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Int J Syst Evol Microbiol 55 (2005), 1465-1470; DOI  10.1099/ijs.0.63352-0
© 2005 International Union of Microbiological Societies

Nocardia polyresistens sp. nov.

Ping Xu1,2,{dagger}, Wen-Jun Li1,{dagger}, Shu-Kun Tang1, Yi Jiang1, Hua-Hong Chen1, Li-Hua Xu1 and Cheng-Lin Jiang1

1 The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, P. R. China
2 New Drug R & D, North China Pharmaceutic Corp., Shijiazhuang, 050015, P. R. China

Correspondence
Wen-Jun Li
wjli{at}ynu.edu.cn


    ABSTRACT
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 ABSTRACT
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A novel actinomycete strain YIM 33361T was isolated from a soil sample collected from Yunnan, China. Comparative 16S rRNA gene sequencing showed that the strain constituted a distinct subclade within the genus Nocardia, displaying more than 3 % sequence divergence from established species. Based on its morphological, chemotaxonomic, phenotypic and genotypic characteristics, strain YIM 33361T (=CCTCC AA 204004T=KCTC 19027T) is proposed as the type strain of a novel species, Nocardia polyresistens sp. nov.


Abbreviations: DAP, diaminopimelic acid

Published online ahead of print on 28 January 2005 as DOI 10.1099/ijs.0.63352-0.

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain YIM 33361T is AY626158.

{dagger}These authors contributed equally to this work. Back


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The application of chemotaxonomic, numerical phenetic and molecular systematic methods has promoted a radical reappraisal of the genus Nocardia (Goodfellow, 1998Go; Goodfellow et al., 1999Go; Lechevalier, 1976Go). This improved classification provides a sound framework for the recognition of additional species (Yassin et al., 2001Go). Members of the genus form extensively branched mycelia and the substrate hyphae fragment into rod-shaped, non-motile elements; aerial hyphae are usually formed but are sometimes only visible microscopically (Goodfellow & Lechevalier, 1989Go; Gordon & Mihm, 1957Go, 1962Go). Nocardiae are also characterized by a number of chemical markers, including the presence of meso-diaminopimelic acid (DAP), arabinose and galactose, mycolic acids and a DNA G+C content of 64–72 % (Goodfellow & Lechevalier, 1989Go; Goodfellow, 1992Go).

Currently, the genus Nocardia encompasses 54 accepted species with validly published names. Much of the emphasis in nocardial systematics has focused on the causal agents of actinomycetoma and nocardiosis (Goodfellow, 1992Go, 1998Go; McNeil & Brown, 1994Go). Little is known about nocardial species diversity, functional activities and commercial value in natural habitats (Kämpfer et al., 2004Go; Maldonado et al., 2000Go; Orchard et al., 1977Go; Orchard & Goodfellow, 1980Go; Saintpierre-Bonaccio et al., 2004Go; Wang et al., 2001Go; Zhang et al., 2003Go). In the course of our screening programme for new antibiotics, several actinomycete strains, which contained both type I and type II polyketide biosynthetic pathway genes, were isolated from soil samples collected from Yunnan Province, China (Xu et al., 2003aGo).

Strain YIM 33361T was isolated from a soil sample after 2 weeks incubation at 28 °C on water/proline (1 % proline in tap water) agar. Biomass for molecular systematic and most of the chemotaxonomic studies was obtained after incubation at 28 °C for 7 days by growing in shake flasks of yeast extract-malt extract broth (ISP 2 broth; Shirling & Gottlieb, 1966Go) supplemented with the vitamin mixture of HV medium (Hayakawa & Nonomura, 1987Go). Cultural characteristics were determined after 2 weeks at 28 °C by methods used in the International Streptomyces Project (ISP; Shirling & Gottlieb, 1966Go) except for modified Sauton's agar (Mordarska et al., 1972Go). Morphological observations of spores and mycelia were made by light microscopy (Olympus microscope BH-2) and scanning electron microscopy (model JEOL JSM 5600LV). Gram (Hucker's modification; Society for American Bacteriologists, 1957Go) and Ziehl–Neelsen (Gordon, 1967Go) preparations were also observed by light microscopy.

