Skip to main content
SpringerLink
Log in

Nonomuraea cypriaca sp. nov., isolated from soil

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

Abstract

A novel actinobacterium, designated strain K274T, was isolated from soil collected from Zafer Cape (Cape Apostolos Andreas), the easternmost tip of Cyprus on the Karpas peninsula, Magusa, Northern Cyprus, and a polyphasic approach was used for characterization of the strain. The isolate was found to have chemotaxonomic and morphological properties associated with members of the genus Nonomuraea. The strain has the highest similarity to Nonomuraea zeae DSM 100528T with 99.1% similarity value. In the phylogenetic dendogram based on 16S rRNA gene sequence, strain K274T was formed a distinct clade together N. zeae DSM 100528T, ‘Nonomuraea basaltis’ 160415 (98.9% similarity), and ‘Nonomuraea lycopersici’ NEAU-DE8(1) (98.2% similarity). The genome sequence of strain K274T was 11.5 Mbp in size with a total of 11,848 protein-coding genes and 75 RNA genes. The genomic G + C content of the novel strain was 69.7 mol%. Both average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) results between the strain and phlyogenetic neighbours were well below the threshold value, and the novelty are supported by phenotypic and chemotaxonomic differences. Because of all these, strain K274T represents a novel species in the genus Nonomuraea, for which the name Nonomuraea cypriaca sp. nov. is proposed. The type strain is K274T (= DSM 45718T = KCTC 29095T).

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

References

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

    Google Scholar 

  • Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87

    CAS  PubMed  PubMed Central  Google Scholar 

  • Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y, Raytselis Y, Sayers EW, Tao T, Ye J, Zaretskaya I (2013) BLAST: a more efficient report with usability improvements. Nucleic Acids Res 41:W29–W33

    PubMed  PubMed Central  Google Scholar 

  • Brenner DJ, Krieg NR, Staley JT, Garrity GM (2005) Bergey’s manual of systematic bacteriology, Vol. 2, the proteobacteria (Part A), 2nd Edn. Springer, NY

    Google Scholar 

  • Chiba S, Suzuki M, Ando K (1999) Taxonomic re-evaluation of ‘Nocardiopsis’ sp. K-252T (= NRRL 15532T): a proposal to transfer this strain to the genus Nonomuraea as Nonomuraea longicatena sp. nov. Int J Syst Bacteriol 49:1623–1630

    PubMed  Google Scholar 

  • Chun J, Goodfellow M (1995) A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240–245

    CAS  PubMed  Google Scholar 

  • Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, 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

    CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Collins CH, Lyne PM, Grange JM, Falkinham JO (eds) (2004) Collins and Lyne’s microbiological methods, 8th edn. Arnold, London, pp 97–98

    Google Scholar 

  • Fang BZ, Hua ZS, Han MX, Zhang ZT, Wang YH, Yang ZW, Zhang WQ, Xiao M, Li WJ (2017) Nonomuraea cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. Int J Syst Evol Microbiol 67:4692–4697

    CAS  PubMed  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 phylogeny: an approach using the bootstrap. Evolution 39:783–791

    PubMed  Google Scholar 

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

    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 

  • Hayakawa M, Nonomura H (1987) Humic acid-vitamin agar, a new medium for selective isolation of soil actinomycetes. J Ferment Technol 65:501–509

    CAS  Google Scholar 

  • Jones KL (1949) Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57:141–145

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005

    Google Scholar 

  • Kelly KL (1964) Inter-society color council-national bureau of standards color-name charts illustrated with centroid colors. US Government Printing Office, Washington

    Google Scholar 

  • Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    CAS  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 

  • Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Google Scholar 

  • Klykleung N, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Pittayakhajonwut P, Tanasupawat S (2020) Nonomuraea phyllanthi sp. nov., an endophytic actinomycete isolated from the leaf of Phyllanthus amarus. Arch Microbiol 202:55–61

    CAS  PubMed  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger. J Liquid Chromatogr 5:2359–2387

    CAS  Google Scholar 

  • Kroppenstedt RM, Goodfellow M (2006) The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora. In: Dworkin M, Falkow S, Schleifer KH, Stackebrandt E (eds) The prokaryotes. Archaea and bacteria: firmicutes, actinomycetes, 3rd edn. Springer, New York, pp 682–724

    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 

  • Lechevalier MP, Lechevalier HA (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443

    CAS  Google Scholar 

  • Ludwig W, Klenk HP (2005) Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) in Bergey’s manual of systematic bacteriology, Vol 2, the proteobacteria (Part A). Springer, New York, pp 49–66

    Google Scholar 

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

    Google Scholar 

  • Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal K, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Google Scholar 

  • Montero-Calasanz JP, Meier-Kolthoff MDC, Zhang D-F, Yaramis A, Rohde M, Woyke T, Kyrpides NC, Schumann P, Li W-J, Göker M (2017) Genome-scale data call for a taxonomic rearrangement of Geodermatophilaceae. Front Microbiol 8:2501

    PubMed  PubMed Central  Google Scholar 

  • Nash P, Krent MM (1991) Culture media. In: Balows A, Hauser WJ, Herrmann KL, Isenberg HD, Shadomy HJ (eds) Manual of clinical microbiology, 3rd edn. American Society for Microbiology, Washington, pp 1268–1270

    Google Scholar 

  • Niemhom N, Chutrakul C, Suriyachadkun C, Thawai C (2017) Nonomuraea stahlianthi sp. nov., an endophytic actinomycete isolated from the stem of Stahlianthus campanulatus. Int J Syst Evol Microbiol 67:2879–2884

