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1 Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, 41080 Sevilla, Spain
2 Hans-Knöll-Institut für Naturstoff-Forschung eV, D-07745 Jena, Germany
Correspondence
Cesareo Saiz-Jimenez
saiz{at}irnase.csic.es
| ABSTRACT |
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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains 20-5T and 23-23T are AY507129 and AY507128, respectively.
| MAIN TEXT |
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In this study, two strains, 20-5T and 23-23T, are described. Strain 20-5T was isolated from a top soil sample collected a few metres from the entrance of Grotta dei Cervi, Porto Badisco, Italy (Laiz et al., 2000
) and strain 23-23T was from a soil sample collected inside the cave. Both strains were isolated using PY-BHI agar (Yokota et al., 1993
) incubated at 28 °C. Cells for chemotaxonomic analyses were prepared in OM79 medium (Prauser & Falta, 1968
), pH adjusted to 7·5, containing (l1): 10 g glucose, 10 g Bacto-Peptone (Difco), 2 g casein hydrolysate, 2 g yeast extract and 6 g NaCl. The following type strains were included for comparative studies: A. fucosus IMET 11529T, A. cerinus subsp. cerinus IMET 11525T, A. cerinus subsp. nitratus IMET 11532T and A. ramosus IMET 11027T.
Cell morphology and cell dimensions were examined using a Zeiss Axioscope 2 phase-contrast microscope equipped with image analysing Axio Vision 2.05 software. Colony morphology of 3- and 14-day-old cultures grown on OM79 was studied using a stereo microscope.
Acid production from a variety of substrates was tested using the API 50 CH system and API 50CHB/E medium (bioMérieux) according to the manufacturer's instructions. Decomposition of adenine, hypoxanthine, xanthine and tyrosine, utilization of organic acids, nitrate reduction, urease activity, catalase and hydrogen sulfide production, hydrolysis of gelatin and Tween 80, methyl red and VogesProskauer, and oxidase activity were analysed as reported previously (Groth et al., 1996
). Indole production and hydrolysis of hippurate were studied as recommended by Smibert & Krieg (1994)
. Casein and starch hydrolysis was examined according to Cowan & Steel (1965)
. Susceptibility to antibiotics was studied by placing antibiotic discs (Oxoid) on OM79 agar plates that were seeded with suspensions of the test strains. The API ZYM galleries (bioMérieux) were used to study enzymic activities.
Analysis of cell wall amino acids, whole cell sugars, menaquinones, polar lipids and the acyl type was carried out as described by Groth et al. (1996)
. Cellular fatty acid profiles were analysed according to standard methods recently described by Gonzalez et al. (2004)
.
Bacterial DNA was extracted following the method described by Marmur (1961)
. The 16S rRNA gene was amplified by PCR using the conserved primers 27F (5'-AGA GTT TGA TCC TGG CTC AG) and 1522R (5'-AAG GAG GTG ATC CAG CCG CA). PCR thermal conditions were as follows: 95 °C for 1 min; 35 cycles of 95 °C for 15 s, 55 °C for 15 s, 72 °C for 2 min; and a final extension cycle at 72 °C for 10 min. Forward and reverse strands of the amplified DNA fragment were sequenced in an ABI 3700 sequencer (Applied Biosystems). A similarity search was performed using the BLAST algorithm (Altschul et al., 1990
) at the NCBI database (National Centre for Biotechnology Information; http://www.ncbi.nlm.nih.gov/). Alignments and phylogenetic relationships were determined by the neighbour-joining method using the ARB software package (Ludwig et al., 1998
).
The G+C content of the DNA was determined according to the fluorimetric method described by Gonzalez & Saiz-Jimenez (2002)
using thermal denaturation temperature. The degree of DNADNA relatedness between the two isolated strains and previously described Agromyces species was determined by measuring the divergence between the thermal denaturation midpoint of homoduplex DNA and heteroduplex DNA (
Tm), as described by De Ley et al. (1970)
. The approximate degrees of DNA relatedness were calculated following the relationship proposed by Rosselló-Mora & Amann (2001)
between
Tm and DNADNA binding.
