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1 Department of Applied Biology, Faculty of Science, King Mongkut's Institute of Technology, Ladkrabang, Bangkok 10520, Thailand
2 Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
3 Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
Correspondence
Somboon Tanasupawat
Somboon.T{at}Chula.ac.th
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, and its description has been emended by Koch et al. (1996) and Stackebrandt et al. (1997), who classified seven genera (Micromonospora, Actinoplanes, Dactylosporangium, Catellatospora, Catenuloplanes, Couchioplanes and Pilimelia) within it. Subsequently, the genera Spirilliplanes, Verrucosispora, Virgisporangium, Asanoa, Longispora and Salinispora have been recognized as novel genera of the family Micromonosporaceae on the basis of their chemotaxonomic characteristics and their phylogenetic positions, inferred from 16S rRNA gene sequences and signature nucleotides of this gene (Koch et al., 1996; Stackebrandt et al., 1997). During an investigation of the actinomycete diversity of soils in southern Thailand, we isolated two strains, TT2-10T and TT2-3, which showed chemotaxonomic characteristics typical of members of the family Micromonosporaceae but which represent a novel phylogenetic lineage. In this report, we describe the polyphasic characterization of these strains and propose their classification in a novel genus and species.
Strains TT2-10T and TT2-3 were isolated from peat swamp forest soil in Pattaloong Province, Thailand. Samples were taken from the soil surface and were kept at 4 °C. The sampling and isolation methods were as described by Thawai et al. (2004), and the pure culture was kept at 4–10 °C on yeast extract-malt extract agar (ISP 2 medium) slants.
Strains TT2-10T and TT2-3 were grown for 14 days at 30 °C on oatmeal-nitrate agar and observed by using light microscopy and scanning electron microscopy (model JSM-5410 LV; JEOL). Samples for scanning electron microscopy were prepared as described previously (Itoh et al., 1989).
Cultural, physiological and biochemical characteristics were examined by using several standard methods; cultural characteristics were tested using 14 day cultures grown at 30 °C on various agar media. Jacal Colour Card L2200 (Japan Colour Research Institute) was used for determining colour designations and names. The decomposition of various compounds was examined using the basal medium recommended by Gordon et al. (1974). Temperature, NaCl and pH tolerances were determined on ISP 2 medium. The utilization of various carbon sources was tested using ISP 9 medium (Shirling & Gottlieb, 1966) supplemented with 1 % (final concentration) carbon source and 0.05 % Casamino acids. Gelatin liquefaction, peptonization of milk, nitrate reduction, cellulose decomposition and starch hydrolysis were determined through cultivation on various media, as described by Arai (1975) and Williams & Cross (1971). Melanin and hydrogen sulphide production were examined on tyrosine agar and peptone-iron agar slants supplemented with 0.1 % (w/v) yeast extract.
Freeze-dried cells used for chemotaxonomic analyses were obtained from cultures grown in yeast extract-malt extract broth (ISP 2 broth) on a rotary shaker at 30 °C. Cell-wall peptidoglycan was prepared and hydrolysed according to the methods of Kawamoto et al. (1981), and the amino acid composition was determined with an automatic amino acid analyser. The isomers of diaminopimelic acid in the cell walls were determined by using the method of Staneck & Roberts (1974). The acyl group of the muramic acid in the peptidoglycan was determined by using the method of Uchida & Aida (1984). The reducing sugars from whole-cell hydrolysates were analysed by using the HPLC method of Mikami & Ishida (1983). The phospholipids in the cells were extracted and analysed by using the method of Minnikin et al. (1984). Fatty acid methyl ester analysis was performed by means of GLC according to the instructions of the Microbial Identification System (MIDI) (Sasser, 1990; Kämpfer & Kroppenstedt, 1996). Isoprenoid quinones were extracted by using the method of Collins et al. (1977) and were analysed by using HPLC [Cosmosil 5C18 column (4.6x150 mm); Nacalai Tesque]. The elution solvent was a mixture of methanol and 2-propanol (2 : 1, v/v).
