Hydrogen regulation of growth, growth yields, and methane gene transcription in Methanobacterium thermoautotrophicum deltaH

Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions

Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.

Bioenergetic characterization of hyperthermophilic archaean Methanocaldococcus sp. FS406-22

Hyperthermophilic archaean Methanocaldococcus sp. FS406-22 (hereafter FS406) is a hydrogenotrophic methanogen isolated from a deep-sea hydrothermal vent. To better understand the energetic requirements of hydrogen oxidation under extreme conditions, the thermodynamic characterization of FS406 incubations is necessary and notably underexplored. In this work, we quantified the bioenergetics of FS406 incubations at a range of temperatures (65, 76, and 85 ℃) and hydrogen concentrations (1.1, 1.4, and 2.1 mm). The biomass yields (C-mol of biomass per mol of H2 consumed) ranged from 0.02 to 0.19. Growth rates ranged from 0.4 to 1.5 h-1. Gibbs energies of incubation based on macrochemical equations of cell growth ranged from - 198 kJ/C-mol to - 1840 kJ/C-mol. Enthalpies of incubation determined from calorimetric measurements ranged from - 4150 kJ/C-mol to - 36333 kJ/C-mol. FS406 growth rates were most comparable to hyperthermophilic methanogen Methanocaldococcus jannaschii. Maintenance energy calculations from the thermodynamic parameters of FS406 and previously determined heterotrophic methanogen data revealed that temperature is a primary determinant rather than an electron donor. This work provides new insights into the thermodynamic underpinnings of a hyperthermophilic hydrothermal vent methanogen and helps to better constrain the energetic requirements of life in extreme environments.

Evolving understanding of rumen methanogen ecophysiology

Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.

The role of oxygen in stimulating methane production in wetlands

Methane (CH4 ), a potent greenhouse gas, is the second most important greenhouse gas contributor to climate change after carbon dioxide (CO2 ). The biological emissions of CH4 from wetlands are a major uncertainty in CH4 budgets. Microbial methanogenesis by Archaea is an anaerobic process accounting for most biological CH4 production in nature, yet recent observations indicate that large emissions can originate from oxygenated or frequently oxygenated wetland soil layers. To determine how oxygen (O2 ) can stimulate CH4 emissions, we used incubations of Sphagnum peat to demonstrate that the temporary exposure of peat to O2 can increase CH4 yields up to 2000-fold during subsequent anoxic conditions relative to peat without O2 exposure. Geochemical (including ion cyclotron resonance mass spectrometry, X-ray absorbance spectroscopy) and microbiome (16S rDNA amplicons, metagenomics) analyses of peat showed that higher CH4 yields of redox-oscillated peat were due to functional shifts in the peat microbiome arising during redox oscillation that enhanced peat carbon (C) degradation. Novosphingobium species with O2 -dependent aromatic oxygenase genes increased greatly in relative abundance during the oxygenation period in redox-oscillated peat compared to anoxic controls. Acidobacteria species were particularly important for anaerobic processing of peat C, including in the production of methanogenic substrates H2 and CO2 . Higher CO2 production during the anoxic phase of redox-oscillated peat stimulated hydrogenotrophic CH4 production by Methanobacterium species. The persistence of reduced iron (Fe(II)) during prolonged oxygenation in redox-oscillated peat may further enhance C degradation through abiotic mechanisms (e.g., Fenton reactions). The results indicate that specific functional shifts in the peat microbiome underlie O2 enhancement of CH4 production in acidic, Sphagnum-rich wetland soils. They also imply that understanding microbial dynamics spanning temporal and spatial redox transitions in peatlands is critical for constraining CH4 budgets; predicting feedbacks between climate change, hydrologic variability, and wetland CH4 emissions; and guiding wetland C management strategies.

Temporal changes in total and metabolically active ruminal methanogens in dairy cows supplemented with 3-nitrooxypropanol

The purpose of this study was to investigate the effect of 3-nitrooxypropanol (3-NOP), a potent methane inhibitor, on total and metabolically active methanogens in the rumen of dairy cows over the course of the day and over a 12-wk period. Rumen contents of 8 ruminally cannulated early-lactation dairy cows were sampled at 2, 6, and 10 h after feeding during wk 4, 8, and 12 of a randomized complete block design experiment in which 3-NOP was fed at 60 mg/kg of feed dry matter. Cows (4 fed the control and 4 fed the 3-NOP diet) were blocked based on their previous lactation milk yield or predicted milk yield. Rumen samples were extracted for microbial DNA (total) and microbial RNA (metabolically active), PCR amplified for the 16S rRNA gene of archaea, sequenced on an Illumina platform, and analyzed for archaea diversity. In addition, the 16S copy number and 3 ruminal methanogenic species were quantified using the real-time quantitative PCR assay. We detected a difference between DNA and RNA (cDNA)-based archaea communities, revealing that ruminal methanogens differ in their metabolic activities. Within DNA and cDNA components, methanogenic communities differed by sampling hour, week, and treatment. Overall, Methanobrevibacter was the dominant genus (94.3%) followed by Methanosphaera, with the latter genus having greater abundance in the cDNA component (14.5%) compared with total populations (5.5%). Methanosphaera was higher at 2 h after feeding, whereas Methanobrevibacter increased at 6 and 10 h in both groups, showing diurnal patterns among individual methanogenic lineages. Methanobrevibacter was reduced at wk 4, whereas Methanosphaera was reduced at wk 8 and 12 in cows supplemented with 3-NOP compared with control cows, suggesting differential responses among methanogens to 3-NOP. A reduction in Methanobrevibacter ruminantium in all 3-NOP samples from wk 8 was confirmed using real-time quantitative PCR. The relative abundance of individual methanogens was driven by a combination of dietary composition, dry matter intake, and hydrogen concentrations in the rumen. This study provides novel information on the effects of 3-NOP on individual methanogenic lineages, but further studies are needed to understand temporal dynamics and to validate the effects of 3-NOP on individual lineages of ruminal methanogens.

