Effect of dilution on methanogenesis, hydrogen turnover and interspecies hydrogen transfer in anoxic paddy soil

Abstract Dilution of anoxic slurries of paddy soil resulted in a proportional decrease of the rates of total methanogenesis and the rate constants of H₂ turnover per gram soil. Dilution did not affect the fraction of H₂/CO₂-dependent methanogenesis which made up 22% of total CH₄ production. However, dilution resulted in a ten fold decrease of the H₂ steady state partial pressure from approximately 4 to 0.4 Pa indicating that H₂/CO₂-dependent methanogenesis was more or less independent of the H₂ pool. The rates of H₂ production calculated from the H₂ turnover rate constants and the H₂ steady state partial pressures accounted for only < 5% of H₂/CO₂-dependent methanogenesis in undiluted soil slurries and for even less after dilution. Upon dilution, the Gibbs free energy available for H₂/CO₂-dependent methanogenesis decreased from −28.4 to only −5.6 kJ per mol. The results indicate that methane was mainly produced from interspecies H₂ transfer within syntrophic bacterial associations and was not significantly affected by the outside H₂ pool.     

Methanosarcina spp. drive vinyl chloride dechlorination via interspecies hydrogen transfer

Two highly enriched cultures containing Dehalococcoides spp. were used to study the effect of aceticlastic methanogens on reductive vinyl chloride (VC) dechlorination. In terms of aceticlastic methanogens, one culture was dominated by Methanosaeta, while the other culture was dominated by Methanosarcina, as determined by fluorescence in situ hybridization. Cultures amended with 2-bromoethanesulfonate (BES), an efficient inhibitor of methanogens, exhibited slow VC dechlorination when grown on acetate and VC. Methanogenic cultures dominated by Methanosaeta had no impact on dechlorination rates, compared to BES-amended controls. In contrast, methanogenic cultures dominated by Methanosarcina displayed up to sevenfold-higher rates of VC dechlorination than their BES-amended counterparts. Methanosarcina-dominated cultures converted a higher percentage of [2-(14)C]acetate to (14)CO(2) when concomitant VC dechlorination took place, compared to nondechlorinating controls. Respiratory indices increased from 0.12 in nondechlorinating cultures to 0.51 in actively dechlorinating cultures. During VC dechlorination, aqueous hydrogen (H(2)) concentrations dropped to 0.3 to 0.5 nM. However, upon complete VC consumption, H(2) levels increased by a factor of 10 to 100, indicating active hydrogen production from acetate oxidation. This process was thermodynamically favorable by means of the extremely low H(2) levels during dechlorination. VC degradation in nonmethanogenic cultures was not inhibited by BES but was limited by the availability of H(2) as electron donor, in cultures both with and without BES. These findings all indicate that Methanosarcina (but not Methanosaeta), while cleaving acetate to methane, simultaneously oxidizes acetate to CO(2) plus H(2), driving hydrogenotrophic dehalorespiration of VC to ethene by Dehalococcoides.     

Coaggregation facilitates interspecies hydrogen transfer between Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus

A thermophilic syntrophic bacterium, Pelotomaculum thermopropionicum strain SI, was grown in a monoculture or coculture with a hydrogenotrophic methanogen, Methanothermobacter thermautotrophicus strain DeltaH. Microscopic observation revealed that cells of each organism were dispersed in a monoculture independent of the growth substrate. In a coculture, however, these organisms coaggregated to different degrees depending on the substrate; namely, a large fraction of the cells coaggregated when they were grown on propionate, but relatively few cells coaggregated when they were grown on ethanol or 1-propanol. Field emission-scanning electron microscopy revealed that flagellum-like filaments of SI cells played a role in making contact with DeltaH cells. Microscopic observation of aggregates also showed that extracellular polymeric substance-like structures were present in intercellular spaces. In order to evaluate the importance of coaggregation for syntrophic propionate oxidation, allowable average distances between SI and DeltaH cells for accomplishing efficient interspecies hydrogen transfer were calculated by using Fick's diffusion law. The allowable distance for syntrophic propionate oxidation was estimated to be approximately 2 mum, while the allowable distances for ethanol and propanol oxidation were 16 mum and 32 mum, respectively. Considering that the mean cell-to-cell distance in the randomly dispersed culture was approximately 30 mum (at a concentration in the mid-exponential growth phase of the coculture of 5 x 10(7) cells ml(-1)), it is obvious that close physical contact of these organisms by coaggregation is indispensable for efficient syntrophic propionate oxidation.     

