search for


Genome sequence of Microbacterium sp. STF-2 isolated from expanded polystyrene in landfill
Korean J. Microbiol. 2024;60(1):38-40
Published online March 31, 2024
© 2024 The Microbiological Society of Korea.

So-Jeong Kim1* , Wook-Hyun Nahm2, Min Han2, and In-Hyun Nam1

1Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Republic of Korea
2Climate Change Response Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Republic of Korea
Correspondence to: *E-mail:;
Tel.: +82-42-868-3311; Fax: +82-42-868-3414
Received December 22, 2023; Revised January 3, 2024; Accepted January 5, 2024.
In this study, we report the genomic information of the microorganism, belonging to the genus Microbacterium, isolated from expanded polystyrene in an unsanitary landfill in South Korea. The draft genome of strain STF-2 is composed of 3.9 Mb (68.4% G + C), including 3,839 protein-coding genes, 5 rRNA genes, and 48 tRNAs. Genes involved in detoxification of heavy metals and degradation of aromatic compound were identified. It might support the potential of strain STF-2 to resist the effects of a variety of contaminated substances in landfill.
Keywords : Microbacterium, landfill, mercury

As the importance of municipal solid waste (MSM) disposal and management increases, landfill-related research has conducted in various fields including study of microbial communities (Meyer-Dombard et al., 2020). To understand the microbial communities in landfill, culture-dependent and culture-independent studies have been conducted (Meyer-Dombard et al., 2020). However, most studies focused on landfill leachate (Meyer-Dombard et al., 2020; Zhao et al., 2021; Gu et al., 2022). In this study, genomic analysis performed of a bacterium isolated from coring sample of landfill during the study to analyze the microbial diversity of landfill.

Sample was carried out using core drilling from landfill. A piece of expanded polystyrene was obtained from a depth of 16 m. The portion of the fragment was moved to a new conical tube and suspended in phosphate saline solution. Serially diluted solutions were spread on R2A plate and a yellow colony among several colonies was selected for further study. To identify the yellow colony, named as STF-2, a genomic DNA was extracted by DNeasy blood & tissue kit (Qiagen). 16S rRNA gene was amplified and sequenced using 27F and 1492R (Lane, 1991). Finally, strain STF-2 was classified to genus Microbacterium belonging to Actinomycetota using Ezbiocloud (Yoon et al., 2017). The production of DNA library (TruSeq Nano DNA kit) and sequencing of strain STF-2 by Illumina HiseqX were performed at Macrogen Inc. The obtained raw reads were qualified by FastQC and assembled by SPAdes (v. 3.15) (Bankevich et al., 2012), with 145 × coverage. The assembled genome was annotated with Prokaryote Genomes Automatic Annotation Pipeline (PGAAP) (Tatusova et al., 2016). Signal peptides and transmembrane structures were predicted using SignalP (Almagro Armenteros et al., 2019) and TMHMM (Krogh et al., 2001), respectively.

The genome of strain STF-2 composes 5 scaffold with a length of 3,935,905 bp (G + C content, 68.4%), including 3,773 coding genes, 5 rRNAs and 48 tRNAs (Table 1). Comparison of 16S rRNA gene with the closet related strain showed 100% similarity with Microbacterium oxydans DSM 20578T but the average nucleotide identity was 86%. It showed that strain STF-2 could be a new species in the genus Microbacterium, according to new species criteria (Jain et al., 2018).

General genomic features of Microbacterium sp. STF-2.

Features STF-2
Length 3,935,905 bp
G + C 68.4
Number of scaffolds 5
Total genes 3,839
Total coding genes 3,773
rRNAs (5S, 16S, 23S) 3*,1,1
tRNAs 48
Accession number JARKMW000000000

*Two partial rRNAs were included.

