The Experts below are selected from a list of 17451 Experts worldwide ranked by ideXlab platform

Ralf Conrad - One of the best experts on this subject based on the ideXlab platform.

  • importance of hydrogenotrophic aceticlastic and methylotrophic Methanogenesis for methane production in terrestrial aquatic and other anoxic environments a mini review
    Pedosphere, 2020
    Co-Authors: Ralf Conrad
    Abstract:

    Abstract Microbial Methanogenesis is a major source of the greenhouse gas methane (CH4). It is the final step in the anaerobic degradation of organic matter when inorganic electron acceptors such as nitrate, ferric iron, or sulfate have been depleted. Knowledge of this degradation pathway is important for the creation of mechanistic models, prediction of future CH4 emission scenarios, and development of mitigation strategies. In most anoxic environments, CH4 is produced from either acetate (aceticlastic Methanogenesis) or hydrogen (H2) plus carbon dioxide (CO2) (hydrogenotrophic Methanogenesis). Hydrogen can be replaced by other CO2-type Methanogenesis, using formate, carbon monoxide (CO), or alcohols as substrates. The ratio of these two pathways is tightly constrained by the stoichiometry of conversion processes. If the degradation of organic matter is complete (e.g., degradation of straw in rice paddies), then fermentation eventually results in production of acetate and H2 at a ratio of > 67% aceticlastic and

  • quantification of carbon flow from stable isotope fractionation in rice field soils with different organic matter content
    Organic Geochemistry, 2007
    Co-Authors: Holger Penning, Ralf Conrad
    Abstract:

    Abstract Rice fields are an important source for the greenhouse gas methane produced by acetoclastic and hydrogenotrophic Methanogenesis. Fractionation of 13 C/ 12 C can in principle be used to quantify the relative contribution of these pathways, but our knowledge of isotopic fractionation during reduction of CO 2 and turnover of acetate in different methanogenic environments is still scarce. We therefore measured δ 13 C signatures in two types of anoxic Italian rice field soils, one with high and one with low degradable organic matter (OM) content. Both soils were incubated in the presence and absence of methyl fluoride, a specific inhibitor of acetoclastic Methanogenesis. Optimization of methyl fluoride concentration resulted in complete inhibition of acetoclastic Methanogenesis. CH 4 was then exclusively produced by hydrogenotrophic Methanogenesis, allowing determination of the isotopic signatures and fractionation factors specific for this methanogenic pathway. Acetate, which was then no longer consumed, accumulated and was used for determination of the isotopic signature of the fermentatively produced acetate (both total acetate and methyl carbon of acetate). Hence, all isotopic signatures, including fractionation factors were determined for the methanogenic soil. These data, were then used for computation of the relative contribution of the two methanogenic pathways. In the high OM soil, the contribution of acetoclastic Methanogenesis to total CH 4 production increased simultaneously with decreasing acetate concentration. In the low OM soil, Methanogenesis from H 2 /CO 2 was clearly greater than theoretically expected. Furthermore, isotope fractionation of hydrogenotrophic Methanogenesis indicated that the in situ energy status of methanogens strongly depended on the availability of organic carbon in the rice field soil system. Collectively, our data show that the study of isotopic fractionation in methanogenic environments allows a deeper insight into the ongoing processes, which may be quite different in the same ecosystem with different content of degradable OM.

  • inhibitory effects of nitrate nitrite no and n2o on Methanogenesis by methanosarcina barkeri and methanobacterium bryantii
    FEMS Microbiology Ecology, 1998
    Co-Authors: Detlef H Kluber, Ralf Conrad
    Abstract:

