A probability matrix for identification of some Streptomycetes.
TL;DR: The character state data obtained for clusters defined at the 77% SSM similarity level in the phenetic numerical classification described by Williams et al. (1983) were used to construct a probabilistic identification matrix and showed that the matrix was theoretically sound.
Abstract: The character state data obtained for clusters defined at the 77.5% SSM similarity level in the phenetic numerical classification described by Williams et al. (1983) were used to construct a probabilistic identification matrix. The 23 phena included were the major clusters (19 Streptomyces, 2 Streptoverticillium and 'Nocardia' mediterranea) and one minor cluster (Streptomyces fradiae). The characters most diagnostic for these clusters were selected using Sneath's CHARSEP and DIACHAR programs. The resulting matrix consisted of 41 characters x 23 phena. Identification scores, determined by Sneath's MATIDEN program were used to evaluate the matrix. Theoretical assessment was achieved by determination of the cluster overlap (OVERMAT), the identification scores for the Hypothetical Medium Organism of each cluster (MOSTTYP), and the scores for randomly selected cluster representatives using the classification data of Williams et al. (1983). The matrix was evaluated practically by the independent re-determination of the characters for the same cluster representatives, which also provided a measure of test error. Finally it was used to identify unknown isolates from a range of habitats. The results showed that the matrix was theoretically sound. Test error was within acceptable limits and did not distort identifications. Of the unknown isolates, 80% were clearly identified with a cluster. It is suggested that the matrix could form the basis for a more objective identification and grouping of the large number of Streptomyces species which have been described.
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TL;DR: The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangia, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while IntrasporangIUM, Nocardioides and Streptoverticillium remained as distinct genera in the familyStreptomycetaceae.
Abstract: Four hundred and seventy-five strains, which included 394 type cultures of Streptomyces and representatives of 14 other actinomycete genera, were studied. Overall similarities of these strains for 139 unit characters were determined by the SSM and SJ coefficients and clustering by the UPGMA algorithm. Test error and overlap between the phena defined were within acceptable limits. Cluster-groups were defined by the SSM coefficient at the 70.1% similarity (S) level and by the SJ coefficient at the 50% S-level. Clusters were distinguished at the 77.5% SSM and 63% SJ S-levels. Groupings obtained with the two coefficients were generally similar, but there were some changes in the definition and membership of cluster-groups and clusters. The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while Intrasporangium, Nocardioides and Streptoverticillium remained as distinct genera in the family Streptomycetaceae. Nocardiopsis dassonvillei also showed strong phenetic affinity to Streptomyces, despite its chemotaxonomic differences. Actinomadura sensu stricto was phenetically distinguishable from Streptomyces and 'Nocardia' mediterranea was recognized as a taxon distinct from both these genera and from Nocardia sensu stricto. Most of the Streptomyces type cultures fell into one large cluster-group. At the 77.5% SSM S-level, they were recovered in 19 major and 40 minor clusters, with 18 strains recovered as single member clusters. The status of the latter as species was therefore confirmed. Most of the minor clusters, consisting of two to five strains, can also be regarded as species. The major clusters varied in size (from 6 to 71 strains) and in there homogeneity. Therefore, it is suggested that they be regarded as species-groups until further information is available. The results provide a basis for the reduction of the large number of Streptomyces species which have been described. They also demonstrate that the previous use of a limited number of subjectively chosen characters to define species-groups or species has resulted in artificial classifications.
1,215 citations
TL;DR: Seven soil samples and seven groundwater samples from a site contaminated with fuel-oil were investigated using several chemical and microbiological techniques and numbers of methylotrophic, denitrifying, sulphate reducing, anaerobic, and hydrocarbon degrading bacteria were found.
Abstract: Seven soil samples and seven groundwater samples from a site contaminated with fuel-oil were investigated using several chemical and microbiological techniques. In soil samples, 500 to 7,500 mg/kg of total hydrocarbons were found. These samples contained no n-alkanes but iso- and branched chain alkanes. No polychlorinated biphenyls could be detected. Microbiological investigations included estimations of total cell counts, viable cell counts on different media, and numbers of methylotrophic, denitrifying, sulphate reducing, anaerobic (with the exception of methanogenic organisms), and hydrocarbon degrading bacteria. Viable and hydrocarbon degrading bacteria were found in all samples. A total of 1,366 pure cultures was characterized morphologically and physiologically and identified by numerical identification using a data base of more than 4,000 reference strains. Groundwater samples were dominated by gram-negative bacteria of the generaPseudomonas, Comamonas, Alcaligenes, andAcinetobacter, which were also found in soil samples. In addition, more grampositive bacteria belonging to the generaArthrobacter, Nocardia, andBacillus could be isolated from soil samples.
