Antonie van Leeuwenhoek

, Volume 94, Issue 4, pp 581–591 | Cite as

Biosystematics of alkaliphilic streptomycetes isolated from seven locations across a beach and dune sand system

  • Sanjay Antony-Babu
  • Michael Goodfellow
Original Paper


Alkaliphilic streptomycetes were isolated from composite sand samples collected from six out of seven locations across a beach and dune sand system using starch-casein-nitrate agar supplemented with cycloheximide and buffered to pH 10.5. The isolates had colonial and chemotaxonomic properties consistent with their classification in the genus Streptomyces. They were assigned to 49 multimembered and 114 single-membered colour-groups given their ability to produce pigments on oatmeal and peptone-yeast-extract-iron agars and to corresponding taxa based on whole-genome rep-PCR banding patterns. Twenty-four isolates representing the colour and rep-PCR groups grew well from pH 5 to 11, and optimally at pH 9, as did phylogenetically close members of the Streptomyces griseus 16S rRNA gene clade. One hundred and twelve representative alkaliphilic streptomycetes formed a heterogeneous but distinct clade in the Streptomyces 16S rRNA gene tree. A 3-dimensional representation of 16S rRNA sequence data showed that the alkaliphilic streptomycetes formed a distinct group in multidimensional taxospace. It is evident that alkaliphilic streptomycetes are common in the beach and dune sand system and that representatives of this community form new centers of taxonomic variation within the genus Streptomyces that can be equated with species.


Alkaliphilic streptomycetes pH profiles Polyphasic taxonomy Selective isolation 



Sanjay Antony-Babu is grateful to the University of Newcastle for an International Research Scholarship and to the School of Biology for a Research Studentship.


