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1 Centre for Environment and Life Sciences, CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
2 CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania, 7001, Australia
3 School of Zoology, University of Tasmania, Private Bag 5, Hobart, Tasmania 7001, Australia
Correspondence
Jason J. Plumb
jason.plumb{at}csiro.au
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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JP7T is AY907891.
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TOPABSTRACTMAIN TEXTREFERENCES |
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, is a member of the order Sulfolobales (Stetter, 1989), and comprises three formally recognized species of facultatively aerobic thermoacidophiles isolated from geothermal or hydrothermal systems. The phylogenetically similar species Acidianus infernus and Acidianus ambivalens and the more distantly related and less thermophilic species Acidianus brierleyi (Fuchs et al., 1996), originally named Sulfolobus brierleyi (Brierley & Brierley, 1973; Zillig et al., 1980), grow as facultative aerobes with the ability to oxidize or reduce elemental sulfur depending on the available oxygen supply and are capable of autotrophic growth. Two recently described species, ‘Acidianus tengchongensis’ and ‘Acidianus manzaensis’, have extended the genotypic and phenotypic diversity within the genus (He et al., 2004; Yoshida et al., 2006).
Moist, sulfur-rich soil was collected from the hot (>80 °C) and acidic (pH 
2) edge of a hot spring within a solfatara on the geothermally active island of Lihir in Papua New Guinea. Sample material was stored for 3 days without temperature control during transfer to the laboratory. Microbial enrichments were performed in 250-ml Erlenmeyer flasks with 70 ml basal medium (Plumb et al., 2002), which contained (per litre) 1.5 g (NH4)2SO4, 0.25 g KH2PO4, 0.25 g MgSO4.7H2O and 0.1 g yeast extract, adjusted to pH 0.8 with 18 M H2SO4, supplemented with 1 % (w/v) chalcopyrite concentrate (88 % CuFeS2, 4 % FeS2 and trace quantities of SiO2, FeS and clinichlore) with a mean particle size of 37.5 µm (P80=85 µm) and 1 % (w/v) sulfidic ore material collected from Lihir. Enrichment cultures were incubated at 72 °C in a shaker incubator at 150 r.p.m. After incubation for 1 week, abundant growth of small, irregular-shaped cocci was detected by using a phase-contrast microscope (Leitz Diaplan). The enrichment culture was subcultured into fresh medium of the same composition once and then maintained on growth medium with 1 % (w/v) chalcopyrite concentrate as the energy source. A pure strain, designated JP7T, was isolated by using serial decimal dilutions to extinction in shake flasks of basal medium at pH 0.8 supplemented with 1 % (w/v) chalcopyrite concentrate. Strain JP7T was maintained routinely in shake flasks with this medium and the incubation conditions given above. Unless specified otherwise, strain JP7T was grown in basal medium at pH 0.8. Cell morphology was similar to other members of the order Sulfolobales, with slightly aspherical shape, and occasional planar sides and edges. Cells occurred singly or occasionally in pairs, the latter particularly during the exponential growth phase. On all growth media, cells ranged between 0.5 and 1.5 µm in diameter and were non-motile. Cells of strain JP7T stained Gram-negative.
