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At least 145 records · Page 8

Methyl-Based Methanogenesis: an Ecological and Genomic Review

Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. In this study, we also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.

methanogens↗

Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi

Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal Archaeoglobi have long been considered nonmethanogenic and their evolutionary history remains elusive. Here, three high-quality metagenomic-assembled genomes (MAGs) retrieved from high-temperature oil reservoir and hot springs, together with three newly assembled Archaeoglobi MAGs from previously reported hot spring metagenomes, are demonstrated to represent a novel genus of Archaeoglobaceae, “Candidatus Methanomixophus.” All “Ca. Methanomixophus” MAGs encode an M methyltransferase (MTR) complex and a traditional type of methyl-coenzyme M reductase (MCR) complex, which is different from the divergent MCR complexes found in “Ca. Polytropus marinifundus.” In addition, “Ca. Methanomixophus dualitatem” MAGs preserve the genomic capacity for dissimilatory sulfate reduction. Comparative phylogenetic analysis supports a laterally transferred origin for an MCR complex and vertical heritage of the MTR complex in this lineage. Metatranscriptomic analysis revealed concomitant in situ activity of hydrogen-dependent methylotrophic methanogenesis and heterotrophic fermentation within populations of “Ca. Methanomixophus hydrogenotrophicum” in a high-temperature oil reservoir.

59 BASIC BIOLOGICAL SCIENCES↗

Proteomic Analysis of Methanococcus voltae Grown in the Presence of Mineral and Nonmineral Sources of Iron and Sulfur

Iron sulfur (Fe-S) proteins are essential and ubiquitous across all domains of life, yet the mechanisms underpinning assimilation of iron (Fe) and sulfur (S) and biogenesis of Fe-S clusters are poorly understood. This is particularly true for anaerobic methanogenic archaea, which are known to employ more Fe-S proteins than other prokaryotes. Here, we utilized a deep proteomics analysis of Methanococcus voltae A3 cultured in the presence of either synthetic pyrite (FeS 2 ) or aqueous forms of ferrous iron and sulfide to elucidate physiological responses to growth on mineral or nonmineral sources of Fe and S. The liquid chromatography-mass spectrometry (LCMS) shotgun proteomics analysis included 77% of the predicted proteome. Through a comparative analysis of intra- and extracellular proteomes, candidate proteins associated with FeS 2 reductive dissolution, Fe and S acquisition, and the subsequent transport, trafficking, and storage of Fe and S were identified. The proteomic response shows a large and balanced change, suggesting that M. voltae makes physiological adjustments involving a range of biochemical processes based on the available nutrient source. Among the proteins differentially regulated were members of core methanogenesis, oxidoreductases, membrane proteins putatively involved in transport, Fe-S binding ferredoxin and radical S-adenosylmethionine proteins, ribosomal proteins, and intracellular proteins involved in Fe-S cluster assembly and storage. This work improves our understanding of ancient biogeochemical processes and can support efforts in biomining of minerals. Clusters of iron and sulfur are key components of the active sites of enzymes that facilitate microbial conversion of light or electrical energy into chemical bonds. The proteins responsible for transporting iron and sulfur into cells and assembling these elements into metal clusters are not well understood. Using a microorganism that has an unusually high demand for iron and sulfur, we conducted a global investigation of cellular proteins and how they change based on the mineral forms of iron and sulfur. Understanding this process will answer questions about life on early earth and has application in biomining and sustainable sources of energy.

59 BASIC BIOLOGICAL SCIENCES↗

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH 4 ), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH 4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH 4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH 4 fluxes. CH 4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH 4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH 4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH 4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH 4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH 4 oxidation pathways in mitigating CH 4 emissions in Amazonian floodplains.

16S rRNA sequencing↗

Four families of folate-independent methionine synthases

Although most organisms synthesize methionine from homocysteine and methyl folates, some have “core” methionine synthases that lack folate-binding domains and use other methyl donors. In vitro , the characterized core synthases use methylcobalamin as a methyl donor, but in vivo , they probably rely on corrinoid (vitamin B12-binding) proteins. We identified four families of core methionine synthases that are distantly related to each other (under 30% pairwise amino acid identity). From the characterized enzymes, we identified the families MesA, which is found in methanogens, and MesB, which is found in anaerobic bacteria and archaea with the Wood-Ljungdahl pathway. A third uncharacterized family, MesC, is found in anaerobic archaea that have the Wood-Ljungdahl pathway and lack known forms of methionine synthase. We predict that most members of the MesB and MesC families accept methyl groups from the iron-sulfur corrinoid protein of that pathway. The fourth family, MesD, is found only in aerobic bacteria. Using transposon mutants and complementation, we show that MesD does not require 5-methyltetrahydrofolate or cobalamin. Instead, MesD requires an uncharacterized protein family (DUF1852) and oxygen for activity.