    In order to elucidate the mechanism of the inhibitory effect of nitrate and its denitrification intermediates nitrite, NO and N2O on Methanogenesis in anoxic environments, we tested possible toxic effects of these N-compounds on the methanogenic bacteria Methanosarcina barkeri and Methanobacterium bryantii which are ubiquitous in methanogenic rice field soils. The different N-compounds inhibited H2-dependent Methanogenesis by these bacteria to different extents. Nitrate showed the weakest inhibition of Methanogenesis in both bacteria, followed by N2O and nitrite for Ms. barkeri, and nitrite and N2O for Mb. bryantii, respectively. In both bacteria, the strongest inhibition was caused by NO. Concentrations of 30 mM nitrate still enabled a CH4 production rate of 25–40% of that before the addition of the N-compound, whereas NO completely inhibited Methanogenesis at concentrations ≥0.8–1.7 μM (equivalent to 50–100 Pa NO partial pressure). Removal of NO by replacing the atmosphere with H2/CO2 (8:2) resulted in resumption of Methanogenesis only if the bacteria had been treated with NO concentrations ≤0.8 μM (50 Pa). Removal of N2O from the cultures resulted in resumption of Methanogenesis if Mb. bryantii had been treated with ≤95 μM N2O (500 Pa) or Ms. barkeri with ≤950 μM N2O (5 kPa). These results show that the denitrification products of nitrate can inhibit CH4 production both reversibly and irreversibly depending on the type of methanogenic bacterium and the applied concentration of the N-compound. In a separate experiment with methanogenic rice field slurries addition of nitrate resulted in immediate inhibition of CH4 production. Nitrate was consumed resulting in the sequential accumulation of nitrite, NO and N2O which were subsequently utilized. Nitrite and N2O reached maximum concentrations that would have been inhibitory in the methanogenic bacterial cultures examined.

  • effects of nitrate nitrite no and n2o on Methanogenesis and other redox processes in anoxic rice field soil
    FEMS Microbiology Ecology, 1998
    Co-Authors: Detlef H Kluber, Ralf Conrad
    Abstract:

    We studied the inhibitory mechanism of nitrate and its denitrification products (nitrite, NO, N2O) on the production of CH4 and the concentrations of reductants (H2, acetate, propionate, etc.) and oxidants (NO−3, NO−2, NO, N2O, Fe(III), SO2−4) in slurries of anoxic Italian rice soil. Addition of each of the N-compounds caused a complete but largely reversible inhibition of Methanogenesis. Nitrate, nitrite and N2O significantly decreased the H2 partial pressure. With nitrate and N2O it decreased below the threshold of methanogens, thus not allowing exergonic production of methane (ΔG>0). Furthermore, significant production of the electron acceptors Fe(III) and/or sulfate was observed after addition of nitrate and N2O, probably due to the oxidation of reduced iron and sulfur species with nitrate and/or N2O as electron acceptors. Methanogenic activity did not resume until all electron acceptors were reduced and, as a consequence, H2 had reached the methanogenic threshold again. Thus competition for H2 with denitrifying bacteria, iron- and sulfate-reducing bacteria seemed to be one important factor for the inhibition of Methanogenesis. Addition of rice straw to reduce competition for electron donors did not prevent inhibition of Methanogenesis after addition of nitrate but decreased the inhibition period. Especially after addition of nitrite and NO, toxic effects may have been more important than competition. Although addition of nitrite or NO caused a decrease of the H2 concentration, exergonic Methanogenesis from H2/CO2 was always possible (ΔG<0). Nevertheless, CH4 production was inhibited. Furthermore, acetate concentrations were generally sufficient for exergonic Methanogenesis in all experiments, even so CH4 production was completely inhibited. Turnover times of [2-14C]acetate to 14CH4 were higher in soil slurry that had resumed Methanogenesis after nitrate inhibition than in the untreated control indicating toxic effects on acetate-utilizing methanogens. However, since the contribution of 14CO2 reduction to CH4 was almost the same (26–29%) in soil slurry that had resumed Methanogenesis after nitrate inhibition as in the untreated control, hydrogenotrophic methanogens must have been affected by toxic N-compounds to a similar extent as acetoclastic methanogens.

John A Leigh - One of the best experts on this subject based on the ideXlab platform.