Energy sources for growth of strain JP7T were tested in shake flask culture incubated aerobically using the basal medium described above. Chemically defined inorganic substrates tested were elemental sulfur (5 g l–1) and FeSO4.7H2O (10 g l–1). A stock solution of FeSO4.7H2O was sterilized by filtration through a 0.2-µm pore size filter. Elemental sulfur was sterilized by heating at 100 °C for 1 h, which was repeated twice on consecutive days. The concentration of Fe2+ was determined spectrophotometrically (Wilson, 1960). Growth on elemental sulfur was determined by phase-contrast microscopy and by measuring total solution sulfur concentration by using inductively coupled plasma optical emission spectroscopy. Although specific detection of sulfate was not performed, it was assumed that elemental sulfur was oxidized completely to sulfate as the pH of the medium decreased significantly, presumably because of production of sulfuric acid. Strain JP7T grew successfully using Fe2+ or sulfur as an energy source, although to lower cell density than growth on chalcopyrite concentrate. Strain JP7T oxidized Fe2+ rapidly compared with uninoculated controls; however, growth using Fe2+ as the sole energy source was not sustained in subsequent subcultures without the addition of elemental sulfur or mineral sulfide or other reduced sulfur compounds. Complex mineral sulfides were also tested as energy sources for growth of strain JP7T. These tests were conducted in shake flasks containing basal medium at pH 0.8. Mineral sulfides tested included pyrite (1 %, w/v), chalcopyrite and arsenopyrite (1–10 %, w/v), which were added as sterilized, finely ground concentrates or finely ground massive sulfides. Growth was monitored with a phase-contrast microscope over three subsequent subcultures where possible. Strain JP7T grew well on all three mineral sulfide substrates and maintained good growth over numerous subcultures on chalcopyrite and arsenopyrite up to a loading of 10 % (w/v). Growth was also observed on chalcopyrite and pyrite in basal medium prepared without yeast extract at pH 0.8 over subsequent subcultures, with a cell density of 108 cells ml–1 achieved after 5–7 days incubation. A significantly higher growth rate on chalcopyrite was achieved when the growth medium contained yeast extract, with a cell density of 108 cells ml–1 achieved after 3 days incubation. These results suggested that strain JP7T is a facultative autotroph, although confirmation of this via uptake of radio-labelled carbon was not performed. Optimal growth was achieved in medium containing NaCl up to a concentration of 0.5 % (w/v). No growth occurred in medium containing NaCl at a concentration of 1 % (w/v). Strain JP7T was less halotolerant than previously described species of the genus Acidianus, which are able to grow in medium containing up to 4 % (w/v) NaCl (Segerer et al., 1986).
Growth of strain JP7T under anaerobic conditions was tested by using H2 or H2S (Na2S.9H2O added at 2 g l–1) as an electron donor and elemental sulfur or ferric iron [Fe2(SO4)3 at 10 g l–1] as a terminal electron acceptor. A. infernus DSM 3191T, A. ambivalens DSM 3772T and A. brierleyi DSM 1651T were included as reference strains in anaerobic growth tests. The media and growth conditions used were as described by Segerer et al. (1986) except that no sodium sulfide was added to the anaerobic media. All cultures showing growth were subcultured twice for confirmation of growth. A. infernus DSM 3191T and A. ambivalens DSM 3772T grew by oxidizing H2 and by reducing elemental sulfur to H2S as expected. A. brierleyi DSM 1651T and strain JP7T did not grow by oxidizing H2 or by reducing elemental sulfur. A. brierleyi has previously been reported to grow by oxidizing H2 and by reducing elemental sulfur (Segerer et al., 1986), although, as discussed below, interpretation of this result is difficult owing to the addition of sodium sulfide (0.75 g l–1) to the anaerobic growth medium. Strain JP7T and A. brierleyi grew by oxidizing H2S and by reducing ferric iron (Fig. 1) both with and without the addition of organic carbon. Strain JP7T and A. brierleyi DSM 1651T grew when sodium sulfide was added at 0.75 g l–1, the concentration used in the anaerobic media prepared by Segerer et al. (1986). This result suggests that the previously reported growth by A. brierleyi with H2 as an energy source may have been due to the oxidation of H2S produced as a result of the addition of sodium sulfide to the anaerobic medium. A. infernus DSM 3191T and A. ambivalens DSM 3772T did not grow via this redox couple. None of the four strains grew in anaerobic medium by oxidizing H2 and reducing ferric iron, in contrast to the results for ‘A. manzaensis’ (Yoshida et al., 2006). Brock & Gustafson (1976) showed that Sulfolobus acidocaldarius grew by oxidizing elemental sulfur or glutamate and by reducing ferric iron and, more recently, ‘A. manzaensis’ was shown to be able to grow by oxidizing elemental sulfur or H2 and by reducing ferric iron (Yoshida et al., 2006). A. brierleyi and A. infernus grew by oxidizing elemental sulfur using molybdate as a terminal electron acceptor (Segerer et al., 1986). All four tested strains grew in anaerobic medium by oxidizing H2S and by reducing elemental sulfur. The inability of strain JP7T to oxidize H2 under sulfur-reducing or ferric-iron-reducing conditions suggests that this strain lacks the hydrogenase used by A. ambivalens for this metabolism (Laska et al., 2003). A number of studies have identified the enzyme systems responsible for aerobic and anaerobic metabolism in A. ambivalens (reviewed by Kletzin et al., 2004). More work is needed to characterize the mechanisms for anaerobic growth of other species of the genus Acidianus.
