Yayoi Sakiyama

Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov.

An anaerobic, thermophilic, thiosulfate-reducing bacterium, strain AZM16c01(T), isolated from a hot spring in Japan [Mori, K., Sunamura, M., Yanagawa, K., Ishibashi, J., Miyoshi, Y., Iino, T., Suzuki, K. & Urabe, T. (2008). Appl Environ Microbiol 74, 6223-6229] was characterized in detail. The 16S rRNA gene sequence analysis had revealed that strain AZM16c01(T) was the first cultivated representative of the candidate phylum OP5. The cells were multicellular filaments with a single polar flagellum. The strain contained iso-C(17 : 0) as the major fatty acid and menaquinone-8(H(6)), menaquinone-8(H(8)) and menaquinone-8(H(10)) as the respiratory quinones. The G+C content of the genomic DNA of strain AZM16c01(T) was 34.6 mol%. Optimum growth was obtained at 65 degrees C, pH 6.5 and in the absence of NaCl, with a doubling time of 10.6 h. On the basis of the results of phylogenetic analysis based on the 16S rRNA gene sequence and the characterization of the strain in this study, we propose the name Caldisericum exile gen. nov., sp. nov. for strain AZM16c01(T) (=NBRC 104410(T)=DSM 21853(T)). In addition, we propose the new phylum name Caldiserica phyl. nov. for the candidate phylum OP5 represented by C. exile gen. nov., sp. nov., and Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov.

Iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber Holothuria edulis, and proposal of Iamiaceae fam. nov.

A novel, Gram-positive bacterial strain, F12(T), was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected from seawater off the coast of Japan. According to 16S rRNA gene sequence analysis, this strain represents a novel, deep-rooting lineage within the class Actinobacteria and clusters with uncultured bacteria and Acidimicrobium ferrooxidans. Compared to species with validly published names, the highest 16S rRNA gene sequence similarity (89.8 %) was to Acidimicrobium ferrooxidans DSM 10331(T). Phylogenetic analyses showed that strain F12(T) represents a distinct phylogenetic lineage related closely to the genus Acidimicrobium. Strain F12(T) contained MK-9(H(6)) as the major menaquinone, whilst 17 : 0, 17 : 1omega8c, 15 : 0 and 16 : 0 were the major cellular fatty acids. The cell-wall peptidoglycan of strain F12(T) was composed of meso-diaminopimelic acid as the diagnostic diamino acid, alanine and glutamic acid (1 : 2 : 1). The cell-wall sugars detected were rhamnose, mannose, arabinose, galactose and xylose. The G+C content of the DNA was 74.4 mol%. From the taxonomic data obtained in this study, the name Iamia majanohamensis gen. nov., sp. nov. is proposed for the isolate, with type strain F12(T) (=NBRC 102561(T)=DSM 19957(T)). The name Iamiaceae fam. nov. is also proposed for the distinct phyletic line represented by the genus Iamia.

Taxonomic and ecological studies of actinomycetes from Vietnam: isolation and genus-level diversity

Actinomycetes were isolated from 109 soil and 93 leaf-litter samples collected at five sites in Vietnam between 2005 and 2008 using the rehydration-centrifugation (RC) method, sodium dodecyl sulfate-yeast extract dilution method, dry-heating method and oil-separation method in conjunction with humic acid-vitamin agar as an isolation medium. A total of 1882 strains were identified as Vietnamese (VN)-actinomycetes including 1080 (57%) streptomycetes (the genus Streptomyces isolates) and 802 (43%) non-streptomycetes. The 16S ribosomal RNA gene sequences of the VN-actinomycetes were analyzed using BLAST searches. The results showed that these isolates belonged to 53 genera distributed among 21 families. Approximately 90% of these strains were members of three families: Streptomycetaceae (1087 strains, 58%); Micromonosporaceae (516 strains, 27%); and Streptosporangiaceae (89 strains, 5%). Motile actinomycetes of the genera Actinoplanes, Kineosporia and Cryptosporangium, which have quite common morphological characteristics, were frequently isolated from leaf-litter samples using the RC method. It is possible that these three genera acquired common properties during a process of convergent evolution. By contrast, strains belonging to the suborder Streptosporangineae were exclusively isolated from soils. A comparison of the sampling sites revealed no significant difference in taxonomic diversity between these sites. Among the non-streptomycetes, 156 strains (19%) were considered as new taxa distributed into 21 genera belonging to 12 families. Interestingly, the isolation of actinomycetes from leaf-litter samples using the RC method proved to be the most efficient way to isolate new actinomycetes in Vietnam, especially the Micromonosporaceae species.

