sp. nov., a blue pigment-producing actinomycete from manganese-contaminated soil Free

Abstract

A novel actinomycete isolate, designated strain MK-45, was isolated from soil sampled at a manganese-contaminated area in Xiangtan, China. The isolate formed extensively branched substrate mycelia and aerial mycelia that differentiated into tightly coiled or spiral spore chains with smooth-surfaced spores. The cell-wall hydrolysates contained -diaminopimelic acid and traces of -diaminopimelic acid. The major menaquinones consisted of MK-9(H), MK-9(H) and MK-9(H). The major polar lipids contained diphosphatidylgycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphotidylinositol and phosphotidylinositol mannosides. The predominant cellular fatty acids were iso-C, C and summed feature 3. Phylogenetic analysis based on the 16S rRNA gene sequences and concatenated partial sequences of the five protein-coding genes indicated that strain MK-45 was a member of the genus and most closely related to GIMN4.002 (99.5 % similarity), CGMCC 4.1680 (99.5 %), CCNWHQ 0031 (99.4 %) and NRRL B12382 (98.9 %), respectively. However, the digital DNA–DNA hybridization values, the average nucleotide identity values and MLSA evolutionary distances between strain MK-45 and them showed that it belonged to a distinct species. Furthermore, the results of morphological, physiological and biochemical tests allowed further phenotypic differentiation of strain MK-45 from the four closely related type strains mentioned above and other species of the genus with which this strain has 98.0–99.2 % 16S rRNA gene sequence similarity. Therefore, it is concluded that strain MK-45 represents a novel species of the genus , for which the name sp. nov. is proposed, with MK-45 (=CICC 11045=KCTC 49099) as the type strain.

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2019-08-01
2024-03-28
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References

  1. Koshy A, Dhevendaran K, Georgekutty MI. Matarajan P. l-Asparaginase activity in Streptomyces plicatus isolated from the alimentary canal of the fish, Gerres filamentous (Cuvier). J Mar Biotechnol 1997; 5:181–185
    [Google Scholar]
  2. Gallagher KA, Fenical W, Jensen PR. Hybrid isoprenoid secondary metabolite production in terrestrial and marine actinomycetes. Curr Opin Biotechnol 2010; 21:794–800 [View Article][PubMed]
    [Google Scholar]
  3. Albarracín VH, Avila AL, Amoroso MJ, Abate CM. Copper removal ability by Streptomyces strains with dissimilar growth patterns and endowed with cupric reductase activity. FEMS Microbiol Lett 2008; 288:141–148 [View Article][PubMed]
    [Google Scholar]
  4. Benimeli CS, Fuentes MS, Abate CM, Amoroso MJ. Bioremediation of lindane-contaminated soil by Streptomyces sp. M7 and its effects on Zea mays growth. Int Biodeterior Biodegradation 2008; 61:233–239 [View Article]
    [Google Scholar]
  5. Desjardin V. Utilisation of supernatants of pure cultures of Streptomyces thermocarboxydus NH50 to reduce chromium toxicity and mobility in contaminated soils. Water, Air, and Soil Pollution: Focus 2003; 3:153–160 [View Article]
    [Google Scholar]
  6. Siñeriz ML, Kothe E, Abate CM. Cadmium biosorption by Streptomyces sp. F4 isolated from former uranium mine. J Basic Microbiol 2009; 49 Suppl 1:S55–S62 [View Article][PubMed]
    [Google Scholar]
  7. Atlas RM. In Parks LC. (editor) Handbook of Microbiological Media Boca Raton: CRC Press; 1993
    [Google Scholar]
  8. Peng YX, Jiang Y, Duan SR, Wj L, Lh X. Selective isolation methods of rare actinomycetes (in Chinese). J Yunnan Univ 2007; 29:86–89
    [Google Scholar]
  9. Jiang CR, Ruan JS. Two new species and a new variety of Ampullarella. Acta Microbiol Sin 1982; 22:207–211
    [Google Scholar]
  10. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  11. Abildgren MP, Lund F, Thrane U, Elmholt S. Czapek-Dox agar containing iprodione and dicloran as a selective medium for the isolation of Fusarium species. Lett Appl Microbiol 1987; 5:83–86 [View Article]
    [Google Scholar]
  12. Ridgway R. Color Standards and Color Nomenclature Washington, DC: The Author; 1912
    [Google Scholar]
  13. Goodfellow M. Numerical taxonomy of some nocardioform bacteria. J Gen Microbiol 1971; 69:33–80 [View Article][PubMed]
    [Google Scholar]
  14. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article][PubMed]
    [Google Scholar]
  15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  16. Shieh WY, Chen YW, Chaw SM, Chiu HH. Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. Int J Syst Evol Microbiol 2003; 53:479–484 [View Article][PubMed]
    [Google Scholar]
  17. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  18. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  19. Kates M. Techniques of Lipidology, 2nd ed. Amsterdam: Elsevier; 1986
    [Google Scholar]
  20. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  21. MIDI Sherlock Microbial Identification System Sherlock Microbial Identification System Newark MIDI Inc: 2005
    [Google Scholar]
  22. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  23. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991 pp. 115–175
    [Google Scholar]
  24. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  25. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  26. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  28. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  29. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  30. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 2012; 35:7–18 [View Article][PubMed]
    [Google Scholar]
  31. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  32. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  33. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  34. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  35. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article][PubMed]
    [Google Scholar]
  36. Wright F, Bibb MJ. Codon usage in the G+C-rich Streptomyces genome. Gene 1992; 113:55–65 [View Article][PubMed]
    [Google Scholar]
  37. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  38. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  39. Zhu HH, Guo J, Yao Q, Yang SZ, Deng MR et al. Streptomyces caeruleatus sp. nov., with dark blue diffusible pigment. Int J Syst Evol Microbiol 2011; 61:507–511 [View Article][PubMed]
    [Google Scholar]
  40. Landwehr W, Kämpfer P, Glaeser SP, Rückert C, Kalinowski J et al. Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov. Int J Syst Evol Microbiol 2018; 68:382–393 [View Article][PubMed]
    [Google Scholar]
  41. Kim SB, Goodfellow M. Streptomyces avermitilis sp. nov., nom. rev., a taxonomic home for the avermectin-producing streptomycetes. Int J Syst Evol Microbiol 2002; 52:2011–2014 [View Article][PubMed]
    [Google Scholar]
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