The bioenergetics of methanogenesis

Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex

The 22nd genetically encoded amino acid, pyrrolysine, plays a unique role in the key step in the growth of methanogens on mono-, di-, and tri-methylamines by activating the methyl group of these substrates for transfer to a corrinoid cofactor. Previous crystal structures of the Methanosarcina barkeri monomethylamine methyltransferase elucidated the structure of pyrrolysine and provide insight into its role in monomethylamine activation. Herein, we report the second structure of a pyrrolysine-containing protein, the M. barkeri trimethylamine methyltransferase MttB, and its structure bound to sulfite, a substrate analog of trimethylamine. We also report the structure of MttB in complex with its cognate corrinoid protein MttC, which specifically receives the methyl group from the pyrrolysine-activated trimethylamine substrate during methanogenesis. Together these structures provide key insights into the role of pyrrolysine in methyl group transfer from trimethylamine to the corrinoid cofactor in MttC.

Importance of thermodynamics dependent kinetic parameters in nitrate-based souring mitigation studies

Souring is the unwanted formation of hydrogen sulfide (H₂S) by sulfate-reducing microorganisms (SRM) in sewer systems and seawater flooded oil reservoirs. Nitrate treatment (NT) is one of the major methods to alleviate souring: The mechanism of souring remediation by NT is stimulation of nitrate reducing microorganisms (NRM) that depending on the nitrate reduction pathway can outcompete SRM for common electron donors, or oxidize sulfide to sulfate. However, some nitrate reduction pathways may challenge the efficacy of NT. Therefore, a precise understanding of souring rate, nitrate reduction rate and pathways is crucial for efficient souring management. Here, we investigate the necessity of incorporating two thermodynamic dependent kinetic parameters, namely, the growth yield (Y), and F_T, a parameter related to the minimum catabolic energy production required by cells to utilize a given catabolic reaction. We first show that depending on physiochemical conditions, Y and F_T for SRM change significantly in the range of [0-0.4] mole biomass per mole electron donor and [0.0006-0.5], respectively, suggesting that these parameters should not be considered constant and that it is important to couple souring models with thermodynamic models. Then, we highlight this further by showing an experimental dataset that can be modeled very well by considering variable F_T. Next, we show that nitrate based lithotrophic sulfide oxidation to sulfate (lNRM₃) is the dominant nitrate reduction pathway. Then, arguing that thermodynamics would suggest that S° consumption should proceed faster than S⁰ production, we infer that the reason for frequently observed S⁰ accumulation is its low solubility. Last, we suggest that nitrate based souring treatment will suffer less from S⁰ accumulation if we (i) act early, (ii) increase temperature and (iii) supplement stoichiometrically sufficient nitrate.

Bentonite Alteration in Batch Reactor Experiments with and without Organic Supplements: Implications for the Disposal of Radioactive Waste

Bentonite is currently proposed as a potential backfill material for sealing high-level radioactive waste in underground repositories due to its low hydraulic conductivity, self-sealing ability and high adsorption capability. However, saline pore waters, high temperatures and the influence of microbes may cause mineralogical changes and affect the long-term performance of the bentonite barrier system. In this study, long-term static batch experiments were carried out at 25 °C and 90 °C for one and two years using two different industrial bentonites (SD80 from Greece, B36 from Slovakia) and two types of aqueous solutions, which simulated (a) Opalinus clay pore water with a salinity of 19 g·L−1, and (b) diluted cap rock solution with a salinity of 155 g·L−1. The bentonites were prepared with and without organic substrates to study the microbial community and their potential influence on bentonite mineralogy. Smectite alteration was dominated by metal ion substitutions, changes in layer charge and delamination during water–clay interaction. The degree of smectite alteration and changes in the microbial diversity depended largely on the respective bentonite and the experimental conditions. Thus, the low charged SD80 with 17% tetrahedral charge showed nearly no structural change in either of the aqueous solutions, whereas B36 as a medium charged smectite with 56% tetrahedral charge became more beidellitic with increasing temperature when reacted in the diluted cap rock solution. Based on these experiments, the alteration of the smectite is mainly attributed to the nature of the bentonite, pore water chemistry and temperature. A significant microbial influence on the here analyzed parameters was not observed within the two years of experimentation. However, as the detected genera are known to potentially influence geochemical processes, microbial-driven alteration occurring over longer time periods cannot be ruled out if organic nutrients are available at appropriate concentrations.