Euzebya tangerina gen. nov., sp. nov., a deeply branching marine actinobacterium isolated from the sea cucumber Holothuria edulis, and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov.

A tangerine-coloured, Gram-positive actinobacterial strain, designated F10(T), was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected in seawater off the coast of Japan. A 16S rRNA gene sequence analysis indicated that strain F10(T) was a member of the class Actinobacteria and was most closely related to Nitriliruptor alkaliphilus ANL-iso2(T) (87.4 % sequence similarity). Phylogenetic analyses showed that strain F10(T) represented a novel, deep-rooted, and distinct phylogenetic lineage within the class Actinobacteria and clustered with N. alkaliphilus and uncultured bacteria. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and rhamnose and galactose as the diagnostic cell-wall sugars. Strain F10(T) contained C₁₆ :₀ω7c, C₁₆:₀ and C₁₇:₁ω8c as the major cellular fatty acids. The predominant isoprenoid quinone was MK-9 (H₄).The G+C content of the DNA was 68.3 mol%. Based on data from the current polyphasic study, it is proposed that the new marine isolate be placed in a novel genus and be considered a novel species designated Euzebya tangerina gen. nov., sp. nov. within the new family, order and subclass Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. in the class Actinobacteria. The type strain of Euzebya tangerina is F10(T) (=NBRC 105439(T) =KCTC 19736(T)).

Flexivirga alba gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae

A novel actinobacterial strain ST13T isolated from soil near wastewater treatment facilities of an electroplating plant was subjected to a polyphasic taxonomic study. Cells of this organism were non-sporulating, and were irregular coccoid to comma shaped. The peptidoglycan of strain ST13T contained glutamic acid, serine, alanine, glycine and lysine, and represented the peptidoglycan type A4α. The whole-cell sugars contained ribose, glucose, galactose, rhamnose and mannose. The predominant menaquinone was MK-8(H4). The major fatty acid was iso-C16:0. The polar lipid contained phosphatidylglycerol. The DNA G+C content was 67.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ST13T fell within the radius of the family Dermacoccaceae, and its closest neighbor was Luteipulveratus mongoliensis MN07-A0370T (95.1%). However, strain ST13T did not make a coherent clade with members of the recognized organisms. On the basis of the phylogenetic and phenotypic characteristics of this actinobacterium, a novel genus and species, Flexivirga alba gen. nov., sp. nov., is proposed. The type strain of F. alba is ST13T (=NBRC 107580T=DSM 24460T).

Kineosporia babensis sp. nov., isolated from plant litter in Vietnam

Three actinomycetes, designated strains VN05A0342, VN05A0351 and VN05A0415(T), were isolated from plant-litter samples collected in the north of Vietnam and examined in a polyphasic taxonomic study. Phylogenetic analysis based on the 16S rRNA gene sequences showed that these isolates were most closely related to the type strain of Kineosporia mikuniensis (98.5 % sequence similarity). Morphological properties (the formation of spore domes and motile spores) and chemotaxonomic data supported the assignment of the three isolates to the genus Kineosporia. The isolates all contained the following: meso-diaminopimelic acid in the peptidoglycan (with small amounts of the ll isomer); ribose, mannose, galactose and glucose as the whole-cell sugars; MK-9(H(4)) as the predominant isoprenoid quinone; C(18 : 1) and C(16 : 0) as the major cellular fatty acids; and phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the phospholipids. The high DNA-DNA relatedness (>71 %) among the three isolates showed that they represented a single species. On the other hand, the DNA-DNA relatedness between the novel isolates and all type strains of Kineosporia species was less than 46 %. The physiological properties of our isolates were distinct from those of all of the Kineosporia species with validly published names, e.g. decomposition of l-tyrosine and aesculin and the utilization of raffinose and d-arabitol. Therefore, strains VN05A0342, VN05A0351 and VN05A0415(T) represent a novel species of the genus Kineosporia, for which the name Kineosporia babensis sp. nov. is proposed. The type strain is VN05A0415(T) (=VTCC-A-0961(T) =NBRC 104154(T)).