59 BASIC BIOLOGICAL SCIENCES↗

NREL's 1MW Water Electrolysis Stack Performance Validation to Pilot-Scale Renewable Natural Gas Production [Slides]

NREL has designed, built, and operates a 1MW water electrolyzer balance-of-plant to support industrial partners and the U.S. Department of Energy in developing next-generation PEM stacks to reduce the cost of hydrogen production. With that hydrogen, we are developing, innovating and de-risking a biomethanation process capable of megawatt-scale deployment that upgrades biogas waste streams to produce pipeline quality renewable natural gas (RNG). Biomethanation is a two-step process using a methanogenic microorganism to convert renewable hydrogen (H 2 ) and waste carbon dioxide (CO 2 ) to renewable methane (CH 4 ) - the primary component in natural gas. Using biogenic CO 2 from biogas sources like dairies, wastewater treatment plants, and landfills allows production of this drop-in direct replacement fuel. Research projects and future R&D topics are also discussed during the presentation.

08 HYDROGEN↗

Bioindicator “fingerprints” of methane-emitting thermokarst features in Alaskan soils

Permafrost thaw increases the bioavailability of ancient organic matter, facilitating microbial metabolism of volatile organic compounds (VOCs), carbon dioxide, and methane (CH 4 ). The formation of thermokarst (thaw) lakes in icy, organic-rich Yedoma permafrost leads to high CH 4 emissions, and subsurface microbes that have the potential to be biogeochemical drivers of organic carbon turnover in these systems. However, to better characterize and quantify rates of permafrost changes, methods that further clarify the relationship between subsurface biogeochemical processes and microbial dynamics are needed. In this study, we investigated four sites (two well-drained thermokarst mounds, a drained thermokarst lake, and the terrestrial margin of a recently formed thermokarst lake) to determine whether biogenic VOCs (1) can be effectively collected during winter, and (2) whether winter sampling provides more biologically significant VOCs correlated with subsurface microbial metabolic potential. During the cold season (March 2023), we drilled boreholes at the four sites and collected cores to simultaneously characterize microbial populations and captured VOCs. VOC analysis of these sites revealed “fingerprints” that were distinct and unique to each site. Total VOCs from the boreholes included > 400 unique VOC features, including > 40 potentially biogenic VOCs related to microbial metabolism. Subsurface microbial community composition was distinct across sites; for example, methanogenic archaea were far more abundant at the thermokarst site characterized by high annual CH 4 emissions. The results obtained from this method strongly suggest that ∼10% of VOCs are potentially biogenic, and that biogenic VOCs can be mapped to subsurface microbial metabolisms. By better revealing the relationship between subsurface biogeochemical processes and microbial dynamics, this work advances our ability to monitor and predict subsurface carbon turnover in Arctic soils.

anaerobic degradation↗

Eight Up-Coming Biotech Tools to Combat Climate Crisis

Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood–Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.

54 ENVIRONMENTAL SCIENCES↗

Archaeal protein containing domain of unknown function 2193 undergoes oligomeric reconfiguration upon iron–sulfur cluster binding

Methanogenic archaea are particularly rich in iron–sulfur proteins, yet their roles remain largely enigmatic. Here, we characterized aMethanococcus voltae(Mvo) protein from the domain of unknown function (DUF) 2193 family, a group of proteins present primarily in archaea and characterized by a conserved cysteine‐rich C‐terminal motif.MvoDUF2193 was heterologously expressed and characterized by a range of spectroscopic and analytical methods. The results demonstrate thatMvoDUF2193 binds a single [4Fe–4S] cluster per subunit and that cluster occupancy regulates the transition from an apo tetramer to a [4Fe–4S] monomeric form. We hypothesize thatMvoDUF2193 serves a regulatory role in the cell, mediated by [Fe–S] cluster binding and changes in oligomeric state.

