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Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.ImportanceAs the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Methane (CH4) is a potent greenhouse gas emitted by archaea in anaerobic environments such as wetland soils. Tidal freshwater wetlands are predicted to become increasingly saline as sea levels rise due to climate change. Previous work has shown that increases in salinity generally decrease CH4 emissions, but with considerable variation, including instances where salinization increased CH4 flux. We measured microbial community composition, biogeochemistry, and CH4 flux from field samples and lab experiments from four different sites across a wide geographic range. We sought to assess how site differences and microbial ecology affect how CH4 emissions are influenced by salinization. CH4 flux was generally, but not always, positively correlated with CO2 flux, soil carbon, ammonium, phosphate, and pH. Methanogen guilds were positively correlated with CH4 flux across all sites, while methanotroph guilds were both positively and negatively correlated with CH4 depending on site. There was mixed support for negative relationships between CH4 fluxes and concentrations of alternative electron acceptors and abundances of taxa that reduce them. CH4/salinity relationships ranged from negative, to neutral, to positive and appeared to be influenced by site characteristics such as pH and plant composition, which also likely contributed to site differences in microbial communities. The activity of site-specific microbes that may respond differently to low-level salinity increases is likely an important driver of CH4/salinity relationships. Our results suggest several factors that make it difficult to generalize CH4/salinity relationships and highlight the need for paired microbial and flux measurements across a broader range of sites.

Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH4). While sulfate loading from seawater intrusion may reduce CH4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH4 fluxes observed in oligohaline sediments.IMPORTANCELow-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.

Methanogenic archaea are chemolithotrophic prokaryotes that can reduce carbon dioxide with hydrogen gas to form methane. These microorganisms make a significant contribution to the global carbon cycle, with methanogenic archaea from anoxic environments estimated to contribute > 500 million tons of global methane annually. Archaeal methanogenesis is dependent on the methanofurans; aminomethylfuran containing coenzymes that act as the primary C1 acceptor molecule during carbon dioxide fixation. Although the biosynthetic pathway to the methanofurans has been elucidated, structural adaptations which confer thermotolerance to Mfn enzymes from extremophilic archaea are yet to be investigated. Here we focus on the methanofuran biosynthetic enzyme MfnB, which catalyses the condensation of two molecules of glyceralde-3-phosphate to form 4‑(hydroxymethyl)-2-furancarboxaldehyde-phosphate. In this study, MfnB enzymes from the hyperthermophile Methanocaldococcus jannaschii and the mesophile Methanococcus maripaludis have been recombinantly overexpressed and purified to homogeneity. Thermal unfolding studies, together with steady-state kinetic assays, demonstrate thermoadaptation in the M. jannaschii enzyme. Molecular dynamics simulations have been used to provide a structural explanation for the observed properties. These reveal a greater number of side chain interactions in the M. jannaschii enzyme, which may confer protection from heating effects by enforcing spatial residue constraints. [ABSTRACT FROM AUTHOR]

Semi‐biological photosynthesis combines synthetic photosensitizers with microbial catalysts to produce sustainable fuels and chemicals from CO2. However, the inefficient transfer of photoexcited electrons to microbes leads to limited CO2 utilization, restricting the catalytic performance of such biohybrid assemblies. Here, we introduce a biological engineering solution to address the inherently sluggish electron uptake mechanism of a methanogen, Methanosarcina barkeri (M. barkeri), by coculturing it with an electron transport specialist, Geobacter sulfurreducens KN400 (KN400), an adapted strain rich with multiheme c‐type cytochromes (c‐Cyts) and electrically conductive protein filaments (e‐PFs) made of polymerized c‐Cyts with enhanced capacity for extracellular electron transfer (EET). Integration of this M. barkeri‐KN400 co‐culture with a synthetic photosensitizer, carbon nitride, demonstrates that c‐Cyts and e‐PFs, emanating from live KN400, transport photoexcited electrons efficiently from the carbon nitride to M. barkeri for methanogenesis with remarkable long‐term stability and selectivity. The demonstrated cooperative interaction between two microbes via direct interspecies electron transfer (DIET) and the photosensitizer to assemble a semi‐biological photocatalyst introduces an ecosystem engineering strategy in solar chemistry to drive sustainable chemical reactions. [ABSTRACT FROM AUTHOR]

Introduction: Molecular hydrogen is produced by the fermentation of organic matter and consumed by organisms including hydrogenotrophic methanogens and sulfate reducers in anoxic marine sediment. The thermodynamic feasibility of these metabolisms depends strongly on organic matter reactivity and hydrogen concentrations; low organic matter reactivity and high hydrogen concentrations can inhibit fermentation so when organic matter is poor, fermenters might form syntrophies with methanogens and/or sulfate reducers who alleviate thermodynamic stress by keeping hydrogen concentrations low and tightly controlled. However, it is unclear how these metabolisms effect porewater hydrogen concentrations in natural marine sediments of different organic matter reactivities. Methods: We measured aqueous concentrations of hydrogen, sulfate, methane, dissolved inorganic carbon, and sulfide with high-depth-resolution and 16S rRNA gene assays in sediment cores with low carbon reactivity in White Oak River (WOR) estuary, North Carolina, and those with high carbon reactivity in Cape Lookout Bight (CLB), North Carolina. We calculated the Gibbs energies of sulfate reduction and hydrogenotrophic methanogenesis. Results: Hydrogen concentrations were significantly higher in the sulfate reduction zone at CLB than WOR (mean: 0.716 vs. 0.437 nM H2) with highly contrasting hydrogen profiles. At WOR, hydrogen was extremely low and invariant (range: 0.41–0.52 nM H2) in the upper 15 cm. Deeper than 15 cm, hydrogen became more variable (range: 0.312–2.56 nM H2) and increased until methane production began at ~30 cm. At CLB, hydrogen was highly variable in the upper 15 cm (range: 0.08–2.18 nM H2). Ratios of inorganic carbon production to sulfate consumption show AOM drives sulfate reduction in WOR while degradation of organics drive sulfate reduction in CLB. Discussion: We conclude more reactive organic matter increases hydrogen concentrations and their variability in anoxic marine sediments. In our AOM-dominated site, WOR, sulfate reducers have tight control on hydrogen via consortia with fermenters which leads to the lower observed variance due to interspecies hydrogen transfer. After sulfate depletion, hydrogen accumulates and becomes variable, supporting methanogenesis. This suggests that CLB's more reactive organic matter allows fermentation to occur without tight metabolic coupling of fermenters to sulfate reducers, resulting in high and variable porewater hydrogen concentrations that prevent AOM from occurring through reverse hydrogenotrophic methanogenesis. [ABSTRACT FROM AUTHOR]