Evidence for the coexistence of direct and riboflavin-mediated interspecies electron transfer in Geobacter co-culture

Geobacter species can secrete free redox-active flavins, but the role of these flavins in the interspecies electron transfer (IET) of Geobacter direct interspecies electron transfer (DIET) co-culture is unknown. Here, we report the presence of a new riboflavin-mediated interspecies electron transfer (RMIET) process in a traditional Geobacter DIET co-culture; in this process, riboflavin contributes to IET by acting as a free-form electron shuttle between free Geobacter species and serving as a bound cofactor of some cytochromes in Geobacter co-culture aggregates. Multiple lines of evidence indicate that RMIET facilitates the primary initiation of syntrophic growth between Geobacter species before establishing the DIET co-culture and provides additional ways alongside the DIET to transfer electrons to achieve electric syntrophy between Geobacter species. Redox kinetic analysis of riboflavin on either Geobacter species demonstrated that the Gmet_2896 cytochrome acts as the key riboflavin reduction site, while riboflavin oxidation by Geobacter sulfurreducens is the rate-limiting step in RMIET, and the RMIET makes only a minor contribution to IET in Geobacter DIET co-culture. The discovery of a new RMIET process in Geobacter DIET co-culture suggests the complexity of IET in syntrophic bacterial communities and provides suggestions for the careful examination of the IET of other syntrophic co-cultures.     

Simultaneous butyrate oxidation by Syntrophomonas wolfei and catalytic olefin reduction in absence of interspecies hydrogen transfer

Methanogenesis by a Syntrophomonas wolfei/ Methanospirillum hungatei coculture was inhibited in presence of ethylene and the hydrogenation catalyst Pd-BaSO₄. However, butyrate oxidation by S. wolfei continued and ethylene was reduced to ethane. Per mol of butyrate oxidized, 2.4 mol acetate was produced and 0.8 mol ethylene was reduced. Acetylene, propylene and butene were less effective as H₂ acceptors than ethylene, and addition of bromoethanesulfonic acid was necessary to inhibit methanogenesis in the presence of the two longer-chain olefins. Other hydrogenation catalysts were less effective in the order Pd-charcoal < PE-asbestos < Pd-PEI beads < Pt-Al₂O₃, Pd-CaCO₃. Optimal ethylene hydrogenation was achieved with still incubation in presence of 7.2 mg Pd-BaSO₄ and 0.7 g sand per ml medium. The higher catabolic rate of S. wolfei in presence of the methanogen indicated that the biological H₂ removal mechanism was more efficient than the catalytic olefin reduction.Abbreviations BES bromoethane sulfonic acid - VFA volatile fatty acid     

Control of interspecies electron transfer flow during anaerobic digestion: dynamic diffusion reaction models for hydrogen gas transfer in microbial flocs

Dynamic reaction diffusion models were used to analyze the consequences of aggregation for syntrophic reactions in methanogenic ecosystems. Flocs from a whey digestor were used to measure all model parameters under the in situ conditions of a particular defined biological system. Fermentation simulations without adjustable parameters could precisely predict the kinetics of H(2) gas production of digestor flocs during syntrophic methanogenesis from ethanol. The results demonstrated a kinetic compartmentalization of H(2) metabolism inside the flocs. The interspecies electron transfer reaction was mildly diffusion controlled. The H(2) gas profiles across the flocs showed high H (2) concentrations inside the flocs at any time. Simulations of the syntrophic metabolism at low substrate concentrations such as in digestors or sediments showed that it is impossible to achieve high H(2) gas turnovers at simultaneously low steady-state H(2) concentrations. This showed a mechanistic contradiction in the concept of postulated low H(2) microenvironments for the anaerobic digestion process. The results of the computer experiments support the conclusion that syntrophic H(2) production may only be a side reaction of H(2) independent interspecies electron transfer in methanogenic ecosystems.     

