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MacArdle SG, Rees DC. Solvent Deuterium Isotope Effects of Substrate Reduction by Nitrogenase from Azotobacter vinelandii. J Am Chem Soc 2022; 144:21125-21135. [DOI: 10.1021/jacs.2c07574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Siobhán G. MacArdle
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Douglas C. Rees
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
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Campbell BJ, Sessions AL, Fox DN, Paul BG, Qin Q, Kellermann MY, Valentine DL. Minimal Influence of [NiFe] Hydrogenase on Hydrogen Isotope Fractionation in H 2-Oxidizing Cupriavidus necator. Front Microbiol 2017; 8:1886. [PMID: 29085342 PMCID: PMC5649130 DOI: 10.3389/fmicb.2017.01886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 09/14/2017] [Indexed: 11/25/2022] Open
Abstract
Fatty acids produced by H2-metabolizing bacteria are sometimes observed to be more D-depleted than those of photoautotrophic organisms, a trait that has been suggested as diagnostic for chemoautotrophic bacteria. The biochemical reasons for such a depletion are not known, but are often assumed to involve the strong D-depletion of H2. Here, we cultivated the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16) under aerobic, H2-consuming, chemoautotrophic conditions and measured the isotopic compositions of its fatty acids. In parallel with the wild type, two mutants of this strain, each lacking one of two key hydrogenase enzymes, were also grown and measured. In all three strains, fractionations between fatty acids and water ranged from -173‰ to -235‰, and averaged -217‰, -196‰, and -226‰, respectively, for the wild type, SH- mutant, and MBH- mutant. There was a modest increase in δD as a result of loss of the soluble hydrogenase enzyme. Fractionation curves for all three strains were constructed by growing parallel cultures in waters with δDwater values of approximately -25‰, 520‰, and 1100‰. These curves indicate that at least 90% of the hydrogen in fatty acids is derived from water, not H2. Published details of the biochemistry of the soluble and membrane-bound hydrogenases confirm that these enzymes transfer electrons rather than intact hydride (H-) ions, providing no direct mechanism to connect the isotopic composition of H2 to that of lipids. Multiple lines of evidence thus agree that in this organism, and presumably others like it, environmental H2 plays little or no direct role in controlling lipid δD values. The observed fractionations must instead result from isotope effects in the reduction of NAD(P)H by reductases with flavin prosthetic groups, which transfer two electrons and acquire H+ (or D+) from solution. Parallels to NADPH reduction in photosynthesis may explain why D/H fractionations in C. necator are nearly identical to those in many photoautotrophic algae and bacteria. We conclude that strong D-depletion is not a diagnostic feature of chemoautotrophy.
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Affiliation(s)
- Brian J Campbell
- Department of Earth Science, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Daniel N Fox
- Undergraduate College of Letters and Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Blair G Paul
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Qianhui Qin
- Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Matthias Y Kellermann
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Wilhelmshaven, Germany
| | - David L Valentine
- Department of Earth Science, University of California, Santa Barbara, Santa Barbara, CA, United States.,Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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Crider BP, Carper SW, Lancaster JR. Electron transfer-driven ATP synthesis in Methanococcus voltae is not dependent on a proton electrochemical gradient. Proc Natl Acad Sci U S A 2010; 82:6793-6. [PMID: 16593614 PMCID: PMC390773 DOI: 10.1073/pnas.82.20.6793] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intracellular ATP levels in whole cells of Methanococcus voltae respond to electron transfer coupled to methanogenesis. ATP synthesis can also be induced by an artificially imposed transmembrane electrical potential [formed by electrogenic movement outwards of potassium (induced by valinomycin) or of protons (induced by an uncoupler], or by a pH gradient (acid outside). These results implicate the existence of a reversible ATPase coupled to electrogenic movement of an ion(s) other than potassium or proton, and that ionophores are competent to catalyze ion movement across the cytoplasmic membrane of this organism (which is the sole membrane structure in this species). ATP synthesis driven by electron transfer is, however, insensitive to the addition of such ionophores. These results indicate that although cells possess an ion-translocating ATPase (possibly involved in the maintenance of internal ionic composition homeostasis), methanogenesis-driven ATP synthesis does not involve the intermediacy of a transmembrane ion gradient. Primarily because methane formation has been previously demonstrated to involve true electron transfer, substrate-level phosphorylation (at least in analogy to other systems) has been generally ruled out. The results presented here suggest that at least one methanogenic bacterium may use a direct linkage of ATP synthesis to electron transfer.