Analysis of a Methanogen and an Actinobacterium Dominating the Thermophilic Microbial Community of an Electromethanogenic Biocathode

Electromethanogenesis refers to the bioelectrochemical synthesis of methane from CO₂ by biocathodes. In an electromethanogenic system using thermophilic microorganisms, metagenomic analysis along with quantitative real-time polymerase chain reaction and fluorescence in situ hybridization revealed that the biocathode microbiota was dominated by the methanogen Methanothermobacter sp. strain EMTCatA1 and the actinobacterium Coriobacteriaceae sp. strain EMTCatB1. RNA sequencing was used to compare the transcriptome profiles of each strain at the methane-producing biocathodes with those in an open circuit and with the methanogenesis inhibitor 2-bromoethanesulfonate (BrES). For the methanogen, genes related to hydrogenotrophic methanogenesis were highly expressed in a manner similar to those observed under H₂-limited conditions. For the actinobacterium, the expression profiles of genes encoding multiheme c-type cytochromes and membrane-bound oxidoreductases suggested that the actinobacterium directly takes up electrons from the electrode. In both strains, various stress-related genes were commonly induced in the open-circuit biocathodes and biocathodes with BrES. This study provides a molecular inventory of the dominant species of an electromethanogenic biocathode with functional insights and therefore represents the first multiomics characterization of an electromethanogenic biocathode.

Transcriptional regulation of methanogenic metabolism in archaea

Methanogenesis is a widespread metabolism of evolutionary and environmental importance that is likely to have originated on early Earth. Microorganisms that perform methanogenesis, termed methanogens, belong exclusively to the domain Archaea. Despite maintaining eukaryotic transcription machinery and homologs of bacterial regulators, archaeal transcription and gene regulation appear to be distinct from either domain. While genes involved in methanogenic metabolism have been identified and characterized, their regulation in response to both extracellular and intracellular signals is less understood. Here, we review recent reports on transcriptional regulation of methanogenesis using two model methanogens, Methanococcus maripaludis and Methanosarcina acetivorans, and highlight directions for future research in this nascent field.

Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman

Serpentinization can generate highly reduced fluids replete with hydrogen (H₂) and methane (CH₄), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH₄ in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH₄ in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH₄ cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, >10), H₂- and CH₄-rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH₄ production and in microbial CH₄ oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH₄ cycling in aquifers that undergo low-temperature serpentinization.IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH₄) cycling, including the abiotic production of hydrogen (H₂) and possibly CH₄ Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth's history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H₂ and CH₄ These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH₄ in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.

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.

Application of in-situ H2-assisted biogas upgrading in high-rate anaerobic wastewater treatment

The H₂-assisted biogas upgrading approach has recently attracted much interest as a low-cost and environmentally friendly alternative to commonly used ex-situ/ physiochemical biogas upgrading techniques. However, most studies conducted to date have been limited to anaerobic solid-waste treatment characterized by flocculant sludge and low organic loading rates (OLR). In an attempt to expand its application to high-rate anaerobic wastewater treatment, an innovative two-stage up-flow anaerobic sludge blanket reactor system was employed using anaerobic granular sludge. We found that the CH₄ content of product gas was consistently >90% and that H₂ and CO₂ concentrations stayed below 5%, even when OLR was increased from 1 to 5 g L^-1 d^-1 and H₂ feeding rates were increased from 0.13 to 0.63 g L^-1 d^-1. We were also able to show that CO (5-10%) in H₂-rich syngas didn't inhibit methanogenesis or had significant impact on microbial community structure, suggesting that H₂-assisted biogas upgrading with H₂-rich syngas is feasible.

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents

The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2, CH4, and metagenome methanogen concentration estimates in 20-40 °C hydrothermal fluids. Model results showed that hyperthermophilic methanogens dominate in systems where a narrow flow path geometry is maintained, while thermophilic methanogens dominate in systems where the flow geometry expands. At Axial Seamount, the residence time of fluid below the surface was 29-33 h. Only 1011 methanogenic cells occupying 1.8-18 m3 of ocean crust per m2 of vent seafloor area were needed to produce the observed CH4 anomalies. We show that variations in local geology at diffuse vents can create fluid flow paths that are stable over space and time, harboring persistent and distinct microbial communities.

Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer

Hyperthermophilic methanogens are often H2 limited in hot subseafloor environments, and their survival may be due in part to physiological adaptations to low H2 conditions and interspecies H2 transfer. The hyperthermophilic methanogen Methanocaldococcus jannaschii was grown in monoculture at high (80 to 83 μM) and low (15 to 27 μM) aqueous H2 concentrations and in coculture with the hyperthermophilic H2 producer Thermococcus paralvinellae The purpose was to measure changes in growth and CH4 production kinetics, CH4 fractionation, and gene expression in M. jannaschii with changes in H2 flux. Growth and cell-specific CH4 production rates of M. jannaschii decreased with decreasing H2 availability and decreased further in coculture. However, cell yield (cells produced per mole of CH4 produced) increased 6-fold when M. jannaschii was grown in coculture rather than monoculture. Relative to high H2 concentrations, isotopic fractionation of CO2 to CH4 (εCO2-CH4) was 16‰ larger for cultures grown at low H2 concentrations and 45‰ and 56‰ larger for M. jannaschii growth in coculture on maltose and formate, respectively. Gene expression analyses showed H2-dependent methylene-tetrahydromethanopterin (H4MPT) dehydrogenase expression decreased and coenzyme F420-dependent methylene-H4MPT dehydrogenase expression increased with decreasing H2 availability and in coculture growth. In coculture, gene expression decreased for membrane-bound ATP synthase and hydrogenase. The results suggest that H2 availability significantly affects the CH4 and biomass production and CH4 fractionation by hyperthermophilic methanogens in their native habitats.IMPORTANCE Hyperthermophilic methanogens and H2-producing heterotrophs are collocated in high-temperature subseafloor environments, such as petroleum reservoirs, mid-ocean ridge flanks, and hydrothermal vents. Abiotic flux of H2 can be very low in these environments, and there is a gap in our knowledge about the origin of CH4 in these habitats. In the hyperthermophile Methanocaldococcus jannaschii, growth yields increased as H2 flux, growth rates, and CH4 production rates decreased. The same trend was observed increasingly with interspecies H2 transfer between M. jannaschii and the hyperthermophilic H2 producer Thermococcus paralvinellae With decreasing H2 availability, isotopic fractionation of carbon during methanogenesis increased, resulting in isotopically more negative CH4 with a concomitant decrease in H2-dependent methylene-tetrahydromethanopterin dehydrogenase gene expression and increase in F420-dependent methylene-tetrahydromethanopterin dehydrogenase gene expression. The significance of our research is in understanding the nature of hyperthermophilic interspecies H2 transfer and identifying biogeochemical and molecular markers for assessing the physiological state of methanogens and possible source of CH4 in natural environments.

Physiology and methane productivity of Methanobacterium thermaggregans

Accumulation of carbon dioxide (CO2), associated with global temperature rise, and drastically decreasing fossil fuels necessitate the development of improved renewable and sustainable energy production processes. A possible route for CO2 recycling is to employ autotrophic and hydrogenotrophic methanogens for CO2-based biological methane (CH4) production (CO2-BMP). In this study, the physiology and productivity of Methanobacterium thermaggregans was investigated in fed-batch cultivation mode. It is shown that M. thermaggregans can be reproducibly adapted to high agitation speeds for an improved CH4 productivity. Moreover, inoculum size, sulfide feeding, pH, and temperature were optimized. Optimization of growth and CH4 productivity revealed that M. thermaggregans is a slightly alkaliphilic and thermophilic methanogen. Hitherto, it was only possible to grow seven autotrophic, hydrogenotrophic methanogenic strains in fed-batch cultivation mode. Here, we show that after a series of optimization and growth improvement attempts another methanogen, M. thermaggregas could be adapted to be grown in fed-batch cultivation mode to cell densities of up to 1.56 g L-1. Moreover, the CH4 evolution rate (MER) of M. thermaggregans was compared to Methanothermobacter marburgensis, the CO2-BMP model organism. Under optimized cultivation conditions, a maximum MER of 96.1 ± 10.9 mmol L-1 h-1 was obtained with M. thermaggregans-97% of the maximum MER that was obtained utilizing M. marburgensis in a reference experiment. Therefore, M. thermaggregans can be regarded as a CH4 cell factory highly suited to be applicable for CO2-BMP.

Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD+ (Rnf) as Electron Acceptors: A Historical Review

Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F₄₂₀H₂, H₂, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E₀′ = −420 mV) with NADH (−320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (−10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H₂-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F₄₂₀H₂-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms—in which they have been found—are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO₂ fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD⁺ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.

Biological hydrogen methanation - A review

Surplus energy out of fluctuating energy sources like wind and solar energy is strongly increasing. Biological hydrogen (H₂) methanation (BHM) is a highly promising approach to move the type of energy from electricity to natural gas via electrolysis and the subsequent step of the Sabatier-reaction. This review provides an overview of the numerous studies concerning the topic of BHM. The technical and biological parameters regarding the research results of these studies are compared and analyzed hereafter. A holistic view on how to overcome physical limitations of the fermentation process, such as gas-liquid mass transfer or a rise of the pH value, and on the enhancement of environmental circumstances for the bacterial biomass are delivered within. With regards to ex-situ methanation, the evaluated studies show a distinct connection between methane production and the methane percentage in the off-gas.

Non-autotrophic methanogens dominate in anaerobic digesters

Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.

