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Microbial Research Discovery Unit, School of Biomolecular and Biomedical Sciences, Faculty of Science, Griffith University, Brisbane, Queensland 4111, Australia
Correspondence
Bharat K. C. Patel
bharat{at}genomes.sci.gu.edu.au
| ABSTRACT |
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-hydroxybutyrateThe GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain FaiI4T is AY078053.
| INTRODUCTION |
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| METHODS |
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Culture media.
Rouf's agar medium (Mulder & Deinema, 1992
) was used for enrichment and isolation. The medium contained (l-1): 1 g yeast extract, 5 g peptone, 0·2 g MgSO4.7H2O, 0·05 g CaCl2, 0·15 g ferric ammonium citrate, 0·05 g MnSO4.4H2O, 0·01 g FeCl3.4H2O, 17 g agar, 10 ml vitamin solution (Wolin et al., 1963
) and 1 ml trace-element solution (Zeikus et al., 1979
). Routine cultivation was performed in the same medium but without agar. Rouf's medium containing 0·06 % or 0·006 % (w/v) yeast extract instead of 1 g l-1 and without peptone and agar (referred to as Rouf's minimal medium) was used to test the physiological properties of the strain. Rouf's medium lacking agar but containing 5 g instead of 1 g yeast extract l-1 (referred to as Rouf's maximal medium) was used to determine the optimal environmental growth parameters. The pH of the medium was adjusted to 7·1 with NaOH when necessary.
Isolation and cellular characterization.
Agar plates were spread directly with 100 µl of the bore-water sample and incubated at 37, 40 and 50 °C for up to 3 days. Several colonies that developed at 40 °C were picked and restreaked onto new plates and the procedure was repeated twice. A colony with a light-pink colour was picked as being representative of several similar colonies, designated strain FaiI4T and studied further. Phase-contrast and electron microscopy of cells were performed as described previously (Andrews & Patel, 1996
). The presence of poly-
-hydroxybutyrate (PHB) was demonstrated by staining lightly heat-fixed cells with Sudan black B [0·3 % (w/v) in 70 % (v/v) ethanol] for 10 min followed by decolorizing with xylene for 10 s, drying and counterstaining with Safrarnine [0·5 % (w/v) in water] for 10 s. Phase-contrast microscopy and spore staining (Smibert & Krieg, 1994
) of early, exponential and late growth phase and 1-week-old cultures was used to determine the presence of spores. Mid-exponential and mid-stationary phase cultures exposed to heat at 70, 80, 90 and 100 °C for 10 and 20 min were used to inoculate fresh medium and incubated at the 41 °C in order to determine heat resistance.
Substrate utilization and physiological studies.
Rouf's minimal medium was used to test for growth on different substrates. Unless otherwise stated, substrates were tested by adding aliquots from 2 or 3 M sterile stock solutions to 5 ml medium to a final concentration of 21 mM. Yeast extract, peptone and casein hydrolysate (Amyl Media) were tested at 0·05 and 0·1 % (w/v), ethanol at 10 and 21 mM, methanol at 0·1, 0·5 and 1·0 % (w/v), N,N-dimethylformamide (DMF) and formamide at 0·15 and 0·5 % (w/v) and nitrilotriacetate (NTA) at concentrations from 0·007 to 0·5 % (w/v). Methane was injected into tubes of autoclaved medium capped with butyl septa, using a syringe with a single-use filter unit (Sartorius) attached at the end to filter-sterilize the gas at the same time. The ratio of methane to air in the tube was roughly 1 : 4. Thiosulfate (5 and 10 mM) was tested as an alternate electron acceptor with 0·02 and 0·003 % yeast extract. The pH was adjusted to 7·1 prior to inoculation when necessary and all tests were carried out in duplicate. Growth was measured as OD600 after incubation at 41 °C for up to 24 h.
API 20E (bioMérieux) and BBL Crystal E/NF (Becton Dickinson) identification kits were used to determine acid production from sugars, nitrate reduction, enzymic hydrolysis and utilization of various substrates using the manufacturers' recommended protocols. Catalase activity was determined on freshly growing colonies using 3 % (v/v) hydrogen peroxide solution. Hydrolysis of starch and casein and determination of oxidative or fermentative catabolism were carried out according to methods described by Smibert & Krieg (1994)
.
Rouf's maximal medium was used to determine pH (range pH 510), temperature (range 2560 °C) and NaCl [range 011 % (w/v)] optima.
Anaerobic growth was tested in TYEG medium (Wynter et al., 1996
). The presence of photosynthetic pigments and carotenoids was determined by scanning acetone extracts of 10 and 50 ml cultures that had been incubated in the dark and in the light, in a Cintra20 spectrophotometer (GBC Scientific Equipment) at wavelengths between 250 and 900 nm.
