| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
2 The DEEP-STAR Group, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
3 NASA Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, CA 91109-8099, USA
Correspondence
Ken Takai
kent{at}jamstec.go.jp
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
Micrographs of cells of Deferribacter desulfuricans sp. nov. SSM1T and graphs showing the effects of temperature, pH and total salt concentration on growth are available as supplementary material in IJSEM Online.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
; 1991; Stetter et al., 1990, 1993; Gonzalez et al., 1995, 1998; Godfroy et al., 1996, 1997; Antoine et al., 1997; Takai & Horikoshi, 2000; Takai et al., 2000; Takai & Fujiwara, 2002). Recently, several investigations using a combination of culture-dependent and -independent analyses have revealed that these sulfur-reducing, heterotrophic thermophiles dominate microbial populations in deep-sea hydrothermal vent chimney structures, specifically on the surfaces of the chimney structures (Harmsen et al., 1997; Takai et al., 2001). However, the community structures of sulfur-reducing, heterotrophic thermophiles other than members of Thermococcales and their ecological contribution remain poorly understood.
From subsamples obtained from the East Pacific Rise (EPR) deep-sea hydrothermal vent site (13 °N), a population of dissimilatory Fe(III)-reducing thermophilic bacteria belonging to Deferribacter was detected by culture-dependent techniques in a deep-sea hydrothermal vent environment (Slobodkin et al., 2001). The genus Deferribacter is represented by a single strain, Deferribacter thermophilus BMAT, isolated from a subseafloor petroleum reservoir (Greene et al., 1997). It is a strictly anaerobic, heterotrophic thermophile, using a variety of organic compounds and hydrogen as energy sources and nitrate, Fe(III) and Mn(IV) as electron acceptors. The versatile energy-generating metabolism and physiological features of members of Deferribacter may indicate that deep-sea hydrothermal vent environments are a potential niche other than subsurface oil reservoirs. In this study, we sought to find sulfur-reducing, heterotrophic thermophiles other than members of Thermococcales and Thermotogales in deep-sea hydrothermal vent environments.
Sample collection, enrichment and purification
Samples from a black smoker vent were obtained from the hydrothermal field at the Suiyo Seamount in the Izu-Bonin Arc, Japan (28°34·287'N, 140°38·663'E), at a depth of 1385 m by the manned submersible Shinkai 2000 in a dive (dive #1237) performed in November 2000. A bulk chimney sample with a vent emission temperature of 310·8 °C was brought to the sea surface in a sample box, which is part of the equipment of the Shinkai 2000, and immediately divided into four different sections (top part of the chimney, surface layer of the chimney, inside structure and vent orifice surface) as described by Takai et al. (2001). The chimney was composed mainly of iron sulfide, and large pyrite or chalcopyrite crystals were observed where hot fluid was emitted (the vent orifice surface). Each of the sample sections (approx. 10 g each) was suspended in 20 ml sterilized MJ synthetic sea water (Sako et al., 1996; Takai et al., 1999) containing 0·05 % (w/v) sodium sulfide in a 100-ml glass bottle (Schott Glaswerke) tightly sealed with a butyl rubber cap under a gas phase of 100 % N2 (100 kPa). These suspended portions of the samples were inoculated (0·1 % volume of the medium) with MJNS medium (described below) supplemented with 0·1 % (w/v) yeast extract and 0·1 % (w/v) tryptone under a gas phase of 80 % H2 and 20 % CO2 (300 kPa). The cultures were incubated onboard at 70 and 85 °C in dry ovens.
Growth of anaerobic, heterotrophic thermophiles was observed in MJNS medium supplemented with 0·1 % (w/v) yeast extract and 0·1 % (w/v) tryptone, which was inoculated only with the sample section from the chimney surface layer (1–3 mm), after 2 days of incubation at 70 and 85 °C. Based on direct cell counting of DAPI-stained samples, the chimney surface layer contained approximately 1·0x108 cells g-1, while the other sample sections had microbial population densities below the detection limit (<103 cells g-1). Unlike previously reported results for a black smoker chimney structure from the Manus Basin deep-sea hydrothermal field (Takai et al., 2001), a sizeable microbial community probably occurred only in the microhabitat along the chimney surface in the Suiyo Seamount deep-sea hydrothermal field.
