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Complete genome sequence of Comamonas sp. NLF-7-7 isolated from biofilter of wastewater treatment plant
Korean J. Microbiol 2019;55(3):309-312
Published online September 30, 2019
© 2019 The Microbiological Society of Korea.

Dong-Hyun Kim1, Kook-Il Han2, Hae Jun Kwon1, Mi Gyeong Kim1, Young Guk Kim1, Doo Ho Choi1, Keun Chul Lee2, Min Kuk Suh2, Han Sol Kim2, Jung-Sook Lee2,3*, and Jong-Guk Kim1*

1School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
2Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
3University of Science and Technology (UST), Daejeon 34113, Republic of Korea
Correspondence to: *(J.G. Kim) E-mail: kimjg@knu.ac.kr; Tel.: +82-53-950-5379; Fax: +82-53-950-5379 /
(J.S. Lee) E-mail: jslee@kribb.re.kr; Tel.: +82-63-570-5618; Fax: +82-63-570-5609
Received August 27, 2019; Revised September 17, 2019; Accepted September 17, 2019.
Abstract
Comamonas sp. NLF-7-7 was isolated from biofilter of wastewater treatment plant. The whole-genome sequence of Comamonas sp. NLF-7-7 was analyzed using the PacBio RS II and Illumina HiSeqXten platform. The genome comprises a 3,333,437 bp chromosome with a G + C content of 68.04%, 3,197 total genes, 9 rRNA genes, and 49 tRNA genes. This genome contained pollutants degradation and floc forming genes such as sulfur oxidization pathway (SoxY, SoxZ, SoxA, and SoxB) and floc forming pathway (EpsG, EpsE, EpsF, EpsG, EpsL, and glycosyltransferase), respectively. The Comamonas sp. NLF-7-7 can be used to the purification of wastewater.
Keywords : Comamonas sp. NLF-7-7, Illumina HiSeqXten, PacBio RS II, wastewater
Body

Large scale of farm cause large scale of wastewater. This wastewater need to pass through wastewater treatment plants and purified. But the water purification process causes a huge amount of odor pollutants. Biofilters are responsible for removing these odor pollutants by specific microorganisms which can degrades pollutants (Wani et al., 1997). A sulfur oxidizing bacteria investigation performed that presence of a SoxB gene indicate presence of the Sox pathway and this means presence of sulfur oxidization ability in organism (Petri et al., 2001; Anandham et al., 2008). During the study of analyzing kinds of cultivable bacteria in Biofilter of the wastewater treatment plants, a novel bacterial strain NLF-7-7 was isolated. Based on phylogenetic, phenotypic and chemotaxonomic data, strains NLF-7-7 (= KCTC 62943) was identified as a novel species as a member of the genus Comamonas within the family Comamonadaceae of Betaproteobacteria. The genus Comamonas, proposed by De Vos et al. (1985), is Gram-negative, aerobic, motile, rod shaped bacteria. And the Comamonas sp. NLF-7-7 is Gram-negative, aerobic, non-motile, rod shaped, and floc forming bacteria. Here we describe the complete genome sequence and annotation of Comamonas sp. NLF-7-7 isolated from biofilter of wastewater treatment plant in Nonsan, Republic of Korea.

The Comamonas sp. NLF-7-7 was grown in Trypticase soy agar (TSA; Difco) for 3~4 days at 30°C under aerobic condition. After lysozyme pretreatment, the genomic DNA was automatically extracted and purified by using Maxwell® 16 Cell DNA Purification Kit. Nucleotides were incorporated into a sequence by the DNA polymerase while reading a template, like circular Single-Molecule Real-Time (SMRT) bell template. Polymerase reads were trimmed to pick up only high quality region. Each polymerase read was divided to form one or more subreads. The DNA library was prepared using PacBio DNA Template Prep Kit 1.0. Sequencing library was prepared by random fragmentation of the DNA sample and this library. Genome sequencing was performed using PacBio RS II and Illumina HiSeqXten platform. The sequencing data was converted into raw data for the analysis.

De novo assembly was performed by using RS HGAP Assembly version 3.0 (Chin et al., 2013). Illumina raw data were filtered by quality for error correction. The assembly was corrected using high quality HiSeqXten reads by Pilon v1.21 (Walker et al., 2014). The genome was annotated using Prokka v1.13 (Seemann, 2014) based on NCBI Prokaryotic Genome Annotation Pipeline. For annotation, predicted protein sets were prepared to perform InterProScan v5.30-69.0 (Jones et al., 2014) and psiblast v2.4.0 (Camacho et al., 2009) with EggNOG database v4.5 (Huerta-Cepas et al., 2016). Circular maps displaying each contigs were generated using Circos v0.69.3. (Krzywinski et al., 2009).