Antibiotic sensitivity.
Sensitivity to antibiotics (penicillin, ampicillin, neomycin, tetracycline, streptomycin, vancomycin, chloramphenicol and spectinomycin) was determined by adding the antibiotic to 10 ml aliquots of Rouf's maximal medium to final concentrations of 10, 50 and 100 µg ml-1. The cultures were incubated under optimal conditions for 24 h and growth was recorded by measuring the OD600. Percentage growth inhibition was calculated from cultures that had been grown under similar conditions in antibiotic-free medium.
DNA G+C content and 16S rRNA sequencing.
Genomic DNA was prepared using a modification of the method of Marmur (1961)
in which achromopeptidase (final concentration 0·8 µg µl-1) was used to improve cell lysis following lysozyme treatment. The genomic DNA was dissolved overnight in 0·1x SSC at a concentration of 20 µg ml-1 and the Tm was determined in 0·1x SSC using Escherichia coli DNA as a reference in a Cintra20 spectrophotometer.
The methods used for 16S rRNA gene amplification and sequencing have been reported previously (Andrews & Patel, 1996
). Sequences generated during this work were assembled into one complete sequence using Bioedit (Hall, 1999
). The consensus sequence was corrected manually for errors and the most homologous sequences, determined against the GenBank database using BLAST (Altschul et al., 1997
) and using the Sequence Match option against the Ribosomal Database Project (Maidak et al., 2001
), were extracted and aligned manually. Sequence uncertainties were omitted from the analysis and phylogeny from 1108 unambiguous nucleotides was determined as described previously (Andrews & Patel, 1996
).
| RESULTS |
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Strain FaiI4T did not grow anaerobically in TYEG medium and did not contain bacteriochlorophyll, indicating that it was not a photosynthetic bacterium. However, carotenoids were present in light- and dark-grown cultures.
Substrate utilization and physiological characteristics
Strain FaiI4T grew on yeast extract, which was absolutely required for growth on other substrates. Strain FaiI4T grew well on acetate, xylose, peptone and casein hydrolysate (Amyl Media) but not on glucose, sucrose, fructose, maltose, cellobiose, glycerol, ethanol, methanol, pyruvate, succinate, methane, benzoate, butyrate, oxalate, citrate, lactate, fumarate, glycine, aesculin, NTA, DMF or formamide as sole sources of carbon and energy in a medium containing 0·06 or 0·006 % yeast extract. Gelatin, but not starch or casein, was hydrolysed. Very weak acid production was observed from glucose and arabinose. Oxidase, urease, tryptophan deaminase, ornithine decarboxylase, arginine dihydrolase, H2S, lysine decarboxylase,
-galactosidase, arabinosidase, glucuronidase, glucosaminidase, xylosidase, indole from tryptophan and acetoin were not produced. Nitroanilidase, glucosidase and catalase were positive. Nitrate was reduced to nitrite. Thiosulfate did not stimulate growth.
Antibiotic susceptibility
Strain FaiI4T did not grow in the presence of 10 µg penicillin, ampicillin, neomycin, tetracycline, streptomycin and chloramphenicol ml-1 or 100 µg spectinomycin ml-1 but growth was inhibited only partially in medium containing 100 µg vancomycin ml-1.
G+C content and 16S rRNA sequence analysis
The G+C content of strain FaiI4T determined by the Tm method was found to be 63·5±0·5 mol%.
BLAST analysis indicated that strain FaiI4T was most closely related to the environmental clone WCHB1-55 (Dojka et al., 1998
) and the taxonomically undescribed strain SJA-9 (Von Wintzingerode et al., 1999
) in the class Alphaproteobacteria, phylum Proteobacteria (as proposed in the 2nd edition of Bergey's Manual of Systematic Bacteriology; Garrity & Holt, 2001
). Methylobacterium species (Patt et al., 1976
; Urakami et al., 1993
; Urakami & Komagata, 1984
) and Bosea thiooxidans (Das et al., 1996
) were the mostly closely related of the taxonomically valid taxa, with a mean similarity value of 93 % (Fig. 2
). Bootstrap analysis gave a high degree of confidence to this relationship (100 %). Strain FaiI4T was slightly less closely related to Chelatococcus asaccharovorans (Auling et al., 1993
; Egli et al., 1988
).