414 citations
TL;DR: Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture.
Abstract: Molecular techniques were employed to document the microbial diversity associated with the marine sponge Rhopaloeides odorabile. The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rDNA analysis. The community structure was extremely diverse with representatives of the Actinobacteria, low-G+C gram-positive bacteria, the beta- and gamma-subdivisions of the Proteobacteria, Cytophaga/Flavobacterium, green sulfur bacteria, green nonsulfur bacteria, planctomycetes, and other sequence types with no known close relatives. FISH probes revealed the spatial location of these bacteria within the sponge tissue, in some cases suggesting possible symbiotic functions. The high proportion of 16S rRNA sequences derived from novel actinomycetes is good evidence for the presence of an indigenous marine actinomycete assemblage in R. odorabile. High microbial diversity was inferred from low duplication of clones in a library with 70 representatives. Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture. Novel media incorporating sponge extracts were used to isolate bacteria not previously recovered from this sponge.
395 citations
Additional excerpts
...erol-asparagine agar (49), actinomycete isolation agar (Difco), yeast malt extract...
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TL;DR: This review addresses the current status of streptomycete taxonomy, highlighting the value of a polyphasic approach that utilizes genotypic and phenotypic traits for the delimitation of species within the genus.
Abstract: The streptomycetes, producers of more than half of the 10,000 documented bioactive compounds, have offered over 50 years of interest to industry and academia. Despite this, their taxonomy remains somewhat confused and the definition of species is unresolved due to the variety of morphological, cultural, physiological and biochemical characteristics that are observed at both the inter- and the intraspecies level. This review addresses the current status of streptomycete taxonomy, highlighting the value of a polyphasic approach that utilizes genotypic and phenotypic traits for the delimitation of species within the genus.
369 citations
Cites background or methods from "A probability matrix for identifica..."
...Williams et al. (1983a), conducted a numerical taxonomic study of streptomycetes and related genera with cell wall 798 International Journal of Systematic and Evolutionary Microbiology 51 Downloaded from www.microbiologyresearch.org by IP: 54.191.40.80 On: Fri, 07 Jul 2017 01:49:04 chemotype I…...
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...Overall the group does show general antimicrobial activity ; 39% produce compounds with antifungal activity, 32% produce compounds with anti-Gram-positive activity and 10% are active against Gram-negative micro-organisms (Williams et al., 1983b)....
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...…developed by Fulton et al. (1995), MseI fingerprints of rRNA operons (RiDiTS) were used to group 98 named streptomycete strains that included members of the phenotypic cluster groups A (subclusters 1–41) and F (subclusters 55–67) according to Williams et al. (1983a) and additional actinomycetes....
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...…relationships within the family Streptomycetaceae and resulted in the reclassification of six additional genera (Actinopycnidium, Actinosporangium, Chainia, Elytrosporangium, Kitasatoa and Microellobosporia) to the Streptomyces genus (Williams et al., 1983a; Goodfellow et al., 1986a–d)....
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...Williams et al. (1983a) used a numerical taxonomic approach based on phenetic characters which resulted in a reduction of the numbers of described Streptomyces species, the 1989 edition of Bergey’s Manual describes 142 species (Williams et al., 1989), in contrast to 463 species described in the…...
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TL;DR: The ecological role of actinomycetes in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate marine strains for search and discovery of new drugs, but continued development of improved cultivation methods and molecular technologies for accessing the marine environment promises to provide access to this significant new source of chemical diversity.
331 citations
References
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Book•
01 Jun 1973
5,901 citations
TL;DR: A review of the currently valid names of bacteria is conducted with the object of retaining only names for those taxa which were adequately described and cultivable, for which there was a Type, Neotype, or Reference strain available.
Abstract: At the meeting of the Judicial Commission
of the ICSB held in Jerusalem on the 29th
March, 1973 an Ad Hoc Committee was
appointed (Minute 22) to organize a review of
the currently valid names of bacteria with the
object of retaining only names for those taxa
which were adequately described and, if
cultivable, for which there was a Type, Neotype
or Reference strain available; to compile these
names under the title of Approved Lists of
Bacterial Names and to publish the lists in the
International Journal of Systematic Bacteriology,
to become effective on January 1, 1980...
2,458 citations
TL;DR: The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangia, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while IntrasporangIUM, Nocardioides and Streptoverticillium remained as distinct genera in the familyStreptomycetaceae.
