Skip to main content
Log in

Adhaeribacter terrigena sp. nov., Isolated from Korean Soil

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

A bacterial strain, designated BT258T, was isolated from a soil sample collected from Uijeongbu-si, Gyeong-do Province, Republic of Korea. Cells were Gram stain negative, aerobic, rod shaped, motile by gliding, and formed light pink-pigmented colonies on agar plates. Growth of the isolate was observed at 10–37 °C and pH 6–7. A 16S rRNA gene sequence analysis revealed that strain BT258T is a member of the genus Adhaeribacter in the family Hymenobacteraceae and had the highest sequence similarity with ‘Adhaeribacter soli’ MA2T (97.1%), Adhaeribacter terreus DNG6T (96.6%), and Adhaeribacter terrae HY02T (96.5%). The predominant respiratory quinone of the isolate was MK-7, the main polar lipid was phosphatidylethanolamine, and the major fatty acids were C15:0 iso (37.7%), summed feature 4 (C17:1 anteiso B/iso-C17:1 I; 16.8%), and C16:0 (10.3%). The draft genome of strain BT258T had a whole length of 4,974,022 bp and DNA G + C content of 46.0 mol%. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the novel isolate and ‘Adhaeribacter soli’ and seven other Adhaeribacter species ranged from 17.9 to 22.7% and 69.7 to 77.9%, respectively. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain BT258T represents a novel species in the genus Adhaeribacter, for which the name Adhaeribacter terrigena sp. nov. is proposed. The type strain is BT258T (= KCTC 72409 T = JCM 34303 T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

Data Availability

The datasets used or analyzed during the current study are available from the corresponding author on reasonable request.

References

  1. Rickard AH, Stead AT, O’May GA, Lindsay S, Banner M et al (2005) Adhaeribacter aquaticus gen. nov., sp. nov., a Gram-negative isolate from a potable water biofilm. Int J Syst Evol Microbiol 55:821–829

    Article  CAS  Google Scholar 

  2. Han JH, Kang S, Kim MK (2021) Adhaeribacter soli sp. nov., a bacterium isolated from soil in Korea. Arch Microbiol 203:163–168

    Article  CAS  Google Scholar 

  3. Kim DU, Kim KW, Kang MS, Kim JY, Jang JH, Kim MK (2018) Adhaeribacter swui sp. nov., isolated from wet mud. Int J Syst Evol Microbiol 68:1096–1100

    Article  CAS  Google Scholar 

  4. Zhang JY, Liu XY, Liu SJ (2009) Adhaeribacter terreus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 59:1595–1598

    Article  CAS  Google Scholar 

  5. Wilson K (1997) Preparation of genomic DNA from bacteria. In: Ausubel FM et al (eds) Current protocols in molecular biology, no supplement 27. Wiley, New York, pp 2.4.1-2.4.5

    Google Scholar 

  6. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  CAS  Google Scholar 

  7. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  Google Scholar 

  8. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  Google Scholar 

  9. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  10. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  Google Scholar 

  11. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  12. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  13. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  Google Scholar 

  14. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  Google Scholar 

  15. Bruzek S, Vestal G, Lasher A, Lima A, Silbert S (2020) Bacterial whole genome sequencing on the Illumina iSeq 100 for clinical and public health laboratories. J Mol Diagn 22:1419–1429

    Article  CAS  Google Scholar 

  16. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  Google Scholar 

  17. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75

    Article  Google Scholar 

  18. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al (2018) RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 46:D851–D860

    Article  CAS  Google Scholar 

  19. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624

    Article  CAS  Google Scholar 

  20. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108

    Article  CAS  Google Scholar 

  21. Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57

    Article  CAS  Google Scholar 

  22. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286

    Article  CAS  Google Scholar 

  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 14:60

    Article  Google Scholar 

  24. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  25. Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070

    CAS  Google Scholar 

  26. Ten LN, Okiria J, Lee JJ, Lee SY, Park S, Lee DS, Kang IK, Kim MK, Jung HY (2018) Spirosoma terrae sp. nov., isolated from soil from Jeju Island. Korea Curr Microbiol 75:492–498

    Article  CAS  Google Scholar 

  27. Kim J, Jung HS, Baek JH, Chun BH, Khan SA, Jeon CO (2021) Paenibacillus silvestris sp. nov., isolated from forest soil. Curr Microbiol 78:822–829

    Article  CAS  Google Scholar 

  28. Khan I, Debnath SC, Alderson YC, G, Athalye M, Schaal A, Parlett JH, et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  Google Scholar 

  29. Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205

    Article  CAS  Google Scholar 

  30. Li W, Ten LN, Lee SY, Lee DH, Jung HY (2018) Spirosoma jeollabukense sp. nov., isolated from soil. Arch Microbiol 200:431–438

    Article  CAS  Google Scholar 

  31. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J Gen App Microbiol 42:457–469

    Article  CAS  Google Scholar 

  32. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Netwark

  33. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    Article  CAS  Google Scholar 

  34. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

    Google Scholar 

  35. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Hana Y, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  Google Scholar 

  36. Meier-Kolthoff JP, Klenk HP, Göker M (2014) Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356

    Article  CAS  Google Scholar 

  37. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    Article  CAS  Google Scholar 

  38. Elderiny N, Lee JJ, Lee YH, Park SJ, Lee SY, Park S, Cho YJ, Ten LN, Jung HY (2017) Adhaeribacter terrae sp. nov., a novel bacterium isolated from soil. Int J Syst Evol Microbiol 67:2922–2927

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank the Brain Pool Program (2020H1D3A2A01103925) of the National Research Foundation (NRF), Republic of Korea, for financial support.

Funding

This work was supported by the Brain Pool Program (Grant No. 2020H1D3A2A01103925) through the National Research Foundation (NRF) funded by the Ministry of Science and ICT, Republic of Korea.

Author information

Authors and Affiliations

Authors

Contributions

All the authors contributed to the study conception and design. LNT analyzed the data and wrote the manuscript, WL performed the experiments and wrote the manuscript, MKK analyzed the genome sequence, IKK analyzed chemotaxonomic data, SYL performed 16S rRNA phylogeny, HYJ designed, planned the study, and reviewed the manuscript. All authors read and approved the final version of the manuscript.

Corresponding author

Correspondence to Hee-Young Jung.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors. Informed consent was obtained from all individual participants included in the study.

Consent for Publication

All authors have given consent for publication.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 646 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ten, L.N., Li, W., Kim, M.K. et al. Adhaeribacter terrigena sp. nov., Isolated from Korean Soil. Curr Microbiol 78, 3328–3333 (2021). https://doi.org/10.1007/s00284-021-02586-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-021-02586-7

Navigation