Biochemistry of Methyl-Coenzyme M Reductase

Methanogens are masters of CO2 reduction. They conserve energy by coupling H2 oxidation to the reduction of CO2 to CH4, the primary constituent of natural gas. They also generate methane by the reduction of acetic acid, methanol, methane thiol, and methylamines. Methanogens produce 109 tons of methane per year and are the major source of the earth’s atmospheric methane. Reverse methanogenesis or anaerobic methane oxidation, which is catalyzed by methanotrophic archaea living in consortia among bacteria that can act as an electron acceptor, is responsible for annual oxidation of 108 tons of methane to CO2. This chapter briefly describes the overall process of methanogenesis and then describes the enzymatic mechanism of the nickel enzyme, methyl-CoM reductase (MCR), the key enzyme in methane synthesis and oxidation. MCR catalyzes the formation of methane and the heterodisulfide (CoBSSCoM) from methyl-coenzyme M (methyl-CoM) and coenzyme B (HSCoB). Uncovering the mechanistic and molecular details of MCR catalysis is critical since methane is an abundant and important fuel and is the second (to CO2) most prevalent greenhouse gas.

Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions

5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.

Response of a rice paddy soil methanogen to syntrophic growth as revealed by transcriptional analyses

Members of Methanocellales are widespread in paddy field soils and play the key role in methane production. These methanogens feature largely in these organisms’ adaptation to low H2 and syntrophic growth with anaerobic fatty acid oxidizers. The adaptive mechanisms, however, remain unknown. In the present study, we determined the transcripts of 21 genes involved in the key steps of methanogenesis and acetate assimilation of Methanocella conradii HZ254, a strain recently isolated from paddy field soil. M. conradii was grown in monoculture and syntrophically with Pelotomaculum thermopropionicum (a propionate syntroph) or Syntrophothermus lipocalidus (a butyrate syntroph). Comparison of the relative transcript abundances showed that three hydrogenase-encoding genes and all methanogenesis-related genes tested were upregulated in cocultures relative to monoculture. The genes encoding formylmethanofuran dehydrogenase (Fwd), heterodisulfide reductase (Hdr), and the membrane-bound energy-converting hydrogenase (Ech) were the most upregulated among the evaluated genes. The expression of the formate dehydrogenase (Fdh)-encoding gene also was significantly upregulated. In contrast, an acetate assimilation gene was downregulated in cocultures. The genes coding for Fwd, Hdr, and the D subunit of F420-nonreducing hydrogenase (Mvh) form a large predicted transcription unit; therefore, the Mvh/Hdr/Fwd complex, capable of mediating the electron bifurcation and connecting the first and last steps of methanogenesis, was predicted to be formed in M. conradii. We propose that Methanocella methanogens cope with low H2 and syntrophic growth by (i) stabilizing the Mvh/Hdr/Fwd complex and (ii) activating formatedependent methanogenesis.

Maximizing efficiency of rumen microbial protein production

Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen.

Microbial diversity in innovative mesophilic/thermophilic temperature-phased anaerobic digestion of sludge

Anaerobic digestion (AD) is one of the few sustainable technologies that both produce energy and treat waste streams. Driven by a complex and diverse community of microbes, AD may be affected by different factors, many of which also influence the composition and activity of the microbial community. In this study, the biodiversity of microbial populations in innovative mesophilic/thermophilic temperature-phased AD of sludge was evaluated by means of fluorescence in situ hybridization (FISH). The increase of digestion temperature drastically affected the microbial composition and selected specialized biomass. Hydrogenotrophic Methanobacteriales and the protein fermentative bacterium Coprothermobacter spp. were identified in the thermophilic anaerobic biomass. Shannon-Weaver diversity (H') and evenness (E) indices were calculated using FISH data. Species richness was lower under thermophilic conditions compared with the values estimated in mesophilic samples, and it was flanked by similar trend of the evenness indicating that thermophilic communities may be therefore more susceptible to sudden changes and less prompt to adapting to operative variations.

Thermophilic anaerobic digestion of thermal pretreated sludge: role of microbial community structure and correlation with process performances

Thermal hydrolysis pretreatment coupled with Thermophilic Anaerobic Digestion (TAD) for Waste Activated Sludge (WAS) treatment is a promising combination to improve biodegradation kinetics during stabilization. However, to date there is a limited knowledge of the anaerobic biomass composition and its impact on TAD process performances. In this study, the structure and dynamics of the microbial communities selected in two semi-continuous anaerobic digesters, fed with untreated and thermal pretreated sludge, were investigated. The systems were operated for 250 days at different organic loading rate. 16S rRNA gene clonal analysis and Fluorescence In Situ Hybridization (FISH) analyses allowed us to identify the majority of bacterial and archaeal populations. Proteolytic Coprothermobacter spp. and hydrogenotrophic Methanothermobacter spp. living in strict syntrophic association were found to dominate in TAD process. The establishment of a syntrophic proteolytic pathway was favoured by the high temperature of the process and enhanced by the thermal pretreatment of the feeding sludge. Proteolytic activity, alone or with thermal pretreatment, occurred during TAD as proven by increasing concentration of soluble ammonia and soluble COD (sCOD) during the process. However, the availability of a readily biodegradable substrate due to pretreatment allowed to significant sCOD removals (more than 55%) corresponding to higher biogas production in the reactor fed with thermal pretreated sludge. Microbial population dynamics analysed by FISH showed that Coprothermobacter and Methanothermobacter immediately established a stable syntrophic association in the reactor fed with pretreated sludge in line with the overall improved TAD performances observed under these conditions.

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH₄ mitigation at the levels of microbiota composition and transcriptional regulation.

