PMMB 2022, 5, 1; a0000276. doi: 10.36877/pmmb.a0000276 http://journals.hh-publisher.com/index.php/pmmb 

Genome Report 

Whole-Genome Sequence of Chelatococcus daeguensis 

Strain M38T9, Isolated from Ulu Slim Hot Spring in 

Malaysia 

Yi Xian Goh1, Kok Gan Chan2,3,4, Kar Wai Hong5* 

 

Article History 
1Department of Computational Biology, High Impact Research Building, 

University of Malaya, Kuala Lumpur, 50603, Malaysia; 

elizabel8683@gmail.com (YXG) 

2Department of Biotechnology, Faculty of Applied Sciences, UCSI University 

Kuala Lumpur, 56000, Kuala Lumpur, Malaysia 

3International Genome Centre, Jiangsu University, Zhenjiang, China. 

4Institute of Biological Sciences, Faculty of Science, University of Malaya, 

50603, Kuala Lumpur, Malaysia; kokgan@um.edu.my (KGC) 

 
5Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome 

and Bioresource Research Strength (MBRS), Jeffrey Cheah School of 

Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon 

Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia 

 

*Corresponding author: Kar-Wai Hong; Novel Bacteria and Drug Discovery 

Research Group (NBDD), Microbiome and Bioresource Research Strength 

(MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash 

University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor 

Darul Ehsan, Malaysia; hong.karwai@monash.edu (KWH) 

 

Received: 13 July 2022; 

Received in Revised Form: 

10 August 2022; 

Accepted: 17 August 2022;  

Available Online: 23 

August 2022 

Abstract: Chelatococcus daeguensis strain M38T9 is a thermotolerant bacterium isolated 

from a hot-spring in Malaysia. The draft genome of C. daeguensis strain M38T9 consists of 

4,218,658 bp assembled into 50 scaffolds. The GC content of the genome is 67.91 %, and the 

sequencing coverage of 184×. There are 4,046 predicted genes, 3,962 protein-coding genes, 

and 53 RNA-coding genes (tRNA: 45, rRNA: 4). The draft genome has been deposited at 

DDBJ/ENA/GenBank under the BioProject accession number PRJNA668056. The raw reads 

were deposited in the Sequence Read Archive (SRA) under accession number 

SRR13805582. Here we report the draft genome of this strain to expand our understanding 

of the genomic information available on the genus Chelatococcus. 

Keywords: Chelatococcus daeguensis; nitrogen metabolism; denitrification; dissimilatory 

nitrate reduction; genome 

 

 

  



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1. Introduction 

The genus Chelatococcus falls within the class of Alphaproteobacteria and was first 

reported as obligately aerobic, Gram-negative bacteria by Auling and colleagues in the year 

1993[1]. According to the List of Prokaryotic names with Standing in Nomenclature 

(LPSN)[2], this genus comprises six species at the time of writing, namely C. 

asaccharovorans, C. caeni, C. composti, C. daeguensis, C. reniformis, and C. sambhunathii 
[1, 3-7]. Most notably, there has been a growing interest in C. daeguensis in the recent years for 

its capability in utilizing a variety of carbon sources and its capability in performing aerobic 

denitrification at high temperatures, as well as its capability in biodegrading crude oil, coal 

and toxic metals[5, 8-11]. To provide insights into the genomic basis for these mechanisms, we 

hereby present the draft genome of C. daeguensis M38T9, isolated from Ulu Slim hot spring, 

Malaysia (3.8986 N 101.4847 E, 110°C, pH 7). 

2. Data Description  

The genomic DNA from M38T9 was extracted using a MasterpureTM DNA 

purification kit  (Epicentre, Illumina Inc., Madison, WI, USA) upon growing the cells at 37°C 

on Luria-Bertani (LB) agar[12]. The quality and quantity of DNA were quantified using 

NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 

2.0 fluorometer (Life Technologies, Carlsbad, CA, USA), respectively[13]. The sequencing 

library was constructed using the Nextera DNA library kit, followed by sequencing 

performed using Illumina HiSeq 2500 platform[14]. The quality of these raw reads was 

checked using FastQC (version 0.11.9)[15], and the low-quality reads were trimmed using 

Trimmomatic (version 0.39)[16] with the default settings for paired-end reads. Subsequently, 

the quality-filtered reads were de novo assembled by Velvet (version 1.2.10)[17]. The quality 

of assembly was analyzed using QUAST (version 5.0.2)[18] and BUSCO (version 3)[19]. The 

assembled gene was annotated using NCBI Prokaryotic Genome Annotation Pipeline 

(PGAP)[20] as well as MicroScope[21]. Default parameters were used for all software unless 

otherwise specified.  