Macrobiont: Cradle for the Origin of Life and Creation of a Biosphere

Although the cellular microorganism is the fundamental unit of biology, the origin of life (OoL) itself is unlikely to have occurred in a microscale environment. The macrobiont (MB) is the macro-scale setting where life originated. Guided by the methodologies of Systems Analysis, we focus on subaerial ponds of scale 3 to 300 m diameter. Within such ponds, there can be substantial heterogeneity, on the vertical, horizontal, and temporal scales, which enable multi-pot prebiotic chemical evolution. Pond size-sensitivities for several figures of merit are mathematically formulated, leading to the expectation that the optimum pond size for the OoL is intermediate, but biased toward smaller sizes. Sensitivities include relative access to nutrients, energy sources, and catalysts, as sourced from geological, atmospheric, hydrospheric, and astronomical contributors. Foreshores, especially with mudcracks, are identified as a favorable component for the success of the macrobiont. To bridge the gap between inanimate matter and a planetary-scale biosphere, five stages of evolution within the macrobiont are hypothesized: prebiotic chemistry → molecular replicator → protocell → macrobiont cell → colonizer cell. Comparison of ponds with other macrobionts, including hydrothermal and meteorite settings, allows a conclusion that more than one possible macrobiont locale could enable an OoL.

The potential for biologically catalyzed anaerobic methane oxidation on ancient Mars

This study examines the potential for the biologically mediated anaerobic oxidation of methane (AOM) coupled to sulfate reduction on ancient Mars. Seven distinct fluids representative of putative martian groundwater were used to calculate Gibbs energy values in the presence of dissolved methane under a range of atmospheric CO2 partial pressures. In all scenarios, AOM is exergonic, ranging from -31 to -135 kJ/mol CH4. A reaction transport model was constructed to examine how environmentally relevant parameters such as advection velocity, reactant concentrations, and biomass production rate affect the spatial and temporal dependences of AOM reaction rates. Two geologically supported models for ancient martian AOM are presented: a sulfate-rich groundwater with methane produced from serpentinization by-products, and acid-sulfate fluids with methane from basalt alteration. The simulations presented in this study indicate that AOM could have been a feasible metabolism on ancient Mars, and fossil or isotopic evidence of this metabolic pathway may persist beneath the surface and in surface exposures of eroded ancient terrains.

Methanosarcina domination in anaerobic sequencing batch reactor at short hydraulic retention time

The Archaea population of anaerobic sequential batch reactor (ASBR) featuring cycle operations under varying hydraulic retention time (HRT) was evaluated for treating a dilute waste stream. Terminal-Restriction Length Polymorphism and clone libraries for both 16S rRNA gene and mcrA gene were employed to characterize the methanogenic community structure. Results revealed that a Methanosarcina dominated methanogenic community was successfully established when using an ASBR digester at short HRT. It was revealed that both 16S rRNA and mcrA clone library could not provide complete community structure, while combination of two different clone libraries could capture more archaea diversity. Thermodynamic calculations confirmed a preference for the observed population structure. The results both experimentally and theoretically confirmed that Methanosarcina dominance emphasizing ASBR's important role in treating low strength wastewater as Methanosarcina will be more adept at overcoming temperature and shock loadings experienced with treating this type of wastewater.

Microbial community analysis of swine wastewater anaerobic lagoons by next-generation DNA sequencing