Despite the importance of alkaline seafloor hydrothermal vents in broadening our understanding of deep-sea hydrothermal ecosystems, little is known about the mobility and concentrations of micronutrient transition metals in these environments. Here, we present new analyses of micronutrient transition metal concentrations in vent fluids from the iconic Lost City Hydrothermal Field (LCHF) and report concentrations of Fe = 2.9–18.3 µmol/kg, Zn = 1.30–5.86 µmol/kg, Cu = 0.43–5.06 µmol/kg, Ni = 86.4–556 nmol/kg, Mn = 8.3–274 nmol/kg, V = 25.9–127 nmol/kg, Mo = 24–94 nmol/kg, Co = 8.0–135 nmol/kg, W = 4.8–16 nmol/kg, and Cd = 1.7–4.5 nmol/kg. We additionally present results of a hydrothermal lherzolite alteration experiment conducted at 300 °C, 500 bar. Transition metal concentrations and major chemical parameters of experimental reaction fluids are broadly similar to LCHF vent fluids, indicating that transition metal concentrations in LCHF vent fluids, and alkaline hydrothermal fluids more generally, reflect metal solubility controlled by underlying rock-buffered hydrothermal reactions. Concentrations of Ni and Mo are especially noteworthy because of their recognized importance for biological methanogenesis (Ni) and nitrogen fixation (Mo). When compared with known biological thresholds, our findings indicate that Ni concentrations in LCHF vent fluids are sufficient to support the robust methane-metabolizing microbial communities observed in the immediate vicinity of LCHF vents and suggest that Ni availability influences the spatial distribution of LCHF methanogens. Furthermore, our laboratory hydrothermal experiments demonstrate that Mo concentrations of similar magnitude to those observed in LCHF vent fluids (and also modern seawater) can be obtained by hydrothermal alteration of ultramafic rocks with Mo-free (Na, Ca) Cl aqueous solution. Thus, we conclude that alkaline hydrothermal fluids were likely similarly enriched in Mo prior to oxidation of the Earth's atmosphere and ocean, providing localized Mo-rich geochemical environments capable of supporting Mo-dependent nitrogen fixation at currently recognized threshold concentrations. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate the effects of different concentrations of hydrogen-rich water (HRW) on in vitro rumen fermentation characteristics and the dynamics of bacterial communities. The experiment included four treatment groups: a control (CON) and hydrogen-rich water (HRW) at 200, 400, and 800 ppb. Each group was analyzed at 12-hour (h) and 48-hour (h) time points with five replicates, totaling 40 samples. The experimental results highlighted the HRW800ppb group as the top production in terms of gas production and CH4 content. In contrast, the HRW200ppb group exhibited significantly lower methane levels at both 12 h and 48 h (P < 0.05). Regarding rumen fermentation, the HRW400ppb group significantly increased the levels of ammonia nitrogen (NH3-N) and microbial crude protein (MCP) at 12 h fermentation, but reduced the dry matter degradation rate (P < 0.05). After 48 h, the HRW400ppb group had highest MCP content (P < 0.05), but no significant differences in NH3-N and dry matter degradation rate compared with the CON group (P > 0.05). Although HRW did not significantly benefit the synthesis of total volatile fatty acids (TVFA) and individual VFA, the HRW800ppb group significantly increased the ratio of acetate to propionate (P < 0.05). Based on CH4 emissions and MCP synthesis, we selected the HRW400ppb group for subsequent bacterial community analysis. Bacterial community analysis showed that at 12 h, compared with the CON group, the Bacterial community analysis revealed that the HRW400ppb group had significant increases in the Simpson index, Firmicutes, Streptococcus, Schwartzia, Prevotellaceae_YAB2003_group, and Oribacterium, and decreases in Prevotella, Ruminobacter, Succinivibrio, unclassified_Succinivibrionaceae, and Prevotellaceae_UCG-003 (P < 0.05). At 48 h, the Prevotellaceae_YAB2003_group and Oribacterium abundances continued to rise significantly, while Rikenellaceae_RC9_gut_group and Succiniclasticum abundances fell in the HRW400ppb group (P < 0.05). Correlation analysis indicated a negative link between CH4 and Streptococcus, and a positive correlation between the abundance of Rikenellaceae_RC9_gut_group and CH4. Collectively, these results indicate that HRW can modulate rumen fermentation and microbial community structure to reduce methane emissions without significantly affecting VFA synthesis, highlighting its potential as drinking water for enhancing ruminant nutrition and mitigating the environmental impact of livestock farming. [ABSTRACT FROM AUTHOR]

Fluctuations in the production of renewable-based electricity have to be compensated by converting and storing the energy for later use. Underground methanation reactors (UMR) are a promising technology to address this issue. The idea is to create a controlled bio-reactor system in a porous underground formation, where hydrogen obtained from renewable energy sources by electrolysis and carbon dioxide from industrial sources are fed into the reactor and converted into methane. Microorganisms, known as methanogenic archaea, catalyze the chemical reaction by using the two non-organic substrates as nutrients for their growth and for their respiratory metabolism. The generated synthetic methane is renewable and capable to compete with the fossil methane. Mathematical models play an important role in the design and planning of such systems. Usually, a numerical solution of the model is required since complex initial-boundary problems cannot be solved analytically. In this paper, an existing bio-reactive transport model for UMR is simplified to such an extent that an analytical solution of the advection-dispersion-reaction equation can be applied. A second analytical solution is used for the case without dispersion. The analytical solutions are shown for both the educt (hydrogen) and the reaction product (methane). In order to examine the applicability of the analytical models, they are compared with the significantly more complex numerical model for a 1D case and a 3D case. It was shown that there is an acceptable agreement between the two analytical solutions and the numerical solution in different spatial plots of hydrogen and methane concentration and in the methane concentration in the withdrawn gas. The mean absolute error in the mole fraction is well below 0.015 in most cases. The spatial distribution of the hydrogen concentration in the comparison to the 3D case shows a higher deviation with a mean absolute error of approx. 0.023. As expected, the model with dispersion shows a slightly lower error in all cases, as only here the gas mixing resulting in smeared displacement fronts can be represented. It is shown that analytical modeling is a good tool to get a first estimation of the behavior of an UMR. It allows to help in the design of well spacing in combination with the injection rate and injected gas composition. Nevertheless, it is recommended to use more complex models for the later detailed analysis, which require a numerical solution. [ABSTRACT FROM AUTHOR]

The first discovery of methanogens led to the formation of a new domain of life known as Archaea. The Archaea domain exhibits properties vastly different from previously known Bacteria and Eucarya domains. However, for a certain multi-step process, a syntrophic relationship between organisms from all domains is needed. This process is called methanogenesis and is defined as the biological production of methane. Different methanogenic pathways prevail depending on substrate availability and the employed order of methanogenic Archaea. Most methanogens reduce carbon dioxide to methane with hydrogen through a hydrogenotrophic pathway. For hydrogen activation, a group of enzymes called hydrogenases is required. Regardless of the methanogenic pathway, electrons are carried between microorganisms by hydrogen. Naturally occurring processes, such as methanogenesis, can be engineered for industrial use. With the growth and emergence of new industries, the amount of produced industrial waste is an ever-growing environmental problem. For successful wastewater remediation, a syntrophic correlation between various microorganisms is needed. The composition of microorganisms depends on wastewater type, organic loading rates, anaerobic reactor design, pH, and temperature. The last step of anaerobic wastewater treatment is production of biomethane by methanogenesis, which is thought to be a cost-effective means of energy production for this renewable biogas. [ABSTRACT FROM AUTHOR]

Precise control of operational parameters in anaerobic digestion reactors is crucial to avoid imbalances that could affect biomethane production and alterations in the microbiota. Restoring the methanogenic microbiota after a failure is essential for recovering methane production, yet no published strategies exist for this recovery. In this study, we restored the methanogenic microbiota in an anaerobic SBR reactor that operates with both biofilm and suspended biomass simultaneously, aiming to treat tequila vinasses. Four strategies were evaluated for restoring the methanogenic microbiota: reducing the initial vinasse concentration, increasing the reaction time (RT), adjusting the carbon/nitrogen (C/N) ratio, and progressively increasing the initial vinasse concentration. Among these, adjusting the C/N ratio emerged as a critical parameter for restoring organic matter removal efficiency and reestablishing methanogenic microbiota. The operational conditions under which the methanogenic activity and microbiota were restored were as follows: Operating the A-SBR with an initial vinasse concentration of 60%, an RT of 168 h, a pH of 6.9 ± 0.2, a temperature of 35 ± 2 °C, and a C/N ratio adjusted to 100/1.9 resulted in stable COD removal efficiency of 93 ± 3% over a year and a high percentage of methanogenic microorganisms in both the suspended microbiota (69%) and biofilm (52%). The normalized methane production (0.332 NL CH4/g CODr) approached the theoretical maximum value (0.35 L CH4/g CODr) after restoring the population and methanogenic activity within the reactor. [ABSTRACT FROM AUTHOR]

Microbial electrosynthesis (MES) has great potential for CO 2 reduction and renewable energy storage. However, high energy consumption and investment costs constrained the practical application of MES. Here, the domestication of halotolerant methanogens was proposed to improve the energy efficiency of MES, and methane metabolism under low and high Na+ concentrations was explored by metagenomic analysis. The Na+ concentration of the catholyte was increased from 4.07 g·L-1 to 23.01 g·L-1, and the reactor maintained great performance after initial inhibition. High-salinity catholyte improved the energy efficiency to 47% and reduced the cathode voltage consumption. Increasing Na+ concentration, microorganisms resisted damage by secreting more extracellular polymers, and maintained methane production through community evolution. The relative abundance of Euryarchaeota increased from 50% to 80%. Methanobrevibacter and Methanobacterium were dominant genera at Na+ of 23.01 g·L-1. Incorporating metagenomic analysis, the methane metabolism at the initial period (Na+:4.07 g·L-1) included a CO 2 -reduction pathway and acetoclastic pathway. However, when Na+ concentration increased to 23.01 g·L-1, the CO 2 -reduction pathway with 4Fe–4S ferredoxin and common pathways was significantly enhanced, in addition, the acetyl metabolism pathway using CO 2 as substrate was also enhanced. Overall, methane metabolism was enhanced, and the metabolic pathways changed with increasing Na⁺ concentration. [Display omitted] • A methanogen community could tolerant 23 g·L-1 Na+ was obtained by domestication. • The halotolerant methanogens improved the energy efficiency of MES by 21%. • The dominant genera were Methanobacterium and Methanobrevibacter accounting for 82%. • The CO 2 -reduction pathway with 4Fe–4S ferredoxin was significantly enhanced. [ABSTRACT FROM AUTHOR]

Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A-cluster within the enzyme acetyl-CoA synthase (ACS) to carbon monoxide (CO) and a methyl group (CH3 +). The methyl group ultimately forms the greenhouse gas methane, whereas CO is converted to the greenhouse gas carbon dioxide (CO2) by a Ni-Fe-S-containing C-cluster within the enzyme carbon monoxide dehydrogenase (CODH). Although structures have been solved of CODH/ACS from acetogens, which use these enzymes to make acetate from CO2, no structure of a CODH/ACS from a methanogen has been reported. In this work, we use cryo-electron microscopy to reveal the structure of a methanogenic CODH and CODH/ACS from Methanosarcina thermophila (MetCODH/ACS). We find that the N-terminal domain of acetogenic ACS, which is missing in all methanogens, is replaced by a domain of CODH. This CODH domain provides a channel for CO to travel between the two catalytic Ni-Fe-S clusters. It generates the binding surface for ACS and creates a remarkably similar CO alcove above the A-cluster using residues from CODH rather than ACS. Comparison of our MetCODH/ACS structure with our MetCODH structure reveals a molecular mechanism to restrict gas flow from the CO channel when ACS departs, preventing CO escape into the cell. Overall, these long-awaited structures of a methanogenic CODH/ACS reveal striking functional similarities to their acetogenic counterparts despite a substantial difference in domain organization. [ABSTRACT FROM AUTHOR]

The ruminal microbiota generates biogenic methane in ruminants. However, the role of host genetics in modifying ruminal microbiota‐mediated methane emissions remains mysterious, which has severely hindered the emission control of this notorious greenhouse gas. Here, we uncover the host genetic basis of rumen microorganisms by genome‐ and transcriptome‐wide association studies with matched genome, rumen transcriptome, and microbiome data from a cohort of 574 Holstein cattle. Heritability estimation revealed that approximately 70% of microbial taxa had significant heritability, but only 43 genetic variants with significant association with 22 microbial taxa were identified through a genome‐wide association study (GWAS). In contrast, the transcriptome‐wide association study (TWAS) of rumen microbiota detected 28,260 significant gene–microbe associations, involving 210 taxa and 4652 unique genes. On average, host genetic factors explained approximately 28% of the microbial abundance variance, while rumen gene expression explained 43%. In addition, we highlighted that TWAS exhibits a strong advantage in detecting gene expression and phenotypic trait associations in direct effector organs. For methanogenic archaea, only one significant signal was detected by GWAS, whereas the TWAS obtained 1703 significant associated host genes. By combining multiple correlation analyses based on these host TWAS genes, rumen microbiota, and volatile fatty acids, we observed that substrate hydrogen metabolism is an essential factor linking host–microbe interactions in methanogenesis. Overall, these findings provide valuable guidelines for mitigating methane emissions through genetic regulation and microbial management strategies in ruminants. Highlights: Using large‐scale matched samples, we reveal the impact of host genetics variants and rumen gene expressions on rumen microbiota in Holstein cattle.Host genetic factors average explained approximately 28% of the microbial abundance variance, whereas rumen gene expression explained 43%.The transcriptome‐wide association study is a promising method for exploring the associations between gene expression and complex phenotypes in direct effector organs.Host–microbial interactions in bovine rumen methanogenesis are possibly involved in substrate hydrogen metabolism and transport. [ABSTRACT FROM AUTHOR]

Increasing plastic pollution is a serious environmental problem as widespread production and inadequate disposal of plastic materials lead to adverse impacts on ecosystems. The structural and functional characteristics of the anaerobic microbial community contacting with extruded polystyrene (XPS) waste were investigated under methanogenic (MG) and nitrate-(NR) and sulfate-reducing (SR) conditions. The presence of XPS in the microbial community was shown to have no negative effect on the processes of biogas formation and, on the contrary, resulted in an increase in the yield of methane and volatile fatty acids and a change in their ratio. Microparticles of different sizes were found in the culture liquid of the variants with XPS: 2.4 × 106/mL (NR), 1.2 × 106/mL (SR), and 0.4 × 106/mL (MG), while no microparticles were found in the control variants. Scanning electron microscopy revealed that in all experimental variants the surface of the polymer became looser, more textured, with formation of irregularities, cracks, and holes. Increased diversity in the microbial community associated with an increase in the number of microbial morphotypes, correlated with the results of high-throughput sequencing of the 16S rRNA gene. When XPS was introduced into an anaerobic community incubated in different donor-acceptor conditions, the number of microbial groups in it increased, as well as the proportion of hydrolytic and acidogenic bacteria (Sedimentibacter, Lentimicrobium), acetogenic syntrophs (Syntrophomonas, Desulfovibrio, Geobacter), and methanogenic archaea (Methanosarcina, Methanobacterium). Our study showed that the XPS waste was not inert for the microbial community, the contact with it resulting in significant changes in its structure and functioning. Changes in the sample surface, emergence of microparticles, and differences in the composition of the intermediate and terminal metabolic products may indicate slow partial degradation of the plastic via fragmentation. However, since the experiments were carried out using household XPS containing various fillers apart from the main polymer, it is probable that, along with polystyrene, additional substances included in its composition (plasticizers, dyes, etc.) are also subject to degradation. The ability of microorganisms to degrade the polymer itself requires further research. [ABSTRACT FROM AUTHOR]

Abstract The objective of this study was to evaluate the effects of different concentrations of hydrogen-rich water (HRW) on in vitro rumen fermentation characteristics and the dynamics of bacterial communities. The experiment included four treatment groups: a control (CON) and hydrogen-rich water (HRW) at 200, 400, and 800 ppb. Each group was analyzed at 12-hour (h) and 48-hour (h) time points with five replicates, totaling 40 samples. The experimental results highlighted the HRW800ppb group as the top production in terms of gas production and CH4 content. In contrast, the HRW200ppb group exhibited significantly lower methane levels at both 12 h and 48 h (P 0.05). Although HRW did not significantly benefit the synthesis of total volatile fatty acids (TVFA) and individual VFA, the HRW800ppb group significantly increased the ratio of acetate to propionate (P

Abstract Background In recent years, there has been a rapid increase in the number of microbial genomes reconstructed through shotgun sequencing, and obtained by newly developed approaches including metagenomic binning and single-cell sequencing. However, our ability to functionally characterize these genomes by experimental assays is orders of magnitude less efficient. Consequently, there is a pressing need for the development of swift and automated strategies for the functional classification of microbial genomes. Results The present work leverages a suite of supervised machine learning algorithms to establish a range of 86 metabolic and other ecological functions, such as methanotrophy and plastic degradation, starting from widely obtainable microbial genome annotations. Tests performed on independent datasets demonstrated robust performance across complete, fragmented, and incomplete genomes above a 70% completeness level for most of the considered functions. Application of the algorithms to the Biogas Microbiome database yielded predictions broadly consistent with current biological knowledge and correctly detecting functionally-related nuances of archaeal genomes. Finally, a case study focused on acetoclastic methanogenesis demonstrated how the developed machine learning models can be refined or expanded with models describing novel functions of interest. Conclusions The resulting tool, MICROPHERRET, incorporates a total of 86 models, one for each tested functional class, and can be applied to high-quality microbial genomes as well as to low-quality genomes derived from metagenomics and single-cell sequencing. MICROPHERRET can thus aid in understanding the functional role of newly generated genomes within their micro-ecological context.

The elevated level of carbon dioxide in the atmosphere has become a pressing concern for environmental health due to its contribution to climate change and global warming. Simultaneously, the energy crisis is a significant issue for both developed and developing nations. In response to these challenges, carbon capture, sequestration, and utilization (CCSU) have emerged as promising solutions within the carbon–neutral bioenergy sector. Numerous technologies are available for CCSU including physical, chemical, and biological routes. The aim of this study is to explore the potential of CCSU technologies, specifically focusing on the use of microorganisms based on their well-established metabolic part. By investigating these biological pathways, we aim to develop sustainable strategies for climate management and biofuel production. One of the key novelties of this study lies in the utilization of microorganisms for CO2 fixation and conversion, offering a renewable and efficient method for addressing carbon emissions. Algae, with its high growth rate and lipid contents, exhibits CO2 fixation capabilities during photosynthesis. Similarly, methanogens have shown efficiency in converting CO2 to methane by methanogenesis, offering a viable pathway for carbon sequestration and energy production. In conclusion, our study highlights the importance of exploring biological pathways, which significantly reduce carbon emissions and move towards a more environmentally friendly future. The output of this review highlights the significant potential of CCSU models for future sustainability. Furthermore, this review has been intensified in the current agenda for reduction of CO2 at considerable extends with biofuel upgrading by the microbial-shift reaction. Graphical abstract for carbon dioxide capture, sequestration, and utilization models [ABSTRACT FROM AUTHOR]

