Abstract
Large numbers of putatively novel streptomycetes were isolated from environmental samples collected from in and around the root system of the tropical angiosperm, Paraserianthes falcataria. Representative isolates were assigned to 37 multi-membered and 107 single membered colour groups based on their ability to form pigments on oatmeal and peptone yeast extract iron agars. The largest taxon, colour group 3, encompassed 94 isolates which had morphological properties typical of members of the Streptomyces violaceusniger clade. Twelve representatives of this taxon chosen on the basis of Curie-point pyrolysis mass spectrometric data were compared with representatives of the validly described species which constitute the Streptomyces violaceusniger clade. Six out of the twelve representative strains were readily distinguished from one another and from the marker strains using a combination of genotypic and phenotypic properties. These organisms were consequently considered to merit species status as Streptomyces asiaticus sp. nov., Streptomyces cangkringensis sp. nov., Streptomyces indonesiensis sp. nov., Streptomyces javensis sp. nov., Streptomyces rhizosphaerius sp. nov. and Streptomyces yogyakartensis sp. nov.
Similar content being viewed by others
References
Al-Tai A, Kim B, Kim SB, Manfio GP & Goodfellow M (1999) Streptomyces malaysiensis sp. nov., a new streptomycete species with rugose, ornamented spores. Int. J. Syst. Bacteriol. 49: 1395–1402
Arcamone FC, Bertazzoli C, Ghione M & Scotti T (1959) Melanosporin and elaiophylin, new antibiotics from S. melanosporus (sive melanosporofaciens) n. sp. G. Microbiol. 71: 207–216
Atalan E, Manfio GP, Ward AC, Kroppenstedt RM & Goodfellow M (2000) Biosystematic studies on novel streptomycetes from soil. Antonie van Leeuwenhoek 77: 337–353
Chun J (1995) Computer-assisted Classification and Identification of Actinomycetes. Ph.D. thesis. University of Newcastle, Newcastle upon Tyne, UK
Chun J & Goodfellow M (1995) A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 45: 240–245
Colquhoun JA, Heald SC, Li L, Tamaoka J, Kato C, Horikoshi K & Bull AT (1998a) Taxonomy and biotransformation activities of some deep-sea actinomycetes. Extremophiles 2: 269–277
Colquhoun JA, Mexson J, Goodfellow M, Ward AC, Horikoshi K & Bull AT (1998b) Novel rhodococci and other mycolate actinomycetes from the deep-sea. Antonie van Leeuwenhoek 74: 27–40
Colquhoun JA, Zulu J, Goodfellow M, Horikoshi K, Ward AC & Bull AT (2000) Rapid characterisation of deep-sea actinomycetes for biotechnology screening programmes. Antonie van Leeuwenhoek 77: 359–367
Crawford DL, Lynch J, Whipps J & Ousley M (1993) Isolation and characterization of actinomycete antagonists of a fungal root pathogen. Appl. Environ. Microbiol. 59: 3889–3905
El-Abyad MS, El-Sayed MA, El-Shanshoury AR & El-Sabbagh SM (1993) Towards the biological control of fungal and bacterial diseases of tomato using antagonistic Streptomyces spp. Plant and Soil 149: 185–193
Embley TM & Stackebrandt E (1997) Species in practice: exploring uncultured prokaryotic diversity in natural samples. In: Claridge MF Dawah HA & Wilson MR (Eds) Species: the Units of Diversity (pp 61–81). Chapman & Hall, London
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368–376
Ferguson EV, Ward AC, Sanglier JJ & Goodfellow M (1996) Evaluation of Streptomyces species-groups by pyrolysis mass spectrometry. Zbl Bakt 285: 169–181
Fitch, WM & Margoliash E (1967) Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome C sequences is of general applicability. Science 155: 279–284
Goodfellow M & Haynes JA (1984) Actinomycetes in marine sediments. In: Ortiz-Ortiz L Bojalil LF & Yakoleff V (Eds) Biological, Biochemical and Biomedical Aspects of Actinomycetes (pp 453–472). Academic Press, Orlando
Goodfellow M, Davenport R, Stainsby FM & Curtis TP (1996) Actinomycete diversity associated with foaming in activated sludge plants. J. Ind. Microbiol. 17: 268–280
Goodfellow M, Stainsby FM, Davenport R, Chun J & Curtis T (1998) Activated sludge foaming: the true extent of actinomycete diversity. Water Sci. Technol. 37: 511–519
