Antonie van Leeuwenhoek

, Volume 108, Issue 6, pp 1383–1390 | Cite as

Micromonospora vulcania sp. nov., isolated from volcanic sediment

  • Feiyu Jia
  • Chongxi Liu
  • Shuyu Zhou
  • Jiansong Li
  • Yue Shen
  • Xuejiao Guan
  • Siyu Guo
  • Meiyue Gao
  • Xiangjing Wang
  • Wensheng Xiang
Original Paper

Abstract

A novel actinobacterial strain, designated strain NEAU-JM2T, was isolated from volcanic sediment collected from Longwan, Jilin province, north China and characterized using a polyphasic approach. The strain was found to have morphological and chemotaxonomic characteristics typical of the members of the genus Micromonospora. Phylogenetic analysis of the16S rRNA gene sequence also indicated that strain NEAU-JM2T should be classified in the genus Micromonospora and showed that close relatives are Micromonospora maoerensis NEAU-MES19T (99.5 %) and Micromonospora matsumotoense JCM 9104T (98.8 %). However, phylogenetic analysis based on the gyrB gene sequence showed that the isolate forms a separate subclade away from the close relatives in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. The low level of DNA–DNA relatedness allowed the isolate to be differentiated from M. maoerensis NEAU-MES19T and M. matsumotoense JCM 9104T. Furthermore, strain NEAU-JM2T could also be distinguished from its close phylogenetic relatives by cultural and physiological characteristics. Therefore, it is proposed that strain NEAU-JM2T represents a novel species of the genus Micromonospora, for which the name Micromonospora vulcania sp. nov. is proposed. The type strain is NEAU-JM2T (=CGMCC 4.7144T = DSM 46711T).

Keywords

Actinobacteria Micromonospora vulcania sp. nov. Polyphasic taxonomy 16S rRNA gene gyrB gene 

Notes

Acknowledgments

This work was supported in part by grants from the National Outstanding Youth Foundation (No. 31225024), the National Natural Science Foundation of China (No. 31471832, 31171913 and 31372006), the National Key Technology R&D Program (No. 2012BAD19B06), the Program for New Century Excellent Talents in University (NCET-11-0953), the Outstanding Youth Foundation of Heilongjiang Province (JC201201), Chang Jiang Scholar Candidates Program for Provincial Universities in Heilongjiang (CSCP), the China Postdoctoral Science Foundation (2014M561319), the Heilongjiang Postdoctoral Fund (LBH-Z14027) and the kindly help of nomenclature expert Aharon Oren.

Supplementary material

10482_2015_591_MOESM1_ESM.doc (2.8 mb)
Supplementary material 1 (DOC 2907 kb)

