search for


Complete genome sequence of Amylibacter sp. IMCC11727 isolated from the East Sea, South Korea
Korean J. Microbiol. 2023;59(2):145-147
Published online June 30, 2023
© 2023 The Microbiological Society of Korea.

Sumin Kim1†, Yeonjung Lim2†, Ilnam Kang1, and Jang-Cheon Cho1*

1Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
2Center for Molecular and Cell Biology, Inha University, Incheon 22212, Republic of Korea
Correspondence to: *E-mail:; Tel.: +82-32-860-7711; Fax: +82-32-232-0541
These authors contributed equally to this work.
Received April 25, 2023; Revised May 10, 2023; Accepted May 12, 2023.
The genus Amylibacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria is known as Gram-negative, aerobic, and rod-shaped bacterium. In this study, we report the complete genome sequence of Amylibacter sp. IMCC11727 (= KCTC 52246 = KACC 18775), isolated from the East Sea of South Korea. The genome of strain IMCC11727 was sequenced using the PacBio RSII platform and subsequently assembled into a single circular contig with a size of 3,452,935 bp and a G + C content of 53.7%. The genome encoded 3,474 protein- coding sequences and genes for 3 rRNAs and 38 tRNAs. Strain IMCC11727 is suggested to be a candidate for a novel species in the genus Amylibacter, with metabolic potential for cobalamin biosynthesis and dimethylsulfoniopropionate (DMSP) degradation.
Keywords : Amylibacter, complete genome, dimethylsulfoniopropionate, OM42 clade, Rhodobacteraceae

The family Rhodobacteraceae comprises Gram-negative, aerobic, and primarily heterotrophic bacteria that are classified within the class Alphaproteobacteria. These microorganisms exhibit a broad distribution across a range of ecological habitats, including marine, freshwater, and soil, and are notable for their extensive metabolic, phenotypic, and ecological diversity (Pujalte et al., 2014). In our previous study, many Rhodobacteraceae strains were isolated from the East Sea (38°13'51'' N, 128°40'53'' E) by using dilution-to-extinction cultivation (Yang et al., 2016).

Among those isolates, strain IMCC11727 exhibited a close relationship with the genus Amylibacter within the family Rhodobacteraceae. This genus was initially proposed by Teramoto and Nishijima (2014) and currently encompasses five species: Amylibacter cionae, Amylibacter kogurei, Amylibacter lutimaris, Amylibacter marinus, and Amylibacter ulvae, all of which were isolated from marine environments. In analysis using the EzBioCloud database (Yoon et al., 2017), the 16S rRNA gene sequence of strain IMCC11727 showed highest similarities (94.89 to 96.98%) to those of type strains of the genus Amylibacter. Since it has been reported that the genus Amylibacter is closely related with strain HTCC2255, a cultured representative of the OM42 (NAC11-7) lineage well-known for its abundance and crucial roles in sulfur and cobalamin cycling in marine environments (Ottesen et al., 2011; Varaljay et al., 2015; Knobloch et al., 2020; Soto et al., 2023), we also analyzed 16S rRNA gene sequence similarity between strains IMCC11727 and HTCC2255. The two strains showed ~96% 16S rRNA gene sequence similarity to each other, implicating a close relationship of strain IMCC11727 with the OM42 lineage.

Genomic DNA of strain IMCC11727 was extracted using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions, from the biomass obtained from a plate culture that was grown at 20°C on Marine Agar 2216 (BD Difco). The genome sequencing was performed using the PacBio RS II platform (Pacific Biosciences) with a 20 kb SMRTbell library (DNA Link, Inc.), resulting in > 1 Gb of raw reads. De novo assembly was conducted with the RS_HGAP_Assembly.2 protocol of SMRT Analysis (v2.3.0) (Chin et al., 2013), producing a single contig with approximately ~235× coverage. This single contig was circularized using Circlator (v1.5.5) (Hunt et al., 2015) and polished using the RS_Resequencing.1 protocol of SMRT Analysis until no variants were called. This process resulted in the final error-corrected genome sequence.

The total length of the complete genome is 3,452,935 bp and the DNA G + C content is 53.7%. A total of 3,474 protein coding sequences were predicted for the genome using Prokka (v1.14.6) (Seemann et al., 2014), with 3 rRNA and 38 tRNA genes (Table 1). ANIb values (Richter et al., 2016) between strain IMCC11727 and the type strains of the genus Amylibacter ranged from 68.1% to 72.5%, suggesting that strain IMCC11727 is a candidate for a novel species in the genus Amylibacter.

General genomic features of the genus Amylibacter, including Amylibacter sp. IMCC11727.

The genomic statistics were analyzed using Prokka (v1.14.6) with consistent options for all genomes, including Amylibacter sp. IMCC11727.

