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1 State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
2 Department of Agricultural and Environmental Science, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
Correspondence
Zhiheng Liu
zhliu{at}sun.im.ac.cn
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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The GenBank accession numbers for the 16S rDNA sequences of A. catellatispora 3.24T, A. glauciflava 80-60T, A. latina DSM 43382T and A. nitritigenes DSM 44137T are respectively AF154127, AF153881, AY035998 and AY035999.
Present address: College of Life Science, Hebei University, Baoding 071002, People's Republic of China. 
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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; Zhang et al., 1998, 2001). This taxon currently includes the genera Actinocorallia Iinuma et al. 1994, Actinomadura Lechevalier and Lechevalier 1968, Spirillospora Couch 1963 and Thermomonospora Henssen 1957, the type genus. Members of these taxa share a range of chemotaxonomic and molecular systematic properties that distinguish them from other actinomycetes (Zhang et al., 1998, 2001; Miyadoh & Miyara, 2001), including near relatives classified in the families Nocardiopsaceae (Rainey et al. 1996) emend. Zhang et al. 2001 and Streptosporangiaceae (Goodfellow et al. 1990) emend. Stackebrandt et al. 1997.
Organisms previously classified as Nocardia dassonvillei, Nocardia madurae and Nocardia pelletieri were the founder members of the genus Actinomadura (Lechevalier & Lechevalier, 1968), though Actinomadura dassonvillei was subsequently reclassified as Nocardiopsis dassonvillei (Meyer, 1976). Following its introduction, the genus Actinomadura became a dumping ground for an assortment of aerobic, Gram-positive, non-acid-fast, non-motile sporoactinomycetes that had cell walls rich in meso-diaminopimelic acid (meso-A2pm), but lacking diagnostic sugars (wall chemotype III sensu Lechevalier & Lechevalier, 1970). The application of chemotaxonomic, molecular systematic and numerical phenetic procedures clearly showed that the genus was in need of taxonomic revision (Athalye et al., 1985; Fischer et al., 1983; Poscher et al., 1985; Kroppenstedt et al., 1990), a task that was initiated by the extensive studies of Zhang et al. (1998, 2001).
The revised genus Actinomadura accommodates aerobic, Gram-positive, non-acid-fast, non-motile actinomycetes that typically form non-fragmenting, extensively branched substrate mycelia and aerial hyphae that differentiate into short to long, straight, hooked or spiral chains of spores with either folded, irregular, smooth, spiny or warty spores. Members of the genus Actinomadura contain meso-A2pm, the sugars galactose, glucose, madurose, mannose and ribose, major proportions of hexahydrogenated menaquinones with nine isoprene units, complex fatty acids, including hexadecanoic, 14-methylpentadecanoic and 10-methyloctadecanoic acids as predominant components and diphosphatidylglycerol and phosphatidylinositol as major phospholipids (Kroppenstedt et al., 1990).
The genus presently contains 28 validly described species, though there is evidence that Actinomadura spadix may merit generic status (Athalye et al., 1985; Ochi et al., 1991; Zhang et al., 2001). Further comparative studies are also needed to establish clear relationships between Actinomadura echinospora, Actinomadura umbrina and Thermomonospora curvata (the type species of the genus), as these organisms are well separated from other Actinomadura species on the basis of 16S and 23S rDNA sequence data (Zhang et al., 2001). Phylogenetic data also indicate that Spirillospora albida, the type species of the genus, has a very close evolutionary relationship with some Actinomadura species.
The aim of the present study was to determine the taxonomic status of two soil isolates, strains 3.24T and 80-60T, which were considered to have phenotypic properties typical of actinomadurae. Isolate 80-60T was invalidly described as ‘Streptomyces glaucoflavus’ by Zhang et al. (1984), but was subsequently shown to have chemical and morphological properties typical of Actinomadura strains (Itoh et al., 1987). The two organisms were examined for a range of genotypic and phenotypic properties and were found to form new centres of taxonomic variation within the genus Actinomadura; the names Actinomadura catellatispora sp. nov. and Actinomadura glauciflava sp. nov. are respectively proposed for strains 3.24T and 80-60T.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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. The isolates were maintained as glycerol suspensions (20 %, v/v), as were the type strains of Actinomadura citrea, Actinomadura coerulea, Actinomadura latina, Actinomadura livida, Actinomadura luteofluorescens, Actinomadura nitritigenes and Actinomadura verrucosospora. Biomass for chemotaxonomic and molecular systematic studies was prepared by growing all of the organisms in shake flasks of modified Sauton's broth (Mordarska et al., 1972) at 28 °C for 7 days. Cells for chemotaxonomic analyses (isolates 3.24T and 80-60T) were washed twice in distilled water and freeze-dried; those for molecular systematic studies (all strains) were washed in NaCl/EDTA buffer (0·1 M EDTA, pH 8·0; 0·1 M NaCl) and stored at -20 °C until required.
