Thermodynamics of H2-consuming and H2-producing metabolic reactions in diverse methanogenic environments under in situ conditions

Metabolic Segregation and Functional Gene Clusters in Anaerobic Digestion Consortia

A combined enrichment experiment and genome-centric meta-omics analysis demonstrated that metabolic specificity, rather than flexibility, governs the anaerobic digestion (AD) ecosystem. This study provides new insights into interspecies electron transfer in the AD process, highlighting a segregation in the metabolism of H2 and formate. Our findings show that H2 acts as the primary electron sink for recycling redox cofactors, including NAD+ and oxidised ferredoxin (Fdox), during primary fermentation, while formate is the dominant electron carrier in secondary fermentation, especially under conditions with elevated H2 concentrations. Importantly, no evidence of biochemical interconversion between H2 and formate was identified in the primary fermenting bacteria or in syntrophs enriched in this study. This segregation of H2 and formate metabolism likely benefits the anaerobic oxidation of butyrate and propionate with a higher tolerance to H2 accumulation. Moreover, this study highlights the functional partitioning among microbial populations in key AD niches: primary fermentation, secondary fermentation (syntrophic acetogenesis), hydrogenotrophic methanogenesis, and acetoclastic methanogenesis. Genome-centric analysis of the AD microbiome identified several key functional gene clusters, which could enhance genome-centric genotype-phenotype correlations, particularly for strict anaerobes that are difficult to isolate and characterise in pure culture.

A climatically significant abiotic mechanism driving carbon loss and nitrogen limitation in peat bogs

Sphagnum-dominated bogs are climatically impactful systems that exhibit two puzzling characteristics: CO2:CH4 ratios are greater than those predicted by electron balance models and C decomposition rates are enigmatically slow. We hypothesized that Maillard reactions partially explain both phenomena by increasing apparent CO2 production via eliminative decarboxylation and sequestering bioavailable nitrogen (N). We tested this hypothesis using incubations of sterilized Maillard reactants, and live and sterilized bog peat. Consistent with our hypotheses, CO2 production in the sterilized peat was equivalent to 8-13% of CO2 production in unsterilized peat, and the increased formation of aromatic N compounds decreased N-availability. Numerous sterility assessments rule out biological contamination or extracellular enzyme activity as significant sources of this CO2. These findings suggest a need for a reevaluation of the fixed CO2:CH4 production ratios commonly used in wetland biogeochemical models, which could be improved by incorporating abiotic sources of CO2 production and N sequestration.

Functional convergence in slow-growing microbial communities arises from thermodynamic constraints

The dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network-independent of species composition and biochemical details-providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by analyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.

Complexity of temperature dependence in methanogenic microbial environments

There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH₄, an important greenhouse gas. Microbial CH₄ production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO₂ and CH₄. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH₄ production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H₂/CO₂ as immediate CH₄ precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH₄ production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (E_a). Interestingly, CH₄ release from defined microbial cultures, from environmental samples and from wetland field sites all show similar E_a values around 100 kJ mol^-1 indicating that CH₄ production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.

Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria

Acetogenic bacteria are a polyphyletic group of organisms that fix carbon dioxide under anaerobic, non-phototrophic conditions by reduction of two mol of CO₂ to acetyl-CoA via the Wood–Ljungdahl pathway. This pathway also allows for lithotrophic growth with H₂ as electron donor and this pathway is considered to be one of the oldest, if not the oldest metabolic pathway on Earth for CO₂ reduction, since it is coupled to the synthesis of ATP. How ATP is synthesized has been an enigma for decades, but in the last decade two ferredoxin-dependent respiratory chains were discovered. Those respiratory chains comprise of a cytochrome-free, ferredoxin-dependent respiratory enzyme complex, which is either the Rnf or Ech complex. However, it was discovered already 50 years ago that some acetogens contain cytochromes and quinones, but their role had only a shadowy existence. Here, we review the literature on the characterization of cytochromes and quinones in acetogens and present a hypothesis that they may function in electron transport chains in addition to Rnf and Ech.

High-rate biological selenate reduction in a sequencing batch reactor for recovery of hexagonal selenium

Recovery of selenium (Se) from wastewater provides a solution for both securing Se supply and preventing Se pollution. Here, we developed a high-rate process for biological selenate reduction to elemental selenium. Distinctive from other studies, we aimed for a process with selenate as the main biological electron sink, with minimal formation of methane or sulfide. A sequencing batch reactor, fed with an influent containing 120 mgSe L^-1 selenate and ethanol as electron donor and carbon source, was operated for 495 days. The high rates (419 ± 17 mgSe L^-1 day^-1) were recorded between day 446 and day 495 for a hydraulic retention time of 6 h. The maximum conversion efficiency of selenate amounted to 96% with a volumetric conversion rate of 444 mgSe L^-1 day^-1, which is 6 times higher than the rates reported in the literature thus far. At the end of the experiment, a highly enriched selenate reducing biomass had developed, with a specific activity of 856 ± 26 mgSe^-1day^-1g_biomass^-1, which was nearly 1000-fold higher than that of the inoculum. No evidence was found for the formation of methane, sulfide, or volatile reduced selenium compounds like dimethyl-selenide or H₂Se, revealing a high selectivity. Ethanol was incompletely oxidized to acetate. The produced elemental selenium partially accumulated in the reactor as pure (≥80% Se of the total mixture of biomass sludge flocs and flaky aggregates, and ~100% of the specific flaky aggregates) selenium black hexagonal needles, with cluster sizes between 20 and 200 µm. The new process may serve as the basis for a high-rate technology to remove and recover pure selenium from wastewater or process streams with high selectivity.