Genomic features Amylibacter sp. IMCC11727 Amylibacter marinus NBRC 110140T Amylibacter ulvae KCTC 32465T Amylibacter cionae CGMCC 1.15880T Amylibacter kogurei 4G11T
Genome size (bp) 3,452,935 2,721,832 3,169,477 4,190,336 2,982,417
G + C content (%) 53.7 52.4 49.2 56.5 48.8
Sequencing method PacBio RS II Illumina HiSeq 4000 Illumina HiSeq X Illumina HiSeq X Illumina MiSeq
Contigs 1 14 25 29 16
Coverage 235.65× 180× 492× 155× 183×
No. of CDSs 3,474 2,660 3,088 3,957 2,885
rRNA genes 3 3 3 3 3
tRNA genes 38 36 39 43 39
tmRNA genes 1 1 1 1 1
GenBank Accession No. CP122960 BSNN01000000 BMZF01000000 BMKA01000000 MDGM01000000

Metabolic reconstruction based on KEGG was performed using BlastKOALA and KEGG-decoder (Graham et al., 2018). The complete gene sets for the Entner-Doudoroff pathway, pentose phosphate pathway (both oxidative and non-oxidative parts), the TCA cycle, and the oxidative phosphorylation system were predicted in the genome, suggesting an aerobic heterotrophic lifestyle for strain IMCC11727. The genome encodes genes for cobalamin (vitamin B12) biosynthesis via early cobalt insertion (anaerobic) pathway and dimethylsulfoniopropionate (DMSP) utilization via the demethylation route, which is also found in the genomes of HTCC2255 and several Amylibacter strains, suggesting ecological roles in cobalamin and sulfur cycling in the ocean in addition to prototrophy for vitamin B12.

Strain and nucleotide sequence accession numbers

Strain IMCC11727 has been deposited in the Korean Collection for Type Cultures (KCTC) under the number KCTC 52246 and in the Korean Agricultural Culture Collection (KACC) under the number KACC 18775. The GenBank/EMBL/DDBJ accession number for the complete genome sequence of strain IMCC11727 is CP122960. The associated BioProject and BioSample accession numbers are PRJNA953190 and SAMN34109428, respectively.

적 요

Amylibacter 속은 Alphaproteobacteria 강의 Rhodobacteraceae 과에 속하며, 그람음성 호기성 간균이다. 이 연구는 대한민국 동해에서 분리된 Amylibacter sp. IMCC11727의 전장 유전체 염기서열을 보고한다. IMCC11727 균주의 유전체는 PacBio RSII 플랫폼을 사용하여 서열이 확보되었으며, 그 결과 3,452,935 bp 크기의 53.7%의 G + C함량을 갖는 원형의 유전체로 조립되었다. 유전체는 3,474개의 CDS, 3개의 rRNA 및 38 개의 tRNA 유전자로 구성되어 있음이 확인되었다. IMCC11727 균주는 Amylibacter 속의 신종 후보 균주로 판단되며, 유전체에서는 코발라민(cobalamin) 생합성 경로와 dimethylsulfoniopropionate (DMSP) 분해경로가 발견되었다.


This research was supported by High Seas Bioresources Program of Korea Institute of Marine Science & Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries (KIMST-20210646) and by the Mid-Career Research Program (NRF-2022R1A2C3008502), through the National Research Foundation (NRF) funded by the Ministry of Sciences and ICT.

Conflict of Interest

The authors declare no conflict of interest.

  1. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston H, and Eichler EEEichler EE, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563-569.
    Pubmed CrossRef
  2. Graham ED, Heidelberg JF, and Tully BJ. 2018. Potential for primary productivity in a globally-distributed bacterial phototroph. ISME J. 12, 1861-1866.
    Pubmed KoreaMed CrossRef
  3. Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, and Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16, 294.
    Pubmed KoreaMed CrossRef
  4. Knobloch S, Jóhannsson R, and Marteinsson VÞ. 2020. Genome analysis of sponge symbiont 'Candidatus Halichondribacter symbioticus' shows genomic adaptation to a host-dependent lifestyle. Environ. Microbiol. 22, 483-498.
    Pubmed CrossRef
  5. Ottesen EA, Marin R III, Preston CM, Young CR, Ryan JP, Scholin CA, and DeLong EF. 2011. Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J. 5, 1881-1895.
    Pubmed KoreaMed CrossRef
  6. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, and Macián MC. 2014. The Family Rhodobacteraceae, pp. 439-512. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, and Thompson F (eds.). The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Springer, Berlin, Germany.
  7. Richter M, Rosselló-Móra R, Oliver Glöckner F, and Peplies J. 2016. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32, 929-931.
    Pubmed KoreaMed CrossRef
  8. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069.
    Pubmed CrossRef
  9. Soto MA, Desai D, Bannon C, LaRoche J, and Bertrand EM. 2023. Cobalamin producers and prokaryotic consumers in the Northwest Atlantic. Environ. Microbiol.. .
  10. Teramoto M and Nishijima M. 2014. Amylibacter marinus gen. nov., sp. nov., isolated from surface seawater. Int. J. Syst. Evol. Microbiol. 64, 4016-4020.
    Pubmed CrossRef
  11. Varaljay VA, Robidart J, Preston CM, Gifford SM, Durham BP, Burns AS, Ryan JP, Marine R 3rd, Kiene RP, and Zehr JPZehr JP, et al. 2015. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME J. 9, 1677-1686.
    Pubmed KoreaMed CrossRef
  12. Yang SJ, Kang I, and Cho JC. 2016. Expansion of cultured bacterial diversity by large-scale dilution-to-extinction culturing from a single seawater sample. Microb. Ecol. 71, 29-43.
    Pubmed CrossRef
  13. 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

September 2023, 59 (3)
Full Text(PDF) Free

Social Network Service

Author ORCID Information