Cultural and morphological studies.
The undisturbed arrangement of the aerial hyphae and spore chain morphology of the isolates was observed from cultures grown on glucose-yeast extract-malt extract agar (ISP 2 medium; Shirling & Gottlieb, 1966) at 28 °C for up to 4 weeks, using the cover-slip technique of Kawato & Shinobu (1959). Growth on the cover-slip was fixed and examined following the procedure described by Zhou et al. (1998). Spore ornamentation was observed by examining gold-coated, dehydrated preparations, using a Hitachi 5-570 SEM.
Biochemical and physiological properties and chemotaxonomy.
The isolates were examined for a broad range of phenotypic properties as described by Athalye et al. (1985).
The diagnostic isomers of A2pm, the predominant menaquinones, sugars, polar lipids and the DNA base composition of the isolates were determined as described by Lu et al. (2001).
DNA extraction and 16S rDNA sequencing.
Standard procedures were used to extract genomic DNA from all of the test organisms (Pitcher et al., 1989; Kim et al., 1998).
PCR amplification of 16S rDNA samples prepared from the isolates and from the type strains of A. latina and A. nitritigenes was carried out as described previously (Kim et al., 1996). The PCR products were purified according to the Wizard PCR purification system (Promega) and then sequenced using a DyeDeoxy Terminator cycle sequencing kit (Applied Biosystems) and universal primers as described previously (Lu et al., 2001). Sequence gel electrophoresis was carried out and nucleotide sequences were obtained automatically using an Applied Biosystems DNA sequencer (model 373A) and software provided by the manufacturer.
Analysis of sequence data.
The almost complete 16S rDNA sequences of the organisms were aligned manually with corresponding sequences of representatives of the family Thermomonosporaceae retrieved from the DDBJ/EMBL/GenBank databases using the program PHYDIT (J. Chun, unpublished data). Evolutionary trees were inferred using the least-squares, maximum-likelihood, maximum-parsimony and neighbour-joining treeing algorithms from the PHYLIP suite of programs (Felsenstein, 1993) and evolutionary distance matrices were generated for the least-squares and neighbour-joining methods as described by Jukes & Cantor (1969). The stability of the groupings was evaluated by bootstrap analyses (1000 replicates) of the neighbour-joining dataset using the programs SEQBOOT and CONSENSE (Felsenstein, 1993).
DNA–DNA relatedness studies.
Levels of DNA–DNA relatedness between isolate 80-60T and the type strains of A. citrea, A. coerulea, A. luteofluorescens, Actinomadura macra and A. verrucosospora were determined, in duplicate, following the procedure described by De Ley et al. (1970).
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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showed that all of the strains fall within the range of the evolutionary radiation occupied by the genus Actinomadura (data not shown). The isolates also exhibited chemical markers typical of members of this taxon, i.e. they contained: meso-A2pm as the wall diamino acid; the sugars galactose, glucose, madurose, mannose and ribose; hexahydrogenated menaquinones with nine isoprene units as the predominant isoprenologue (
80 %), minor amounts (10–12 %) of tetra- and octahydrogenated components with nine isoprene units, diphosphatidylglycerol and phosphatidylinositol as major polar lipids; and complex mixtures of fatty acids, notably major proportions of hexadecanoic (40 % of total fatty acids), 14-methylpentadecanoic (20 %) and 10-methyloctadecanoic (20 %) acids. These chemical properties distinguish the isolates from members of the family Thermomonosporaceae, apart from those classified in the genus Actinomadura (Kroppenstedt et al., 1990; Miyadoh & Miyara, 2001). In addition, strains 3.24T and 80-60T have G+C-rich DNA (70·8 and 72·0 mol%, respectively), but lack mycolic acids.
The phenotypic properties of the isolates are also consistent with their classification in the genus Actinomadura. The organisms are aerobic, non-motile, Gram-positive, non-acid/alcohol-fast actinomycetes that form extensively branched, non-fragmenting substrate mycelia. Isolate 80-60T produces abundant bluish-green aerial hyphae on ISP 2 medium (Shirling & Gottlieb, 1966) that differentiate into short, curved or hooked or spiral (one turn) spore chains with a warty ornamentation (Fig. 1a). In contrast, strain 3.24T formed short, straight chains of smooth-surfaced spores on the aerial mycelium (Fig. 1b).
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. Strain 3.24T is most closely related to the type strain of A. livida; the two organisms share 96·8 % 16S rDNA similarity, which corresponds to 45 nt differences at 1450 locations. Much higher 16S rDNA similarities have been found between representatives of validly described Actinomadura species. The type strains of A. citrea and A. coerulea, for instance, share 99·4 % similarity, which corresponds to 8 nt differences at 1450 sites. Representatives of these taxa have a DNA–DNA relatedness value of 48 % (Poscher et al., 1985), a value well below the 70 % cut-off point recommended by Wayne et al. (1987) for the delineation of genomic species.