The identity of strain M38T9 was first determined using Microflex LT (Bruker 

Daltonics, Bremen, Germany), and the strain M38T9 was identified as Chelatococcus 

species[22]. The 16S ribosomal RNA (rRNA) gene of strain M38T9 was compared with the 

EzBiocloud Database[23]. Interestingly, the 16S rRNA gene of strain M38T9 showed the 

highest sequence identity with the 16S rRNA genes of C. daeguensis and C. sambhunathii, 

both at 99.72% of identity. However, the estimated average nucleotide identity (ANI) value 

determined by autoMLST[24] suggested the strain M38T9 is likely to be C. daeguensis as the 

estimated ANI for strain M38T9 by referring to C. danguensis strain M3 is 100% (p-

value=0.000). 

The draft genome of C. daeguensis strain M38T9 consists of 4,218,658 bp assembled 

into 50 scaffolds, with N50 and L50 of 311,252 bp and 6 bp, respectively. The GC content of 

the genome is 67.91 %, and the sequencing coverage of 184×. There are 4,046 predicted 

genes, 3,962 protein-coding genes, and 53 RNA-coding genes (tRNA: 45, rRNA: 4). The 



PMMB 2022, 5, 1; a0000276 3 of 5 

 

draft genome has been deposited at DDBJ/ENA/GenBank under the BioProject accession 

number PRJNA668056. The raw reads were deposited in the Sequence Read Archive (SRA) 

under accession number SRR13805582. The version described in this paper is the first 

version. 

 

Figure 1. Complete pathway of dissimilatory nitrate reduction and denitrification in C. daeguensis strain TAD1, 

M3 and M38T9. 

 

By comparing the metabolic pathway of three C. daeguensis strains, namely TAD1 

(NCBI accession number: CP018095.1), M3 (NCBI accession number: LQQT01000000), 

and M38T9 (NCBI accession number: JAFDUY010000000), a complete metabolic pathway 

of denitrification has been identified (Figure 1). The denitrification metabolic pathway 

comprises of periplasmic nitrate reductase complex NapAB which reduces nitrate (NO3
-) to 

nitrite (NO2
-), copper-containing nitrite reductase NirK which further reduces NO2

- to nitric 

oxide (NO), nitric oxide reductase complex NorBC which reduces NO to nitrous oxide 

(N2O), and nitrous oxide reductase NosZ which reduces N2O to nitrogen (N2). Similarly, via 

comparative genomics, the complete pathway of dissimilatory nitrate reduction was 

identified in all three strains. The dissimilatory nitrate reduction comprises periplasmic 

nitrate reductase complex NapAB, which reduces nitrate (NO3
-) to nitrite (NO2

-), followed 

by nitrite reductase, which reduces nitrite (NO2
-) to ammonia (NH3). This genome report 

provided vital insights into the genomic basis for these mechanisms. 

 

Author Contributions: YXG and KWH conducted the experiments and analyzed the data. KWH and KGC 

provided vital guidance, technical support, and proofreading for the work. All authors approved the final draft. 

Funding: This work was supported by the University of Malaya via PPP Grant (PG085-2015B) awarded to 

KWH, and High Impact Research Grants (UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1, no. 

H-50001-A000027 and A-000001-50001) which are awarded to Kok-Gan Chan. 

Conflicts of Interest: The authors declare no conflict of interest. 



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References 

1. Auling G, Busse HJ, Egli T, et al. description of the Gram-negative, obligately aerobic, nitrilotriacetate 

(NTA)-utilizing bacteria as Chelatobacter heintzii, gen. nov., sp. nov., and Chelatococcus 

asaccharovorans, gen. nov., sp. nov. Syst Appl Microbiol 1993; 16(1): 104-112. 

2. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, et al. TYGS and LPSN: a database tandem for fast 

and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2021; 

50(D1): D801-D807. 

3. Jin L, Ko SR, Lee HG, et al. Chelatococcus caeni sp. nov., isolated from a biofilm reactor sludge sample. 

Int J Syst Evol Microbiol 2015; 65(Pt_3): 885-889. 