Abstract: Four hundred and seventy-five strains, which included 394 type cultures of Streptomyces and representatives of 14 other actinomycete genera, were studied. Overall similarities of these strains for 139 unit characters were determined by the SSM and SJ coefficients and clustering by the UPGMA algorithm. Test error and overlap between the phena defined were within acceptable limits. Cluster-groups were defined by the SSM coefficient at the 70.1% similarity (S) level and by the SJ coefficient at the 50% S-level. Clusters were distinguished at the 77.5% SSM and 63% SJ S-levels. Groupings obtained with the two coefficients were generally similar, but there were some changes in the definition and membership of cluster-groups and clusters. The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while Intrasporangium, Nocardioides and Streptoverticillium remained as distinct genera in the family Streptomycetaceae. Nocardiopsis dassonvillei also showed strong phenetic affinity to Streptomyces, despite its chemotaxonomic differences. Actinomadura sensu stricto was phenetically distinguishable from Streptomyces and 'Nocardia' mediterranea was recognized as a taxon distinct from both these genera and from Nocardia sensu stricto. Most of the Streptomyces type cultures fell into one large cluster-group. At the 77.5% SSM S-level, they were recovered in 19 major and 40 minor clusters, with 18 strains recovered as single member clusters. The status of the latter as species was therefore confirmed. Most of the minor clusters, consisting of two to five strains, can also be regarded as species. The major clusters varied in size (from 6 to 71 strains) and in there homogeneity. Therefore, it is suggested that they be regarded as species-groups until further information is available. The results provide a basis for the reduction of the large number of Streptomyces species which have been described. They also demonstrate that the previous use of a limited number of subjectively chosen characters to define species-groups or species has resulted in artificial classifications.
1,215 citations
TL;DR: Taylor and Decker (1947) showed that various plant pathogenic actinomycetes could be separated from nonpathogenic isolates on the basis of their reactions on carbon compounds, as well as other criteria.
Abstract: Attention has recently been focused on the identification of the actinomycetes because of the ability of some members of this group to produce antibiotics. The determinative procedures now in use are based primarily on morphology, pigmentation, and growth characteristics on media composed of complex natural substrates. With such media one can often observe a variety of pigments and colony types produced by the same organism. In inexperienced hands, this leads to difficulties in interpretation of results, and one is often forced to designate a particular isolate as one of several species rather than one distinct species. To aid in the identification of a group of antibiotic-producing actinomycetes under study, an intensive investigation of their utilization of carbon compounds in chemically defined media was undertaken. Prior to the current investigations a number of workers had studied the utilization of carbon compounds by some species in this group. Beijerinck (1900), Sames (1900), Caminiti (1913), Fousek (cited by Waksman, 1919), Krainsky (1914), and Gray and Thornton (1928) each tested a few materials and found that various members of this group could grow on media containing different carbon sources. More extensive tests on carbon compounds were made by Salzmann (1907), Munter (1913), and Waksman (1919). Recently Taylor and Decker (1947) showed that various plant pathogenic actinomycetes could be separated from nonpathogenic isolates on the basis of their reactions on carbon compounds, as well as other criteria. The studies of Cochrane (1947) also indicated that different species in the genus Actinomyces might be separated on the basis of acid production.
773 citations
TL;DR: Type specimens (strains) of the 100 species for which emended characterizations have been completed, are now deposited in the American Type Culture Collection and the Centraalbureau voor Schimmelcultures for distribution to other culture collections of the world as reference cultures.
Abstract: Confusion exists in taxonomy and nomenclature of the genus Streptomyces (Actinomycetales) and related genera because of inadequate descriptions for the species or lack of uniformity in criteria and methods for their characterization. More than 40 collaborating laboratories representing 18 nations are joined in an international effort to assemble and redescribe authentic type strains or neotype strains for the named species in the genera Streptomyces and Streptoverticillium. Uniform descriptive criteria and standardized methods and media, developed under the supervision of the Subcommittee on Taxonomy of Actinomycetes, American Society for Microbiology and the Subcommittee on Taxonomy of Actinomycetes of the International Committee on Bacteriological Nomenclature, have been officially adopted for this purpose. The type strain for each species (identified only by code number) is studied under these standard procedures in cooperating laboratories in 3 different nations. Data returned by these collaborators, including photo micrographs and electron micrographs, were used to prepare the illustrated standardized emendations to descriptions for 100 Streptomyces (Actinomyces) or Streptoverticillium species included in this report. Emendations to descriptions for additional species will be included in reports to follow. Type specimens (strains) of the 100 species for which emended characterizations have been completed, are now deposited in the American Type Culture Collection and the Centraalbureau voor Schimmelcultures for distribution to other culture collections of the world as reference cultures.
338 citations