Family Thermomonosporaceae Research Articles

Thermomonospora catenispora sp. nov., isolated from mushroom compost.

A novel thermophilic actinomycete, designated strain 3-22-3T, was isolated from mushroom compost collected in Nanning, Guangxi Province, China. The organism produced white aerial mycelium and short spore chains of non-motile oval spores with a ridged surface on the aerial mycelium. Strain 3-22-3T contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars were galactose, glucose, madurose and ribose. Major fatty acids were iso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. MK-9(H6) and MK-9(H4) were the predominant menaquinones. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, ninhydrin-positive glycophospholipids, glycolipids and unidentified phospholipids. The G+C content of the genomic DNA was 72.5 mol%. The 16S rRNA gene sequence analysis indicated that strain 3-22-3T belonged to the genus Thermomonospora and showed the highest sequence similarity to Thermomonospora curvata DSM 43183T (96.3 %). On the 16S rRNA gene tree of closely related species and type species of all genera in the family Thermomonosporaceae, strain 3-22-3T formed a distinct phyletic line together with Thermomonospora curvata DSM 43183T. Furthermore, the chemotaxonomic characteristics of strain 3-22-3T were congruent with the description of the genus Thermomonospora, but the morphological characteristics of strain 3-22-3T were significantly different from Thermomonosporacurvata. Based on the phenotypic and phylogenetic data, strain 3-22-3T represents a novel species of the genus Thermomonospora, and the name Thermomonospora catenispora sp. nov. is proposed. The type strain is 3-22-3T (=CGMCC 4.7155T=DSM 46802T=ATCC BAA-2627T).

Actinomadura hankyongense sp. nov. Isolated From Soil of Ginseng Cultivating Field.

A Gram-positive, rod-shaped, non-spore-forming, and aerobic bacterium (Gsoil 556T) was isolated from soil of a ginseng field and subjected to its taxonomic position. Based on 16S rRNA gene sequence similarity, strain Gsoil 556T was shown to belong to the genus Actinomadura of the family Thermomonosporaceae and was closely related to A. montaniterrae CYP1-1BT (99.3%), A. nitritigenes DSM 44137T (98.7%), and A. rudentiformis HMC1T (98.5%), while it showed less than 98.4% sequence similarity to the other species of this genus. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that it is most closely related to A. rudentiformis HMC1T and A. nitritigenes DSM 44137T. The DNA G+C content was 73.1mol%. The peptidoglycan was meso-diaminopimelic acid and the whole-cell sugar contained fucose, galactose, glucose, mannose, and ribose. The predominant menaquinone (KK) was MK-9(H8) [55%] and MK-9(H6) [45%]. The major cellular fatty acids were C14:0, C16:0, C18:1 ω9c and summed feature 3 (C16:1 ω6c/C16:1 ω7c). All these data supported the affiliation of strain Gsoil 556T to the genus Actinomadura. The DNA-DNA hybridization between strain Gsoil 556T and its phylogenetically closest relatives were less than 40%. Furthermore, the results of physiological and biochemical tests enabled strain Gsoil 556T to be differentiated genotypically and phenotypically from currently known Actinomadura species. Therefore, strain Gsoil 556T represents a novel species of the genus Actinomadura, for which the name Actinomadura hankyongense sp. nov. is proposed. The type strain Gsoil 556T (=KACC 19438T=LMG 30327T).

English

An actinomycete strain T16-1 demonstrated the maximum poly (L-Lactide)-degrading activity when cultured in basal liquid medium at 50°C. According to 16S rDNA sequence analysis, chemotaxonomic and DNA-DNA hybridization revealed that strain T16-1 belong to the family Thermomonosporaceae, genus Actinomadura. On the basis of phenotypic and phylogenic data, strain T16-1 which is a novel PLA-degrading thermophilic actinomycete was identified as Actinomadura keratinilytica, but the color of its colony on ISP plates, NaCl tolerant and utilization of mannitol, raffinose and arabinose were different. Partial sequence of poly (L-lactide) depolymerase gene from strain T16-1 was demonstrated. The gene consisting of 222 amino acids was related to serine protease from Streptomyces sp. with 43 to 46% identity. Key words: Actinomadura keratinilytica, cloning, identification, poly (L-lactide).