The enrichment cultures grown at 70 °C contained predominantly bent, flexible rods, with a small population of highly motile irregular coccoids, while the cultures at 85 °C had a population of highly motile coccoids alone. Since the highly motile, irregular coccoids were probably members of the Thermococcales, a pure culture of bent, flexible rods grown at 70 °C was obtained by using the dilution-to-extinction technique at 65 °C (Takai & Horikoshi, 2000). The culture in the tube showing growth at the highest dilution was designated strain SSM1T (=JCM 11476T =DSM 14783T). Purity was confirmed routinely by microscopic examination and by repeated partial sequencing of the 16S rRNA gene using several PCR primers.
Morphology
Cells were routinely observed under a phase-contrast Olympus BX51 microscope with the Olympus Camedia C3030 digital camera system. Transmission electron microscopy of negatively stained cells was carried out as described by Zillig et al. (1990). Cells grown in MJNS medium supplemented with 0·1 % (w/v) yeast extract and 0·1 % (w/v) tryptone at 62 °C in the mid-exponential phase of growth were negatively stained with 2 % (w/v) uranyl acetate and observed under a JEOL JEM-1210 electron microscope at an accelerating voltage of 120 kV. Cells of strain SSM1T were Gram-negative and were bent, flexible rods, which were about 1·5–2·5 µm long and 0·3–0·7 µm wide in the exponential growth phase (see Fig. A, available as supplementary material in IJSEM Online). In the stationary growth phase, the cells tended to be long and spiral-shaped (Supplementary Fig. B). Each of the cells in the exponential growth phase appeared to have a polar flagellum, although no motility was evident in the laboratory cultures. These morphological features were quite similar to those of D. thermophilus BMAT (Greene et al., 1997).
Growth characteristics
Strain SSM1T was routinely cultivated in MJNS medium supplemented with 0·1 % (w/v) yeast extract and 0·1 % (w/v) tryptone. MJNS medium consisted of (l-1 MJ synthetic sea water): 1 ml vitamin solution (Balch et al., 1979), 50 mg sodium selenite, 30 mg sodium tungstate, 1 mg resazurin, 10 mM NaNO3, 3 % (w/v) elemental sulfur, 20 g NaHCO3 and 0·5 g Na2S.9H2O (Sako et al., 1996; Takai et al., 1999). To prepare the supplemented medium, sodium selenite, sodium tungstate, resazurin, yeast extract (1 g) and tryptone (1 g) were dissolved in 1 l MJ synthetic sea water and the pH of the medium was adjusted to around 7·0 with NaOH before autoclaving. After autoclaving under an air atmosphere, a concentrated solution of vitamins (Balch et al., 1979), NaHCO3, NaNO3, elemental sulfur and Na2S (pH adjusted to 7·0) were added to the medium under gas purging with 80 % H2 and 20 % CO2. These solutions were sterilized separately by autoclaving except for the vitamins and elemental sulfur, which were respectively filter-sterilized and steam-sterilized (three times at 95 °C for 3 h). The medium was dispensed at 20 % of the total bottle (Schott Glaswerke) or tube (Iwaki glass) volume and containers were tightly sealed with a butyl rubber stopper under a gas phase of 80 % H2 and 20 % CO2 at 300 kPa. All experiments described below were conducted in duplicate.
The effects of temperature, pH and total salt concentration on growth were tested. With MJNS medium supplemented with 0·1 % (w/v) yeast extract and 0·1 % (w/v) tryptone, strain SSM1T grew over the temperature range of about 40–70 °C, showing optimal growth at 60–65 °C, and the generation time at 62 °C, pH 6·5, was about 40 min (see Supplementary Fig. C in IJSEM Online at http://ijs.sgmjournals.org). No growth was observed at 35 or 75 °C. To determine the effect of pH on growth, the pH of MJNS medium containing 0·1 % (w/v) yeast extract and tryptone was adjusted to various levels with 10 mM acetate/acetic acid buffer (pH 4–5), MES (pH 5–6), PIPES (pH 6–7), HEPES (pH 7–7·5) and Tris (pH 8–9·5). Growth of strain SSM1T at 62 °C occurred at pH 5·0–7·5, with optimum growth at about pH 6·5 (Supplementary Fig. D). The pH was found to be stable during the cultivation period. The effect of total salt concentration on growth was determined using MJNS medium supplemented with 0·1 % (w/v) yeast extract and 0·1 % (w/v) tryptone, in which varying dilutions of 4xMJ synthetic sea water were used (1xMJ synthetic sea water contains 30 g NaCl l-1). Isolate SSM1T grew over the range of total salt concentration between 18 and 96 g l-1, with optimum growth at 36 g total salt l-1 at 62 °C, pH 6·5 (Supplementary Fig. E). Compared with D. thermophilus BMAT, strain SSM1T can grow at slightly higher temperatures.