The test strain was examined for a range of phenotypic properties using standard procedures (Goodfellow, 1971Go; Williams et al., 1983Go). In addition, acid production from carbohydrates was carried out using media and methods described by Gordon et al. (1974)Go. The utilization of sole carbon and sole nitrogen sources was investigated after Gordon & Mihm (1957)Go and Tsukamura (1966)Go. Resistance to lysozyme was determined by the method of Gordon et al. (1974)Go. Tolerance to temperature (10, 27, 30, 37 and 45 °C), sodium chloride (4, 7, 10 and 13 %) and phenol (0·1, 0·2, 0·5 and 1·0 %) was tested using modified Bennett's agar (Williams et al., 1983Go). Resistance to antibiotics was examined using amikacin (30 µg), aureomycin (30 µg), ciprofloxacin (10 µg), chloramphenicol (30 µg), erythromycin (15 µg), gentamicin sulfate (10 µg), kanamycin (15 µg), netilmicin (10 µg), novobiocin (30 µg), oleandomycin (10 µg), penicillin G (10 U), polymyxin B (300 U), streptomycin sulfate (10 µg), terramycin (30 µg), tetracycline (30 µg), tobramycin sulfate (10 µg) and vancomycin (10 µg) discs (Goodfellow & Orchard, 1974Go) with glucose-yeast extract agar (Gordon & Mihm, 1962Go) as the basal medium; the results were recorded following incubation at 28 °C for up to 14 days. Colours and hues were determined according to Kelly (1964)Go.

Cell wells were purified and amino acids of peptidoglycan were analysed by TLC (Lechevalier & Lechevalier, 1980Go; Jiang et al., 2001Go). Analysis of whole-cell sugar composition followed procedures described by Becker et al. (1965)Go and Lechevalier & Lechevalier (1980)Go. Phospholipid analysis was carried out as described by Lechevalier et al. (1981)Go. The acid methanolysis procedure was used to detect mycolic acids (Minnikin et al., 1975Go). Menaquinones were determined using the procedures of Collins et al. (1977)Go. Biomass for the quantitative fatty acid analysis was prepared by scraping growth from TSA plates [trypticase soy broth (BBL), 3 % (w/v); Bacto agar (Difco), 1·5 % (w/v)] that had been incubated for 3 days at 28 °C. The fatty acids were extracted, methylated and analysed using the standard MIDI (Microbial Identification) system (Sasser, 1990Go; Kämpfer & Kroppenstedt, 1996Go).

Genomic DNA extraction and PCR amplification of the 16S rRNA gene from strain YIM 33361T were carried out using procedures described by Xu et al. (2003b)Go. The nearly complete resultant 16S rRNA gene sequence (1511 nucleotides) was aligned manually with corresponding almost-complete sequences of representative Nocardia species retrieved from the DDBJ, EMBL and GenBank databases by using BLAST (Altschul et al., 1997Go) and BLAST 2 sequences (Tatusova & Madden, 1999Go). Phylogenetic analysis was performed using the software packages PHYLIP (Felsenstein, 1993Go) and MEGA version 2.1 (Kumar et al., 2001Go) after multiple alignment of data by CLUSTAL X (Thompson et al., 1997Go); distances (distance options) according to the Kimura two-parameter model (Kimura, 1980Go, 1983Go) and clustering with the neighbour-joining method (Saitou & Nei, 1987Go). The topology of the tree was evaluated by performing a bootstrap analysis (Felsenstein, 1985Go) using 1000 resamplings. Arthrobacter globiformis was used as the outgroup.

The chromosomal DNA for genomic DNA G+C content analysis was extracted as described by Marmur (1961)Go. The DNA G+C base content of strain YIM 33361T was determined by the thermal denaturation method (Mandel & Marmur, 1968Go).

Strain YIM 33361T has phenotypic properties consistent with its classification in the genus Nocardia (Goodfellow et al., 1999Go). The organism is aerobic, Gram-positive, slightly acid–alcohol-fast. It developed well on several media including ISP 2 agar, glycerol-asparagine agar (ISP 5 medium; Shirling & Gottlieb, 1966Go), potato agar (DSMZ medium 129) and modified Bennett's agar (Jones, 1949Go), showed moderate growth on oatmeal agar (ISP 3 medium; Shirling & Gottlieb, 1966Go), inorganic salts-starch agar (ISP 4 medium; Shirling & Gottlieb, 1966Go), modified Sauton's agar (Mordarska et al., 1972Go) and nutrient agar (Waksman, 1961Go) and grew poorly on Czapek's agar (Shirling & Gottlieb, 1966Go) (Table 1Go). Diffusible pigments were not produced on any tested medium. Morphological features were observed on modified Bennett's agar. The substrate mycelium branched extensively and fragmented into non-motile, rod-shaped elements. The white aerial mycelium was also well developed. Sporotrichetes of up to seven spores were borne on both substrate and aerial hyphae.


