Shanti Ratnakomala

Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp. nov. and Actinokineospora cianjurensis sp. nov., isolated from soil and plant litter.

Six actinomycete strains isolated from soil and plant-litter samples in Indonesia were studied for their taxonomic position by using a polyphasic approach. Phylogenetically, all the strains were located in the broad cluster of the genus Actinokineospora. Chemotaxonomic data [cell-wall diamino acid, meso-diaminopimelic acid; cell-wall peptidoglycan, type III (A1γ); major sugars, galactose and arabinose; major menaquinone, MK-9(H₄); major fatty acid, iso-C₁₆:₀; major phospholipid, phosphatidylethanolamine] supported the affiliation of all six strains to the genus Actinokineospora. The results of DNA-DNA hybridization with DNA from type strains of Actinokineospora species with validly published names revealed three DNA-DNA relatedness groups. Group I (ID03-0561(T)) showed low relatedness to the other strains studied. The three strains in group II (ID03-0784(T), ID03-0808 and ID03-0809) formed a group with high relatedness (98-100 %) and showed low relatedness to the other strains studied. The two strains in group III (ID03-0810(T) and ID03-0813) showed 58-68 % relatedness to Actinokineospora terrae NBRC 15668(T) and showed low relatedness (2-24 %) to the other strains studied. The description of three novel species is proposed: Actinokineospora baliensis sp. nov., for the single strain in group I (type strain ID03-0561(T) =BTCC B-554(T) =NBRC 104211(T)), Actinokineospora cibodasensis sp. nov., for the strains in group II (type strain ID03-0784(T) =BTCC B-555(T) =NBRC 104212(T)), and Actinokineospora cianjurensis sp. nov., for the strains in group III (type strain ID03-0810(T) =BTCC B-558(T) =NBRC 105526(T)).

Dietzia timorensis sp. nov., isolated from soil.

An actinomycete strain, ID05-A0528(T), was isolated using the SDS-yeast extract pre-treatment method from soil under mahogany (Swietenia mahogani) trees in West Timor, Indonesia, and was examined by using a polyphasic taxonomic approach. Chemotaxonomic and phylogenetic characterizations demonstrated that the novel strain belongs to the genus Dietzia. 16S rRNA gene sequencing studies showed that the strain was related to Dietzia cinnamea (97.2 %). Results of phenotypic and phylogenetic analyses determined that strain ID05-A0528(T) is different from the known species of the genus Dietzia. It is proposed that the isolate should be classified as a representative of a novel species of the genus Dietzia, with the name Dietzia timorensis sp. nov. The type strain is ID05-A0528(T) (=BTCC B-560(T) =NBRC 104184(T)).

Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil

Two actinomycete strains, ID05-A0653(T) and ID06-A0464(T), were isolated from soils of West Timor and Lombok island, respectively, in Indonesia. 16S rRNA gene sequence analysis clearly demonstrated that the isolates belonged to the family Pseudonocardiaceae and were closely related to the genus Actinophytocola. Strains ID05-A0653(T) and ID06-A0464(T) exhibited 98.1 and 98.2 % 16S rRNA gene sequence similarity, respectively, with Actinophytocola oryzae GMKU 367(T). The isolates grew well on ISP media and produced white aerial mycelium. Short spore chains were formed directly on the substrate mycelium. The isolates contained meso-diaminopimelic acid, arabinose and galactose as cell-wall components, MK-9(H(4)) as the sole isoprenoid quinone, iso-C(16 : 0) as the major cellular fatty acid and phosphatidylethanolamine as the diagnostic polar lipid. The DNA G+C contents of strains ID05-A0653(T) and ID06-A0464(T) were 69.7 and 71.2 mol%, respectively. On the basis of phenotypic characteristics, DNA-DNA relatedness and 16S rRNA gene sequence comparisons, strains ID05-A0653(T) and ID06-A0464(T) each represent a novel species of the genus Actinophytocola, for which the names Actinophytocola timorensis sp. nov. (type strain ID05-A0653(T)  = BTCC B-673(T)  = NBRC 105524(T)) and Actinophytocola corallina sp. nov. (type strain ID06-A0464(T)  = BTCC B-674(T)  = NBRC 105525(T)) are proposed.

Streptomyces baliensis sp. nov., isolated from Balinese soil

The taxonomic positions of actinomycete strains ID03-0915T and ID03-0825, isolated from soil on the Indonesian island of Bali, were examined using a polyphasic taxonomic approach. The morphological and chemotaxonomic characteristics of these organisms are typical of the genus Streptomyces. Phylogenetic analyses performed using almost-complete 16S rRNA gene sequences demonstrated that the strains were closely related to Streptomyces glauciniger and Streptomyces lilacinus. However, DNA-DNA hybridization and phenotypic characteristics revealed that the strains differed from known Streptomyces species. Therefore, we conclude that strains ID03-0915T and ID03-0825 (=BTCC B-563) represent a novel species of the genus Streptomyces, for which we propose the name Streptomyces baliensis sp. nov. The type strain is strain ID03-0915T (=BTCC B-608T=NBRC 104276T).

Actinoplanes bogoriensis sp. nov., a novel actinomycete isolated from leaf litter.

