Ratchanee Mingma

Amycolatopsis samaneae sp. nov., isolated from roots of Samanea saman (Jacq.) Merr.

A novel actinomycete, designated strain RM287(T), was isolated from surface-sterilized roots of Samanea saman (Jacq.) Merr., collected from Bangkok, Thailand. The status of the novel strain was determined using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism formed a distinct phyletic line within the radiation of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain RM287(T) was most closely related to Amycolatopsis mediterranei IMSNU 20056(T) (97.4 %), A. rifamycinica DSM 46095(T) (97.2 %), A. kentuckyensis NRRL B-24129(T) (97.2 %), A. pretoriensis DSM 44654(T) (97 %) and A. australiensis DSM 44671(T) (97 %). The novel organism was found to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the dignostic diamino acid in the cell-wall peptidoglycan and arabinose and galactose as the diagnostic sugars. The major menaquinone was MK-9(H(4)). The major fatty acids were iso-C(16 : 0) iso-C(15 : 0), iso 2-OH-C(16 : 0) and iso-C(17 : 0). The DNA G+C content was 71.7 mol%. Phenotypic data clearly distinguished the novel isolate from its closest relatives. The combined genotypic and phenotypic data indicated that strain RM287(T) represented a novel species of the genus Amycolatopsis. The proposed name for this organism is Amycolatopsis samaneae sp. nov., with the type strain RM287(T) ( = TISTR 1919(T) = BCC 35842(T) = NBRC 106095(T)).

Sphaerisporangium rufum sp. nov., an endophytic actinomycete from roots of Oryza sativa L.

An endophytic actinomycete, strain R10-82(T), isolated from surface-sterilized roots of rice (Oryza sativa L.) was studied using a polyphasic approach. Strain R10-82(T) produced branching substrate mycelia and developed spherical spore vesicles on aerial hyphae containing non-motile spores. The major cellular fatty acids were iso-C16 : 0, iso-C14 : 0 and 10-methyl C17 : 0. The predominant menaquinones were MK-9, MK-9(H2), MK-9(H4) and MK-9(H6). Rhamnose, ribose, madurose, mannose and glucose were detected in whole-cell hydrolysates. The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol mannosides, hydroxylphosphatidylethanolamine and ninhydrin-positive phosphoglycolipids. These morphological and chemotaxonomic data were similar to those of the genus Sphaerisporangium. Analysis of the 16S rRNA gene sequence revealed that strain R10-82(T) was related most closely to Sphaerisporangium cinnabarinum JCM 3291(T) (98.3 % similarity). The DNA G+C content of strain R10-82(T) was 74 mol%. DNA-DNA relatedness data in combination with differences in the biochemical and physiological properties suggested that strain R10-82(T) should be classified as representing a novel species of the genus Sphaerisporangium, for which the name Sphaerisporangium rufum is proposed. The type strain is R10-82(T) ( = BCC 51287(T) = NBRC 109079(T)). An emended description of the genus Sphaerisporangium is also provided.

Microbispora thailandensis sp. nov., an actinomycete isolated from cave soil.

The taxonomic position of actinomycete strain NN276T, isolated from cave soil, was studied using the polyphasic taxonomic approach. A phylogenetic tree based on 16S ribosomal RNA (rRNA) gene sequences showed that the isolate formed a distinct evolutionary linage with the genus Microbispora, with M. mesophila JCM 3151T as its closest phylogenetic neighbor (97.9% similarity). The organism contained meso-diaminopimelic acid and the N-acetyl type of peptidoglycan. Madurose was detected in the whole-cell hydrolasate. The predominant menaquinones were MK-9(H4), MK-9(H2) and MK-9. Mycolic acids were not detected. Major phospholipids were diphosphatidylglycerol, hydroxy-phosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major cellular fatty acid was iso-C16: 0 and G+C content 70 mol%. DNA–DNA hybridization demonstrated that the isolate was distinct from M. mesophila JCM 3151T. On the basis of phenotypic and genotypic data, it is proposed that strain NN276T represents a novel species of the genus Microbispora, hence the name Microbispora thailandensis sp. nov. The type strain is strain NN276T (=BCC 41490T=NRRL B-24806T=NBRC 107569T).

