Abstract
Two actinobacterial strains, YIM 65001T and YIM 65002T, were isolated from surface-sterilized plant tissues collected from Yunnan Province, south-west China, and their taxonomic positions were determined by using a polyphasic approach. The DNA G+C contents of strains YIM 65001T and YIM 65002T were 71.9 and 72.6 mol%, respectively. The two strains had chemotaxonomic markers that were consistent with their classification in the genus Dietzia. Phylogenetic analysis based on almost-complete 16S rRNA gene sequences indicated that strain YIM 65001T was related most closely to Dietzia maris DSM 43672T and that strain YIM 65002T was related most closely to Dietzia natronolimnaea CBS 107.95T. Levels of 16S rRNA gene sequence similarity between strains YIM 65001T and YIM 65002T and the type strains of other recognized members of the genus Dietzia were 95.8–99.8 %. DNA–DNA hybridization experiments confirmed the separate genomic status of strains YIM 65001T and YIM 65002T. Strains YIM 65001T and YIM 65002T showed significant phenotypic differences between each other and their closest recognized neighbours. On the basis of their phenotypic and phylogenetic distinctiveness, the two novel isolates were identified as representing two novel species of the genus Dietzia, for which the names Dietzia schimae sp. nov. (type strain YIM 65001T=CCTCC AA 207015T=DSM 45139T) and Dietzia cercidiphylli sp. nov. (type strain YIM 65002T=CCTCC AA 207016T=DSM 45140T) are proposed.
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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains YIM 65001T and YIM 65002T are EU375845 and EU375846, respectively.
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Two-dimensional thin-layer chromatograms of phospholipids of strains YIM 65001T and YIM 65002T and a table detailing the fatty acid profiles of strains YIM 65001T and YIM 65002T and of the type strains of closely related Dietzia species are available as supplementary material with the online version of this paper.
The genus Dietzia was first proposed by Rainey et al. (1995) to accommodate organisms previously classified as Rhodococcus maris (Nesterenko et al., 1982). Since Dietzia maris was originally isolated from halibut by Harrison (1929), members of the genus have been isolated from various habitats such as marine, soil and hospital environments (Colquhoun et al., 1998; Duckworth et al., 1998; Mayilraj et al., 2006; Yassin et al., 2006; Jones et al., 2008). During an investigation into the diversity of endophytic actinobacteria from pharmaceutically important plants, two novel strains, designated YIM 65001T and YIM 65002T, were isolated from surface-sterilized plant tissues. The aim of the present study was to determine the taxonomic status of these organisms.
Samples of Schima sp. and Cercidiphyllum japonicum were collected from Yunnan Province, south-west China, and were surface-sterilized according to the method of Coombs & Franco (2003). Strain YIM 65001T was isolated from the surface-sterilized stem of Schima sp., and strain YIM 65002T was isolated from the surface-sterilized root of C. japonicum by using tap water-yeast extract agar medium (Coombs & Franco, 2003). The purified strains were cultivated and maintained on trypticase soy agar medium (TSA; Difco). Cell morphology was observed by using light microscopy (BH2; Olympus) and electron microscopy (JEM-1010; JEOL). Colony colour was determined by comparison with colour chips from the ISCC-NBS colour chart standard samples (Kelly, 1964).
Phenotypic properties, and growth at various temperatures, pH values and NaCl concentrations were examined as described by Xu et al. (2005) by growing the strains on trypticase soy broth (TSB) as the basal medium. Oxidase activity was determined from the oxidation of tetramethyl-p-phenylenediamine (Kovacs, 1956). Catalase activity was determined by use of 3 % H2O2, and bubble production was identified as indicating a positive reaction. API 50 CH test kits (bioMérieux) were used to investigate several physiological and biochemical characteristics according to the manufacturer's instructions. Hydrolysis of starch, gelatin, and Tweens 20, 40 and 80 was determined as described by Smibert & Krieg (1994). Nitrate reduction was determined according to Lányí (1987). The following tests were performed as described by Goodfellow (1986): Voges–Proskauer, methyl red, and the production of H2S and indole. Cell morphology and physiological and biochemical test results are given in detail in Table 1⇓ and in the species descriptions below.