An iron corrosion-assisted H2-supplying system: a culture method for methanogens and acetogens under low H2 pressures

H₂ is an important fermentation intermediate in anaerobic environments. Although H₂ occurs at very low partial pressures in the environments, the culture and isolation of H₂-utilizing microorganisms is usually carried out under very high H₂ pressures, which might have hampered the discovery and understanding of microorganisms adapting to low H₂ environments. Here we constructed a culture system designated the "iron corrosion-assisted H₂-supplying (iCH) system" by connecting the gas phases of two vials (one for the iron corrosion reaction and the other for culturing microorganisms) to achieve cultures of microorganisms under low H₂ pressures. We conducted enrichment cultures for methanogens and acetogens using rice paddy field soil as the microbial source. In the enrichment culture of methanogens under canonical high H₂ pressures, only Methanobacterium spp. were enriched. By contrast, Methanocella spp. and Methanoculleus spp., methanogens adapting to low H₂ pressures, were specifically enriched in the iCH cultures. We also observed selective enrichment of acetogen species by the iCH system (Acetobacterium spp. and Sporomusa spp.), whereas Clostridium spp. predominated in the high H₂ cultures. These results demonstrate that the iCH system facilitates culture of anaerobic microorganisms under low H₂ pressures, which will enable the selective culture of microorganisms adapting to low H₂ environments.

Electrophysiology of the Facultative Autotrophic Bacterium Desulfosporosinus orientis

Electroautotrophy is a novel and fascinating microbial metabolism, with tremendous potential for CO₂ storage and valorization into chemicals and materials made thereof. Research attention has been devoted toward the characterization of acetogenic and methanogenic electroautotrophs. In contrast, here we characterize the electrophysiology of a sulfate-reducing bacterium, Desulfosporosinus orientis, harboring the Wood-Ljungdahl pathway and, thus, capable of fixing CO₂ into acetyl-CoA. For most electroautotrophs the mode of electron uptake is still not fully clarified. Our electrochemical experiments at different polarization conditions and Fe⁰ corrosion tests point to a H₂- mediated electron uptake ability of this strain. This observation is in line with the lack of outer membrane and periplasmic multi-heme c-type cytochromes in this bacterium. Maximum planktonic biomass production and a maximum sulfate reduction rate of 2 ± 0.4 mM day^–1 were obtained with an applied cathode potential of −900 mV vs. Ag/AgCl, resulting in an electron recovery in sulfate reduction of 37 ± 1.4%. Anaerobic sulfate respiration is more thermodynamically favorable than acetogenesis. Nevertheless, D. orientis strains adapted to sulfate-limiting conditions, could be tuned to electrosynthetic production of up to 8 mM of acetate, which compares well with other electroacetogens. The yield per biomass was very similar to H₂/CO₂ based acetogenesis. Acetate bioelectrosynthesis was confirmed through stable isotope labeling experiments with Na-H¹³CO₃. Our results highlight a great influence of the CO₂ feeding strategy and start-up H₂ level in the catholyte on planktonic biomass growth and acetate production. In serum bottles experiments, D. orientis also generated butyrate, which makes D. orientis even more attractive for bioelectrosynthesis application. A further optimization of these physiological pathways is needed to obtain electrosynthetic butyrate production in D. orientis biocathodes. This study expands the diversity of facultative autotrophs able to perform H₂-mediated extracellular electron uptake in Bioelectrochemical Systems (BES). We characterized a sulfate-reducing and acetogenic bacterium, D. orientis, able to naturally produce acetate and butyrate from CO₂ and H₂. For any future bioprocess, the exploitation of planktonic growing electroautotrophs with H₂-mediated electron uptake would allow for a better use of the entire liquid volume of the cathodic reactor and, thus, higher productivities and product yields from CO₂-rich waste gas streams.

It does not always take two to tango: "Syntrophy" via hydrogen cycling in one bacterial cell

Interspecies hydrogen transfer in anoxic ecosystems is essential for the complete microbial breakdown of organic matter to methane. Acetogenic bacteria are key players in anaerobic food webs and have been considered as prime candidates for hydrogen cycling. We have tested this hypothesis by mutational analysis of the hydrogenase in the model acetogen Acetobacterium woodii. Hydrogenase-deletion mutants no longer grew on H₂ + CO₂ or organic substrates such as fructose, lactate, or ethanol. Heterotrophic growth could be restored by addition of molecular hydrogen to the culture, indicating that hydrogen is an intermediate in heterotrophic growth. Indeed, hydrogen production from fructose was detected in a stirred-tank reactor. The mutant grew well on organic substrates plus caffeate, an alternative electron acceptor that does not require molecular hydrogen but NADH as reductant. These data are consistent with the notion that molecular hydrogen is produced from organic substrates and then used as reductant for CO₂ reduction. Surprisingly, hydrogen cycling in A. woodii is different from the known modes of interspecies or intraspecies hydrogen cycling. Our data are consistent with a novel type of hydrogen cycling that connects an oxidative and reductive metabolic module in one bacterial cell, “intracellular syntrophy.”