Dunaliella salina from saline environments of the central coast of Peru

An evaluation of the algal flora of the Salinas de Huacho on the coast of Peru between 1984 and 1990 was carried out by collection of algal mats and natural waters from a variety of habitats and by microscopic examination. D. salina occurred in lagoons and pools with a salinity range of 165\% to 350\% and formed planktonic and benthic communities. The benthic palmelloid stage of D. salina was found at higher salinities. Aplanospore formation was also observed. Associated halophilic species included D. viridis, Oscillatoria tenuis and Pleurocapsa entophysaloides. D. salina was also found at two other salinas on the central Peruvian coast (Chilca and Otuma).     

Mechanism of action of adenosylcobalamin: hydrogen transfer in the inactivation of diol dehydratase by glycerol

We have investigated the kinetic characteristics of the inactivation of the adenosylcobalamin-dependent enzyme propanediol dehydratase by glycerol, (RS)-1,1-dideuterioglycerol, (R)-1,1-dideuterioglycerol, and perdeuterioglycerol in the presence of 1,2-propanediol and 1,1-dideuterio-1,2-propanediol. The results imply that hydrogen (or deuterium) attached to C-1 of 1,2-propanediol participates in the inactivation process and contributes to the expression of a kinetic isotope effect on the rate of inactivation. The mechanism for this inactivation must involve the cofactor as an intermediate hydrogen carrier, presumably in the form of 5'-deoxyadenosine. Moreover, a mechanism involving a rate-determining transfer of hydrogen from an intermediate containing three equivalent hydrogens quantitatively accounts for all of the results. When diol dehydratase holoenzyme is inactivated by [1-3H]glycerol, 5'-deoxyadenosine which is enriched in tritium by a factor of 2.1 over that in glycerol can be isolated from the reaction mixture.     

互营氧化产甲烷微生物种间电子传递研究进展

甲烷是重要的温室气体,也是典型的可再生性生物质能源。目前约70%的大气甲烷排放来源于产甲烷微生物过程。在产甲烷环境中,产甲烷菌与互营细菌形成互营关系,从而克服有机质厌氧分解反应的热力学能垒,实现短链脂肪酸和醇类物质的互营氧化产甲烷过程。该过程中,种间电子传递是关键步骤。本文首先概述了甲烷的研究意义及微生物互营降解有机质产甲烷的过程,然后分别综述了种间H2转移、种间甲酸转移和种间直接电子传递这3种种间电子传递机制的起源、发展、研究现状和未来所需要解决的研究问题。     

Modeling of interspecies electron transfer in anaerobic microbial communities

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Cyclic GMP phosphodiesterase from bovine retina. Evidence for interspecies conservation.

A light-activated phosphodiesterase (PDE) from retinal rod outer segments (ROS) has been strongly implicated as a possible mediator in the propagation of the visual response. In view of the probable importance of this enzyme in the visual system, a comparison of the PDE proteins from ROS of different evolutionary species was made. Partial purification of the PDE, as measured by enzymic activity, followed by resolution of the protein components on sodium dodecyl sulphate/polyacrylamide-gel electrophoresis, indicated that the major Coomassie Blue-staining species in the ROS of all species studied is a doublet of 84000-88000 Da. After radioiodination, this doublet was converted in all but the frog proteins into a single band of 85000 Da. Two-dimensional tryptic peptide mapping of the radioiodinated peptides indicated that at least six major peptides of the putative PDE have been conserved in all of the species studies. If this protein is indeed associated with PDE activity, such conserved peptides may play an important role in the catalytic and/or regulatory functions of the enzyme.     