  • exploring hydrogenotrophic Methanogenesis a genome scale metabolic reconstruction of methanococcus maripaludis
    Journal of Bacteriology, 2016
    Co-Authors: Matthew A Richards, John A Leigh, Juan Zhang, Stephen W Ragsdale, Nathan D. Price
    Abstract:

    ABSTRACT Hydrogenotrophic Methanogenesis occurs in multiple environments, ranging from the intestinal tracts of animals to anaerobic sediments and hot springs. Energy conservation in hydrogenotrophic methanogens was long a mystery; only within the last decade was it reported that net energy conservation for growth depends on electron bifurcation. In this work, we focus on Methanococcus maripaludis, a well-studied hydrogenotrophic marine methanogen. To better understand hydrogenotrophic Methanogenesis and compare it with methylotrophic Methanogenesis that utilizes oxidative phosphorylation rather than electron bifurcation, we have built iMR539, a genome scale metabolic reconstruction that accounts for 539 of the 1,722 protein-coding genes of M. maripaludis strain S2. Our reconstructed metabolic network uses recent literature to not only represent the central electron bifurcation reaction but also incorporate vital biosynthesis and assimilation pathways, including unique cofactor and coenzyme syntheses. We show that our model accurately predicts experimental growth and gene knockout data, with 93% accuracy and a Matthews correlation coefficient of 0.78. Furthermore, we use our metabolic network reconstruction to probe the implications of electron bifurcation by showing its essentiality, as well as investigating the infeasibility of aceticlastic Methanogenesis in the network. Additionally, we demonstrate a method of applying thermodynamic constraints to a metabolic model to quickly estimate overall free-energy changes between what comes in and out of the cell. Finally, we describe a novel reconstruction-specific computational toolbox we created to improve usability. Together, our results provide a computational network for exploring hydrogenotrophic Methanogenesis and confirm the importance of electron bifurcation in this process. IMPORTANCE Understanding and applying hydrogenotrophic Methanogenesis is a promising avenue for developing new bioenergy technologies around methane gas. Although a significant portion of biological methane is generated through this environmentally ubiquitous pathway, existing methanogen models portray the more traditional energy conservation mechanisms that are found in other methanogens. We have constructed a genome scale metabolic network of Methanococcus maripaludis that explicitly accounts for all major reactions involved in hydrogenotrophic Methanogenesis. Our reconstruction demonstrates the importance of electron bifurcation in central metabolism, providing both a window into hydrogenotrophic Methanogenesis and a hypothesis-generating platform to fuel metabolic engineering efforts.

  • metabolic versatility in methanogens
    Current Opinion in Biotechnology, 2014
    Co-Authors: Kyle C Costa, John A Leigh
    Abstract:

    Methanogenesis is an anaerobic metabolism responsible for the generation of >90% of the methane formed on Earth today, with important implications for fuels production and global warming. Although methanogenic Archaea have been cultured for over 70 years, key insights regarding electron flow and energy conservation in Methanogenesis have only recently emerged. Fundamental differences between two metabolic types of Methanogenesis, hydrogenotrophic and methylotrophic, are now understood, with implications for metabolic versatility and the potential for engineering of methanogens to utilize new substrates. The development of model species with genetic and bioinformatic tools has advanced the field and holds potential for further characterizing and engineering of Methanogenesis. Our understanding of a related pathway, anaerobic methane oxidation, is in its infancy.

  • hydrogen regulation and global responses to electron carbon and nitrogen sources of methanococcus maripaludis
    2013
    Co-Authors: John A Leigh
    Abstract:

    Methanogens catalyze the critical, methane-producing step (called Methanogenesis) in the anaerobic decomposition of organic matter. This project has generated the first predictive model of global gene regulation of Methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. maripaludis through integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 58 different steady-state and time course experiments that were performed in chemostats or batch cultures, under a spectrum of environmental perturbations that modulated Methanogenesis. Analyses of the EGRIN model have revealed novel components of Methanogenesis that included at least three additional protein-coding genes of previously unknown function as well as one non-coding RNA. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to inter-coordinate key steps of Methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel transcription factors in the regulation of phosphate-dependent repression of formate dehydrogenase a key enzyme inmore » the Methanogenesis pathway. The EGRIN model demonstrates regulatory affiliations within Methanogenesis as well as between Methanogenesis and other cellular functions. In addition, we have published an analysis of transcriptome architecture in M. maripaludis and an analysis of the effects of H2 and formate on growth yield and regulation of Methanogenesis in M. maripaludis.« less