Pseudonocardia babensis sp. nov., isolated from plant litter

A novel actinomycete, designated strain VN05A0561(T), was isolated from plant litter collected at Ba Be National Park, Vietnam. The substrate mycelia and spore chains fragmented in a manner similar to nocardioform actinomycetes; the spores had smooth surfaces and were rod-shaped. Strain VN05A0561(T) had the following chemotaxonomic characteristics: meso-diaminopimelic acid in the cell-wall peptidoglycan, arabinose and galactose as characteristic sugars, MK-8(H₄) as the major isoprenoid quinone, phosphatidylcholine as the diagnostic phospholipid and iso-C₁₆:₀ as the major cellular fatty acid. Strain VN05A0561(T) shared low levels of 16S rRNA gene sequence similarity (< 97 %) with the type strains of recognized species of the genus Pseudonocardia and could be differentiated from its closest phylogenetic relatives based on phenotypic characteristics. These results suggested that strain VN05A0561(T) represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia babensis sp. nov. is proposed. The type strain is VN05A0561(T) (=VTCC-A-1757(T)=NBRC 105793(T)).

Streptomyces catbensis sp. nov., isolated from soil.

Strain VN07A0015(T) was isolated from soil collected on Cat Ba Island, Vietnam. The taxonomic position of strain VN07A0015(T) was near Streptomyces aomiensis M24DS4(T) (98.5% 16S rRNA gene sequence similarity) and Streptomyces scabrisporus NBRC 100760(T) (95.6%), and it clustered within them; however, this cluster was distant from the type strains of other species of the genus Streptomyces. The aerial mycelia of strain VN07A0015(T) were greyish and formed imperfect spiral spore chains (retinaculiaperti type) with smooth-surfaced spores. The morphological features of strain VN07A0015(T) were different from those of the type strains of S. aomiensis and S. scabrisporus. The chemotaxonomic characteristics of strain VN07A0015(T) were typical for all members of the genus Streptomyces, which possessed ll-type diaminopimelic acid, menaquinone MK-9(H6, H8) and the major fatty acids iso-C(16 : 0) and iso-C(15 : 0). DNA-DNA relatedness between strain VN07A0015(T) and S. aomiensis NBRC 106164(T) was less than 30%. In addition, some physiological and biochemical traits differed from those of S. aomiensis. Therefore, we propose that strain VN07A0015(T) be classified in the genus Streptomyces as a representative of Streptomyces catbensis sp. nov. (type strain VN07A0015(T) = VTCC-A-1889(T) = NBRC 107860(T)).

Screening for actinomyces isolated from soil with the ability to inhibit Xanthomonas oryzae pv. oryzae causing rice bacterial blight disease in Vietnam

Bacterial blight disease caused by Xanthomonas oryzae pv. oryzae ( Xoo ) is one of the major diseases in rice culture of Northen Vietnam, as well as other rice-growing regions of the world. In this study, we isolated and screened for actinomycete strains from Vietnam with the ability to inhibit Xoo isolates from northern Vietnam. From 90 actinomycete strains taken from soil in northern Vietnam in 2010, we screened for their antagonistic activity against 10 races of Xoo causing rice bacterial blight disease. Three actinomycete strains were found to inhibit all 10 Xoo races. Among the three strains, a strain namely VN10-A-44 was shown not to have the ability to produce toxic compounds and was selected for further study. The strain was identified as Streptomyces virginiae by 16S ribosomal RNA gene sequencing. We replaced soybean meal with tofu waste in antibiotic producing medium to improve antagonistic activity of VN10-A-44 against the Xoo pathogen and to make use of tofu waste for large-scale fermentation of VN10-A-44. We found that replacing soybean meal with 20 and 30 g of tofu waste/litter in the antibiotic producing medium gave the largest inhibition zone against the Xoo pathogen. Key words : Xanthomonas oryzae pv. oryzae , rice bacterial blight disease, Streptomyces virginiae , Vietnam.