Emission of hydrogen from deep and shallow freshwater environments

In-situ partial pressures of hydrogen in anoxic profundal lake sediments reached values of up to 5 Pa which were more than 5 orders of magnitude lower than the partial pressures of methane. Analysis of gas bubbles collected from anoxic submerged paddy soil showed H₂ partial pressures in the range of 1.8 ± 1.3 Pa being ca. 4 orders of magnitude lower than the CH₄ partial pressures. H₂ emission rates, on the other hand, were less than 3 orders of magnitude lower than the CH₄ emission rates indicating that H₂ and CH₄ were oxidized to a different extent in the rhizosphere of the soil before they reached the atmosphere, or that H₂ was produced by the plants. More than 70% of the emitted H₂ reached the atmosphere via plant-mediated flux. The rest was emitted via ebullition from the anoxic soil and, in addition, was produced in the paddy water. A significant amount of H₂ was indeed found to be produced in the water under conditions where thallic algae and submerged parts of the rice plants produced oxygen by photosynthesis. Very little H₂ was emitted via molecular diffusion through the paddy water; in addition, this amount was less than expected from the degree of supersaturation and the diffusional emission rate of CH₄ indicating a relatively high rate of H₂ consumption in the surface film of the paddy water. The total H₂ source strength of rice paddies and other freshwater environments was estimated to be less than 1 Tg yr^-1, being negligible in the atmospheric budget of H₂.     

微生物种间直接电子传递机理及应用研究进展

微生物胞内产生的电子转移到其他电子受体而获得能量的过程称为微生物胞外电子传递,其中,另一微生物作为电子受体时发生的电子传递称为微生物种间电子传递。根据微生物种间电子传递机制,可分间接种间电子传递和种间直接电子传递。由于种间直接电子传递不需要其他物质介导,因此较间接种间电子传递效率更高、能量利用更高。本文系统阐述了微生物进行胞外电子传递的机理及应用,重点分析了种间直接电子传递机理,并概述种间直接电子传递应用领域,为寻找更多电连接的微生物群落以及应用微生物提供参考。     

微生物种间直接电子传递研究进展

一直以来氢气和甲酸被认为是微生物间电子传递的中间电子传递体.近年来的研究发现,微生物之间可以通过种间直接电子传递(DIET)来替代氢气/甲酸传递.DIET作为一种新发现的微生物间电子传递途径,其电子传递效率要高于传统的种间氢气/甲酸传递.DIET这一新发现改变了微生物互营生长代谢必须依赖氢气或甲酸等电子载体的传统认识,...     

Availability, uptake and turnover of glycerol in hypersaline environments

Abstract A sensitive assay for glycerol and other polyols was developed, based on periodate oxidation to formaldehyde, followed by a colorimetric assay with 3-methyl-2-benzothiazolone hydrazone. Apparent glycerol concentrations thus measured in saltern crystallizer ponds were around 20–36 μM, while in the Dead Sea, during a Dunaliella bloom, values were up to 27 μM. However, these values probably overestimate the glycerol concentrations present, as shown by labeled glycerol uptake experiments. Values of [K + S_n] (natural concentration + affinity constant) in saltern ponds were as low as 0.76–1.4 μM, with V_max values of 193–303 nmol 1⁻¹h⁻¹, and turnover times between 2.6–7.2 h at 35°C. Similar measurements in the Dead Sea were: [K + S_n] 0.07–1.41 μM, V_max values 160–426 nmol 1⁻¹h⁻¹, and turnover times in the range of 0.45–3.3 h.     

Compatible solutes of organisms that live in hot saline environments

The accumulation of organic solutes is a prerequisite for osmotic adjustment of all microorganisms. Thermophilic and hyperthermophilic organisms generally accumulate very unusual compatible solutes namely, di-myo-inositol-phosphate, di-mannosyl-di-myo-inositol-phosphate, di-glycerol-phosphate, mannosylglycerate and mannosylglyceramide, which have not been identified in bacteria or archaea that grow at low and moderate temperatures. There is also a growing awareness that some of these compatible solutes may have a role in the protection of cell components against thermal denaturation. Mannosylglycerate and di-glycerol-phosphate have been shown to protect enzymes and proteins from thermal denaturation in vitro as well, or better, than compatible solutes from mesophiles. The pathways leading to the synthesis of some of these compatible solutes from thermophiles and hyperthermophiles have been elucidated. However, large numbers of questions remain unanswered. Fundamental and applied interest in compatible -solutes and osmotic adjustment in these organisms, drives research that, will, in the near future, allow us to understand the role of compatible solutes in osmotic protection and thermoprotection of some of the most fascinating organisms known on Earth.