Streptomyces oryzae sp. nov., an endophytic actinomycete isolated from stems of rice plant

An actinomycete strain S16–07T, isolated from surface-sterilized stems of rice plant (Oryza sativa L.), was characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences indicated affiliation of the strain belonged to the genus Streptomyces. The highest levels of sequence similarity were found with Streptomyces smyrnaeus SM3501T (97.7% similarity), S. abikoensis NBRC 13860T (97.6% similarity) and S. thermocarboxydovorans NBRC 16324T (97.5% similarity). The cell wall of strain S16–07T contained LL-diaminopimelic acid. The predominant menaquinones were MK-9(H6) and MK-9(H8). Phospholipids detected were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, hydroxy-phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine and phosphatidylinositol mannosides. The major cellular fatty acids were ai-C15:0, i-C16:0 and ai-C17:0. The G+C content of strain S16–07T was 70.4 mol%. On the basis of the phylogeny of the isolate and its differences from the most closely related species, the isolate S16–07T represents a novel species for which the name S. oryzae sp. nov. is proposed. The type strain is S16–07T (=BCC 60400T=NBRC 109761T).

Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis

The taxonomic position of a rhizosphere soil isolate, designated strain SR8.15T, was determined by using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a well-separated sub-branch within the radiation encompassing the genus Saccharopolyspora. Highest levels of 16S rRNA gene sequence similarity were found between strain SR8.15T and Saccharopolyspora shandongensis CGMCC 4.3530T (98.9%) and Saccharopolyspora spinosa DSM 44228T (98.5%). However, these strains shared low levels of DNA-DNA relatedness (<26%). Strain SR8.15T had chemical characteristics consistent with its classification in the genus Saccharopolyspora. It contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The diagnostic phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The main menaquinone was MK-9(H4). No mycolic acid was detected. The predominant cellular fatty acid was iso-C16:0. The G+C content of the genomic DNA of strain SR8.15T was 70.3 mol%. Strain SR8.15T had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from its combined genotypic and phenotypic properties that strain SR8.15T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora phatthalungensis sp. nov. is proposed. The type strain is SR8.15T (=TISTR 1921T=BCC 35844T=NRRL B-24798T).

Nonomuraea purpurea sp. nov., an actinomycete isolated from mangrove sediment

A polyphasic approach was used to verify the novel actinomycete, strain 1SM4-01T, isolated from mangrove sediment collected from Ranong Province, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism was a member of the genus Nonomuraea and was most closely related to Nonomuraea syzygii GKU 164T (98.7 % sequence similarity), Nonomuraea rhizophila YIM 67092T (98.4 %), Nonomuraea solani NEAU-Z6T (98.4 %), Nonomuraea monospora PT708T (98.3 %) and Nonomuraea thailandensis KC-061T (98.2 %). The strain produced branching aerial mycelium which differentiated into straight chains of rough-surfaced spores borne at the end of a short sporophore. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with madurose, mannose and ribose as the main sugars. MK-9(H4) was a major menaquinone of this strain. The acyl type of peptidoglycan was N-acetyl. The predominant cellular fatty acids were C17 : 1ω8c and iso-C16 : 0. Phospholipids consisted of diphosphatidylglycerol, hydroxy-phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, aminophospholipids and unidentified lipids. The G+C content of the genomic DNA was 70.4 mol%. On the basis of phenotypic characteristics, DNA-DNA relatedness and phylogenetic distinctiveness, strain 1SM4-01T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea purpurea sp. nov. is proposed. The type strain is 1SM4-01T (=BCC 60397T=NBRC 109647T).

