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1 Departamento de Biologia Celular, Universidade de Brasilia, DF 70910900, Brazil
2 Fundacão Tropical de Pesquisas e Tecnologia, ‘Andre Tosello’, Rua Latino Coelho 1301, 13087-010, Campinas (SP), Brazil
3 Departamento de Bioquimica e Biofisica, Universidade Federal de Goias, GO 74001970, Brazil
4 Department of Agricultural and Environmental Science, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
Correspondence
Michael Goodfellow
m.goodfellow{at}ncl.ac.uk
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Present address: CPQBA/UNICAMP, CP 6171, CEP 13083-970 Campinas, SP, Brazil. 
Present address: KRIBB, 52 Oun-dong, Yusong-gu, Taejon, 305-333, Republic of Korea.
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; Goodfellow et al., 1999). The genus currently accommodates 26 recognized species, which form a clade within the evolutionary radiation occupied by mycolic-acid-containing actinomycetes, that is, by actinomycetes that comprise the suborder Corynebacterineae Stackebrandt et al. 1997. The taxonomic status of most of the species is supported by a rich combination of molecular systematic and numerical phenetic data (Goodfellow et al., 1999; Hamid et al., 2001; Maldonado et al., 2001; Yassin et al., 2001a, b). The improved classification of the genus provides a framework for the recognition of additional nocardial species.
It seems likely that soil is the primary reservoir of nocardiae (Cross et al., 1976; Orchard et al., 1977), though members of the genus are better known as causal agents of actinomycete mycetoma and nocardioses (McNeil & Brown, 1994; Goodfellow, 1998; Hamid et al., 2001). Little is known about the biology of nocardiae in natural habitats, though they have been considered to form part of the autochthonous soil microflora (Orchard, 1979, 1981). There is also evidence that nocardial species diversity in natural and artificial habitats is grossly underestimated (Orchard & Goodfellow, 1980; Wang et al., 1999; Maldonado et al., 2001). It is important to establish the species richness of nocardiae in natural ecosystems in order to determine the roles that specific nocardiae play in organic-matter turnover; representatives of such novel taxa also form high-quality biological material for exploitable biology (Bull et al., 2000).
The Brazilian Cerrado is an extensive species-rich ecosystem that contains commercially significant actinomycetes (Huddleston et al., 1997; Esposito et al., 1998). In a search for novel actinomycetes indigenous to this ecosystem, an unusual strain was isolated and provisionally assigned to the genus Nocardia by using morphological criteria. The aim of the present study was to determine the taxonomic status of this organism by using a polyphasic taxonomic approach.
Strain Y9T was isolated on an R5 agar plate (Hopwood et al., 1985) that had been incubated for 4 days at 30 °C, following incubation with a soil sample collected from a Cerrado cultivated field of corn and Brachiaria grass; the sample had been kept for 5 months at 4 °C and treated with CaCO3 prior to the preparation of a dilution series. The isolate was maintained on modified Bennett's agar (Jones, 1949) at room temperature and as suspensions of mycelial fragments in glycerol (20 %, v/v) at -80 °C. Biomass for chemotaxonomic studies was grown in shake flasks of modified Bennett's broth for 5 days at 28 °C and harvested by centrifugation; the resultant pellets were washed twice with distilled water.
The colonial and micromorphological properties of the tested strain were observed using standard procedures following inoculation on modified Bennett's agar plates for 14 days at 30 °C. The remaining phenotypic properties were scored following established procedures (Isik et al., 1999). The isomeric form of diaminopimelic acid (A2pm) of strain Y9T was determined by TLC of whole-organism hydrolysates (Staneck & Roberts, 1974). Standard procedures were also used for the extraction and analysis of mycolic acids (Minnikin et al., 1975), whole-organism sugars (Schaal, 1985) and isoprenoid quinones and polar lipids (Minnikin et al., 1984), using appropriate controls. The base composition of DNA of the strain was determined using the reverse-phase HPLC method described by Tamaoka (1994) and the HPLC conditions outlined by Gerke et al. (1984). DNA–DNA hybridizations were made, in duplicate, between Nocardia africana SD769T (=DSM 44491T) and Nocardia veterana N1071T (=DSM 44445T) and between Nocardia strain Y9T and the former two strains, under the auspices of the identification service at the Deutsche Sammlung von Mikroorganismen und Zellkulturen (Braunschweig, Germany), as described by Kim et al. (1999). Genomic DNA was extracted and amplified from single colonies grown on modified Bennett's agar using a procedure (Chun & Goodfellow, 1995) slightly modified from that of Pitcher et al. (1989). PCR amplification of the 16S rRNA gene was performed as described by Wang et al. (2001), and the resultant PCR product was purified by using the Wizard PCR purification system (Promega) according to the manufacturer's instructions. The purified PCR products were sequenced using a Taq Dye Deoxy Terminator cycle sequencing kit (Applied Biosystems) and two universal primers, as described previously (Lu et al., 2001). Sequence gel electrophoresis was carried out and the nucleotide sequence obtained automatically by using an Applied Biosystems DNA sequencer (model 373A) and software provided by the manufacturer.
The 16S rDNA sequence of the test organism was aligned manually against nucleotide sequences of representative Nocardia strains retrieved from the Ribosomal Database Project (Maidak et al., 1997) and the GenBank database, using the PHYDIT program (J. Chun, unpublished data). Evolutionary trees were inferred using the least-squares (Fitch & Margoliash, 1967), maximum-likelihood (Felsenstein, 1981), maximum-parsimony (Kluge & Farris, 1969) and neighbour-joining (Saitou & Nei, 1987) routines from the PHYLIP suite of programs (Felsenstein, 1993). The algorithm of Jukes & Cantor (1969) was used to generate evolutionary distance matrices for the least-squares and neighbour-joining methods. The robustness of the unrooted trees was evaluated by bootstrap analysis of 1000 resamplings, using the SEQBOOT and CONSENSE programs from the PHYLIP package (Felsenstein, 1993).