Chromosomal DNA was isolated from cells grown in ISP 2 broth according to the method of Tamaoka (1994). The G+C content of the DNA was determined using the HPLC method of Tamaoka & Komagata (1984). An equimolar mixture of nucleotides for analysis of the DNA G+C content (Yamasa Shoyu) was digested by bacterial alkaline phosphatase into nucleosides and used as the quantitative standard. DNA–DNA relatedness was measured fluorometrically using the microplate hybridization method devised by Ezaki et al. (1989). Hybridization was carried out at 55 °C for 2 h.
Genomic DNA extraction, PCR-mediated amplification of the 16S rRNA gene and sequencing of the PCR products were carried out as described by Nakajima et al. (1999). The 16S rRNA gene sequence was multiply aligned with selected sequences from the GenBank/EMBL/DDBJ databases using CLUSTAL W, version 1.81 (Thompson et al., 1994). Alignments were verified manually and adjusted prior to the construction of a phylogenetic tree. The phylogenetic tree was constructed using the neighbour-joining (Saitou & Nei, 1987) and maximum-parsimony methods (Kluge & Farris, 1969) in MEGA, version 2.1. Confidence values for the branches of the phylogenetic tree were determined using bootstrap analyses (Felsenstein, 1985) based on 1000 resamplings. 16S rRNA gene sequence similarities among closely related genera were calculated manually after pairwise alignments had been obtained using CLUSTAL X (Thompson et al., 1997). Gaps and ambiguous nucleotides were eliminated from the calculations.
Strains TT2-10T and TT2-3 produced well-developed substrate mycelia on ISP 2 agar, oatmeal agar (ISP 3), inorganic salts-starch agar (ISP 4), peptone-yeast extract-iron agar (ISP 6), tyrosine agar (ISP 7) and glucose-asparagine agar. Aerial mycelia and spores were absent on these media, but white aerial mycelia were formed with cultivation on oatmeal-nitrate agar. Spore chains were borne on the aerial mycelia and each consisted of more than 10 spores (Fig. 1). The spore surface appeared to be smooth. Spores were cylindrical, approximately 0.3–0.4 x 0.5–1.0 µm in size and non-motile. The colonies of strains TT2-10T and TT2-3 were yellow to vivid yellow–orange in colour; soluble pigments were not produced on most of the media tested, with the exception of a yellow pigment on oatmeal agar. The physiological and biochemical characteristics of the strains are presented in the species description.
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); the peptidoglycan was of type A1
(described by Schleifer & Kandler, 1972). The acyl type of the cell-wall muramic acid was glycolyl. The strains contained glucose, galactose, xylose, arabinose, mannose and ribose as whole-cell sugars, but rhamnose was not detected. This result suggests that the whole-cell sugar profile was pattern D of Lechevalier & Lechevalier (1970). The characteristic phospholipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, phosphatidylethanolamine and unidentified ninhydrin-negative phospholipids, but phosphatidylcholine was not present. This pattern corresponds to phospholipid type II of Lechevalier et al. (1977). The cellular fatty acid compositions are shown in Table 1. The major fatty acids of strains TT2-10T and TT2-3 were iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. This pattern corresponds to fatty acid type 3b of Kroppenstedt (1985). Mycolic acids were absent. The predominant menaquinones were MK-9(H4) and MK-9(H6) and small amounts of MK-9(H2) and MK-9(H8) were also present. The DNA G+C contents for strains TT2-10T and TT2-3 were 72.2 and 72.3 mol%, respectively.