  • h2 independent growth of the hydrogenotrophic methanogen methanococcus maripaludis
    Mbio, 2013
    Co-Authors: Kyle C Costa, Michael A. Jacobs, John A Leigh
    Abstract:

    ABSTRACT Hydrogenotrophic methanogenic Archaea require reduced ferredoxin as an anaplerotic source of electrons for Methanogenesis. H 2 oxidation by the hydrogenase Eha provides these electrons, consistent with an H 2 requirement for growth. Here we report the identification of alternative pathways of ferredoxin reduction in Methanococcus maripaludis that operate independently of Eha to stimulate Methanogenesis. A suppressor mutation that increased expression of the glycolytic enzyme glyceraldehyde-3-phosphate:ferredoxin oxidoreductase resulted in a strain capable of H 2 -independent ferredoxin reduction and growth with formate as the sole electron donor. In this background, it was possible to eliminate all seven hydrogenases of M. maripaludis . Alternatively, carbon monoxide oxidation by carbon monoxide dehydrogenase could also generate reduced ferredoxin that feeds into Methanogenesis. In either case, the reduced ferredoxin generated was inefficient at stimulating Methanogenesis, resulting in a slow growth phenotype. As Methanogenesis is limited by the availability of reduced ferredoxin under these conditions, other electron donors, such as reduced coenzyme F 420 , should be abundant. Indeed, when F 420 -reducing hydrogenase was reintroduced into the hydrogenase-free mutant, the equilibrium of H 2 production via an F 420 -dependent formate:H 2 lyase activity shifted markedly toward H 2 compared to the wild type. IMPORTANCE Hydrogenotrophic methanogens are thought to require H 2 as a substrate for growth and Methanogenesis. Here we show alternative pathways in methanogenic metabolism that alleviate this H 2 requirement and demonstrate, for the first time, a hydrogenotrophic methanogen that is capable of growth in the complete absence of H 2 . The demonstration of alternative pathways in methanogenic metabolism suggests that this important group of organisms is metabolically more versatile than previously thought.

  • Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic Methanogenesis
    Proceedings of the National Academy of Sciences of the United States of America, 2012
    Co-Authors: Thomas J. Lie, Kyle C Costa, William B. Whitman, Boguslaw Lupa, Suresh Korpole, John A Leigh
    Abstract:

    Despite decades of study, electron flow and energy conservation in methanogenic Archaea are still not thoroughly understood. For methanogens without cytochromes, flavin-based electron bifurcation has been proposed as an essential energy-conserving mechanism that couples exergonic and endergonic reactions of Methanogenesis. However, an alternative hypothesis posits that the energy-converting hydrogenase Eha provides a chemiosmosis-driven electron input to the endergonic reaction. In vivo evidence for both hypotheses is incomplete. By genetically eliminating all nonessential pathways of H2 metabolism in the model methanogen Methanococcus maripaludis and using formate as an additional electron donor, we isolate electron flow for Methanogenesis from flux through Eha. We find that Eha does not function stoichiometrically for Methanogenesis, implying that electron bifurcation must operate in vivo. We show that Eha is nevertheless essential, and a substoichiometric requirement for H2 suggests that its role is anaplerotic. Indeed, H2 via Eha stimulates Methanogenesis from formate when intermediates are not otherwise replenished. These results fit the model for electron bifurcation, which renders the methanogenic pathway cyclic, and as such requires the replenishment of intermediates. Defining a role for Eha and verifying electron bifurcation provide a complete model of Methanogenesis where all necessary electron inputs are accounted for.

Nicole R Buan - One of the best experts on this subject based on the ideXlab platform.