Transcription regulation in the third domain

The ability of organisms to sense and respond to their environment is essential to their survival. This is no different for members of the third domain of life, the Archaea. Archaea are found in diverse and often extreme habitats. However, their ability to sense and respond to their environment at the level of gene expression has been understudied when compared to bacteria and eukaryotes. Over the last decade, the field has expanded, and a variety of unique and interesting regulatory schemes have been unraveled. In this review, the current state of knowledge of archaeal transcription regulation is explored.

Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis

Hydrogenotrophic methanogenic Archaea are defined by an H2 requirement for growth. Despite this requirement, many hydrogenotrophs are also capable of growth with formate as an electron donor for methanogenesis. While certain responses of these organisms to hydrogen availability have been characterized, responses to formate starvation have not been reported. Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H2 excess or formate excess. Analysis of the growth yields of several mutants suggests that this phenomenon occurs independently of the storage of intracellular carbon or a transcriptional response to methanogenesis. Using microarray analysis, we found that the expression of genes encoding coenzyme F420-dependent steps of methanogenesis, including one of two formate dehydrogenases, increased with H2 starvation but with formate occurred at high levels regardless of limitation or excess. One gene, encoding H2-dependent methylene-tetrahydromethanopterin dehydrogenase, decreased in expression with either H2 limitation or formate limitation. Expression of genes for the second formate dehydrogenase, molybdenum-dependent formylmethanofuran dehydrogenase, and molybdenum transport increased specifically with formate limitation. Of the two formate dehydrogenases, only the first could support growth on formate in batch culture where formate was in excess.

Functional responses of methanogenic archaea to syntrophic growth

Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H₂ directly as reductant, versus those using the reduced deazaflavin (coenzyme F₄₂₀). The greater importance of direct reduction by H₂ was supported by improved syntrophic growth of a deletion mutant in an F₄₂₀-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism.

Linking energy production and protein synthesis in hydrogenotrophic methanogens

Hydrogenotrophic methanogens possessing the hydrogen-dependent dehydrogenase Hmd also encode paralogs of this protein whose function is poorly understood. Here we present biochemical evidence that the two inactive Hmd paralogs of Methanocaldococcus jannaschii, HmdII and HmdIII, form binary and ternary complexes with several components of the protein translation apparatus. HmdII and HmdIII, but not the active dehydrogenase Hmd, bind with micromolar binding affinities to a number of tRNAs and form ternary complexes with tRNA(Pro) and prolyl-tRNA synthetase (ProRS). Fluorescence spectroscopy experiments also suggest that binding of HmdII and ProRS involves distinct binding determinants on the tRNA. These biochemical data suggest the possibility of a regulatory link between energy production and protein translation pathways that may allow a rapid cellular response to altered environmental conditions.

Comparative proteomic analysis of Methanothermobacter themautotrophicus ΔH in pure culture and in co-culture with a butyrate-oxidizing bacterium

To understand the physiological basis of methanogenic archaea living on interspecies H₂ transfer, the protein expression of a hydrogenotrophic methanogen, Methanothermobacter thermautotrophicus strain ΔH, was investigated in both pure culture and syntrophic coculture with an anaerobic butyrate oxidizer Syntrophothermus lipocalidus strain TGB-C1 as an H₂ supplier. Comparative proteomic analysis showed that global protein expression of methanogen cells in the model coculture was substantially different from that of pure cultured cells. In brief, in syntrophic coculture, although methanogenesis-driven energy generation appeared to be maintained by shifting the pathway to the alternative methyl coenzyme M reductase isozyme I and cofactor F₄₂₀-dependent process, the machinery proteins involved in carbon fixation, amino acid synthesis, and RNA/DNA metabolisms tended to be down-regulated, indicating restrained cell growth rather than vigorous proliferation. In addition, our proteome analysis revealed that α subunits of proteasome were differentially acetylated between the two culture conditions. Since the relevant modification has been suspected to regulate proteolytic activity of the proteasome, the global protein turnover rate could be controlled under syntrophic growth conditions. To our knowledge, the present study is the first report on N-acetylation of proteasome subunits in methanogenic archaea. These results clearly indicated that physiological adaptation of hydrogenotrophic methanogens to syntrophic growth is more complicated than that of hitherto proposed.

More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus

The hydrogenotrophic methanogens Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus can easily be mass cultured. They have therefore been used almost exclusively to study the biochemistry of methanogenesis from H₂ and CO₂, and the genomes of these two model organisms have been sequenced. The close relationship of the two organisms is reflected in their genomic architecture and coding potential. Within the 1,607 protein coding sequences (CDS) in common, we identified approximately 200 CDS required for the synthesis of the enzymes, coenzymes, and prosthetic groups involved in CO₂ reduction to methane and in coupling this process with the phosphorylation of ADP. Approximately 20 additional genes, such as those for the biosynthesis of F₄₃₀ and methanofuran and for the posttranslational modifications of the two methyl-coenzyme M reductases, remain to be identified.