The quest for scientifically advanced and sustainable solutions is driven by growing environmental and economic issues associated with coal mining, processing, and utilization. Consequently, within the coal industry, there is a growing recognition of the potential of microbial applications in fostering innovative technologies. Microbial-based coal solubilization, coal beneficiation, and coal dust suppression are green alternatives to traditional thermochemical and leaching technologies and better meet the need for ecologically sound and economically viable choices. Surfactant-mediated approaches have emerged as powerful tools for modeling, simulation, and optimization of coal-microbial systems and continue to gain prominence in clean coal fuel production, particularly in microbiological co-processing, conversion, and beneficiation. Surfactants (surface-active agents) are amphiphilic compounds that can reduce surface tension and enhance the solubility of hydrophobic molecules. A wide range of surfactant properties can be achieved by either directly influencing microbial growth factors, stimulants, and substrates or indirectly serving as frothers, collectors, and modifiers in the processing and utilization of coal. This review highlights the significant biotechnological potential of surfactants by providing a thorough overview of their involvement in coal biodegradation, bioprocessing, and biobeneficiation, acknowledging their importance as crucial steps in coal consumption. [ABSTRACT FROM AUTHOR]

Holocellulose (HC) fraction extracted from date-pits was evaluated as a novel feed additive for ruminant feeding. This study was performed to investigate the effectiveness of the HC additive on rumen fermentation, methane (CH4) production, and diet degradability over 24 h of in vitro incubation. Three independent incubation trials were conducted over three consecutive weeks, employing the same in vitro methodology to assess four treatment doses in a completely randomized design. The experimental diet incorporated four increasing doses of HC, containing HC at 0 (HC0), 10 (HC10), 20 (HC20), and 30 (HC30) g/kg dry matter (DM). In vitro gas production (GP) and CH4 production, volatile fatty acids (VFAs) concentration, protozoa accounts, degraded organic matter (DOM), metabolizable and net energy (ME and NE), and hydrogen (H2) estimates were measured. No significant differences in ruminal pH were observed as the HC doses gradually increased. All incremental doses of HC additive over 24 h resulted in a linear increase in GP (P < 0.001), DOM (P < 0.001), total VFAs (P = 0.011), and propionate (P < 0.001) concentrations, as well as estimated energy (ME and NE) (P < 0.05) and microbial protein (P = 0.017) values. However, the inclusion of increasing doses of HC in the diet displayed linear reductions in the net CH4 production (ml/kg DOM; P = 0.002), protozoa abundance (P = 0.027); acetate (P = 0.029), and butyrate (P < 0.001) concentrations, the acetate-to-propionate ratio (P < 0.001), and the estimated net H2 production concentration (P = 0.049). Thus, the use of date-pits HC additive generated positive ruminal fermentability, including increased total VFAs and a reduction in the acetate-to-propionate ratio, leading to decreased CH4 output over 24 h of in vitro incubation. Hence, HC could be considered a potent feed additive (at up to 30 g/kg DM), demonstrating promising CH4-mitigating competency and thereby enhancing energy-use efficiency in ruminants. [ABSTRACT FROM AUTHOR]

3-Nitrooxypropanol (3-NOP) is a nitrooxy compound that specifically targets methyl-coenzyme M reductase (MCR), ultimately resulting in a reduction in methane production. In this study, we undertook an in vitro investigation of the effects of different dosages of 3-NOP on ruminal fermentation parameters, methane production, and the microbial community. A single-factor completely randomized design was adopted, comprising a control treatment (C), where no 3-NOP was added to the fermentation substrate, and three 3-NOP treatments, where 0.025 mg (low-dose treatment, LD), 0.05 mg (medium-dose treatment, MD), or 0.1 mg (high-dose treatment, HD) was added to 1 g of fermentation substrate (DM basis), followed by incubation for 24 h in vitro. The results showed that, compared with the control treatment, the three dosages of 3-NOP reduced total gas production, methane production, and acetate production (all p < 0.01). In contrast, 3-NOP treatment increased H2 production and the molar proportions of propionate and butyrate (all p ≤ 0.02), resulting in a decrease in the acetate-propionate ratio (p < 0.01). Meanwhile, the microbial profiles were not altered by the treatments, but the relative abundances of Prevotella, Methanobrevibacter, and Ophryoscolex were increased by the MD and HD treatments (all p < 0.01), whereas those of Methanosarcina, Methanosaeta, Sphaerochaeta, RFN20, Entodinium, and Diplodinium were decreased by the HD treatment (all p ≤ 0.03). Moreover, the results of a correlation analysis showed that there was a certain correlation between these microorganisms and total gas production, methane production, H2 production, acetate, propionate, and butyrate. In summary, under in vitro conditions, the addition of 3-NOP to the diet affected the microbial community structure, thereby altering the ruminal fermentation pattern and reducing methane production. Our results indicated that 0.05 mg per g of dietary DM is the recommended inclusion ratio for 3-NOP in the diet of lambs. [ABSTRACT FROM AUTHOR]

Mitigation of enteric methane (CH4) emissions from ruminant livestock represents an opportunity to improve the sustainability, productivity, and profitability of beef and dairy production. Ruminal methanogenesis can be mitigated via two primary strategies: (1) alternative electron acceptors and (2) enzymatic inhibition of methanogenic pathways. The former utilizes the thermodynamic favorability of certain reactions such as nitrate/nitrite reduction to ammonia (NH3) while the latter targets specific enzymes using structural analogs of CH4 and methanogenic cofactors such as bromochloromethane (BCM). In this study, we investigated the effects of four additives and their combinations on CH4 production by rumen microbes in batch culture. Sodium nitrate (NaNO3), sodium sulfate (Na2SO4), and 3-nitro-1-propionate (3NPA) were included as thermodynamic inhibitors, whereas BCM was included as a enzymatic inhibitor. Individual additives were evaluated at three levels of inclusion in experiments 1 and 2. Highest level of each additive was used to determine the combined effect of NaNO3 + Na2SO4 (NS), NS + 3NPA (NSP), and NSP + BCM (NSPB) in experiments 3 and 4. Experimental diets were high, medium, and low forage diets (HF, MF, and LF, respectively) and consisted of alfalfa hay and a concentrate mix formulated to obtain the following forage to concentrate ratios: 70:30, 50:50, and 30:70, respectively. Diets with additives were placed in fermentation culture bottles and incubated in a water bath (39°C) for 6, 12, or 24h. Microbial DNA was extracted for 16S rRNA and ITS gene amplicon sequencing. In experiments 1 and 2, CH4 concentrations in control cultures decreased in the order of LF, MF, and HF diets, whereas in experiments 3 and 4, CH4 was highest in MF diet followed by HF and LF diets. Culture pH and NH3 in the control decreased in the order of HF, MF, to LF as expected. NaNO3 decreased (p < 0.001) CH4 and butyrate and increased acetate and propionate (p < 0.03 and 0.003, respectively). Cultures receiving NaNO3 had an enrichment of microorganisms capable of nitrate and nitrite reduction. 3NPA also decreased CH4 at 6h with no further decrease at 24 h (p < 0.001). BCM significantly inhibited methanogenesis regardless of inclusion levels as well as in the presence of the thermodynamic inhibitors (p < 0.001) while enriching succinate producers and assimilators as well as propionate producers (p adj < 0.05). However, individual inclusion of BCM decreased total short chain fatty acid (SCFA) concentrations (p < 0.002). Inhibition of methanogenesis with BCM individually and in combination with the other additives increased gaseous H2 concentrations (p < 0.001 individually and 0.028 in combination) while decreasing acetate to propionate ratio (p < 0.001). Only the cultures treated with BCM in combination with other additives significantly (padj < 0.05) decreased the abundance of Methanobrevibacter expressed as log fold change. Overall, the combination of thermodynamic and enzymatic inhibitors presented a promising effect on ruminal fermentation in-vitro, inhibiting methanogenesis while optimizing the other fermentation parameters such as pH, NH3, and SCFAs. Here, we provide a proof of concept that the combination of an electron acceptor and amethane analogmay be exploited to improvemicrobial effciency via methanogenesis inhibition. [ABSTRACT FROM AUTHOR]

