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Complete genome sequence of Ottowia sp. SB7-C50, a heterotrophic sulfur-oxidizing bacterium isolated from a wastewater treatment system
Korean J. Microbiol. 2023;59(4):350-352
Published online December 31, 2023
© 2023 The Microbiological Society of Korea.

Ji-Hyun Nam1,2, Se-Hwan Kang2, Tatsuya Unno2, and Dong-Hun Lee2*

1Division of Antimicrobial Resistance Research, Center for Infectious Diseases Research, National Institute of Infectious Diseases, National Institute of Health, Cheongju 28160, Republic of Korea
2Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
Correspondence to: *E-mail: donghun@cbnu.ac.kr; Tel.: +82-43-261-3261; Fax: +82-43-264-9600
Received October 30, 2023; Revised November 13, 2023; Accepted November 14, 2023.
Abstract
A novel heterotrophic sulfur-oxidizing bacterium, Ottowia sp. SB7-C50, was isolated from a wastewater treatment system in Korea. The strain SB7-C50 was facultatively anaerobic and used thiosulfate as an additional electron donor. The complete genome of strain SB7-C50 consists of a single circular chromosome (3,611,735 bp with G + C content of 67.49%). The complete genome included a total of 3,214 protein-coding genes, 3 rRNAs, 41 tRNAs, and 3 non-coding RNAs. The strain SB7-C50 had a sulfur oxidation system composed of thiosulfate oxidation carrier protein, sulfur oxidation c-type cytochrome, thiosulfohydrolase, and sulfite dehydrogenase. In addition, strain SB7-C50 had nitrate reductase and nitrite reductase.
Keywords : Ottowia, activated sludge, denitrification, sulfur-oxidizing bacteria
Body

The processes using denitrifying bacteria have been used for the removal of nitrogen in wastewater treatment systems. However, in a denitrification process for industrial wastewater with low C/N ratios, an external carbon source is usually needed (Ahmed et al., 2023). A variety of electron donors can be used for denitrification, and inorganic compounds were proposed as an alternative source of electron donors to reduce carbon use (Pang and Wang, 2021). Moreover, the autotrophic or mixotrophic denitrification process has been studied for wastewater treatment (Capua et al., 2019; Zhang et al., 2023).

The genus Ottowia, belongs to the Comamonadaceae family, was first proposed by Spring et al. (2004) and 9 species have been validly published: O. thiooxydans, O. pentelensis, O. beijingensis, O. konkukae, O. oryzae, O. flava, O. caeni, O. testudinis, and O. massiliensis (https://lpsn.dsmz.de). In this report, we describe the genome sequence and annotation of Ottowia sp. SB7-C50 isolated from a wastewater treatment system of a meat-processing plant in Gimcheon-si, Republic of Korea (36.15°N, 128.12°E). The strain SB7-C50 was capable of facultatively anaerobic growth with nitrate and nitrite as electron acceptors. Thiosulfate could be utilized by strain SB7-C50 as an additional electron donor for mixotrophic growth. This was consistent with the characteristics of other strains of the genus Ottowia (Cao et al., 2014; Heo et al., 2018; Busse et al., 2022).

For the whole genome sequencing, the strain SB7-C50 was incubated aerobically on Nutrient Agar without NaCl (BD) at 30°C for 2 days. The genomic DNA was extracted and purified using Wizard® HMW DNA Extraction Kit (Promega). The sequencing of the whole genome was performed on the Oxford Nanopore MinION platform with SQK-NBD114.24 Kit and FLO-MIN114 (R10.4.1) flow cell (ONT). A total of 386,927,623 bp with 84,884 reads (average read length 4,558 bp, 108x coverage) were produced and de novo assembly was performed by Flye (Kolmogorov et al., 2019). The complete genome of strain SB7-C50 consisted of one circular chromosome with 3,611,735 bp (G + C content of 67.49%). Genome annotation and functional characterization of genes were performed by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016). A total of 3,444 genes were predicted from the genome sequence, and 3,214 protein-coding genes and 47 RNAs (3 rRNAs, 41 tRNAs, and 3 ncRNAs) were identified as described in Table 1.

Genome features of Ottowia sp. SB7-C50
Features Chromosome
Genome size (bp) 3,611,735
G + C content (mol%) 67.49
Total number of genes 3,444
Protein-coding genes 3,214
rRNA genes (5S, 16S, 23S) 3 (1, 1, 1)
tRNA genes 41
ncRNA genes 3
Pseudogenes 183


Genomic similarities between strain SB7-C50 and three type strains of the genus Ottowia were calculated using the ANI calculator at the EZBioCloud server (http://www.ezbiocloud.net) (Yoon et al., 2017). The OrthoANI value between strain SB7-C50 and O. beijingensis (DSM 100246T) was 84.32%, while it was 83.16% with O. testudinis (CCM 9138T) and 80.29% with O. oryzae (KACC 19325T). Strain SB7-C50 had one copy of 16S rRNA gene, and the 16S rRNA gene sequence of strain SB7-C50 was compared with those of other type strains using the EzBioCloud server. Strain SB7-C50 was mostly related to O. beijingensis (97.93%) and O. testudinis (97.45%), and shared 94.91 to 96.14% sequence similarity with the other type strains of genus Ottowia.

The comparative sequence analysis revealed that strain SB7-C50 had a sulfur oxidation (Sox) system composed of thiosulfate oxidation carrier protein (SoxYZ), sulfur oxidation c-type cytochrome (SoxXA), thiosulfohydrolase (SoxB), and sulfite dehydrogenase (SoxC). Except for SoxX, the Sox proteins of strain SB7-C50 showed high similarities of amino acid sequence (more than 87.6%) with O. testudinis and O. beijingensis. In addition, strain SB7-C50 had nitrate reductase and nitrite reductase for a partial pathway of denitrification. The genomic information of strain SB7-C50 may contribute to the development of alternative denitrification processes for wastewater with poor carbon sources.

Strain and nucleotide sequence accession numbers

Ottowia sp. SB7-C50 has been deposited at the Korean Collection for Type Cultures (KCTC) under the preservation number of KCTC 32378. The GenBank accession number for the genome sequence of Ottowia sp. SB7-C50 is CP136995. The associated BioProject and BioSample accession numbers are PRJNA1027767 and SAMN37803623, respectively.

적 요

국내 폐수처리장에서 신규 종속영양 황산화 세균 Ottowia sp. SB7-C50을 분리 배양하였다. SB7-C50 균주는 통성혐기성이었으며 티오황산염을 추가 전자 공여체로 이용하였다. SB7-C50 균주의 전체 게놈은 단일 원형 염색체 (3,611,735 bp, G + C 함량 67.49%)로 구성된다. 전체 3,214개의 단백질 암호 유전자, 3개의 rRNA 유전자, 41개의 tRNA 및 3개의 non-coding RNA가 확인되었다. SB7-C50 균주는 티오황산염 산화 운반 단백질, 황 산화 c형 시토크롬, 티오설포가수분해효소 및 아황산염 탈수소효소로 구성된 황 산화 시스템을 가지고 있다. 또한, SB7-C50 균주는 탈질 반응을 위한 질산염 환원효소와 아질산염 환원효소를 가지고 있었다.

Acknowledgments

This work was supported by the academic research program of Chungbuk National University in 2023.

Conflict of Interest

The authors have no conflict of interest to report.

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