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Int J Syst Evol Microbiol 55 (2005), 153-157; DOI  10.1099/ijs.0.63199-0
© 2005 International Union of Microbiological Societies

Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.

Valme Jurado1, Ingrid Groth2, Juan M. Gonzalez1, Leonila Laiz1 and Cesareo Saiz-Jimenez1

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


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A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA–DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).


Published online ahead of print on 22 October 2004 as DOI 10.1099/ijs.0.63199-0.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains 20-5T and 23-23T are AY507129 and AY507128, respectively.


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The genus Agromyces, with the type species Agromyces ramosus, was established by Gledhill & Casida (1969)Go for filamentous, nutritionally fastidious, catalase- and oxidase-negative soil isolates. Zgurskaya et al. (1992)Go emended the description of the genus and added two species, each with two subspecies, Agromyces cerinus subsp. cerinus, A. cerinus subsp. nitratus, Agromyces fucosus subsp. fucosus and A. fucosus subsp. hippuratus, which are characterized by rapid growth on simple media and positive catalase and oxidase reactions. Recently, the reclassification of A. fucosus subsp. hippuratus as Agromyces hippuratus has been proposed (Ortiz-Martinez et al., 2004Go). Currently, the genus Agromyces encompasses ten species, among them Agromyces mediolanus (Suzuki et al., 1996Go), comprising the former misclassified species ‘Corynebacterium mediolanum’ and ‘Flavobacterium dehydrogenans’ and soil isolates lacking a mycelial growth phase. The remaining recognized species at the time of writing are Agromyces albus (Dorofeeva et al., 2003Go), Agromyces aurantiacus (Li et al., 2003Go), Agromyces bracchium, Agromyces luteolus and Agromyces rhizospherae (Takeuchi & Hatano, 2001Go).

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., 2000Go) and strain 23-23T was from a soil sample collected inside the cave. Both strains were isolated using PY-BHI agar (Yokota et al., 1993Go) incubated at 28 °C. Cells for chemotaxonomic analyses were prepared in OM79 medium (Prauser & Falta, 1968Go), pH adjusted to 7·5, containing (l–1): 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 Voges–Proskauer, and oxidase activity were analysed as reported previously (Groth et al., 1996Go). Indole production and hydrolysis of hippurate were studied as recommended by Smibert & Krieg (1994)Go. Casein and starch hydrolysis was examined according to Cowan & Steel (1965)Go. 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)Go. Cellular fatty acid profiles were analysed according to standard methods recently described by Gonzalez et al. (2004)Go.

Bacterial DNA was extracted following the method described by Marmur (1961)Go. 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., 1990Go) 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., 1998Go).

The G+C content of the DNA was determined according to the fluorimetric method described by Gonzalez & Saiz-Jimenez (2002)Go using thermal denaturation temperature. The degree of DNA–DNA 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 ({Delta}Tm), as described by De Ley et al. (1970)Go. The approximate degrees of DNA relatedness were calculated following the relationship proposed by Rosselló-Mora & Amann (2001)Go between {Delta}Tm and DNA–DNA 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, 1994Go) 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. 1Go.



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Fig. 1. Phylogenetic tree showing the relationships between species of the genus Agromyces and the two studied isolates (Agromyces salentinus 20-5T and Agromyces neolithicus 23-23T). Sequences used in this analysis were from A. fucosus, A. hippuratus, A. cerinus, A. ramosus, A. rhizospherae, A. albus, A. aurantiacus, A. luteolus, A. mediolanus, A. bracchium, A. salentinus and A. neolithicus.

 
A broad range of physiological characteristics also distinguished strains 20-5T and 23-23T from each other, including differences in the decomposition of gelatin and urea, reduction of nitrate, acid production from numerous different carbon sources, enzymic activities tested by the API ZYM galleries and sensitivity to some antibiotics (Table 1Go).


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Table 1. Characteristics that can be used to differentiate strains 20-5T and 23-23T from their closest relatives within the genus Agromyces

Taxa: 1, strain 20-5T; 2, strain 23-23T; 3, A. fucosus IMET 11529T; 4, A. ramosus IMET 11027T; 5, A. cerinus subsp. nitratus IMET 11532T; 6, A. cerinus subsp. cerinus IMET 11525T. Tested strains are all negative for hydrolysis of adenine and Tween 80 and positive for hydrolysis of aesculin and starch. Benzoate and DL-tartrate are not utilized by any of these strains. All strains are positive for the production of hydrogen sulfide. Voges–Proskauer, methyl red and indole tests gave negative results for all strains. All strains are susceptible to chloramphenicol (30 µg), imipenem (10 µg), ofloxacin (10 µg), oxytetracycline (30 µg), rifampicin (30 µg), tetracycline (30 µg), vancomycin (30 µg) and ovobiocin (5 µg) and sensitive to lincomycin (2 µg). All strains have alkaline phosphatase activity; none of them has lipase (C14) activity. –, Negative; +, positive; (+) weakly positive; +/–, variable; (+/–), weak and variable; ND, not determined.

 
Differences in the compositions of menaquinones, whole cell sugars, polar lipids, acyl type and cell wall amino acids are shown in Table 2Go. The predominant fatty acids of strains 20-5T and 23-23T were iso-C15 : 0 (6·0 and 12·8 %, respectively), anteiso-C15 : 0 (52·0 and 37·8 %), iso-C16 : 0 (12·9 and 13·0 %), iso-C17 : 0 (2·2 and 3·4 %) and anteiso-C17 : 0 (24·8 and 31·9 %).


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Table 2. Chemotaxonomic characteristics of strains 20-5T and 23-23T

For both strains, the acyl type was acetyl. Components are given in order of abundance (most abundant first).

 
The DNA G+C content underlined the distinct taxonomic position of the two strains within the genus Agromyces. The DNA G+C contents of strains 20-5T and 23-23T were 72·3 and 65·3 mol%, respectively. DNA–DNA relatedness studies showed significant differences between strains 20-5T and 23-23T (9 °C; corresponding to approximately 45 % relatedness) and between these two strains and the most closely related Agromyces species, A. ramosus (14 and 14 °C for strains 20-5T and 23-23T, respectively; corresponding to approximately 20 % relatedness), A. cerinus subsp. nitratus (16 and 11 °C; 10 and 35 % relatedness, respectively), A. cerinus subsp. cerinus (15 and 11 °C; 15 and 35 % relatedness, respectively) and A. fucosus (9 and 8 °C; corresponding to 45 and 50 % relatedness, respectively). Thus, DNA–DNA relatedness results showed differences below the species threshold (5 °C; Stackebrandt & Goebel, 1994Go) between strains 20-5T and 23-23T and their closest relatives within the genus Agromyces.

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 0·5–0·7 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 20–28 °C). Colonies are circular, convex, smooth and yellow. Colony diameter is about 1 mm. Phenotypic characteristics, including antibiotic susceptibility, are reported in Table 1Go. 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 0·3–0·5 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 1Go. 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
 
V. J. and L. L. are grateful for fellowships from the Spanish Ministry of Science and Technology (I3P programme) and J. M. G. is grateful for a contract from the Spanish Ministry of Science and Technology, ‘Ramón y Cajal’ programme. This study was supported by project BTE2002-04492-C02-01. We thank Christiane Weigel and Carmen Schult for their technical assistance.


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