  • a multienzyme complex channels substrates and electrons through acetyl coa and methane biosynthesis pathways in methanosarcina
    PLOS ONE, 2014
    Co-Authors: Dillon J Lieber, Jennie L Catlett, Nandu Madayiputhiya, Renu Nandakumar, Madeline M Lopez, William W Metcalf, Nicole R Buan
    Abstract:

    Multienzyme complexes catalyze important metabolic reactions in many organisms, but little is known about the complexes involved in biological methane production (Methanogenesis). A crosslinking-mass spectrometry (XL-MS) strategy was employed to identify proteins associated with coenzyme M-coenzyme B heterodisulfide reductase (Hdr), an essential enzyme in all methane-producing archaea (methanogens). In Methanosarcina acetivorans, Hdr forms a multienzyme complex with acetyl-CoA decarbonylase synthase (ACDS), and F420-dependent methylene-H4MPT reductase (Mer). ACDS is essential for production of acetyl-CoA during growth on methanol, or for Methanogenesis from acetate, whereas Mer is essential for Methanogenesis from all substrates. Existence of a Hdr:ACDS:Mer complex is consistent with growth phenotypes of ACDS and Mer mutant strains in which the complex samples the redox status of electron carriers and directs carbon flux to acetyl-CoA or Methanogenesis. We propose the Hdr:ACDS:Mer complex comprises a special class of multienzyme redox complex which functions as a “biological router” that physically links Methanogenesis and acetyl-CoA biosynthesis pathways.

Shungui Zhou - One of the best experts on this subject based on the ideXlab platform.

  • nanofe3o4 as solid electron shuttles to accelerate acetotrophic Methanogenesis by methanosarcina barkeri
    Frontiers in Microbiology, 2019
    Co-Authors: Jingyuan Wang, Li Fu, Ting Zhou, Yahai Lu, Linpeng Yu, Shungui Zhou
    Abstract:

    Magnetite nanoparticles (nanoFe3O4) have been reported to facilitate direct interspecies electron transfer (DIET) between syntrophic bacteria and methanogens thereby improving syntrophic Methanogenesis. However, whether or how nanoFe3O4 affects acetotrophic Methanogenesis remain unknown. Herein, we demonstrate the unique role of nanoFe3O4 in accelerating methane production from direct acetotrophic Methanogenesis in Methanosarcina-enriched cultrures, which was further confirmed by pure cultures of Methanosarcina barkeri. Compared with other nanomaterials of higher electrical conductivity such as carbon nanotubes (CNTs) and graphite, nanoFe3O4 with mixed valence Fe(II) and Fe(III) had the most significant stimulatory effect on methane production, suggesting its redox activity rather than electrical conductivity led to enhanced Methanogenesis by M. barkeri. Cell morphology and spectroscopy analysis revealed that nanoFe3O4 penetrated into the cell membrane and cytoplasm of M. barkeri. These results provide the unprecedented possibility that nanoFe3O4 in the cell membrane of methanogens serve as electron shuttles to facilitate intracellular electron transfer and thus enhance methane production. This work has important implications not only for understanding the mechanisms of mineral-methanogen interaction but also for optimizing engineered methanogenic processes.

  • secondary mineralization of ferrihydrite affects microbial Methanogenesis in geobacter methanosarcina cocultures
    Applied and Environmental Microbiology, 2016
    Co-Authors: Jia Tang, Ziyang Tang, Li Zhuang, Zhen Yu, Shungui Zhou
    Abstract:

    ABSTRACT The transformation of ferrihydrite to stable iron oxides over time has important consequences for biogeochemical cycling of many metals and nutrients. The response of methanogenic activity to the presence of iron oxides depends on the type of iron mineral, but the effects of changes in iron mineralogy on Methanogenesis have not been characterized. To address these issues, we constructed methanogenic cocultures of Geobacter and Methanosarcina strains with different ferrihydrite mineralization pathways. In this system, secondary mineralization products from ferrihydrite are regulated by the presence or absence of phosphate. In cultures producing magnetite as the secondary mineralization product, the rates of Methanogenesis from acetate and ethanol increased by 30.2% and 135.3%, respectively, compared with a control lacking ferrihydrite. Biogenic magnetite was proposed to promote direct interspecies electron transfer between Geobacter and Methanosarcina in a manner similar to that of c-type cytochrome and thus facilitate Methanogenesis. Vivianite biomineralization from ferrihydrite in the presence of phosphate did not significantly influence the Methanogenesis processes. The correlation between magnetite occurrence and facilitated Methanogenesis was supported by increased rates of methane production from acetate and ethanol with magnetite supplementation in the defined cocultures. Our data provide a new perspective on the important role of iron biomineralization in biogeochemical cycling of carbon in diverse anaerobic environments. IMPORTANCE It has been found that microbial Methanogenesis is affected by the presence of iron minerals, and their influences on Methanogenesis are associated with the mineralogical properties of the iron minerals. However, how changes in iron mineralogy affect microbial Methanogenesis has not been characterized. To address this issue, we constructed methanogenic cocultures of Geobacter and Methanosarcina strains with different ferrihydrite mineralization pathways. The experimental results led to two contributions, i.e., (i) the transformation of iron minerals might exert an important influence on Methanogenesis under anaerobic conditions and (ii) both biogenic and chemical magnetite can accelerate syntrophic ethanol oxidization between Geobacter metallireducens and Methanosarcina barkeri. This study sheds new light on the important role of iron biomineralization in the biogeochemical cycling of carbon in diverse anaerobic environments, particularly in iron-rich natural and agricultural wetland soils.

