Geology topics

Derek R. Lovley

Publications and source records attributed to Derek R. Lovley.

At least 37 records · Page 2Linked to original sources

USGS1995

Growth of strain SES-3 with arsenate and other diverse electron acceptors

The selenate-respiring bacterial strain SES-3 was able to use a variety of inorganic electron acceptors to sustain growth. SES-3 grew with the reduction of arsenate to arsenite, Fe(III) to Fe(II), or thiosulfate to sulfide. It also grew in medium in which elemental sulfur, Mn(IV), nitrite, trimethylamine N -oxide, or fumarate was provided as an electron acceptor. Growth on oxygen was microaerophilic. There was no growth with arsenite or chromate. Washed suspensions of cells grown on selenate or nitrate had a constitutive ability to reduce arsenate but were unable to reduce arsenite. These results suggest that strain SES-3 may occupy a niche as an environmental opportunist by being able to take advantage of a diversity of electron acceptors.

Applied and Environmental Microbiology↗

USGS1995

Fe(III) and S0 reduction by Pelobacter carbinolicus

There is a close phylogenetic relationship between Pelobacter species and members of the genera Desulfuromonas and Geobacter , and yet there has been a perplexing lack of physiological similarities. Pelobacter species have been considered to have a fermentative metabolism. In contrast, Desulfuromonas and Geobacter species have a respiratory metabolism with Fe(III) serving as the common terminal electron acceptor in all species. However, the ability of Pelobacter species to reduce Fe(III) had not been previously evaluated. When a culture of Pelobacter carbinolicus that had grown by fermentation of 2,3- butanediol was inoculated into the same medium supplemented with Fe(III), the Fe(III) was reduced. There was less accumulation of ethanol and more production of acetate in the presence of Fe(III). P. carbinolicus grew with ethanol as the sole electron donor and Fe(III) as the sole electron acceptor. Ethanol was metabolized to acetate. Growth was also possible on Fe(III) with the oxidation of propanol to propionate or butanol to butyrate if acetate was provided as a carbon source. P. carbinolicus appears capable of conserving energy to support growth from Fe(III) respiration as it also grew with H 2 or formate as the electron donor and Fe(III) as the electron acceptor. Once adapted to Fe(III) reduction, P. carbinolicus could also grow on ethanol or H 2 with S 0 as the electron acceptor. P. carbinolicus did not contain detectable concentrations of the c -type cytochromes that previous studies have suggested are involved in electron transport to Fe(III) in other organisms that conserve energy to support growth from Fe(III) reduction. These results demonstrate that P. carbinolicus may survive in some sediments as an Fe(III) or S 0 reducer rather than growing fermentatively on rare substrates or syntrophically as an ethanol-oxidizing acetogen. These studies also suggest that the ability to use Fe(III) as a terminal electron acceptor may be an important unifying feature of the Geobacter-Desulfuromonas- Pelobacter branch of the delta Proteobacteria .

Applied and Environmental Microbiology↗

USGS1994

Stimulated anoxic biodegradation of aromatic hydrocarbons using Fe(III) ligands

Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing the bioavailability of Fe(III) by adding suitable ligands provides a potential alternative to oxygen addition for the bioremediation of petroleum-contaminated aquifers.Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing the bioavailability of Fe(III) by adding suitable ligands provides a potential alternative to oxygen addition for the bioremediation of petroleum-contamined aquifers.

Nature↗

USGS1993

Aspects of the biogeochemistry of methane in Mono Lake and the Mono Basin of California

