Enzymology of one-carbon metabolism in methanogenic pathways

Purification of Waste-Generated Biogas Mixtures Using Covalent Organic Framework's High CO2 Selectivity

Development of crystalline porous materials for selective CO2 adsorption and storage is in high demand to boost the carbon capture and storage (CCS) technology. In this regard, we have developed a β-keto enamine-based covalent organic framework (VM-COF) via the Schiff base polycondensation technique. The as-synthesized VM-COF exhibited excellent thermal and chemical stability along with a very high surface area (1258 m2 g-1) and a high CO2 adsorption capacity (3.58 mmol g-1) at room temperature (298 K). The CO2/CH4 and CO2/H2 selectivities by the IAST method were calculated to be 10.9 and 881.7, respectively, which were further experimentally supported by breakthrough analysis. Moreover, theoretical investigations revealed that the carbonyl-rich sites in a polymeric backbone have higher CO2 binding affinity along with very high binding energy (-39.44 KJ mol-1) compared to other aromatic carbon-rich sites. Intrigued by the best CO2 adsorption capacity and high CO2 selectivity, we have utilized the VM-COF for biogas purification produced by the biofermentation of municipal waste. Compared with the commercially available activated carbon, VM-COF exhibited much better purification ability. This opens up a new opportunity for the creation of functionalized nanoporous materials for the large-scale purification of waste-generated biogases to address the challenges associated with energy and the environment.

Review: Biological consequences of the inhibition of rumen methanogenesis

Decreasing enteric CH4 emissions from ruminants is important for containing global warming to 1.5 °C and avoid the worst consequences of climate change. However, the objective of mitigating enteric CH4 emissions is difficult to reconcile with the forecasted increase in production of ruminant meat and milk, unless CH4 production per animal and per kilogram of animal product are decreased substantially. Chemical compound 3-nitrooxypropanol and bromoform-containing red algae Asparagopsis are currently the most potent inhibitors of rumen methanogenesis, but their average efficacy would have to be increased to mitigate enteric CH4 emissions to contain global warming to 1.5 °C, if the demand for ruminant products increases as predicted. We propose that it may be possible to enhance the efficacy of inhibitors of methanogenesis through understanding the mechanisms that cause variation in their efficacy across studies. We also propose that a more thorough understanding of the effects of inhibiting methanogenesis on rumen and postabsorptive metabolism may help improve feed efficiency and cost-effectiveness as co-benefits of the methanogenesis inhibition intervention. For enhancing efficacy, we examine herein how different inhibitors of methanogenesis affect the composition of the rumen microbial community and discuss some mechanisms that may explain dissimilar sensitivities among methanogens to different types of inhibitors. For improving feed efficiency and cost-effectiveness, we discuss the consequences of inhibiting methanogenesis on rumen fermentation, and how changes in rumen fermentation can in turn affect postabsorptive metabolism and animal performance. The objectives of this review are to identify knowledge gaps of the consequences of inhibiting methanogenesis on rumen microbiology and rumen and postabsorptive metabolism, propose research to address those knowledge gaps and discuss the implications that this research can have for the efficacy and adoption of inhibitors of methanogenesis. Depending on its outcomes, research on the microbiological, biochemical, and metabolic consequences of the inhibition of rumen methanogenesis could help the adoption of feed additives inhibitors of methanogenesis to mitigate enteric CH4 emissions from ruminants to ameliorate climate change.

Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications

Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.

Responses of CH4, N2O, and NH3 emissions to different slurry pH values of 5.5-10.0: Characteristics and mechanisms

Animal slurry storage is a significant source of greenhouse gas (GHG) and ammonia (NH3) emissions. pH is a basic but key factor that could pose great influence on gas emissions, but the simultaneous evaluation of its influence on GHG and NH3 emissions and the understanding of its underlying mechanism are not enough. In this work, pH was adjusted between 5.5 and 10.0 by a step of 0.5 unit by adding lactic acid and sodium hydroxide (NaOH) properly and frequently to the stored slurry during a 43-day storage period. The cumulative NH3 emissions were linearly correlated with the slurry pH, with R2 being 0.982. Maintaining the slurry pH at 5.5-6.0 could reduce NH3 emissions by 69.4%-85.1% compared with the non-treated group (CK). The pH ranges for maximum methane (CH4) and nitrous oxide (N2O) emissions were 7.5-8.5 and 6.5-8.5, respectively, and the slurry under pH 7.5-8.5 showed the highest GHG emissions. Acidification to pH 5.5 helped reduce the CH4, N2O, and total GHG emissions by 98.0%, 29.3%, and 81.7%, respectively; while alkalinization to pH 10.0 helped achieve the mitigation effects of 74.1%, 24.9%, and 30.6%, respectively. The Pearson's correlation factor between CH4 and the gene copy of mcrA under different pH values was 0.744 (p < 0.05). Meanwhile, the correlation factors between N2O and the gene copies of amoA, narG, and nirS were 0.644 (p < 0.05), 0.719 (p < 0.05), and 0.576 (p = 0.081), respectively. The gene copies of mcrA, amoA, narG, and nirS were maintained at the lowest level under pH 5.5. These results recommended keeping slurry pH lower than 5.5 with lactic acid can help control GHG and NH3 emissions simultaneously and effectively.

Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase

All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.

Methane emission reduction oriented extracellular electron transfer and bioremediation of sediment microbial fuel cell: A review

Sediment is the internal and external source of water environment pollution, so sediment remediation is the premise of water body purification. Sediment microbial fuel cell (SMFC) can remove the organic pollutants in sediment by electroactive microorganisms, compete with methanogens for electrons, and realize resource recycling, methane emission inhibiting and energy recovering. Due to these characteristics, SMFC have attracted wide attention for sediment remediation. In this paper, we comprehensively summarized the recent advances of SMFC in the following areas: (1) The advantages and disadvantages of current applied sediment remediation technologies; (2) The basic principles and influencing factors of SMFC; (3) The application of SMFC for pollutant removal, phosphorus transformation and remote monitoring and power supply; (4) Enhancement strategies for SMFC in sediments remediation such as SMFC coupled with constructed wetland, aquatic plant and iron-based reaction. Finally, we have summarized the drawback of SMFC and discuss the future development directions of applying SMFC for sediment bioremediation.

Hydrogenotrophic pathway dominates methanogenesis along the river-estuary continuum of the Yangtze River

Rivers are considered as an important source of methane (CH₄) to the atmosphere, but our understanding for the methanogenic pathway in rivers and its linkage with CH₄ emission is very limited. Here, we investigated the diffusive flux of CH₄ and its stable carbon isotope signature (δ¹³C-CH₄) along the river-estuary continuum of the Yangtze River. The diffusive CH₄ flux was estimated to 27.9 ± 11.4 μmol/m²/d and 36.5 ± 24.4 μmol/m²/d in wet season and dry season, respectively. The δ¹³C-CH₄ values were generally lower than -60‰, with the fractionation factor (α_c) higher than 1.055 and the isotope separation factor (ε_c) ranged from 55 to 100. In situ microbial composition showed that hydrogenotrophic methanogens accounts for over 70% of the total reads. Moreover, the incubation test showed that the headspace CH₄ concentration by adding CO₂/H₂ to the sediment was orders of magnitude higher than that by adding trimethylamine and sodium acetate. These results jointly verified the river-estuary continuum is a minor CH₄ source and dominated by hydrogenotrophic pathway. Based on the methanogenic pathway here and previous reported data in the same region, the historical variation of diffusive CH₄ flux was calculated and results showed that CH₄ emission has reduced 82.5% since the construction of Three Gorges Dam (TGD). Our study verified the dominant methanogenic pathway in river ecosystems and clarified the effect and mechanism of dam construction on riverine CH₄ emission.

Semi-wet methanogen cathode composed of oak white charcoal for developing sustainable microbial fuel cells

The present study aimed to evaluate a semi-wet biocathode composed of oak white charcoal and agarose gel as an alternative to the standard carbon felt biocathodes used in microbial fuel cells (MFCs). The MFC containing the oak white charcoal cathode (Oak-MFC) recorded a higher current value than that of the MFC containing a carbon felt cathode (CF-MFC). The Oak-MFC produced approximately 4.0-fold more electrons in the external circuit and 1.7-fold more methane (CH₄) than the CF-MFC. A real-time PCR targeting mcrA showed that the number of methanogens adhering to the oak white charcoal cathode was approximately 15-fold that adhering to the carbon felt cathode. These results suggest that the methanogens attached to the cathode of both MFCs received electrons and CH₄ was produced from carbon dioxide (CO₂). Furthermore, Oak-MFC performed better than CF-MFC, thereby suggesting that oak white charcoal bound by agarose gel can be used as an alternative methanogen cathode. The propionic acid degradation rate of Oak-MFC was faster than that of CF-MFC suggesting that the cathodic reaction may affect the anodic reaction. The use of oak-derived electrode as a methanogen cathode also could contribute to sustainable forest management and promote regular thinning of oak trees. Further, its use will enable carbon fixation and efficient energy conversion from CO₂ to CH₄, thus contributing to sustainable energy use.