  • Methanogenesis affected by the co occurrence of iron iii oxides and humic substances
    FEMS Microbiology Ecology, 2014
    Co-Authors: Shungui Zhou, Jielong Xu, Guiqin Yang, Li Zhuang
    Abstract:

    Iron oxides and humic substances (humics) have substantial effects on biochemical processes, such as Methanogenesis, due to their redox reactivity and ubiquitous presence. This study aimed to investigate how Methanogenesis is affected by the common occurrence of these compounds, which has not been considered to date. The experiment was conducted with anoxic paddy soil microcosms receiving a humics surrogate compound (anthraquinone-2,6-disulfonate, AQDS) and three iron(III) oxides (ferrihydrite, hematite, and magnetite) differing in crystallinity and conductivity. Ferrihydrite suppressed Methanogenesis, whereas AQDS, hematite, and magnetite facilitated Methanogenesis. CH4 production in co-occurring ferrihydrite + AQDS, hematite + AQDS, and magnetite + AQDS cultures was 4.1, 1.3, and 0.9 times greater than the corresponding cultures without AQDS, respectively. Syntrophic cooperation between Geobacter and Methanosarcina occurred in the Methanogenesis-facilitated cultures. Experimental results suggested that the conductive characteristics of iron(III) oxides was an important factor determining the methanogenic response to the co-occurrence of iron(III) oxides and humics in anaerobic paddy soil. This work indicated that the type of iron(III) oxides may significantly affect carbon cycling under anoxic conditions in natural wetlands.

Tianze Song - One of the best experts on this subject based on the ideXlab platform.

  • snapshot of methanogen sensitivity to temperature in zoige wetland from tibetan plateau
    Frontiers in Microbiology, 2015
    Co-Authors: Tianze Song
    Abstract:

    Zoige wetland in Tibetan plateau represents a cold environment at high altitude where significant methane emission has been observed. However, it remains unknown how the production and emission of CH4 from Zoige wetland will respond to a warming climate. Here we investigated the temperature sensitivity of methanogen community in a Zoige wetland soil under the laboratory incubation conditions. One soil sample was collected and the temperature sensitivity of the methanogenic activity, the structure of methanogen community and the methanogenic pathways were determined. We found that the response of Methanogenesis to temperature could be separated into two phases, a high sensitivity in the low temperature range and a modest sensitivity under mesophilic conditions, respectively. The aceticlastic methanogens Methanosarcinaceae were the main methanogens at low temperatures, while hydrogenotrophic Methanobacteriales, Methanomicrobiales and Methanocellales were more abundant at higher temperatures. The total abundance of mcrA genes increased with temperature indicating that the growth of methanogens was stimulated. The growth of hydrogenotrophic methanogens, however, was faster than aceticlastic ones resulting in the shift of methanogen community. Determination of carbon isotopic signatures indicated that methanogenic pathway was also shifted from mainly aceticlastic Methanogenesis to a mixture of hydrogenotrophic and aceticlastic Methanogenesis with the increase of temperature. Collectively, the shift of temperature responses of Methanogenesis was in accordance with the changes in methanogen composition and methanogenic pathway in this Zoige wetland sample. It appears that the aceticlastic Methanogenesis dominated at low temperatures is more sensitive than the hydrogenotrophic one at higher temperatures.