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Affiliation(s)
- B P Crider
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
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Sandbeck KA, Reeburgh WS. Microbiological preparation of 3H-labelled methane. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580271107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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Daniels L, Zeikus JG. Convenient biological preparation of pure high specific activity 14C-labelled methane. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580200104] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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6
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Blaut M, Müller V, Gottschalk G. Proton translocation coupled to methanogenesis from methanol + hydrogen inMethanosarcina barkeri. FEBS Lett 2002. [DOI: 10.1016/0014-5793(87)80112-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Lancaster J. A unified scheme for carbon and electron flow coupled to ATP synthesis by substrate-level phosphorylation in the methanogenic bacteria. FEBS Lett 2001. [DOI: 10.1016/0014-5793(86)81214-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Affiliation(s)
- A D Moodie
- Department of Biochemistry and Microbiology, University of St Andrews, UK
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Rajagopal BS, Lespinat PA, Fauque G, LeGall J, Berlier YM. Mass-spectrometric studies of the interrelations among hydrogenase, carbon monoxide dehydrogenase, and methane-forming activities in pure and mixed cultures of Desulfovibrio vulgaris, Desulfovibrio desulfuricans, and Methanosarcina barkeri. Appl Environ Microbiol 1989; 55:2123-9. [PMID: 2508553 PMCID: PMC203043 DOI: 10.1128/aem.55.9.2123-2129.1989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The activities of pure and mixed cultures of Desulfovibrio vulgaris and Methanosarcina barkeri in the exponential growth phase were monitored by measuring changes in dissolved-gas concentration by membrane-inlet mass spectrometry. M. barkeri grown under H2-CO2 or methanol produced limited amounts of methane and practically no hydrogen from either substrate. The addition of CO resulted in a transient H2 production concomitant with CO consumption. Hydrogen was then taken up, and CH4 production increased. All these events were suppressed by KCN, which inhibited carbon monoxide dehydrogenase activity. Therefore, with both substrates, H2 appeared to be an intermediate in CO reduction to CH4. The cells grown on H2-CO2 consumed 4 mol of CO and produced 1 mol of CH4. Methanol-grown cells reduced CH3OH with H2 resulting from carbon monoxide dehydrogenase activity, and the ratio was then 1 mol of CH4 to 1 mol of CO. Only 12CH4 and no 13CH4 was obtained from 13CO, indicating that CO could not be the direct precursor of CH4. In mixed cultures of D. vulgaris and M. barkeri on lactate, an initial burst of H2 was observed, followed by a lower level of production, whereas methane synthesis was linear with time. Addition of CO to the mixed culture also resulted in transient extra H2 production but had no inhibitory effect upon CH4 formation, even when the sulfate reducer was D. vulgaris Hildenborough, whose periplasmic iron hydrogenase is very sensitive to CO. The hydrogen transfer is therefore probably mediated by a less CO-sensitive nickel-iron hydrogenase from either of both species.
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Affiliation(s)
- B S Rajagopal
- Section d'Enzymologie et Biochimie Bactérienne, CEN Cadarache, Saint Paul Lez Durance, France
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Sparling R, Daniels L. Source of carbon and hydrogen in methane produced from formate by Methanococcus thermolithotrophicus. J Bacteriol 1986; 168:1402-7. [PMID: 3782041 PMCID: PMC213652 DOI: 10.1128/jb.168.3.1402-1407.1986] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Methanococcus thermolithotrophicus is able to produce methane either from H2-CO2 or from formate. The route of formate entry into the methanogenic pathway was investigated by using 2H2O or [13C]formate and analysis by mass spectrometry. When cells (H2-CO2 or formate grown) were transferred to formate medium in 95% 2H water, the proportion of 2H in methane was 95%. When cells (H2-CO2 or formate grown) were transferred to media containing [13C]formate in the presence of H2-CO2 or He-CO2, the ratio of 13CH4 to 12CH4 increased over time parallel to the ratio of 13CO2 to 12CO2. The cells catalyzed a significant exchange of label between [13C]formate and 13CO2.