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The temperature range for growth of strain JP7T was determined via a temperature gradient incubator (Terratec Asia Pacific) and by application of the Ratkowsky equation (Ratkowsky et al., 1983; Plumb et al., 2002; Franzmann et al., 2005). For this test, strain JP7T was grown in a mineral-sulfide-free medium that enabled non-destructive turbidimetric measurement of growth. The medium contained (per litre) 0.4 g MgSO4.7H2O, 0.4 g (NH4)2SO4, 0.4 g KH2PO4, 4.0 g K2S4O6, 20.0 g FeSO4.7H2O and 1.0 g meat extract, with pH adjusted to 0.8 with 18 M H2SO4. The potassium tetrathionate, ferrous sulfate and meat extract were added as filter-sterilized solutions to the basal medium after sterilization by autoclaving at 121 °C for 20 min. Biomass in cultures grown at 24 different temperatures ranging from 40 to 85 °C was quantified by measuring the optical density at 550 nm. The square root of the inverse of the time taken to reach an optical density of 0.25 at each temperature was plotted against temperature and the plot was fitted by using the Ratkowsky equation. Extrapolated minimum, optimum and maximum temperatures for growth were 45.2±1.3, 74.4±0.7 and 82.5±0.8 °C, respectively. At the temperature closest to the extrapolated optimum at which strain JP7T was grown (72.9 °C), the generation time of strain JP7T in this mixotrophic medium was 8.4 h. Strain JP7T was not as thermophilic as A. infernus or A. ambivalens, which grew optimally at 90 and 80 °C, respectively (Segerer et al., 1986; Zillig et al., 1986), but was more thermophilic than A. brierleyi, which grew optimally at 70 °C (Segerer et al., 1986).
The pH range for growth of strain JP7T was determined by using two different approaches. Growth at different pH was tested with either basal medium containing chalcopyrite concentrate (1 %, w/v) or basal medium supplemented with FeSO4.7H2O (10 g l–1). The pH of the medium was adjusted by using concentrated H2SO4. All pH measurements were made at room temperature by using a SenTix HW electrode and a pH 330i meter (WTW). Standard solutions of pH 2.0 and pH 1.0 buffer (Merck) were used for calibration and to test the accuracy of low pH readings. Inoculated and uninoculated control flasks were set up in duplicate. As stated above, strain JP7T required a small amount of sulfur or mineral sulfide in the growth medium in order to maintain successful growth over repeated subcultures; however, the inclusion of sulfur or mineral sulfide causes significant changes in pH of the medium owing either to acid production via sulfur oxidation or to acid consumption via mineral sulfide oxidation, and the resulting change in pH makes assessment of the pH range for growth difficult. In order to minimize changes in pH of the medium due to addition of sulfur or mineral sulfide, the effect of pH on the growth of strain JP7T was tested in basal medium containing Fe2+ as the sole energy source. Inoculum was prepared by growing strain JP7T in basal medium at pH 0.8 or 1.8 with chalcopyrite concentrate (1 %, w/v). All flasks were incubated in a shaker operated at 72 °C, with shaking at 150 r.p.m. Cultures grown on chalcopyrite were monitored by using a Helber counting chamber and phase-contrast microscopy. In cultures grown on ferrous sulfate, oxidation of Fe2+ was monitored by measuring the Fe2+ concentration spectrophotometrically (Wilson, 1960). Strain JP7T grew and oxidized Fe2+ over a broad range of pH. At the extremes of the pH range tested (pH 0.4 and 3.0) strain JP7T oxidized the least Fe2+ (Fig. 2a). Strain JP7T oxidized Fe2+ at a similar rate at pH 0.8, 1.0 and 1.4, although a slight lag prior to achieving the maximum oxidation rate was observed at pH 0.8 and 