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that strain 80-60T belongs to the A. luteofluorescens subclade. The taxonomic integrity of this group is supported by a bootstrap value of 61 % and by results obtained with all four treeing algorithms. Strain 80-60T is most closely related to the type strain of A. citrea. The two organisms share 98·4 % 16S rDNA similarity, which corresponds to 23 nt differences at 1450 sites. DNA–DNA relatedness studies are now commonly used to resolve the finer taxonomic relationships between representatives of such closely related species. In the present investigation, it is evident that isolate 80-60T belongs to a distinct genomic species, as it shares mean DNA–DNA relatedness values of 62 % with A. luteofluorescens JCM 4491T, 53 % with A. citrea JCM 3295T and A. verrucosospora JCM 3147T and 38 % with A. coerulea JCM 3320T. These strains can also be distinguished from one another, and from isolate 3.24T, using a range of phenotypic properties (Table 1).
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; Lipski & Altendorf, 1995).
Description of Actinomadura catellatispora sp. nov.
Actinomadura catellatispora (ca.tell.a.ti.spo'ra. L. n. catella small chain; Gr. n. spora a seed; N.L. fem. n. catellatispora organism forming small chains of spores).
Aerobic, Gram-positive, non-acid/alcohol-fast, non-motile actinomycete that forms an extensively branched, non-fragmenting, light-yellow substrate mycelium on glucose-yeast extract-malt extract agar (ISP 2 medium). Short chains of spores (0·85 µm diameter) are formed on the aerial mycelium. The spore surface is smooth and the aerial spore mass is yellow. Diffusible pigments are not formed. Aesculin and gelatin are degraded but not casein, hypoxanthine, starch, tyrosine or xanthine. Nitrate is reduced. The organism is chemo-organotrophic, has an oxidative type of metabolism and grows at temperatures between 18 and 35 °C. Isolated from a mud sample taken from a sewage ditch in Zhanjiang City, Canton Province, southern China. The type strain is isolate 3.24T (=AS 4.1522T =IFO 16341T), which has a DNA G+C content of 70·8 mol%. The species description is based upon a single strain and hence serves as the description of the type strain.
Description of Actinomadura glauciflava sp. nov.
Actinomadura glauciflava (glau'ci.fla.va. L. fem. adj. glauca bluish-green; L. adj. flaveus yellow; N.L. adj. glauciflava bluish-green yellow).
The description is based on data taken from this and earlier studies (Zhang et al., 1984; Itoh et al., 1987). Aerobic, Gram-positive, non-acid/alcohol-fast, non-motile actinomycete that forms an extensively branched, non-fragmenting, substrate mycelium that carries aerial hyphae which differentiate into curved or hooked or spiral chains of spores (1 µm diameter) on glucose-yeast extract-malt extract agar (ISP 2 medium). The spore surface is warty, the aerial spore mass is bluish-green. A yellow diffusible pigment is produced. Aesculin, casein, gelatin, starch and hypoxanthine are degraded, but not tyrosine or xanthine. Nitrate is reduced. The organism is chemo-organotrophic, has an oxidative type of metabolism and grows at temperatures between 18 and 35 °C. Isolated from soil collected in Yunnan Province, southern China. The type strain is isolate 80-60T (=AS 4.1202T =IFO 14668T =JCM 16161T), which has a DNA G+C content of 72 mol%. The species description is based on a single strain and hence serves as the description of the type strain.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Couch, J. N. (1963). Some new genera and species of Actinoplanaceae. J Elisha Mitchell Sci Soc 79, 53–70.
De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 143–153.[Medline]
Felsenstein, J. (1993). PHYLIP (phylogenetic inference package), version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle, WA, USA.
Fischer, A., Kroppenstedt, R. M. & Stackebrandt, E. (1983). Molecular-genetic and chemotaxonomic studies on Actinomadura and Nocardiopsis. J Gen Microbiol 129, 3433–3446.[Medline]
Fitch, W. M. & Margoliash, E. (1967). Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155, 279–284.
Goodfellow, M., Stanton, L. J., Simpson, K. E. & Minnikin, D. E. (1990). Numerical and chemical classification of Actinoplanes and some related actinomycetes. J Gen Microbiol 136, 19–36.
Henssen, A. (1957). Beiträge zür Morphologie and Systematik der thermophilen Actinomyceten. Arch Mikrobiol 26, 373–414.[CrossRef][Medline]
Holt, J. G., Krieg, N. R., Sneath, P. H. A., Staley, J. T. & Williams, S. T. (editors) (1994). Bergey's Manual of Determinative Bacteriology, 9th edn. Baltimore: Williams & Wilkins.