The oxygen sensitivity of strain SSM1T was tested with MJNS medium supplemented with 0·1 % (w/v) yeast extract and 0·1 % (w/v) tryptone under a gas phase replaced with a mixture of 80 % H2, 19 % CO2 and 1 % O2 (300 kPa) or a mixture of 80 % H2, 19·9 % CO2 and 0·1 % O2 (300 kPa). Strain SSM1T grew only under strictly anaerobic culture conditions and was extremely sensitive to oxygen (Table 1). In contrast to the oxygen-resistant growth (at an oxygen concentration of up to 0·6 % in the gas phase) observed for D. thermophilus BMAT, growth of strain SSM1T was completely inhibited in the presence of 0·1 % oxygen.
|
). In an attempt to determine potential energy sources for heterotrophic growth, yeast extract, peptone, tryptone, Casamino acids (each at 0·2 %, w/v), formate, acetate, glycerol, citrate, tartrate, fumarate, malate, succinate, propionate, maleate, lactate, oxalate, thioglycolate, pyruvate, each of 20 amino acids (each at 5 mM), 0·025 % (v/v) methanol, 0·05 % (v/v) ethanol, 0·1 % (v/v) 2-propanol, glucose, galactose, sucrose, fructose, lactose, maltose, arabinose, trehalose and starch (each at 0·1 %, w/v) were examined in MJNS medium under a gas phase of 80 % H2+20 % CO2 (300 kPa), 80 % N2+20 % CO2 (300 kPa) or 100 % N2 (300 kPa). Strain SSM1T was able to grow on yeast extract, tryptone, peptone, casein, Casamino acids, ethanol, citrate, tartrate, fumarate, malate, succinate, propionate, lactate, oxalate, pyruvate, acetate or formate as sole energy and carbon sources. Yeast extract, tryptone, peptone, pyruvate and acetate yielded the highest level of growth. 2-Propanol, methanol, maleate, thioglycolate, glycerol, various amino acids and sugars did not support growth as sole energy and carbon sources. Strain SSM1T grew better in the presence of hydrogen than in the presence of nitrogen or argon (Table 1). This indicates that hydrogen serves as a supplementary energy source for growth of strain SSM1T, similar to D. thermophilus BMAT.
The use of nitrate, nitrite, elemental sulfur, sulfite, thiosulfate, sulfate, soluble (ferric citrate) or insoluble (ferrihydrite) iron (III), manganese (IV) (vernadite), selenite, selenate, arsenate, arsenite or fumarate as potential sole electron acceptors in place of nitrate and elemental sulfur was examined in MJNS medium with acetate as an energy source (Table 1). Ferric citrate, ferrihydrite [Fe(OH)3] and vernadite (MnO2) were prepared as described by Kostka & Nealson (1998). These tests were performed under anaerobic conditions in the absence of Na2S.9H2O to avoid chemical reduction of the potential electron acceptors by the reductant. To ensure that conditions were anaerobic, the media were purged with vigorous bubbling with 80 % H2+20 % CO2 or 80 % N2+20 % CO2 for 30 min and then compressed with 80 % H2+20 % CO2 (300 kPa) or 80 % N2+20 % CO2 (300 kPa). Nitrate, elemental sulfur or arsenate was required as a potential electron acceptor for growth of strain SSM1T, while nitrite, sulfite, thiosulfate, sulfate, soluble or insoluble iron (III), manganese (IV), selenite, selenate and arsenite did not support growth (Table 1). The requirement for elemental sulfur as the primary electron acceptor and the inability to utilize iron (III) or manganese (IV) observed for strain SSM1T were distinct from the inorganic substrate requirements of strain BMAT.
The time-course of consumption of acetate and reduction of elemental sulfur, nitrate or arsenate and concomitant bacterial growth of strain SSM1T were examined with MJNS medium supplemented with 5 mM acetate and each of 3 % (w/v) elemental sulfur, 5 mM nitrate or 2 mM arsenate under a gas phase of 80 % H2+20 % CO2 (300 kPa). The concentration of nitrogen in the gas phase during growth was measured using a Micro GC CP2002 gas chromatograph (GL Sciences). Anion samples (nitrate, nitrite and acetate) were analysed by ion chromatography using a Shim-pack IC column (Shimadzu). The diazotization method was employed to determine the concentrations of nitrate and nitrite (Matsunaga & Nishimura, 1969) independently from ion chromatography and Nessler's reagent was employed to measure the ammonium ion concentration in the medium (Allen et al., 1974). Sulfide was analysed quantitatively using the methylene blue method (Fonselius, 1983). Determination of arsenate and arsenite was performed as described previously (Johnson & Pilson, 1972).