  1. Anderson AS, Wellington EMH (2001) The taxonomy of Streptomyces and related genera. Int J Syst Evol Microbiol 51:797–814PubMedGoogle Scholar
  2. Antony-Babu S, Okorafor LA, Stach JEM, Goodfellow M (2007) Alkaliphilic streptomycetes: prospective new candidates for bioprospecting. In: Proceedings of the 14th international symposium on the biology of actinomycetes, University of Newcastle, UK, p 110Google Scholar
  3. Atalan E, Manfio GP, Ward AC, Kroppenstedt RM, Goodfellow M (2000) Biosystematic studies on novel streptomycetes from soil. Antonie Van Leeuwenhoek 77:337–353. doi: 10.1023/A:1002682728517 PubMedCrossRefGoogle Scholar
  4. Basilio A, Gonzalez I, Vicente MF, Gorrochategui J, Cabello A, Gonzalez A et al (2003) Patterns of antimicrobial activities from soil actinomycetes isolated under different conditions of pH and salinity. J Appl Microbiol 95:814–823. doi: 10.1046/j.1365-2672.2003.02049.x PubMedCrossRefGoogle Scholar
  5. Bentley SD, Chater KF, Cerdeno-Tarraga AM et al (2002) Complete genome sequence of the model actinomycete “Streptomyces coelicolor A3(2)”. Nature 417:141–147. doi: 10.1038/417141a PubMedCrossRefGoogle Scholar
  6. Bérdy J (2005) Bioactive microbial metabolites. J Antibiot (Tokyo) 58:1–26Google Scholar
  7. British Standards Institution (1995) Soil quality. Chemical methods. Determination of organic and total carbon after dry combustion (elementary analysis). British Standard 7755-3.8. British Standards Institution, LondonGoogle Scholar
  8. Bruntner C, Binder T, Pathom-aree W, Goodfellow M, Bull AT, Potterat O et al (2005) Frigocyclinone, a novel angucyclinone antibiotic produced by a Streptomyces griseus strain from Antarctica. J Antibiot (Tokyo) 58:346–349Google Scholar
  9. Bull AT, Stach JEM, Ward AC, Goodfellow M (2005) Marine actinobacteria: perspectives, challenges, future directions. Antonie Van Leeuwenhoek 87:65–79. doi: 10.1007/s10482-004-6562-8 CrossRefGoogle Scholar
  10. Chun J (1995) Computer-assisted classification and identification of actinomycetes. Department of Agriculture and Environmental Sciences, University of Newcastle, Newcastle-upon-TyneGoogle Scholar
  11. Dieter A, Hamm A, Fiedler HP, Goodfellow M, Műller WEG, Brun R et al (2003) Pyrocoll, an antibiotic, antiparasitic and antitumor compound produced by a novel alkaliphilic Streptomyces strain. J Antibiot 56:639–646Google Scholar
  12. Duangmal K, Ward AC, Goodfellow M (2005) Selective isolation of members of the Streptomyces violaceoruber clade from soil. FEMS Microbiol Lett 245:321–327. doi: 10.1016/j.femsle.2005.03.028 PubMedCrossRefGoogle Scholar
  13. Fahmy T, Aubry P (2003) XLSTAT-pro, version 7.0, ParisGoogle Scholar
  14. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol Int J Org Evol 39:783–791. doi: 10.2307/2408678 Google Scholar
  15. Fiedler HP, Bruntner C, Bull AT, Ward AC, Goodfellow M, Potterat O et al (2005) Marine actinomycetes as a source of novel secondary metabolites. Antonie Van Leeuwenhoek 87:37–42. doi: 10.1007/s10482-004-6538-8 PubMedCrossRefGoogle Scholar
  16. Goodfellow M, Dawson D (1978) Qualitative and quantitative studies of bacteria colonizing Picea sitchensis litter. Soil Biol Biochem 10:303–307. doi: 10.1016/0038-0717(78)90027-5 CrossRefGoogle Scholar
  17. Goodfellow M, Haynes JA (1984) Actinomycetes in marine sediments. In: Ortiz-Ortiz L, Bojalil LF, Yakoleff V (eds) Biological and biomedical aspects of actinomycetes. Academic Press, New York, pp 452–472Google Scholar
  18. Goodfellow M, Ferguson EV, Sanglier JJ (1992) Numerical classification and identification of Streptomyces species—a review. Gene 115:225–233. doi: 10.1016/0378-1119(92)90563-5 PubMedCrossRefGoogle Scholar
  19. Goodfellow M, Kumar Y, Labeda DP, Sembiring L (2007) The Streptomyces violaceusniger clade: a home for streptomycetes with rugose ornamented spores. Antonie Van Leeuwenhoek 92:173–199. doi: 10.1007/s10482-007-9146-6 PubMedCrossRefGoogle Scholar
  20. Graf E, Schneider K, Nicholson G, Ströbele M, Jones AL, Goodfellow M et al (2007) Elloxazinones A and B, new aminophenoxazinones from Streptomyces griseus Acta 2871. J Antibiot 60:277–284PubMedGoogle Scholar
  21. Häne BG, Jäger K, Drexler H (1993) The Pearson product-moment correlation coefficient is better suited for identification of DNA fingerprint profiles than band matching algorithms. Electrophoresis 14:967–972. doi: 10.1002/elps.11501401154 PubMedCrossRefGoogle Scholar