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Table 1. Cultural characteristics of strain YIM 33361T on various media

Colours were determined according to Kelly (1964)Go.

 
Whole-organism hydrolysates of strain YIM 33361T were rich in meso-DAP, arabinose and galactose (cell wall chemotype IV sensu Lechevalier & Lechevalier, 1970Go) and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides (phospholipid type II sensu Lechevalier et al., 1977Go). The menaquinones were MK-8(H4{omega}-cycl.) (85 %) and MK-8(H2) (15 %). It was also characterized by the presence of mycolic acids that co-migrated (Rf value around 0·47) with those from marker strains of Nocardia. The fatty acid profile contained mainly straight-chain saturated, unsaturated and 10-methyl-branched fatty acids. The predominant components, as a proportion of the total fatty acid composition, were i-C15 : 0 (1·33 %), ai-C15 : 0 (5·73 %), i-C16 : 0 (1·76 %), cis7-C16 : 1 (1·33 %), i-2-OH-C15 : 0 (5·69 %), C16 : 0 (22·14 %), i-C17 : 0 (2·16 %), ai-C17 : 0 (2·72 %), C17 : 0 (1·53 %), cis6,9-C18 : 2 (10·86 %), cis9-C18 : 1 (10·05 %), C18 : 0 (21·16 %) and 10-methyl-C18 : 0 (10·5 %). The G+C content of genomic DNA was 65·6 mol%. Detailed results of the physiological features are indicated in Table 2Go and in the species description.


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Table 2. Phenotypic properties that separate strain YIM 33361T from related Nocardia species

Data were taken from this and previous studies (Maldonado et al., 2000Go; Wang et al., 2001Go; Zhang et al., 2003Go; Yassin et al., 2001Go; Albuquerque de Barros et al., 2003Go; Kämpfer et al., 2004Go; Saintpierre-Bonaccio et al., 2004Go; Kageyama et al., 2004aGo, bGo). Symbols: +, utilization; –, no utilization; D, doubtful; W, weak; ND, not determined.

 
A database search demonstrated that the strain YIM 33361T belongs to the family Nocardiaceae (Stackebrandt et al., 1997Go) and that the determined sequence contains all the signature nucleotides characteristic of the genus Nocardia (Chun & Goodfellow, 1995Go). The rooted phylogenetic tree (Fig. 1Go) indicated that strain YIM 33361T formed a distinct subclade within the genus Nocardia. Low 16S rRNA gene sequence similarity values (<97 %) were found with all species with validly published names of the genus Nocardia. The closest relatives of strain YIM 33361T were Nocardia pseudobrasiliensis DSM 44290T (AF430042) and Nocardia paucivorans DSM 44386T (AF430041) which both showed 96·92 % similarity (46 nucleotide differences in 1492 sites).



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Fig. 1. Phylogenetic dendrogram obtained by neighbour-joining analysis based on 1396 bp of 16S rRNA gene sequences, showing the position of strain YIM 33361T among its phylogenetic neighbours. Numbers on branch nodes are bootstrap percentages (1000 resamplings). Sequence accession numbers are given in parentheses. The sequence of Arthrobacter globiformis DSM 20124T (X80736) was used as the root (not shown). Bar, 0·01 substitutions per nucleotide position.

 
This is also supported by phenotypic data, as at least three differences in phenotypic properties were observed between strain YIM 33361T and the species with validly published names of the genus Nocardia (Table 2Go). Strain YIM 33361T, N. paucivorans IMMIB D-1632T and N. pseudobrasiliensis ATCC 51512T can also be distinguished easily by their physiological properties. Each of the two strains shows seven differences in comparison with the characteristics of strain YIM 33361T(Table 2Go).