When any electron acceptor was provided, the concentration of acetate decreased as the number of cells increased (Fig. 1a), indicating that acetate was consumed during growth. Although the amount of elemental sulfur was not quantified, the concentrations of nitrate and arsenate decreased and the concentrations of sulfide, nitrite and arsenite increased during growth of strain SSM1T (Fig. 1). Since the control media without bacterial inocula did not demonstrate acetate consumption or the reduction of elemental sulfur, nitrate or arsenate to sulfide, nitrite or arsenite (data not shown), bacterial reduction of elemental sulfur, nitrate and arsenate occurred during growth. The accumulated concentrations of nitrite and arsenite were stoichiometrically equivalent to the concentrations of nitrate and arsenate reduced (Fig. 1b, c). In addition, strain SSM1T was unable to utilize nitrite or arsenite as potential electron acceptors (Table 1). Hence, nitrite and arsenite were likely the end products of nitrate and arsenate reduction. On the basis of these results, strain SSM1T was found to be a respiratory elemental sulfur-, nitrate- or arsenate-reducing heterotroph.
|
Fatty acid and DNA base compositions
The cellular fatty acid composition was analysed using cells grown in the standard medium at 62 °C in the late-exponential growth phase. Lyophilized cells (300 mg) were placed in a Teflon-lined, screw-capped tube containing 5 ml anhydrous methanolic HCl and heated at 100 °C for 3 h. The resulting fatty acid methyl esters (FAMEs) were extracted twice with n-hexane and concentrated under a stream of nitrogen gas. The FAMEs were analysed using a gas-liquid chromatograph (model GC-380; GL Science) or gas-liquid chromatography-mass spectrometer (GCMS-QP5050; Shimadzu). The FAMEs standard (C4–C24) was purchased from Supelco. The major cellular fatty acids of strain SSM1T were iso-C14 : 0 (8·3 %), iso-C15 : 0 (10·3 %), anteiso-C15 : 0 (23·3 %), iso-C16 : 0 (7·3 %), iso-C17 : 0 (7·3 %), anteiso-C17 : 0 (19·4 %), iso-C18 : 0 (11·6 %), C18 : 0 (4·3 %), iso-C19 : 0 (4·4 %) and anteiso-C19 : 0 (3·7 %).
Genomic DNA of strain SSM1T was prepared as described by Marmur & Doty (1962). The G+C content of DNA was determined by direct analysis of deoxyribonucleotides on HPLC (Tamaoka & Komagata, 1984). Non-methylated DNA from bacteriophage 
(49·8 mol% G+C; TaKaRa) was used as a reference. The G+C content of the genomic DNA of strain SSM1T was 38·6 mol%, which is slightly higher than that of D. thermophilus BMAT (Table 2).
|
; Lane, 1985). The nearly complete sequence (1446 bp) of the 16S rRNA gene from strain SSM1T was sequenced directly on both strands using the dideoxynucleotide chain termination method with a DNA sequencer model 3100 (Perkin-Elmer Applied Biosystems). The rDNA sequence was analysed using the gapped-BLAST search algorithm (Altschul et al., 1997; Benson et al., 1998) and was found to be most closely related (98·1 %) to that of D. thermophilus BMAT (Greene et al., 1997). This suggests that strain SSM1T belongs to the genus Deferribacter.
The nearly complete sequence was manually realigned to 16S rDNA data from the Ribosomal Data Project II (RDP-II) (Maidak et al., 2000) based on alignments determined using the Sequence Aligner program of RDP-II. Phylogenetic analyses were restricted to nucleotide positions that could be unambiguously aligned. Evolutionary distance matrix analysis (using the Kimura two-parameter method, the least-squares distance method and a transition/transversion rate of 2·0) and neighbour-joining analysis were performed using the PHYLIP package (version 3.5; obtained from J. Felsenstein, University of Washington, Seattle, WA, USA). Bootstrap analysis was performed to provide confidence estimates for phylogenetic tree topologies. The phylogenetic tree indicated that strain SSM1T is closely related to D. thermophilus BMAT, as determined by sequence similarity analysis (Fig. 2). Phylogenetically related bacterial species were the nitrate-, nitrite- or arsenate-reducing mesophile Chrysiogenes arsenatis BAL-1T (Macy et al., 1996), the slightly thermophilic, fermentative bacterium Flexistipes sinusarabici MAS 10T isolated from deep-sea brine water (Fiala et al., 1990) and the Fe(III)-, Co(III)- or sulfur-reducing mesophile Geovibrio ferrireducens PAL-1T (Caccavo et al., 1996). These bacterial strains may be classified into a phylogenetic group with the genus Deferribacter at the order or phylum level with a potential common ancestor, based on the phylogenetic tree (Fig. 2).
|
. D. thermophilus BMAT (=ACM 5093T) was obtained from the Australian Collection of Microorganisms. It was cultivated under the optimal conditions as described previously (Greene et al., 1997). The mean hybridization rate was 5·8 %, indicating that strain SSM1T could be genotypically differentiated from the previously described species of the genus Deferribacter.