Phosphine as a Biosignature Gas in Exoplanet Atmospheres

A long-term goal of exoplanet studies is the identification and detection of biosignature gases. Beyond the most discussed biosignature gas O₂, only a handful of gases have been considered in detail. In this study, we evaluate phosphine (PH₃). On Earth, PH₃ is associated with anaerobic ecosystems, and as such, it is a potential biosignature gas in anoxic exoplanets. We simulate the atmospheres of habitable terrestrial planets with CO₂- and H₂-dominated atmospheres and find that PH₃ can accumulate to detectable concentrations on planets with surface production fluxes of 10¹⁰ to 10¹⁴ cm^-2 s^-1 (corresponding to surface concentrations of 10s of ppb to 100s of ppm), depending on atmospheric composition and ultraviolet (UV) irradiation. While high, the surface flux values are comparable to the global terrestrial production rate of methane or CH₄ (10¹¹ cm^-2 s^-1) and below the maximum local terrestrial PH₃ production rate (10¹⁴ cm^-2 s^-1). As with other gases, PH₃ can more readily accumulate on low-UV planets, for example, planets orbiting quiet M dwarfs or with a photochemically generated UV shield. PH₃ has three strong spectral features such that in any atmosphere scenario one of the three will be unique compared with other dominant spectroscopic molecules. Phosphine's weakness as a biosignature gas is its high reactivity, requiring high outgassing rates for detectability. We calculate that tens of hours of JWST (James Webb Space Telescope) time are required for a potential detection of PH₃. Yet, because PH₃ is spectrally active in the same wavelength regions as other atmospherically important molecules (such as H₂O and CH₄), searches for PH₃ can be carried out at no additional observational cost to searches for other molecular species relevant to characterizing exoplanet habitability. Phosphine is a promising biosignature gas, as it has no known abiotic false positives on terrestrial planets from any source that could generate the high fluxes required for detection.

Complex Multimeric [FeFe] Hydrogenases: Biochemistry, Physiology and New Opportunities for the Hydrogen Economy

Hydrogenases are key enzymes of the energy metabolism of many microorganisms. Especially in anoxic habitats where molecular hydrogen (H₂) is an important intermediate, these enzymes are used to expel excess reducing power by reducing protons or they are used for the oxidation of H₂ as energy and electron source. Despite the fact that hydrogenases catalyze the simplest chemical reaction of reducing two protons with two electrons it turned out that they are often parts of multimeric enzyme complexes catalyzing complex chemical reactions with a multitude of functions in the metabolism. Recent findings revealed multimeric hydrogenases with so far unknown functions particularly in bacteria from the class Clostridia. The discovery of [FeFe] hydrogenases coupled to electron bifurcating subunits solved the enigma of how the otherwise highly endergonic reduction of the electron carrier ferredoxin can be carried out and how H₂ production from NADH is possible. Complexes of [FeFe] hydrogenases with formate dehydrogenases revealed a novel enzymatic coupling of the two electron carriers H₂ and formate. These novel hydrogenase enzyme complex could also contribute to biotechnological H₂ production and H₂ storage, both processes essential for an envisaged economy based on H₂ as energy carrier.

Formate and Hydrogen as Electron Shuttles in Terminal Fermentations in an Oligotrophic Freshwater Lake Sediment

The energetic situation of terminal fermentations in methanogenesis was analyzed by pool size determinations in sediment cores taken in the oligotrophic Lake Constance, Germany. Distribution profiles of fermentation intermediates and products were measured at three different water depths (2, 10, and 80 m). Methane concentrations were constant below 10 cm of sediment depth. Within the methanogenic zone, concentrations of formate, acetate, propionate, and butyrate varied between 1 and 40 μM, and hydrogen was between 0.5 and 5 Pa. From the distribution profiles of the fermentation intermediates, Gibbs free energy changes for their interconversion were calculated. Pool sizes of formate and hydrogen were energetically nearly equivalent, with -5 ± 5 kJ per mol difference of free energy change (ΔG) for a hypothetical conversion of formate to hydrogen plus CO2 The ΔG values for conversion of fatty acids to methanogenic substrates and their further conversion to methane and CO2 were calculated with hydrogen and with formate as intermediates. Syntrophic propionate oxidation reached energetic equilibrium with formate as the sole electron carrier but was sufficiently exergonic if at least some of the electrons were transferred via hydrogen. The energetic consequences of formate versus hydrogen transfer in secondary and methanogenic fermentations indicate that both carrier systems are probably used simultaneously to optimize the energy yields for the partners involved.IMPORTANCE In the terminal steps of methane formation in freshwater lake sediments, fermenting bacteria cooperate syntrophically with methanogens and homoacetogens at minimum energy increments via interspecies electron transfer. The energy yields of the partner organisms in these cooperations have so far been calculated based mainly on in situ hydrogen partial pressures. In the present study, we also analyzed pools of formate as an alternative electron carrier in sediment cores of an oligotrophic lake. The formate and hydrogen pools appeared to be energetically nearly equivalent and are likely to be used simultaneously for interspecies electron transfer. Calculations of reaction energies of the partners involved suggest that propionate degradation may also proceed through the Smithella pathway, which converts propionate via butyrate and acetate to three acetate residues, thus circumventing one energetically difficult fatty acid oxidation step.

Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats

Desulfitobacterium hafniense Y51 has been widely used in investigations of perchloroethylene (PCE) biodegradation, but limited information exists on its other physiological capabilities. We investigated how D. hafniense Y51 confronts the debilitating limitations of not having enough electron donor (lactate), or electron acceptor (fumarate) during cultivation in chemostats. The residual concentrations of the substrates supplied in excess were much lower than expected. Transcriptomics, proteomics and fluxomics were integrated to investigate how this phenomenon was regulated. Through diverse regulation at both transcriptional and translational levels, strain Y51 turned to fermenting the excess lactate and disproportionating the excess fumarate under fumarate- and lactate-limiting conditions respectively. Genes and proteins related to the utilization of a variety of alternative electron donors and acceptors absent from the medium were induced, apparently involving the Wood-Ljungdahl pathway. Through this metabolic flexibility, D. hafniense Y51 may be able to switch between different metabolic capabilities under limiting conditions.

Bridging spatially segregated redox zones with a microbial electrochemical snorkel triggers biogeochemical cycles in oil-contaminated River Tyne (UK) sediments

Marine sediments represent an important sink for a number of anthropogenic organic contaminants, including petroleum hydrocarbons following an accidental oil spill. Degradation of these compounds largely depends on the activity of sedimentary microbial communities linked to biogeochemical cycles, in which abundant elements such as iron and sulfur are shuttled between their oxidized and reduced forms. Here we show that introduction of a small electrically conductive graphite rod ("the electrochemical snorkel") into an oil-contaminated River Tyne (UK) sediment, so as to create an electrochemical connection between the anoxic contaminated sediment and the oxygenated overlying water, has a large impact on the rate of metabolic reactions taking place in the bulk sediment. The electrochemical snorkel accelerated sulfate reduction processes driven by organic contaminant oxidation and suppressed competitive methane-producing reactions. The application of a comprehensive suite of chemical, spectroscopic, biomolecular and thermodynamic analyses suggested that the snorkel served as a scavenger of toxic sulfide via a redox interaction with the iron cycle. Taken as a whole, the results of this work highlight a new strategy for controlling biological processes, such as bioremediation, through the manipulation of the electron flows in contaminated sediments.

Syntrophomonas wolfei Uses an NADH-Dependent, Ferredoxin-Independent [FeFe]-Hydrogenase To Reoxidize NADH

Syntrophomonas wolfei syntrophically oxidizes short-chain fatty acids (four to eight carbons in length) when grown in coculture with a hydrogen- and/or formate-using methanogen. The oxidation of 3-hydroxybutyryl-coenzyme A (CoA), formed during butyrate metabolism, results in the production of NADH. The enzyme systems involved in NADH reoxidation in S. wolfei are not well understood. The genome of S. wolfei contains a multimeric [FeFe]-hydrogenase that may be a mechanism for NADH reoxidation. The S. wolfei genes for the multimeric [FeFe]-hydrogenase (hyd1ABC; SWOL_RS05165, SWOL_RS05170, SWOL_RS05175) and [FeFe]-hydrogenase maturation proteins (SWOL_RS05180, SWOL_RS05190, SWOL_RS01625) were coexpressed in Escherichia coli, and the recombinant Hyd1ABC was purified and characterized. The purified recombinant Hyd1ABC was a heterotrimer with an αβγ configuration and a molecular mass of 115 kDa. Hyd1ABC contained 29.2 ± 1.49 mol of Fe and 0.7 mol of flavin mononucleotide (FMN) per mole enzyme. The purified, recombinant Hyd1ABC reduced NAD+ and oxidized NADH without the presence of ferredoxin. The HydB subunit of the S. wolfei multimeric [FeFe]-hydrogenase lacks two iron-sulfur centers that are present in known confurcating NADH- and ferredoxin-dependent [FeFe]-hydrogenases. Hyd1ABC is a NADH-dependent hydrogenase that produces hydrogen from NADH without the need of reduced ferredoxin, which differs from confurcating [FeFe]-hydrogenases. Hyd1ABC provides a mechanism by which S. wolfei can reoxidize NADH produced during syntrophic butyrate oxidation when low hydrogen partial pressures are maintained by a hydrogen-consuming microorganism.IMPORTANCE Our work provides mechanistic understanding of the obligate metabolic coupling that occurs between hydrogen-producing fatty and aromatic acid-degrading microorganisms and their hydrogen-consuming partners in the process called syntrophy (feeding together). The multimeric [FeFe]-hydrogenase used NADH without the involvement of reduced ferredoxin. The multimeric [FeFe]-hydrogenase would produce hydrogen from NADH only when hydrogen concentrations were low. Hydrogen production from NADH by Syntrophomonas wolfei would likely cease before any detectable amount of cell growth occurred. Thus, continual hydrogen production requires the presence of a hydrogen-consuming partner to keep hydrogen concentrations low and explains, in part, the obligate requirement that S. wolfei has for a hydrogen-consuming partner organism during growth on butyrate. We have successfully expressed genes encoding a multimeric [FeFe]-hydrogenase in E. coli, demonstrating that such an approach can be advantageous to characterize complex redox proteins from difficult-to-culture microorganisms.

Hydrogen or formate: Alternative key players in methanogenic degradation

Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration. Recent evidence from biochemical and molecular biological studies indicates that several secondary fermenters can use both hydrogen and formate for electron release, and may do so even simultaneously. Numerous strictly anaerobic bacteria contain enzymes which equilibrate hydrogen and formate pools to energetically equal values, and recent measurements in sewage digestors and biogas reactors indicate that - beyond occasional fluctuations - the pool sizes of hydrogen and formate are indeed energetically nearly equivalent. Nonetheless, a thermophilic archaeon from a submarine hydrothermal vent, Thermococcus onnurineus, can obtain ATP from the conversion of formate to hydrogen plus bicarbonate at 80°C, indicating that at least in this extreme environment the pools of formate and hydrogen are likely to be sufficiently different to support such an unusual type of energy conservation.