Actinomadura rupiterrae sp. nov., isolated from cliff soil

A novel actinomycete strain, designated CS5-AC15T, was isolated from a soil sample collected from a cliff on Mara Island, Jeju, Republic of Korea, and subjected to a polyphasic taxonomic analysis. The isolate produced well-developed, yellow substrate mycelium and white aerial mycelium that differentiated into straight or flexuous chains of smooth-surfaced spores. 16S rRNA gene sequence analyses showed that the organism belonged to the family Thermomonosporaceae and formed a tight cluster with the type strain of Actinomadura oligospora (97.4 % sequence similarity). Chemotaxonomic characteristics were consistent with its assignment to the genus Actinomadura in that the isolate had meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall, madurose as the characteristic sugar, N-acetyl type of murein in the peptidoglycan, MK-9(H6) and MK-9(H8) as major menaquinones and a polar lipid profile containing diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospholipids. Mycolic acids were not detected. The predominant fatty acids were C16:0, C18:1ω9c and iso-C16:0. The DNA G+C content was 70.9 mol%. DNA relatedness of strain CS5-AC15T and A. oligospora JCM 10648T was 37.9±0.7 %. On the basis of the phenotypic, phylogenetic and DNA-DNA hybridization data, strain CS5-AC15T is assigned to a novel species of the genus Actinomadura, for which the name Actinomadura rupiterrae sp. nov. is proposed (type strain CS5-AC15T=KCTC 19559T=DSM 45251T).

Actinomadura meridiana sp. nov., isolated from mountain soil

A novel actinomycete, designated strain DLS-45(T), was isolated from soil from the surface of a rock collected from the peak of Darangshi Oreum (Small Mountain) in Jeju, Republic of Korea. Substrate mycelium was well developed, but aerial mycelium was scant on most of the media tested. Spherical to subspherical spores on the aerial mycelium were in chains that were arranged in hooks and their surfaces were warty. The combination of morphological and chemical features supported the classification of the new isolate in the genus Actinomadura. The neighbour-joining tree based on 16S rRNA gene sequences showed that the strain belonged to the family Thermomonosporaceae and formed a coherent cluster with Actinomadura pelletieri IMSNU 22169(T) (98.0% sequence similarity). The other closest relatives were Actinomadura bangladeshensis 3-46-b(3)(T) (98.2%) and Actinomadura chokoriensis 3-25-a(11)(T) (97.9%). Levels of DNA-DNA relatedness between strain DLS-45(T) and the type strains of the phylogenetic relatives were less than 17%. A battery of phenotypic, genotypic and DNA-DNA relatedness data indicated that strain DLS-45(T) represented a novel species of the genus Actinomadura, for which the name Actinomadura meridiana sp. nov. is proposed. The type strain is strain DLS-45(T) (=KCTC 19558(T)=DSM 45252(T)).

Complete genome sequence of Thermomonospora curvata type strain (B9).

Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Actinomadura scrupuli sp. nov., isolated from rock

A novel actinomycete, designated strain R-Ac121(T), was isolated from a small stone collected from an agricultural field in Jeju, Republic of Korea. The organism formed abundant vegetative mycelium that was branched and twisted. The reverse colour of colonies was brownish-yellow. Non-motile, wrinkled arthrospores were produced directly on the substrate mycelium. Aerial mycelium and sporangia were not observed. A neighbour-joining tree based on 16S rRNA gene sequences indicated that the isolate formed a distinct clade within the radiation of the family Thermomonosporaceae. The highest 16S rRNA gene sequence identity was found with the type strain of Spirillospora rubra (97.3 % sequence similarity) followed by those of Actinoallomurus purpureus (97.0 %), Actinomadura alba (96.5 %), Actinomadura fibrosa (96.5 %) and Actinomadura echinospora (96.4 %). The cell wall contained meso-diaminopimelic acid. The whole-cell sugars were rhamnose, glucose, ribose, xylose and arabinose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The major menaquinone was MK-9(H(6)) and the predominant fatty acids were iso-C(16 : 0), C(16 : 0), C(17 : 1)ω8c and 10-methyl C(17 : 0). The DNA G+C content was 71.8 mol%. The combination of morphological, chemotaxonomic and phylogenetic data clearly supports the separation of the organism from recognized species of the genus Actinomadura and related genera. On the basis of the data presented here, strain R-Ac121(T) represents a novel species of the genus Actinomadura, for which the name Actinomadura scrupuli sp. nov. is proposed. The type strain is strain R-Ac121(T) (=KCTC 19488(T) =DSM 45225(T)).

Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus sp. nov., Actinoallomurus iriomotensis sp. nov., Actinoallomurus luridus sp. nov., Actinoallomurus purpureus sp. nov. and Actinoallomurus yoronensis sp. nov.