    CAS  PubMed  Google Scholar 

  • Nonomura H, Ohara Y (1971) Distribution of actinomycetes in soil. XI. Some new species of the genus Actinomadura Lechevalier. J Ferment Technol 49:904–912

    Google Scholar 

  • Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M (2018) Genome-based taxonomic classification of the Phylum Actinobacteria. Front Microbiol 9:2007–2123

    PubMed  PubMed Central  Google Scholar 

  • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 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 

  • Saricaoglu S, Nouioui I, Ay H, Saygin H, Bektas KI, Guven K, Cetin D, Klenk HP, Isik K, Sahin N (2018) Nonomuraea insulae sp. Nov., isolated from forest soil. Antonie Van Leeuwenhoek 111(11):2051–2059

    CAS  PubMed  Google Scholar 

  • Saricaoglu S, Saygin H, Topkara AR, Gencbay T, Guven K, Cetin D, Sahin N, Isik K (2020) Nonomuraea basaltis sp. nov., a siderophore-producing actinobacteria isolated from surface soil of basaltic parent material. Arch Microbiol 202:1535–1543

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Saygin H, Nouioui I, Ay H, Guven K, Cetin D, Klenk HP, Goodfellow M, Sahin N (2020a) Polyphasic classification of Nonomuraea strains isolated from the Karakum Desert and description of Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov. Int J Syst Evol Microbiol 70(1):636–647

    CAS  PubMed  Google Scholar 

  • Saygin H, Ay H, Guven K, Cetin D, Sahin N (2020b) Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili. Int J Syst Evol Microbiol 70:2750–2759

    CAS  PubMed  Google Scholar 

  • Shen Y, Jia FY, Liu CX, Li JS, Guo SY, Zhou SY, Wang XJ, Xiang WS (2016) Nonomuraea zeae sp. nov., isolated from the rhizosphere of corn (Zea mays L.). Int J Syst Evol Microbiol 66:2259–2264

    CAS  PubMed  Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Google Scholar 

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

    Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    CAS  PubMed  PubMed Central  Google Scholar 

  • Starke R, Pylro VS, Morais DK (2020) 16S rRNA gene copy number normalization does not provide more reliable conclusions in metataxonomic surveys. Microb Ecol. https://doi.org/10.1007/s00248-020-01586-7

    Article  PubMed  PubMed Central  Google Scholar 

  • Suksaard P, Mingma R, Srisuk N, Matsumoto A, Takahashi Y, Duangmal K (2016) Nonomuraea purpurea sp. nov., an actinomycete isolated from mangrove sediment. Int J Syst Evol Microbiol 66:4987–4992

    CAS  PubMed  Google Scholar 

  • Sungthong R, Nakaew N (2015) The genus Nonomuraea: a review of a rare actinomycete taxon for novel metabolites. J Basic Microbiol 55:554–565

    PubMed  Google Scholar 

  • Waksman SA (1961) The actinomycetes, classification, identification and description of genera and species, vol 2. Williams and Wilkins, Baltimore

    Google Scholar 

  • Waksman SA (1967) The actinomycetes. A summary of current knowledge. Ronald Press, New York

    Google Scholar 

  • Wang XJ, Zhao JW, Liu CX, Wang JD, Shen Y, Jia FY, Wang L, Zhao J, Yu C, Xiang WS (2013) Nonomuraea solani sp.nov. an actinomycete isolated from eggplant root (Solanum melongena L.). Int J Syst Evol Microbiol 63:2418

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang S, Liu C, Zhang Y, Zhao J, Zhang X, Yang L, Wang X, Xiang W (2014) Nonomuraea guangzhouensis sp nov, and Nonomuraea harbinensis sp nov, two novel actinomycetes isolated from soil. Antonie Van Leeuwenhoek 105(1):109–118

    CAS  PubMed  Google Scholar 

  • Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL (2016) Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 45:D535–D542

    PubMed  PubMed Central  Google Scholar 

  • Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813

    CAS  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 Z, Wang Y, Ruan J (1998) Reclassification of Thermomonospora and Microtetraspora. Int J Syst Bacteriol 48:411–422

    PubMed  Google Scholar 

  • Zhao J, Mu S, Zhao Q, Jiang S, Cao P, Guo X, Wang X, Xiang W (2018) Nonomuraea rhizosphaerae sp nov, an actinomycete isolated from the rhizosphere soil of a rubber tree (Hevea brasiliensis Muell. Arg). Antonie Van Leeuwenhoek 111(11):2009–2016

    PubMed  Google Scholar 

  • Zheng W, Zhao J, Li D, Jiang H, Han L, Zhao X, Chen Y, Wang X, Xiang W (2018) Nonomuraea lycopersici sp. nov., isolated from the root of tomato plants (Solanum lycopersicum L.). Antonie Van Leeuwenhoek 111:1095–1103

    PubMed  Google Scholar 

Download references

Acknowledgements

Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk).

Author information

Authors and Affiliations

  1. Department of Medical Services and Techniques, Vocational School of Health Services, Sinop University, 57000, Sinop, Turkey

    Aysel Veyisoglu

Authors
  1. Aysel Veyisoglu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Aysel Veyisoglu.

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 and/or animals performed by any of the authors. The formal consent is not required in this study.

Additional information

Communicated by Erko Stackebrandt.

Publisher's Note

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

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Veyisoglu, A. Nonomuraea cypriaca sp. nov., isolated from soil. Arch Microbiol 203, 2639–2645 (2021). https://doi.org/10.1007/s00203-021-02202-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-021-02202-z

Keywords

Search

Navigation