Biochemistry & Molecular Biology↗

Candidatus Nanopusillus

The genus Candidatus Nanopusillus is comprised of small coccoid cells (~100–400 nm) that live epibiotically on the surface of archaeal hosts. The first described species, Candidatus Nanopusillus acidilobi, is an anaerobic, hyperthermophilic acidophile whose best growth is observed at 82°C, pH 3.6, cultivated from a hot spring in Yellowstone National Park. Ca. Nanopusillus acidilobi cells associate with the Crenarchaeota host organism Acidilobus sp. 7A. Archaeal flagella (archaella) have been predicted from the genome sequence and shown to be expressed in the proteome. Additionally, a second putative species, Candidatus Nanopusillus massiliensis, was recently reported from human dental plaque and associates with the methanogen Methanobrevibacter oralis. The genome consists of a single scaffold which is highly fragmented by spans of ambiguous nucleotides, with 16S rRNA gene fragments from Bacteria. Both species have small genomes (~0.6 Mb) encoding few biosynthetic genes and no apparent ATP synthase complex genes, suggesting that the nanoarchaeotes rely on their host for the production of major cellular precursors.

acidophile↗

Development of molecular cluster models to probe pyrite surface reactivity

Abstract The recent discovery that anaerobic methanogens can reductively dissolve pyrite and utilize dissolution products as a source of iron and sulfur to meet their biosynthetic demands for these elements prompted the development of atomic‐scale nanoparticle models, as maquettes of reactive surface sites, for describing the fundamental redox steps that take place at the mineral surface during reduction. The given report describes our computational approach for modeling n (FeS 2 ) nanoparticles originated from mineral bulk structure. These maquettes contain a comprehensive set of coordinatively unsaturated Fe (II) sites that are connected via a range of persulfide (S 2 2− ) ligation. In addition to the specific maquettes with n = 8, 18, and 32 FeS 2 units, we established guidelines for obtaining low‐energy structures by considering the pattern of ionic, covalent, and magnetic interactions among the metal and ligand sites. The developed models serve as computational nano‐reactors that can be used to describe the reductive dissolution mechanism of pyrite to better understand the reactive sites on the mineral, where microbial extracellular electron‐transfer reactions can occur.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Differential effects of press vs. pulse seawater intrusion on microbial communities of a tidal freshwater marsh

Abstract Tidal freshwater marshes (TFMs) are threatened by seawater intrusion, which can affect microbial communities and alter biogeochemical processes. Here, we report on a long‐term, large‐scale manipulative field experiment that investigated continuous (press) and episodic (pulse, 2 months/yr) inputs of brackish water on microbial communities in a TFM. After 2.5 yr, microbial diversity was lower in press treatments than in control (untreated) plots whereas diversity in pulse plots was unaffected by brackish water additions. Sulfate reducer abundance increased in response to both press and pulse treatments whereas methanogens did not differ among treatments. Our results, along with other lab and field measurements that show reduced soil respiration and extracellular enzyme activity suggest that continuous seawater intrusion will decrease macrophyte C inputs that reduce bacterial diversity in ways that also diminish ecosystem carbon cycling.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial communities for valorizing biomass using the carboxylate platform to produce volatile fatty acids: A review

The carboxylate platform employs a diverse microbial consortium of anaerobes in which the methanogens are inhibited. Nearly all biomass components are digested to a mixture of C1-C8 monocarboxylic acids and their corresponding salts. The methane-arrested anaerobic digestion proceeds readily without needing to sterilize biomass or equipment. It accepts a wide range of feedstocks (e.g., agricultural residues, municipal solid waste, sewage sludge, animal manure, food waste, algae, and energy crops), and produces high product yields. This review highlights several important aspects of the platform, including its thermodynamic underpinnings, influences of inoculum source and operating conditions on product formation, and downstream chemical processes that convert the carboxylates to hydrocarbon fuels and oxygenated chemicals. Furthermore, this review further establishes the carboxylate platform as a viable and economical route to industrial biomass utilization.