Ten actinomycete strains that form chains of spiral or looped spores were isolated from soil and dung samples in Japan. They contained D- and L-lysine, meso-diaminopimelic acid (A2pm), D-glutamic acid and D- and L-alanine in the cell-wall peptidoglycan, madurose as a characteristic whole-cell sugar, MK-9(H6) and MK-9(H8) as the major isoprenoid quinones and iso-C16:0 as the major cellular fatty acid and showed genomic DNA G+C contents of 69-74 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolated actinomycete strains consistently formed a monophyletic cluster with Actinomadura spadix NBRC 14099T and a separate line of descent in the phylogenetic cluster of the family Thermomonosporaceae. Actinomadura spadix NBRC 14099T also contained D- and L-lysine in addition to meso-A2pm. This genetic and phenotypic evidence revealed that the actinomycete strains could be clearly differentiated from the other members of the family Thermomonosporaceae and that they warranted separate genus status. We conclude that Actinomadura spadix should be assigned the status of the type species of a new genus as Actinoallomurus spadix gen. nov., comb. nov. (type strain NBRC 14099T=ATCC 27298T=BCRC 13386T=CBS 261.72T=CIP 105479T=DSM 43459T=JCM 3146T=KCTC 9252T=NCIMB 11118T=NRRL B-16128T). Further, we conclude that the ten new isolates should be assigned to the novel species Actinoallomurus amamiensis sp. nov. (type strain TT00-28T=NBRC 103682T=KCTC 19537T), Actinoallomurus caesius sp. nov. (type strain A3015T=NBRC 103678T=KCTC 19535T), Actinoallomurus coprocola sp. nov. (type strain TT04-09T=NBRC 103688T=KCTC 19542T), Actinoallomurus fulvus sp. nov. (type strain TT99-66T=NBRC 103680T=KCTC 19536T), Actinoallomurus iriomotensis sp. nov. (type strain TT02-47T=NBRC 103685T=KCTC 19539T), Actinoallomurus luridus sp. nov. (type strain TT02-15T=NBRC 103683T=KCTC 19538T), Actinoallomurus purpureus sp. nov. (type strain TTN02-30T=NBRC 103687T=KCTC 19541T) and Actinoallomurus yoronensis sp. nov. (type strain TTN02-22T=NBRC 103686T=KCTC 19540T).

Actinomadura alba sp. nov., isolated from soil in Yunnan, China

A novel actinomycete, strain YIM 45681(T), which was isolated from soil in a suburb of Kunming, Yunnan Province, China, was subjected to phenotypic and genotypic characterization. The micro-organism, which produces short spore chains arranged in spirals on the aerial mycelium, was shown to have meso-diaminopimelic acid in the cell wall. The sugars present in whole-cell hydrolysates were ribose, xylose, galactose, madurose and glucose. The predominant menaquinones were MK-9(H(4)), MK-9(H(6)) and MK-9(H(2)). The phospholipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C(16 : 1) H, C(17 : 1) omega 8c, 10-methyl C(17 : 0) and C(16 : 0). A comparative analysis of 16S rRNA gene sequences indicated that the organism formed a distinct clade within the evolutionary radiation of the family Thermomonosporaceae, and that it was closely associated with members of the genus Actinomadura. A broad range of phenotypic and genetic data supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura alba sp. nov. is proposed, with YIM 45681(T) (=DSM 45045(T) =CCTCC AA206005(T)) as the type strain.

Actinomadura hallensis sp. nov., a novel actinomycete isolated from Mt. Halla in Korea

A novel actinomycete, strain H647-1T, which was isolated from soil of Mt. Halla, Jeju Island, Republic of Korea, was subjected to phenotypic and genotypic characterization. The organism, which produces warty spore chains arranged in hooks or spirals on the aerial mycelium, was shown to have chemotaxonomic characteristics consistent with assignment to the genus Actinomadura. A comparative analysis of 16S rRNA gene sequences indicated that the organism formed a distinct clade within the evolutionary radiation of the family Thermomonosporaceae and that it was closely associated with members of the genus Actinomadura, but possessed a 22 nt extended loop between positions 453 and 479 of the 16S rRNA gene sequence (Escherichia coli numbering). A broad range of phenotypic and genetic data supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura hallensis sp. nov. is proposed. The type strain is strain H647-1T (= IMSNU 50760T = KCTC 9992T = KCCM 42245T = NRRL B-24436T).