  22. He L, Li W, Huang Y, Wang L, Liu Z, Lanoot B et al (2005) Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Bacteriol 55:1939–1944Google Scholar
  23. Hedlund BP, Staley JT (2004) Microbial endemism and biogeography. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 225–231Google Scholar
  24. Höltzel A, Dieter A, Schmid DG, Brown R, Goodfellow M, Beil W et al (2003) Lactonamycin Z, an antibiotic and antitumor compound produced by Streptomyces sanglieri strain AK 623. J Antibiot 56:1058–1061PubMedGoogle Scholar
  25. Hozzein WN, Ali MIA, Hammouda O, Mousa AS, Li W-J, Xu L-H et al (2008) Streptomyces sannurensis sp. nov., a novel alkaliphilic streptomycete isolated from Wadi Sannur in Egypt. Antonie Van Leeuwenhoek (in press)Google Scholar
  26. Huang Y, Li W, Wang L, Lanoot B, Vancanneyt M, Rodriguez C et al (2004) Streptomyces glauciniger sp. nov., a novel mesophilic streptomycete isolated from soil in south China. Int J Syst Evol Microbiol 54:2085–2089. doi: 10.1099/ijs.0.63158-0 PubMedCrossRefGoogle Scholar
  27. Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T et al (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21:526–531. doi: 10.1038/nbt820 PubMedCrossRefGoogle Scholar
  28. Jones KL (1949) Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57:141–145Google Scholar
  29. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic Press, New York, pp 21–123Google Scholar
  30. Kelly KL (1964) Inter-Society Color Council–National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors. US Government Printing Office, Washington, DCGoogle Scholar
  31. Kieser T, Bibb MJ, Buttner M, Chater KF, Hopwood DA (2000) Practical Streptomyces genetics. The John Innes Foundation, Norwich, pp 162–170Google Scholar
  32. Kim B, Sahin N, Minnikin DE, Zakrzewska-Czerwinska J, Mordarski M, Goodfellow M (1999) Classification of thermophilic streptomycetes, including the description of Streptomyces thermoalcalitolerans sp. nov. Int J Syst Evol Microbiol 49:7–17CrossRefGoogle Scholar
  33. Kim SB, Seong CN, Jeon SJ, Bae KS, Goodfellow M (2004) Taxonomic study of neutrotolerant acidophilic actinomycetes isolated from soil and description of Streptomyces yeochonensis sp. nov. Int J Syst Evol Microbiol 54:211–214. doi: 10.1099/ijs.0.02519-0 PubMedCrossRefGoogle Scholar
  34. Kumar Y, Goodfellow M (2008) Five new species of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis comb. nov., Streptomyces himastatinicus sp. nov., Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp. nov. and Streptomyces ruanii sp. nov. Int J Syst Evol Microbiol (in press)Google Scholar
  35. Kűster E, Williams ST (1964) Selection of media for isolation of streptomycetes. Nature 202:928–929. doi: 10.1038/202928a0 CrossRefGoogle Scholar
  36. Lanoot B, Vancanneyt M, Hoste B, Vandemeulebroecke K, Cnockaert MC, Dawyndt P et al (2005) Grouping of streptomycetes using 16S-ITS RFLP fingerprinting. Res Microbiol 156:755–762. doi: 10.1016/j.resmic.2005.01.017 PubMedCrossRefGoogle Scholar
  37. Liu Z, Shi Y, Zhang Y, Zhou Z, Lu Z, Li W et al (2005) Classification of Streptomyces griseus (Krainsky 1914) Waksman and Henrici 1948 and related species and the transfer of ‘Microstreptospora cinerea’ to the genus Streptomyces as Streptomyces yanii sp. nov. Int J Syst Evol Microbiol 55:1605–1610. doi: 10.1099/ijs.0.63654-0 PubMedCrossRefGoogle Scholar
  38. Manfio GP, Zakrzewska-Czerwinska J, Atalan E, Goodfellow M (1995) Towards minimal standards for description of Streptomyces species. Biotechnologia 7:242–283Google Scholar
  39. Manfio GP, Atalan E, Zakrzewska-Czerwinska J, Mordarski M, Rodriguez C, Collins MD et al (2003) Classification of novel soil streptomycetes as Streptomyces aureus sp. nov., Streptomyces laceyi sp. nov. and Streptomyces sanglieri sp. nov. Antonie Van Leeuwenhoek 83:245–255. doi: 10.1023/A:1023332427794 PubMedCrossRefGoogle Scholar
  40. Mao J, Tang Q, Zhang Z, Wang W, Wei D, Huang Y et al (2007) Streptomyces radiopugnans sp. nov., a radiation-resistant actinomycete isolated from radiation-polluted soil in China. Int J Syst Evol Microbiol 57:2578–2582. doi: 10.1099/ijs.0.65027-0 PubMedCrossRefGoogle Scholar
  41. Mehta VJ, Thumar JT, Singh SP (2006) Production of alkaline protease from an alkaliphilic actinomycete. Bioresour Technol 97:1650–1654. doi: 10.1016/j.biortech.2005.07.023 PubMedCrossRefGoogle Scholar
