) were sequenced using the Illumina 151 bp pair-end library. De novo assembly was conducted using the CANU version 1.8 (Nurk et al., 2020) 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 HNIBRBA226 was determined to be a circular chromosome of 3,746,993 bp, with the DNA G + C content of 33.5% and depth of 100×. The genome encodes 3,208 coding DNA sequences (CDSs), 7 rRNAs (5S, 16S, and 23S), and 39 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 HNIBRBA226 genome shared 96.1% of ANI with the P7-3-5T genome. Metabolic reconstruction based on KEGG was pathways and orthology assignments were obtained using BlastKOALA (Kanehisa et al., 2016). The results suggested an anaerobic heterotrophic lifestyle for strain HNIBRBA226. Genes for dissimilatory nitrate reduction (locus tag: 08405, 08410, 08180, 08185), folate biosynthesis (03810, 06125, 15960), ABC transporter for Zinc/Manganese/Iron(II) (02210) were encoded on the HNIBRBA226 and P7-3-5T genomes, but two cellulase genes (05005, 08300) only on the HNIBRBA226 genome. Cellulose is a prevalent marine polysaccharide found in seaweeds (Kouzuma and Fujii, 2018) and Algibacter members may play a role in the degradation of seaweeds.

General genomic features of strains Algibacter luteus HNIBRBA226 and P7-3-5T
Genomic features HNIBRBA226 P7-3-5T
GenBank accession no. CP128313 ALIH00000000
Genome length (Mb) 3.74 3.38
G + C content (%) 33.48 33.33
No. of contigs 1 51
No. of total predicted genes 3,259 2,977
No. of total coding sequences 3,208 2,959
No. of rRNA (23S, 16S, 5S) 7 6
No. of tRNA 39 36
Presence of cellulase + -


Strain and nucleotide sequence accession numbers

Strain HNIBRBA226 has been deposited at the Bank of Bioresources from Island and Coast (BOBIC) under the number HNIBR BC-28. The GenBank/EMBL/DDBJ accession number for the complete genome sequence of strain HNIBRBA 226 is CP128313. The associated BioProject and BioSample accession numbers are PRJNA914060 and SAMN32317180, respectively.

적 요

Algibacter 속은 Bacteroidota 문의 Flavobacteraceae 과에 속하며, 그람-음성 통성혐기성 간균이며 활주세균이다. 이 연구는 연안 해수에서 분리된 Algibacter luteus HNIBRBA226의 전장 유전체 염기서열을 보고한다. HNIBRBA226 균주는 A. luteus P7-3-5T와 99.9% 16S rRNA 유전자 상동성을 보였다. HNIBRBA226 유전체는 3,746,993 bp 크기의 33.5%의 G + C함량을 갖는 원형의 유전체로 조립되었다. HNIBRBA226 유전체는 3,208개의 CDS, 7개의 rRNA 및 39개의 tRNA 유전자로 구성되어 있음이 확인되었다. HNIBRBA226 유전체는 A. luteus P7-3-5T 유전체와 96.1% 이상의 유전체 염기서열 평균 유사도를 보였으며, 고유하게 셀룰로오스 가수분해 효소를 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