The genome statistics are showed in Table 1. Total number of raw reads of strain NLF-7-7 was 1,856,190. Complete genome of Comamonas sp. NLF-7-7 was composed of a 3,333,437 bp chromosome, genome coverage is 362X and G + C content is 68.04%. The genome contains 3,079 CDSs, 49 tRNAs and 9 rRNAs (5S, 16S, 23S) were annotated (Fig. 1). A total of 3,012 genes were matched to EggNOG database. We found a cluster of genes that involved in some pollutants degradation and floc forming pathway. The genome showed presence of SoxY, SoxZ, SoxA, and SoxB, which have role in sulfur oxidization pathway. And the genome showed presence of phenol hydroxylation protein like Phenol hydroxylase P1 protein mphL, Phenol hydroxylase P2 protein dmpM, Phenol hydroxylase P5 protein dmpP and tmoA. In the description, Stingele et al. (1999) reported that Eps proteins and glycosyltransferase had a function of flocculation (exopolysaccharide biosynthesis) of bacteria. The genome sequence of this strain contained Eps protein and various glycosyltransferase gene like EpsD, EpsE, EpsF, EpsG, and EpsL, and Glycosyltransferase Gtf1, Ubiquinone biosynthesis O-methyltransferase ubiG4, UDP-N-acetyl-D-mannosaminuronic acid transferase wecG, D-inositol-3-phosphate glycosyltransferase mshA1, and O-antigen biosynthesis glycosyltransferase WbnK, respectively. The complete genome information of Comamonas sp. NLF-7-7 will contribute to understanding of the biological functions of Comamonas sp. NLF-7-7 in the wastewater.

General features of Comamonas sp. NLF-7-7

Property Value
Genome assembly
 Assemble method RS HGAP Assembly version 3.0
 Genome coverage 364X
Genome features
 Genome size (bp) 3,333,437
 G+C content (%) 68.04
 No. of contigs 1
 Total genes 3,197
 Protein-coding genes 3,079
 Pseudo genes 57
 rRNA genes (5S, 16S, 23S) 9 (3, 3, 3)
 tRNA genes 49
 CDS assigned by COG 3,012
 GenBank Accession No. CP042344

Fig. 1.

Chromosome map of Comamonas sp. NLF-7-7. Marked characteristics are shown from outside to the center; coding sequences on forward strand, coding sequences on reverse strand, Transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), GC content, and GC skew.



Based on the 16S rRNA gene sequence similarity and average nucleotide identity, the most closely related strain with strain NLF-7-7 is Comamonas badia KCTC 12244T with the values of 95.81% and 81.91%, respectively.

Nucleotide sequence accession number

Comamonas sp. NLF-7-7 has been deposited in the Korean Collection for Type Cultures under accession number KCTC 62943. The GenBank/EMBL/DDBJ accession number for the genome sequence of Comamonas sp. NLF-7-7 is CP042344.

적 요

본 연구에서는 폐수처리장의 바이오필터로부터 Comamonas sp. NLF-7-7 균주를 분리하고 유전체서열을 PacBio RS II와 Illumina HiSeqXten 플랫폼을 사용하여 분석하였다. 염색체의 크기는 3,333,437 bp로 G + C 구성 비율은 68.04%, 총 유전자수는 3,197개, rRNA는 9개 및 tRNA는 49개로 구성되었다. 본 유전체는 오염물질분해와 플록형성에 관여하는 황산화 경로 유전자(SoxY, SoxZ, SoxASoxB)와 플록형성 경로 유전자(EpsG, EpsE, EpsF, EpsG, EpsL 및 glycosyltransferase)를 포함하고 있다. 이러한 Comamonas sp. NLF-7-7 균주는 폐수를 정화하는데 활용될 수 있다.

Acknowledgements

This research was supported by project for Cooperative R&D between Industry, Academy, and Research Institute funded Korea Ministry of SMEs and Startups in 2018 Grants No. S2597396, and also from the Korea Research Institute of Bioscience & Biotechnology (KRIBB) Research Initiative Program.

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