Anaerobic lagoons are a standard practice for the treatment of swine wastewater. This practice relies heavily on microbiological processes to reduce concentrated organic material and nutrients. Despite this reliance on microbiological processes, research has only recently begun to identify and enumerate the myriad and complex interactions that occur in this microbial ecosystem. To further this line of study, we utilized a next-generation sequencing (NGS) technology to gain a deeper insight into the microbial communities along the water column of four anaerobic swine wastewater lagoons. Analysis of roughly one million 16S rDNA sequences revealed a predominance of operational taxonomic units (OTUs) classified as belonging to the phyla Firmicutes (54.1%) and Proteobacteria (15.8%). At the family level, 33 bacterial families were found in all 12 lagoon sites and accounted for between 30% and 50% of each lagoon's OTUs. Analysis by nonmetric multidimensional scaling (NMS) revealed that TKN, COD, ORP, TSS, and DO were the major environmental variables in affecting microbial community structure. Overall, 839 individual genera were classified, with 223 found in all four lagoons. An additional 321 genera were identified in sole lagoons. The top 25 genera accounted for approximately 20% of the OTUs identified in the study, and the low abundances of most of the genera suggests that most OTUs are present at low levels. Overall, these results demonstrate that anaerobic lagoons have distinct microbial communities which are strongly controlled by the environmental conditions present in each individual lagoon.

Structure and expression of the genes, mcrBDCGA, which encode the subunits of component C of methyl coenzyme M reductase in Methanococcus vannielii

The genes that encode the alpha, beta, and gamma subunits of component C of methyl coenzyme M reductase (mcrA, mcrB, and mcrG) in Methanococcus vannielii have been cloned and sequenced, and their expression in Escherichia coli has been demonstrated. These genes are organized into a five-gene cluster, mcrBDCGA, which contains two genes, designated mcrC and mcrD, with unknown functions. The mcr genes are separated by very short intergenic regions that contain multiple translation stop codons and strong ribosomebinding sequences. Although the genome of M. vannielii is 69 mol% A+T, there is a very strong preference in the mcrA, mcrB, and mcrG genes for the codon with a C in the wobble position in the codon pairs AA(U) (C) (asparagine), GA(U) (C) (aspartic acid), CA(U) (C) (histidine), AU(U) (C) (isoleucine), UU(U) (C) (phenylalanine), and UA(U) (C) (tyrosine). The mcrC and mcrD genes do not show this codon preference and frequently have U or A in the wobble position. As the codon pairs listed above are likely to be translated by the same tRNA with a G in the first anticodon position, the presence of C in the wobble position might ensure maximum efficiency of translation of transcripts of these very highly expressed genes.

Electron transfer-driven ATP synthesis in Methanococcus voltae is not dependent on a proton electrochemical gradient

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.

Effect of gramicidin on methanogenesis by various methanogenic bacteria

Methanogenesis by Methanobacterium thermoautotrophicum strains was extremely sensitive to gramicidin, total inhibition being observed at 0.2 mug/ml. In contrast, methane synthesis by Methanococcus voltae, Methanogenium marisnigri, Methanosarcina mazei, and Methanospirillum hungatei were resistant to the highest concentrations of gramicidin tested (40 mug/ml), although spheroplasts of Methanospirillum hungatei were extremely sensitive. Other species tested showed intermediate sensitivity to gramicidin, methanogenesis inhibition occurring at 4 to 20 mug/ml.

Production of ethane, ethylene, and acetylene from halogenated hydrocarbons by methanogenic bacteria

Several methanogenic bacteria were shown to produce ethane, ethylene, and acetylene when exposed to the halogenated hydrocarbons bromoethane, dibromo- or dichloroethane, and 1,2-dibromoethylene, respectively. They also produced ethylene when exposed to the coenzyme M analog and specific methanogenic inhibitor bromoethanesulfonic acid. The production of these gases from halogenated hydrocarbons has a variety of implications concerning microbial ecology, agriculture, and toxic waste treatment. All halogenated aliphatic compounds tested were inhibitory to methanogens. Methanococcus thermolithotrophicus, Methanococcus deltae, and Methanobacterium thermoautotrophicum DeltaH and Marburg were completely inhibited by 7 muM 1,2-dibromoethane and, to various degrees, by 51 to 1,084 muM 1,2-dichloroethane, 1,2-dibromoethylene, 1,2-dichloroethylene, and trichloroethylene. In general, the brominated compounds were more inhibitory. The two Methanococcus species were fully inhibited by 1 muM bromoethanesulfonic acid, whereas both Methanobacterium strains were only partly inhibited by 2,124 muM. Coenzyme M protected cells from bromoethanesulfonic acid but not from any of the other inhibitors.