The results of long-term studies of the conjugate distribution of methane (CH4) and sulfide sulfur (Ssulfide) concentrations in the bottom sediments of watercourses of the steppe zone of the European part of Russia are analyzed. In addition to CH4 and Ssulfide, Eh and pH values, humidity and density were determined in different sediment horizons; CH4, dry residue, and pH values were determined in water. Concentrations of CH4 in the watercourses vary from <0.1 to 2007.0 μL/L (median 24.3 μL/L), with the largest number of values (72%) in the range 10.1–100.0 μL/L. The concentrations of CH4 and Ssulfide in the bottom sediments of watercourses are quite high and vary, respectively, from <0.01 to 51.0 µg/g of wet sediment (median 1.35 µg/g) and from <0.001 to 4.50 mg/g of wet sediment (median 0.813 mg/g). Usually, the CH4 and Ssulfide concentrations increase from the surface layer to the subsurface horizons, and then decrease. The difference between the distributions of Ssulfide and CH4 is the more frequent occurrence of maximum concentrations of Ssulfide in less deep sediment horizons. Seasonal changes were recorded in the vertical distribution of CH4 and Ssulfide not only in terms of their concentrations, but also in the position of maximum and minimum values. There is a weak positive correlation between the concentrations of CH4 and Ssulfide, which indicates the synchronous formation of these gases in separate layers of sediments of the studied watercourses. The positive correlation established between the CH4 concentrations in water and 0–2 cm layer of bottom sediments indicates that the sediments are an important source of CH4 in water and its emission into the atmosphere. [ABSTRACT FROM AUTHOR]

Background: In recent years, there has been a rapid increase in the number of microbial genomes reconstructed through shotgun sequencing, and obtained by newly developed approaches including metagenomic binning and single-cell sequencing. However, our ability to functionally characterize these genomes by experimental assays is orders of magnitude less efficient. Consequently, there is a pressing need for the development of swift and automated strategies for the functional classification of microbial genomes. Results: The present work leverages a suite of supervised machine learning algorithms to establish a range of 86 metabolic and other ecological functions, such as methanotrophy and plastic degradation, starting from widely obtainable microbial genome annotations. Tests performed on independent datasets demonstrated robust performance across complete, fragmented, and incomplete genomes above a 70% completeness level for most of the considered functions. Application of the algorithms to the Biogas Microbiome database yielded predictions broadly consistent with current biological knowledge and correctly detecting functionally-related nuances of archaeal genomes. Finally, a case study focused on acetoclastic methanogenesis demonstrated how the developed machine learning models can be refined or expanded with models describing novel functions of interest. Conclusions: The resulting tool, MICROPHERRET, incorporates a total of 86 models, one for each tested functional class, and can be applied to high-quality microbial genomes as well as to low-quality genomes derived from metagenomics and single-cell sequencing. MICROPHERRET can thus aid in understanding the functional role of newly generated genomes within their micro-ecological context. [ABSTRACT FROM AUTHOR]

Methanogens often inhabit sulfidic environments that favor the precipitation of transition metals such as iron (Fe) as metal sulfides, including mackinawite (FeS) and pyrite (FeS2). These metal sulfides have historically been considered biologically unavailable. Nonetheless, methanogens are commonly cultivated with sulfide (HS-) as a sulfur source, a condition that would be expected to favor metal precipitation and thus limit metal availability. Recent studies have shown that methanogens can access Fe and sulfur (S) from FeS and FeS2 to sustain growth. As such, medium supplied with FeS2 should lead to higher availability of transition metals when compared to medium supplied with HS-. Here, we examined how transition metal availability under sulfidic (i.e., cells provided with HS-as sole S source) versus non-sulfidic (cells provided with FeS2 as sole S source) conditions impact the metalloproteome of Methanosarcina barkeri Fusaro. To achieve this, we employed size exclusion chromatography coupled with inductively coupled plasma mass spectrometry and shotgun proteomics. Significant changes were observed in the composition and abundance of iron, cobalt, nickel, zinc, and molybdenum proteins. Among the differences were alterations in the stoichiometry and abundance of multisubunit protein complexes involved in methanogenesis and electron transport chains. Our data suggest that M. barkeri utilizes the minimal iron-sulfur cluster complex and canonical cysteine biosynthesis proteins when grown on FeS2 but uses the canonical Suf pathway in conjunction with the tRNA-Sep cysteine pathway for iron-sulfur cluster and cysteine biosynthesis under sulfidic growth conditions. [ABSTRACT FROM AUTHOR]

Various environmental factors, including H2 availability, metabolic tradeoffs, optimal growth temperature, stochasticity, and hydrology, were examined to determine if they affect microbial competition between three autotrophic thermophiles. The thiosulfate reducer Desulfurobacterium thermolithotrophum (Topt72°C) was grown in mono- and coculture separately with the methanogens Methanocaldococcus jannaschii (Topt82°C) at 72°C and Methanothermococcus thermolithotrophicus (Topt65°C) at 65°C at high and low H2 concentrations. Both methanogens showed a metabolic tra deoff shifting from high growth rate-low cell yield at high H2 concentrations to low growth rate-high cell yield at low H2 concentrations and when grown in coculture with the thiosulfate reducer. In 1:1 initial ratios, D. thermolithotrophum outcompeted both methanogens at high and low H2, no H2S was detected on low H2, and it grew with only CO2 as the electron acceptor indicating a similar metabolic tradeoff with low H2. When the initial methanogen-to-thiosulfate reducer ratio varied from 1:1 to 104:1 with high H2, D. thermolithotrophum always outcompeted M. jannaschii at 72°C. However, M. thermolithotrophicus outcompeted D. thermolithotrophum at 65°C when the ratio was 103:1. A reactive transport model that mixed pure hydrothermal fluid with cold seawater showed that hyperthermophilic methanogens dominated in systems where the residence time of the mixed fluid above 72°C was sufficiently high. With shorter residence times, thermophilic thiosulfate reducers dominated. If residence times increased with decreasing fluid temperature along the flow path, then thermophilic methanogens could dominate. Thermophilic methanogen dominance spread to previously thiosulfate-reducer-dominated conditions if the initial ratio of thermophilic methanogen-to-thiosulfate reducer increased. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the sulfur hexafluoride (SF6) tracer technique for estimating methane (CH4) emissions in dual-flow continuous culture systems (DFCCS). In experiment 1 (Exp1), fermenters were filled with water, and known CH4 concentrations (0, 1.35, 2.93, or 4.43 g/d) were injected using permeation tubes with SF6 release rates (3.30 or 9.65 mg/d). Headspace gas was collected using canisters, and the SF6 technique estimated CH4 recovery. Experiment 2 (Exp2) involved a DFCCS fermentation trial with ruminal fluid from three Holstein cows, testing diets with soybean meal or its partial replacement (50%) by Chlorella or Spirulina. Headspace gas was collected at intervals post-feeding. Standard curves for SF6 and CH4 quantification were inadequate for DFCCS samples, with the CH4:SF6 ratio differing from standards, indicating the data needs further SF6 release rate evaluation. In Exp1, a high correlation (r = 0.97) was found between infused and calculated CH4, indicating good repeatability. Low and high SF6 rates performed similarly at low CH4 infusion, but high SF6 overestimated CH4 at high infusion. Exp2 showed CH4 emissions irrespective of SF6 rate and indicated reduced CH4 emissions and increased NDF degradation with algae-containing diets. Further evaluation of the SF6 tracer technique is warranted for DFCCS. [ABSTRACT FROM AUTHOR]

Carbon capture, utilization, and storage (CCUS) is an important component in many national net-zero strategies, and ensuring that CO2 can be safely and economically stored in geological systems is critical. Recent discoveries have shown that microbial processes (e.g., methanogenesis) can modify fluid composition and fluid dynamics within the storage reservoir. Oil reservoirs are under high pressure, but the influence of pressure on the petroleum microbial community has been previously overlooked. To better understand microbial community dynamics in deep oil reservoirs, we designed an experiment to examine the effect of high pressure (12 megapascals [MPa], 60 °C) on nitrate-reducing, sulfate-reducing, and methanogenic enrichment cultures. Cultures were exposed to these conditions for 90 d and compared with a control exposed to atmospheric pressure (0.1 MPa, 60 °C). The degradation characteristic oil compounds were confirmed by thin-layer analysis of oil SARA (saturates, aromatics, resins, and asphaltenes) family component rods. We found that the asphaltene component in crude oil was biodegraded under high pressure, but the concentration of asphaltenes increased under atmospheric pressure. Gas chromatography analyses of saturates showed that short-chain saturates (C8–C12) were biodegraded under high and atmospheric pressure, especially in the methanogenic enrichment culture under high pressure (the ratio of change was −81%), resulting in an increased relative abundance of medium- and long-chain saturates. In the nitrate-reducing and sulfate-reducing enrichment cultures, long-chain saturates (C22–C32) were biodegraded in cultures exposed to high-pressure and anaerobic conditions, with a ratio of change of −8.0% and −2.3%, respectively. However, the relative proportion of long-chain saturates (C22–C32) increased under atmospheric pressure. Gas Chromatography Mass Spectrometry analyses of aromatics showed that several naphthalene series compounds (naphthalene, C1-naphthalene, and C2-naphthalene) were biodegraded in the sulfate-reducing enrichment under both atmospheric pressure and high pressure. Our study has discerned the linkages between the biodegradation characteristics of crude oil and pressures, which is important for the future application of bioenergy with CCUS (bio-CCUS). [ABSTRACT FROM AUTHOR]