Microbial diversity arising from thermodynamic constraints

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments.

Improving the stability of thermophilic anaerobic digesters treating SS-OFMSW through enrichment with compost and leachate seeds

This paper examines the potential of improving the stability of thermophilic anaerobic digestion of source-sorted organic fraction of municipal solid waste (SS-OFMSW) by adding leachate and compost during inoculation. For this purpose, two stable thermophilic digesters, A (control) and B (with added leachate and compost), were subjected to a sustained substrate shock by doubling the organic loading rate for one week. Feeding was suspended then gradually resumed to reach the pre-shock loading rate (2 gVS/l/d). Digester A failed, exhibiting excessive increase in acetate and a corresponding decrease in pH and methane generation, and lower COD and solids removal efficiencies. In contrast, digester B was able to restore its functionality with 90% recovery of pre-shock methane generation rate at stable pH, lower hydrogen levels, and reduced VFAs and ammonia accumulation.

Desulfofrigus sp. prevails in sulfate-reducing dilution cultures from sediments of the Benguela upwelling area

Sediments of coastal upwelling areas are generally characterized by a high content of organic carbon that is mainly degraded via anaerobic microbial processes including sulfate reduction as a major terminal oxidation step. Despite the high importance of sulfate reduction in these sediments, the identity of sulfate-reducing bacteria (SRB) has remained almost unknown. Here, we applied a cultivation-based approach using selective enrichment conditions to study the diversity and distribution of active SRB in sediments along a transect perpendicular to the continental slope off the coast of Namibia (Meteor-cruise M76/1). To promote growth of the most abundant SRB, dilution series were prepared and amended with hydrogen, acetate, or a mixture of monomers representing typical substrates for SRB. Growth of SRB could be detected in the presence of all electron donors and from sediment down to 4 m depth. 16S rRNA gene-based DGGE analysis and sequencing revealed the predominance of SRB related to psychrophiles in particular to the genus Desulfofrigus, which made up 1 % of the total microbial community, accounting for an absolute abundance of up to 4.8 × 10(7)  cells mL(-1) . In general, the abundance of cultured SRB changed with depth and between the different sampling sites and correlated with the content of organic carbon as previously reported. Growth of chemolithotrophic SRB in relatively high dilution steps and the enrichment of methanogens as well as acetogens from deeper sediment point to a competition between hydrogen-utilizing microbial processes and their biogeochemical significance in deep sediment layers of the Benguela upwelling area.

Energy sources for chemolithotrophs in an arsenic- and iron-rich shallow-sea hydrothermal system

The hydrothermally influenced sediments of Tutum Bay, Ambitle Island, Papua New Guinea, are ideal for investigating the chemolithotrophic activities of micro-organisms involved in arsenic cycling because hydrothermal vents there expel fluids with arsenite (As(III)) concentrations as high as 950 μg L(-1) . These hot (99 °C), slightly acidic (pH ~6), chemically reduced, shallow-sea vent fluids mix with colder, oxidized seawater to create steep gradients in temperature, pH, and concentrations of As, N, Fe, and S redox species. Near the vents, iron oxyhydroxides precipitate with up to 6.2 wt% arsenate (As(V)). Here, chemical analyses of sediment porewaters from 10 sites along a 300-m transect were combined with standard Gibbs energies to evaluate the energy yields (-ΔG(r)) from 19 potential chemolithotrophic metabolisms, including As(V) reduction, As(III) oxidation, Fe(III) reduction, and Fe(II) oxidation reactions. The 19 reactions yielded 2-94 kJ mol(-1) e(-) , with aerobic oxidation of sulphide and arsenite the two most exergonic reactions. Although anaerobic As(V) reduction and Fe(III) reduction were among the least exergonic reactions investigated, they are still potential net metabolisms. Gibbs energies of the arsenic redox reactions generally correlate linearly with pH, increasing with increasing pH for As(III) oxidation and decreasing with increasing pH for As(V) reduction. The calculated exergonic energy yields suggest that micro-organisms could exploit diverse energy sources in Tutum Bay, and examples of micro-organisms known to use these chemolithotrophic metabolic strategies are discussed. Energy modeling of redox reactions can help target sampling sites for future microbial collection and cultivation studies.

Genesis of acetate and methane by gut bacteria of nutritionally diverse termites

The evolution of different feeding guilds in termites is paralleled by differences in the activity of their gut microbiota. In wood-feeding termites, carbon dioxide-reducing acetogenic bacteria were found to generally outprocess carbon dioxide-reducing methanogenic bacteria for reductant (presumably hydrogen) generated during microbial fermentation in the hindgut. By contrast, acetogenesis from hydrogen and carbon dioxide was of little significance in fungus-growing and soil-feeding termites, which evolved more methane than their wood- and grass-feeding counterparts. Given the large biomass of termites on the earth and especially in the tropics, these findings should help refine global estimates of carbon dioxide reduction in anoxic habitats and the contribution of termite emissions to atmospheric methane concentrations.