Comparison with related species
Phylogenetic analysis indicated that strain SSM1T is most closely related to D. thermophilus BMAT, which was isolated from a subseafloor oil reservoir in the North Sea (Greene et al., 1997), and is likely a member of the genus Deferribacter. Most of the morphological, physiological and molecular characteristics of strain SSM1T are similar to those of D. thermophilus BMAT (Table 2). However, strain SSM1T differs markedly from D. thermophilus BMAT with respect to several physiological features (Table 2). The most distinctive feature is the utilization of electron acceptors; strain SSM1T is able to use elemental sulfur as a primary electron acceptor but is unable to reduce iron (III) or manganese (IV), which are the primary electron acceptors for D. thermophilus BMAT. In addition, the growth rate of strain SSM1T is higher than that of D. thermophilus BMAT under the optimal conditions for each of the strains and the temperature range and optimum of strain SSM1T are shifted to slightly higher values than those of D. thermophilus BMAT (Table 2). Growth of D. thermophilus BMAT is resistant to microaerobic conditions (0·6 % oxygen in the gas phase), whereas strain SSM1T is extremely sensitive to oxygen (Table 2). DNA hybridization analysis clearly showed that strain SSM1T can be differentiated genetically from D. thermophilus BMAT at the species level. On the basis of these physiological and genetic properties of strain SSM1T (=JCM 11476T=DSM 14783T), we propose that it be classified as the type strain of Deferribacter desulfuricans sp. nov.
In the report on the isolation of the first Deferribacter species, from a subsurface oil reservoir, Greene et al. (1997) suggested the occurrence of an ecological niche for iron- or manganese-reducing thermophiles in oil-bearing rocks commonly containing iron and manganese oxides and hydroxides. An ecological niche containing abundant iron, manganese oxides and hydroxides might be more likely to occur in relatively oxidative microhabitats such as chimney surface areas in deep-sea hydrothermal vent environments. Recent investigations on an iron-reducing microbial population in the EPR deep-sea hydrothermal vent environment suggested the abundant occurrence of a thermophilic iron-reducing microbial population, predominantly represented by members of Thermococcus and Deferribacter, in relatively oxidative microhabitats (Slobodkin et al., 2001). A body of evidence has demonstrated that sulfidogenic, thermophilic bacteria and archaea, mainly consisting of sulfur-reducing members of Thermotogales and Thermococcales, are predominantly present in global subsurface oil-reservoir environments other than marine hydrothermal systems (L'Haridon et al., 1995; Orphan et al., 2000; Slobodkin et al., 1999; Stetter et al., 1993; Takahata et al., 2000). In addition to members of Thermotogales and Thermococcales, sulfur-reducing and/or metal-reducing members of Deferribacter such as D. desulfuricans SSM1T and D. thermophilus BMAT may be widely distributed in global deep-sea hydrothermal systems and subsurface oil-reservoir environments and may represent significant microbial components.
Description of Deferribacter desulfuricans sp. nov.
Deferribacter desulfuricans (de.sul.fu'ri.cans. L. pref. de from; L. n. sulfur sulfur; N.L. part. adj. desulfuricans reducing sulfur).
Bent, flexible rods, with a mean length of 1·5–2·5 µm and mean width of 0·3–0·7 µm. Cells stain Gram-negative and occur singly in the exponential growth phase and as long, spiral forms in the stationary phase. Exhibits no evident motility with a polar flagellum. Strictly anaerobic and obligately heterotrophic. The temperature range for growth is 40–70 °C, with the optimum being 60–65 °C. The pH range for growth is 5·0–7·5, with optimum growth at pH 6·5. Sea salts are required for growth and the concentration range is 18–96 g l-1, with optimum growth at 36 g l-1. Growth uses organic compounds such as yeast extract, tryptone, peptone, casein, Casamino acids, ethanol, citrate, tartrate, fumarate, malate, succinate, propionate, lactate, oxalate, pyruvate, acetate and formate as sole energy and carbon sources. Elemental sulfur, nitrate or arsenate are absolutely required for growth as electron acceptors, being respectively reduced to sulfide, nitrite and arsenite. Ammonium and nitrate serve as nitrogen sources. The G+C content of genomic DNA is 38·6 mol% (by HPLC). The 16S rDNA sequence exhibits 98·5 % similarity to that of D. thermophilus BMAT. The DNA–DNA relatedness to D. thermophilus BMAT is low (5·8 %).
