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Complete genome sequence analysis of Idiomarina abyssalis MSP-CT isolated from marine sediment, Jeju Island
Korean J. Microbiol. 2021;57(4):280-282
Published online December 31, 2021
© 2021 The Microbiological Society of Korea.

Minji Kim and Soo-Je Park*

Department of Biology, Jeju National University, Jeju 63243, Republic of Korea
Correspondence to: E-mail: sjpark@jejunu.ac.kr;
Tel.: +82-64-754-3524; Fax: +82-64-756-3541
Received August 30, 2021; Revised October 13, 2021; Accepted October 18, 2021.
Abstract
The genus Idiomarina belongs to the class Altermonadales has been known as a Gram-stain-negative and halophile. Also, the members of the genus Idiomarina as an aerobic heterotroph have little understanding of their abilities in nature. The present study isolated strain MSP-CT from the marine sediment and analyzed its single complete genome sequence. The circularized- complete genome size and G + C content were about 2.61 Mb and 47.1%, respectively. The single chromosome encoded 2,425 coding sequences with protein, 12 ribosomal RNA, and 56 transfer RNA genes. Strain MSP-CT genome encoded genes for biosynthesis for various vitamins, partial denitrification, and phosphorus uptake. Also, the genome harbored cbb3 and bd oxidases as a high affinity for oxygen under low-oxygen conditions. Taken together, strain MSP-CT might contribute to nutrient cycling and have a resistance against environmental stress in marine sediment.
Keywords : Idiomarina, complete genome, marine sediment
Body

The coastal marine sediment characters are continuously affected by freshwater runoff and soil particle sedimentation. During tide to go in and out, microorganisms in the estuarine zone would suffer various environmental stresses such as salinity and nutrient gradients due to mixing freshwater or evaporation. This study investigated the bacterial diversity based on the cultivation using different salt concentrations ranged 0.5 to 15% (w/v, NaCl). For bacterial isolation, the sediment sample (33°27'15" N, 126°18'23"E) was harvested using a sterilized spatula and quickly mixed with the autoclaved high salt-natural seawater (HNS) medium adjusted to 15% (w/v) NaCl. The mixture was serially diluted (ten-fold) to 10-5 with HNS medium. Then 100 µl of the aliquot from the final diluted sample (10-5) was spread on marine agar (BD Difco) plates adjusted to 15% (w/v, NaCl; named high-salt marine agar, HSM) and incubated at 25°C for two weeks under aerobic conditions. We selected several strains based on colony morphology and color under naked eyes. To obtain the single colony, the colonies had been successively transferred to the new HSM agar plates. Finally, we isolated one strain, designed MSP-CT at 15% (w/v) NaCl culture condition. The isolated strain MSP-CT has been deposited at the Korean Culture Center for Microorganisms (KCCM) as KCCM 43407.

To analyze the phylogenetic and taxonomic position, we extracted the gDNA of the strain MSP-CT using a commercial DNA extraction kit (GeneAll Biotechnology Co., Ltd.) and amplified the 16S ribosomal RNA gene sequence, according to the previous study (Kim et al., 2020). Then, we found that the strain MSP-CT was most closely related to Idiomarina abyssalis KMM 227T (LGOW01000020, 99.86% 16S rRNA gene sequence similarity) using EzBioCloud server (https://www.ezbiocloud.net/). The genus Idiomarina of the family Idiomarinaceae and the type species, Idiomarina abyssalis isolated as deep-sea bacteria from the Pacific Ocean was firstly proposed by Ivanova et al. (2000). Also, they require sodium ions for growth and possess Q-8 as predominant ubiquinone (Chen et al., 2019).

Whole-genome sequencing was performed at DNA Link, Inc. using the Pacific Biosciences RSII instrument (Pacific Biosciences). A single SMRT cell produced a total of 2.2 Gb (849 × in depth) in 323,617 polymerase reads that passed filtering. We obtained a single contig closed using RS HGAP assembly (v2.3). To estimate genome completeness and quality, we used CheckM v1.1.3 (Parks et al., 2015). The resulting assembled contigs were annotated by NCBI Prokaryotic Genome Annotation Pipeline (PGAP) with GeneMarkS-2+ version 5.2, using the best-placed reference protein method (Angiuoli et al., 2008). In addition, protein sequences were annotated using BLAST hit against the NCBI NR database and performed using Kyoto Encyclopedia of Genes and Genomes (KEGG) database references, as described previously (Kim et al., 2020). Finally, the assembled sequence length of the strain MSP-CT is 2,610,628 bp with 47.10% G + C content. The CheckM estimation result indicated genome completeness at 99.66% with 0.16% contamination and 0.0% strain heterogeneity.