Electron transfer in syntrophic communities of anaerobic bacteria and archaea

Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to overcome energy barriers and break down compounds that they cannot digest by themselves. Here, we review the transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities. We also describe the process of reverse electron transfer, which is a key requirement in obligately syntrophic interactions. Anaerobic methane oxidation coupled to sulphate reduction is also carried out by syntrophic communities of bacteria and archaea but, as we discuss, the exact mechanism of this syntrophic interaction is not yet understood.

Effect of seasonal changes in quantities of biowaste on full scale anaerobic digester performance

A 750,000l digester located in Roppen/Austria was studied over a 2-year period. The concentrations and amounts of CH4, H2, CO2 and H2S and several other process parameters like temperature, retention time, dry weight and input of substrate were registered continuously. On a weekly scale the pH and the concentrations of NH4+ -N and volatile fatty acids (acetic, butyric, iso-butyric, propionic, valeric and iso-valeric acid) were measured. The data show a similar pattern of seasonal gas production over 2 years of monitoring. The consumption of VFA and not the hydrogenotrophic CH4 production appeared to be the limiting factor for the investigated digestion process. Whereas the changes in pH and the concentrations of most VFA did not correspond with changes in biogas production, the ratio of acetic to propionic acid and the concentration of H2 appeared to be useful indicators for reactor performance. However, the most influential factors for the anaerobic digestion process were the amount and the quality of input material, which distinctly changed throughout the year.

Effect of competitive terminal electron acceptor processes on dechlorination of cis-1,2-dichloroethene and 1,2-dichloroethane in constructed wetland soils

Thermodynamic calculations were coupled with time-series measurements of chemical species (parent and daughter chlorinated solvents, H(2), sulfite, sulfate and methane) to predict the anaerobic transformation of cis-1,2-dichloroethene (cis-1,2-DCE) and 1,2-dichloroethane (1,2-DCA) in constructed wetland soil microcosms inoculated with a dehalorespiring culture. For cis-1,2-DCE, dechlorination occurred simultaneously with sulfite and sulfate reduction but competitive exclusion of methanogenesis was observed due to the rapid H(2) drawdown by the dehalorespiring bacteria. Rates of cis-1,2-DCE dechlorination decreased proportionally to the free energy yield of the competing electron acceptor and proportionally to the rate of H(2) drawdown, suggesting that H(2) competition between dehalorespirers and other populations was occurring, affecting the dechlorination rate. For 1,2-DCA, dechlorination occurred simultaneously with methanogenesis and sulfate reduction but occurred only after sulfite was completely depleted. Rates of 1,2-DCA dechlorination were unaffected by the presence of competing electron-accepting processes. The absence of a low H(2) threshold suggests that 1,2-DCA dechlorination is a cometabolic transformation, occurring at a higher H(2) threshold, despite the high free energy yields available for dehalorespiration of 1,2-DCA. We demonstrate the utility of kinetic and thermodynamic calculations to understand the complex, H(2)-utilizing reactions occurring in the wetland bed and their effect on rates of dechlorination of priority pollutants.

Influence of extrinsic factors on granulation in UASB reactor

The aim of this mini-review is to synthesize and analyze information on how the process of granulation is affected by environmental and operational conditions in the reactor. The factors reviewed are temperature, pH, alkalinity, organic loading rate, upflow velocity, nature and strength of substrate, nutrients, multivalent cations and heavy metals, microbial ecology of seed sludge, exo-cellular polymer, and addition of natural and synthetic polymers. Careful temperature control and adequate alkalinity is required for generation and maintenance of granules. Nature and strength of substrate in conjunction with intra-granular diffusion to a large extent determines the microstructure of the granules. The divalent cations such as calcium and iron may enhance granulation by ionic bridging and linking exo-cellular polymers. However, their presence in excess may lead to cementation due to precipitation leading to increased ash content and mass transfer limitation. The addition of external additives such as ionic polymers may enhance granulation in the upflow anaerobic sludge blanket reactors.

Effect of temperature on anaerobic ethanol oxidation and methanogenesis in acidic peat from a northern wetland

The effects of temperature on rates and pathways of CH4 production and on the abundance and structure of the archaeal community were investigated in acidic peat from a mire in northern Scandinavia (68 degrees N). We monitored the production of CH4 and CO2 over time and measured the turnover of Fe(II), ethanol, and organic acids. All experiments were performed with and without specific inhibitors (2-bromoethanesulfonate [BES] for methanogenesis and CH3F for acetoclastic methanogenesis). The optimum temperature for methanogenesis was 25 degrees C (2.3 micromol CH4.g [dry weight](-1) . day(-1)), but the activity was relatively high even at 4 degrees C (0.25 micromol CH4. g [dry weight](-1) . day(-1)). The theoretical lower limit for methanogenesis was calculated to be at -5 degrees C. The optimum temperature for growth as revealed by real-time PCR was 25 degrees C for both archaea and bacteria. The population structure of archaea was studied by terminal restriction fragment length polymorphism analysis and remained constant over a wide temperature range. Hydrogenotrophic methanogenesis accounted for about 80% of the total methanogenesis. Most 16S rRNA gene sequences that were affiliated with methanogens and all McrA sequences clustered with the exclusively hydrogenotrophic order Methanobacteriales, correlating with the prevalence of hydrogenotrophic methanogenesis. Fe reduction occurred parallel to methanogenesis and was inhibited by BES, suggesting that methanogens were involved in Fe reduction. Based upon the observed balance of substrates and thermodynamic calculations, we concluded that the ethanol pool was oxidized to acetate by the following two processes: syntrophic oxidation with methanogenesis (i) as an H2 sink and (ii) as a reductant for Fe(III). Acetate accumulated, but a considerable fraction was converted to butyrate, making volatile fatty acids important end products of anaerobic metabolism.

