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Int J Syst Evol Microbiol 53 (2003), 1553-1559; DOI  10.1099/ijs.0.02595-0
© 2003 International Union of Microbiological Societies

Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae

Atsuko Matsumoto1, Yoko Takahashi1, Mayumi Shinose1, Akio Seino1, Yuzuru Iwai2 and Satoshi Omura1,2

1 Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
2 The Kitasato Institute, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan

Correspondence
Yoko Takahashi
ytakaha{at}lisci.kitasato-u.ac.jp


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 METHODS
 RESULTS AND DISCUSSION
 REFERENCES
 
A novel actinomycete strain was isolated from a soil sample collected in Japan by using gellan gum as a solidifying agent. Spore-chains from the short sporophores were straight and each had more than 20 spores per chain. Spores possessed no motility. Cell-wall peptidoglycan contained meso-diaminopimelic acid, glycine, alanine and glutamic acid; whole-cell hydrolysates contained arabinose, galactose and xylose. The acyl type of the peptidoglycan was glycolyl. The predominant menaquinones were MK-10(H4) and MK-10(H6); MK-10(H8) was a minor component. Mycolic acids were not detected. The diagostic phospholipid was phosphatidylethanolamine. Cellular fatty acids included heptadecenoic (C17 : 1), 14-methylpentadecanoic (i-C16 : 0) and octadecenoic (C18 : 1) acids. The G+C content of the DNA was 70 mol%. On the basis of morphogical and chemotaxonomic properties and phylogenetic analysis based on 16S rDNA sequence data, it is proposed that this strain should be classified in a novel genus and species, Longispora albida gen. nov., sp. nov., in the family Micromonosporaceae. The type strain is K97-0003T (=NRRL B-24201T=JCM 11711T).

Abbreviations: DAP, diaminopimelic acid

Published online ahead of print on 11 April 2003 as DOI 10.1099/ijs.0.02595-0.

The GenBank/EMBL/DDBJ accession number for the 16S rDNA sequence of strain K97-0003T is AB089241.


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
METHODS
 RESULTS AND DISCUSSION
 REFERENCES
 
Members of the order Actinomycetales offer possibilities for the discovery of new bioactive compounds. Many new bioactive metabolites have been found from Streptomyces strains that were isolated from soil, in which strains of this genus are distributed at a high frequency. An efficient way to find new bioactive metabolites is by the discovery of new micro-organisms and many approaches have been used for this purpose, e.g. isolation from plants or soil in particular environments, pre-treatments of soil samples and changing the formulation of isolation media. As one of these various approaches, we tried to isolate actinomycete strains by using gellan gum, which was used for selective isolation of the genus Actinobispora Jiang et al. 1991Go by Suzuki et al. (1998)Go as a solidifying agent, instead of agar. As a result, we isolated strain K97-0003T, which produces actinohivin, a novel anti-HIV (human immunodeficiency virus) protein found in the culture broth of the strain by a syncytium formation assay system (Chiba et al., 2001Go).

Strain K97-0003T grew better on gellan gum media than on agar media. Morphological and chemotaxonomic properties of the strain indicated that it belonged to the family Micromonosporaceae (Krasil'nikov 1938Go, emend. Koch et al. 1996Go). Phylogenetic analysis based on 16S rDNA sequence data showed that the strain formed a lineage within the family Micromonosporaceae, but not within any existing genus. Therefore, we propose that the strain should be classified as a novel genus and species, Longispora albida gen. nov., sp. nov.


   METHODS
TOP
 ABSTRACT
 INTRODUCTION
 METHODS
RESULTS AND DISCUSSION
 REFERENCES
 
Micro-organisms.
Strain K97-0003T was isolated from a soil sample collected at Suginami, Tokyo, Japan, by culture on water/proline/gellan gum medium [tap water, 1 % proline, 1 % gellan gum (Kanto Chemical); unadjusted pH] at 27 °C.

Morphology.
Morphological characteristics of the strain were observed by scanning electron microscopy (model JSM-5600; JEOL) following incubation on 1/10 V8 juice/gellan gum medium [2 % V8 juice (Campbell's soup), 0·03 % CaCO3, 1 % gellan gum, tap water, pH 7·2] that contained 0·06 % CaCl2.2H2O for 20 days at 27 °C and fixation by 4 % osmium tetroxide vapour.