Differential characteristics between strains YIM 65001T and YIM 65002T and the type strains of recognized Dietzia species
Strains: 1, YIM 65001T; 2, YIM 65002T; 3, D. psychralcaliphila ILA-1T; 4, D. natronolimnaea CBS 107.95T; 5, D. kunjamensis K30-10T; 6, D. maris DSM 43672T; 7, D. cinnamea IMMIB RIV-399T; 8, D. papillomatosis N 1280T. Data for all strains except D. cinnamea IMMIB RIV-399T and D. papillomatosis N 1280T (Yassin et al., 2006; Jones et al., 2008) are from the present study. +, Positive; w, weakly positive; −, negative; nd, not determined.
The cellular fatty acid composition was determined as described by Sasser (1990), by using the Microbial Identification System (MIDI). For other chemotaxonomic analyses, freeze-dried cells were obtained from cultures grown in TSB for 5 days at 28 °C. The amino acids and sugars of whole-cell hydrolysates were determined by using TLC as described by Staneck & Roberts (1974). Phospholipids were extracted and identified according to standard procedures (Minnikin et al., 1979; Collins & Jones, 1980). Menaquinones were extracted (Collins et al., 1977) and separated by HPLC (Tamaoka et al., 1983). The presence of mycolic acids was demonstrated by using TLC (Minnikin et al., 1980). The G+C content of the genomic DNA was determined by using the HPLC method according to Mesbah et al. (1989).
Strains YIM 65001T and YIM 65002T contained meso-diaminopimelic acid as the diamino acid. Whole-cell hydrolysates were rich in arabinose and galactose. For the two strains, the predominant menaquinone was MK-8(H2) (100 % for both). Mycolic acids were present, and these co-migrated with those of Dietzia kunjamensis K30-10T; it was thus inferred that the mycolic acids in strains YIM 65001T and YIM 65002T contained 33–40 carbon atoms (Mayilraj et al., 2006). Polar lipid analysis showed that strains YIM 65001T and YIM 65002T contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. However, strain YIM 65002T also contained phosphatidylinositol mannoside, which was absent from strain YIM 65001T (see Supplementary Fig. S1 available in IJSEM Online). The DNA G+C contents of strains YIM 65001T and YIM 65002T were 71.9 and 72.6 mol%, respectively. These values are consistent with those of recognized members of the genus Dietzia, which range from 66.1 to 73.0 mol% (Rainey et al., 1995; Duckworth et al., 1998; Yumoto et al., 2002; Yassin et al., 2006; Mayilraj et al., 2006). The fatty acid profiles of the two novel strains are described in detail in Supplementary Table S1 (available in IJSEM Online) and in the species descriptions below.
Genomic DNA extraction, amplification and 16S rRNA gene sequencing were performed as described by Li et al. (2007). Phylogenetic analysis was performed by using mega version 2.1 (Kumar et al., 2001) after multiple alignment of the data by clustal_x (Thompson et al., 1997). Evolutionary distances and Knuc values were calculated and clustering was performed by using the neighbour-joining method (Saitou & Nei, 1987). The topology of the resultant tree was evaluated by bootstrap analysis of the neighbour-joining data based on 1000 resamplings (Felsenstein, 1985). The phylogenetic positions of strains YIM 65001T and YIM 65002T revealed that these two taxa were closely associated with the genus Dietzia but formed separate subclades with their most closely related neighbours (Fig. 1⇓). A 16S rRNA gene sequence similarity value of 98.1 % was found between strains YIM 65001T and YIM 65002T. Strain YIM 65001T showed 16S rRNA gene sequence similarities of 99.8, 99.0, 97.9, 97.8, 97.3 and 96.1 % to D. maris DSM 43672T, D. kunjamensis K30-10T, Dietzia cinnamea IMMIB RIV-399T, Dietzia natronolimnaea CBS 107.95T, Dietzia psychralcaliphila ILA-1T and Dietzia papillomatosis N 1280T, respectively. Strain YIM 65002T displayed 16S rRNA gene sequence similarities of 99.5, 98.7, 98.2, 97.6, 97.3 and 95.8 % to D. natronolimnaea CBS 107.95T, D. psychralcaliphila ILA-1T, D. maris DSM 43672T, D. cinnamea IMMIB RIV-399T, D. kunjamensis K30-10T and D. papillomatosis N 1280T, respectively.