Uncoupling of Methanogenesis from Growth of Methanosarcina barkeri by Phosphate Limitation

Production of methane by Methanosarcina barkeri from H(2)-CO(2) was studied in fed-batch culture under phosphate-limiting conditions. A transition in the kinetics of methanogenesis from an exponentially increasing rate to a constant rate was due to depletion of phosphate from the medium. The period of exponentially increasing rate of methanogenesis was extended by increasing the initial concentration of phosphate in the medium. Addition of phosphate during the constant period changed the kinetics to an exponentially increasing rate of methanogenesis, indicating the reversibility of phosphate depletion. The relation between methanogenesis and growth of M. barkeri was investigated by measuring the incorporation of phosphorus, supplied as KH(2)PO(4), in the medium. At a low (1 muM) initial concentration of phosphate in the medium and during the constant period of methanogenesis, there was no net cell growth. At a higher (10 muM) initial concentration of phosphate, cell growth proceeded linearly with time after phosphate had been removed from the medium by uptake into cells.

Steady state characteristics of acclimated hydrogenotrophic methanogens on inorganic substrate in continuous chemostat reactors

A Monod model has been used to describe the steady state characteristics of the acclimated mesophilic hydrogenotrophic methanogens in experimental chemostat reactors. The bacteria were fed with mineral salts and specific trace metals and a H(2)/CO(2) supply was used as a single limited substrate. Under steady state conditions, the growth yield (Y(CH4)) reached 11.66 g cells per mmol of H(2)/CO(2) consumed. The daily cells generation average was 5.67 x 10(11), 5.25 x 10(11), 4.2 x 10(11) and 2.1 x 10(11) cells/l-culture for the dilutions 0.071/d, 0.083/d, 0.1/d and 0.125/d, respectively. The maximum specific growth rate (mu(max)) and the Monod half-saturation coefficient (K(S)) were 0.15/d and 0.82 g/L, respectively. Using these results, the reactor performance was simulated. During the steady state, the simulation predicts the dependence of the H(2)/CO(2) concentration (S) and the cell concentration (X) on the dilution rate. The model fitted the experimental data well and was able to yield a maximum methanogenic activity of 0.24 L CH(4)/g VSS.d. The dilution rate was estimated to be 0.1/d. At the dilution rate of 0.14/d, the exponential cells washout was achieved.

Isolation and characterization of methanophenazine and function of phenazines in membrane-bound electron transport of Methanosarcina mazei Gö1

A hydrophobic, redox-active component with a molecular mass of 538 Da was isolated from lyophilized membranes of Methanosarcina mazei Gö1 by extraction with isooctane. After purification on a high-performance liquid chromatography column, the chemical structure was analyzed by mass spectroscopy and nuclear magnetic resonance studies. The component was called methanophenazine and represents a 2-hydroxyphenazine derivative which is connected via an ether bridge to a polyisoprenoid side chain. Since methanophenazine was almost insoluble in aqueous buffers, water-soluble phenazine derivatives were tested for their ability to interact with membrane-bound enzymes involved in electron transport and energy conservation. The purified F42OH2 dehydrogenase from M. mazei Gö1 showed highest activity with 2-hydroxyphenazine and 2-bromophenazine as electron acceptors when F420H2 was added. Phenazine-1-carboxylic acid and phenazine proved to be less effective. The Km values for 2-hydroxyphenazine and phenazine were 35 and 250 microM, respectively. 2-Hydroxyphenazine was also reduced by molecular hydrogen catalyzed by an F420-nonreactive hydrogenase which is present in washed membrane preparations. Furthermore, the membrane-bound heterodisulfide reductase was able to use reduced 2-hydroxyphenazine as an electron donor for the reduction of CoB-S-S-CoM. Considering all these results, it is reasonable to assume that methanophenazine plays an important role in vivo in membrane-bound electron transport of M. mazei Gö1.

