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Draft genome sequence of Weizmannia coagulans BA375 isolated from saltern soil in Korea
Korean J. Microbiol. 2021;57(2):116-118
Published online June 30, 2021
© 2021 The Microbiological Society of Korea.

So-Jeong Kim1*, Jong-Geol Kim2, Gi-Yong Jung1, Jisoo Park3, and Eun-Jin Yang3

1Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Republic of Korea
2Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan 54538, Republic of Korea
3Division of Polar Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
Correspondence to: E-mail: sojkim86@kigam.re.kr; Tel.: +82-42-868-3311; Fax: +82-42-868-3414
Received April 6, 2021; Revised May 12, 2021; Accepted June 1, 2021.
Abstract
The strain Weizmannia coagulans BA375, which was isolated from soil of a saltern, produced 1,4-β-xylanase and acetylxylan esterase. The draft genome sequence of the strain W. coagulans BA375 was determined using Illumina MiSeq platform. The genome comprises 82 contigs with genome size of 3,060,890 bp long and GC content of 46.9%. The draft genome contains 2,785 protein-coding genes, 130 pseudogenes and 117 RNA genes including 33 ribosomal RNA genes, 80 transfer RNA (tRNA) genes and 4 non-coding RNA (ncRNA) genes. The strain W. coagulans BA375 has polyprenyl glycosylphosphotransferase gene which is involved in biosynthesis of exopolysaccharides.
Keywords : Weizmannia coagulans, draft genome sequence, exopolysaccharide, Illumina MiSeq, xylanase
Body

Manganese is an abundant element in the Earth’s crust and plays a key role in biogeochemical cycles. Some microorganisms are known to be associated with the manganese cycle. Recently, the first chemolithotrophic manganese oxidizer was isolated, and its genomic properties were reported (Yu and Leadbetter, 2020). Previously, only heterotrophic manganese-oxidizing bacteria were known (Nealson, 2006). One strain, Aurantimonas manganoxydans SI85-9A1, is a known heterotrophic Mn(II) oxidizer that produces Mn(III/IV) oxides (Dick et al., 2008). The genus Aurantimonas has been isolated from various environments such as deep-sea sediment (Li et al., 2017), marine (Anderson et al., 2009), cave (Jurado et al., 2006), coral (Denner et al., 2003), root (Liu et al., 2016), and air (Weon et al., 2007). DM33-3 was isolated from a water column of the Amundsen Sea Polynya, Antarctica. For preparation of inoculum, microbial cells from the seawater were collected under vacuum through a sterile membrane filter (pore diameter of 0.2 µm, Adcantec Tokyo) and was incubated in marine broth (Difco) at 15°C. To obtain isolate, the enrichment culture was spread on marine agar 2216 (MA; Difco). Among the colonies, a bacterial strain was isolated and purified. Its cells were routinely cultured at 25°C on MA and deposited at the Korea Culture Type Collection (KCTC) as KCTC 72499.

DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen) for genome sequencing. The DNA library was prepared using the TruSeq DNA Nano kit and the genome sequencing was performed using Illumina Hiseq 6000 at Microgen. Automated annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline. Bacterial universal primers 27F and 1492R were used to amplify 16S rRNA gene sequence (Lane, 1991). The similarity of 16S rRNA gene was conducted using EzBioCloud (Yoon et al., 2017). 16S rRNA gene analysis revealed that the isolate had 100% similarity with Aurantimonas coralicida DSM14790. Digital comparisons of genomic sequence of strain DM33-3 and DSM14790, ANI and AAI were analyzed by JSpiecesWS and compareM, respectively. The ANI and AAI values were 97.8% and 96.1%, respectively. Based on the value of species boundaries (Konstantinidis and Tiedje, 2005; Konstantinidis et al., 2006), strain DM33-3 is considered a new strain of Aurantimonas coralicida.