59 BASIC BIOLOGICAL SCIENCES↗

Machine learning-aided inverse design for biogas upgrading through biological CO 2 conversion

The biogas upgrading process through bioconversion of CO 2 to CH 4 by hydrogenotrophic methanogens is an attractive strategy for energy decarbonation. Many studies have optimized operational parameters to improve key performance indicators such as CH 4 % and H 2 utilization efficiency. However, inconsistent laboratory conditions make it challenging to compare results. Existing models for analyzing operating conditions can only assess the impact of individual conditions and lack the ability to simultaneously optimize multiple conditions. To address this, two XGBoost models were built with R 2 of 0.779 and 0.903 with data collected from literatures and were embedded into multi-objective partitive swarm optimization algorithm to optimal operating conditions. Predictions were compared with experimental validations under optimized conditions, revealing an 8.50% and 2.95% relative error in CH 4 % and H 2 conversion rate, respectively. This approach streamlines biogas upgrading processes, offering a data-driven solution to enhance efficiency and consistency in the pursuit of sustainable methane production.

Biogas upgrading↗

Improving anaerobic digestion of sewage sludge to renewable natural gas by the Advanced Pretreatment & Anaerobic Digestion technology (APAD): Pilot testing

Conventional anaerobic digestion (AD) of sewage sludge in wastewater treatment facilities suffers from low carbon conversion efficiency (CCE = 40%) and requires costly CO2 removal for injection of the produced CH4 into the natural gas grid. To address these limitations, we developed the Advanced Pretreatment and Anaerobic Digestion (APAD) process. This integrates Advanced Wet Oxidation & Steam Explosion (AWOEx) pretreatment of residual sludge after conventional AD, followed by biogas upgradation using a novel methanogenic strain, Methanothermobacter wolfeii BSEL, converting CO2 with H2 into CH4 or RNG (renewable natural gas). Pilot-scale results demonstrated that AWOEx pretreatment achieved a CCE of 62% for the residual sludge, 68% higher than the conventional AD process. The CH4 production was further increased by 79%. Subsequent biogas upgrading in a trickling bed reactor with H2 further enhanced total methane output by 100% and resulted in a final CO2 concentration of =3%. The integrated APAD process achieved a remarkable overall CCE of 83%, resulting in a 200% increase in RNG output when compared to conventional AD. Techno-economic analysis revealed that AWOEx pretreatment alone reduced sludge treatment costs from $494 to $253 per ton of dry solids. The complete APAD process incurred a higher cost of treatment of $530 per ton, driven by prices for bottled H2. The process did, however, show gains in energy recovery and decarbonization. Renewable H2, which may reduce in price in the near future, can positively improve the economics of biogas upgrading for the APAD process.

Life Cycle Assessment (LCA)↗

Non-mercury methylating microbial taxa are integral to understanding links between mercury methylation and elemental cycles in marine and freshwater sediments

The goal of this study was to explore the role of non-mercury (Hg) methylating taxa in mercury methylation and to identify potential links between elemental cycles and Hg methylation. Statistical approaches were utilized to investigate the microbial community and biochemical functions in relation to methylmercury (MeHg) concentrations in marine and freshwater sediments. Sediments were collected from the methylation zone (top 15 cm) in four Hg-contaminated sites. Both abiotic (e.g., sulfate, sulfide, iron, salinity, total organic matter, etc.) and biotic factors (e.g., hgcA, abundances of methylating and non-methylating taxa) were quantified. Random forest and stepwise regression were performed to assess whether non-methylating taxa were significantly associated with MeHg concentration. Co-occurrence and functional network analyses were constructed to explore associations between taxa by examining microbial community structure, composition, and biochemical functions across sites. Regression analysis showed that approximately 80% of the variability in sediment MeHg concentration was predicted by total mercury concentration, the abundances of Hg methylating taxa, and the abundances of the non-Hg methylating taxa. The co-occurrence networks identified Paludibacteraceae and Syntrophorhabdaceae as keystone non Hg methylating taxa in multiple sites, indicating the potential for syntrophic interactions with Hg methylators. Strong associations were also observed between methanogens and sulfate-reducing bacteria, which were likely symbiotic associations. The functional network results suggested that non-Hg methylating taxa play important roles in sulfur respiration, nitrogen respiration, and the carbon metabolism-related functions methylotrophy, methanotrophy, and chemoheterotrophy. Interestingly, keystone functions varied by site and did not involve carbon- and sulfur-related functions only. In conclusion, our findings highlight associations between methylating and non-methylating taxa and sulfur, carbon, and nitrogen cycles in sediment methylation zones, with implications for predicting and understanding the impact of climate and land/sea use changes on Hg methylation.