The type strain, strain SSM1T (=JCM 11476T=DSM 14783T), was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.
Antoine, E., Cilia, V., Meunier, J. R., Guezennec, J., Lesongeur, F. & Barbier, G. (1997). Thermosipho melanensis sp. nov., a new thermophilic anaerobic bacterium belonging to the order Thermotogales, isolated from deep-sea hydrothermal vents in the Southwestern Pacific Ocean. Int J Syst Bacteriol 47, 1118–1123.
Balch, W. E., Fox, G. E., Magrum, L. J., Woese, C. R. & Wolfe, R. S. (1979). Methanogens: reevaluation of a unique biological group. Microbiol Rev 43, 260–296.
Benson, D. A., Boguski, M. S., Lipman, D. J., Ostell, J. & Ouellette, B. F. F. (1998). GenBank. Nucleic Acids Res 26, 1–7.
Caccavo, F., Jr, Coates, J. D., Rossello-Mora, R. A., Ludwig, W., Schleifer, K. H., Lovley, D. R. & McInerney, M. J. (1996). Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium. Arch Microbiol 165, 370–376.[CrossRef][Medline]
DeLong, E. F. (1992). Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89, 5685–5689.
Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.
Fiala, G., Woese, C. R., Langworthy, T. A. & Stetter, K. O. (1990). Flexistipes sinusarabici, a novel genus and species of eubacteria occurring in the Atlantis II Deep brines of the Red Sea. Arch Microbiol 154, 120–126.[CrossRef]
Fonselius, S. H. (1983). Determination of hydrogen sulfide. In Sea Water Analysis, pp. 73–80. Edited by K. Grasshoff, M. Ehrhardt & K. Kremling. Weinheim: Verlag Chemie.
Godfroy, A., Meunier, J.-R., Guezennec, J., Lesongeur, F., Raguénès, G., Rimbault, A. & Barbier, G. (1996). Thermococcus fumicolans sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent in the North Fiji Basin. Int J Syst Bacteriol 46, 1113–1119.
Godfroy, A., Lesongeur, F., Raguénès, G., Quérellou, J., Antoine, E., Meunier, J.-R., Guezennec, J. & Barbier, G. (1997). Thermococcus hydrothermalis sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Int J Syst Bacteriol 47, 622–626.
Gonzalez, J. M., Kato, C. & Horikoshi, K. (1995). Thermococcus peptonophilus sp. nov., a fast-growing, extremely thermophilic archaebacterium isolated from deep-sea hydrothermal vents. Arch Microbiol 164, 159–164.[CrossRef][Medline]
Gonzalez, J. M., Masuchi, Y., Robb, F. T., Ammerman, J. W., Maeder, D. L., Yanagibayashi, M., Tamaoka, J. & Kato, C. (1998). Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles 2, 123–130.[CrossRef][Medline]
Greene, A. C., Patel, B. K. C. & Sheehy, A. J. (1997). Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir. Int J Syst Bacteriol 47, 505–509.
Harmsen, J. M., Prieur, D. & Jeanthon, C. (1997). Distribution of microorganisms in deep-sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichment culture of thermophilic subpopulations. Appl Environ Microbiol 63, 2876–2883.[Abstract]
Johnson, D. L. & Pilson, M. E. Q. (1972). Spectrophotometric determination of arsenite, arsenate, and phosphate in natural water. Anal Chim Acta 58, 289–299.[CrossRef]
Kostka, J. & Nealson, K. H. (1998). Isolation, cultivation and characterization of iron- and manganese-reducing bacteria. In Techniques in Microbial Ecology, pp. 58–78. Edited by R. S. Burlage, R. Atlas, D. Stahl, G. Geesey & G. Sayler. New York: Oxford University Press.
Lane, D. J. (1985). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–176. Edited by E. Stackebrandt & M. Goodfellow. New York: Wiley.
L'Haridon, S., Reysenbach, A.-L., Glenat, P., Prieur, D. & Jeanthon, C. (1995). Hot subterranean biosphere in a continental oil reservoir. Nature 377, 223–224.