Cultural and physiological characteristics.
Cultural and physiological characteristics of the strain were determined following incubation for 2 weeks at 27 °C on media recommended by Waksman (1961)Go and the International Streptomyces Project (Shirling & Gottlieb, 1966Go). Colour names and hue numbers were determined according to the Color Harmony Manual (Taylor et al., 1958Go). The ability of the strain to grow on a range of sole carbon sources at 1 % (w/v) was determined in carbon utilization media (Pridham & Gottlieb, 1948Go) with agar or gellan gum and agar medium of yeast nitrogen base without amino acids (Difco), as described by Asano & Kawamoto (1986)Go. NaCl tolerance and pH and temperature ranges for growth were determined on yeast extract/malt extract agar (ISP medium 2). Media for spore formation were as follows: ISP media (2, 3 and 7), glucose/peptone, nutrient, water/proline (1 % proline, tap water), 1/10 V8 and 1/10 V8 that contained 0·06 % CaCl2.2H2O; 1·5 % agar or 1 % gellan gum was used as the solidifying agent.

Chemotaxonomic characterization.
Isomers of diaminopimelic acid (DAP) in whole-cell hydrolysates were determined by TLC following standard methods (Becker et al., 1965Go; Hasegawa et al., 1983Go) and the N-acyl types of muramic acid were determined by the method of Uchida & Aida (1977)Go. Purified cell wall was obtained by the method of Kawamoto et al. (1981)Go and the amino acid composition of hydrolysed cell walls was determined by TLC. Whole-cell sugars were analysed after Becker et al. (1965)Go, presence of mycolic acids was examined by TLC following Tomiyasu (1982)Go and phospholipids were extracted and identified following the method of Minnikin et al. (1977)Go. Menaquinones were extracted and purified by the method of Collins et al. (1977)Go, then analysed by HPLC (model 802-SC; Jasco) on a chromatograph equipped with a CAPCELL PAK C18 column (Shiseido) (Tamaoka et al., 1983Go). Methyl esters of cellular fatty acids were prepared by direct transmethylation with methanolic hydrochloride and analysed by using GLC (model GC-17A; Shimadzu) with a DB-23 capillary column (0·25 mmx30 m; J&W Scientific) (Suzuki & Komagata, 1983Go).

DNA base composition.
Chromosomal DNA was prepared by using the procedure of Marmur (1961)Go and the G+C content of the DNA preparations was determined by the HPLC method of Tamaoka & Komagata (1984)Go.

Analysis of 16S rDNA sequence.
Chromosomal DNA was prepared by using the same method as above. 16S rDNA was PCR-amplified by using previously described methods (Takahashi et al., 2002Go) and was sequenced directly on an ABI model 377A automatic DNA sequencer by using a PRISM Ready Reaction Dye Primer Cycle Sequencing kit (Applied Biosystems). CLUSTAL W software (Thompson et al., 1994Go) was used for multiple alignment of selected sequences, for calculating evolutionary distances (Kimura, 1980Go) and similarity values and for constructing a phylogenetic tree based on the neighbour-joining method (Saitou & Nei, 1987Go). Data were resampled with 1000 bootstrap replications (Felsenstein, 1985Go). For the phylogenetic tree by the maximum-likelihood method, PAUP* version 4.0 beta 8 (Swofford, 2001Go) was used.


   RESULTS AND DISCUSSION
TOP
 ABSTRACT
 INTRODUCTION
 METHODS
 RESULTS AND DISCUSSION
REFERENCES
 
Cultural and morphological characteristics
After incubation for 2 weeks at 27 °C, strain K97-0003T grew well on yeast extract/malt extract agar, oatmeal agar, peptone/yeast extract/iron agar and nutrient agar, but aerial mycelia did not grow (Table 1Go). After substitution of agar by gellan gum, aerial mycelia grew slightly on a few media and spores were produced well on 1/10 V8 gellan gum medium that contained CaCl2 (Table 2Go).


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  		Table 1. Growth and cultural characteristics of strain K97-0003T

Strain K97-0003T did not grow on inorganic salts/starch agar (ISP medium 4), sucrose/nitrate agar, glucose/nitrate agar or glycerol/calcium malate agar. No aerial mycelia were produced on any medium.

 

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  		Table 2. Aerial mycelium formation of strain K97-0003T on various media

-, Negative; +t, trace aerial mycelium observed with a light microscope; +, poor aerial mycelium; ++, aerial mycelium produced (better than +).

 
Short sporophores branched from the vegetative mycelia; spore-chains from the sporophores were straight and each had more than 20 spores per chain. Spores were cylindrical, 0·4–0·5x1·0–1·4 µm and had a smooth surface (Fig. 1Go). Whirls, sclerotic granules, sporangia and flagellated spores were not observed.