54 ENVIRONMENTAL SCIENCES↗

Clumped 13 CH 2 D and 12 CHD 2 compositions of methyl groups from wood and synthetic monomers: Methods, experimental and theoretical calibrations, and initial results

Methyl groups are found in numerous biogenic and synthetic materials including geologically preserved materials such as wood. The carbon and hydrogen isotope compositions of methyl groups are used as tracers in biogeochemical cycles, as paleothermometers, and to determine the hydrogen isotopic composition of ancient rain. Here we present analyses of resolved 13 C–D ( 13 CH 2 D) and D–D ( 12 CHD 2 ) clumped isotope compositions of methyl groups as new variables for the study of methyl groups in the present and past. We first present chemical methods to extract, purify, and derivatize methyl groups from methoxyl (R–O–CH 3 ) groups as CH 3 F and CH 3 Cl, and high-resolution mass spectrometric techniques to determine the clumped isotope compositions of these species. We achieve precisions for 13 C–D clumping of ±0.25‰ and D–D clumping of ±2.5‰. We anchor our clumped isotopic measurements to a thermodynamic reference frame by first calculating the theoretical temperature dependences of 13 C–D and D–D clumping in CH 3 Cl, then placing our measurements onto this reference frame through experimental internal isotopic equilibration of CH 3 Cl at 200 °C. Finally, we provide and analyze an initial dataset of clumped 13 C–D and D–D compositions of methyl groups from various commercial/synthetic monomers and environmental woods. We observe ranges in clumped isotope compositions of ~11‰ in 13 C–D and ~48‰ in D–D, and systematic differences within these ranges between methyl groups from commercial monomers and wood. Specifically, commercial clumped 13 C–D compositions are between 0 and 3‰, which correspond to apparent equilibrium temperatures between 170 °C and the infinite temperature limit. In contrast, the clumped 13 C–D compositions of wood methoxyl groups are distinctively high (9.50–11.25‰) and 3–6‰ higher than would be expected if formed in internal isotopic equilibrium at Earth-surface temperatures. Commercial/synthetic methyl and wood methoxyl clumped D–D compositions are also distinct: -5 to +13‰ in commercial monomers vs. -35 to -8‰ in wood—such negative values cannot result from formation in isotopic equilibrium and require kinetic processes to have occurred. Overall, these results indicate that wood methoxyl groups are formed out of isotopic equilibrium and that clumped isotope compositions of methyl groups may be useful tracers of methyl group sources and sinks in the environment. For instance, isotopic clumping in methyl groups may be useful for understanding controls on isotopic clumping in methane produced by methylotrophic methanogens.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Contributions of anoxic microsites to soil carbon protection across soil textures

Anoxic microsites, zones of oxygen depletion in otherwise oxic soils, may slow soil C turnover. However, the abundance of anoxic microsites and their contribution to soil C protection is yet undefined. In this study, we determine the contribution of anoxic microsites to soil C protection in soils of three distinct textures (clay loam, loam, sandy loam) across a range of soil moistures. We examined the influence of soil oxygen supply by increasing oxygen content in the incubation atmosphere (oxygen enrichment) and through disaggregation. We attributed increases in CO 2 efflux to the aeration of anoxic microsites. The contribution of anoxic microsites to soil C protection increased with decreasing clay content. Clay loam CO 2 efflux was relatively unaffected by aeration. Moderately moist, loam soils had CO 2 effluxes that did not increase with oxygen enrichment but increased by 375% upon disaggregation. Sandy loam soil CO 2 efflux increased by 50–75% with oxygen enrichment and 250% with disaggregation. Geochemical and microbial data reveal that anoxic microsite abundance also increased with decreasing clay content. The proportion of acid extractable Fe present as Fe(II) increased with decreasing clay content, and methanogens were more abundant in loam and sandy loam soils. Our results suggest that oxygen demand, rather than supply, can regulate anoxic microsite formation and that anoxic protection of soil C can be diminished through physical disruption of soil structure. Our findings further illustrate that anoxic microsites should be included in conceptual models of soil C protection to avoid soil C loss and improve predictions of soil C response to disturbance.

58 GEOSCIENCES↗