Heterogeneity of ribosomal proteins among Streptomyces species and its application to identification

The ribosomal proteins from 11 Streptomyces strains representing various numerical taxonomic clusters were compared by two-dimensional PAGE. The protein patterns were specific for each species and were unaffected by acridine dye treatment, suggesting genetic stability of ribosomal proteins. An attempt was made to identify one strain of Streptomyces by both traditional taxonomic methods and analysis of the ribosomal protein patterns. Both methods identified the strain as Streptomyces lavendulae, and protein pattern analysis also showed that Streptomyces avidinii was closely related to this species. The practical application of ribosomal protein patterns in Streptomyces taxonomy was therefore demonstrated.     

Polyacrylamide gel electrophoresis analysis of ribosomal protein: a new approach for actinomycete taxonomy.

The ribosomal (r)-proteins from eleven Streptomyces strains representing various numerical taxonomic clusters were compared by two-dimensional polyacrylamide-gel electrophoresis (2D-PAGE). The protein patterns were specific for each species. An attempt was made to identify one strain of Streptomyces by both traditional taxonomic methods and 2D-PAGE analysis of the r-protein patterns. Both methods identified the strain as Streptomyces lavendulae, and protein pattern analysis also showed that S. griseolavendus was a variant of S. lavendulae. Actinomycete r-protein AT-L30 exhibited electrophoretic mobility that is specific for each genus. On the basis of this observation, we analyzed AT-L30 r-proteins from numerous strains of species belonging to the genera Actinomadura, Microtetraspora, Streptosporangium, Nocardia, Rhodococcus and mycolate-less wall chemotype-IV actinomycetes. The results strongly supported the conclusions of previous work and thus proved the efficacy of r-protein analysis as a novel approach for taxonomy of actinomycetes.     

链霉菌的rep-PCR基因指纹分析

对重复片段PCR(repPCR)基因指纹分析应用于链霉菌分子分型进行研究,结果表明repPCR基因指纹分析具有分辨率高、稳定、重现性好、简便易行等特点,在一定程度上与16S rDNA 序列比较结果相一致,是一种快速而有效的DNA指纹技术,能反映出链霉菌种和菌株水平的基因型、系统发育和分类学关系,可应用于种及以下水平的分类和快速鉴定,尤其适用于分析大量的菌株或分离株。     

Phylogenetic study of the species within the family Streptomycetaceae

Species of the genus Streptomyces, which constitute the vast majority of taxa within the family Streptomycetaceae, are a predominant component of the microbial population in soils throughout the world and have been the subject of extensive isolation and screening efforts over the years because they are a major source of commercially and medically important secondary metabolites. Taxonomic characterization of Streptomyces strains has been a challenge due to the large number of described species, greater than any other microbial genus, resulting from academic and industrial activities. The methods used for characterization have evolved through several phases over the years from those based largely on morphological observations, to subsequent classifications based on numerical taxonomic analyses of standardized sets of phenotypic characters and, most recently, to the use of molecular phylogenetic analyses of gene sequences. The present phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters. Many of the observed clades are consistent with earlier morphological and numerical taxonomic studies, but it is apparent that insufficient variation is present in the 16S rRNA gene sequence within the species of this family to permit bootstrap-supported resolution of relationships between many of the individual clusters.     

Numerical phenetic classification of clinically significant aerobic sporoactinomycetes and related organisms

Clinically significant aerobic sporoactinomycetes, notably agents of mycetoma, were examined for a balanced set of unit characters and the resultant data analysed using standard numerical taxonomic procedures. All save two of the one hundred and seventy three tested strains were assigned to three multimembered cluster-groups, which encompassed sixteen major (4–7 strains), ten minor (2–3 strains) and forty single membered clusters, in an analysis based on the simple matching coefficient and unweighted pair group method with arithmetic averages algorithm. The three cluster-groups were equated with the genus Actinomadura (including Actinocorallia and Streptomyces somaliensis strains), and the genera Nocardiopsis and Streptomyces, and Thermobifida and Thermomonospora, respectively. In a corresponding principal co-ordinates analysis four multimembered groups corresponding to the genera Actinomadura, Nocardiopsis, Streptomyces, and Thermobifida and Thermomonospora were recognised. The causal agents of actinomycetoma were not only assigned to established taxa, notably, to Actinomadura latina, Actinomadura madurae, Actinomadura pelletieri and Streptomyces somaliensis, but also to additional centres of taxonomic variation which were equated with the rank of species. Most of the streptomycetes isolated from clinical material were assigned to clusters equated with the species Streptomyces albus and Streptomyces anulatus. The numerical taxonomic data were used to generate a frequency matrix designed to facilitate the identification of clinically significant Actinomadura, Nocardiopsis and Streptomyces strains to the species level; rapid enzyme tests accounted for eleven out of the twenty-one diagnostic tests. This revised version was published online in June 2006 with corrections to the Cover Date.     