Studying gene regulation in methanogenic archaea

Methanogenic archaea are a unique group of strictly anaerobic microorganisms characterized by their ability, and dependence, to convert simple C1 and C2 compounds to methane for growth. The major models for studying the biology of methanogens are members of the Methanococcus and Methanosarcina species. Recent development of sophisticated tools for molecular analysis and for genetic manipulation allows investigating not only their metabolism but also their cell cycle, and their interaction with the environment in great detail. One aspect of such analyses is assessment and dissection of methanoarchaeal gene regulation, for which, at present, only a handful of cases have been investigated thoroughly, partly due to the great methodological effort required. However, it becomes more and more evident that many new regulatory paradigms can be unraveled in this unique archaeal group. Here, we report both molecular and physiological/genetic methods to assess gene regulation in Methanococcus maripaludis and Methanosarcina acetivorans, which should, however, be applicable for other methanogens as well.

Correlation of methane production and functional gene transcriptional activity in a peat soil

The transcription dynamics of subunit A of the key gene in methanogenesis (methyl coenzyme M reductase; mcrA) was studied to evaluate the relationship between process rate (methanogenesis) and gene transcription dynamics in a peat soil ecosystem. Soil methanogen process rates were determined during incubation of peat slurries at temperatures from 4 to 37 degrees C, and real-time quantitative PCR was applied to quantify the abundances of mcrA genes and transcripts; corresponding transcriptional dynamics were calculated from mcrA transcript/gene ratios. Internal standards suggested unbiased recovery of mRNA abundances in comparison to DNA levels. In comparison to those in pure-culture studies, mcrA transcript/gene ratios indicated underestimation by 1 order of magnitude, possibly due to high proportions of inactive or dead methanogens. Methane production rates were temperature dependent, with maxima at 25 degrees C, but changes in abundance and transcription of the mcrA gene showed no correlation with temperature. However, mcrA transcript/gene ratios correlated weakly (regression coefficient = 0.76) with rates of methanogenesis. Methanogen process rates increased over 3 orders of magnitude, while the corresponding maximum transcript/gene ratio increase was only 18-fold. mcrA transcript dynamics suggested steady-state expression in peat soil after incubation for 24 and 48 h, similar to that in stationary-phase cultures. mcrA transcript/gene ratios are therefore potential in situ indicators of methanogen process rate changes in complex soil systems.

Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide

Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp(-1)) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO(2) but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII-c(3), Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2.

Specific DNA binding of a potential transcriptional regulator, inosine 5'-monophosphate dehydrogenase-related protein VII, to the promoter region of a methyl coenzyme m reductase I-encoding operon retrieved from Methanothermobacter thermautotrophicus strain DeltaH

Two methyl coenzyme M reductases (MCRs) encoded by the mcr and mrt operons of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus DeltaH are expressed in response to H(2) availability. In the present study, cis elements and trans-acting factors responsible for the gene expression of MCRs were investigated by using electrophoretic mobility shift assay (EMSA) and affinity particle purification. A survey of their operator regions by EMSA with protein extracts from mrt-expressing cultures restricted them to 46- and 41-bp-long mcr and mrt upstream regions, respectively. Affinity particle purification of DNA-binding proteins conjugated with putative operator regions resulted in the retrieval of a protein attributed to IMP dehydrogenase-related protein VII (IMPDH VII). IMPDH VII is predicted to have a winged helix-turn-helix DNA-binding motif and two cystathionine beta-synthase domains, and it has been suspected to be an energy-sensing module. EMSA with oligonucleotide probes with unusual sequences showed that the binding site of IMPDH VII mostly overlaps the factor B-responsible element-TATA box of the mcr operon. The results presented here suggest that IMPDH VII encoded by MTH126 is a plausible candidate for the transcriptional regulator of the mcr operon in this methanogen.

Archaeal chromatin proteins histone HMtB and Alba have lost DNA-binding ability in laboratory strains of Methanothermobacter thermautotrophicus

Alignments of the sequences of the all members of the archaeal histone and Alba1 families of chromatin proteins identified isoleucine residues, I19 in HMtB and I39 in MtAlba, in Methanothermobacter thermautotrophicus, at locations predicted to be directly involved in DNA binding. In all other HMfB family members, residue 19 is an arginine (R19), and either arginine or lysine is present in almost all other Alba1 family members at the structural site equivalent to I39 in MtAlba. Electrophoretic mobility shift assays revealed that recombinant HMtB and MtAlba do not bind DNA, but variants constructed with R19 and R39, respectively, bound DNA; and whereas MtAlba(I19) did not bind RNA, MtAlba(R19) bound both single stranded RNA and tRNA. Amplification and sequencing of MT0254 (encodes HMtB) and MT1483 (encodes MtAlba) from several Methanothermobacter thermautotrophicus lineages has revealed that HMtB and MtAlba had arginine residues at positions 19 and 39, respectively, in the original isolate and that spontaneous mutations must have occurred, and been fixed, in some laboratory lineages that now have HMtB(I19) and MtAlba(I39). The retention of these variants suggests some continuing functions and fusion of the HMtB(I19) sequence to HMtA2 resulted in a protein that folds to form a histone fold heterodimer that binds and compacts DNA. The loss of DNA binding by HMtB(I19) does not therefore prevent HMtB from participating in DNA interactions as one partner of an archaeal histone heterodimer.

Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli

Methanothermobacter thermautotrophicus strain DeltaH is a model hydrogenotrophic methanogen, for which the complete genome sequence and extensive biochemical information are available. Little is known, however, about how this organism regulates its cellular functions in response to environmental stimuli. In this study, whole-genome oligonucleotide microarrays were constructed for M. thermautotrophicus and used to gain insights into how this organism responds to different environmental stimuli, including hydrogen depletion, shifts in pH and temperature and the occurrence of toxics (hydrogen peroxide and ammonia). Our analysis confirmed that methanogenesis genes (including mtd, mer, frh and mcr) were upregulated under hydrogen-limited conditions, while some of them were affected by other environmental stimuli. Concerning stress responses of this organism, several unique features were revealed. First, there was no universal stress response in this organism. Second, genes for alternative redox enzymes, such as rubrerythrin, were upregulated under the oxidative stress, but those for typical antioxidant enzymes were not. Third, genes relevant to the modification of cell surface structures were differentially expressed under stress conditions. Finally, energy-requiring CO(2) assimilation systems were downregulated under stress conditions. These findings suggest that M. thermautotrophicus has complex transcriptional regulation mechanisms that facilitate it to survive in unstable ecosystems such as an anaerobic digester.

Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea

The use of molecular hydrogen as electron donor for energy generation is a defining characteristic of the hydrogenotrophic methanogens, an ancient group that dominates the phylum Euryarchaeota. We present here a global study of changes in mRNA abundance in response to hydrogen availability for a hydrogenotrophic methanogen. Cells of Methanococcus maripaludis were grown by using continuous culture to deconvolute the effects of hydrogen limitation and growth rate, and microarray analyses were conducted. Hydrogen limitation markedly increased mRNA levels for genes encoding enzymes of the methanogenic pathway that reduce or oxidize the electron-carrying deazaflavin, coenzyme F(420). F(420)-dependent redox functions in energy-generating metabolism are characteristic of the methanogenic Archaea, and the results show that their regulation is distinct from other redox processes in the cell. Rapid growth increased mRNA levels of the gene for an unusual hydrogenase, the hydrogen-dependent methylenetetrahydromethanopterin dehydrogenase.

Coupling of Methanothermobacter thermautotrophicus methane formation and growth in fed-batch and continuous cultures under different H2 gassing regimens

In nature, H2- and CO2-utilizing methanogenic archaea have to couple the processes of methanogenesis and autotrophic growth under highly variable conditions with respect to the supply and concentration of their energy source, hydrogen. To study the hydrogen-dependent coupling between methanogenesis and growth, Methanothermobacter thermautotrophicus was cultured in a fed-batch fermentor and in a chemostat under different 80% H(2)-20% CO2 gassing regimens while we continuously monitored the dissolved hydrogen partial pressures (pH2). In the fed-batch system, in which the conditions continuously changed the uptake rates by the growing biomass, the organism displayed a complex and yet defined growth behavior, comprising the consecutive lag, exponential, and linear growth phases. It was found that the in situ hydrogen concentration affected the coupling between methanogenesis and growth in at least two respects. (i) The microorganism could adopt two distinct theoretical maximal growth yields (YCH4 max), notably approximately 3 and 7 g (dry weight) of methane formed mol-1, for growth under low (pH2 < 12 kPa)- and high-hydrogen conditions, respectively. The distinct values can be understood from a theoretical analysis of the process of methanogenesis presented in the supplemental material associated with this study. (ii) The in situ hydrogen concentration affected the "specific maintenance" requirements or, more likely, the degree of proton leakage and proton slippage processes. At low pH2 values, the "specific maintenance" diminished and the specific growth yields approached YCH4 max, indicating that growth and methanogenesis became fully coupled.

Association between Archaeal prolyl- and leucyl-tRNA synthetases enhances tRNA(Pro) aminoacylation

Aminoacyl-tRNA synthetase-containing complexes have been identified in different eukaryotes, and their existence has also been suggested in some Archaea. To investigate interactions involving aminoacyl-tRNA synthetases in Archaea, we undertook a yeast two-hybrid screen for interactions between Methanothermobacter thermautotrophicus proteins using prolyl-tRNA synthetase (ProRS) as the bait. Interacting proteins identified included components of methanogenesis, protein-modifying factors, and leucyl-tRNA synthetase (LeuRS). The association of ProRS with LeuRS was confirmed in vitro by native gel electrophoresis and size exclusion chromatography. Determination of the steady-state kinetics of tRNA(Pro) charging showed that the catalytic efficiency (k(cat)/K(m)) of ProRS increased 5-fold in the complex with LeuRS compared with the free enzyme, whereas the K(m) for proline was unchanged. No significant changes in the steady-state kinetics of LeuRS aminoacylation were observed upon the addition of ProRS. These findings indicate that ProRS and LeuRS associate in M. thermautotrophicus and suggest that this interaction contributes to translational fidelity by enhancing tRNA aminoacylation by ProRS.