Biological control of hog waste odor through stimulated microbial Fe(III) reduction

Odor control and disposal of swine waste have inhibited expansion of swine production facilities throughout the United States. Swine waste odor is associated primarily with high concentrations of volatile fatty acids (VFAs). Here, we demonstrate that stimulated Fe(III) reduction in hog manure can rapidly remove the malodorous compounds and enhance methane production by 200%. As part of these studies, we enumerated the indigenous Fe(III)-reducing population in swine waste and identified members of the family Geobacteraceae as the dominant species. These organisms were present at concentrations as high as 2 x 10(5) cells g(-1). Several pure cultures of Fe(III) reducers, including Geobacter metallireducens, Geobacter humireducens, Geobacter sulfurreducens, Geobacter grbiciae, Geothrix fermentans, and Geovibrio ferrireducens, readily degraded some or all of the malodorous VFAs found in swine manure. In contrast, Shewanella algae did not degrade any of these compounds. We isolated an Fe(III) reducer, Geobacter strain NU, from materials collected from primary swine waste lagoons. This organism degraded all of the malodorous VFAs tested and readily grew in swine waste amended with Fe(III). When raw waste amended with Fe(III) was inoculated with strain NU, the VFA content rapidly decreased, corresponding with an almost complete removal of the odor. In contrast, the raw waste without Fe(III) or strain NU showed a marked increase in VFA content and a rapid pH drop. This study showed that Fe(III) supplementation combined with appropriate bioaugmentation provides a simple, cost-effective approach to deodorize and treat swine waste, removing a significant impediment to the expansion of pork production facilities.

Stable-isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil

Propionate is an important intermediate of the degradation of organic matter in many anoxic environments. In methanogenic environments, due to thermodynamic constraints, the oxidation of propionate requires syntrophic cooperation of propionate-fermenting proton-reducing bacteria and H(2)-consuming methanogens. We have identified here microorganisms that were active in syntrophic propionate oxidation in anoxic paddy soil by rRNA-based stable-isotope probing (SIP). After 7 weeks of incubation with [(13)C]propionate (<10 mM) and the oxidation of approximately 30 micromol of (13)C-labeled substrate per g dry weight of soil, we found that archaeal nucleic acids were (13)C labeled to a larger extent than those of the bacterial partners. Nevertheless, both terminal restriction fragment length polymorphism and cloning analyses revealed Syntrophobacter spp., Smithella spp., and the novel Pelotomaculum spp. to predominate in "heavy" (13)C-labeled bacterial rRNA, clearly showing that these were active in situ in syntrophic propionate oxidation. Among the Archaea, mostly Methanobacterium and Methanosarcina spp. and also members of the yet-uncultured "rice cluster I" lineage had incorporated substantial amounts of (13)C label, suggesting that these methanogens were directly involved in syntrophic associations and/or thriving on the [(13)C]acetate released by the syntrophs. With this first application of SIP in an anoxic soil environment, we were able to clearly demonstrate that even guilds of microorganisms growing under thermodynamic constraints, as well as phylogenetically diverse syntrophic associations, can be identified by using SIP. This approach holds great promise for determining the structure and function relationships of further syntrophic or other nutritional associations in natural environments and for defining metabolic functions of yet-uncultivated microorganisms.

Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: effect of temperature

Methanogenic degradation of organic matter is an important microbial process in lake sediments. Temperature may affect not only the rate but also the pathway of CH4 production by changing the activity and the abundance of individual microorganisms. Therefore, we studied the function and structure of a methanogenic community in anoxic sediment of Lake Dagow, a eutrophic lake in north-eastern Germany. Incubation of sediment samples (in situ 7.5 degrees C) at increasing temperatures (4, 10, 15, 25, 30 degrees C) resulted in increasing production rates of CH4 and CO2 and in increasing steady-state concentrations of H2. Thermodynamic conditions for H2/CO2 -dependent methanogenesis were only exergonic at 25 and 30 degrees C. Inhibition of methanogenesis with chloroform resulted in the accumulation of methanogenic precursors, i.e., acetate, propionate, and isobutyrate. Mass balance calculations indicated that less CH4 was formed via H2 at 4 degrees C than at 30 degrees C. Conversion of 14CO2 to 14CH4 also showed that H2/CO2 -dependent methanogenesis contributed less to total CH4 production at 4 degrees C than at 30 degrees C. [2-14 C]Acetate turnover rates at 4 degrees C accounted for a higher percentage of total CH4 production than at 30 degrees C. Collectively, these results showed a higher contribution of H2-dependent methanogenesis and a lower contribution of acetate-dependent methanogenesis at high versus low temperature. The archaeal community was characterized by cloning, sequencing, and phylogenetic analysis of the 16S rRNA genes retrieved from the sediment. Sequences were affiliated with Methanosaetaceae, Methanomicrobiaceae, and three deeply branching euryarchaeotal clusters, i.e., group III, Rice cluster V, and a novel euryarchaeotal cluster, the LDS cluster. Terminal restriction fragment length polymorphism (T-RFLP) analysis showed that 16S rRNA genes affiliated to Methanosaetaceae (20-30%), Methanomicrobiaceae (35-55%), and group III (10-25%) contributed most to the archaeal community. Incubation of the sediment at different temperatures (4-30 degrees C) did not result in a systematic change of the archaeal community composition, indicating that change of temperature primarily affected the activity rather than the structure of the methanogenic community.