Coenzyme F430 is a nickel‐containing tetrapyrrole, serving as the prosthetic group of methyl‐coenzyme M reductase in methanogenic and methanotrophic archaea. During coenzyme F430 biosynthesis, the tetrapyrrole macrocycle is reduced by the nitrogenase‐like CfbC/D system consisting of the reductase component CfbC and the catalytic component CfbD. Both components are homodimeric proteins, each carrying a [4Fe‐4S] cluster. Here, the ligands of the [4Fe‐4S] clusters of CfbC2 and CfbD2 were identified revealing an all cysteine ligation of both clusters. Moreover, the midpoint potentials of the [4Fe‐4S] clusters were determined to be −256 mV for CfbC2 and −407 mV for CfbD2. These midpoint potentials indicate that the consecutive thermodynamically unfavorable 6 individual "up‐hill" electron transfers to the organic moiety of the Ni2+‐sirohydrochlorin a,c‐diamide substrate require an intricate interplay of ATP‐binding, hydrolysis, protein complex formation and release to drive product formation, which is a common theme in nitrogenase‐like systems. [ABSTRACT FROM AUTHOR]

This document is a research article published in the journal Frontiers in Microbiology. It acknowledges the contributions of a researcher named Barny to the field of methanogen research and the broader microbial field. The article highlights Barny's work in clarifying the taxonomy of methanogens and recognizes his wider contributions as an editor. The article also includes information about the funding sources for the research and acknowledges the authors and reviewers who contributed to the research topic. It concludes with a statement about potential conflicts of interest and a note from the publisher. [Extracted from the article]

The aim of this study was to evaluate the effects of the level and type of essential oils (EOs) derived from oregano (ORO), thyme (THO), clove (CLO), and cinnamon (CIO), when used as feed additives, on in vitro rumen fermentation and methanogenesis. This was achieved by conducting a metaanalysis that integrated data from relevant studies. A total of 17 articles were included comprising 154 data points. The collected data were subsequently analysed using a mixed model methodology implemented in a SAS software version 9.4. The findings showed that the level of EOs exerted a significant (P < 0.01) linear effect, resulting in increased pH, decreased volume of total gas, CH4, and NH3, reduced total volatile fatty acids (VFA) levels, dry matter digestibility (DMD), organic matter digestibility (OMD), and bacterial population. A quadratic effect was also observed with respect to reduced (P < 0.01) CO2 and propionate (C3 ) levels. Additionally, the protozoan population demonstrated a linear decrease (P < 0.05), while butyrate (C4) concentration exhibited a quadratic increase (P < 0.05). However, increasing levels of EOs did not affect the acetate (C2)- and methanogen-producing bacterial populations. With respect to different EO types, ORO and THO significantly reduced (P < 0.05) total gas (30–41%) and CH4 production (38–39%) compared to the control. ORO and CLO in turn significantly decreased (P < 0.05) C3 generation (5–7%), while ORO increased C4 levels (14%) compared to the control. Moreover, CLO, CIO, and THY administration led to a decrease in OMD (8–23%). Due to the limited dataset on microbial population, the diverse types of EOs showed no significant impact on bacterial, protozoan, or methanogen populations. In conclusion, while specific doses of EOs can suppress ruminal methane emissions, they can also inhibit rumen fermentation processes. Among the EOs examined, ORO demonstrated the most potent antimicrobial ability against methanogenesis. [ABSTRACT FROM AUTHOR]

The environmental impacts of livestock agriculture include the production of greenhouse gasses (GHG) such as methane (CH4) through enteric fermentation. Recent advances in our understanding of methanogenesis have led to the development of animal feed additives (AFA) that can reduce enteric CH4 emissions. However, many interacting factors impact hydrogen (H2) and CH4 production and AFA efficacy, including animal factors, basal diet, particle and fluid outflow, microbial populations, rumen fluid pH, and fermentative cofactor dynamics. Characterizing the response of rumen fermentation to AFA is essential for optimizing AFA implementation. Mechanistic models of enteric fermentation are constructed to represent physiological and microbial processes in the rumen and can be updated to characterize the dependency of AFA efficacy on basal diet and the impacts of AFA on fermentation. The objective of this article is to review the current state of rumen mechanistic modeling, contrasting the representation of key pools in extant models with a particular emphasis on representation of CH4 production. Additionally, we discuss the first rumen mechanistic models to include AFA and emphasize future model needs for improved representation of rumen dynamics under CH4-inhibition due to AFA supplementation, including the representation of microbial populations, rumen pH, fractional outflow rates, and thermodynamic control of fermentative pathways.

IntroductionMolecular hydrogen is produced by the fermentation of organic matter and consumed by organisms including hydrogenotrophic methanogens and sulfate reducers in anoxic marine sediment. The thermodynamic feasibility of these metabolisms depends strongly on organic matter reactivity and hydrogen concentrations; low organic matter reactivity and high hydrogen concentrations can inhibit fermentation so when organic matter is poor, fermenters might form syntrophies with methanogens and/or sulfate reducers who alleviate thermodynamic stress by keeping hydrogen concentrations low and tightly controlled. However, it is unclear how these metabolisms effect porewater hydrogen concentrations in natural marine sediments of different organic matter reactivities.MethodsWe measured aqueous concentrations of hydrogen, sulfate, methane, dissolved inorganic carbon, and sulfide with high-depth-resolution and 16S rRNA gene assays in sediment cores with low carbon reactivity in White Oak River (WOR) estuary, North Carolina, and those with high carbon reactivity in Cape Lookout Bight (CLB), North Carolina. We calculated the Gibbs energies of sulfate reduction and hydrogenotrophic methanogenesis.ResultsHydrogen concentrations were significantly higher in the sulfate reduction zone at CLB than WOR (mean: 0.716 vs. 0.437 nM H2) with highly contrasting hydrogen profiles. At WOR, hydrogen was extremely low and invariant (range: 0.41–0.52 nM H2) in the upper 15 cm. Deeper than 15 cm, hydrogen became more variable (range: 0.312–2.56 nM H2) and increased until methane production began at ~30 cm. At CLB, hydrogen was highly variable in the upper 15 cm (range: 0.08–2.18 nM H2). Ratios of inorganic carbon production to sulfate consumption show AOM drives sulfate reduction in WOR while degradation of organics drive sulfate reduction in CLB.DiscussionWe conclude more reactive organic matter increases hydrogen concentrations and their variability in anoxic marine sediments. In our AOM-dominated site, WOR, sulfate reducers have tight control on hydrogen via consortia with fermenters which leads to the lower observed variance due to interspecies hydrogen transfer. After sulfate depletion, hydrogen accumulates and becomes variable, supporting methanogenesis. This suggests that CLB’s more reactive organic matter allows fermentation to occur without tight metabolic coupling of fermenters to sulfate reducers, resulting in high and variable porewater hydrogen concentrations that prevent AOM from occurring through reverse hydrogenotrophic methanogenesis.

ABSTRACT The ruminant-microorganism symbiosis is unique by providing high-quality food from fibrous materials but also contributes to the production of one of the most potent greenhouse gases—methane. Mitigating methanogenesis in ruminants has been a focus of interest in the past decades. One of the promising strategies to combat methane production is the use of feed supplements, such as seaweeds, that might mitigate methanogenesis via microbiome modulation and direct chemical inhibition. We conducted in vitro investigations of the effect of three seaweeds (Ascophyllum nodosum, Asparagopsis taxiformis, and Fucus vesiculosus) harvested at different locations (Iceland, Scotland, and Portugal) on methane production. We applied metataxonomics (16S rRNA gene amplicons) and metagenomics (shotgun) methods to uncover the interplay between the microbiome’s taxonomical and functional states, methanogenesis rates, and seaweed supplementations. Methane concentration was reduced by A. nodosum and F. vesiculosus, both harvested in Scotland and A. taxiformis, with the greatest effect of the latter. A. taxiformis acted through the reduction of archaea-to-bacteria ratios but not eukaryotes-to-bacteria. Moreover, A. taxiformis application was accompanied by shifts in both taxonomic and functional profiles of the microbial communities, decreasing not only archaeal ratios but also abundances of methanogenesis-associated functions. Methanobrevibacter “SGMT” (M. smithii, M. gottschalkii, M. millerae or M. thaueri; high methane yield) to “RO” (M. ruminantium and M. olleyae; low methane yield) clades ratios were also decreased, indicating that A. taxiformis application favored Methanobrevibacter species that produce less methane. Most of the functions directly involved in methanogenesis were less abundant, while the abundances of the small subset of functions that participate in methane assimilation were increased.IMPORTANCEThe application of A. taxiformis significantly reduced methane production in vitro. We showed that this reduction was linked to changes in microbial function profiles, the decline in the overall archaeal community counts, and shifts in ratios of Methanobrevibacter “SGMT” and “RO” clades. A. nodosum and F. vesiculosus, obtained from Scotland, also decreased methane concentration in the total gas, while the same seaweed species from Iceland did not.