Above-ambient levels of methane and higher hydrocarbons were detected in the atmosphere of the Mono Basin. These gases emanated from several different sources, including natural gas seeps (thermogenic and biogenic), and methanogenic activity in sediments. Seeps were distributed over nearly 33% of the lake bottom and were also present in the exposed former lakebed. They originated from one or more natural gas deposits that underlie the basin. Seeps associated with hot springs had a thermogenic character, whereas the others had the characteristics of bacterially formed gases. The radiocarbon content of methane in all seep gases was low (5-11% modern carbon), indicating an age of greater than about 20,000 years. Dissolved methane increased with depth in the sediments, ultimately reaching saturation levels (1-3 mM). The outward diffusive flux of methane into the anoxic bottom waters elevated concentrations to 60 µM during the 1984-1988 meromictic interval. The radiocarbon content of hypolimnion methane was equivalent to that of the dissolved inorganic carbon (~80% modern carbon), indicating derivation from current methanogenic activity. Oxidation by anaerobic bacteria was the major sink for this methane. Methane that escaped oxidation transited to the epilimnion where it attained supersaturation (0.1-3.0 µM) relative to the atmosphere. Measured outward fluxes over a 2-year period were highly variable, ranging from 0.01 to 4.82 mmoles CH 4 m -2 d -1 . Bacterial activity was detected in the sediments of the hypolimnion High rates of sulfate reduction (~200 µmoles L -1 d -1 ) were measured in the upper 5-cm interval but decreased > 10-fold with depth. The highest rate of methanogenic activity was ~1 µmole L -1 d -1 , as measured by reduction of 14 CO 2 . Bacteria metabolized dimethylsulfide, trimethylamine, acetate, and glucose to primarily CO 2 and some CH 4 . Turnovers of glucose (k = 0.16 d -1 ) and trimethylamine (k = 0.09 d -1 ) were highest in the upper 2.5-cm interval and decreased as much as 10-fold with depth. These results confirm that a low rate of methanogenic activity occurs in this extreme environment and is the source of methane to the hypolimnion.

California↗

USGS1993

Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals

The gram-negative metal-reducing microorganism, previously known as strain GS-15, was further characterized. This strict anaerobe oxidizes several short-chain fatty acids, alcohols, and monoaromatic compounds with Fe(III) as the sole electron acceptor. Furthermore, acetate is also oxidized with the reduction of Mn (IV), U (VI), and nitrate. In whole cell suspensions, the c -type cytochrome(s) of this organism was oxidized by physiological electron acceptors and also by gold, silver, mercury, and chromate. Menaquinone was recovered in concentrations comparable to those previously found in gram-negative sulfate reducers. Profiles of the phospholipid ester-linked fatty acids indicated that both the anaerobic desaturase and the branched pathways for fatty acid biosynthesis were operative. The organism contained three lipopolysaccharide hydroxy fatty acids which have not been previously reported in microorganisms, but have been observed in anaerobic freshwater sediments. The 16S rRNA sequence indicated that this organism belongs in the delta proteobacteria. Its closest known relative is Desulfuromonas acetoxidans . The name Geobacter metallireducens is proposed.

Archives of Microbiology↗

USGS1993

Enzymatic iron and uranium reduction by sulfate-reducing bacteria

The potential for sulfate-reducing bacteria (SRB) to enzymatically reduce Fe(III) and U(VI) was investigated. Five species of Desulfovibrio as well as Desulfobacterium autotrophicum and Desulfobulbus propionicus reduced Fe(III) chelated with nitrilotriacetic acid as well as insoluble Fe(III) oxide. Fe(III) oxide reduction resulted in the accumulation of magnetite and siderite. Desulfobacter postgatei reduced the chelated Fe(III) but not Fe(III) oxide. Desulfobacter curvatus, Desulfomonile tiedjei , and Desulfotomaculum acetoxidans did not reduce Fe(III). Only Desulfovibrio species reduced U(VI). U(VI) reduction resulted in the precipitation of uraninite. None of the SRB that reduced Fe(III) or U(VI) appeared to conserve enough energy to support growth from this reaction. However, Desulfovibrio desulfuricans metabolized H 2 down to lower concentrations with Fe(III) or U(VI) as the electron acceptor than with sulfate, suggesting that these metals may be preferred electron acceptors at the low H 2 concentrations present in most marine sediments. Molybdate did not inhibit Fe(III) reduction by D. desulfuricans . This indicates that the inability of molybdate to inhibit Fe(III) reduction in marine sediments does not rule out the possibility that SRB are important catalysts for Fe(III) reduction. The results demonstrate that although SRB were previously considered to reduce Fe(III) and U(VI) indirectly through the production of sulfide, they may also directly reduce Fe(III) and U(VI) through enzymatic mechanisms. These findings, as well as our recent discovery that the S o -reducing microorganism Desulfuromonas acetoxidans can reduce Fe(III), demonstrate that there are close links between the microbial sulfur, iron, and uranium cycles in anaerobic marine sediments.