1.0. Slower rates of Fe2+ oxidation were observed at other test pH values, but rates of Fe2+ oxidation at these pH values were greater than occurred in the uninoculated controls. Growth on chalcopyrite concentrate was observed at all pH values tested up to a pH of 2.2. A comparison of the growth of strain JP7T on chalcopyrite over a range from pH 0.4 to 1.0 was made (Fig. 2b). At such a low pH, acid production or consumption by the mineral sulfide does not change pH effectively. Growth at pH 0.4, 0.6 and 0.8 occurred after an initial lag period; however, the growth rate and maximum cell density achieved at pH 0.8 and 1.0 were almost identical. In another test, cell growth was maintained over numerous subcultures in basal medium with chalcopyrite (1 %, w/v) at pH 0.35. At this extremely low pH, cells remained intact but were smaller in size and slightly refractile in appearance, probably because of their stressed condition. The pH range for growth of strain JP7T extended to significantly lower values than for other species of Acidianus. According to Segerer et al. (1986) and Zillig et al. (1986), the lower pH limit for growth of A. infernus, A. ambivalens and A. brierleyi was pH 1.0, with optimal growth occurring between pH 1.5 and 2.0.
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) available at http://www.ncbi.nlm.nih.gov. The sequence was then aligned against reference sequences of species of Acidianus by using the program ARB (Ludwig et al., 2004). A phylogenetic tree was constructed by using distance matrix calculations and the neighbour-joining method (Saitou & Nei, 1987) available in the ARB program. The stability of tree nodes was evaluated by using bootstrap resampling (Felsenstein, 1985). Construction of a similarity matrix was performed also within ARB by using representative sequences from the Sulfolobales. The 16S rRNA gene sequence of strain JP7T was most closely related to that of ‘A. manzaensis’ NA-1, with a similarity of 97.2 %. The 16S rRNA gene sequences of A. ambivalens DSM 3772T, A. infernus DSM 3191T and A. brierleyi DSM 1651T shared similarity of 92.6, 92.3 and 91.2 %, respectively, with that of strain JP7T. On the basis of 16S rRNA gene sequence analysis, there is probably some doubt as to whether A. brierleyi should be included in the genus Acidianus, although it shares many phenotypic similarities with other members of this genus. Similarity of the 16S rRNA gene sequence of strain JP7T to those of the type strains of two other representatives of the Sulfolobaceae, Metallosphaera prunae and Sulfolobus solfataricus, was 90 and 87.7 %, respectively. A phylogenetic tree generated from 16S rRNA gene sequence data from members of the Sulfolobales (Fig. 3) shows strain JP7T clustering with ‘A. manzaensis’. The positioning of strain JP7T with other species of the genus Acidianus was well supported according to bootstrap analysis.
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, but without the use of the bead-beating step. The DNA was purified by using the UltraClean PCR Clean-up kit (MO BIO Laboratories Inc.). Agarose gel electrophoresis was used to confirm the extraction of high-molecular-mass genomic DNA. The DNA was hydrolysed with P1 nuclease and the nucleotides were dephosphorylated with bovine alkaline phosphatase (Mesbah et al., 1989). The G+C content was determined by analysing the resultant deoxyribonucleosides by HPLC (Shimadzu Corp.). The column used for analysis was a VYDAC 201SP54 (C18, 5 µm, 250x4.6 mm) equipped with a 201GD54H guard column (Vydac). The DNA G+C content of strain JP7T was 31.1 mol%, which is close to that of A. ambivalens (31 mol%), A. infernus (32.7 mol%) and A. brierleyi (31.5 mol%) (Segerer et al., 1986; Zillig et al., 1986).