The Microbial Logic behind the Prevalence of Incomplete Oxidation of Organic Compounds by Acetogenic Bacteria in Methanogenic Environments

Microbial degradation of organic material in methanogenic ecosystems is a multistep process in which subsequent groups use the products of the first groups of organisms in the chain as substrates. The acetogenic bacteria in these systems produce both H2 and acetate. In the present minireview a thermodynamic approach is taken to evaluate the logic behind this duality. The evaluation shows that at the H2 partial pressures that usually occur in methanogenic ecosystems the acetogenic oxidation of known acetogenic substrates such as propionate, butyrate, and benzoate yields more energy than their complete oxidation to H2/CO2. Also, H2 partial pressures needed to achieve complete hydrogenogenic oxidation of these acetogenic substrates would have to be so low that H2 would be virtually unavailable to the hydrogenotrophic bacteria, in casu the methanogens.

Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil

Temperature is an important factor controlling CH(4) production in anoxic rice soils. Soil slurries, prepared from Italian rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37 degrees C or in a temperature gradient block covering the same temperature range at intervals of 1 degrees C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH(4) production rates increased with temperature, with an apparent activation energy of 61 kJ mol(-1). Steady-state partial pressures of the methanogenic precursor H(2) also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H(2) plus CO(2)-dependent methanogenesis was kept at -20 to -25 kJ mol of CH(4)(-1) over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 microM. Simultaneously, the relative contribution of H(2) as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to (14)CH(4), so that the carbon and electron flow to CH(4) was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal Methanobacteriaceae, Methanomicrobiaceae, Methanosaetaceae, Methanosarcinaceae, and Rice clusters I, III, IV, V, and VI, which were all present in the rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I and Methanosaetaceae were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring Methanosarcinaceae decreased and the more modest Methanosaetaceae increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.

Kinetics of syntrophic cultures: a theoretical treatise on butyrate fermentation

Numerous microbial conversions in methanogenic environments proceed at (Gibbs) free energy changes close to thermodynamic equilibrium. In this paper we attempt to describe the consequences of this thermodynamic boundary condition on the kinetics of anaerobic conversions in methanogenic environments. The anaerobic fermentation of butyrate is used as an example. Based on a simple metabolic network stoichiometry, the free energy change based balances in the cell, and the flux of substrates and products in the catabolic and anabolic reactions are coupled. In butyrate oxidation, a mechanism of ATP-dependent reversed electron transfer has been proposed to drive the unfavorable oxidation of butyryl-CoA to crotonyl-CoA. A major assumption in our model is that ATP-consumption and electron translocation across the cytoplasmic membrane do not proceed according to a fixed stoichiometry, but depend on the cellular concentration ratio of ATP and ADP. The energetic and kinetic impact of product inhibition by acetate and hydrogen are described. A major consequence of the derived model is that Monod-based kinetic description of this type of conversions is not feasible, because substrate conversion and biomass growth are proposed to be uncoupled. It furthermore suggests that the specific substrate conversion rate cannot be described as a single function of the driving force of the catabolic reaction but depends on the actual substrate and product concentrations. By using nonfixed stoichiometries for the membrane associated processes, the required flexibility of anaerobic bacteria to adapt to varying environmental conditions can be described.

Metabolic regulation in methanogenic archaea during growth on hydrogen and CO2

Methanogenic Archaea represent a unique group of micro-organisms in their ability to derive their energy for growth from the conversion of their substrates to methane. The common substrates are hydrogen and CO2. The energy obtained in the latter conversion is highly dependent on the hydrogen concentration which may dramatically vary in their natural habitats and under laboratory conditions. In this review the bio-energetic consequences of the variations in hydrogen supply will be investigated. It will be described how the organisms seem to be equipped as to their methanogenic apparatus to cope with extremes in hydrogen availability and how they could respond to hydrogen changes by the regulation of their metabolism.

The importance of hydrogen in landfill fermentations

Forty-two samples taken from two landfills were monitored for CH(inf4) production and apparent steady-state H(inf2) concentration. The rates of methanogenesis in these samples ranged from below the detection limit to 1,900 (mu)mol kg (dry weight)(sup-1) day(sup-1), and the median steady-state hydrogen concentration was 1.4 (mu)M in one landfill and 5.2 (mu)M in the other. To further investigate the relationship between hydrogen concentration and methanogenesis, a subset of seven landfill samples was selected on basis of their rates of CH(inf4) production, H(inf2) concentrations, sample pHs, and moisture contents. Samples with H(inf2) concentrations of <20 nM had relatively small amounts of volatile fatty acids (VFAs) (undetectable to 18.6 mmol of VFA kg [dry weight](sup-1)), while samples with H(inf2) concentrations of >100 nM had relatively high VFA levels (133 to 389 mmol of VFA kg [dry weight](sup-1)). Samples with high H(inf2) and VFA contents had relatively low pH values (<=6.3). However, methanogenic and syntrophic bacteria were present in all samples, so the lack of methanogenesis in some samples was not due to a lack of suitable inocula. The low rates of methanogenesis in these samples were probably due to inhibitory effects of low pH and VFA accumulation, resulting from a thermodynamic uncoupling of fatty acid oxidation. As in other anaerobic ecosystems, H(inf2) is a critical intermediate that may be used to monitor the status of landfill fermentations.