Iinuma, S., Yokota, A., Hasegawa, T. & Kanamaru, T. (1994). Actinocorallia gen. nov., a new genus of the order Actinomycetales. Int J Syst Bacteriol 44, 230–234.
Itoh, T., Kudo, T. & Seino, A. (1987). Chemotaxonomic studies on new genera of actinomycetes proposed in Chinese papers. Actinomycetologica 1, 43–59.
Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
Kawato, M. & Shinobu, R. (1959). Streptomyces herbaricolor sp. nov., supplement: a single technique for microscopical observation. Mem Osaka Univ Lib Arts Educ 8, 114.
Kim, D., Chun, J., Sahin, N., Hah, Y. C. & Goodfellow, M. (1996). Analysis of thermophilic clades within the genus Streptomyces by 16S ribosomal DNA sequence comparisons. Int J Syst Bacteriol 46, 581–587.
Kim, S. B., Falconer, C., Williams, E. & Goodfellow, M. (1998). Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int J Syst Bacteriol 48, 59–68.
Kluge, A. G. & Farris, F. S. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 1–32.
Kroppenstedt, R. M., Stackebrandt, E. & Goodfellow, M. (1990). Taxonomic revision of the actinomycete genera Actinomadura and Microtetraspora. Syst Appl Microbiol 13, 148–160.
Lechevalier, H. A. & Lechevalier, M. P. (1968). A critical evaluation of the genera of aerobic actinomycetes. In The Actinomycetales, pp. 393–405. Edited by H. Prauser. Jena: Gustav Fischer.
Lechevalier, M. P. & Lechevalier, H. (1970). Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20, 435–443.
Lipski, A. & Altendorf, K. (1995). Actinomadura nitritigenes sp. nov., isolated from experimental biofilters. Int J Syst Bacteriol 45, 717–723.
Lu, Z., Liu, Z., Wang, L., Zhang, Y., Qi, W. & Goodfellow, M. (2001). Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., novel actinomycetes from soil. Int J Syst Evol Microbiol 51, 319–325.[Abstract]
Meyer, J. (1976). Nocardiopsis, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26, 487–493.
Meyer, J. (1979). New species of the genus Actinomadura. Zentbl Allg Mikrobiol 19, 37–44.
Miyadoh, S. & Miyara, T. (2001). Family Thermomonosporaceae. In Identification Manual of Actinomycetes, pp. 281–291. Edited by the Society for Actinomycetes, Japan. Tokyo: Business Center for Academic Societies.
Mordarska, H., Mordarski, M. & Goodfellow, M. (1972). Chemotaxonomic characters and classification of some nocardioform bacteria. J Gen Microbiol 71, 77–86.[Medline]
Ochi, K., Miyadoh, S. & Tamura, T. (1991). Polyacrylamide gel electrophoresis analysis of ribosomal protein AT-L30 as a novel approach to actinomycete taxonomy: application to the genera Actinomadura and Microtetraspora. Int J Syst Bacteriol 41, 234–239.
Pitcher, D. G., Saunders, N. A. & Owen, R. J. (1989). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8, 151–156.
Poscher, J., Kroppenstedt, R. M., Fischer, A. & Stackebrandt, E. (1985). DNA : DNA reassociation and chemotaxonomic studies on Actinomadura, Microbispora, Microtetraspora, Micropolyspora and Nocardiopsis. Syst Appl Microbiol 6, 264–270.
Rainey, F. A., Ward-Rainey, N., Kroppenstedt, R. M. & Stackebrandt, E. (1996). The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 46, 1088–1092.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.
Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L. (1997). Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47, 479–491.
Trujillo, M. E. & Goodfellow, M. (1997). Polyphasic taxonomic study of clinically significant actinomadurae including the description of Actinomadura latina sp. nov. Zentbl Bakteriol 285, 212–233.
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
Zhang, G., Xing, G. & Yan, X. (1984). Studies of classification of Streptomycetaceae. III. A new genus – Streptomycoides in the Streptomycetaceae. Acta Microbiol Sin 24, 189–194.
Zhang, Z., Wang, Y. & Ruan, J. (1998). Reclassification of Thermomonospora and Microtetraspora. Int J Syst Bacteriol 48, 411–422.
Zhang, Z., Kudo, T., Nakajima, Y. & Wang, Y. (2001). Clarification of the relationship between the members of the family Thermomonosporaceae on the basis of 16S rDNA, 16S–23S rRNA internal transcribed spacer and 23S rDNA sequences and chemotaxonomic analyses. Int J Syst Evol Microbiol 51, 373–383.[Abstract]
Zhou, Z.-H., Liu, Z.-H., Qian, Y.-D., Kim, S. B. & Goodfellow, M. (1998). Saccharopolyspora spinosporotrichia sp. nov., a novel actinomycete from soil. Int J Syst Bacteriol 48, 53–58.
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