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Int J Syst Evol Microbiol 54 (2004), 235-239; DOI  10.1099/ijs.0.02586-0
© 2004 International Union of Microbiological Societies

Amycolatopsis decaplanina sp. nov., a novel member of the genus with unusual morphology

Joachim Wink1, Julia Gandhi2, Reiner M. Kroppenstedt3, Gerhard Seibert1, Bettina Sträubler3, Peter Schumann3 and Erko Stackebrandt3

1 Aventis Pharma Deutschland GmbH, Drug Innovation and Approval, Natural Products, 65926 Frankfurt, Germany
2 School of Life Sciences and Chemical Technology, 535 Clementi Road, Singapore 599489
3 DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany

Correspondence
Joachim Wink
joachim.wink{at}aventis.com


    ABSTRACT
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Strain DSM 44594T, which produces the glycopeptide antibiotic decaplanin, is a member of the genus Amycolatopsis based on 16S rRNA gene sequence analysis and chemotaxonomic properties. It is the first member of this genus that is reported to form pseudosporangia, which resemble those of members of the genus Kibdelosporangium. Phylogenetically, the novel taxon is related to Amycolatopsis orientalis, Amycolatopsis lurida, Amycolatopsis azurea, Amycolatopsis japonica and Amycolatopsis keratiniphila. Morphological, cultural and physiological properties, the production of a unique glycolipid and DNA–DNA similarity of <55 % with phylogenetically related strains reveal that strain DSM 44594T represents a novel species of the genus, for which the name Amycolatopsis decaplanina sp. nov. (type strain, FH 1845T=DSM 44594T=NRRL B-24209T) is proposed.


Abbreviations: A2pm, diaminopimelic acid

Published online ahead of print on 8 August 2003 as DOI 10.1099/ijs.0.02586-0.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains DSM 44594T, DSM 44213T and DSM 43134T are AJ508237, AJ508236 and AJ577997, respectively.


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In the course of a screening programme in Hoechst, Frankfurt, for new antibiotics that are active against methicillin-resistant strains of Staphylococcus aureus, the strain that produces the new antibiotic decaplanin (Eur. Pat., 1990, EP 356894) was isolated from a soil sample from India. Strain FH 1845T (=DSM 44594T=NRRL B-24209T) displays activity against a wide range of Gram-positive bacteria, including enterococci and clinical isolates, that are resistant to commonly applied antibiotics (Sanchez et al., 1992Go).

Micrographs of the strain described in this study are shown in Fig. 1Go. Morphological and physiological characteristics of DSM 44594T were observed on various agar cultures as described by Shirling & Gottlieb (1966)Go: yeast extract/malt extract agar (ISP 2), oatmeal agar (ISP 3), inorganic salt/starch agar (ISP 4), glycerol/asparagine agar (ISP 5), peptone/yeast extract/iron agar (ISP 6) and tyrosine agar (ISP 7), incubated for 10 days at 28 °C. For scanning electron microscopy (Grabley et al., 1992Go), the strain was grown on ISP 3 agar. A honey-yellow vegetative mycelium developed on all ISP media tested (RAL colour code 1005; Deutsches Institut für Gütesicherung und Kennzeichnung e.V. – Reichsausschuß für Lieferbedingungen). Aerial mycelium was only formed on ISP 3 medium and a soluble red pigment was produced on ISP 7 medium. After 7–10 days on ISP 3 medium, sporangium-like elements were formed. These elements showed a smooth surface and a regular shape under the scanning electron microscope. Spores were not detected either inside or outside the pseudosporangia.



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Fig. 1. Pseudosporangia formation in strain DSM 44594T grown on ISP 3 medium for 14 days at 28 °C. Top, light microscopy (x200); bottom, scanning electron microscopy (x1000).

 
Utilization of carbohydrates was investigated on ISP 9 medium (Shirling & Gottlieb, 1966Go) by using a 12-well microtitre plate technique. Sodium chloride tolerance was also tested on 6-well microtitre plates by using a technique based on the method of Kutzner et al. (1986)Go. A fingerprint of enzymic activities was obtained by using API 20E and API ZYM test strips (Smith et al., 1972Go; Humble et al., 1977Go; Kilian, 1978Go). Reactions are indicated in the species description.

To determine the antimicrobial spectrum (Williams et al., 1989Go), bacteria were grown on Mueller–Hinton agar and fungi on Czapek Dox agar. Antibacterial activity was seen after cultivation on ISP 2, ISP 3 and starch media, especially against Staphylococcus aureus, Micrococcus luteus, Streptomyces murinus and Bacillus subtilis. Antifungal activity was not detected.

For metabolite production, Amycolatopsis strains were incubated in four different media: a soymeal medium, a starch medium and ISP 2 and 3 media for 7 days in a shaking flask culture at 28 °C. After cultivation, the whole culture was extracted with methanol, evaporated and dissolved in water.