It is apparent from both phenotypic and phylogenetic results that strains 20-5T and 23-23T are members of the genus Agromyces. The comparison of 16S rRNA gene sequences revealed significant differences below the generally accepted species threshold (97 %) (Stackebrandt & Goebel, 1994
) between the two isolates and all previously described species of the genus Agromyces (
96 % similarity). Phylogenetic analysis indicated that A. ramosus, A. fucosus and A. cerinus subsp. nitratus are the closest relatives to strains 20-5T and 23-23T, with similarity values ranging between 95 and 96 %. A phylogenetic tree showing the relationships between members of the genus Agromyces and strains 20-5T and 23-23T is shown in Fig. 1
.
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Based on the results of the polyphasic approach presented in this study, it is proposed that strains 20-5T and 23-23T represent two novel species of the genus Agromyces, Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov., respectively.
Description of Agromyces salentinus sp. nov.
Agromyces salentinus (sa.len.ti'nus. N.L. masc. adj. salentinus referring to Salentine Peninsula, the location of Grotta dei Cervi, the area from which the organism was isolated).
Cells form branching hyphae (width 0·50·7 µm) that break up into irregular diphtheroid and rod-like non-motile fragments. Gram-positive, aerobic and microaerophilic, growing between 10 and 37 °C (optimal growth at 2028 °C). Colonies are circular, convex, smooth and yellow. Colony diameter is about 1 mm. Phenotypic characteristics, including antibiotic susceptibility, are reported in Table 1
. In addition, acid is also produced from starch, amygdalin, D-arabinose, arbutin, cellobiose, aesculin, fructose, L-fucose, galactose, glucose, glycerol, glycogen and mannose. Grows in up to 4 % NaCl. Predominant menaquinones are MK-12 and MK-11. Amino acid composition of the cell wall includes diaminobutyric acid, glutamic acid, glycine and alanine. Whole cell sugars are rhamnose, glucose, galactose, arabinose and ribose. Major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, an unknown glycolipid and four unknown phospholipids. Acyl type is acetyl. Predominant fatty acids are anteiso-C15 : 0 and anteiso-C17 : 0.
Type strain is 20-5T (=HKI 0320T=DSM 16198T=NCIMB 13990T). The G+C content of the type strain is 72·3 mol%.
Description of Agromyces neolithicus sp. nov.
Agromyces neolithicus (ne.o.li'thi.cus. N.L. masc. adj. neolithicus referring to the origin of the neolithic paintings in Grotta dei Cervi, the source of the soil from which the organism was isolated).
Cells form branching hyphae (width 0·30·5 µm) that break up into irregular diphtheroid and rod-like non-motile fragments. Gram-positive, aerobic and microaerophilic, growing between 15 and 37 °C (optimal growth at 28 °C). Colonies are circular, convex, smooth and beige. Colony diameter is about 1 mm. Phenotypic characteristics, including antibiotic susceptibility, are reported in Table 1
. In addition, acid is also produced from starch, D-arabinose, arbutin, cellobiose, aesculin, fructose, L-fucose, galactose, glucose, glycerol, glycogen and mannose. No growth occurs in 4 % NaCl. Predominant menaquinones are MK-13 and MK-12. Amino acid composition of the cell wall includes diaminobutyric acid, glutamic acid, glycine and alanine. Whole cell sugars are glucose, galactose and mannose. Major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, two unknown phospholipids and an unknown glycolipid. Predominant fatty acids are anteiso-C15 : 0 and anteiso-C17 : 0.
Type strain is 23-23T (=HKI 0321T=DSM 16197T=NCIMB 13989T). The G+C content of the type strain is 65·3 mol%.
| ACKNOWLEDGEMENTS |
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