References

  1. Alain K, Holler T, Musat F, Elvert M, Treude T, Krüger M (2006) Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania. Environ Microbiol 8:574–590CrossRefPubMedGoogle Scholar
  2. Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. 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. Fang BZ, Liu CX, Guan XJ, Song J, Zhao JW, Liu H, Li C, Ning WX, Wang XJ, Xiang WS (2015) Two new species of the genus Micromonospora: Micromonospora palomenae sp. nov. and Micromonospora harpali sp. nov. isolated from the insects. Antonie Van Leeuwenhoek 108:141–150CrossRefPubMedGoogle Scholar
  5. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  6. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefPubMedGoogle Scholar
  7. 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
  8. Garcia LC, Martínez-Molina E, Trujillo ME (2010) Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum. Int J Syst Evol Microbiol 60:331–337CrossRefPubMedGoogle Scholar
  9. Genilloud O (2012) Genus I Micromonospora. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn., The ActinobacteriaSpringer, New York, pp 1039–1057Google 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. Hayakawa M, Nonomura H (1987) Humic acid-vitamin agar, a new medium for the selective isolation of soil actinobacteria. J Ferment Technol 65:501–509CrossRefGoogle Scholar
  12. 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
  13. Kelly KL (1964) Inter-society color council-national bureau of standards color-name charts illustrated with centroid colors published in USGoogle Scholar
  14. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow M (2000) Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinobacterial. Int J Syst Evol Microbiol 50:2031–2036CrossRefPubMedGoogle Scholar
  15. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721CrossRefPubMedGoogle Scholar
  16. 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
  17. Kroppenstedt RM (1985) Fatty acid and menaquinone analysis of actinomycetes and related organisms. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics, vol 20., Society for applied bacteriology technical seriesAcademic Press, New York, pp 173–199Google Scholar
  18. Lechevalier MP, Lechevalier HA (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443CrossRefGoogle Scholar
  19. Lechevalier MP, Lechevalier HA (1980) The chemotaxonomy of actinobacteria. In: Dietz A, Thayer DW (eds) Actinobacterial taxonomy, vol 6. Society of Industrial Microbiology, Arlington, pp 227–291Google Scholar
  20. Lechevalier MP, Stern AE, Lechevalier HA (1981) Phospholipids in the taxonomy of actinomycetes. Zentralbl Bakteriol Hyg Abt 1(Suppl 11):111–116Google Scholar
  21. Mandel M, Marmur J (1968) Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195–206CrossRefGoogle Scholar
  22. 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
  23. 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
  24. Ørskov J (1923) Investigations into the morphology of the ray fungi. Levin and Munksgaard, CopenhagenGoogle Scholar
  25. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  26. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340CrossRefGoogle Scholar
  27. 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 607–654Google Scholar
  28. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  29. Thawai C (2015) Micromonospora costi sp. nov., isolated from a leaf of Costus speciosus. Int J Syst Evol Microbiol 65:1456–1461CrossRefPubMedGoogle Scholar
  30. Thompson JD, Gibson TJ, Plewniak F (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 5:4876–4882CrossRefGoogle Scholar
  31. Waksman SA (1961) The Actinobacteria, vol. 2, Classification, identification and descriptions of genera and species. Williams and Wilkins, BaltimoreGoogle Scholar
  32. Waksman SA (1967) The Actinobacteria. A summary of current knowledge. Ronald, New YorkGoogle Scholar
  33. 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
  34. 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
  35. 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
  36. Xiang WS, Yu C, Liu CX, Zhao JW, Yang LY, Xie BJ, Li L, Hong K, Wang XJ (2014) Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger). Int J Syst Evol Microbiol 64:495–500CrossRefPubMedGoogle Scholar
  37. Xie QY, Lin HP, Li L, Brown R, Goodfellow M, Deng ZX, Hong K (2012) Verrucosispora wenchangensis sp. nov., isolated from mangrove soil. Antonie Van Leeuwenhoek 102:1–7CrossRefPubMedGoogle Scholar
  38. Yakimov MM, Giuliano L, Crisafi E, Chernikova TN, Timmis KN, Golyshin PN (2002) Microbial community of saline mud volcano at San Biagio-Belpasso, Mt. Etna (Italy). Environ Microbiol 4:249–256CrossRefPubMedGoogle Scholar
  39. Yokota A, Tamura T, Hasegawa T, Huang LH (1993) Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 43:805–812CrossRefGoogle Scholar
  40. Zhang YJ, Liu H, Zhang XH, Wang SR, Liu CX, Yu C, Wang XJ, Xiang WS (2014) Micromonospora violae sp. nov., isolated from a root of Viola philippica Car. Antonie Van Leeuwenhoek 106:219–225CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Feiyu Jia
    • 1
  • Chongxi Liu
    • 1
  • Shuyu Zhou
    • 1
  • Jiansong Li
    • 1
  • Yue Shen
    • 1
  • Xuejiao Guan
    • 1
  • Siyu Guo
    • 1
  • Meiyue Gao
    • 1
  • Xiangjing Wang
    • 1
  • Wensheng Xiang
    • 1
    • 2
  1. 1.Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education CommitteeNortheast Agricultural UniversityHarbinPeople’s Republic of China
  2. 2.State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China

Personalised recommendations