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  • 1
    Electronic Resource
    Electronic Resource
    Selective isolation of members of the Streptomyces violaceoruber clade from soil (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 245 (2005), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Large numbers of filamentous actinomycetes which formed distinctive red coloured colonies were isolated from three out of four composite soil samples using a medium designed to be selective for members of the Streptomyces violaceoruber clade, a taxon which includes the model organisms “Streptomyces coelicolor” A3(2) and “Streptomyces lividans” 66. The isolation medium, dextran-histidine-sodium chloride-mineral salts agar supplemented with antibacterial and antifungal antibiotics, also supported the growth of representatives of the S. violaceoruber clade. One hundred and ninety one representatives of the isolates that produced red colour colonies on the isolation medium were distributed into four colour groups based on their ability to form distinctive pigments and morphological properties typical of members of the S. violaceoruber clade, an assignment that was confirmed by corresponding 16S rRNA gene sequencing studies. The selective isolation and characterisation procedures used in the present investigation provide a practical means of determining the taxonomic diversity, geographical distribution and roles of representatives of the S. violaceoruber clade in natural habitats.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsle.2005.03.028
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  • 2
    Electronic Resource
    Electronic Resource
    Rapid identification of streptomycetes by artificial neural network analysis of pyrolysis mass spectra (1993)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 114 (1993), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract An artificial neural network was trained to distinguish between three putatively novel species of Streptomyces using normalised, scaled pyrolysis mass spectra from three representative strains of each of the taxa, each sampled in triplicate. Once trained, the artificial neural network was challenged with spectral data from the original organisms, the ‘training set’, from additional members of the putative novel taxa and from over a hundred strains representing six other actinomycete genera. All of the streptomycetes were correctly identified but many of the other actinomycetes were mis-identified. A modified network topology was developed to recognise the mass spectral patterns of the non-streptomycete strains. The resultant neural network correctly identified the streptomycetes, whereas all of the remaining actinomycetes were recognised as unknown organisms. The improved artificial neural network provides a rapid, reliable and cost-effective method of identifying members of the three target streptomycete taxa.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1993.tb06560.x
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  • 3
    Electronic Resource
    Electronic Resource
    Novel rhodococci and other mycolate actinomycetes from the deep sea (1998)
    Springer
    Antonie van Leeuwenhoek 74 (1998), S. 27-40 
    Details
    ISSN: 1572-9699
    Keywords: deep sea ; mycolata ; polyphasic taxonomy ; pyrolysis mass spectrometry ; Rhodococcus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A large number of mycolate actinomycetes have been recovered from deep-sea sediments in the NW Pacific Ocean using selective isolation methods. The isolates were putatively assigned to the genus Rhodococcus on the basis of colony characteristics and mycolic acid profiles. The diversity among these isolates and their relationship to type strains of Rhodococcus and other mycolate taxa were assessed by Curie point pyrolysis mass spectrometry (PyMS). Three major (A, C, D) and two minor (B, E) groups were defined by PyMS. Cluster A was a large group of isolates recovered from sediment in the Izu Bonin Trench (2679 m); Cluster C comprised isolates from both the Izu Bonin Trench (6390 and 6499 m) and from the Japan Trench (4418, 6048 and 6455 m). These Cluster C isolates showed close similarity to Dietzia maris and this was subsequently confirmed using molecular methods. Cluster D contained isolates recovered from a sediment taken from a depth of 1168m in Sagami Bay and were identified as members of the terrestrial species Rhodococcus luteus. Clusters B and E had close affinities with members of the genera Gordonia and Mycobacterium. The presence of Thermoactinomyces in certain of the deep-sea sediments studied was indicative of the movement of terrestrial material into the ocean depths. 16S ribosomal RNA gene sequence analyses produced excellent definition of most genera of the mycolata, and indicated that the among the deep sea isolates (1) were novel species of Corynebacterium, Gordonia and Mycobacterium, and (2) a Sea of Japan isolate the phylogenetic depth of which suggests the possibility of a new genus. Polyphasic taxonomic analysis revealed considerable diversity among the deep sea rhodococci and evidence for recently diverged species or DNA groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1001743625912
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  • 4