Neighbour-joining tree based on 16S rRNA gene sequences showing the phylogenetic relationships among strains YIM 65001T and YIM 65002T and related species. Bootstrap values (expressed as percentages of 1000 replications) of greater than 50 % are given at nodes. Bar, 1 substitution per 100 nt.
Genomic relatedness between strains YIM 65001T and YIM 65002T and their most closely related phylogenetic neighbours, i.e. the type strains of D. maris, D. natronolimnaea, D. psychralcaliphila and D. kunjamensis, was determined according to the DNA–DNA reassociation method described by He et al. (2005). Strain YIM 65001T displayed low levels of DNA–DNA relatedness to YIM 65002T (43.2 %), D. maris DSM 43672T (42.1 %), D. kunjamensis K30-10T (44.0 %), D. natronolimnaea CBS 107.95T (53.3 %) and D. psychralcaliphila ILA-1T (51.1 %). Strain YIM 65002T displayed a moderate level of DNA–DNA relatedness to D. kunjamensis K30-10T (59.6 %), and lower levels to D. psychralcaliphila ILA-1T (42.7 %), D. natronolimnaea CBS 107.95T (27.8 %) and D. maris DSM 43672T (32.9 %). These data further supported the conclusions drawn by Duckworth et al. (1998) and Yassin et al. (2006) that representatives of Dietzia species with 16S rRNA gene sequence similarities of greater than 98 % share DNA–DNA relatedness values well below 70 %, the recommended threshold value for the delineation of genomic species (Wayne et al., 1987). D. cinnamea IMMIB RIV-399T is allocated to Risk Group 2 and restrictions are placed on its use and distribution. However, strains YIM 65001T and YIM 65002T could be distinguished easily from their closest relatives based on differences in several phenotypic characteristics (see Table 1⇑). In view of these facts, we did not investigate the DNA–DNA relatedness of strains YIM 65001T and YIM 65002T with respect to D. cinnamea IMMIB RIV-399T. Given their genomic distinctiveness together with differences in some phenotypic properties, we suggest that strains YIM 65001T and YIM 65002T represent two novel species of the genus Dietzia, for which the names Dietzia schimae sp. nov. and Dietzia cercidiphylli sp. nov. are proposed, respectively.
Description of Dietzia schimae sp. nov.
Dietzia schimae (schi′ma.e. N.L. gen. n. schimae of the plant genus Schima, isolated from a stem sample of Schima sp.).
Forms circular, smooth, opaque and deep pink colonies on TSA plates. Short, rod-shaped cells exhibit snapping division and produce V-forms. Aerobic, Gram-positive, non-motile, non-spore-forming and non-acid-fast. Catalase is produced. Negative for oxidase, Voges–Proskauer and methyl red tests, production of H2S and indole, milk coagulation and peptonization, and hydrolysis of gelatin, urea and starch. Positive for nitrate reduction and hydrolysis of Tweens 20, 40 and 80. Tolerates up to 15 % NaCl and grows at temperatures between 10 and 45 °C, with an optimum growth temperature of 28 °C. Grows at pH 6.0–9.0 with optimum growth at pH 7.0. Utilizes aesculin, cellobiose, d-fructose, d-glucose, glycerol, d-lactose, d-mannose and sucrose, but not d-adonitol, amygdalin, l-arabinose, d-arabinose, l-arabitol, d-arabitol, arbutin, dulcitol, erythritol, l-fucose, d-fucose, d-galactose, gentiobiose, glycogen, inositol, inulin, d-lyxose, maltose, d-mannitol, melezitose, melibiose, methyl α-d-glucopyranoside, methyl α-d-mannopyranoside, methyl β-d-xylopyranoside, N-acetylglucosamine, potassium gluconate, potassium 2-ketogluconate, potassium 5-ketogluconate, raffinose, l-rhamnose, d-ribose, salicin, d-sorbitol, l-sorbose, starch, d-tagatose, trehalose, turanose, xylitol, l-xylose or d-xylose. The diagnostic amino acid is meso-diaminopimelic acid, and arabinose and galactose are present in whole-cell hydrolysates. Phospholipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone is MK-8(H2). Mycolic acids are present. Major fatty acids are C14 : 0, C16 : 1ω6c/C16 : 1ω7c, C16 : 0, C17 : 1ω7c, C17 : 1 anteiso B/iso I, 10-methyl C17 : 0, 10-methyl C18 : 0 (tuberculostearic acid), iso-C19 : 0 and anteiso-C19 : 0. The DNA G+C content of the type strain is 71.9 mol%.
