Saccharopolyspora oryzae sp. nov., isolated from rhizosphere soil of the wild rice species Oryza rufipogon

A novel actinobacterium, designated as strain WRP15-2T, was isolated from rhizosphere soil of rice plant (Oryza rufipogon). The strain was Gram-stain-positive, aerobic, and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain WRP15-2T fell into the genus Saccharopolyspora. The strain shared the highest 16S rRNA gene sequence similarity with the type strains Saccharopolyspora kobensis JCM 9109T (99.1%), Saccharopolyspora indica VRC122T (98.9%), and Saccharopolyspora antimicrobica DSM 45119T (98.7%). However, the digital DNA-DNA hybridization and average nucleotide identity values among these strains confirmed that the microorganism represented a novel member of the genus Saccharopolyspora. Chemotaxonomic data revealed that strain WRP15-2T possessed MK-9(H4) as the predominant menaquinone. It contained meso-diaminopimelic acid as the diagnostic diaminopimelic acid and arabinose, galactose, and ribose as predominant whole-cell sugars. The detected phospholipids were dominated by phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxy-phosphatidylmethylethanolamine, and phosphatidylcholine. The predominant cellular fatty acids were iso-C16:0, C16:0, and iso-C15:0. The G + C content of the genomic DNA was 69.5%. Based on these genotypic and phenotypic data, it is supported that strain WRP15-2T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora oryzae sp. nov. is proposed. The type strain is WRP15-2T ( = TBRC 15728T = NBRC 115560T).

Streptomyces silvisoli sp. nov., a polyene producer, and Streptomyces tropicalis sp. nov., two novel actinobacterial species from peat swamp forests in Thailand

Two novel actinobacterial strains, designated RB6PN23T and K1PA1T, were isolated from peat swamp soil samples in Thailand and characterized using a polyphasic taxonomic approach. The strains were filamentous Gram-stain-positive bacteria containing ll-diaminopimelic acid in their whole-cell hydrolysates. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strain RB6PN23T was most closely related to Streptomyces rubrisoli (99.1 % sequence similarity) and Streptomyces ferralitis (98.5%), while strain K1PA1T showed 98.8 and 98.7% sequence similarities to Streptomyces coacervatus and Streptomyces griseoruber, respectively. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species-level thresholds (95-96 % ANI and 70 % dDDH). The genomes of strains RB6PN23T and K1PA1T were estimated to be 7.88 Mbp and 7.39 Mbp in size, respectively, with DNA G+C contents of 70.2 and 73.2 mol%. Moreover, strains RB6PN23T and K1PA1T encode 37 and 24 putative biosynthetic gene clusters, respectively, and in silico analysis revealed that these new species have a high potential to produce unique natural products. Genotypic and phenotypic characteristics confirmed that strains RB6PN23T and K1PA1T represented two novel species in the genus Streptomyces. The names proposed for these strains are Streptomyces silvisoli sp. nov. (type strain RB6PN23T=TBRC 17040T=NBRC 116113T) and Streptomyces tropicalis sp. nov. (type strain K1PA1T=TBRC 17041T=NBRC 116114T). Additionally, a giant linear polyene compound, neotetrafibricin A, exhibiting antifungal activity in strain RB6PN23T, was identified through HPLC and quadrupole time-of-flight MS analysis. The crude extract from the culture broth of strain RB6PN23T exhibited strong antifungal activity against Fusarium verticillioides, Fusarium fujikuroi and Bipolaris zeicola. This finding suggests that strain RB6PN23T could be a promising candidate for biological control of fungal diseases.

Streptomyces humicola sp. nov., a novel actinobacterium isolated from peat swamp forest soil in Thailand

A polyphasic approach was used to describe strain RB6PN25^T, an actinobacterium isolated from peat swamp forest soil in Rayong Province, Thailand. The strain was a Gram-stain-positive and filamentous bacterium that contained ll-diaminopimelic acid, mannose and ribose in whole-cell hydrolysates. MK-9(H₈) was the major menaquinone. The major fatty acids were iso-C_16 : 0, anteiso-C_15 : 0 and iso-C_15 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified glycophospholipids, two unidentified aminolipids and an unidentified phospholipid. The 16S rRNA gene sequences analysis indicated that it was most closely related to Streptomyces rubrisoli DSM 42083^T (97.6 %) and Streptomyces palmae TBRC 1999^T (97.4 %). Strain RB6PN25^T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with S. rubrisoli DSM 42083^T (78.6 %, 23.2 %) and S. palmae TBRC 1999^T (76.0 %, 22.6 %). The DNA G+C content of strain RB6PN25^T was 69.9%. The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses reveal that strain RB6PN25^T represents a novel species of the genus Streptomyces, for which the name Streptomyces humicola sp. nov. is proposed. The type strain is RB6PN25^T (=TBRC 14819^T=NBRC 115204^T).

Streptomyces acididurans sp. nov., isolated from peat swamp forest soil

A novel actinomycete, designated strain KK5PA1^T, was isolated from a soil sample collected from Kuan Kreng peat swamp forest, Nakhon Si Thammarat Province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces. Strain KK5PA1^T was most closely related to Streptomyces bryophytorum NEAU-HZ10^T (98.0 %) and Streptomyces guanduensis 701^T (97.6 %). The G+C content of the genomic DNA was 72.3 mol%. Digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain KK5PA1^T and those of S. bryophytorum DSM 42138^T(25.1 and 79.1 %) and S. guanduensis DSM 41944^T(25.1 and 79.7%) were below the thresholds of 70 and 96 % for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain KK5PA1^T possessed MK-9(H₆) and MK-9(H₈) as the predominant menaquinones. It contained ll-diaminopimelic acid as the diagnostic diamino acid and galactose, glucose, mannose and ribose as whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside, two unidentified aminolipids, five unidentified phospholipids and an unidentified lipid. The predominant cellular fatty acids were iso-C_16 : 0, anteiso-C_15 : 0 and C_16 : 0. On the basis of these genotypic and phenotypic data, it is proposed that strain KK5PA1^T represents a novel species of the genus Streptomyces, for which the name Streptomyces acididurans sp. nov. is proposed. The type strain is strain KK5PA1^T (=TBRC 13094^T=NBRC 114802^T).

Pseudonocardia acidicola sp. nov., a novel actinomycete isolated from peat swamp forest soil

A novel actinobacterium, designated strain K10HN5^T, was isolated from a peat soil sample collected from Kantulee peat swamp forest, Surat Thani Province, Thailand and its taxonomic position was determined using a polyphasic approach. Strain K10HN5^T contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose in its whole-cell hydrolysates. The predominant menaquinone was MK-8(H₄). The major fatty acids were iso-C_16 : 0, iso-C_15 : 0 and iso-C_16 : 1H. Mycolic acids were not present. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, hydroxyphosphatidylmethylethanolamine and phosphatidylinositol. The 16S rRNA gene sequence analysis indicated that it was closely related to Pseudonocardia bannensis DSM 45300^T (97.9 %) and Pseudonocardia xinjiangensis JCM 11839^T (97.9 %). Strain K10HN5^T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with P. bannensis DSM 45300^T (82.6, 28.7 %) and P. xinjiangensis JCM11839^T (76.3, 22.2 %). The DNA G+C content of strain K10HN5^T was 72.4 mol%. Based on polyphasic data, strain K10HN5^T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia acidicola sp. nov. is proposed. The type strain is K10HN5^T (=TBRC 10048^T=NBRC 113897^T).