Analysis of whole-cell diaminopimelic acid (A2pm) isomers and sugars was done by the method of Hasegawa et al. (1983)Go. Phospholipids and menaquinones were analysed by the method of Kutzner et al. (1986)Go. To determine the whole-cell fatty acid profile, the fast method with trimethylsulfonium hydroxide (TMSH) was used (Müller et al., 1990Go). Major fatty acids were i-C15 : 0 (22·5 %), C17 : 0 (11·4 %) and i-C16 : 0 (10·3 %), whilst i-C14 : 0 (6·4 %), ai-C15 : 0 (9·4 %), i-C15 : 0 2-OH (8·7 %), C15 : 0 (7·6 %), C17 : 1 (5·8 %), C16 : 0 (3·3 %), C15 : 1 (2·1 %), i-C17 : 0 (1·7 %), ai-C17 : 0 (3·4 %), i-C16 : 0 2-OH (2·8 %), ai-C15 : 0 2-OH (1·9 %), C17 : 0 2-OH (1·5 %) and 10-methyl i-C17 : 0 (1·2 %) occurred in smaller amounts. Phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine phosphatidylinositol and phosphatidylinositol mannoside. Menaquinones were MK-8(H4) and MK-9(H4). The peptidoglycan diamino acid was meso-A2pm; cell-wall sugars were arabinose and galactose.

Genomic DNA extraction, PCR-mediated amplification of the 16S rRNA gene and purification of PCR products were carried out as described previously (Rainey et al., 1996Go). The almost-complete 16S rRNA gene sequence of strain DSM 44594T (1464 nt) was aligned manually against 16S rRNA gene sequences of representatives of the main actinobacterial lineages and then against members of the genus Amycolatopsis. Pairwise evolutionary distances were computed by using the correction of Jukes & Cantor (1969)Go. A phylogenetic dendrogram (Fig. 2Go) was reconstructed from the distance matrix by using the treeing algorithm of DeSoete (1983)Go. Strain DSM 44594T was related closely to Amycolatopsis azurea DSM 43854T (99·2 % sequence similarity), Amycolatopsis orientalis IMSNU 20058T (99·0 %), Amycolatopsis japonica DSM 44213T (99·1 %) and Amycolatopsis keratiniphila DSM 44409T (99·1 %) (Al-Musallam et al., 2003Go). Sequence similarity values with less closely related members of the genus ranged between 95·0 and 98·8 %.



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Fig. 2. 16S rDNA dendrogram (DeSoete, 1983Go), displaying the phylogenetic position of strain DSM 44594T and phylogenetically related members of the genus Amycolatopsis. Numbers indicate percentages of 1000 bootstrap resamplings. More distantly related members of the genus served as a root. Bar, 1 % sequence divergence.

 
Automated ribotyping of the isolates was accomplished by using the RiboPrinter (Qualicon) system (Bruce, 1996Go) and PvuII as the standard restriction enzyme for cutting genomic DNA. Whilst the patterns of the type strains of A. japonica and A. orientalis bear some similarity, those of other strains, including DSM 44594T, are different (Fig. 3Go). For DNA–DNA reassociation experiments, DNA was isolated by using a French pressure cell (Thermo Spectronic) and was purified by chromatography on hydroxyapatite as described by Cashion et al. (1977)Go. DNA–DNA hybridizations were carried out in duplicate, according to methods described by De Ley et al. (1970)Go and Huß et al. (1983)Go, at 69 °C in 2x SSC that contained 10 % DMSO. Renaturation rates were calculated by using the computer program TRANSFER.BAS (Jahnke, 1992Go). DNA similarities were determined for strain DSM 44594T and its closest phylogenetic relatives. Strain DSM 44594T and A. azurea DSM 43854T, which share high 16S rRNA gene sequence similarity, showed 55·7 % DNA–DNA hybridization (mean of two determinations of 55·2 and 56·2 %). Similarly low values were found for strain DSM 44594T and the type strains of A. orientalis DSM 40040T (50·5 %, mean of 47 and 54 %) and A. lurida DSM 43134T (31·5 %, mean of 32 and 31 %). The type strains of the latter two species share only 44·5 % DNA similarity. The remote DNA relatedness of organisms that share >99·0 % 16S rRNA gene sequence similarity has recently been reported by Wink et al. (2003)Go.



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Fig. 3. Diversity of normalized PvuII ribotype patterns found within strain DSM 44594T and phylogenetically related Amycolatopsis strains.