    Electronic Resource
    Electronic Resource
    Genomic and phenomic differentiation of Rhodococcus equi and related strains (2000)
    Springer
    Antonie van Leeuwenhoek 78 (2000), S. 331-340 
    Details
    ISSN: 1572-9699
    Keywords: Pyrolysis mass spectrometry ; Rhodococcus equi ; 16S rDNA sequencing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract 16S rDNA sequence and pyrolysis mass spectrometric analyses were carried out on representatives of Rhodococcus equi and marker strains of genera that encompass mycolic acid containing actinomycetes. The R. equi strains formed a monophyletic clade within the evolutionary radiation occupied by members of the genera Nocardia and Rhodococcus. The 16S rDNA sequence data also showed R. equi to be an heterogeneous taxon. This heterogeneity was underscored by the pyrolysis mass spectrometric data. These observations are in line with those of previous studies where similar profiles of relatedness were found between pyrolysis mass spectral data and the results of DNA:DNA pairing and numerical phenetic studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1010282616110
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  • 5
    Electronic Resource
    Electronic Resource
    Resolution of batch variations in pyrolysis mass spectrometry of bacteria by the use of artificial neural network analysis (1995)
    Springer
    Antonie van Leeuwenhoek 68 (1995), S. 253-260 
    Details
    ISSN: 1572-9699
    Keywords: pyrolysis mass spectrometry ; batch variation ; artificial neural network ; bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A simple, but stringent, three group model of bacterial interstrain identity (two cultures of the same strain ofEscherichia coli) and difference (a culture of a serologically distinct strain) was used in multiple serial weekly subcultures for five weeks to demonstrate the effect of both growth-related (phenotypic) and machine-related variation on pyrolysis mass spectra. An aliquot of serum from a single sample was included in each pyrolysis batch to distinguish machine drift from culture drift. Conventional principal component (PC) canonical variate (CV) analysis was successful within each pyrolysis batch but the variations between batches precluded the use of data from more than one batch in successful PCCV analysis. In contrast, artificial neural networks (ANNs) trained with data from one batch could be successfully used to identify groups in data from non-contemporaneous pyrolysis batches. Although the ANN method will require validation in more complex settings than this simple model, it is a promising approach to the problem of batch constraint in pyrolysis mass spectrometry.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00871823
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  • 6
    Electronic Resource
    Electronic Resource
    Biosystematics and diversity amongst novel carboxydotrophic actinomycetes (1993)
    Springer
    Antonie van Leeuwenhoek 64 (1993), S. 325-340 
    Details
    ISSN: 1572-9699
    Keywords: Carboxydotrophic actinomycetes ; numerical taxonomy ; chemical characterisation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Fifty-four carboxydotrophic actinomycetes isolated from soils and composts were compared through 119 unit characters with representative mesophilic and thermophilic streptomycetes. The data were examined using the Jaccard, pattern and simple matching coefficients and clustering achieved using the unweighted pair group method with arithmetic averages algorithm. Acceptable cophenetic correlation and test error values allowed confidence to be placed in the resultant numerical taxonomies. The carboxydotrophic actinomycetes, which were distinct from cluster-groups corresponding to the mesophilic and thermophilic streptomycetes, formed two major cluster-groups the members of which were examined for the presence of diagnostic chemical markers. All but two of the carboxydotrophic actinomycetes had a profile of chemical properties consistent with their assignment to the genusStreptomyces. Quantitative fatty acid data were examined using the SIMCA package and the two statistically significant groups obtained corresponded with the cluster-groups circumscribed in the numerical phenetic analysis. Members of the two groups were also distinguished on the basis of their phospholipid composition. The two strains that containedmeso- as opposed to LL-diaminopimelic acid in their peptidoglycan also showed a distinct chemotaxonomic profile. It was concluded that the carboxydotrophic actinomycetes form a novel and taxonomically diverse group.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00873091
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  • 7
    Electronic Resource
    Electronic Resource
    The Nocardia salmonicida clade, including descriptions of Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov. (2000)
    Springer
    Antonie van Leeuwenhoek 78 (2000), S. 367-377 
    Details
    ISSN: 1572-9699
    Keywords: Nocardial systematics ; polyphasic taxonomy ; the Nocardia salmonicida clade