Freeze-dried biomass collected from cultures of strain JP7T was used to characterize the cell membrane phospholipids. Biomass was placed in a thick-walled test tube along with 3 ml of a mixture containing 10 : 1 : 1 methanol/CHCl3/concentrated HCl. The test tube was capped and the mixture was heated overnight at 95 °C in a water bath. After cooling, 1 ml water was added and the reaction mixture was extracted three times with 1.8 ml portions of a 4 : 1 mixture of n-hexane and CH2Cl2. The extracts were pooled and the solvent was removed under a stream of N2. The ether lipids were stored at –20 °C. Gas chromatographic analysis was carried out by using a Hewlett Packard 5890 gas chromatograph equipped with an on-column auto-injector and a flame-ionization detector that was maintained at 405 °C. The capillary column used was a 2.5-m polyimide-clad SGE HT5, with an internal diameter of 0.25 mm and a film thickness of 0.1 µm (SGE International). Samples were injected with the injector and column at 30 °C. The oven temperature was maintained for 2 min, then increased at 35 °C min–1 to 350 °C and then at 5 °C min–1 to 400 °C. At the end of the run, the oven was cooled at a rate of 30 °C min–1 in order to reduce the likelihood of column damage as a result of rapid temperature change. The carrier gas was helium and the head pressure was 35 kPa. The ether lipids eluted as well-separated peaks. The concentrations of glycerol dialkyl glycerol tetraethers (GDGTs) and glycerol dialkyl calditol tetraethers (calditols) were determined. Analysis of the ether lipids in strain JP7T showed an almost 50 : 50 split between GDGTs and calditols. Cyclized forms of each of these tetraethers with one to eight mid-chain cyclopentyl rings were detected, with the majority of tetraethers containing six rings. Although the distribution of cyclized tetraether lipids varies according to factors such as temperature and pH, this ether lipid profile was consistent with profiles of members of the Sulfolobales grown at high temperature (De Rosa et al., 1983).
The phenotypic and genotypic characteristics described above suggest that strain JP7T is a member of the genus Acidianus. Differences in 16S rRNA gene sequence, aerobic and anaerobic growth, temperature range for growth and pH range for growth justify the conclusion that strain JP7T represents a novel species of the genus Acidianus. The name Acidianus sulfidivorans sp. nov. is proposed for this novel species.
Emended description of Acidianus Segerer et al. 1986
Cells are Gram-negative and occur singly or occasionally in pairs during exponential growth; the cells have an irregular coccoid morphology (sometimes lobed or showing sharp bends, and resembling tetrahedrons, pyramids, discs or dishes). Cells are non-motile. Cell width is between 0.5 and 2 µm, depending on culture conditions. A surrounding envelope about 25 nm wide covering the cell membrane is evident in thin section. The envelope is composed of subunits in a hexagonal array. The cells are facultative aerobes. Lithotrophic growth occurs aerobically by means of S0 oxidation, mineral sulfide oxidation or Fe2+ oxidation. Anaerobic growth occurs by means of S0 or ferric iron reduction with H2 or H2S. The cells are autotrophic and mixotrophic and may grow organotrophically on yeast extract without S0 in the presence of O2. The organisms are thermoacidophiles, thriving between pH 0.35 and 6 and between 45 and 96 °C. They grow in the presence of 0.1 % NaCl and may grow in media containing up to 4 % NaCl. Neither muramic acid nor meso-diaminopimelic acid is present, indicating the absence of murein. Elongation factor 2 is sensitive to adenosine diphosphate ribosylation by diphtheria toxin. Cells contain isopranyl ether lipids, which consist of GDGTs and calditols, including lipids with mid-chain cyclopentyl rings, and also caldariellaquinone. Members of the genus are resistant to vancomycin, ampicillin and kanamycin (150 µg ml–1 each). DNA-dependent RNA polymerase shows incomplete immunological cross-reactions with antibody against DNA-dependent RNA polymerase from Sulfolobus acidocaldarius DSM 639T. The purified DNA has a G+C content of 31–33 mol%. Members of the genus occur in acidic solfataras and in marine hydrothermal systems. The type species is Acidianus infernus.
Description of Acidianus sulfidivorans sp. nov.