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  		Fig. 1. Scanning electron micrograph of spore-chains of strain K97-0003T, grown on 1/10 V8+CaCl2 gellan gum medium for 20 days at 27 °C. Bar, 1 µm.

 
Physiological characteristics
Strain K97-0003T grew at 12–37 °C and the optimum range was 21–33 °C. No melanoid pigment was produced; tests for reduction of nitrate, liquefaction of gelatin and coagulation and peptonization of milk were positive. Hydrolysis of starch was negative on gellan gum medium and the strain did not grow on agar medium. The strain utilized D-glucose, but not L-arabinose, D-fructose, myo-inositol, D-mannitol, melibiose, raffinose, L-rhamnose, sucrose or D-xylose, on agar and gellan gum media. Cellulose was not decomposed. The pH range for growth was 6–9. The strain did not grow in the presence of 2 % NaCl.

Chemotaxonomic characteristics
Strain K97-0003T contained arabinose, galactose and xylose in whole-cell hydrolysates. Cell-wall peptidoglycan contained meso-DAP, glycine, alanine and glutamic acid. The acyl type of the peptidoglycan was glycolyl. Predominant menaquinones were MK-10(H4) and MK-10(H6) and a minor menaquinone component was MK-10(H8). Mycolic acids were not detected. The only phospholipid detected was phosphatidylethanolamine; phosphatidylcholine, phosphatidylglycerol and an unidentified phospholipid that contains glucosamine were absent. This corresponds to phospholipid pattern II sensu of Lechevalier et al. (1977)Go. Predominant cellular fatty acid components were heptadecenoic (C17 : 1, 24 %), 14-methylpentadecanoic (i-C16 : 0, 20 %) and octadecenoic (C18 : 1, 16 %) acids (Table 3Go). The G+C content of the DNA was 70 mol%.


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  		Table 3. Fatty acid composition of strain K97-0003T

 
The acyl type of strain K97-0003T was glycolyl; mycolic acids were absent. These two characteristics show that this strain is a member of the family Micromonosporaceae, the family Glycomycetaceae or the genus Microbacterium (Orla-Jensen, 1919Go) in the family Microbacteriaceae (Table 4Go). However, its morphology and chemotaxonomic characters differed from those of members of the genus Microbacterium and of the only genus, Glycomyces (Labeda et al., 1985Go), of the family Glycomycetaceae. As a result, this strain was placed in the family Micromonosporaceae.


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  		Table 4. Comparison of morphological and chemotaxonomic characteristics of strain K97-0003T and genera that contain N-glycolyl muramic acid in the peptidoglycan and no mycolic acids

Taxa: 1, K97-0003T; 2, Micromonospora; 3, Actinoplanes; 4, Asanoa; 5, Catellatospora; 6, Catenuloplanes; 7, Couchioplanes; 8, Dactylosporangium; 9, Pilimelia; 10, Spirilliplanes; 11, Verrucosispora; 12, Virgisporangium; 13, Glycomyces; 14, Microbacterium. Data were taken from Labeda et al. (1985)Go, Stackebrandt & Kroppenstedt (1987)Go, Vobis (1989)Go, Goodfellow et al. (1990)Go, Evtushenko et al. (1991)Go, Tamura et al. (1994Go, 1997Go, 2001)Go, Rheims et al. (1998)Go, Takeuchi & Hatano (1998)Go, Kudo et al. (1999)Go, Lee et al. (2000)Go, Lee & Hah (2002)Go and Zlamala et al. (2002)Go. ND, Not determined; D, a substantial proportion of species differ.

 
At present, the family Micromonosporaceae consists of eleven genera: Actinoplanes (Couch, 1950Go), Asanoa (Lee & Hah, 2002Go), Catellatospora (Asano & Kawamoto, 1986Go), Catenuloplanes (Yokota et al., 1993Go), Couchioplanes (Tamura et al., 1994Go), Dactylosporangium (Thiemann et al., 1967Go), Micromonospora (Ørskov, 1923Go), Pilimelia (Kane, 1966Go), Spirilliplanes (Tamura et al., 1997Go), Verrucosispora (Rheims et al., 1998Go) and Virgisporangium (Tamura et al., 2001Go). Although these genera are similar to each other, their cultural, morphological and chemotaxonomic characteristics differ somewhat. Genera that have spore-chains similar to those of strain K97-0003T are Asanoa, Catellatospora, Catenuloplanes, Couchioplanes and Spirilliplanes. The latter three possess motile spores; the two genera that do not possess them, Asanoa and Catellatospora, share this trait with strain K97-0003T. However, the genera Asanoa and Catellatospora make distinctive spore-chains that are borne directly from the vegetative hyphae that grow on the surface of agar media and do not produce true aerial mycelia. This indicates that strain K97-0003T does not belong to any known genus.