Hopkins DW, O'Donnell AG & MacNaughton SJ (1991a) Evaluation of a dispersion and elutriation technique for sampling microorganisms from soil. Soil Biol. Biochem. 23: 227–232
Hopkins DW, MacNaughton SJ & O'Donnell AG (1991b) A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil. Soil Biol. Biochem. 23: 217–225
Jensen HL (1931) Contribution to our knowledge of the Actinomycetales. II. The definition and subdivision of the genus Actinomyces, with a preliminary account of Australian soil actinomycetes. Proc. Linn. Soc. NSW 56: 345–370
Jones KL (1949) Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J. Bacteriol. 57: 141–145
Kämpfer P, Kroppenstedt RM & Dott W (1991) A numerical classification of the genera Streptomyces and Streptoverticillium using miniaturized physiological tests. J. Gen. Microbiol. 137: 1831–1891
Kay HE, Coutinho HLC, Fattori M, Manfio GP, Goodacre R, Nuti MP, Basaglia M & Beringer JE (1994) The identification of Bradyrhizobium japonicum strains isolated from Italian soils. Microbiology 140: 2333–2339
Kelly KL (1958) Central notations for the revised ISCC-NBS color name blocks. J. Res. Nat. Bureau Standards USA 61: 427
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. Bacteriol 49: 7–17
Kim B, Al-Tai AM, Kim SB, Somasundaram P & Goodfellow M (2000) Streptomyces thermocoprophilus sp. nov., a cellulasefree endo-xylanase-producing streptomycete. Int. J. Syst. Evol. Microbiol 50: 505–509
Kim SB, Falconer C, Williams E & Goodfellow M (1998) Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int. J. Syst. Bacteriol 48: 59–68
Kovach WL (1988) Multivariate methods of analysing paleoecological data. In DiMichelle WA & Wing SL (Eds) The Paleontological Society Special Publications. Methods and Application of Plant Paleontology (pp 72–104)
Küster E (1959) Outline of a comparative study of criteria used in characterization of the actinomycetes. Int. Bull. Bacteriol. Nomencl. Taxon 9: 97–104
Küster E & Williams ST (1964) Selection of media for isolation of streptomycetes. Nature 202: 928–929
Labeda DP (1993) DNA relatedness among strains of the Streptomyces lavendulae phenotypic cluster group. Int. J. Syst. Bacteriol. 43: 822–825
Labeda DP (1998) DNA relatedness among the Streptomyces fulvissimus and Streptomyces griseoviridis phenotypic cluster groups. Int. J. Syst. Bacteriol. 48: 829–832
Labeda DP & Lyons AJ (1991) The Streptomyces violaceusniger cluster is heterogeneous in DNA relatedness among strains: Emendation of the descriptions of Streptomyces violaceusniger and Streptomyces hygroscopicus. Int. J. Syst. Bacteriol. 41: 398–401
Labeda DP & Lyons AJ (1992) DNA relatedness among strains of the sweet potato pathogen Streptomyces ipomoea (Person and Martin 1940) Waksman and Henrici 1948. Appl. Environ. Microbiol. 58: 532–535
Li L, Kato C & Horikoshi K (1999) Bacterial diversity in deep sea sediments from different depths. Biodiver. Conserv. 8: 659–677
MacNaughton SJ & O'Donnell AG (1994) Tuberculostearic acid as a means of estimating the recovery (using dispersal and differential centrifugation) of actinomycetes from soil. J. Microbiol. Meth. 20: 69–77
Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ & Woese CR (1997) The Ribosomal Database Project (RDP). Nucleic Acid Res. 25: 109–111
Manfio GP (1995) Towards Minimal Standards for the Description of Streptomyces species. Ph.D. thesis. University of Newcastle, Newcastle upon Tyne, UK
Manfio GP, Zakrzewska-Czerwinska J, Atalan E & Goodfellow M (1995) Towards minimal standards for the description of Streptomyces species. Biotechnologia 7–8: 242–253
Marilley L & Aragno M (1999) Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Applied Soil Ecology 13: 127–136
Miller JJ, Liljeroth E, Henken G & van Veen JA (1990) Fluctuations in the fluorescent pseudomonad and actinomycete populations of rhizosphere and rhizoplane during the growth of spring wheat. Can. J. Microbiol. 36: 254–258
National Bureau of Standards (1964) The ISCC-NBS Colour Manual Charts Illustrated with Centroid Colours. Supplement to NBS, Circular 553
Rothrock CS & Gottlieb D (1984) Role of antibiosis in antagonism of Streptomyces hygroscopicus var. geldanus to Rhizoctonia solani in soil. Can. J. Microbiol. 30: 1440–1447