The complete genome of the strain MSP-CT, estimated by PGAP, included 2,505 predicted genes, 12 ribosomal RNA, and 56 transfer RNA genes (Table 1). With the similarity for 16S rRNA gene sequence was high (99.86%), the result (76.30%) of digital DNA-DNA Hybridization (DDH) estimated by Genome-to-Genome Distance Calculator (GGDC) (Meier-Kolthoff et al., 2013) indicated that strain MSP-CT is the same species with Idiomarina abyssalis KMM 227T (GCA_001294685). Based on the results for potential metabolic characterizations estimated by Clusters of Orthologous Groups (COGs) and KEGG analyses, we had no significant differences for the genomics traits between strains MSP-CT and KMM 227T.

Idiomarina abyssalis MSP-CT genome assembly and its general features

Genome features Value
Assembled length (Mb) 2.61
GC content (%) 47.1
No. of total predicted genes* 2,505
No. of total coding sequences* 2,433
No. of coding sequences with protein* 2,425
No. of rRNA (23S, 16S, 5S)* 12 (4, 4, 4)
No. of tRNA* 56

*Predicted by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP); annotation method, Best-placed reference protein set; GeneMarkS-2+ (version 5.2).



KEGG analysis (n = 1,621) showed that the complete genome of the strain MSP-CT has putative metabolic traits such as iron uptake (CcmABCD) from the environment, biosynthesis for cofactors and vitamins, and glyoxylate cycle as an anabolic tricarboxylic acid cycle. Although strain MSP-CT has been identified as heterotrophs, most genes for nutrient transporters were lacked in the genome, except for PstSCBA (phosphate) and MlaCDEBF (phospholipid). In addition, genes for partial denitrification (nitrate to nitrous oxide; narGHI, nirK, and norBC) have been identified in the genome. These results deduce that the strain MSP-CT produces and supplies growth factors to other organisms (Sañudo-Wilhelmy et al., 2014), and contributes to phosphorus and nitrogen cycle in marine sediment (Herbert, 1999; Martínez et al., 2013; Karl and Björkman, 2015).

Unexpectedly, the strain MSP-CT genome harbored many proteins for chemotaxis, entire flagellar assembly, and type IV pilus assembly (i.e., twitching motility or biofilm formation) (Craig et al., 2019). The genome harbored cbb3 and bd oxidases as a high oxygen affinity under low-oxygen conditions (Pitcher and Watmough, 2004; Giuffrè et al., 2014). In addition, it deduces that the strain MSP-CT might have a resistance to oxidative and nitrosative stress via cytochrome bd oxidase (Giuffrè et al., 2014). Taken together, strain MSP-CT might have a ecological advantages under nutrient starvation.

Nucleotide sequence accession numbers

The complete genome sequence of the strain MSP-CT (= KCCM 43407) has been deposited at DDBJ/ENA/GenBank under the accession number CP081832.

적 요

Altermonadales 과에 속하는 Idiomarina속은 그람 음성 및 호염성 세균으로 알려져 있다. 호기적 종속 영양체인 Idiomarina 속 세균들은 자연계에서 그들의 능력에 대하여 제한된 정보들만 알고 있다. 본 연구에서는 해양 침전물로부터 분리된 MSP-CT 균주의 완전한 게놈 서열을 분석하였다. 전장 게놈 크기와 G + C 함량은 각각 약 2.61 Mbp와 47.1%였다. 본 전장 게놈은, 2,425개의 단백질을 암호화하는 서열을 비롯하여, 12개의 리보솜 RNA, 56개의 운반 RNA 유전자를 포함하였다. MSP-CT 균주의 게놈은 다양한 비타민 생합성, 부분 탈질화와 인 흡수에 관련된 유전자를 암호화한다. 또한 본 게놈은 저 산소 조건에서 높은 산소 친화력을 지닌 cbb3bd 산화효소를 가지고 있었다. 이러한 결과를 바탕으로, MSP-CT 균주는 해양 퇴적물 환경의 물질 순환에 기여하며, 환경적 스트레스를 잘 견딜 수 있는 것으로 예측된다.

Acknowledgments

This research was supported by the 2021 scientific promotion program funded by Jeju National University.

Conflict of Interest

The authors have no conflict of interest to report.

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