Acidianus sulfidivorans (sul.fi.di.vo'rans. N.L. n. sulfidum sulfide; L. part. adj. vorans devouring; N.L. part. adj. sulfidivorans sulfide-devouring).
Displays the following properties in addition to those given in the emended genus description. Cells are 0.5–1.5 µm in diameter. Growth is obligately chemolithotrophic. Good growth occurs under aerobic conditions on elemental sulfur, ferrous iron, pyrite and other mineral sulfides. Under anaerobic conditions, ferric iron or elemental sulfur serve as the terminal electron acceptor for growth via oxidation of H2S. Cells do not grow using elemental sulfur as a terminal electron acceptor for oxidation of H2. Cells are facultatively autotrophic, as they grow when provided with CO2 as the sole source of carbon and heterotrophically using yeast extract or meat extract as a carbon source. Cells do not grow organotrophically. Cells grow over a range of temperatures from 45 to 83 °C, with optimum growth at 74 °C. The pH range for growth is 0.35–3.0, with optimal growth at pH 0.8–1.4. Optimal growth occurs at up to 0.5 % (w/v) NaCl. The DNA G+C content is 31.1 mol%. Cell-membrane lipids consist of a mixture of GDGTs and glycerol dialkyl calditol tetraethers, most of which are cyclized tetraethers.
The type strain, JP7T (=DSM 18786T=JCM 13667T), was isolated from the sulfur-rich acidic edge of a solfataric hot spring.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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Brierley, C. L. & Brierley, J. A. (1973). A chemolithoautotrophic and thermophilic microorganism isolated from an acidic hot spring. Can J Microbiol 19, 183–188.[Medline]
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De Rosa, M., Gambacorta, A., Nicolaus, B., Chappe, B. & Albrecht, P. (1983). Isoprenoid ethers; backbone of complex lipids of the archaebacterium Sulfolobus solfataricus. Biochim Biophys Acta 753, 249–256.
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Franzmann, P. D., Haddad, C. M., Hawkes, R. B., Robertson, W. J. & Plumb, J. J. (2005). Effects of temperature on the rates of iron and sulfur oxidation by selected bioleaching Bacteria and Archaea: application of the Ratkowsky equation. Miner Eng 18, 1304–1314.[CrossRef]
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He, Z.-G., Zhong, H. & Li, Y. (2004). Acidianus tengchongensis sp. nov., a new species of acidothermophilic archaeon isolated from an acidothermal spring. Curr Microbiol 48, 159–163.[CrossRef][Medline]
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Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363–1371.
Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.
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Plumb, J. J., Gibbs, B., Stott, M. B., Robertson, W. J., Gibson, J. A. E., Nichols, P. D., Watling, H. R. & Franzmann, P. D. (2002). Enrichment and characterisation of thermophilic acidophiles for the bioleaching of mineral sulphides. Miner Eng 15, 787–794.[CrossRef]
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Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Segerer, A., Neuner, A. M., Kristjansson, J. K. & Stetter, K. O. (1986). Acidianus infernus gen. nov., sp. nov., and Acidianus brierleyi comb. nov.: facultatively aerobic, extremely acidophilic thermophilic sulfur-metabolizing archaebacteria. Int J Syst Bacteriol 36, 559–564.
Stetter, K. O. (1989). Order III. Sulfolobales ord. nov. In Bergey's Manual of Systematic Bacteriology, vol. 3, pp. 2250–2253. Edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. G. Holt. Baltimore: Williams & Wilkins.
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Zillig, W., Stetter, K. O., Wunderl, S., Schulz, W., Priess, H. & Scholz, I. (1980). The Sulfolobus-"Caldariella" group: taxonomy on the basis of the structure of DNA-dependent RNA polymerases. Arch Mikrobiol 125, 259–269.
Zillig, W., Yeats, S., Holz, I., Böck, A., Rettenberger, M., Gropp, F. & Simon, G. (1986). Desulfurolobus ambivalens, gen. nov., sp. nov., an autotrophic archaebacterium facultatively oxidising or reducing sulfur. Syst Appl Microbiol 8, 197–203.
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