Environmental impact of biomethanogenesis

The environmental impact of biomethanogenesis is related to its ecological role, accumulation and effect as a greenhouse gas, and application in anaerobic digestion for conversion of biomass and wastes to methane and compost. Biological formation of methane is the process by which bacteria decompose organic matter using carbon dioxide as an electron acceptor in the absence of dioxygen or other electron acceptors. This microbial activity is responsible for carbon recycling in anaerobic environments, including wetlands, rice fields, intestines of animals sediments, and manures. The mixed consortium of microorganisms involved includes a unique group of bacteria, the methanogens, which may be considered to be in a separate kingdom based on genetic and phylogenetic variance from all other life forms. Because methane is a significant and increasing greenhouse gas, its source fluxes and their potential reduction are of concern. Biomethanogenesis may be harnessed for reduction of wastes and conversion of renewable resources to significant quantities of substitute natural gas which could mitigate carbon dioxide and other pollutants related to use of fossil fuels.

Identification, Biosynthesis, and Function of 1,3,4,6-Hexanetetracarboxylic Acid in Methanobacterium thermoautotrophicum ΔH

An unusual compound, 1,3,4,6-hexanetetracarboxylic acid, was identified by 1 H and 13 C two-dimensional nuclear magnetic resonance spectroscopy and gas chromatography-mass spectrometry as one of the major components of the small-molecule pool in Methanobacterium thermoautotrophicum ΔH under optimal conditions of cell growth. Incorporation of 13 C- and 2 H-labeled acetates was consistent with the biosynthesis of this tetracarboxylic acid from α-ketoglutarate, two molecules of acetyl-coenzyme A, and one molecule of CO 2 , as established for the tetracarboxylic acid moiety of methanofuran. 13 CO 2 pulse- 12 CO 2 chase methodology was used to establish the turnover rate for this compound. In contrast to the two other major solutes in this bacterium, cyclic 2,3-diphosphoglycerate and glutamate, which are key metabolic intermediates, this free tetracarboxylic acid was metabolically inactive, with a half-life that exceeded the cell doubling time. Hence, this molecular pool cannot serve as a metabolic intermediate in cell biosynthesis. The functional role of free tetracarboxylate as a conservative part of a system that maintains high positive internal osmotic pressure in this bacterium is proposed.

Cyclic 2,3-diphosphoglycerate as a component of a new branch in gluconeogenesis in Methanobacterium thermoautotrophicum delta H

A unique compound, cyclic 2,3-diphosphoglycerate (cDPG), is the major soluble carbon and phosphorus solute in Methanobacterium thermoautotrophicum delta H under optimal conditions of cell growth. It is a component of an unusual branch in gluconeogenesis in these bacteria. [U-13C]acetate pulse-[12C]acetate chase methodology was used to observe the relationship between cDPG and other metabolites (2-phosphoglycerate and 2,3-diphosphoglycerate [2-PG and 2,3-DPG, respectively]) of this branch. It was demonstrated that cells could grow exponentially under conditions in which 2-PG and 2,3-DPG, rather than cDPG, were the major solutes. While the total concentration of these three phosphorylated molecules was maintained, rapid interconversion of 13C label among them was observed. Label flow from 2-PG to 2,3-DPG to cDPG to polymer is the usual direction in this pathway in exponentially growing cells, while the reverse reactions sometimes predominate in the stationary phase. Evidence of the presence of a polymeric compound in this pathway was provided by 13C nuclear magnetic resonance (one-dimensional and two-dimensional INADEQUATE) studies of solubilized cell debris.

Production of Specifically Labeled Compounds by Methanobacterium espanolae Grown on H 2 -CO 2 plus [ 13 C]Acetate

Methanobacterium espanolae , an acidiphilic methanogen, required acetate for maximal growth on H 2 -CO 2 . In the presence of 5 to 15 mM acetate, at a growth pH of 5.5, the μ max was 0.05 h -1 . M. espanolae consumed 12.3 mM acetate during 96 h of incubation at 35°C with shaking at 100 rpm. At initial acetate levels of 2.5 to 10.0 mM, the amount of biomass produced was dependent on the amount of acetate in the medium. 13 C nuclear magnetic resonance spectra of protein hydrolysates obtained from cultures grown on [1- 13 C]- or [2- 13 C]acetate indicated that an incomplete tricarboxylic acid pathway, operating in the reductive direction, was functional in this methanogen. The amino acids were labeled with a very high degree of specificity and at greater than 90% enrichment levels. Less than 2% label randomization occurred between positions primarily labeled from either the carboxyl or methyl group of acetate, and very little label was transferred to positions primarily labeled from CO 2 . The labeling pattern of carbohydrates was typical for glucogenesis from pyruvate. This methanogen, by virtue of the properties described above and its ability to incorporate all of the available acetate (10 mM or lower) from the growth medium, has advantages over other microorganisms for use in the production of specifically labeled compounds.