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| DISCUSSION |
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Penicillin and a number of other antibiotics that inhibit members of domain Bacteria also inhibited the growth of strain FaiI4T, suggesting an affiliation to this group of microbes. This was confirmed by analysis of the 16S rRNA gene which, in addition, indicated that the closest relatives of the isolate were C. asaccharovorans, B. thiooxidans and Methylobacterium species, respectively members of the families Beijerinckiaceae, Bradyrhizobiaceae and Methylobacteriaceae of the Alphaproteobacteria. Strain FaiI4T was placed almost equidistantly amongst them, with a similarity value of approximately 93 %. This relationship remained stable even with the selection of different members of the Alphaproteobacteria in the analysis. The high bootstrap value obtained for these datasets also suggests that strain FaiI4T is a deep-branching member of the Alphaproteobacteria and should be accorded generic status.
Strain FaiI4T is a strictly non-spore-forming aerobe, stains Gram-negative, is catalase-positive and does not produce indole or hydrolyse starch; these phenotypic properties are common to C. asaccharovorans, B. thiooxidans and Methylobacterium species. However, numerous other properties of strain FaiI4T are different from those of these close phylogenetic relatives (Table 1
). Strain FaiI4T has the highest optimum growth temperature (41 °C) and has a restricted substrate range for growth in comparison with these close relatives. In addition, the G+C content of the DNA of strain FaiI4T (63 mol%) is very different from those of B. thiooxidans (68 mol%) and Methylobacterium species (6671 mol%), but is similar to that of C. asaccharovorans. A number of other key metabolic differences also exist. Strain FaiI4T is unable to utilize NTA as a carbon source, a key differentiating property of C. asaccharovorans, a property that is also unique amongst bacteria. All 14 Methylobacterium species are characterized by their pink-pigmented colonies, production of PHB and extreme nutritional versatility in their ability to grow on organic substrates as well as C1 compounds, such as methane and methanol. Therefore, they are commonly referred to as the pink-pigmented facultatively methylotrophic microbes. Strain FaiI4T also produces pink colonies and PHB, but it has a number of key nutritional differences when compared with its four closest phylogenetic neighbours, namely Methylobacterium radiotolerans, Methylobacterium aminovorans, Methylobacterium extorquens and Methylobacterium organophilum, including its inability to grow on the C1 compounds tested (Table 1
).
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The phylogenetic and phenotypic evidence presented above suggests that strain FaiI4T cannot be assigned to any known taxon. We therefore propose to describe it as representative of a novel species of a new genus, Microvirga subterranea gen. nov., sp. nov.
Description of Microvirga gen. nov.
Microvirga (Mi.cro.vir'ga. Gr. adj. mikros small; L. fem. n. virga rod; N.L. fem. n. Microvirga a small rod).
Strictly aerobic, small, rod-shaped cells that stain Gram-negative and produce light-pink colonies. The optimum temperature for growth is 41 °C, with a temperature range for growth between 25 and 45 °C. Does not grow on glucose but uses xylose. Reduces nitrate to nitrite. Cells are susceptible to antibiotics that inhibit members of domain Bacteria. Bacteriochlorophyll is absent but carotenoids are present. PHB is produced. Thiosulfate does not stimulate growth. 16S rDNA sequence analysis indicates that it is a member of the Alphaproteobacteria, phylum Proteobacteria, placed almost equidistantly between C. asaccharovorans and B. thiooxidans, respectively members of the families Beijerinckiaceae and Bradyrhizobiaceae, as its nearest phylogenetic relatives. The type species is Microvirga subterranea.
Description of Microvirga subterranea sp. nov.
Microvirga subterranea (sub.ter.ra'ne.a. L. fem. adj. subterranea underground, subterranean).
In addition to the properties described for the genus, the following properties apply. After 48 h, colonies (diameter 0·52 mm) are light pink, convex, smooth and circular with entire margins. Cells are rod-shaped (1x1·54 µm), stain Gram-negative and possess a typical Gram-negative type cell wall ultrastructure, are motile by a single polar flagellum and do not form spores. Cells from old cultures are pleomorphic and contained large intracellular granules. Does not grow at 50 °C; optimum pH is 7·0 (pH range for growth 69). Grows on yeast extract, which is absolutely required for growth. Grows on casein hydrolysate, tryptone, xylose and acetate as sole carbon and energy sources but not on other carbohydrates, organic acids, alcohols, methane, glycine, aesculin, NTA, DMF or formamide. Gelatin, but not starch or casein, is hydrolysed. Very weak acid production is detected from glucose and arabinose. Catalase is produced but not oxidase, urease, indole or acetoin. Nitrite is produced from nitrate. Sensitive to penicillin, ampicillin, chloramphenicol, tetracycline, streptomycin and neomycin but resistant to vancomycin and spectinomycin. The G+C content of the type strain is 63·5±0·5 mol%.
The type strain, strain FaiI4T (=ATCC BAA-295T =DSM 14364T), was isolated from the geothermal waters of a bore (bore register no. 3768) tapping the GAB of Australia.
| ACKNOWLEDGEMENTS |
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