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Teixeira M, Moura I, Fauque G, Czechowski M, Berlier Y, Lespinat PA, Le Gall J, Xavier AV, Moura JJ. Redox properties and activity studies on a nickel-containing hydrogenase isolated from a halophilic sulfate reducer Desulfovibrio salexigens. Biochimie 1986; 68:75-84. [PMID: 3015250 DOI: 10.1016/s0300-9084(86)81071-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A soluble hydrogenase from the halophilic sulfate reducing bacterium Desulfovibrio salexigens, strain British Guiana (NCIB 8403) has been purified to apparent homogeneity with a final specific activity of 760 mumoles H2 evolved/min/mg (an overall 180-fold purification with 20% recovery yield). The enzyme is composed of two non-identical subunits of molecular masses 62 and 36 kDa, respectively, and contains approximately 1 Ni, 12-15 Fe and 1 Se atoms/mole. The hydrogenase shows a visible absorption spectrum typical of an iron-sulfur containing protein (A400/A280 = 0.275) and a molar absorbance of 54 mM-1cm-1 at 400 nm. In the native state (as isolated, under aerobic conditions), the enzyme is almost EPR silent at 100 K and below. However, upon reduction under H2 atmosphere a rhombic EPR signal develops at g-values 2.22, 2.16 and around 2.0, which is optimally detected at 40 K. This EPR signal is reminiscent of the nickel signal C (g-values 2.19, 2.16 and 2.02) observed in intermediate redox states of the well characterized D. gigas nickel containing hydrogenase and assigned to nickel by 61 Ni isotopic substitution (J.J.G. Moura, M. Teixeira, I. Moura, A.V. Xavier and J. Le Gall (1984), J. Mol. Cat., 23, 305-314). Upon longer incubation with H2 the "2.22" EPR signal decreases. During the course of a redox titration under H2, this EPR signal attains a maximal intensity around--380 mV. At redox states where this "2.22" signal develops (or at lower redox potentials), low temperature studies (below 10 K) reveals the presence of other EPR species with g-values at 2.23, 2.21, 2.14 with broad components at higher fields. This new signal (fast relaxing) exhibits a different microwave power dependence from that of the "2.22" signal, which readily saturates with microwave power (slow relaxing). Also at low temperature (8 K) typical reduced iron-sulfur EPR signals are concomitantly observed with gmed approximately 1.94. The catalytic properties of the enzyme were also followed by substrate isotopic exchange D2/H+ and H2 production measurements.
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Daniels L, Sparling R, Sprott GD. The bioenergetics of methanogenesis. BIOCHIMICA ET BIOPHYSICA ACTA 1984; 768:113-63. [PMID: 6236847 DOI: 10.1016/0304-4173(84)90002-8] [Citation(s) in RCA: 157] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The reduction of CO2 or any other methanogenic substrate to methane serves the same function as the reduction of oxygen, nitrate or sulfate to more reduced products. These exergonic reactions are coupled to the production of usable energy generated through a charge separation and a protonmotive-force-driven ATPase. For the understanding of how methanogens derive energy from C-1 unit reduction one must study the biochemistry of the chemical reactions involved and how these are coupled to the production of a charge separation and subsequent electron transport phosphorylation. Data on methanogenesis by a variety of organisms indicates ubiquitous use of CH3-S-CoM as the final electron acceptor in the production of methane through the methyl CoM reductase and of 5-deazaflavin as a primary source of reducing equivalents. Three known enzymes serve as catalysts in the production of reduced 5-deazaflavin: hydrogenase, formate dehydrogenase and CO dehydrogenase. All three are potential candidates for proton pumps. In the organisms that must oxidize some of their substrate to obtain electrons for the reduction of another portion of the substrate to methane (e.g., those using formate, methanol or acetate), the latter two enzymes may operate in the oxidizing direction. CO2 is the most frequent substrate for methanogenesis but is the only substrate that obligately requires the presence of H2 and hydrogenase. Growth on methanol requires a B12-containing methanol-CoM methyl transferase and does not necessarily need any other methanogenic enzymes besides the methyl-CoM reductase system when hydrogenase is present. When bacteria grow on methanol alone it is not yet clear if they get their reducing equivalents from a reversal of methanogenic enzymes, thus oxidizing methyl groups to CO2. An alternative (since these and acetate-catabolizing methanogens possess cytochrome b) is electron transport and possible proton pumping via a cytochrome-containing electron transport chain. Several of the actual components of the methanogenic pathway from CO2 have been characterized. Methanofuran is apparently the first carbon-carrying cofactor in the pathway, forming carboxy-methanofuran. Formyl-FAF or formyl-methanopterin (YFC, a very rapidly labelled compound during 14C pulse labeling) has been implicated as an obligate intermediate in methanogenesis, since methanopterin or FAF is an essential component of the carbon dioxide reducing factor in dialyzed extract methanogenesis. FAF also carries the carbon at the methylene and methyl oxidation levels.(ABSTRACT TRUNCATED AT 400 WORDS)
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Šmigáň P, Friederová A, Rusňák P, Greksák M. Effect of 2,4-dinitrophenol and ionophores on growth and methanogenesis inMethanobacterium thermoautotrophicum. Folia Microbiol (Praha) 1984. [DOI: 10.1007/bf02887762] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sauer FD, Mahadevan S, Erfle JD. Methane synthesis by membrane vesicles and a cytoplasmic cofactor isolated from Methanobacterium thermoautotrophicum. Biochem J 1984; 221:61-9. [PMID: 6466320 PMCID: PMC1144003 DOI: 10.1042/bj2210061] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Methanobacterium thermoautotrophicum when grown on ordinary culture medium has a tough cell wall which is lysozyme-resistant and difficult to disrupt by physical means. The cell wall, however, can be weakened by the addition of D-sorbitol to the growth medium and the organisms form protoplasts after lysozyme addition. This technique allowed the isolation of two types of intracellular small vesicles: (a) isolated by disruption of the total cell population (lysozyme-sensitive and lysozyme-resistant cells) by ultrafrequency sound and (b) isolated by osmotic lysis of protoplasts. For the first time, a small vesicle fraction isolated as in (a) was capable of synthesizing methane from CO2 and H2 without cytoplasm. There was, however, an absolute requirement for a small, heat-stable, oxygen-sensitive cofactor which was isolated from the cytoplasm. Methane synthesis with this vesicle fraction was inhibited by the detergent deoxycholate, and by the protonophores 2,4-dinitrophenol and carbonyl cyanide m-chlorophenylhydrazone. Mg2+-ATPase appeared to be located on the outer or cytoplasmic surface of the small vesicle fraction isolated as in (b). The results were consistent with a previously made suggestion [Sauer, Erfle & Mahadevan (1981) J. Biol. Chem. 256, 9843-9848] that the interior of the small intracellular vesicles becomes acid during methane synthesis.
