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Complete genome sequence of Thermaerobacter sp. FW80, an aerobic extremely thermophilic bacterium isolated from a food waste compost
Korean J. Microbiol. 2019;55(4):462-464
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

Ji-Hyun Nam1, Tae-U Kim2, and Dong-Hun Lee2*

1Division of Antimicrobial Resistance, Center for Infectious Diseases Research, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju 28160, Republic of Korea
2Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
Correspondence to: *E-mail: donghun@cbnu.ac.kr;
Tel.: +82-43-261-3261; Fax: +82-43-264-9600
Received December 2, 2019; Revised December 7, 2019; Accepted December 9, 2019.
Abstract

A novel aerobic extremely thermophilic bacterium, Thermaerobacter sp. FW80, was isolated from food waste compost in Korea. The strain FW80 grew at a temperature of 50~85°C (optimum 77°C). The complete genome of strain FW80 consists of one 2.95 Mb chromosome and two circular plasmids with 77.62 and 8.46 kb, respectively. The complete genome included a total of 2,206 protein-coding genes, 6 rRNAs, 46 tRNAs, and 4 non-coding RNAs. The strain FW80 had Clp protease, ribosomal proteins, and heat-shock proteins distinct from other thermophilic bacteria. The genomic information of FW80 may provide insights into bacterial adaptation to hot environments.

Keywords : Thermaerobacter, extremely thermophilic bacterium, food waste compost, heat-shock protein
Body

Although many hyperthermophiles are Archaea, extremely thermophilic bacteria growing at a temperature above 75°C also have been isolated from hot environments. The genus Thermaerobacter, belongs to the Clostridiales family Incertae Sedis XVII, was first proposed by Takai et al. (1999) and 5 species have been validly published: T. marianensis (Takai et al., 1999), T. nagasakiensis (Nunoura et al., 2002), T. subterraneus (Spanevello et al., 2002), T. litoralis (Tanaka et al., 2006), and T. composti (Yabe et al., 2009). The optimum growth temperature of T. marianensis is 75°C, while other species show optimum growth at 70°C. In this report, we describe the genome sequence and annotation of Thermaerobacter sp. FW80 isolated from a food waste compost in Korea. Strain FW80 grows optimally at 77°C, with a temperature range of 50~85°C.

For the whole genome sequencing, the strain FW80 was incubated aerobically in Marine Broth 2216 (Difco) at 77°C for 3 days. The genomic DNA was extracted and purified using MagAttract HMW DNA kit (Qiagen). The sequencing of the whole genome was performed on the PacBio RS II platform (Pacific Biosciences) by DNA Link Inc.

A single circular chromosome (2,953,026 bp with G + C content of 73.4%) and two plasmids (77,620 bp with G + C content of 66.9% and 8,456 bp with G + C content of 69.2%) were obtained through de novo assembly with Hierarchical Genome Assembly Process (Chin et al., 2013). Genome annotation and functional characterization of genes were performed by the NCBI Prokaryotic Genome Annotation Pipeline (Tatusova et al., 2016) and the Integrated Microbial Genomes and Microbiomes (Chen et al., 2019). A total of 2,519 genes were predicted from the genome sequence, and 2,206 protein-coding genes and 56 RNAs (6 rRNAs, 46 tRNAs, and 4 ncRNAs) were identified as described in Table 1.

Genome features of Thermaerobacter sp. FW80

FeaturesChromosomePlasmid 1Plasmid 2
Genome size (bp)2,953,02677,6208,456
G + C content (%)73.466.969.2
Total genes2,4416612
Protein-coding genes2,1385711
rRNA genes (5S, 16S, 23S)6 (2, 2, 2)00
tRNA genes4600
ncRNA genes400
Pseudogenes24791

Genomic similarities between strain FW80 and two type strains of the genus Thermaerobacter were calculated using the ANI calculator at the EZBioCloud server (http://www.ezbiocloud.net) (Yoon et al., 2017). The OrthoANI value between strain FW80 and T. subterraneus was 83.13%, while it was 83.07% with T. marianensis.

Strain FW80 had two copies of 16S rRNA genes, in which a single nucleotide was different at the position of 1,488 bp. The 16S rRNA gene sequences of strain FW80 were compared with those of other type strains using the EzBioCloud server. Strain FW80 was mostly related to T. composti (99.7 and 99.8%) and shared 97.4 to 98.2% sequence similarity with the other type strains of genus Thermaerobacter.

The comparative sequence analysis revealed that strain FW80 had Clp protease, ribosomal proteins, and heat-shock proteins distinct from other thermophilic bacteria. DnaK protein of strain FW80 showed high similarities of amino acid sequence (more than 91%) with those of Thermaerobacter species, while low similarities (less than 72%) was observed with other thermophilic bacteria such as Caldicoprobacter, Calderihabitans, and Thermoclostridium. DnaJ and GrpE proteins also showed a similar pattern with thermophilic bacteria at a similarity level of 57 and 52%, respectively. The genomic information of strain FW80 may provide insights into bacterial adaptation to hot environments.

Nucleotide sequence accession number

Thermaerobacter sp. FW80 has been deposited at the Korean Collection for Type Cultures under the preservation number of KCTC 43180. The GenBank accession numbers for the genome sequence of Thermaerobacter sp. FW80 are CP037895, CP037896, and CP037897.

적 요

음식물쓰레기 퇴비 시료로부터 신규 호기성 호열성 세균 Thermaerobacter sp. FW80을 분리하였다. FW80 균주는 50~85°C에서 생장하였으며, 최적 생장 온도는 77°C였다. FW80 균주의 유전체는 약 2.95 Mb의 염색체와 77.62 및 8.46 kb 크기의 플라스미드 2개로 구성되어 있다. 전체 2,206개의 단백질 암호 유전자, 6개의 rRNA, 46개의 tRNA, 4개의 non- coding RNA가 확인되었다. 균주 FW80은 다른 고온세균들과 구분되는 특유의 Clp 단백질분해효소, 리보좀 단백질, 열충격단백질을 가지고 있으며, FW80의 유전체 정보는 고온 환경에서의 세균의 적응에 대한 통찰력을 제공할 것으로 생각된다.

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December 2019, 55 (4)