Marine Geology↗

USGS1993

Anaerobes into heavy metal: Dissimilatory metal reduction in anoxic environments

Within the last decade, a novel form of microbial metabolism of major environmental significance has been elucidated. In this process, known as dissimilatory metal reduction, specialized microorganisms, living in anoxic aquatic sediments and ground water, oxidize organic compounds to carbon dioxide with metals serving as the oxidant. Recent studies have demonstrated that this metabolism explains a number of important geochemical phenomena in ancient and modern sedimentary environments, affecting not only the cycling of metals but also the fate of organic matter. Furthermore, this metabolism may have practical application in remediation of environments contaminated with toxic metals and/or organics.

Trends in Ecology and Evolution↗

USGS1993

Dissimilatory Fe(III) reduction by the marine microorganism Desulfuromonas acetoxidans

The ability of the marine microorganism Desulfuromonas acetoxidans to reduce Fe(III) was investigated because of its close phylogenetic relationship with the freshwater dissimilatory Fe(III) reducer Geobacter metallireducens. Washed cell suspensions of the type strain of D. acetoxidans reduced soluble Fe(III)-citrate and Fe(III) complexed with nitriloacetic acid. The c -type cytochrome(s) of D. acetoxidans was oxidized by Fe(III)-citrate and Mn(IV)-oxalate, as well as by two electron acceptors known to support growth, colloidal sulfur and malate. D. acetoxidans grew in defined anoxic, bicarbonate-buffered medium with acetate as the sole electron donor and poorly crystalline Fe(III) or Mn(IV) as the sole electron acceptor. Magnetite (Fe 3 O 4 ) and siderite (FeCO 3 ) were the major end products of Fe(III) reduction, whereas rhodochrosite (MnCO 3 ) was the end product of Mn(IV) reduction. Ethanol, propanol, pyruvate, and butanol also served as electron donors for Fe(III) reduction. In contrast to D. acetoxidans, G. metallireducens could only grow in freshwater medium and it did not conserve energy to support growth from colloidal S 0 reduction. D. acetoxidans is the first marine microorganism shown to conserve energy to support growth by coupling the complete oxidation of organic compounds to the reduction of Fe(III) or Mn(IV). Thus, D. acetoxidans provides a model enzymatic mechanism for Fe(III) or Mn(IV) oxidation of organic compounds in marine and estuarine sediments. These findings demonstrate that 16S rRNA phylogenetic analyses can suggest previously unrecognized metabolic capabilities of microorganisms.

Applied and Environmental Microbiology↗

USGS1991

Release of 226Ra from uranium mill tailings by microbial Fe(III) reduction

Uranium mill tailings were anaerobically incubated in the presence of H 2 with Alteromonas putrefaciens , a bacterium known to couple the oxidation of H 2 and organic compounds to the reduction of Fe(III) oxides. There was a direct correlation between the extent of Fe(III) reduction and the accumulation of dissolved 226 Ra. In sterile tailings in which Fe(III) was not reduced, there was negligible leaching of 226 Ra. The behavior of Ba was similar to that of Ra in inoculated and sterile systems. These results demonstrate that under anaerobic conditions, microbial reduction of Fe(III) may result in the release of dissolved 226 Ra from uranium mill tailings.

Applied Geochemistry↗

USGS1991

Microbial reduction of uranium

Reduction of the soluble, oxidized form of uranium, U(VI), to insoluble U(IV) is an important mechanism for the immobilization of uranium in aquatic sediments and for the formation of some uranium ores 1–10 . U(VI) reduction has generally been regarded as an abiological reaction in which sulphide, molecular hydrogen or organic compounds function as the reductant 1,2,5,11 . Microbial involvement in U(VI) reduction has been considered to be limited to indirect effects, such as microbial metabolism providing the reduced compounds for abiological U(VI) reduction and microbial cell walls providing a surface to stimulate abiological U(VI) reduction 1,12,13 . We report here, however, that dissimilatory Fe(III)-reducing microorganisms can obtain energy for growth by electron transport to U(VI). This novel form of microbial metabolism can be much faster than commonly cited abiological mechanisms for U(VI) reduction. Not only do these findings expand the known potential terminal electron acceptors for microbial energy transduction, they offer a likely explanation for the deposition of uranium in aquatic sediments and aquifers, and suggest a method for biological remediation of environments contaminated with uranium.