Shotgun Proteomics of Methanococcus jannaschii and Insights into Methanogenesis

Methanococcus jannaschii is an autotrophic hyperthermophilic archaeon isolated from an oceanic hydrothermal vent. Its primary pathway for energy production is methanogenesis from H2 and CO2. High-throughput Multidimensional Protein Identification Technology based on microcapillary LC/LC/ MS/MS was used to investigate the proteome of M. jannaschii and the methanogenesis pathway in cells grown in complex medium with high H2 supply. A total of 963 proteins have been unambiguously identified. The identified proteins represent approximately 54% of the whole genome of M. jannaschii. About 44% of the identified proteins are either conserved hypothetical or hypothetical proteins. We identified 83-95% of the proteins predicted to be involved in amino acid biosynthesis, cellular processes, central intermediary metabolism, energy metabolism, protein synthesis, transcription, and purine, pyridine, nucleoside, and nucleotide synthesis. Over 40% of these proteins have better than 50% sequence coverage. Approximately 90% of the predicted methanogenesis proteins were detected. In contrast, only 27-37% of predicted hypothetical proteins, proteins involved in transport and binding, and proteins with regulatory functions were identified. High peptide number, spectrum count, and sequence coverage have been used as indicators of high expression levels and are in good agreement with codon bias analysis. Predicted intein peptides were detected in MJ1043 (DNA-directed RNA polymerase, subunit A"), MJ0542 (phosphoenolpyruvate synthase), MJ0782 (transcription initiation factor IIB), and MJ1422 (putative replication factor C subunit). New peptides created by protein splicing were detected in MJ0885 (DNA dependent DNA polymerase), MJ0542, and MJ0782. The methanogenesis pathway and the enzymes involved are also discussed.

Methane production by mixed ruminal cultures incubated in dual-flow fermentors

This study evaluated the effects of dilution rate and forage-to-concentrate ratio on gas production by rumen microbes. Continuous cultures were used to monitor methane production at three liquid dilution rates (3.2, 6.3, or 12.5%/h) and three forage-to-concentrate ratios (70:30, 50:50, or 30:70). Filtered ruminal contents were allowed 6 d of adaptation to diets followed by 7 d of data collection. Forage consisted of pelleted alfalfa and the concentrate mix included ground corn, soybean meal, and a mineral and vitamin premix. The experiment was replicated in a split-plot design. Total volatile fatty acid production averaged 58.0 mmol/d and was not affected by treatment. Molar proportion of acetate increased with increasing forage-to-concentrate ratio. Molar proportion of propionate tended to decrease at dilution rate of 12.5%/h and increased with the medium and low forage-to-concentrate ratio. Culture pH tended to be greater at a dilution rate of 12.5%/h. Methane production that was calculated from stoichiometric equations was not affected by treatments. However, methane production based on methane concentration in fermentor headspace resulted in an interaction effect of treatments. Stoichiometric equations underestimated methane output at higher dilution rates and with high forage diets. Total diet fermentability was lowest at dilution rate of 3.2%/h. Increasing dilution rates increased microbial yield; increasing the proportion of concentrate improved microbial efficiency. Dilution rate and forage-to-concentrate ratio altered the partition of substrate by microbes. Methane production based on actual concentrations differed from values estimated using stoichiometry of end-product appearance.

Differential expression of methanogenesis genes of Methanothermobacter thermoautotrophicus (formerly Methanobacterium thermoautotrophicum) in pure culture and in cocultures with fatty acid-oxidizing syntrophs

The expression of genes involved in methanogenesis in a thermophilic hydrogen-utilizing methanogen, Methanothermobacter thermoautotrophicus strain TM, was investigated both in a pure culture sufficiently supplied with H(2) plus CO(2) and in a coculture with an acetate-oxidizing hydrogen-producing bacterium, Thermacetogenium phaeum strain PB, in which hydrogen partial pressure was constantly kept very low (20 to 80 Pa). Northern blot analysis indicated that only the mcr gene, which encodes methyl coenzyme M reductase I (MRI), catalyzing the final step of methanogenesis, was expressed in the coculture, whereas mcr and mrt, which encodes methyl coenzyme M reductase II (MRII), the isofunctional enzyme of MRI, were expressed at the early to late stage of growth in the pure culture. In contrast to these two genes, two isofunctional genes (mtd and mth) for N(5),N(10)-methylene-tetrahydromethanopterin dehydrogenase, which catalyzes the fourth step of methanogenesis, and two hydrogenase genes (frh and mvh) were expressed both in a pure culture and in a coculture at the early and late stages of growth. The same expression pattern was observed for Methanothermobacter thermoautotrophicus strain DeltaH cocultured with a thermophilic butyrate-oxidizing syntroph, Syntrophothermus lipocalidus strain TGB-C1. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole proteins of M. thermoautotrophicus strain TM obtained from a pure culture and a coculture with the acetate-oxidizing syntroph and subsequent N-terminal amino acid sequence analysis confirmed that MRI and MRII were produced in the pure culture, while only MRI was produced in the coculture. These results indicate that under syntrophic growth conditions, the methanogen preferentially utilizes MRI but not MRII. Considering that hydrogenotrophic methanogens are strictly dependent for growth on hydrogen-producing fermentative microbes in the natural environment and that the hydrogen supply occurs constantly at very low concentrations compared with the supply in pure cultures in the laboratory, the results suggest that MRI is an enzyme primarily functioning in natural methanogenic ecosystems.

TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIEalpha

In the archaeon Methanobacterium thermoautotrophicum, MTH1669 encodes a protein with a sequence related to the N-terminal sequences of the alpha-subunits of eucaryal general transcription factor TFIIE. The recombinant MTH1669 gene product has been purified and shown to stimulate transcription in vitro from M. thermoautotrophicum promoters that were almost inactive or much less active in reaction mixtures that contained only M. thermoautotrophicum RNA polymerase, TATA-binding protein and transcription factor B. As all complete archaeal genome sequences contain an MTH1669 homolog, the protein encoded by this gene is apparently the first characterized example of a transcription activator, here designated TFE, that may be universally present in the Archaea.