Energetics of methanogenesis studied in vesicular systems

Methanogenesis is restricted to a group of prokaryotic microorganisms which thrive in strictly anaerobic habitats where they play an indispensable role in the anaerobic food chain. Methanogenic bacteria possess a number of unique cofactors and coenzymes that play an important role in their specialized metabolism. Methanogenesis from a number of simple substrates such as H2 + CO2, formate, methanol, methylamines, and acetate is associated with the generation of transmembrane electrochemical gradients of protons and sodium ions which serve as driving force for a number of processes such as the synthesis of ATP via an ATP synthase, reverse electron transfer, and solute uptake. Several unique reactions of the methanogenic pathways have been identified that are involved in energy transduction. Their role and importance for the methanogenic metabolism are described.

Purification and properties of a F420-nonreactive, membrane-bound hydrogenase from Methanosarcina strain Gö1

The distribution of the F420-reactive and F420-nonreactive hydrogenases from the methylotrophic Methanosarcina strain Gö1 indicated a membrane association of the F420-nonreactive enzyme. The membrane-bound F420-nonreactive hydrogenase was purified 42-fold to electrophoretic homogeneity with a yield of 26.7%. The enzyme had a specific activity of 359 mumol H2 oxidized.min-1.mg protein-1. The purification procedure involved dispersion of the membrane fraction with the detergent Chaps followed by anion exchange, hydrophobic and hydroxylapatite chromatography. The aerobically prepared enzyme had to be reactivated anaerobically. Maximal activity was observed at 80 degrees C. The molecular mass as determined by native gel electrophoresis and gel filtration was 77,000 and 79,000, respectively. SDS gel electrophoresis revealed two polypeptides with molecular masses of 60,000 and 40,000 indicating a 1:1 stoichiometry. The purified enzyme contained 13.3 mol S2-, 15.1 mol Fe and 0.8 mol Ni/mol enzyme. Flavins were not detected. The amino acid sequence of the N-termini of the subunits showed a higher degree of homology to eubacterial uptake-hydrogenases than to F420-dependent hydrogenases from other methanogenic bacteria. The physiological function of the F420-nonreactive hydrogenase from Methanosarcina strain Göl is discussed.

Anaerobic digestion of lignocellulosic biomass and wastes. Cellulases and related enzymes

Anaerobic digestion represents one of several commercially viable processes to convert woody biomass, agricultural wastes, and municipal solid wastes to methane gas, a useful energy source. This process occurs in the absence of oxygen, and is substantially less energy intensive than aerobic biological processes designed for disposal purposes. The anaerobic conversion process is a result of the synergistic effects of various microorganisms, which serve as a consortium. The rate-limiting step of this conversion process has been identified as the hydrolysis of cellulose, the major polymeric component of most biomass and waste feedstocks. Improvements in process economics therefore rely on improving the kinetic and physicochemical characteristics of cellulose degrading enzymes. The most thoroughly studied cellulase enzymes are produced by aerobic fungi, namely Trichoderma reesei. However, the pH and temperature optima of fungal cellulases make them incompatible for use in anaerobic digestion systems, and the major populations of microorganisms involved in cellulase enzyme production under anaerobic digestion conditions are various bacterial producers. The current state of understanding of the major groups of bacterial cellulase producers is reviewed in this paper. Also addressed in this review are recently developed methods for the assessment of actual cellulase activity levels, reflective of the digester "hydrolytic potential," using a series of detergent extractive procedures.