Saitou N & Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425
Sanglier JJ, Whitehead D, Saddler GS, Ferguson EV & Goodfellow M(1992) Pyrolysis mass spectrometry as a method for the classi-fication, identification and selection of actinomycetes. Gene 115: 235–242
Sardi P, Saracchi M, Quaroni B, Petrolini B, Borgonovi & Nesli S (1992) Isolation of endophytic Streptomyces strains from surface-sterilised roots. Appl. Environ. Microbiol. 58: 2691–2698
Sembiring L (2000) Selective Isolation and Characterisation of Streptomycetes Associated with the Rhizosphere of the Tropical Legume Paraserianthes falcataria (L) Nielsen. Ph.D. thesis. University of Newcastle, Newcastle upon Tyne, UK
Sembiring L, Goodfellow M & Ward AC (2000) The Streptomyces violaceusniger clade: a home for streptomycetes producing rugose spores. Int. J. Syst. Evol. Microbiol. (in press)
Shirling EB & Gottlieb D (1966) Methods for characterisation of Streptomyces species. Int. J. Syst. Bacteriol. 16: 313–340
Smith J, Putnam A & Nair M (1990) In vitro control of Fusarium diseases of Asparagus officinalis L. with a Streptomyces or its polyene antibiotic, faerifungin. J. Agric. Food. Chem. 38: 1729–1733
Sneath PHA & Sokal RR (1973) Numerical Taxonomy: The Principles and Practice of Numerical Classification. W.H. Freeman, Baltimore
Sokal RR & Michener CD (1958) A statistical method for evaluating systematic relationships. Kan. Univ. Sci. Bull. 38: 1409–1438
Staneck JL & Roberts GD (1974) Simplified approach to identi-fication of aerobic actinomycetes by thin-layer chromatography. Appl. Microbiol. 28: 225–231
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F & Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tool. Nucleic Acid Res. 24: 4876–4882
Trejo-Estrada SR, Paszczynski A & Crawford DL (1998a) Antibiotics and enzymes produced by the biocontrol agent Streptomyces violaceusniger YCED-9. J. Ind. Microbiol. Biotech. 21: 81–90
Trejo-Estrada SR, Sepulveda SR & Crawford DL (1998b) In vitro and in vivo antagonism of Streptomyces violaceusniger YCED9 against fungal pathogens of turfgrass. Wrld. J. Microbiol. Biotech. 14: 865–872
Trujillo M & Goodfellow M (1997) Polyphasic taxonomic study of clinically significant actinomadurae including the description of Actinomadura latina sp. nov. Zbl. Bakt. 285: 212–233
Upton M (1994) Ecological Approaches to the Selective Isolation of Actinomycetes for Bioactivity Screening. Ph.D. thesis, University of Newcastle, Newcastle upon Tyne, UK
Vickers JC & Williams ST (1987) An assessment of plate inoculation procedures for the enumeration and isolation of soil streptomycetes. Microbios Lett. 35: 113–117
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 (pp 553–561). Academic Press, London
Waksman SA & Curtis RE (1916) The actinomyces of the soil. Soil Sci. 1: 99–134
Watson ET & Williams ST (1974) Studies on the ecology of actinomycetes in soil. VII. Actinomycetes in a coastal belt. Soil Biol. Biochem. 6: 43–52
Wayne LG, Brenner DJ, Colwell RR & 9 other authors (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463–464
Williams ST & Vickers JC (1988) Detection of actinomycetes in the natural environment – problems and perspectives. In: Okami Y, Beppu T & Ogawara H (Eds) Biology of Actinomycetes '88 (pp 265–270). Japan Scientific Societies Press, Tokyo
Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA & Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J. Gen. Microbiol. 129: 1743–1813
Williams ST, Lanning S & Wellington EMH (1984) Ecology of actinomycetes. In: Goodfellow M, Mordarski M & Williams ST (Eds) The Biology of the Actinomycetes (pp 481–528). Academic Press, London
You MP, Sivasithamparam K & Kurteboke DI (1996) Actinomycetes in organic mulch used in avocado plantations and their ability to suppress Phytophthera cinnamoni. Biol. Fertil. Soils 22: 237–242
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Sembiring, L., Ward, A.C. & Goodfellow, M. Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria . Antonie Van Leeuwenhoek 78, 353–366 (2000). https://doi.org/10.1023/A:1010226515202
Issue Date:
DOI: https://doi.org/10.1023/A:1010226515202