Dietzia timorensis sp. nov., isolated from soil

Abstract

An actinomycete strain, ID05-A0528T , 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 (5BTCC B-560 T 5NBRC 104184 T ).The genus Dietzia is a member of the suborder Corynebacterineae (Stackebrandt et al., 1997) and encompasses eight species at the time of writing, including Dietzia papillomatosis, Dietzia schimae and Dietzia cercidiphylli (Jones et al., 2008;Li et al., 2008). Known species of the genus Dietzia were originally isolated from several sources, including clinical materials, such as an alkaline soda lake, a perianal swab, a drain pool of a fish-egg processing plant, soil, the skin of an immunocompetent patient, and plant tissue (Duckworth et al., 1998;Yumoto et al., 2002;Yassin et al., 2006;Mayilraj et al., 2006;Jones et al., 2008;Li et al., 2008). Some strains identified as representing species of the genus Dietzia show degradation of hydrocarbons, including n-alkanes (Rainey et al., 1995;Chaillan et al., 2004;Yumoto et al., 2002). Additionally, Takeishi et al. (2006) reported xylanolytic strains of the genus Dietzia isolated from the hindgut and faeces of Trypoxylus dichotomus larvae. Hence, the discovery of additional species of this genus will help in understanding their ecological roles and provide bioresources for industrial applications, including bioremediation.Strain ID05-A0528 T was isolated from a soil sample collected under mahogany trees in West Timor. The SDS-yeast extract pre-treatment method (Hayakawa & Nonomura, 1989) and humic acid-vitamin agar (Hayakawa & Nonomura, 1987) containing nalidixic acid (20 mg l -1 ) were used in the isolation. The pre-treatment method was used to enhance the spore germination of actinomycetes and to decrease the number of nonfilamentous bacteria on the isolation plates. The aim of the present study was to determine the taxonomic position of isolate ID05-A0528 T using a polyphasic approach.The colonial properties of strain ID05-A0528 T were recorded from a modified Bennett's agar plate (Jones, 1949) that had been incubated for 14 days at 28 u C. Gramstaining was examined by using Hucker's method (Gerhardt, 1981). Motility was examined in hanging drops by light microscopy using culture grown on Bennett's agar plates. Morphology of the cells was observed using light microscopy. Tests for aesculin and arbutin hydrolysis (Williams et al., 1983), nitrate reduction (Gordon & Mihm,The...

Characterization of human clinical isolates of Dietzia species previously misidentified as Rhodococcus equi

“…The interpretive breakpoints used for all drugs except vancomycin were those recommended by the CLSI for mycobacteria, nocardiae, and other aerobic actinomycetes. As no interpretive criteria for vancomycin have been established for this group of organisms, the breakpoints for susceptible (≤4), intermediate (8)(9)(10)(11)(12)(13)(14)(15)(16), and resistant (≥32) were those of the Food and Drug Administration (FDA) for infections other than S. aureus.…”

“…All strains were negative for growth on MacConkey, indole reaction, utilization of acetamide, Simmon's citrate, motility, arylsulfatase production, and hydrolysis of casein, hypoxanthine, tyrosine, and xanthine. On triple sugar iron agar slants, all clinical isolates and type strains gave an alkaline slant and no change in the butt c Clinical isolates W5004 and W5026 d Gordon's base medium [22] e King's base medium [21] Two isolates were resistant and three isolates were susceptible c Seven isolates were resistant and two isolates were susceptible d As no interpretive criteria for vancomycin have been established for actinomycetes, the breakpoints for susceptible (≤4), intermediate (8)(9)(10)(11)(12)(13)(14)(15)(16), and resistant (≥32) were those of the Food and Drug Administration (FDA) for infections other than Staphylococcus aureus strains were different from that of R. equi type strain, except for Dm/Ds clinical isolate W4994.…”

“…This genus consisted of ten validly described species at the time of the present study: D. aerolata [8], D. cercidiphylli [9], D. cinnamea [10], D. kunjamensis [11], D. maris [7], D. natronolimnaea [12], D. papillomatosis [13], D. psychralcaliphila [14], D. schimae [9], and D. timorensis [15]. Members of this genus are distributed in diverse habitats such as marine, soil, and hospital environments [10][11][12]16].…”

Identification of Atypical Rhodococcus -Like Clinical Isolates as Dietzia spp. by 16S rRNA Gene Sequencing

“…The CA155 16S rRNA gene was 99% identical to that from Dietzia timorensis ID05-A0528. This species was proposed to classify a soil isolate from West Timor, Indonesia, and has recently been validly recognized as a novel Dietzia species (24). This is the first reported isolation of the alkaliphilic D. natronolimnaea and the recently established species D. timorensis from human specimens.…”

Genus Diversity of Actinomycetes in Cibinong Science Center, West Java, Indonesia

“…During the collaborative research on ecology and taxonomy of actinomycetes in Indonesia between Indonesia and Japan, we have collected thousands of actinomycetes isolates from several sites in Indonesia. Some interesting new taxa has been reported, including Streptomyces baliensis sp nov. from Bali (Otoguro et al 2009), Dietzia timorensis from Timor (Yamamura et al 2010); Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp.…”