An extracellular type of intradiol ring-cleavage dioxygenase (MicroSTF_17290) was found in this genome, which catalyzes the decyclization reaction of aromatic ring structures (Kumar et al., 2018). Also, the genome of strain STF-2 encoded Poly(3-hydroxyburyate) (PHB) depolymerase family esterase (MicroSTF_02155). PHB depolymerase is known as the enzyme that hydrolyzes PHB, which is one of the biodegradable plastics. The availability of plastic degradation of strain STF-2 need to check in further study because the gene encoded PHB depolymerase was intracellular type.

Since MSM includes industrial wastes, consumer electronics and household products that contain mercury, mercury can affect the microbial ecosystem in landfills (Lee et al., 2016). This genome contained organomercurial lyase (MerB, MicroSTF_111570) and mercuric reductase (MerA, MicroSTF_111575), that can detoxify methylmercury and inorganic mercury to gaseous elemental mercury. In addition, genes related to heavy metal resistance were observed in the genome such as chromate resistance protein ChrB (MicroSTF_11405) and arsenate reductase ArsC (MicroSTF_05220). The detoxification mechanisms of heavy metals of strain STF-2 might enhance the survival ability in landfill.

Nucleotide sequence accession number

Strain STF-2 has been deposited at Korean Collection for Type Cultures as KCTC 49960 and the genome sequence has been deposited at GenBank under the accession number JARKMW000000000.

적 요

본 연구는 대한민국의 비위생 매립지에서 채취한 스티로폼 시료로부터 분리한 Microbacterium 속에 속하는 미생물의 게놈 정보를 보고한다. STF-2 균주의 게놈 초안은 3,839개의 단백질 코딩 유전자, 5개의 rRNA 유전자 및 48개의 tRNA를 포함하여 3.9 Mb (68.4% G + C)로 구성된다. 중금속 해독 및 방향족 화합물 분해에 관여하는 유전자가 확인되었다. 이는 다양한 오염 물질의 영향에 저항하는 STF-2 균주의 잠재력을 뒷받침할 수 있다.

  1. Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, and Nielsen H. 2019. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37, 420-423.
    Pubmed CrossRef
  2. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, and Prjibelski ADPrjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477.
    Pubmed KoreaMed CrossRef
  3. Gu Z, Feng K, Li Y, and Li Q. 2022. Microbial characteristics of the leachate contaminated soil of an informal landfill site. Chemosphere 287, 132155.
    Pubmed CrossRef
  4. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, and Aluru S. 2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114.
    Pubmed KoreaMed CrossRef
  5. Krogh A, Larsson B, von Heijne G, and Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580.
    Pubmed CrossRef
  6. Kumar A, Wang L, Ng CY, and Maranas CD. 2018. Pathway design using de novo steps through uncharted biochemical spaces. Nat. Commun. 9, 184.
    Pubmed KoreaMed CrossRef
  7. Lane DJ. 1991. 16S/23S rRNA sequencing, pp. 115-175. In Stackebrandt E, Goodfellow M (ed.). Nucleic Acid Techniques in Bacterial Systematic. John Wiley and Sons, New York, USA.
  8. Lee SW, Lowry GV, and Hsu-Kim H. 2016. Biogeochemical transformations of mercury in solid waste landfills and pathways for release. Environ. Sci. Process Impacts 18, 176-189.
    Pubmed CrossRef
  9. Meyer-Dombard DR, Bogner JE, and Malas J. 2020. A review of landfill microbiology and ecology: a call for modernization with 'Next Generation' technology. Front. Microbiol. 11, 1127.
    Pubmed KoreaMed CrossRef
  10. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.
    Pubmed KoreaMed CrossRef
  11. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, and Chun J. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613-1617.
    Pubmed KoreaMed CrossRef
  12. Zhao R, Liu J, Feng J, Li X, and Li B. 2021. Microbial community composition and metabolic functions in landfill leachate from different landfills of China. Sci. Total Environ. 767, 144861.
    Pubmed CrossRef

March 2024, 60 (1)
Full Text(PDF) Free

Social Network Service

Author ORCID Information

Funding Information