The almost complete 16S rDNA sequence (1460 nt) obtained for strain Y9T was compared with those of related actinomycetes and found to contain all of the signature nucleotides expected for members of the suborder Corynebacterineae and the family Nocardiaceae (Stackebrandt et al., 1997). The high 16S rDNA sequence similarities found between the tested strain and representatives of the genus Nocardia (94·0–98·8 %) support its inclusion in this taxon. The 16S rDNA nucleotide sequence of strain Y9T also contains the signature nucleotides characteristic of members of the genus Nocardia (Chun & Goodfellow, 1995).
It is evident from the 16S rDNA sequence data that strain Y9T forms a distinct subclade in the nocardial tree together with N. africana, Nocardia vaccinii and N. veterana (Fig. 1). The taxonomic integrity of this subclade was supported by all four treeing algorithms and by the 86 % bootstrap value obtained in the neighbour-joining analysis. Strain Y9T shares 16S rDNA nucleotide similarity of 98·8 % with N. africana, 98·1 % with N. vaccinii and 99·0 % with N. veterana, values that respectively correspond to 17, 27 and 14 differences at 1420 nt sites. Higher 16S rDNA similarity values have been recorded between representatives of several validly described Nocardia species found to have DNA–DNA relatedness values well below the 70 % cut-off point recommended by Wayne et al. (1987) for the delineation of genomic species of bacteria. The type strains of Nocardia brevicatena and Nocardia paucivorans, for instance, were found to share 16S rRNA gene sequence similarity of 99·6 % and a DNA relatedness value of 61·9 % (Yassin et al., 2000a). Similarly, the type strains of Nocardia carnea and Nocardia flavorosea were shown to share a high 16S rRNA nucleotide similarity value (99·2 % or 12 nucleotide differences) and a mean DNA relatedness value of 5 % when the N. carnea strain was used as the probe (Chun et al., 1998). In the present study, Nocardia strain Y9T showed a mean DNA–DNA relatedness value of 60·5 % with N. africana SD769T and 58 % with N. veterana N1071T; the corresponding value between the N. africana and N. veterana strains was 47·8 %.
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; Goodfellow et al., 1999). The organism is an aerobic, Gram-positive, acid–alcohol-fast actinomycete that forms an extensive branched substrate mycelium that fragments into irregular, rod-shaped, non-motile elements and supports pinkish-white aerial hyphae on modified Bennett's agar. The strain was also shown to produce whole-organism hydrolysates rich in meso-A2pm, arabinose and galactose (wall chemotype IV sensu Lechevalier & Lechevalier, 1970), to have major amounts of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides (phospholipid type II sensu Lechevalier et al., 1977), to have mycolic acids that co-migrated (Rf value of about 0·47) with those extracted from marker Nocardia strains and to have DNA with a G+C content of 68·8 mol%. The isolate also contained predominant amounts of hexahydrogenated menaquinones with eight isoprene units where the end two were cyclized; this menaquinone is characteristic of representatives of the genera Nocardia and Skermania (Chun et al., 1997; Goodfellow et al., 1999). The biochemical, degradative and growth profiles of strain Y9T also serve to distinguish it from the type strains of the validly described species of Nocardia (Table 1).
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Description of Nocardia cerradoensis sp. nov
Nocardia cerradoensis (cer.ra.do.en'sis. N.L. fem. adj. cerradoensis pertaining to the Cerrado, soil of which was the source of the organism).
Aerobic, Gram-positive, catalase-positive, slightly acid–alcohol-fast, non-motile actinomycete that produces an orange substrate mycelium that fragments in situ into irregular rod-shaped elements. Pinkish-white aerial hyphae are formed. Orange to tan colonies are produced on modified Bennett's agar. Colony elevation is convex to irregular, and colony margins are filamentous. Diffusible pigments are not produced. Aesculin and urea are hydrolysed and nitrate is reduced. Does not degrade adenine, casein, elastin, hypoxanthine, tyrosine, uric acid or xanthine. Grows well at 30 °C but does not grow at 45 °C. D(-)-Arabinose, dulcitol, D(-)-fructose, D(+)-glucose, glycerol, inulin, D(+)-maltose, D(+)-mannose, D(+)-melibiose, methyl 
-D-glucoside, D(-)-ribose, salicin, D(+)-sucrose and D(+)-trehalose (all at 1 %, w/v), acetate, benzoate, fumarate, m-hydroxybenzoic acid, DL-malate, pyruvate and succinate (at 0·1 %, w/v) are used as sole carbon sources for energy and growth, but adonitol, arbutin, D(+)-cellobiose, meso-erythritol, ethanol, D(-)-fucose, D(+)-galactose, glycogen, meso-inositol, D(+)-lactose, D(+)-melezitose, D(+)-raffinose, xylitol, D(+)-xylose, isoamyl alcohol, isobutanol (at 1 %, w/v), benzoate, butyrate, gluconate and p-hydroxybenzoic acid (at 0·1 %, w/v) are not. L-Glutamate, L-leucine, L-proline and L-valine are used as sole carbon and nitrogen sources, but acetamide, L-alanine, L-aspartic acid, gelatin, monoethanolamine, L-phenylalanine, uric acid and urea (all at 0·1 %, w/v) are not. The G+C content of the DNA is 68·8 mol%. The organism was isolated from Cerrado soil in Brazil. The type strain is Y9T (=CCT 5601T =DSM 44546T). The species description is based on a single strain and hence it serves as the type strain.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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Chun, J. & Goodfellow, M. (1995). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45, 240–245.
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