Macy, J. M., Nunan, K., Hagen, K. D., Dixon, D. R., Harbour, P. J., Cahill, M. & Sly, L. I. (1996). Chrysiogenes arsenatis gen. nov., sp. nov., a new arsenate-respiring bacterium isolated from gold mine wastewater. Int J Syst Bacteriol 46, 1153–1157.
Maidak, B. L., Cole, J. R., Lilburn, T. G. & 9 other authors (2000). The RDP (Ribosomal Database Project) continues. Nucleic Acids Res 28, 173–174.
Marmur, J. & Doty, P. (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109–118.[Medline]
Matsunaga, K. & Nishimura, M. (1969). Determination of nitrate in sea water. Anal Chim Acta 43, 350–353.[CrossRef]
Orphan, V. J., Taylor, L. T., Hafenbradl, D. & DeLong, E. F. (2000). Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microbiol 66, 700–711.
Pledger, R. J. & Baross, J. A. (1989). Characterization of an extremely thermophilic archaebacterium isolated from a black smoker polychaete (Paralvinella sp.) at the Juan de Fuca Ridge. Syst Appl Microbiol 12, 249–256.
Pledger, R. J. & Baross, J. A. (1991). Preliminary description and nutritional characterization of a chemoorganotrophic archaeobacterium growing at temperatures of up to 110 °C isolated from a submarine hydrothermal vent environment. J Gen Microbiol 137, 203–211.
Sako, Y., Takai, K., Ishida, Y., Uchida, A. & Katayama, Y. (1996). Rhodothermus obamensis sp. nov., a modern lineage of extremely thermophilic marine bacteria. Int J Syst Bacteriol 46, 1099–1104.
Slobodkin, A. I., Jeanthon, C., L'Haridon, S., Nazina, T., Miroshnichenko, M. & Bonch-Osmolovskaya, E. (1999). Dissimilatory reduction of Fe(III) by thermophilic bacteria and archaea in deep subsurface petroleum reservoirs of western Siberia. Curr Microbiol 39, 99–102.[CrossRef][Medline]
Slobodkin, A., Campbell, B., Cary, S. C., Bonch-Osmolovskaya, E. & Jeanthon, C. (2001). Evidence for the presence of thermophilic Fe(III)-reducing microorganisms in deep-sea hydrothermal vents at 13°N (East Pacific Rise). FEMS Microbiol Ecol 36, 235–243.[Medline]
Stetter, K. O., Fiala, G., Huber, G., Huber, R. & Segerer, A. (1990). Hyperthermophilic microorganisms. FEMS Microbiol Rev 75, 117–124.[CrossRef]
Stetter, K. O., Huber, R., Blöchl, E., Kurr, M., Eden, R. D., Fielder, M., Cash, H. & Vance, I. (1993). Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 365, 743–745.
Takahata, Y., Nishijima, M., Hoaki, T. & Maruyama, T. (2000). Distribution and physiological characteristics of hyperthermophiles in the Kubiki oil reservoir in Niigata, Japan. Appl Environ Microbiol 66, 73–79.
Takai, K. & Fujiwara, Y. (2002). Hydrothermal vents: biodiversity in deep-sea hydrothermal vents. In Encyclopedia of Environmental Microbiology, pp. 1604–1617. Edited by G. Bitton. New York: Wiley.
Takai, K. & Horikoshi, K. (2000). Thermosipho japonicus sp. nov., an extremely thermophilic bacterium isolated from a deep-sea hydrothermal vent in Japan. Extremophiles 4, 9–17.[Medline]
Takai, K., Inoue, A. & Horikoshi, K. (1999). Thermaerobacter marianensis gen. nov., sp. nov., an aerobic extremely thermophilic marine bacterium from the 11 000 m deep Mariana Trench. Int J Syst Bacteriol 49, 619–628.
Takai, K., Sugai, A., Itoh, T. & Horikoshi, K. (2000). Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 50, 489–500.[Abstract]
Takai, K., Komatsu, T., Inagaki, F. & Horikoshi, K. (2001). Distribution of archaea in a black smoker chimney structure. Appl Environ Microbiol 67, 3618–3629.
Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.
Zillig, W., Holz, I., Janekovic, D. & 7 other authors (1990). Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides. J Bacteriol 172, 3959–3965.
