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Genome sequence of Undibacterium aquatile 14-3-2 isolated from CO2-rich groundwater
Korean J. Microbiol. 2021;57(3):216-219
Published online September 30, 2021
© 2021 The Microbiological Society of Korea.

So-Jeong Kim1*, Gi-Yong Jung1,2, Dong-Hun Kim1, and Kyung-Seok Ko1

1Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Republic of Korea
2Department of Biological Science and Biotechnology, Microbiology & Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
Correspondence to: E-mail: sojkim86@kigam.re.kr; Tel.: +82-42-868-3311; Fax: +82-42-868-3414
Received June 18, 2021; Revised August 17, 2021; Accepted August 17, 2021.
Abstract
We report the draft genome sequence of Undibacterium aquatile strain 14-3-2, isolated from natural CO2-rich groundwater. The genome of strain 14-3-2 comprises 12 scaffolds with a chromosome length of 4,032,713 bp and 49.8% G + C content. The draft genome contains 3,544 protein-coding genes, 3 rRNA genes, and 50 tRNAs. Additionally, genes involved in biosynthesis of cofactors and vitamin and glycoside hydrolases were identified throughout the draft genome, which might be crucial factors for the survival of strain 14-3-2 in an oligotrophic groundwater environment.
Keywords : Undibacterium aquatile, CO2-rich, groundwater
Body

Recently, many species of the genus Undibacterium were isolated from water such as lake, water fall, drinking water, and purified water system (Kämpfer et al., 2007; Eder et al., 2011; Kim et al., 2014; Du et al., 2015). Furthermore, the genus Undibacterium was one of the predominant genera in biofilm on biodegradable plastic (Morohoshi et al., 2018) and chlorinated anthracite filters (de Vera et al., 2018). Members of this genus are generally reported to Gram-staining negative, oxidase-positive, rod-shaped, motile by means of a single polar flagellum and chemoheterotrophic (Chen et al., 2017).

During the national-wide investigation of the microbial diversity of groundwater in the Republic of Korea, Undibacterium-like strain was isolated from natural CO2-rich groundwater. The groundwater sample, which has been used for drinking water, was collected from Daebak-ri, Sejong-si, Republic of Korea (36.4822 N, 127.3400 E). Detailed information of the sampling site (DPW-2 well) was described in previous study (Ham et al., 2017). The cells were harvested by using 0.1 µm pore size filter and inoculated into artificial freshwater medium (Jung et al., 2019) containing 0.5 mM glycerol and 1% CO (v/v) as electron donors. After one month of cultivation at 25°C, the extinction culture was spread on Reasoner’s 2A (R2A) agar and repetitively transferred to new medium in order to get a single colony. Finally, one strain was isolated and designated as into strain 14-3-2. Strain 14-3-2 was closely related to Undibacterium aquatile CCTCC AB 2015119T on the basis of the 16S rRNA gene sequence similarity (98.67% similarity). Strain 14-3-2 was grown at 10~35°C (optimum 25°C) and NaCl 0~0.5% (wt/v).

The genomic DNA was extracted using a commercial DNA extraction kit (DNeasy Blood & Tissue Kit) according to the manufacturer’s instructions. Whole-genome sequencing was performed at Macrogen Inc. using the Hiseq 4000 sequencing platform (Illumina Inc.). Total read bases about 2.0 Gb (after passed filtering) were used into contig assembly. The sequence depth was calculated as 145× average genome coverage. Paired reads were qualified with FastQC and assembled by SPAdes (ver. 3.13). The reconstructed genome was annotated by NCBI Prokaryotic Genome Annotation Pipeline (Tatusova et al., 2016). The draft genome of strain 14-3-2 was composed 4,032,713 bp of chromosome (12 scaffolds) with a DNA G + C content of 49.8%. The genome contains 3,614 genes, 3,544 protein-coding genes (CDSs), 3 rRNA genes, and 50 tRNA genes (Table 1). The average nucleotide identity (ANI) of genomes between strain 14-3-2 and U. aquatile CCTCC AB 2015119T was 96.1% based on OrthoANIu (Yoon et al., 2017). The higher ANI value than the criterion for interspecies identity (Jain et al., 2018) indicating that strain 14-3-2 was represented a strain of U. aquatile.