Ni(II) and Ni(I) forms of pentaalkylamide derivatives of cofactor F430 of Methanobacterium thermoautotrophicum

A series of pentaalkylamide forms of F430 and of its 12,13-diepimer have been generated and characterized. Carbodiimide-assisted N-hydroxysulfosuccinimide activation of all five peripheral carboxylates of the F430 macrocycle allows nucleophilic attack by a number of primary amines (RNH2, R- = CH3-, CH3CH2-, CF3CH2-, CH3(CH2)3-) generating the pentaalkylamide derivatives. The identity of each derivative has been verified by fast-atom bombardment mass spectrometry (FAB-MS). The solubility of these derivatives in aprotic organic solvents varies as the amine alkyl substituent (R-) is changed. Electrochemical measurements have shown that the Ni(II/I) reduction potentials in N,N-dimethylformamide (DMF) are approximately -1 V (Ag/AgCl). Reduction by sodium amalgam in THF generates the Ni(I) form of the F430 diepimer pentabutylamide. The visible and EPR spectra of this Ni(I) species are very similar to the corresponding spectra of Ni(I) F430M (Jaun, B. and Pfaltz, A. (1986) J. Chem. Soc. Chem. Commun. 1327-1329.).

Unexpected Errors in Gas Chromatographic Analysis of Methane Production by Thermophilic Bacteria

Unexpected errors in methane measurement by gas chromatography occurred when samples at thermophilic temperatures were analyzed. With a standard curve prepared at room temperature (25°C), stoppered bottles incubated and sampled at 37 to 85°C showed more methane upon analysis than bottles incubated at 25°C: values at 50, 63, and 85°C were 109, 126, and 125%, respectively, of the 25°C value. All variation between 4 and 50°C can be explained by the temperature difference between culture bottle and sampling syringe, and the variation of methane concentration can be predicted by the gas law. Between 50 and 63°C, there was a more dramatic rise than predicted by theory. These variations are important to consider if thermophilic methane production is to be measured accurately. Methods to avoid errors are discussed.

Immunocytochemical localization of the coenzyme F420-reducing hydrogenase in Methanosarcina barkeri Fusaro

The cytological localization of the 8-hydroxy-5-deazaflavin (coenzyme F420)-reducing hydrogenase of Methanosarcina barkeri Fusaro was determined by immunoelectron microscopy, using a specific polyclonal rabbit antiserum raised against the homogeneous deazaflavin-dependent enzyme. In Western blot (immunoblot) experiments this antiserum reacted specifically with the native coenzyme F420-reducing hydrogenase, but did not cross-react with the coenzyme F420-nonreducing hydrogenase activity also detectable in crude extracts prepared from methanol-grown Methanosarcina cells. Immunogold labelling of ultrathin sections of anaerobically fixed methanol-grown cells from the exponential growth phase revealed that the coenzyme F420-reducing hydrogenase was predominantly located in the vicinity of the cytoplasmic membrane. From this result we concluded that the deazaflavin-dependent hydrogenase is associated with the cytoplasmic membrane in intact cells of M. barkeri during growth on methanol as the sole methanogenic substrate, and a possible role of this enzyme in the generation of the electrochemical proton gradient is discussed.

Thiosulfate, polythionates and elemental sulfur assimilation and reduction in the bacterial world

Among sulfur compounds, thiosulfate and polythionates are present at least transiently in many environments. These compounds have a similar chemical structure and their metabolism appears closely related. They are commonly used as energy sources for photoautotrophic or chemolithotrophic microorganisms, but their assimilation has been seldom studied and their importance in bacterial physiology is not well understood. Almost all bacterial strains are able to cleave these compounds since they possess thiosulfate sulfur transferase, thiosulfate reductase or S-sulfocysteine synthase activities. However, the role of these enzymes in the assimilation of thiosulfate or polythionates has not always been clearly established. Elemental sulfur is, on the contrary, very common in the environment. It is an energy source for sulfur-reducing eubacteria and archaebacteria and many sulfur-oxidizing archaebacteria. A phenomenon still not well understood is the 'excessive assimilatory sulfur metabolism' as observed in methanogens which perform a sulfur reduction which exceeds their anabolic needs without any apparent benefit. In heterotrophs, assimilation of elemental sulfur is seldom described and it is uncertain whether this process actually has a physiological significance. Thus, reduction of thiosulfate and elemental sulfur is a common but incompletely understood feature among bacteria. These activities could give bacteria a selective advantage, but further investigations are needed to clarify this possibility. Presence of thiosulfate, polythionates and sulfur reductase activities does not imply obligatorily that these activities play a role in thiosulfate, polythionates or sulfur assimilation as these compounds could be merely intermediates in bacterial metabolism. The possibility also exists that the assimilation of these sulfur compounds is just a side effect of an enzymatic activity with a completely different function. As long as these questions remain unanswered, our understanding of sulfur and thiosulfate metabolism will remain incomplete.

