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Complete genome sequence of polybutylene adipate terephthalate-degrading Rhizobacter sp. strain SBD 7-3, isolated from soil
Korean J. Microbiol. 2023;59(4):366-367
Published online December 31, 2023
© 2023 The Microbiological Society of Korea.

Jehyeong Yeon, Han Suk Choi, Joon-hui Chung, Young-Joon Ko, Dayeon Kim, Sihyun An, Jae-Hyung Ahn, and Hang-Yeon Weon*

Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju 55365, Republic of Korea
Correspondence to: *E-mail: why@korea.kr; Tel.: +82-63-238-3027; Fax: +82-63-238-3834
Received November 17, 2023; Revised December 16, 2023; Accepted December 18, 2023.
Abstract
Rhizobacter sp. SBD 7-3, a polybutylene adipate terephthalate (PBAT)-degrading strain, was isolated from upland soil that has been installed by biodegradable mulching films in Yeongwol province, Republic of Korea. The genome analysis revealed strain SBD 7-3 genome comprised one chromosome (5,594,180 bp) and two plasmids (200,976 bp; 142,941 bp), with G + C contents of 67.6%, 60.7%, and 61.4% respectively. The genome contained 5,540 protein-encoding genes, 58 tRNA genes, and 3 rRNA genes. Several genes linked to the breakdown of PBAT are found throughout the genome.
Keywords : Rhizobacter sp. SBD 7-3, PBAT-degrading bacterium, whole genome sequence
Body

Polybutylene adipate terephthalate (PBAT) is a biodegradable polymer used to produce various plastic products. PBAT can be rapidly biodegraded by microorganisms under soil conditions within a few months (Wu et al., 2023). Rhizobacter sp. strain SBD7-3 was isolated using a minimal agar medium (Ahn et al., 2018) containing 0.1% PBAT and 1.0% R2A broth under aerobic conditions at 28°C from upland soil that has been installed by biodegradable mulching films during the last few years, in Yeongwol province, Republic of Korea. Strain SBD7-3 showed PBAT degradation activity on a minimal agar medium (Ahn et al., 2018) supplemented with 0.1% PBAT and 1% R2A broth. The strain was identified as a member of the genus Rhizobacter through a phylogenetic comparison of the 16S rRNA gene sequence. The 16S rRNA gene sequence of strain SBD7-3 showed 97.8% similarity to that of Rhizobacter gummiphilus NBRC 109400T (Imai et al., 2013).

Genomic DNA of strain SBD7-3 was extracted by the Maxwell RSC Tissue DNA kit (Promega) and was subsequently sequenced using the PacBio Sequel System and Illumina HiSeq platform at Macrogen Inc. The long and short-read data sets were assembled using the Microbial Assembly application (SMRT Link version 11.0) by Macrogen Inc. Gene prediction and functional annotation were performed using the NCBI Prokaryotic Genomes Annotation Pipeline (Tatusova et al., 2016) and Rapid Annotation Subsystem Technology (Aziz et al., 2008).

The complete genome sequence of Rhizobacter sp. SBD7-3 consisted of one chromosome and two plasmids 5,938,097 bp with an average DNA G + C content of 67.5%. The genome contained 5,540 coding sequences (CDS), 58 tRNAs, and 3 rRNAs (Table 1). According to Orthologous Average Nucleotide Index (OrthoANI, OAT v0.93), strains SBD7-3 exhibited 77.3% nucleotide sequence identity with Rhizobacter gummiphilus NCRC 109400T.

Genome features of Rhizobacter gummiphilus SBD7-3
Genome feature Value
Contig 3
Genome size (bp) 5,938,097
G + C content (%) 67.5
Total genes 5,530
Protein-coding genes (CDSs) 5540
tRNAs 58
rRNAs (5S, 16S, 23S) 3 (1, 1, 1)
GenBank accession No. CP136336–136338


The backbones of PBAT include terephthalate moiety similar to polyethylene terephthalate (PET), so various PET hydrolyzing enzymes (cutinase, esterases and lipases) can also degrade PBAT (Wu et al., 2023). PBAT degradation activity has been reported in relation to lipase extracted from Pelosinus fermentans (Biundo et al., 2016). The genome of strain SBD7-3 also encoded a lipase (locus_tag RXV79_01540, 01550) similar to the lipase extracted from Pelosinus fermentans, capable of degrading PBAT (Biundo et al., 2016). Many genes related to the degradation of PBAT were found to be present in the genome, which provides essential information for facilitating the breakdown of PBAT (Urbanek et al., 2020).

Nucleotide sequence accession number

Rhizobacter sp. SBD7-3 has been deposited in the Korean Agricultural Culture Collection with the accession number KACC 92562P. GenBank accession number CP136336–136338 have been assigned to this whole-genome study.

적 요

대한민국 영월의 생분해성 멀칭 필름을 사용한 농경지 토양에서 분리한 Rhizobacter sp. SBD 7-3 균주는 PBAT를 분해할 수 있었다. SBD 7-3 균주는 하나의 염색체(5,594,180 bp)와 두 개의 플라스미드(200,976 bp; 142,941 bp)로 이루어져 있으며, G + C 함량은 각각 67.6%, 60.7%, 61.4%이었다. SBD 7-3 균주의 유전체는 단백질 암호화 유전자 5,540개, tRNA 유전자 58개, 그리고 rRNA 유전자 3개로 이루어져 있다. SBD 7-3 균주의 유전체에는 여러 유전자가 PBAT 분해에 관여하고 있었다.

Acknowledgments

This study was made possible by the support of “Cooperative Research Program for Agricultural Science & Technology Development (Project No. PJ017097)”, Rural Development Administration, Republic of Korea.

Conflict of Interest

The authors have no conflict of interest to report.

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