Abstract The ruminal microbiota generates biogenic methane in ruminants. However, the role of host genetics in modifying ruminal microbiota‐mediated methane emissions remains mysterious, which has severely hindered the emission control of this notorious greenhouse gas. Here, we uncover the host genetic basis of rumen microorganisms by genome‐ and transcriptome‐wide association studies with matched genome, rumen transcriptome, and microbiome data from a cohort of 574 Holstein cattle. Heritability estimation revealed that approximately 70% of microbial taxa had significant heritability, but only 43 genetic variants with significant association with 22 microbial taxa were identified through a genome‐wide association study (GWAS). In contrast, the transcriptome‐wide association study (TWAS) of rumen microbiota detected 28,260 significant gene–microbe associations, involving 210 taxa and 4652 unique genes. On average, host genetic factors explained approximately 28% of the microbial abundance variance, while rumen gene expression explained 43%. In addition, we highlighted that TWAS exhibits a strong advantage in detecting gene expression and phenotypic trait associations in direct effector organs. For methanogenic archaea, only one significant signal was detected by GWAS, whereas the TWAS obtained 1703 significant associated host genes. By combining multiple correlation analyses based on these host TWAS genes, rumen microbiota, and volatile fatty acids, we observed that substrate hydrogen metabolism is an essential factor linking host–microbe interactions in methanogenesis. Overall, these findings provide valuable guidelines for mitigating methane emissions through genetic regulation and microbial management strategies in ruminants.

Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane, and its activity accounts for nearly all biologically produced methane released into the atmosphere. The assembly of MCR is an intricate process involving the installation of a complex set of posttranslational modifications and the unique Ni-containing tetrapyrrole called coenzyme F430. Despite decades of research, details of MCR assembly remain largely unresolved. Here, we report the structural characterization of MCR in two intermediate states of assembly. These intermediate states lack one or both F430 cofactors and form complexes with the previously uncharacterized McrD protein. McrD is found to bind asymmetrically to MCR, displacing large regions of the alpha subunit and increasing active-site accessibility for the installation of F430-shedding light on the assembly of MCR and the role of McrD therein. This work offers crucial information for the expression of MCR in a heterologous host and provides targets for the design of MCR inhibitors.

Abstract Different from the Qaidam basin with about 320 billion m3 microbial gas, only limited microbial gases were found from the Junggar basin with similarly abundant type III kerogen. To determine whether microbial gases have not yet identified, natural gas samples from the Carboniferous to Cretaceous in the Junggar basin have been analyzed for chemical and stable isotope compositions. The results reveal some of the gases from the Mahu sag, Zhongguai, Luliang and Wu-Xia areas in the basin may have mixed with microbial gas leading to straight ethane to butane trends with a “dogleg” light methane in the Chung’s plot. Primary microbial gas from degradation of immature sedimentary organic matter is found to occur in the Mahu sag and secondary microbial gas from biodegradation of oils and propane occurred in the Zhongguai, Luliang and Beisantai areas where the associated oils were biodegraded to produce calcites with δ13C values from + 22.10‰ to + 22.16‰ or propane was biodegraded leading to its 13C enrichment. Microbial CH4 in the Mahu sag is most likely to have migrated up from the Lower Wuerhe Formation coal-bearing strata by the end of the Triassic, and secondary microbial gas in Zhongguai and Beisantan uplifts may have generated after the reservoirs were uplifted during the period of the Middle and Late Jurassic. This study suggests widespread distribution of microbial gas and shows the potential to find large microbial gas accumulation in the basin.

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. 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.

The world's oceans are challenged by climate change linked warming with typically highly populated coastal areas being particularly susceptible to these effects. Many studies of climate change on the marine environment use large, short-term temperature manipulations that neglect factors such as long-term adaptation and seasonal cycles. In this study, a Baltic Sea 'heated' bay influenced by thermal discharge since the 1970s from a nuclear reactor (in relation to an unaffected nearby 'control' bay) was used to investigate how elevated temperature impacts surface water microbial communities and activities. 16S rRNA gene amplicon based microbial diversity and population structure showed no difference in alpha diversity in surface water microbial communities, while the beta diversity showed a dissimilarity between the bays. Amplicon sequencing variant relative abundances between the bays showed statistically higher values for, e.g., Ilumatobacteraceae and Burkholderiaceae in the heated and control bays, respectively. RNA transcript-derived activities followed a similar pattern in alpha and beta diversity with no effect on Shannon's H diversity but a significant difference in the beta diversity between the bays. The RNA data further showed more elevated transcript counts assigned to stress related genes in the heated bay that included heat shock protein genes dnaKJ, the co-chaperonin groS, and the nucleotide exchange factor heat shock protein grpE. The RNA data also showed elevated oxidative phosphorylation transcripts in the heated (e.g., atpHG) compared to control (e.g., atpAEFB) bay. Furthermore, genes related to photosynthesis had generally higher transcript numbers in the control bay, such as photosystem I (psaAC) and II genes (psbABCEH). These increased stress gene responses in the heated bay will likely have additional cascading effects on marine carbon cycling and ecosystem services. [ABSTRACT FROM AUTHOR]

In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) catalyzes the formation of formylmethanofuran through reducing CO2. Heterodisulfide reductase (Hdr) provides two low potential electrons for the Fmd reaction using a flavin‐based electron‐bifurcating mechanism. [NiFe]‐hydrogenase (Mvh) or formate dehydrogenase (Fdh) complexes with Hdr and provides electrons to Hdr from H2 and formate, or the reduced form of F420, respectively. Recently, an Fdh‐Hdr complex was purified as a 3‐MDa megacomplex that contained Fmd, and its three‐dimensional structure was elucidated by cryo‐electron microscopy. In contrast, the Mvh‐Hdr complex has been characterized only as a complex without Fmd. Here, we report the isolation and characterization of a 1‐MDa Mvh‐Hdr‐Fmd megacomplex from Methanothermobacter marburgensis. After anion‐exchange and hydrophobic chromatography was performed, the proteins with Hdr activity eluted in the 1‐ and 0.5‐MDa fractions during size exclusion chromatography. Considering the apparent molecular mass and the protein profile in the fractions, the 1‐MDa megacomplex was determined to be a dimeric Mvh‐Hdr‐Fmd complex. The megacomplex fraction contained a polyferredoxin subunit MvhB, which contains 12 [4Fe‐4S]‐clusters. MvhB polyferredoxin has never been identified in the previously purified Mvh‐Hdr and Fmd preparations, suggesting that MvhB polyferredoxin is stabilized by the binding between Mvh‐Hdr and Fmd in the Mvh‐Hdr‐Fmd complex. The purified Mvh‐Hdr‐Fmd megacomplex catalyzed electron‐bifurcating reduction of [13C]‐CO2 to form [13C]‐formylmethanofuran in the absence of extrinsic ferredoxin. These results demonstrated that the subunits in the Mvh‐Hdr‐Fmd megacomplex are electronically connected for the reduction of CO2, which likely involves MvhB polyferredoxin as an electron relay. [ABSTRACT FROM AUTHOR]

Methane (CH4) is a potent greenhouse gas emitted by archaea in anaerobic environments such as wetland soils. Tidal freshwater wetlands are predicted to become increasingly saline as sea levels rise due to climate change. Previous work has shown that increases in salinity generally decrease CH4 emissions, but with considerable variation, including instances where salinization increased CH4 flux. We measured microbial community composition, biogeochemistry, and CH4 flux from field samples and lab experiments from four different sites across a wide geographic range. We sought to assess how site differences and microbial ecology affect how CH4 emissions are influenced by salinization. CH4 flux was generally, but not always, positively correlated with CO2 flux, soil carbon, ammonium, phosphate, and pH. Methanogen guilds were positively correlated with CH4 flux across all sites, while methanotroph guilds were both positively and negatively correlated with CH4 depending on site. There was mixed support for negative relationships between CH4 fluxes and concentrations of alternative electron acceptors and abundances of taxa that reduce them. CH4/salinity relationships ranged from negative, to neutral, to positive and appeared to be influenced by site characteristics such as pH and plant composition, which also likely contributed to site differences in microbial communities. The activity of site‐specific microbes that may respond differently to low‐level salinity increases is likely an important driver of CH4/salinity relationships. Our results suggest several factors that make it difficult to generalize CH4/salinity relationships and highlight the need for paired microbial and flux measurements across a broader range of sites. Plain Language Summary: Sea level rise will lead to increases in salinity in coastal wetlands and estuaries. Salinity is a key variable that controls the amount of greenhouse gases emitted from coastal wetlands, but we do not know if increases in salinity will increase or decrease emissions of the potent greenhouse gas methane, which is produced by microorganisms in wetlands. We examined salinity‐methane relationships at four different sites in the United States, and assessed how environmental factors and microorganism communities affected those relationships. We found discrepancies in salinity‐methane relationships that are likely driven by site‐specific communities of microorganisms that may respond differently to increasing salinity. Relationships between methane emissions and environmental variables were not consistent across sites, highlighting the difficulty of making generalizations about methane emissions from coastal wetlands and how they will respond to seawater intrusion. Key Points: Salinity‐methane relationships are variable across sitesRelationships between nutrients, alternative electron acceptors, and methane flux were not consistent across sitesCoastal wetland microbial consortia are site‐specific and may respond differently to seawater intrusion, with implications for methane flux [ABSTRACT FROM AUTHOR]

