Korean Journal of Microbiology (2019) Vol. 55, No. 3, pp. 309-312 pISSN 0440-2413DOI https://doi.org/10.7845/kjm.2019.9099 eISSN 2383-9902Copyright ⓒ 2019, The Microbiological Society of Korea

Complete genome sequence of Comamonas sp. NLF-7-7 isolated from

biofilter of wastewater treatment plant

Dong-Hyun Kim1, Kook-Il Han

2, Hae Jun Kwon

1, Mi Gyeong Kim

1, Young Guk Kim

1, Doo Ho Choi

1, Keun Chul Lee

2,

Min Kuk Suh2, Han Sol Kim

2, Jung-Sook Lee

2,3* , and Jong-Guk Kim1*

1School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic

of Korea2Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic

of Korea3University of Science and Technology (UST), Daejeon 34113, Republic of Korea

폐수처리장의 바이오 필터로부터 분리된 Comamonas sp. NLF-7-7 균주의

유전체 염기서열 해독

김동현1 ･ 한국일

2 ･ 권해준

1 ･ 김미경

1 ･ 김영국

1 ･ 최두호

1 ･ 이근철

2 ･ 서민국

2 ･ 김한솔

2 ･ 이정숙

2,3* ･ 김종국1*

1경북대학교,

2한국생명공학연구원 생물자원센터,

3과학기술연학대학원대학교

(Received August 27, 2019; Revised September 17, 2019; Accepted September 17, 2019)

*For correspondence. (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

Comamonas sp. NLF-7-7 was isolated from biofilter of waste-

water 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 gly-

cosyltransferase), 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

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

310 ∙ Kim et al.

미생물학회지 제55권 제3호

Table 1. 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

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.

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.

Complete sequence of Comamonas sp. NLF-7-7 ∙ 311

Korean Journal of Microbiology, Vol. 55, No. 3

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.

적 요

본 연구에서는 폐수처리장의 바이오필터로부터 Comamonas

sp. NLF-7-7 균주를 분리하고 유전체서열을 PacBio RS II와

Illumina HiSeqXten 플랫폼을 사용하여 분석하였다. 염색체

의 크기는 3,333,437 bp로 G + C 구성 비율은 68.04%, 총 유전

자수는 3,197개, rRNA는 9개 및 tRNA는 49개로 구성되었다.

본 유전체는 오염물질분해와 플록형성에 관여하는 황산화 경

로 유전자(SoxY, SoxZ, SoxA 및 SoxB)와 플록형성 경로 유전자

(EpsG, EpsE, EpsF, EpsG, EpsL 및 glycosyltransferase)를 포

함하고 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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