The type strain, YIM 65001T (=CCTCC AA 207015T= DSM 45139T), was isolated from a surface-sterilized stem sample of Schima sp. collected from Yunnan Province, south-west China.
Description of Dietzia cercidiphylli sp. nov.
Dietzia cercidiphylli (cer.ci.di.phyl′li. N.L. gen. n. cercidiphylli of the plant genus Cercidiphyllum, isolated from root sample of Cercidiphyllum japonicum).
Forms circular, smooth, opaque and reddish orange colonies on TSA plates. Short, rod-shaped cells exhibit snapping division and produce V-forms. Aerobic, Gram-positive, non-motile, non-spore-forming and non-acid-fast. Catalase is produced. Negative for oxidase, Voges–Proskauer and methyl red tests, production of H2S and indole, nitrate reduction, milk coagulation and peptonization, and hydrolysis of gelatin and starch. Positive for hydrolysis of urea, and Tweens 20, 40 and 80. Tolerates up to 10 % NaCl and grows at temperatures between 10 and 37 °C, with an optimum growth temperature of 28 °C. Grows at pH 6.0–9.0, with optimum growth at pH 7.0. Utilizes l-arabinose, arbutin, d-fructose, d-glucose, d-lactose, d-lyxose, maltose, d-mannose, potassium 5-ketogluconate, sucrose, d-tagatose and turanose, but not d-adonitol, aesculin, amygdalin, d-arabinose, l-arabitol, d-arabitol, cellobiose, dulcitol, erythritol, l-fucose, d-fucose, d-galactose, gentiobiose, glycerol, glycogen, inositol, inulin, d-mannitol, melezitose, melibiose, methyl α-d-glucopyranoside, methyl α-d-mannopyranoside, methyl β-d-xylopyranoside, N-acetylglucosamine, potassium gluconate, potassium 2-ketogluconate, raffinose, l-rhamnose, d-ribose, salicin, d-sorbitol, l-sorbose, starch, trehalose, xylitol, l-xylose or d-xylose. The diagnostic amino acid is meso-diaminopimelic acid, and arabinose and galactose are present in whole-cell hydrolysates. Phospholipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The predominant menaquinone is MK-8(H2). Mycolic acids are present. Major fatty acids are C14 : 0, iso-C16 : 0, C16 : 1ω6c/C16 : 1ω7c, 10-methyl C16 : 0, C16 : 0, C17 : 1ω8c, C17 : 1ω7c, C18 : 1ω7c, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). The DNA G+C content of the type strain is 72.6 mol%.
The type strain, YIM 65002T (=CCTCC AA 207016T=DSM 45140T), was isolated from a surface-sterilized root sample of Cercidiphyllum japonicum collected from Yunnan Province, south-west China.
Acknowledgments
We are grateful to Professor Jean Euzéby for his help with nomenclature. This research was supported by the National Basic Research Program of China (no. 2004CB719601), the National Natural Science Foundation of China (nos 30560001, 30600001), the Yunnan Provincial International cooperative Program (no. 2005GH21), the Key Project of the Chinese Ministry of Education (no. 206139) and the Ministry of Science and Technology, PR China (2006DFA33550). W.-J. L. was also supported by the Program for New Century Excellent Talent in University (NCET).