Nature↗

USGS1991

Electron transport in the dissimilatory iron reducer, GS-15

Mechanisms for electron transport to Fe(III) were investigated in GS-15, a novel anaerobic microorganism which can obtain energy for growth hy coupling the complete oxidation of organic acids or aromatic compounds to the reduction of Fe(III) to Fe(II). The results indicate that Fe(III) reduction proceeds through a type b cytochrome and a membrane-bound Fe(III) reductase which is distinct from the nitrate reductase.

Applied and Environmental Microbiology↗

USGS1990

Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57 Fe Mo¨ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 × 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of 110 faces which are capped and truncated by 111 end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization.

Earth and Planetary Science Letters↗

USGS1990

Rates of microbial metabolism in deep coastal plain aquifers

Rates of microbial metabolism in deep anaerobic aquifers of the Atlantic coastal plain of South Carolina were investigated by both microbiological and geochemical techniques. Rates of [2- 14 C]acetate and [U- 14 C]glucose oxidation as well as geochemical evidence indicated that metabolic rates were faster in the sandy sediments composing the aquifers than in the clayey sediments of the confining layers. In the sandy aquifer sediments, estimates of the rates of CO 2 production (millimoles of CO 2 per liter per year) based on the oxidation of [2- 14 C] acetate were 9.4 × 10 −3 to 2.4 × 10 −1 for the Black Creek aquifer, 1.1 × 10 −2 for the Middendorf aquifer, and <7 × 10 −5 for the Cape Fear aquifer. These estimates were at least 2 orders of magnitude lower than previously published estimates that were based on the accumulation of CO 2 in laboratory incubations of similar deep subsurface sediments. In contrast, geochemical modeling of groundwater chemistry changes along aquifer flowpaths gave rate estimates that ranged from 10 −4 to 10 −6 mmol of CO 2 per liter per year. The age of these sediments (ca. 80 million years) and their organic carbon content suggest that average rates of CO 2 production could have been no more than 10 −4 mmol per liter per year. Thus, laboratory incubations may greatly overestimate the in situ rates of microbial metabolism in deep subsurface environments. This has important implications for the use of laboratory incubations in attempts to estimate biorestoration capacities of deep aquifers. The rate estimates from geochemical modeling indicate that deep aquifers are among the most oligotrophic aquatic environments in which there is ongoing microbial metabolism.

South Carolina↗

USGS1989

Oxidation of aromatic contaminants coupled to microbial iron reduction

THE contamination of sub-surface water supplies with aromatic compounds is a significant environmental concern1,2. As these contaminated sub-surface environments are generally anaerobic, the microbial oxidation of aromatic compounds coupled to nitrate reduction, sulphate reduction and methane production has been studied intensively1-7. In addition, geochemical evidence suggests that Fe(III) can be an important electron acceptor for the oxidation of aromatic compounds in anaerobic groundwater. Until now, only abiological mechanisms for the oxidation of aromatic compounds with Fe(III) have been reported8-12. Here we show that in aquatic sediments, microbial activity is necessary for the oxidation of model aromatic compounds coupled to Fe(III) reduction. Furthermore, a pure culture of the Fe(III)-reducing bacterium GS-15 can obtain energy for growth by oxidizing benzoate, toluene, phenol or p-cresol with Fe(III) as the sole electron acceptor. These results extend the known physiological capabilities of Fe(III)-reducing organisms and provide the first example of an organism of any type which can oxidize an aromatic hydrocarbon anaerobically.

Nature↗

USGS1989

Requirement for a microbial consortium to completely oxidize glucose in Fe(III)- reducing sediments

In various sediments in which Fe(III) reduction was the terminal electron-accepting process, [ 14 C]glucose was fermented to 14 C-fatty acids in a manner similar to that observed in methanogenic sediments. These results are consistent with the hypothesis that, in Fe(III)-reducing sediments, fermentable substrates are oxidized to carbon dioxide by the combined activity of fermentative bacteria and fatty acid-oxidizing, Fe(III)-reducing bacteria.