 
On the basis of 16S rRNA gene sequence similarity and chemotaxonomic properties, strain DSM 44594T is classified as a member of the genus Amycolatopsis. Species of this genus have not previously been described to form sporangium-like structures that are surrounded by a well-defined wall and in which spores are not observed. Strain DSM 44594T produces the glycopeptide antibiotic decaplanin. The formation of glycopeptide antibiotics has also been reported for some phylogenetically related species, such as vancomycin by A. orientalis (Pittenger & Brigham, 1956Go), ristocetin by A. lurida (Grundy et al., 1956–1957Go) and azureamycin by A. azurea (Omura et al., 1979Go). Amycolatopsis mediterranei, on the other hand, being less closely related to these organisms, produces the antibiotic rifamycin.

Strain DSM 44594T differs from related Amycolatopsis species in cultural properties. Whilst the substrate mycelium is honey-yellow on all ISP media, A. azurea forms steel-blue to purple–violet colonies, A. orientalis and A. lurida form yellow to beige colonies, A. japonica forms white colonies on some ISP media and Amycolatopsis keratiniphila has sand-yellow colonies. Based on carbohydrate utilization patterns and the API ZYM and API 20E panels (Table 1Go), strain DSM 44594T has highest similarity to A. orientalis and A. lurida, but has more pronounced differences from A. azurea, A. japonica and other species (data not shown; Chun et al., 1999Go; Kim et al., 2002Go).


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Table 1. Utilization of carbohydrates and enzymic activities of strain DSM 44594T and type strains of related Amycolatopsis species

Taxa: 1, Strain DSM 44594T; 2, A. azurea DSM 43854T; 3, A. japonica DSM 44213T; 4, A. keratiniphila DSM 44409T; 5, A. orientalis DSM 40040T; 6, A. lurida DSM 43134T. All strains utilized glucose and arabinose and were positive for N-acetyl-{beta}-glucosamidase, chymotrypsin and acid phosphatase activities, acetoin production and gelatinase. No strain utilized rhamnose and all were negative for {beta}-glucuronidase, tryptophan deaminase and production of H2S and indole.

 
Stackebrandt & Goebel (1994)Go recommended a binary threshold value of about 97 % 16S rRNA gene sequence similarity between strains, above which it was advised to perform DNA–DNA reassociation experiments in order to determine whether or not organisms should be affiliated to the same species. Some members of the genus Amycolatopsis, however, are significantly more closely related than this by 16S rRNA gene sequence similarity (around 99·0 %), but DNA–DNA reassociation values are significantly below 70 %, the recommended threshold value for species delineation (Wayne et al., 1987Go). For example, Amycolatopsis methanolica NCIB 11946T and Amycolatopsis thermoflava NBRC 14333T share 99·8 % sequence similarity and the corresponding DNA–DNA binding value was 21 %; similarly, 16S rRNA gene sequence similarity between Amycolatopsis eurytherma NCIMB 13795T and strains NCIB 11946T and NBRC 14333T was also 99·2 % and the corresponding DNA–DNA binding values were 60 and 2 %, respectively (Chun et al., 1999Go; Kim et al., 2002Go). The phylogenetically closest neighbour of the decaplanin-producing strain DSM 44594T is A. azurea DSM 43854T, which shares 99·2 % 16S rRNA gene sequence similarity. Similar values were found for the type strains of A. orientalis and A. lurida. As the corresponding DNA–DNA reassociation value was determined to be <56 %, we refrained from testing the binding rate for strain DSM 44594T and other Amycolatopsis species. We consider that strain DSM 44594T represents a distinct species with respect to phylogenetic position and genomic, morphological and metabolic uniqueness, for which we propose the name Amycolatopsis decaplanina sp. nov.

Description of Amycolatopsis decaplanina sp. nov.
Amycolatopsis decaplanina (de.ca.pla.ni'na. N.L. fem. adj. decaplanina formed from the name of the antibiotic decaplanin, which is produced by the organism).

Aerobic, non-motile, Gram-positive, catalase-positive actinomycete that forms extensively branched substrate mycelium. After 7–10 days on ISP medium 3, regular-shaped to globose and smooth-surfaced sporangium-like elements (pseudosporangia) are formed. Spores are not detected either inside or outside the pseudosporangia. Colonies are honey-yellow on ISP media 1–7. Aerial mycelium is formed only on ISP medium 3. A soluble red pigment is only produced on ISP medium 7. Melanoid pigment is not produced. Carbohydrate utilization and enzymic relation towards the API ZYM and API 20E substrate panels are indicated in Table 1Go. Major fatty acids (>10 %) are i-C15 : 0, i-C16 : 0 and C17 : 0. Menaquinones are MK-8(H4) and MK-9(H4). Produces the glycopeptide antibiotic decaplanin.

Type strain is FH 1845T (=DSM 44594T=NRRL B-24209T). Isolated from soil in India.


    ACKNOWLEDGEMENTS
 
We thank Hans Trüper for advice on the species name and Jolantha Swiderski for phylogenetic analyses.


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