Sphaerisporangium siamense sp. nov., an actinomycete isolated from rubber-tree rhizospheric soil

A Gram-positive aerobic actinomycete, designated SR14.14T, isolated from the rhizospheric soil of rubber tree was determined taxonomically using a polyphasic approach. The organism contained meso-diaminopimelic acid and the N-acetyl type of peptidoglycan. The predominant menaquinones were MK-9, MK-9(H2) and MK-9(H4). Madurose was detected in the whole-cell hydrolysates. Mycolic acids were not presented. Major phospholipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol mannoside. Major cellular fatty acid was iso-C16: 0 and the G+C content was 71.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence suggested that the isolate belongs to the genus Sphaerisporangium. The sequence similarity value between the strain SR14.14T and its closely related species, Sphaerisporangium album, was 97.8%. DNA–DNA hybridization values between them were well below 70%. Based on genotypic and phenotypic data, strain SR14.14T represents a novel species in the genus Sphaerisporangium, for which the name Sphaerisporangium siamense sp. nov. is proposed. The type strain is SR14.14T (=BCC 41491T=NRRL B-24805T=NBRC 107570T).

Three novel species of the genus Kibdelosporangium; Kibdelosporangium kanagawaense sp. nov., Kibdelosporangium rhizosphaerae sp. nov. and Kibdelosporangium rhizovicinum sp. nov.

The taxonomic positions of three actinomycete isolates, K08-0175T, K10-0543T and K12-0791T, which were isolated from plant root and rhizospheric soil samples were subjected to a polyphasic taxonomic study. On the basis of the results of phylogenetic analysis and morphological and chemotaxonomic characteristics, these three strains were classified as representing members of the genus Kibdelosporangium. These strains were observed to produce both long chains of rod-shaped spores and sporangium-like structures with well-defined walls on aerial hyphae. Phylogenetic position, DNA-DNA hybridization and comparison of the phylogenetically closest relatives revealed that these three strains were clearly distinguishable from each other and from their closest phylogenetic relatives. Therefore, three novel species are proposed as Kibdelosporangium kanagawaense sp. nov. [type strain K08-0175T (=NBRC 112388T=TBRC 6786T)], Kibdelosporangiumrhizosphaerae sp. nov. [type strain K10-0543T (=NBRC 112389T=TBRC 6787T)] and Kibdelosporangium rhizovicinum sp. nov. [type strain K12-0791T (=NBRC 112390T=TBRC 6788T)].

Cryptosporangium eucalypti sp. nov., an actinomycete isolated from Eucalyptus camaldulensis roots

A novel actinomycete, designated strain EURKPP3H10T, was isolated from surface-sterilized roots of Eucalyptus camaldulensis Dehnh., collected from Kamphaengphet Silvicultural Research Station, Kamphaengphet province, Thailand. The taxonomic position of strain EURKPP3H10T was studied using a polyphasic approach. Phylogenetic evaluation based on 16S rRNA gene sequence analysis showed that strain EURKPP3H10T belongs to the genus Cryptosporangium, with the highest sequence similarity to Cryptosporangium cibodasense LIPI11-2-Ac046T (99.2 %). Colonies of strain EURKPP3H10T were orange yellow. Spherical sporangia with motile spores were observed. The strain contained meso-diaminopimelic acid and acofriose, arabinose, galactose, glucose, mannose, xylose and ribose in whole-cell hydrolysates. The predominant menaquinones were MK-9(H8) and MK-9(H6). The major fatty acids were iso-C16 : 0, C17 : 1ω8c, C18 : 1ω9c and C17 : 0. The polar lipids of the strain were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unknown lipids. The DNA G+C content of the genomic DNA was 71.5 mol%. Based on comparative analysis of physiological, biochemical and chemotaxonomic data, including DNA-DNA hybridization, strain EURKPP3H10T represents a novel species of the genus Cryptosporangium, for which the name Cryptosporangium eucalypti sp. nov. is proposed. The type strain is EURKPP3H10T (=BCC 77605T=NBRC 111482T).