Key message: In upland forests, trunk CH4 emissions exhibit significant intra-individual spatial variability, which was explained by variations in both CH4 concentration and CH4 production rates in the sapwood. Methane (CH4) emissions from tree trunks in upland forests should be scaled accurately to assess the role of tree trunk in the forest CH4 budget. As the chambers used to measure emissions cover only a small part of the large surface area of tree trunks, it is necessary to understand the intra-individual spatial variability of trunk CH4 emissions. To assess this spatial variability, we measured trunk CH4 flux at nine locations per individual on four trees in a cool-temperate upland forest for which microbial production of CH4 inside the trunk is likely an important source of the emission. To know the origin of this variability and the underlying processes, we also measured the potential rate of CH4 production and CH4 concentrations in both sapwood and characterized wood and bark. Up to 15-fold intra-individual spatial variations in CH4 fluxes were observed in target trees. The variability in emissions within an individual was primarily shown by the variation of the sapwood CH4 concentration which was further explained by the variation in potential CH4 production rate. The radial CH4 diffusivity calculated from concentration gradients and emissions was not related to the measured characteristics of either wood or bark. We emphasized the importance of sampling trunk CH4 flux at multiple locations on the surface of a tree trunk in order to capture the spatial variability, a prerequisite for estimating tree-level CH4 emissions. [ABSTRACT FROM AUTHOR]

Hydrocarbon pollution has led to the destruction of farmlands and fishing settlements in the Niger Delta. In this study, DNA metabarcoding was used to investigate bacterial response during the remediation of an artisanal refining site. Total petroleum hydrocarbons reduced from 93,720 mg kg–1 on timepoint zero to 9,029.76 mg kg–1 on day 91. Bacterial species distribution significantly reduced during remediation. The most responsive phyla to the remediation approach were Proteobacteria and Cyanobacteria. Pathways for hydrocarbon degradation were differentially abundant during remediation. Overall, nutrient addition and intermittent tillage improved bacterial energy yield and the degradation of hydrocarbons. [ABSTRACT FROM AUTHOR]

Microbial electrochemical systems (MESs) can enhance methane production in anaerobic digestion, but their performance is hindered by inadequate electron transfer between the cathode and microbes. Magnetite–zeolite (MZ)‐based catalysts accelerate electron exchange; however, the optimal loading of MZ is crucial for maximizing MES performance. In this study, different loadings of the MZ catalyst ranging from 0 to 2 mg cm−2 on the cathode were evaluated to obtain an optimum loading for maximizing methane recovery from MES. Electrochemical analyses demonstrated enhanced electrochemical reduction kinetics of the cathode with increased MZ loading from 0 to 2 mg cm−2. Among the tested loadings, the MES with 1 mg cm−2 MZ on the cathode exhibited the highest methane production rate at 548 mL L−1 d−1, surpassing other MES operations with 2 and 0.5 mg cm−2 (499 and 434 mL L−1 d−1, respectively). Additionally, the MES with 1 mg cm−2 MZ demonstrated the highest soluble chemical oxygen demand removal efficiency of 87% and total coulomb recovery of 1444.06C ± 42.60C, with the lowest amount of volatile fatty acids accumulation. Consequently, MZ is recommended as a superior catalyst for enhancing MES performance and suggested to utilize 1 mg cm−2 MZ loading on the cathode to maximize methane production. [ABSTRACT FROM AUTHOR]

Different from the Qaidam basin with about 320 billion m3 microbial gas, only limited microbial gases were found from the Junggar basin with similarly abundant type III kerogen. To determine whether microbial gases have not yet identified, natural gas samples from the Carboniferous to Cretaceous in the Junggar basin have been analyzed for chemical and stable isotope compositions. The results reveal some of the gases from the Mahu sag, Zhongguai, Luliang and Wu-Xia areas in the basin may have mixed with microbial gas leading to straight ethane to butane trends with a "dogleg" light methane in the Chung's plot. Primary microbial gas from degradation of immature sedimentary organic matter is found to occur in the Mahu sag and secondary microbial gas from biodegradation of oils and propane occurred in the Zhongguai, Luliang and Beisantai areas where the associated oils were biodegraded to produce calcites with δ13C values from + 22.10‰ to + 22.16‰ or propane was biodegraded leading to its 13C enrichment. Microbial CH4 in the Mahu sag is most likely to have migrated up from the Lower Wuerhe Formation coal-bearing strata by the end of the Triassic, and secondary microbial gas in Zhongguai and Beisantan uplifts may have generated after the reservoirs were uplifted during the period of the Middle and Late Jurassic. This study suggests widespread distribution of microbial gas and shows the potential to find large microbial gas accumulation in the basin. [ABSTRACT FROM AUTHOR]

Biowaste fermentation is a promising technology for low‐carbon print bioenergy and biochemical production. Although it is believed that the microbiome determines both the fermentation efficiency and the product profiles of biowastes, the explicit mechanisms of how microbial activity controls fermentation processes remained to be unexplored. The current study investigated the microbiome dynamics and fermentation product profiles of biowaste fermentation under different organic loads (5, 20, and 40 g‐VS/L) and with additives that potentially modulate the fermentation process via methanogenesis inhibition (2‐bromoethanesulfonate) or electron transfer promotion (i.e., reduced iron, magnetite iron, and activated carbon). The overall fermentation products yields were 440, 373 and 208 CH4‐eq/g‐VS for low‐, medium‐ and high‐load fermentation. For low‐ and medium‐load fermentation, volatile fatty acids (VFAs) were first accumulated and were gradually converted to methane. For high‐load fermentation, VFAs were the main fermentation products during the entire fermentation period, accounting for 62% of all products. 16S rRNA‐based analyses showed that both 2‐bromoethanesulfonate addition and increase of organic loads inhibited the activity of methanogens and promoted the activity of distinct VFA‐producing bacterial microbiomes. Moreover, the addition of activated carbon promoted the activity of H2‐producing Bacteroides, homoacetogenic Eubacteriaceae and methanogenic Methanosarcinaceae, whose activity dynamics during the fermentation led to changes in acetate and methane production. The current results unveiled mechanisms of microbiome activity dynamics shaping the biowaste fermentation product profiles and provided the fundamental basis for the development of microbiome‐guided engineering approaches to modulate biowaste fermentation toward high‐value product recovery. [ABSTRACT FROM AUTHOR]

Aquatic ecosystems are large contributors to global methane (CH4) emissions. Eutrophication significantly enhances CH4-production as it stimulates methanogenesis. Mitigation measures aimed at reducing eutrophication, such as the addition of metal salts to immobilize phosphate (PO43−), are now common practice. However, the effects of such remedies on methanogenic and methanotrophic communities—and therefore on CH4-cycling—remain largely unexplored. Here, we demonstrate that Fe(II)Cl2 addition, used as PO43- binder, differentially affected microbial CH4 cycling-processes in field experiments and batch incubations. In the field experiments, carried out in enclosures in a eutrophic pond, Fe(II)Cl2 application lowered in-situ CH4 emissions by lowering net CH4-production, while sediment aerobic CH4-oxidation rates—as found in batch incubations of sediment from the enclosures—did not differ from control. In Fe(II)Cl2-treated sediments, a decrease in net CH4-production rates could be attributed to the stimulation of iron-dependent anaerobic CH4-oxidation (Fe-AOM). In batch incubations, anaerobic CH4-oxidation and Fe(II)-production started immediately after CH4 addition, indicating Fe-AOM, likely enabled by favorable indigenous iron cycling conditions and the present methanotroph community in the pond sediment. 16S rRNA sequencing data confirmed the presence of anaerobic CH4-oxidizing archaea and both iron-reducing and iron-oxidizing bacteria in the tested sediments. Thus, besides combatting eutrophication, Fe(II)Cl2 application can mitigate CH4 emissions by reducing microbial net CH4-production and stimulating Fe-AOM. [ABSTRACT FROM AUTHOR]