Methanogenic bacteria in human vaginal samples

Twelve vaginal samples were collected from separate patients, processed anaerobically, and added to methanogenic enrichment medium. Methanogenic activity was detected in two samples, both of which were from patients with bacterial vaginosis. None of the samples from healthy patients yielded positive methanogen cultures. One sample from a patient with bacterial vaginosis did not show any detectable methanogenic activity. Two methanogen isolates were obtained from one of the methanogen-positive samples, and both were identified as Methanobrevibacter smithii on the basis of morphological, cultural, and immunological features.

Elemental metals as electron sources for biological methane formation from CO2

Several elemental metals were examined as potential electron donors for methanogenic bacteria, using both a single tube system where the metal was in direct contact with the cells, and a two-flask system, where metal and cells were not in direct contact, but had contact via the gas phase. With all organisms examined in the direct contact system, Fe degree, Al degree and Zn degree served as electron donors for methanogenesis; some organisms used Ni degree or Sn degree as low-level electron donors. Of the metals tested, methanogenesis from H2 + CO2 was inhibited by direct contact with Zn degree or Cu degree, but not by Fe degree or Al degree. Ni degree and Co degree were inhibitory to some methanogens, with Ni degree being particularly inhibitory to the thermophilic strains tested. With all organisms examined in the two-flask system, Fe degree and Zn degree served as good electron sources for both methanogenesis and growth; Co degree generated a very low level of methane and Cu degree did not work at all. In either system V degree, Ti degree or Cd degree did not serve as electron donors. The results suggest that some elemental metals (notably Fe degree, Al degree and Zn degree) produce gaseous H2 by cathodic depolarization which is then consumed by the methanogen, thus accelerating oxidation of the metal by its metabolic activity. All of these reactions are thermodynamically favorable; however, some other metals that are clearly favorable for such a reaction on thermodynamic grounds (Ti degree and V degree) are very stable and do not serve as electron donors.

ATP synthesis coupled to methane formation from methyl-CoM and H2 catalyzed by vesicles of the methanogenic bacterial strain Gö1

Methanogenesis from methyl-CoM and H2, as catalyzed by inside-out vesicle preparations of the methanogenenic bacterium strain Gö1, was associated with ATP synthesis. That this ATP synthesis proceeded via an uncoupler-sensitive transmembrane proton gradient was concluded from the following results: 1. Various inhibitors that affected methane formation (e.g. 2-bromomethanesulfonate) also prevented ATP synthesis. 2. The protonophore 3,5-di-tert-butyl-4-hydroxybenzylidenemalononitrile, in combination with the K+ ionophore valinomycin, inhibited ATP synthesis completely without affecting methanogenesis. 3. The ATP synthase inhibitor diethylstilbestrol inhibited ATP synthesis. 4. Addition of the detergent sulfobetaine inhibited both methane formation and ATP synthesis; the former but not the latter could be restored by adding titanium(III) citrate as electron donor. In addition it was shown that ATP synthesis could also be driven by transmembrane proton gradients artificially imposed on the vesicles. Furthermore net methanogenesis-dependent ATP formation was shown by measuring [32P]phosphate incorporation.

Sodium, protons, and energy coupling in the methanogenic bacteria

In this review, I focus on the bioenergetics of the methanogenic bacteria, with particular attention directed to the roles of transmembrane electrochemical gradients of sodium and proton. In addition, the mechanism of coupling ATP synthesis to methanogenic electron transfer is addressed. Evidence is reviewed which suggests that the methanogens possess great diversity in their bioenergetic machinery. In particular, in some methanogens the primary ion which is translocated coupled to metabolic energy is the proton, while others appear to utilize sodium. In addition, ATP synthesis driven by methanogenic electron transfer is accomplished in some organisms by a chemiosmotic mechanism and is coupled by a more direct mechanism in others. A possible explanation for this diversity (which is consistent with the relatedness of these organisms to each other and to other members of the Archaebacteria as determined by molecular biological techniques) is discussed.