In conclusion, the genotypic and phenotypic data show that strain YIM 33361T forms a novel species of the genus Nocardia, for which we propose the name Nocardia polyresistens sp. nov.

Description of Nocardia polyresistens sp. nov.
Nocardia polyresistens [poly.re.sis'tens. Gr. adj. polus many; L. part. adj. resistens resisting; N.L. part. adj. polyresistens resisting many (antibiotics)].

Aerobic, Gram-positive, catalase-positive and slightly acid–alcohol-fast. Aerial mycelium and substrate mycelium are extensively branched and fragment irregularly into rod-shaped, non-motile elements. A pale-yellow to moderate orange–yellow substrate mycelium carries sparse to abundant, white aerial hyphae on yeast extract-malt extract agar, Czapek's agar, modified Sauton's agar, modified Bennett's agar, potato agar and nutrient agar. A pale-yellow to yellow–white substrate mycelium bears pale-yellow to yellow–white aerial hyphae on glycerol-asparagine or inorganic salts-starch agar. Diffusible pigments are not formed. Ribose, glucose, mannose, fructose, sorbose, melibiose, xylose, sucrose, arabinose, galactose, maltose, lactose, cellobiose, raffinose, melezitose, mannitol, inositol, xylitol, dulcitol, adonitol, salicin, glycerol and dextrin are utilized as sole carbon and energy sources, but not rhamnose, trehalose, sorbitol, arabitol, acetate, malonate, citrate, oxalate or tartrate. Acid is not formed from these tested carbon sources. L-Valine, L-proline (weak), L-asparagine, L-tyrosine (weak), L-alanine and L-histidine are used as sole nitrogen sources, but not acetamide, L-hydroxyproline, L-lysine, L-methionine, L-tryptophan, L-threonine, L-glutamic acid, glycine, L-arginine, L-cysteine or phenylalanine. Urea, xanthine, hypoxanthine, amygdalin, keratin and chitin are hydrolysed. Tweens 20 and 80 are degraded, but not cellulose, starch, allantoin, glucosamine, aesculin, DNA or adenine. Tests for gelatin hydrolysis, nitrate reduction, melanin production, milk coagulation and peptonization, H2S production and resistance to KCN are negative. Grows between 28 and 37 °C, from pH 7 to 9, and in the presence of phenol at 0·1 %, but not in the presence of sodium chloride. Resistant to lysozyme, penicillin G, ciprofloxacin, vancomycin, polymyxin B, erythromycin, terramycin, aureomycin (weak), tobramycin, gentamicin sulfate, amikacin, netilmicin, novobiocin, kanamycin and oleandomycin but sensitive to tetracycline, streptomycin and chloramphenicol. The cell wall of strain YIM 33361T contains meso-DAP. Whole-cell sugars are galactose and arabinose. MK-8(H4{omega}-cycl.) is the major menaquinone and a minor amount of MK-8(H2) is also present. The phospholipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids are C16 : 0 (22·14 %), cis6,9-C18 : 2 (10·86 %), cis9-C18 : 1 (10·05 %), C18 : 0 (21·16 %) and 10-methyl-C18 : 0 (10·5 %). The G+C content of genomic DNA of the type strain is 65·6 mol%.

The type strain, YIM 33361T (=CCTCC AA 204004T=KCTC 19027T), was isolated from soil in Yunnan, China.


    ACKNOWLEDGEMENTS
 
This research was supported by the National Basic Research Program of China (project no. 2004CB719601), the National Natural Science Foundation of China (project no. 30270004) and the Yunnan Provincial Natural Science Foundation (project no. 2004 C0002Q).


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W.-J. Li, P. Xu, P. Schumann, Y.-Q. Zhang, R. Pukall, L.-H. Xu, E. Stackebrandt, and C.-L. Jiang
Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia
Int J Syst Evol Microbiol, July 1, 2007; 57(7): 1424 - 1428.
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Int. J. Syst. Evol. Microbiol.Home page
P. Kampfer, B. Huber, S. Buczolits, K. Thummes, I. Grun-Wollny, and H.-J. Busse
Nocardia acidivorans sp. nov., isolated from soil of the island of Stromboli
Int J Syst Evol Microbiol, June 1, 2007; 57(6): 1183 - 1187.
[Abstract] [Full Text] [PDF]


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