A novel actinomycete, designated LIPI11-2-Ac043T, was isolated from leaf litter collected in Indonesia. According to phylogenetic analysis based on the 16S rRNA gene sequence comparisons, strain LIPI11-2-Ac043T was closely related to Actinoplanes abujensis A4029T (99.3%) and Actinoplanes brasiliensis DSM 43805T (98.8%). Spores of strain LIPI11-2-Ac043T were motile and the sporangia were spherical. The predominant menaquinone was MK-9(H6) and the principal polar lipids were phosphatidylinositol, phosphatidylethanolamine, phosphatidylglycerol and diphospatidylglycerol. The whole-cell sugars were galactose, glucose and mannose; rhibose, arabinose and xylose were also detected as minor components. The major fatty acids were anteiso-C15:0, iso-C16:0, iso-C15:0 and anteiso-C17:0. These data supported the affiliation of strain LIPI11-2-Ac043T to the genus Actinoplanes. Meanwhile, the results of DNA–DNA hybridization and physiological and biochemical tests indicated that strain LIPI11-2-Ac043T can be distinguished from its closest related species. Therefore, strain LIPI11-2-Ac043T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes bogoriensis sp. nov. is proposed. The type strain is LIPI11-2-Ac043T (=InaCC A522T=NBRC 110975T).

Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove.

A novel spherical actinobacterium, designated RS-2-3T, was isolated from the rhizosphere of a mangrove growing on Rambut Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain RS-2-3T was related to the members of the genus Kocuria. The highest 16S rRNA gene sequence similarity value was observed with Kocuria marina KMM 3905T (97.0 %). The peptidoglycan type of strain RS-2-3T was found to be A3α with an interpeptide bridge comprising l-Ala4-5. The predominant menaquinone was MK-7(H2) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 71.8 mol%. These characteristics were consistent with those of members of the genus Kocuria. Meanwhile, physiological and biochemical characteristics revealed that strain RS-2-3T differed from the species of the genus Kocuria with validly published names. Therefore, strain RS-2-3T represents a novel species of the genus Kocuria, for which the name Kocuria pelophila sp. nov. is proposed. The type strain is RS-2-3T (=NBRC 110990T=InaCC A704T).

Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter

A novel Gram-stain-positive actinobacterium, designated PS-14-7(T), was isolated from the rhizosphere of a mangrove on Pramuka Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. The peptidoglycan type of strain PS-14-7(T) was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-8(H4) and the major fatty acids were anteiso-C(15 : 0), C(16 : 0) and iso-C(16 : 0). The DNA G+C content was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain PS-14-7(T) was closely related to Serinibacter salmoneus Kis4-28(T) (99.6%). However, DNA-DNA hybridization and phenotypic characteristics revealed that strain PS-14-7(T) differed from Serinibacter salmoneus . Therefore, strain PS-14-7(T) represents a novel species of the genus Serinibacter , for which the name Serinibacter tropicus sp. nov. is proposed. The type strain is PS-14-7(T) ( = NBRC 110108(T) = InaCC A 515(T)). An emended description of the genus Serinibacter is also proposed.

Diversity of Streptomyces from Eka Karya Botanical Garden, Bali

A total of 229 strains of actinomycetes were isolated and identified by full sequence of 16S rRNA gene analysis. Samples consisted of 18 soil and 20 leaf-litter were collected from Eka Karya Botanical Garden, Bali Island, Indonesia. Two isolation methods, i.e. SDS-Yeast Extract (SY) and Rehydration-Centrifugation (RC) were used in this study. Based on 16S rRNA gene analysis, isolated actinomycetes may be grouped into 28 genera. Based on molecular analysis of 16S rRNA gene similarities showed that isolated actinomycetes of Eka Karya Botanical Garden origin is diverse. Analysis on 144 isolates from soil samples, resulted in 24 genera and more than 87 species. Streptomyces is the most dominant genus where 65 isolates or 45 persen from isolated actinomycetes belong to this genus. It was followed by Actinoplanes (25 isolates = 17 persen). From leaf-litter samples, the total number of 85 isolates may be grouped into 9 genera and more than 41 species. The most dominated genus is Actinoplanes (42 isolates = 49 persen) followed by Catenuloplanes (16 isolates = 19 persen). Biotropia, Vol. 23 No. 1, 2016. P: 42 - 51

Actinoplanes tropicalis sp. nov. and Actinoplanes cibodasensis sp. nov., isolated from leaf litter

Two actinomycete strains, designated LIPI11-2-Ac034T and LIPI11-2-Ac042T, were isolated from leaf litter collected from Cibodas Botanical Garden, West Java, Indonesia. Phylogenetic analysis based on 16S rRNA gene sequences suggested that both isolates belong to the genus Actinoplanes. These isolates were closely related to Actinoplanes ferrugineus and Actinoplanes durhamensis with similarity values of 98.2 % and 97.7 % respectively, for strain LIPI11-2-Ac034T, and 99.0 % and 97.4-97.7 % respectively for strain LIPI11-2-Ac042T. Both isolates grew well on ISP 7 medium with brown soluble pigment production. Spores were motile and sporangia were irregular. The isolates contained meso-diaminopimelic acid in cell-wall hydrolysates, and mannose, glucose and galactose in whole-cell hydrolysates. The predominant menaquinone of strain LIPI11-2-Ac034T was MK-9(H4) while that of strain LIPI11-2-Ac042T was MK-9(H6). The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0 for strain LIPI11-2-Ac034T, and iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 for strain LIPI11-2-Ac042T. Phosphatidylethanolamine was detected as the diagnostic polar lipid. The DNA G+C contents of strains LIPI11-2-Ac034T and LIPI11-2-Ac042T were 71.5 and 70.7 mol%, respectively. Based on the differential phenotypic characteristics and the results of DNA-DNA hybridization and phylogenetic analysis, it is proposed that strains LIPI11-2-Ac034T and LIPI11-2-Ac042T represent two novel species of the genus Actinoplanes, for which the names Actinoplanes tropicalis sp. nov. (type strain LIPI11-2-Ac034T = InaCC A459T = NBRC 110973T) and Actinoplanes cibodasensis sp. nov. (type strain LIPI11-2-Ac042T = InaCC A458T = NBRC 110974T) are proposed.