Skip to main content
SpringerLink
Log in

Deinococcus detaillensis sp. nov., isolated from humus soil in Antarctica

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

A Gram-staining-positive, non-motile, coccus or short-rod-shaped bacterium, designated H1T, was isolated from a humus soil sample in the Detaille Island of Antarctica. The 16S rRNA gene sequence result indicated that strain H1T shared the highest 16S rRNA gene sequence identity with the type strain of Deinococcus alpinitundrae (96.2%). Growth of strain H1T occurred at 4–25 °C, pH 6.0–8.0 and in the presence of 0–1.0% NaCl (w/v). The respiratory quinone was MK-8. The major fatty acids were C16:0, C17:0 cyclo and summed feature 3 (C16:1 ω7c/C16:1 ω6c). The polar lipids were aminoglycophospholipid, aminophospholipid, glycolipid and glycophospholipid. The cell wall peptidoglycan type was A3β. The genomic DNA G + C content was 61.3 mol%. The average nucleotide identity (ANI) between strain H1T and the closely related Deinococcus members was below the cut-off level (95–96%) for species identification. Based on the above results, strain H1T represents a novel species of the genus Deinococcus, for which the name Deinococcus detaillensis sp. nov. is proposed. Type strain is H1T (= CGMCC 1.13938T = JCM 33291T).

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

Abbreviations

ANI:

Average nucleotide identity

AGPL:

Aminoglycophospholipid

APL:

Aminophospholipid

GL:

Glycolipid

GPL:

Glycophospholipid

References

  • Asker D, Awad TS, Beppu T, Ueda K (2009) Deinococcus aquiradiocola sp. nov., isolated from a radioactive site in Japan. Int J Syst Evol Microbiol 59:144–149

    CAS  PubMed  Google Scholar 

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brooks BW, Murray RGE (1981) Nomenclature for “Micrococcus radiodurans” and other radiation-resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Syst Evol Microbiol 31:353–360

    Google Scholar 

  • Buchfink B, Xie C, Huson D (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60

    CAS  PubMed  Google Scholar 

  • Callegan RP, Nobre MF, McTernan PM, Battista JR, Navarro-González R, McKay CP, da Costa MS, Rainey FA (2008) Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments. Int J Syst Evol Microbiol 58:1252–1258

    CAS  PubMed  Google Scholar 

  • Chen W, Wang B, Hong H, Yang H, Liu SJ (2012) Deinococcus reticulitermitis sp. nov., isolated from a termite gut. Int J Syst Evol Microbiol 62:78–83

    CAS  PubMed  Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycani based on 2, 4-diaminobutyric acid. J Appl Bacteriol 48:459–470

    CAS  Google Scholar 

  • Collins M, Pirouz T, Goodfellow M, Minnikin D (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  PubMed  Google Scholar 

  • de Groot A, Chapon V, Servant P, Christen R, Saux MF, Sommer S, Heulin T (2005) Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol 55:2441–2446

    PubMed  Google Scholar 

  • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dong N, Li HR, Yuan M, Zhang XH, Yu Y (2015) Deinococcus antarcticus sp. nov., isolated from soil. Int J Syst Evol Microbiol 65:331–335

    CAS  PubMed  Google Scholar 

  • Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO (2015) Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 8(3):e1319

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol Int J org Evol 39:783–791

    Google Scholar 

  • Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R, Burghardt J, Chung AP, da Costa MS (1997) Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol 47:939–947

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov., an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24:710–715

    CAS  PubMed  Google Scholar 

  • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    CAS  PubMed  Google Scholar 

  • Hirsch P, Gallikowski CA, Siebert J, Peissl K, Kroppenstedt R, Schumann P, Stackebrandt E, Anderson R (2004) Deinococcus frigens sp. nov., Deinococcus saxicola sp.nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica. Syst Appl Microbiol 27:636–664

    CAS  PubMed  Google Scholar 

  • Im WT, Jung HM, Ten LN, Kim MK, Bora N, Goodfellow M, Lim S, Jung J, Lee ST (2008) Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 58:2348–2353

    CAS  PubMed  Google Scholar 

  • Joo ES, Lee JJ, Kang MS, Lim S, Jeong SW, Kim EB, Jeon SH, Srinivasan S, Kim MK (2016) Deinococcus actinosclerus sp. nov., a novel bacterium isolated from soil of a rocky hillside. Int J Syst Evol Microbiol 66:1003–1008

    CAS  Google Scholar 

  • Kim EB, Kang MS, Joo ES, Jeon SH, Jeong SW, Lim SY, Jung HY, Srinivasan S, Kim MK (2017) Deinococcus ruber sp. nov., a radiation-resistant bacterium isolated from soil. Int J Syst Evol Microbiol 67:72–76