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Large numbers of strains selectively isolated from soil, water and deteriorating vulcanised natural rubber pipe rings were provisionally assigned to the genus Nocardia. Twenty-eight representative isolates were found to have chemical and morphological properties typical of nocardiae. These organisms formed a monophyletic clade in the 16S rDNA tree together with Nocardia salmonicida. Three of the strains, isolates S1, W30 and R89, were distinguished from one another and from representatives of the validly described species of Nocardia using genotypic and phenotypic data. These organisms were considered to merit species status and were named Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov. respectively. Additional comparative studies are needed to resolve the finer taxonomic relationships of the remaining isolates assigned to the Nocardia salmonicida clade and to further unravel the extent of nocardial diversity in artificial and natural ecosystems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1010230632040
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  • 8
    Electronic Resource
    Electronic Resource
    Rapid characterisation of deep-sea actinomycetes for biotechnology screening programmes (2000)
    Springer
    Antonie van Leeuwenhoek 77 (2000), S. 359-367 
    Details
    ISSN: 1572-9699
    Keywords: actinomycetes ; deep-sea ; dereplication ; pyrolysis mass spectrometry ; screening
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A continual need in natural product discovery is dereplication, that is the ability to exclude previously tested microorganisms from screening programmes. Whole-cell fingerprinting techniques offer an ideal solution to this problem because of their rapidity and reproducibility, dependence on small samples, and automation. One such technique, Curie-point pyrolysis mass spectrometry (PyMS), has been deployed for the characterisation of a unique collection of actinomycetes recovered from Pacific Ocean sediments approximately 2000 to 6500 m below sea level. This paper addresses the question: to what extent are pyrogroups, defined on the basis of PyMS fingerprinting, related to classifications derived from more conventional microbial systematics? A collection of 44 randomly chosen deep-sea rhodococci were coded and subjected to a double-blind PyMS and numerical taxonomic (NT) analysis; the latter sorted the strains into clusters (taxospecies) using large sets of equally weighted phenotypic data. At the end of the experiment the codes were disclosed and the NT classification shown to generate 6 homogeneous clusters corresponding to different deep-sea sites. The matching of these clusters with the resulting pyrogroups was very high with an overall congruence of nearly 98%. Thus, PyMS characterisation is directly ascribable to the phenotypic variation being sought for biotechnology screens. Moreover, the exquisite discriminatory power of PyMS readily revealed infraspecific diversity in these industrially important bacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1002627314735
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  • 9
    Electronic Resource
    Electronic Resource
    Biosystematic studies on novel streptomycetes from soil (2000)
    Springer
    Antonie van Leeuwenhoek 77 (2000), S. 337-353 
    Details
    ISSN: 1572-9699
    Keywords: minimal standards ; phenetic classification ; selective isolation ; streptomycetes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Members of three putatively novel Streptomyces species, designated Streptomyces groups A, B and C, were repeatedly isolated from environmental samples taken from four hay meadow plots at Cockle Park Experimental Farm, Northumberland (UK). Representative isolates were found to have properties consistent with their classification in the genus Streptomyces and were recovered in three taxa using different phenotypic criteria, namely morphological and pigmentation properties, rapid enzyme tests, and whole-organism fatty acid, protein electrophoretic and pyrolysis mass-spectrometric data. The isolates were rapidly characterised as three taxonomic groups using pyrolysis mass spectrometry. The three taxa were also distinguished from one another and from validly described species of Streptomyces using rapid enzyme tests based on the fluorophores 7-amino-methylcoumarin and 4-methylumbelliferone, and computer-assisted identification procedures. The results indicate that selective isolation and rapid characterisation of streptomycetes using pyrolysis mass spectrometry provide a practical way of determining the phenotypic species diversity of streptomycetes in natural habitats. The experimental data also indicate that representative sampling of cultivable streptomycetes from soil can best be achieved using a multi-step extraction procedure coupled with the use of selective isolation procedures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1002682728517
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  • 10
    Electronic Resource
    Electronic Resource
    Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria (2000)
    Springer
    Antonie van Leeuwenhoek 78 (2000), S. 353-366 
    Details
    ISSN: 1572-9699
    Keywords: polyphasic taxonomy ; rugose-ornamented spores ; streptomycetes ; Streptomyces violaceusniger clade
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1010226515202
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