Genomic features of strain 14-3-2

Genomic features 14-3-2
Genome size (bp) 4,032,713 bp
Number of scaffolds 12
G + C content (%) 49.8
Genome coverage 145×
Total genes 3,614
Protein-coding genes (CDS) 3,544
rRNAs (5S, 16S, 23S) 3 (1, 1, 1)
tRNAs 50
GenBank Accession No. JAENGS010000000.1


The draft genome harbored genes involved in denitrification processes from nitrate (NO3-) to nitrous oxide (N2O) and various types of terminal oxidases (high affinity and low affinity for oxygen) (Table 2). These genes were also observed in the genome of strain CCTCC AB 2015119T. Genes for biosynthesis of cofactors and vitamins such as thiamine, riboflavin, biotin, cobalamin and heme were also observed in this genome. In addition, strain 14-3-2 possesses 15 genes encoding glycoside hydrolases (GH1, GH3, GH8, GH28, GH44, GH64, cellulose, and alpha-amylase) which potentially suggest the utilization of various carbohydrates. In particular, cellulolytic activity can be applied to reduce biofilm formation on the surfaces (Nahm et al., 2017) such as water supply systems.

Genes related to respiration in the genome of strain 14-3-2

Function Locus tag Annotation
Dissimilatory nitrate reduction Undi14_14560 respiratory nitrate reductase subunit gamma, NarI
Undi14_14565 nitrate reductase molybdenum cofactor assembly chaperone, NarJ
Undi14_14570 nitrate reductase subunit beta, NarH
Undi14_14575 nitrate reductase subunit alpha, NarG
Undi14_14580 NarK family nitrate/nitrite MFS transporter
Undi14_14585 NarK/NasA family nitrate transporter
Undi14_14450 nitrite reductase (NO-forming), NirS
Undi14_14225 nitrite reductase, copper-containing, NirK
Undi14_14460 Rrf2 family transcriptional regulator
Undi14_14465 nitric-oxide reductase large subunit, NorB
Oxygen respiration
(High affinity for oxygen)
Undi14_12565 cytochrome bd-I oxidase subunit, CydX
Undi14_12570 cytochrome d ubiquinol oxidase subunit II
Undi14_12575 cytochrome ubiquinol oxidase subunit I
Undi14_13855 cytochrome c oxidase accessory protein CcoG
Undi14_13860 cytochrome-c oxidase, cbb3-type subunit III
Undi14_13865 cbb3-type cytochrome c oxidase subunit 3
Undi14_13870 cytochrome-c oxidase, cbb3-type subunit II
Undi14_13875 cytochrome-c oxidase, cbb3-type subunit I
Oxygen respiration
(low affinity for oxygen)
Undi14_14415 cytochrome o ubiquinol oxidase subunit IV, CyoD
Undi14_14420 cytochrome o ubiquinol oxidase subunit III, CyoC
Undi14_14425 cytochrome o ubiquinol oxidase subunit I, CyoB
Undi14_14430 ubiquinol oxidase subunit II, CyoA
Undi14_08645 cytochrome c oxidase subunit 3
Undi14_08655 cytochrome c oxidase assembly protein
Undi14_08660 cytochrome c oxidase subunit I
Undi14_08665 cytochrome c oxidase subunit II


Recently, poly (3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH)-degrading strains, Undibacterium sp. KW1 and YM2, were isolated from biofilm on the surface of the PHBH film in the freshwater (Morohoshi et al., 2020). These two PHBH degrading bacteria possess extracellular PHA depolymerases, however, strain 14-3-2 had one gene coding intracellular type PHA depolymerase (Undi14_14150). It is possible that strain 14-3-2 can degrade the polyhydroxyalkanoate (PHA), synthesized by a wide range of bacteria in diverse environments, and utilize reduced molecular as a carbon source. The draft genome sequence of strain 14-3-2 will provide the molecular mechanism for survival under oligotrophic groundwater environment.

Nucleotide sequence accession numbers

Strain 14-3-2 has been deposited as KCTC 82081 and NBRC 114685 in culture collections, KCTC and NBRC, respectively. The genome sequence of strain 14-3-2 was deposited in GenBank under the accession number JAENGS010000000.1.

적 요

자연 탄산 지하수로부터 분리된 Undibacterium aquatile 14-3-2의 유전체 정보를 보고한다. 균주 14-3-2의 유전체는 12개의 scaffold로 구성되어 4,032,713 bp, G + C는 49.8%이며, 3,544개 단백질 코딩 유전자, 3개의 rRNA 및 50개의 tRNA를 가진다. 이 유전체는 다양한 조효소와 비타민 및 글라이코시드 가수분해 효소를 코딩하는 유전자를 포함하고 있다. 이러한 특징은 빈영양상태인 지하수 환경에서 이 균주가 살아갈 수 있도록 도와줄 것이다.

Acknowledgments

This work was supported by the National Research Council of Science & Technology (NST) grant by the Korean government (MSIP) (Project code: CAP-19-05-KIGAM).

Conflict of Interest

The authors have no conflicts of interest to report.

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