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, Actinoplanes Couch 1950, Pilimelia Kane 1966, Dactylosporangium Thiemann et al. 1967, Catellatospora Asano and Kawamoto 1986, Catenuloplanes Yokota et al. 1993, Couchioplanes Tamura et al. 1994, Spirilliplanes Tamura et al. 1997, Verrucosispora Rheims et al. 1998, Virgisporangium Tamura et al. 2001, Asanoa Lee and Hah 2002, Longispora Matsumoto et al. 2003 and Salinispora Maldonado et al. 2005. The morphological characteristics of strains TT2-10T and TT2-3 were similar to those of members of the genera Longispora, Catellatospora, Catenuloplanes, Asanoa, Couchioplanes and Spirilliplanes in terms of spore-chain production, but these genera (except Longispora) could be distinguished on the basis of spore motility and true aerial mycelium production. The genus Longispora seems to be the genus most closely related to strains TT2-10T and TT2-3, but the major menaquinones and fatty acid composition of its members distinguished them from strains TT2-10T and TT2-3. These results indicated that strains TT2-10T and TT2-3 do not belong to any known genera in the family Micromonosporaceae. Differential characteristics for the isolates and members of related genera in the family Micromonosporaceae are shown in Table 2.
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). 16S rRNA gene sequence similarities between strain TT2-10T and members of the family Micromonosporaceae ranged from 91.3 % (with Longispora albida) to 93.8 % (with Salinispora arenicola), and strain TT2-10T showed 99.7 % sequence similarity to strain TT2-3; these similarities represent 127, 96 and 4 nucleotide differences, respectively. Additionally, strains TT2-10T and TT2-3 had no more than 93 % sequence similarity with members of any of the other families with which they were compared. Furthermore, the 16S rRNA gene sequences of strains TT2-10T and TT2-3 contained the majority of the signature nucleotides of members of the family Micromonosporaceae (Stackebrandt et al., 1997), except for variations at some positions (position 502 : 543, U–G; position 747, G; and position 811, C; Escherichia coli numbering). On the basis of phenotypic and genotypic data, strains TT2-10T and TT2-3 are readily distinguishable from the members of all established genera in the family Micromonosporaceae. Therefore, we propose that strains TT2-10T and TT2-3 should be classified in a novel genus and species, for which the name Actinocatenispora thailandica gen. nov., sp. nov. is proposed.
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Gram-positive, non-acid-fast, non-motile and aerobic organisms with branching substrate hyphae. Aerial hyphae are formed and bear spore chains each consisting of more than 10 spores. Spores are cylindrical (0.3–0.4x0.5–1.0 µm) and the spore surface is smooth. In general, substrate mycelia are yellow to vivid orange in colour. Cell wall contains glutamic acid, glycine, alanine and meso-diaminopimelic acid. The N-acyl group of the cell-wall muramic acid is glycolyl. Galactose, xylose, arabinose, glucose, mannose and ribose are detected as whole-cell sugars. Contains phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, phosphatidylglycerol and unidentified ninhydrin-negative phospholipids as cellular phospholipids (phospholipid pattern type II). Predominant menaquinones are MK-9(H4) and MK-9(H6); MK-9(H2) and MK-9(H8) are minor components. Mycolic acids are not detected. The DNA G+C content is 72 mol%. Habitat is soil. The type species is Actinocatenispora thailandica.
Description of Actinocatenispora thailandica sp. nov.
Actinocatenispora thailandica (thai.lan'di.ca. N.L. fem. adj. thailandica of Thailand, where the type strain was isolated).
The description of the morphological, chemotaxonomic and general characteristics are as described for the genus. White aerial mycelia are formed on oatmeal-nitrate agar. Soluble yellow pigment present on oatmeal agar. The type strain utilizes D-glucose, D-mannitol, D-melibiose, D-raffinose, glycerol, myo-inositol, salicin and cellobiose but not D-ribose, L-rhamnose, lactose, D-galactose, L-arabinose or D-fructose. Positive for reduction of nitrate, weakly positive for peptonization of milk and gelatin liquefaction and negative for hydrolysis of starch, formation of melanin and H2S production. The optimal temperature for growth is 25–30 °C. No growth occurs above 40 °C. Minimum pH tolerated is 4.5. Maximum NaCl concentration for growth is 7 %. The major cellular fatty acid components are iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. The DNA G+C content of the type strain is 72 mol%.
The type strain, TT2-10T (=JCM 12343T=PCU 235T=DSM 44816T), was isolated from peat swamp forest soil in Pattaloong Province, Thailand.
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ACKNOWLEDGEMENTS |
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