Characterization and comparative studies ofStreptomyces sp. 246 producing a cytostatic antibiotic

The authors submit the results of taxonomic comparative studies of the strainStreptomyces sp. 246, which produces a polypeptide type cytostatic antibiotic. Strain 246 is characterized by tufts of straight sporophores of the “Rectus-Flexibilis” type, smooth spores arranged in chains (over 10 spores in a chain), yellow aerial and substrate mycelium, a negative test for melanin synthesis, utilization of glucose, arabinose, xylose, mannitol, fructose and rhamnose and inability to grow on sucrose, inositol, raffinose and cellulose. The taxonomic characters ofStreptomyces sp. 246 are identical with those of the strainStreptomyces chrysomallus JA 1449-1 and differ manifestly from those ofStreptomyces antibioticus strains (producing actinomycins, antimycin A and oleandomycin), fromStreptomyces cinereoruber ETH 7451 (producing rhodomycin) and from the strainStreptomyces sp. 4127 (producing actinomycin D).     

THE USE OF PROTEIN-SEROLOGICAL CHARACTERS IN THE SYSTEMATICS OF THE FAMILY OLEACEAE

Serological analyses of soluble seed proteins of 12 representative taxa of the family Oleaceae by the techniques of Ouchterlony, presaturation, and immunoelectrophoresis (IEP) yielded complementary taxonomic information. Ouchterlony reactions differentiated among protein extracts of three species, and the combined serological techniques permitted the detection of protein differences of respective taxa of the two subfamilies Jasminoideae and Oleoideae. IEP enabled the separation of the 12 taxa investigated and the distribution into the two subfamilies, by the differential electrophoretic positions of precipitin arcs, which were consistent with members of each of the two subfamilies. Presaturation data, when analyzed by two cluster analysis computer programs, were taxonomically significant. One program, which calculated amalgamation distances from the presaturation data, clustered the 12 taxa into subgroups which corresponded to tribes, and within two groups, which corresponded to two subfamilies. A monothetic clustering program provided theoretical information on evolution of taxa within the family Oleaceae based on serological correspondences obtained from the presaturation data; the subfamily Jasminoideae was found phylogenetically primitive and the subfamily Oleoideae was advanced. Additionally, IEP data supported those theories suggesting that taxa of the Oleoideae evolved from taxa of the Jasminoideae. The groupings of taxa and different information obtained from the cluster analyses of data and all serological techniques reinforced each other, as well as contemporary taxonomic and phylogenetic treatments of taxa of the family Oleaceae. This research demonstrated the taxonomic value of protein-serological data, particularly as applied to the taxonomy of the Oleaceae.     

Molecular and phenotypic comparison of phaeochromycin-producing strains of <Emphasis Type="Italic">Streptomyces phaeochromogenes</Emphasis> and <Emphasis Type="Italic">Streptomyces ederensis</Emphasis>

Streptomyces strain LL-P018 produces the phaeochromycins, novel anti-inflammatory polyketides. This organism was identified as a strain of Streptomyces phaeochromogenes by physiological and genetic taxonomic analysis. In order to gain greater taxonomic perspective, LL-P018 was compared to related strains from major culture collections by 16S rRNA gene sequence, ribotype, HPLC-MS metabolite profile, and rpoB sequence. Using BioNumerics software, genetic and chemical fingerprint data were integrated via multivariate cluster analysis into a single, robust comparison. Based upon this analysis, strain LL-P018 is very closely related to the type strains of both S. phaeochromogenes and Streptomyces ederensis, indicating that these two types may in fact represent a single species. This novel comparative multi-cluster analysis is most useful for clarifying relationships between closely related species.     

The biodiversity of actinomycetes in Lake Baikal

The taxonomic analysis of 107 actinomycete strains isolated from the bottom sediments and water of Lake Baikal showed that most of the water isolates belong to the genus Streptomyces and most of the sediment isolates belong to the genus Micromonospora. In the sediments, the number of actinomycetes increased with depth (down to 200 m). Eight Streptomyces isolates were identified to a species level.     

DNA-DNA hybridization in the systematics of Streptomyces.

