Streptomyces urticae sp. nov., isolated from rhizosphere soil of Urtica urens L.

  • Chenyu Piao
  • Ling Ling
  • Junwei Zhao
  • Liying Jin
  • Shanwen Jiang
  • Xiaowei Guo
  • Xiangjing Wang
  • Wensheng Xiang
Original Paper

Abstract

Two novel Gram-stain positive, spore-forming, aerobic actinomycetes, designated NEAU-PCY-1T and NEAU-PCY-2, were isolated from rhizosphere soil of Urtica urens L. collected from Anshan, Liaoning Province, northeast China. The 16S rRNA gene sequence analysis showed that strains NEAU-PCY-1T and NEAU-PCY-2 exhibited 99.8% similarity with each other and are closely related to Streptomyces abietis DSM 42080T (98.2, 98.3%) and Streptomyces fildesensis DSM 41987T (98.0, 98.1%). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the two strains formed a cluster with these two closely related species. Moreover, DNA–DNA hybridization results and some phenotypic, physiological and biochemical properties differentiated the two strains from their close relatives in the genus Streptomyces. Based on a polyphasic taxonomy study, strains NEAU-PCY-1T and NEAU-PCY-2 are considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces urticae sp. nov. is proposed, with NEAU-PCY-1T (= DSM 105115T = CCTCC AA 2017015T) as the type strain.

Keywords

Streptomyces urticae sp. nov. Polyphasic taxonomy 16S rRNA gene Rhizosphere soil of Urtica urens L. 

Notes

Acknowledgements

This work was supported in part by grants from the National Natural Science Foundation of China (Nos. 31572070, 31672092 and 31471832), Chang Jiang Scholar Candidates Program for Provincial Universities in Heilongjiang (CSCP). We are grateful to Prof. Aharon Oren for helpful advice on the specific epithet.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

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.

Supplementary material

10482_2018_1072_MOESM1_ESM.docx (2.8 mb)
Supplementary material 1 (DOCX 2841 kb)