4. Zhang Z, Zhao J, Yu C, et al. Chelatococcus composti sp. nov., isolated from penicillin fermentation 

fungi residue with pig manure co-compost. Int J Syst Evol Microbiol 2017; 67(3): 565-569. 

5. Yoon JH, Kang SJ, Im WT, et al. Chelatococcus daeguensis sp. nov., isolated from wastewater of a textile 

dye works, and emended description of the genus Chelatococcus. Int J Syst Evol Microbiol 2008; 58(9): 

2224-2228. 

6. Gu Z, Liu Y, Wang N, et al. Chelatococcus reniformis sp. nov., isolated from a glacier. Int J Syst Evol 

Microbiol 2016; 66(11): 4525-4529. 

7. Panday D and Das SK. Chelatococcus sambhunathii sp. nov., a moderately thermophilic 

alphaproteobacterium isolated from hot spring sediment. Int J Syst Evol Microbiol 2010; 60(4): 861-865. 

8. Ke CY, Lu GM, Wei YL, et al. Biodegradation of crude oil by Chelatococcus daeguensis HB-4 and its 

potential for microbial enhanced oil recovery (MEOR) in heavy oil reservoirs. Bioresour Technol 2019; 

287: 121442. 

9. Liang W, Huang S, Liu J, et al. Removal of nitric oxide in a biotrickling filter under thermophilic 

condition using Chelatococcus daeguensis. J Air Waste Manag Assoc 2012; 62(5): 509-516. 

10. Li H, Huang S, and Zhang Y. Cr(VI) removal from aqueous solution by thermophilic denitrifying 

bacterium Chelatococcus daeguensis TAD1 in the presence of single and multiple heavy metals. J 

Microbiol 2016; 54(9): 602-610. 

11. Yang Y, Huang S, Zhang Y, et al. Nitrogen removal by Chelatococcus daeguensis TAD1 and its 

denitrification gene identification. Appl Biochem Biotechnol 2014; 172(2): 829-839. 

12. Ser HL, Ab Mutalib NS, Yin WF, et al. Genome sequence of Streptomyces antioxidans MUSC 164T 

isolated from mangrove forest. Prog Microbes Mol Biol 2018; 1(1). 

13. Torres M., Hong KW, Chong TM, et al. Genomic analyses of two Alteromonas stellipolaris strains reveal 

traits with potential biotechnological applications. Sci Rep 2019; 9(1): 1215. 



PMMB 2022, 5, 1; a0000276 5 of 5 

 

14. Letchumanan V, Tan WS, Yin WF, et al. Genome sequence of Vibrio sp. OULL4 isolated from shellfish. 

Prog Microbes Mol Biol 2020; 3(1). 

15. Brown J, Pirrung M, and McCue LA. FQC Dashboard: integrates FastQC results into a web-based, 

interactive, and extensible FASTQ quality control tool. Bioinform 2017; 33(19): 3137-3139. 

16. Bolger AM, Lohse M, and Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. 

Bioinform 2014; 30(15): 2114-2120. 

17. Zerbino DR, and Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. 

Genome Res 2008; 18(5): 821-829. 

18. Gurevich A, Saveliev V, Vyahhi N, et al. QUAST: quality assessment tool for genome assemblies. 

Bioinform 2013; 29(8): 1072-1075. 

19. Simão FA, Waterhouse RM, Ioannidis P, et al. BUSCO: assessing genome assembly and annotation 

completeness with single-copy orthologs. Bioinform 2015; 31(19): 3210-3212. 

20. Tatusova T, DiCuccio M, Badretdin A, et al. NCBI prokaryotic genome annotation pipeline. Nucleic 

Acids Res 2016; 44(14): 6614-6624. 

21. Vallenet D, Engelen S, Mornico D, et al. MicroScope: a platform for microbial genome annotation and 

comparative genomics. Database 2009; 2009. 

22. Hong KW, Hani AA, Murni CNA, et al. Comparative genomic and phylogenetic analysis of a toxigenic 

clinical isolate of Corynebacterium diphtheriae strain B-D-16-78 from Malaysia. Infect, Genet Evol 

2017; 54: 263-270. 

23. Yoon SH, Ha SM, Kwon S, et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA 

gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67(5):1613-1617. 

24. Alanjary M, Steinke K, and Ziemert N. AutoMLST: an automated web server for generating multi-locus 

species trees highlighting natural product potential. Nucleic Acids Res 2019; 47(W1): W276-W282. 

 

 

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