This article has been cited by other articles:
|
|
 |
|
  A. Gittel, K. B. Sorensen, T. L. Skovhus, K. Ingvorsen, and A. Schramm Prokaryotic Community Structure and Sulfate Reducer Activity in Water from High-Temperature Oil Reservoirs with and without Nitrate Treatment Appl. Envir. Microbiol., November 15, 2009; 75(22): 7086 - 7096. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. B. Slobodkina, T. V. Kolganova, N. A. Chernyh, J. Querellou, E. A. Bonch-Osmolovskaya, and A. I. Slobodkin Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1508 - 1512. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Blum, S. Han, B. Lanoil, C. Saltikov, B. Witte, F. R. Tabita, S. Langley, T. J. Beveridge, L. Jahnke, and R. S. Oremland Ecophysiology of "Halarsenatibacter silvermanii" Strain SLAS-1T, gen. nov., sp. nov., a Facultative Chemoautotrophic Arsenate Respirer from Salt-Saturated Searles Lake, California Appl. Envir. Microbiol., April 1, 2009; 75(7): 1950 - 1960. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Imachi, S. Sakai, H. Hirayama, S. Nakagawa, T. Nunoura, K. Takai, and K. Horikoshi Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney Int J Syst Evol Microbiol, October 1, 2008; 58(10): 2258 - 2265. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Iino, T. Nakagawa, K. Mori, S. Harayama, and K.-i. Suzuki Calditerrivibrio nitroreducens gen. nov., sp. nov., a thermophilic, nitrate-reducing bacterium isolated from a terrestrial hot spring in Japan Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1675 - 1679. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Hirayama, M. Sunamura, K. Takai, T. Nunoura, T. Noguchi, H. Oida, Y. Furushima, H. Yamamoto, T. Oomori, and K. Horikoshi Culture-Dependent and -Independent Characterization of Microbial Communities Associated with a Shallow Submarine Hydrothermal System Occurring within a Coral Reef off Taketomi Island, Japan Appl. Envir. Microbiol., December 1, 2007; 73(23): 7642 - 7656. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, M. Miyazaki, T. Nunoura, H. Hirayama, H. Oida, Y. Furushima, H. Yamamoto, and K. Horikoshi Sulfurivirga caldicuralii gen. nov., sp. nov., a novel microaerobic, thermophilic, thiosulfate-oxidizing chemolithoautotroph, isolated from a shallow marine hydrothermal system occurring in a coral reef, Japan. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1921 - 1929. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, H. Hirayama, T. Nakagawa, Y. Suzuki, K. H. Nealson, and K. Horikoshi Lebetimonas acidiphila gen. nov., sp. nov., a novel thermophilic, acidophilic, hydrogen-oxidizing chemolithoautotroph within the 'Epsilonproteobacteria', isolated from a deep-sea hydrothermal fumarole in the Mariana Arc Int J Syst Evol Microbiol, January 1, 2005; 55(1): 183 - 189. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, H. Hirayama, T. Nakagawa, Y. Suzuki, K. H. Nealson, and K. Horikoshi Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2325 - 2333. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. E. Hoeft, T. R. Kulp, J. F. Stolz, J. T. Hollibaugh, and R. S. Oremland Dissimilatory Arsenate Reduction with Sulfide as Electron Donor: Experiments with Mono Lake Water and Isolation of Strain MLMS-1, a Chemoautotrophic Arsenate Respirer Appl. Envir. Microbiol., May 1, 2004; 70(5): 2741 - 2747. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, K. H. Nealson, and K. Horikoshi Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the {varepsilon}-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field Int J Syst Evol Microbiol, January 1, 2004; 54(1): 25 - 32. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Inagaki, K. Takai, H. Kobayashi, K. H. Nealson, and K. Horikoshi Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing {varepsilon}-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough Int J Syst Evol Microbiol, November 1, 2003; 53(6): 1801 - 1805. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, S. Nakagawa, Y. Sako, and K. Horikoshi Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, strictly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system Int J Syst Evol Microbiol, November 1, 2003; 53(6): 1947 - 1954. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. L. Miroshnichenko, A. I. Slobodkin, N. A. Kostrikina, S. L'Haridon, O. Nercessian, S. Spring, E. Stackebrandt, E. A. Bonch-Osmolovskaya, and C. Jeanthon Deferribacter abyssi sp. nov., an anaerobic thermophile from deep-sea hydrothermal vents of the Mid-Atlantic Ridge Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1637 - 1641. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Nakagawa, K. Takai, K. Horikoshi, and Y. Sako Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney Int J Syst Evol Microbiol, May 1, 2003; 53(3): 863 - 869. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
) of D. desulfuricans SSM1T. Acetate (5 mM; 
) and elemental sulfur (3 %, w/v), nitrate (5 mM) or arsenate (2 mM) were tested. Concentrations of supplied electron acceptor (
) and product (
) are shown as appropriate.