Maryland, Minnesota↗

USGS1989

Hydrogen and formate oxidation coupled to dissimilatory reduction of iron or manganese by Alteromonas putrefaciens

The ability of Alteromonas putrefaciens to obtain energy for growth by coupling the oxidation of various electron donors to dissimilatory Fe(III) or Mn(IV) reduction was investigated. A. putrefaciens grew with hydrogen, formate, lactate, or pyruvate as the sole electron donor and Fe(III) as the sole electron acceptor. Lactate and pyruvate were oxidized to acetate, which was not metabolized further. With Fe(III) as the electron acceptor, A. putrefaciens had a high affinity for hydrogen and formate and metabolized hydrogen at partial pressures that were 25-fold lower than those of hydrogen that can be metabolized by pure cultures of sulfate reducers or methanogens. The electron donors for Fe(III) reduction also supported Mn(IV) reduction. The electron donors for Fe(III) and Mn(IV) reduction and the inability of A. putrefaciens to completely oxidize multicarbon substrates to carbon dioxide distinguish A. putrefaciens from GS-15, the only other organism that is known to obtain energy for growth by coupling the oxidation of organic compounds to the reduction of Fe(III) or Mn(IV). The ability of A. putrefaciens to reduce large quantities of Fe(III) and to grow in a defined medium distinguishes it from a Pseudomonas sp., which is the only other known hydrogen-oxidizing, Fe(III)-reducing microorganism. Furthermore, A. putrefaciens is the first organism that is known to grow with hydrogen as the electron donor and Mn(IV) as the electron acceptor and is the first organism that is known to couple the oxidation of formate to the reduction of Fe(III) or Mn(IV). Thus, A. putrefaciens provides a much needed microbial model for key reactions in the oxidation of sediment organic matter coupled to Fe(III) and Mn(IV) reduction.

Applied and Environmental Microbiology↗

USGS1988

Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments

Factors controlling the concentration of dissolved hydrogen gas in anaerobic sedimentary environments were investigated. Results, presented here or previously, demonstrated that, in sediments, only microorganisms catalyze the oxidation of H2 coupled to the reduction of nitrate, Mn(IV), Fe(III), sulfate, or carbon dioxide. Theoretical considerations suggested that, at steady-state conditions, H2 concentrations are primarily dependent upon the physiological characteristics of the microorganism(s) consuming the H2 and that organisms catalyzing H2 oxidation, with the reduction of a more electrochemically positive electron acceptor, can maintain lower H2 concentrations than organisms using electron acceptors which yield less energy from H2 oxidation. The H2 concentrations associated with the specified predominant terminal electron-accepting reactions in bottom sediments of a variety of surface water environments were: methanogenesis, 7-10 nM; sulfate reduction, 1-1.5 nM; Fe(III) reduction, 0.2 nM; Mn(IV) or nitrate reduction, less than 0.05 nM. Sediments with the same terminal electron acceptor for organic matter oxidation had comparable H2 concentrations, despite variations in the rate of organic matter decomposition, pH, and salinity. Thus, each terminal electron-accepting reaction had a unique range of steady-state H2 concentrations associated with it. Preliminary studies in a coastal plain aquifer indicated that H2 concentrations also vary in response to changes in the predominant terminal electron-accepting process in deep subsurface environments. These studies suggest that H2 measurements may aid in determining which terminal electron-accepting reactions are taking place in surface and subsurface sedimentary environments.

Geochimica et Cosmochimica Acta↗

USGS1987

Anaerobic production of magnetite by a dissimilatory iron-reducing microorganism

The potential contribution of microbial metabolism to the magnetization of sediments has only recently been recognized. In the presence of oxygen, magnetotactic bacteria can form intracellular chains of magnetite while using oxygen or nitrate as the terminal electron acceptor for metabolism 1 . The production of ultrafine-grained magnetite by magnetotactic bacteria in surficial aerobic sediments may contribute significantly to the natural remanent magnetism of sediments 2–4 . However, recent studies on iron reduction in anaerobic sediments suggested that bacteria can also generate magnetite in the absence of oxygen 5 . We report here on a sediment organism, designated GS-15, which produces copious quantities of ultrafine-grained magnetite under anaerobic conditions. GS-15 is not magnetotactic, but reduces amorphic ferric oxide to extracellular magnetite during the reduction of ferric iron as the terminal electron acceptor for organic matter oxidation. This novel metabolism may be the mechanism for the formation of ultrafine-grained magnetite in anaerobic sediments, and could account for the accumulation of magnetite in ancient iron formations and hydrocarbon deposits.

Nature↗