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Jarrell KF, Sprott GD. The effects of ionophores and metabolic inhibitors on methanogenesis and energy-related properties of Methanobacterium bryantii. Arch Biochem Biophys 1983; 225:33-41. [PMID: 6311108 DOI: 10.1016/0003-9861(83)90004-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The effects of numerous ionophores and inhibitors were tested on methane synthesis, intracellular ATP and potassium concentrations, and the proton motive force of the methanogenic archaebacterium Methanobacterium bryantii. M. bryantii had an internal pH near 6.8 (and hence little delta pH during growth) with an electrical potential of --127 mV in growth medium and --105 mV in a pH 6.5 buffer. The study has identified agents which, in M. bryantii, can effectively cause a decline of intracellular ATP (gramicidin, acetylene) and potassium concentrations (gramicidin, nigericin), inhibit methane synthesis (acetylene, gramicidin, nigericin, triphenylmethylphosphonium bromide), eliminate the electrical potential (high extracellular potassium ion concentrations), and dissipate artificially imposed, inside alkaline, pH gradients (monensin, nigericin, carbonyl cyanide m-chlorophenylhydrazone). Carbonyl cyanide m-chlorophenylhydrazone was generally ineffective in media or buffers reduced with cysteine-sulfide but could be effective in cysteine-free solutions reduced with hydrogen sulfide.
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Volfová O, Suchardová O, Krumphanzl V. Anaerobic degradation of cellulose and formation of methane. Folia Microbiol (Praha) 1982; 27:354-62. [PMID: 7141336 DOI: 10.1007/bf02883139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The existing knowledge of anaerobic digestion of cellulose-containing wastes and methane formation is reviewed. Mutual relationships between the individual phases of this complex process and the mechanism of methane biosynthesis are discussed in three sections: (1) Non-methanogenic phase and digestion of cellulose; (2) methanogenic phase and methanogenesis; (3) mixed cultures and their advantages.
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Fallon RD. Influences of pH, Temperature, and Moisture on Gaseous Tritium Uptake in Surface Soils. Appl Environ Microbiol 1982; 44:171-8. [PMID: 16346053 PMCID: PMC241986 DOI: 10.1128/aem.44.1.171-178.1982] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In South Carolina surface soils, the uptake of gaseous tritium (T
2
, HT, or both) showed a broad optimal temperature response from about 20 to 50°C, with the highest rates at 35 to 45°C. The optimal pH was in the range of 4 to 7. Uptake rates declined at the wet and dry extremes in soil moisture content. Inhibition seen upon the addition of hydrogen or carbon monoxide to the soil atmosphere suggested that hydrogenase may be responsible for T
2
-HT uptake in soil. During the period of most rapid recovery in a 36-day incubation of reinoculated, sterilized soil, T
2
-HT uptake rates doubled every 2 to 4 days. Thus, T
2
-HT uptake appears to be biologically mediated. Soil uptake of T
2
-HT was not severely limited by pH, temperature, or moisture in the soils tested. Thus, rapid exchange of gaseous tritium into soil water must be expected and accounted for in modeling the isotope distributions around nuclear facilities.
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Affiliation(s)
- R D Fallon
- E. I. du Pont de Nemours & Co., Inc., Savannah River Laboratory, Aiken, South Carolina 29808
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Purification and properties of an 8-hydroxy-5-deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34788-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Sauer F, Erfle J, Mahadevan S. Evidence for an internal electrochemical proton gradient in Methanobacterium thermoautotrophicum. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68706-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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