Phylogenetic analysis
The almost-complete 16S rDNA sequence (1496 nt) [positions 10–1506, according to the Escherichia coli numbering system of Brosius et al. (1978)Go] was determined for strain K97-0003T; a 1443 nt fragment, between positions 35 and 1475, was used for phylogenetic analysis and compared with 16S rDNA database sequences of members of the class Actinobacteria. Phylogenetic analysis based on this large dataset revealed that strain K97-0003T fell within the cluster of the family Micromonosporaceae and was clearly separated from members of the genera Glycomyces and Microbacterium (data not shown). Fig. 2Go shows the phylogenetic tree constructed by the neighbour-joining method; this tree revealed that strain K97-0003T branched deeply within the family Micromonosporaceae and belonged to no previously known genera in this family. The tree constructed by the maximum-likelihood method supported this result.



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  		Fig. 2. Phylogenetic tree showing the position of strain K97-0003T based on 16S rDNA analysis. Numbers at nodes indicate the level (%) of bootstrap support based on neighbour-joining analysis of 1000 resampled datasets. Only values >50 % are shown. Bar, 1 nucleotide substitution per 100 nucleotides.

 
The pattern of 16S rDNA signature nucleotides (Stackebrandt et al., 1997Go) differed only from that of the family Micromonosporaceae at position 502 (A). Sequence similarity values with other members of the family Micromonosporaceae were also low: Catellatospora citrea subsp. citrea, Virgisporangium aurantiacum, Asanoa ferruginea, Dactylosporangium aurantiacum, Pilimelia terevasa, Catenuloplanes japonicus, Verrucosispora gifhornensis, Spirilliplanes yamanashiensis, Micromonospora chalcea, Couchioplanes caeruleus subsp. caeruleus and Actinoplanes philippinensis (91·8–93·0 %).

From the above chemotaxonomic and morphological characteristics and phylogenetic analysis, we propose that strain K97-0003T should be classified in a novel genus and species, Longispora albida gen. nov., sp. nov.

Description of Longispora gen. nov.
Longispora (Lon.gi.spo'ra. L. adj. longus long; Gr. fem. n. spora spore; N.L. fem. n. Longispora long spore).

Cells are Gram-positive, aerobic, non-acid-fast and non-motile. Spore-chains are straight and have more than 20 spores on the tip of short sporophores that branch from vegetative mycelia. Cell-wall peptidoglycan contains meso-DAP, glycine and alanine; arabinose, galactose and xylose are detected in whole-cell hydrolysates. The acyl type is glycolyl. Predominant menaquinones are MK-10(H4) and MK-10(H6); a minor component is MK-10(H8). Mycolic acids are not detected. The diagnostic phospholipid is phosphatidylethanolamine (phospholipid type II). Habitat is soil. Mesophilic. The type species is Longispora albida.

Description of Longispora albida sp. nov.
Longispora albida (al.bi'da. L. fem. adj. albida somewhat white).

General morphological, chemotaxonomic and growth characteristics are as given above for the genus. Spores are cylindrical (0·4–0·5x1·0–1·4 µm) and have a smooth surface. Temperature range for growth is 12–37 °C and the optimum range is 21–33 °C. Growth occurs at pH 6–9. Melanoid pigment is not produced; positive for reduction of nitrate, liquefaction of gelatin and coagulation and peptonization of milk. D-glucose is utilized but L-arabinose, D-fructose, myo-inositol, D-mannitol, melibiose, raffinose, L-rhamnose, sucrose and D-xylose are not. Cellulose is not decomposed. Growth is better on gellan gum media than on agar media. No growth in the presence of 2 % NaCl. Predominant cellular fatty acid components are C17 : 1, iso-C16 : 0 and C18 : 1. The G+C content of the DNA is 70 mol%.

The type strain is K97-0003T (=NRRL B-24201T=JCM 11711T).


   ACKNOWLEDGEMENTS
 
We thank Mitsuko Matsura for assistance in this study. This study was supported in part by the Grant of the 21st Century COE Program, Ministry of Education, Culture, Sports, Science and Technology (MEXT).


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 ABSTRACT
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