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Draft genome sequence of Raoultella ornithinolytica Nonyl 4-3 isolated from wastewater effluent
Korean J. Microbiol. 2021;57(2):114-115
Published online June 30, 2021
© 2021 The Microbiological Society of Korea.

Do-Hoon Lee, Eun-Mi Hwang, and Chang-Jun Cha*

Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
Correspondence to: E-mail: cjcha@cau.ac.kr; Tel.: +82-31-670-4840; Fax: +82-31-675-0432
Received April 23, 2021; Revised May 20, 2021; Accepted May 27, 2021.
Abstract
A nonylphenol-degrading bacterium designated Raoultella ornithinolytica Nonyl 4-3 was isolated from a wastewater effluent. Genome sequencing of strain Nonyl 4-3 was performed using the PacBio RSII system. The draft genome was composed of 6,205,705 bp with a G + C content of 55.3%. Genome analysis revealed that strain Nonyl 4-3 harbored a variety of monooxygenases and dioxygenases which are key enzymes involved with nonylphenol degradation.
Keywords : Raoultella ornithinolytica, degradation, genome, nonylphenol, wastewater
Body

Raoultella species were previously considered as members of the genus Klebsiella in the family Enterobacteriaceae. Later, differences in phylogeny and genotypes reclassified these species as the separate genus Raoultella. Members of Raoultella are a Gram-negative, aerobic, rod-shaped, and non-spore-forming. The genome size of four type strains of validly published species in the genus Raoultella ranged from 5.27 Mbp to 5.67 Mbp with 55.1–57.4% G + C content.

Strain Nonyl 4-3 was isolated from a wastewater effluent in Anseong (37°00'44.1"N, 127°14'32.9"E), Republic of Korea, using nonylphenol as a sole carbon source in minimal medium (NaNO3 0.5 g, [NH4]2SO4 1.0 g, KH2PO4 2.5 g, Na2HPO4 1.0 g, CaCl2 0.03 g, MgCl2 0.02 g per L). The genomic DNA of strain Nonyl 4-3 was extracted using the DNeasy Blood and tissue kit (Qiagen) following the manufacturer’s protocols. The genome of strain Nonyl 4-3 was sequenced using the single molecule real-time sequencing platform on PacBio RSII 20K (ChunLab). The sequencing depth was 231× coverage. The genome was assembled by the Hierarchical Genome Assembly Process (HGAP) using the SMRT Analysis software v2.3.0. Protein-coding genes (CDSs) and rRNA and tRNA genes were computationally predicted using Prodigal v2.6 (Hyatt et al., 2010), HMMER3 (Eddy, 1998), and tRNAscan-SE v1.3 (Lowe and Eddy, 1997), respectively. Functional annotation of the predicted proteins was performed using the SEED and COG databases (Tatusov et al., 2000; Overbeek et al., 2005). The average nucleotide identity (ANI) was calculated using OrthoANIu (Yoon et al., 2017). The ANI value between strain Nonyl 4-3 and the type strain of Raoultella ornithinolytica was determined to be 99.4%, indicating that strain Nonyl 4-3 should be identified as R. ornithinolytica. The draft genome of strain Nonyl 4-3 consisted of three chromosomal contigs (5,775,447 bp, 25,277 bp, and 31,741 bp in length) and two megaplasmids (211,610 bp and 161,630 bp). The average G + C content of the genome was 55.4%. The genome contained 5,911 CDSs, 25 rRNA genes, and 85 tRNA genes (Table 1). Nonylphenol is one of the hazardous endocrine disruptors known as environmental hormone. Previous studies revealed that two enzymes octylphenol monooxygenase and nonylphenol monooxygenase were key enzymes involved in the degradation of nonylphenol by ipso-hydroxylation (Porter et al., 2012; Takeo et al., 2012). However, genes highly homologous to these monooxygenase genes could not be identified in the genome of strain Nonyl 4-3. This suggests the presence of novel mechanisms that differ from the previously known nonylphenol degradation mechanism. Thirty-three monooxygenase and 30 dioxygenase genes were identified in the genome of strain Nonyl 4-3 as candidate genes for nonylphenol degradation. Strain Nonyl 4-3 capable of degrading nonylphenol can be a potential candidate to be used for bioremediation purposes. The genome information of this strain will be valuable for further studies to identify novel nonylphenol degradation mechanisms.

Genome features of Raoultella ornithinolytica Nonyl 4-3

Genome feature Value
No. of contigs 5
Genome size (bp) 6,205,705
Sequencing depth of coverage 231.59×
N50 (bp) 5,775,447
G + C content (%) 55.3
No. of CDSs (coding sequences) 5,911
No. of rRNA genes 25
No. of tRNA genes 85


Nucleotide sequence accession number(s)

The draft genome sequence of strain Nonyl 4-3 has been deposited at DDBJ/ENA/GenBank under the accession number JAGQDL000000000. The version described in this paper is version JAGQDL010000000. This strain is available from the National Institute of Biological Resources (NIBR) with the deposition number NIBRBAC000499650.

적 요

노닐페놀 분해능이 있는 세균 Raoultella ornithinolytica Nonyl 4-3를 폐수 방류수에서 분리하였다. 균주 Nonyl 4-3의 유전체 염기 서열은 PacBio RSII 시스템을 사용하여 결정되었다. 유전체 초안은 6,205,705 bp 및 55.3%의 G + C 함량으로 구성되어 있었다. 균주 Nonyl 4-3에서 노닐페놀 분해와 관련된 핵심 효소인 monooxygenase와 dioxygenase를 다양하게 보유하고 있음을 유전체 분석을 통하여 밝혔다.

Acknowledgments

This work was supported by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR201518201).

Conflict of Interest

The authors have no conflicts of interest to report.

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June 2021, 57 (2)