References

  1. Carvalho AR, Costa G, Figueirinha A, Liberal J, Prior JAV, Lopes MC, Cruz MT, Batista MT (2017) Urtica spp.: phenolic composition, safety, antioxidant and anti-inflammatory activities. Food Res Int 99:485–494CrossRefPubMedGoogle Scholar
  2. Collins MD (1985) Chemical methods in bacterial systematics. In: Goodfellow M, Minnikin DE (eds) Isoprenoid quinone analyses in bacterial classification and identification. Academic Press, London, pp 267–284Google Scholar
  3. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142CrossRefPubMedGoogle Scholar
  4. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  5. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefPubMedGoogle Scholar
  6. Fujii K, Satomi M, Fukui Y, Matsunobu S, Morifuku Y, Enokida Y (2013) Streptomyces abietis sp. nov., a cellulolytic bacterium isolated from soil of a pine forest. Int J Syst Evol Microbiol 63:4754–4759CrossRefPubMedGoogle Scholar
  7. Gao B, Gupta RS (2012) Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 76:66–112CrossRefPubMedPubMedCentralGoogle Scholar
  8. Gao RX, Liu CX, Zhao JW, Jia FY, Yu C, Yang LY, Wang XJ, Xiang WS (2014) Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie Van Leeuwenhoek 105:307–315CrossRefPubMedGoogle Scholar
  9. Goodfellow M, Fiedler HP (2010) A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie Van Leeuwenhoek 98:119–142CrossRefPubMedGoogle Scholar
  10. Gordon RE, Barnett DA, Handerhan JE, Pang C (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63CrossRefGoogle Scholar
  11. Hatano K, Nishii T, Kasai H (2003) Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA-DNA hybridization and sequences of gyr B, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev. Int J Syst Evol Microbiol 53:1519–1529CrossRefPubMedGoogle Scholar
  12. Huang MJ, Fei JJ, Salam N, Kim CJ, Hozzein WN, Xiao M, Huang HQ, Li WJ (2016) Streptomyces zhihengii sp. nov., isolated from rhizospheric soil of Psammosilene tunicoides. Arch Microbiol 198:743–749CrossRefPubMedGoogle Scholar
  13. Huss VAR, Festl H, Schleifer KH (1983) Studies on the spectrometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192CrossRefPubMedGoogle Scholar
  14. Jones KL (1949) Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57:141–145PubMedPubMedCentralGoogle Scholar
  15. Kelly KL (1964) Inter-society colour council-national bureau of standards colour-name charts illustrated with centroid colours published in USGoogle Scholar
  16. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow M (2000) Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 50:2031–2036CrossRefPubMedGoogle Scholar
  17. Kim KO, Shin KS, Kim MN, Shin KS, Labeda DP, Han JH, Kim SB (2012) Reassessment of the status of streptomyces setonii and reclassification of streptomyces fimicarius as a later synonym of streptomyces setonii and streptomyces albovinaceus as a later synonym of streptomyces globisporus based on combined 16S rRNA/gyrB gene sequence analysis. Int J Syst Evol Microbiol 62(Pt 12):2978CrossRefPubMedGoogle Scholar
  18. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  19. Lechevalier HA, Lechevalier MP (1970a) A critical evaluation of the genera of aerobic actinomycetes. In: Prauser H (ed) The actinomycetes. Gustav Fischer, Jena, pp 393–405Google Scholar
  20. Lechevalier MP, Lechevalier HA (1970b) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443CrossRefGoogle Scholar
  21. Lechevalier MP, Lechevalier HA (1980) The chemotaxonomy of actinomycetes. In: Dietz A, Thayer DW (eds) Actinomycete taxonomy special publication, vol 6. Society of Industrial Microbiology, Arlington, pp 227–291Google Scholar
  22. Lechevalier MP, De Bièvre C, Lechevalier HA (1977) Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260CrossRefGoogle Scholar
  23. Luo XX, Sun Y, Xie SN, Wan CX, Zhang LL (2016) Streptomyces indoligenes sp. nov., isolated from rhizosphere soil of Populus euphratica. Int J Syst Evol Microbiol 66:2424–2428CrossRefPubMedGoogle Scholar
  24. Mandel M, Marmur J (1968) Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12:195–206CrossRefGoogle Scholar
  25. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM, Brooks P, Se-viour RJ (2000) A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 30:178–182CrossRefPubMedGoogle Scholar
  26. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M (1980) Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr 188:221–233CrossRefGoogle Scholar
  27. 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 2:233–241CrossRefGoogle Scholar
  28. Mzid M, Ben Khedir S, Ben Salem M, Regaieg W, Rebai T (2017a) Antioxidant and antimicrobial activities of ethanol and aqueous extracts from Urtica urens. Pharm Biol 55:775–781CrossRefPubMedGoogle Scholar
  29. Mzid M, Ghlissi Z, Salem MB, Khedir SB, Chaabouni K, Ayedi F, Sahnoun Z, Hakim A, Rebai T (2017b) Chemoprotective role of ethanol extract of Urtica urens L. against the toxicity of imidacloprid on endocrine disruption and ovarian morphometric in female rats, GC/MS analysis. Biomed Pharmacother 97:518–527CrossRefPubMedGoogle Scholar
  30. Nguyen TM, Kim J (2015) Description of Streptomyces fabae sp. nov., a producer of antibiotics against microbial pathogens, isolated from soybean (Glycine max) rhizosphere soil. Int J Syst Evol Microbiol 65:4151–4156CrossRefPubMedGoogle Scholar
  31. Olano C, Mendez C, Salas JA (2009) Antitumor compounds from marine actinomycetes. Mar Drugs 7:210–248CrossRefPubMedPubMedCentralGoogle Scholar
  32. Parte AC (2014) LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:613–616CrossRefGoogle Scholar
  33. Qin S, Li J, Zhang YQ, Zhu WY, Zhao GZ, Xu LH, Li WJ (2009) Plantactinospora mayteni gen. nov., sp. nov., a member of the family Micromonosporaceae. Int J Syst Evol Microbiol 59:2527–2533CrossRefPubMedGoogle Scholar
  34. Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and Bacteria. Antonie Van Leeuwenhoek 110:455–456CrossRefPubMedGoogle Scholar
  35. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  36. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340CrossRefGoogle Scholar
  37. Smibert RM, Krieg NR (1994) Phenotypic characterisation. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington DC, pp 607–654Google Scholar
  38. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.06. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  39. Waksman SA (1961) The Actinomycetes, vol. 2, Classification, identification and descriptions of genera and species. Baltimore: Williams and WilkinsGoogle Scholar
  40. Waksman SA (1967) The actinomycetes a summary of current knowledge. Ronald Press, New YorkGoogle Scholar
  41. Waksman SA, Henrici AT (1943) The nomenclature and classification of the actinomycetes. J Bacteriol 46:337–341PubMedPubMedCentralGoogle Scholar
  42. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  43. Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams and Wilkins, Baltimore, pp 2452–2492Google Scholar
  44. Wu C, Lu X, Qin M, Wang Y, Ruan J (1989) Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 16:176–178Google Scholar
  45. Xiang WS, Liu CX, Wang XJ, Du J, Xi LJ, Huang Y (2011) Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 61:1165–1169CrossRefPubMedGoogle Scholar
  46. Xie QY, Lin HP, Li L, Brown R, Goodfellow M, Deng Z, Hong K (2012) Verrucosispora wenchangensis sp. nov., isolated from mangrove soil. Antonie Van Leeuwenhoek 102:1–7CrossRefPubMedGoogle Scholar
  47. Yokota A, Tamura T, Hasegawa T, Huang LH (1993) Catenuloplanes japonicas gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 43:805–812CrossRefGoogle Scholar
  48. 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 67:1613–1617CrossRefPubMedPubMedCentralGoogle Scholar
  49. Zhou SY, Li ZL, Bai L, Yan K, Zhao JW, Lu C, Liu CX, Wang XJ, Xiang WS (2017) Streptomyces castaneus sp. nov., a novel actinomycete isolated from the rhizosphere of Peucedanum praeruptorum Dunn. Arch Microbiol 199:45–50CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Chenyu Piao
    • 1
    • 2
  • Ling Ling
    • 2
  • Junwei Zhao
    • 1
    • 2
  • Liying Jin
    • 2
  • Shanwen Jiang
    • 2
  • Xiaowei Guo
    • 2
  • Xiangjing Wang
    • 2
  • Wensheng Xiang
    • 1
    • 2
  1. 1.State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China
  2. 2.Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education CommitteeNortheast Agricultural UniversityHarbinPeople’s Republic of China

Personalised recommendations