  42. Mikami Y, Miyashita K, Arai T (1982) Diaminopimelic acid profiles of alkalophilic and alkaline-resistant strains of actinomycetes. J Gen Microbiol 128:1709–1712PubMedGoogle Scholar
  43. Ōmura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M et al (2001) Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Natl Acad Sci USA 98:22215–12220Google Scholar
  44. Pridham TG, Tresner HD (1974) Genus I. Streptomyces Waksman and Henrici 1943, 339. In: Buchanan RE, Gibbons NE (eds) Bergey’s manual of determinative bacteriology. The Williams and Wilkins Co., Baltimore, pp 748–829Google Scholar
  45. Reed JF, Cummings RW (1945) Soil reaction-glass electrodes and colorimetric methods for determining pH values in soil. Soil Sci 59:97–104. doi: 10.1097/00010694-194501000-00015 CrossRefGoogle Scholar
  46. Rohlf FJ (1988) NTSYS-pc: numerical taxonomy and multivariate analysis system. Applied Biostatistics Inc., SetauketGoogle Scholar
  47. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  48. Sembiring L, Ward AC, Goodfellow M (2000) Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria. Antonie Van Leeuwenhoek 78:353–366. doi: 10.1023/A:1010226515202 PubMedCrossRefGoogle Scholar
  49. Seong CN, Goodfellow M, Ward AC, Hah YC (1993) Numerical classification of acidophilic actinomycetes isolated from acid soil in Korea. Korean J Microbiol 31:355–363Google Scholar
  50. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313Google Scholar
  51. Solingen P, Meijer D, Kleij WA, Barnett C, Bolle R, Power SD et al (2001) Cloning and expression of an endocellulase gene from a novel streptomycete isolated from an East African soda lake. Extremophiles 5:333–341. doi: 10.1007/s007920100198 PubMedCrossRefGoogle Scholar
  52. Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Environ Microbiol 28:226–231Google Scholar
  53. Strohl WR (2004) Antimicrobials. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 336–355Google Scholar
  54. Taber WA (1960) Evidence for the existence of acid-sensitive actinomycetes in soil. Can J Microbiol 6:503–514CrossRefGoogle Scholar
  55. Van de Peer Y, De Wachter R (1994) Treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570PubMedGoogle Scholar
  56. Vasavada SH, Thumar JT, Singh SP (2006) Secretion of a potent antibiotic by salt-tolerant and alkaliphilic actinomycete Streptomyces sannanensis strain RJT-1. Curr Sci 91:1393–1397Google Scholar
  57. Versalovic J, Koeuth T, Lupski JR (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831. doi: 10.1093/nar/19.24.6823 PubMedCrossRefGoogle Scholar
  58. Vickers JC, Williams ST, Ross GW (1984) A taxonomic approach to selective isolation of streptomycetes from soil. In: Ortiz-Ortiz L, Bojalil LF, Yakoleff V (eds) Biological biochemical and biomedical aspects of actinomycetes. Academic Press, London, pp 553–561Google Scholar
  59. Watson ET, Williams ST (1974) Studies on ecology of actinomycetes in soil. VII. Actinomycetes in a coastal sand belt. Soil Biol Biochem 6:43–52. doi: 10.1016/0038-0717(74)90010-8 CrossRefGoogle Scholar
  60. Watve MG, Tickoo R, Jog MM, Bhole BD (2001) How many antibiotics are produced by the genus Streptomyces? Arch Microbiol 176:386–390. doi: 10.1007/s002030100345 PubMedCrossRefGoogle Scholar
  61. Williams ST, Vickers JC (1988) Detection of actinomycetes in the natural environment: problems and perspectives. In: Okami Y, Beppu T, Ogawara K (eds) Biology of actinomycetes. Japan Scientific Societies Press, Tokyo, pp 265–270Google Scholar
  62. Williams ST, Davies FL, Mayfield CI, Khan MR (1971) Studies on the ecology of actinomycetes in soil. II. The pH requirements of streptomycetes from two acid soils. Soil Biol Biochem 3:187–195. doi: 10.1016/0038-0717(71)90014-9 CrossRefGoogle Scholar
  63. Williams ST, Lanning S, Wellington EMH (1984) Ecology of actinomycetes. In: Goodfellow M, Mordarski M, Williams ST (eds) The biology of the actinomycetes. Academic Press, Inc., London, pp 481–528Google Scholar
  64. Xu C, Wang L, Cui Q, Huang Y, Liu Z, Zhang G et al (2006) Novel neutrotolerant acidophilic Streptomyces species isolated from acidic soils in China: Streptomyces guandensis sp. nov., Streptomyces paucisporeus sp. nov., Streptomyces rubidus sp. nov. and Streptomyces yanglinensis sp. nov. Int J Syst Evol Bacteriol 56:1109–1115Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.School of BiologyUniversity of NewcastleNewcastle-upon-TyneUK

Personalised recommendations