The DNA relatedness among strains in several different phenotypically defined Streptomyces species clusters was evaluated. It was found that the data from DNA-relatedness studies do not necessarily agree with the clustering generated using numerical taxonomic techniques. A study of the morphologically heterogeneous 'S. cyaneus' cluster showed that morphological criteria traditionally used to classify and identify Streptomyces species still have value, since strains in DNA-relatedness cluster groups were also similar morphologically (i.e., they had similar spore color, surface properties, and sporophore morphology). An evaluation of DNA relatedness among strains in the S. violaceusniger and S. lavendulae clusters indicated that, if anything, the genus is underspeciated, based on the number of single-member clusters observed. A study of strains of the sweet potato pathogen, S. ipomoea, collected in various locations in the United States and Japan indicated, not surprisingly, that all of the strains belong to the same species.     

A serological study of the systematics of the Juglandaceae

The purpose of this investigation was to obtain serological data useful in determining taxonomic relationships of the walnut family (Juglandaceae). Antisera were elicited from seed proteins of Juglans nigra and Carya illinoensis and subsequently tested against various taxa of the Fagales and the Anacardiaceae using the Ouchterlony double diffusion technique. Serological correspondence was observed to be: (a) very strong among members of the Juglandaceae; (b) moderate with members of the Fagales; and (c) weak with members of the Anacardiaceae. These results support Takhtajan and Cronquist who place the Juglandaceae close to the Fagales.     

Conversion of Kepone by Methanosarcina thermophila

Abstract Amino acid sequences of protease inhibitors ( Streptomyces subtilisin inhibitor-like proteins) widely distributed in Streptomyces were compared to clarify the taxonomic status of three strains of Streptomyces spp., S. coelicolor A3(2), S. lividans 66 and S. coelicolor Müller, which are closely related by conventional taxonomical procedures. The sequence comparison indicated that S. coelicolor A3(2) is distinct from the type strain S. coelicolor Müller, but belongs to the same taxon as S. lividans 66.     

Classification of acidophilic, neutrotolerant and neutrophilic streptomycetes by nucleotide sequencing of 5S ribosomal RNA.

Complete 5S ribosomal RNA sequences were obtained for four acidophilic actinomycetes, seven neutrophilic streptomycetes and a strain of Streptoverticillium baldaccii. All of the organisms contained RNAs belonging to the 120 nucleotide type. An evolutionary tree was generated after combining the test data with results from similar studies on representative Gram-positive bacteria. The acidophilic, neutrotolerant and neutrophilic actinomycetes were recovered in a distinct cluster that was equated with the genus Streptomyces. The sequence data support the view that the genera Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be considered as synonyms of the genus Streptomyces. The recovery of the Streptoverticillium baldaccii strain on the fringe of the Streptomyces cluster is also consistent with current trends in the taxonomy of these organisms. Further work is needed to determine the taxonomic status of the two streptomycete subgroups that comprised the streptomycete cluster.     

防治哈密瓜疫霉病抗生素产生菌的鉴定

从乌鲁木齐郊区土壤中分离到一株拮抗性放线菌,编号为Ｍ＿２。通过形态、培养特征、生理生化特性及细胞壁组分分析等研究,鉴定为链霉菌属的一个新亚种,定名为萨拉赛链霉菌乌鲁木齐亚种（Ｓｔｒｅｐｔｏｍｙｃｅｓｓａｒａｃｃｔｉｃｕｓｖａｒ．Ｕｒｕｍｕｑｉｅｎｓｅｎ．Ｖａｒ）。     

Structure of anionic carbohydrate-containing cell wall polymers in several representatives of the order actinomycetales

A new teichoic acid was identified in the cell walls of Streptomyces griseoviridis VKM Ac-622T, Streptomyces sp. VKM Ac-2091, and Actinoplanes campanulata VKM Ac-1319T. The polymer is poly(glycosylglycerol phosphate). The repeating units of the polymer, alpha-galactopyranosyl-(1-->3)-2-acetamido-2-deoxy-beta-galactopyran+ ++ osyl-(1-->1)-glycerols, are in phosphodiester linkage at C-3 of glycerol and C-6 of galactose. The structures of cell wall teichoic acids in the strains Streptomyces chryseus VKM Ac-200T and "Streptomyces subflavus" VKM Ac-484 similar in morphology and growth characteristics are also identical: 1,5-poly(ribitol phosphate) substituted at C-4(2) by 2-acetamido-2-deoxy-beta-glucopyranosyl residues and 1,3-poly(glycerol phosphate). The taxonomic aspects of these results are discussed.     