The genomic size of Aurantimonas coralicida DM33-3 is 4,620,302 bp with 49 scaffolds and 66.6% of the G + C content. The coverage of the genome is 286.0×. Total genes are predicted to be 4,423, with one ribosomal operon (Table 1). The genome has complete glycolysis and TCA cycle. Similar to Aurantimonas manganoxydans SI85-9A1, the manganese oxidizer, duplicate manganese-oxidizing related gene cluster (H9Q09_15580 - 15610 and H9Q09_20460 - 20480) and RubisCO (H9Q09_17670 - 17675) are found in this genome. However, the function of RubisCO in A. manganoxydans SI85-9A1 is unclear (Caspi et al., 1996). Strain DM33-3 contains the sox gene cluster (SoxGTRSVWXYZABCD; H9Q09_00175 - 00235). These genes are also found in the genome of DSM14790. This might support the growth of strain DM33-3 with thiosulfate oxidation in the environment.

Genomic features of Aurantimonas coralicida DM33-3 and related strains

Description A. coralicida DM33-3 A. coralicida DSM14790 A. manganoxydans SI85-9A1
Size (bp) 4,620,302 4,615,647 4,325,257
GC content 66.6 66.7 66.7
Number of contigs 49 38 35
Number of coding genes 4,415 4,275 3,650
rRNA (5S, 16S, 23S) 3, 1, 1 3, 1, 5 3, 3, 3
tRNA 45 48 50
Accession number JACSGS010000000 ATXK01000000 AAPJ01000000


The genome includes one cytochrome bd-type quinol oxidase (H9Q09_17750 - 17755; high affinity for oxygen), two cbb3-type cytochrome c oxidases (H9Q09_01970 - 02005 and H9Q09_21295 - 21310; high affinity for oxygen), and three cytochrome c oxidases (H9Q09_04305 - 04310, H9Q09_12435 - 12455, and H9Q09_21985 - 22005; low affinity for oxygen). Compared with DSM 14790, the genome of strain DM33-3 had an additional cbb3-type cytochrome c oxidase. Furthermore, genes related to respiratory nitrate reductase (H9Q09_21845 - 21860) are observed in this genome, which are absent in the genomes of A. manganoxydans SI85-9A1 and A. coralcida DSM14790. This shows that strain DM33-3 might live at various oxygen levels and under anaerobic conditions. The genome also contains heavy metal detoxification systems such as arsenic reductase (H9Q09_03245 - 03260) and mercury reductase (H9Q09_09930 - 09945).

Taken together, strain DM33-3 may adapt various environments by thiosulfate oxidation, a wide range of oxygen respiration, and heavy metal detoxification compared to previous isolates. Thus, this report provides new insights into the ecology of manganese-oxidizing groups from the Amundsen Sea Polynya.

Nucleotide sequence accession number(s)

The genome of Aurantimonas coralicida DM33-3 has been deposited in NCBI under accession number JACSGS0100 00000. Strain DM33-3 is deposited at KCTC as KCTC 72499.

적 요

아문젠해 폴리냐로부터 분리한 Auramtimonas coralicida DM33-3 균주의 유전체 정보를 제공한다. 이 유전체는 4,620,302 bp, 4,415개의 단백질 코딩 유전자, 1개의 rRNA 오페론, 45개의 rRNA를 가진다. 망간과 티오황산염 산화 유전자가 발견되었다. 또한 다양한 산소 친화도를 가지는 말단산화 효소와 질산염 환원 효소를 암호화하는 유전자를 포함하고 있다. 이는 아문젠해 폴리냐에서 DM33-3 균주가 생지화학적 순환(망간, 황, 질소 순환)에 다양한 잠재적 역할을 할 수 있음을 보여 준다.

Acknowledgments

This work was supported by the Basic Research Project of the Korea Institute of Geoscience and Mineral Resources (21-3412-1) and a grant (PE21110) from the Korea Polar Research Institute.

Conflict of Interest

The authors have no conflicts of interest to report.

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June 2021, 57 (2)