    CAS  PubMed  Google Scholar 

  • Kim DU, Lee H, Lee S, Park S, Yoon JH, Zhao L, Kim MK, Ahn JH, Ka JO (2018) Deinococcus multiflagellatus sp. nov., isolated from a car air-conditioning system. Antonie Van Leeuwenhoek 111:619–627

    PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207

    CAS  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703–704

    CAS  PubMed  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367

    CAS  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lai WA, Kämpfer P, Arun AB, Shen FT, Huber B, Rekha PD, Young CC (2006) Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L. Int J Syst Evol Microbiol 56:787–791

    CAS  PubMed  Google Scholar 

  • Li J, Kudo C, Tonouchi A (2018) Description of Deinococcus populi sp. nov. from the trunk surface of a Japanese aspen tree. Arch Microbiol 200:291–297

    CAS  PubMed  Google Scholar 

  • Lin H, Wang Y, Huang J, Lai Q, Xu Y (2017) Deinococcus planocerae sp. nov., isolated from a marine flatworm. Antonie Van Leeuwenhoek 110:811–817

    PubMed  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    CAS  PubMed  PubMed Central  Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18

    PubMed  PubMed Central  Google Scholar 

  • Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95

    CAS  Google Scholar 

  • Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185

    PubMed  PubMed Central  Google Scholar 

  • Narsing Rao MP, Dong ZY, Kan Y, Dong L, Li S, Xiao M, Kang YQ, Zhang K, Li WJ (2020) Description of Paenibacillus tepidiphilus sp. nov., isolated from a tepid spring. Int J Syst Evol Microbiol 20:20. https://doi.org/10.1099/ijsem.0.004004

    Article  CAS  Google Scholar 

  • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055

    CAS  PubMed  PubMed Central  Google Scholar 

  • Parte AC (2018) LPSN - list of prokaryotic names with standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 68:1825–1829

    PubMed  Google Scholar 

  • Powers EM (1995) Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK (2016) Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 8:12–24

    Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. Microbial ID, Inc, Newark

    Google Scholar 

  • Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4:41

    Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882

    CAS  PubMed  PubMed Central  Google Scholar 

  • van Dongen S, Abreu-Goodger C (2012) Using MCL to extract clusters from networks. Methods Mol Biol 804:281–295

    PubMed  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang YQ, Sun CH, Li WJ, Yu LY, Zhou JQ, Zhang YQ, Xu LH, Jiang CL (2007) Deinococcus yunweiensis sp. nov., a gamma- and UV-radiation-resistant bacterium from China. Int J Syst Evol Microbiol 57:370–375

    CAS  PubMed  Google Scholar 

Download references

Funding

This research work was supported by Science and Technology Research Project of Shaanxi Province Academy of Sciences (2018nk-01), the Foundation of Science and Technology in Shaanxi (2017NY-139), National Natural Science Foundation of China (Grant nos. 31560034 and 31760009), Basic Scientific R & D Program for Public Welfare Institutes in Xinjiang (KY2019023).

Author information

Author notes

  1. Kun Zhang, Jing Zhu and Shuai Li contributed equally to this work.

Authors and Affiliations

  1. Shaanxi Institute of Microbiology, Xi’an, 710043, PR China

    Kun Zhang, Ning-Mei Li & Yi Wan

  2. Xinjiang Laboratory of Special Environmental Microbiology, Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China

    Jing Zhu, Qi-Yong Tang & Zhi-Dong Zhang

  3. State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China

    Shuai Li, Manik Prabhu Narsing Rao & Wen-Jun Li

  4. The High School Affiliated To Renmin University of China, Beijing, 100080, PR China

    Ang-Yang Guo

  5. School of Medicine, Xizang Minzu University, Xianyang, 712082, PR China

    Zhao Jiang

Authors
  1. Kun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jing Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shuai Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Manik Prabhu Narsing Rao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ning-Mei Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ang-Yang Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zhao Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Qi-Yong Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yi Wan
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Zhi-Dong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Wen-Jun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Zhi-Dong Zhang or Wen-Jun Li.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest.

Additional information

Communicated by Erko Stackebrandt.

Publisher's Note

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

The 16S rRNA gene sequence of strain H1T has been deposited in GenBank under the accession number MN116004. The GenBank/EMBL/DDBJ accession numbers for genome sequences of strain H1T and Deinococcus alpinitundrae LMG 24283T are VKDB00000000 and WXZL00000000, respectively.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file 1 (DOCX 2695 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, K., Zhu, J., Li, S. et al. Deinococcus detaillensis sp. nov., isolated from humus soil in Antarctica. Arch Microbiol 202, 2493–2498 (2020). https://doi.org/10.1007/s00203-020-01920-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-020-01920-0

Keywords

Search

Navigation