Classification of novel soil streptomycetes as Streptomyces aureus sp. nov., Streptomyces laceyi sp. nov. and Streptomyces sanglieri sp. nov

The taxonomic positions of soil isolates known as Streptomyces groups A, B and C were clarified. Comparative 16S rDNA sequence studies indicated that representatives of all three taxa formed distinct phyletic lines within the Streptomyces tree though the group A strains were shown to be related to Streptomyces griseus and associated validly described species. The taxonomic integrity of all three groups was highlighted by DNA:DNA relatedness and ribotype data though the group A strains encompassed a higher degree of genetic variation than the group B and C strains. In light of these and earlier phenotypic data it is proposed that Streptomyces groups A, B and C be given species status as Streptomyces sanglieri sp. nov., Streptomyces aureus sp. nov. and Streptomyces laceyi sp. nov., respectively. This revised version was published online in June 2006 with corrections to the Cover Date.     

Streptomyces oceani sp. nov., a new obligate marine actinomycete isolated from a deep-sea sample of seep authigenic carbonate nodule in South China Sea

A novel aerobic actinomycete strain, designated as SCSIO 02100(T), was isolated from a deep sea sediment sample collected from Northern South China Sea at a depth of 578 m. This isolate requires sea water or a sodium-supplemented medium for growth. BLAST searches based on the almost full length of the 16S rRNA gene sequence, showed that strain SCSIO 02100(T) had the highest similarities with Streptomyces armeniacus (JCM 3070(T)) (97.1 %). Phylogenetic trees reconstructed on the basis of 16S rRNA gene sequences revealed that strain SCSIO 02100(T) formed a distinct lineage with S. nanshensis SCSIO 01066(T) with 96.9 % similarity. Further analysis of the polyphasic taxonomic data, including morphological, phenotypic and chemotaxonomic properties, showed that strain SCSIO 02100(T) could be readily distinguished from the most closely related members of the genus Streptomyces. Thus, based on the polyphasic taxonomic data, a novel species, Streptomyces oceani sp. nov., is proposed, with the type strain SCSIO 02100(T) (=DSM 42043(T) = CGMCC 4.7007(T)).     

Differential Growth Inhibition of Diaporthe and Phomopsis Isolates by the Metabolic Activity of Five Actinomycetes

Fifty-five cultures derived from Diaporthe perithecia and Phomopsis pycnidia found on diverse host plant species collected at different times and sites in Vojvodina, Yugoslavia, showed distinguishing quantitative reactions to the fungistatic activity of five actinomycetes obtained as fortuitous laboratory contaminants coming from field material. Streptomyces albidoflavus , S. albus , S. diastaticus , Streptomyces sp., and Streptoverticillium sp. could be ranked by their growth-inhibitory potential, with S. albus showing the strongest, and Streptomyces sp. the lowest. The responses of the fungi varied depending on the tested actinomycetes, but two major groups could be distinguished: A, which encompased the isolates that were less affected by the proximity of the actinomycetes; and B, with those which exhibited high sensitivity in all the experiments. Group A was typically represented by Diaporthe arctii , Phomopsis longicolla, and the Phomopsis type-1 cultures from Xanthium italicum; group B was typically represented by Diaporthe/Phomopsis helianthi, Phomopsis type-2 cultures from X. italicum , and isolates from Lactuca serriola . The results obtained underscore the dissimilarities between D. arctii and D. helianthi , and corroborate the value of the physiological aspects of congeneric isolates in considering taxonomic problems in the coelomicete genus Phomopsis.     

Description of <Emphasis Type="Italic">Streptomyces neopeptinius</Emphasis> sp. nov., an actinobacterium with broad spectrum antifungal activities

A streptomycete strain producing broad-spectrum antifungal substances was taxonomically characterized. The strain, designated KNF 2047(T) (= SH-09(T) = KCTC 10586BP(T)), was found to form extensively branching aerial and substrate mycelia, and produce spiny-ornamented spores with loose spiral chains. The whole cell hydrolyzates contained major amount of LL-diaminopimelic acid. The major fatty acids of the phospholipids were saturated and branched fatty acids containing 14~17 carbons, and the major isoprenoid quinones were hexa-and octa-hydrogenated menaquinones with 9 isoprene units. The phylogenetic analysis using the 16S rRNA gene indicated that the strain belongs to the genus Streptomyces but forms an independent phyletic line. These results clearly demonstrate that strain KNF2047(T) forms a new center of taxonomic variation within Streptomyces, for which the name Streptomyces neopeptinius sp. nov. is proposed.