Inhibition of Methylmercury and Methane Formation by Nitrous Oxide in Arctic Tundra Soil Microcosms

Climate warming causes permafrost thaw predicted to increase toxic methylmercury (MeHg) and greenhouse gas [i.e., methane (CH₄), carbon dioxide (CO₂), and nitrous oxide (N₂O)] formation. A microcosm incubation study with Arctic tundra soil over 145 days demonstrates that N₂O at 0.1 and 1 mM markedly inhibited microbial MeHg formation, methanogenesis, and sulfate reduction, while it slightly promoted CO₂ production. Microbial community analyses indicate that N₂O decreased the relative abundances of methanogenic archaea and microbial clades implicated in sulfate reduction and MeHg formation. Following depletion of N₂O, both MeHg formation and sulfate reduction rapidly resumed, whereas CH₄ production remained low, suggesting that N₂O affected susceptible microbial guilds differently. MeHg formation strongly coincided with sulfate reduction, supporting prior reports linking sulfate-reducing bacteria to MeHg formation in the Arctic soil. This research highlights complex biogeochemical interactions in governing MeHg and CH₄ formation and lays the foundation for future mechanistic studies for improved predictive understanding of MeHg and greenhouse gas fluxes from thawing permafrost ecosystems.

Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China

Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH₄). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO₃^-), sulfate (SO₄^2-), and nitrous oxide (N₂O) flux, among them, soil N substances (TN, NO₃^-, N₂O) have essential regulatory roles in the AOM process, while NO₃^- and N₂O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH₄ sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH₄ biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.

Characterization of Biofilm Microbiome Formation Developed on Novel 3D-Printed Zeolite Biocarriers during Aerobic and Anaerobic Digestion Processes

Background: Aerobic or anaerobic digestion is involved in treating agricultural and municipal waste, and the addition of biocarriers has been proven to improve them further. We synthesized novel biocarriers utilizing zeolites and different inorganic binders and compared their efficiency with commercially available biocarriers in aerobic and anaerobic digestion systems. Methods: We examined BMP and several physicochemical parameters to characterize the efficiency of novel biocarriers on both systems. We also determined the SMP and EPS content of synthesized biofilm and measured the adherence and size of the forming biofilm. Finally, we characterized the samples by 16S rRNA sequencing to determine the crucial microbial communities involved. Results: Evaluating BMP results, ZSM-5 zeolite with bentonite binder emerged, whereas ZSM-5 zeolite with halloysite nanotubes binder stood out in the wastewater treatment experiment. Twice the relative frequencies of archaea were found on novel biocarriers after being placed in AD batch reactors, and >50% frequencies of Proteobacteria after being placed in WWT reactors, compared to commercial ones. Conclusions: The newly synthesized biocarriers were not only equally efficient with the commercially available ones, but some were even superior as they greatly enhanced aerobic or anaerobic digestion and showed strong biofilm formation and unique microbiome signatures.

Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures

Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.

Exploring Gut Microbiome in Predicting the Efficacy of Immunotherapy in Non-Small Cell Lung Cancer

We performed various analyses on the taxonomic and functional features of the gut microbiome from NSCLC patients treated with immunotherapy to establish a model that may predict whether a patient will benefit from immunotherapy. We collected 65 published whole metagenome shotgun sequencing samples along with 14 samples from our previous study. We systematically studied the taxonomical characteristics of the dataset and used both the random forest (RF) and the multilayer perceptron (MLP) neural network models to predict patients with progression-free survival (PFS) above 6 months versus those below 3 months. Our results showed that the RF classifier achieved the highest F-score (85.2%) and the area under the receiver operating characteristic curve (AUC) (95%) using the protein families (Pfam) profile, and the MLP neural network classifier achieved a 99.9% F-score and 100% AUC using the same Pfam profile. When applying the model trained in the Pfam profile directly to predict the treatment response, we found that both trained RF and MLP classifiers significantly outperformed the stochastic predictor in F-score. Our results suggested that such a predictive model based on functional (e.g., Pfam) rather than taxonomic profile might be clinically useful to predict whether an NSCLC patient will benefit from immunotherapy, as both the F-score and AUC of functional profile outperform that of taxonomic profile. In addition, our model suggested that interactive biological processes such as methanogenesis, one-carbon, and amino acid metabolism might be important in regulating the immunotherapy response that warrants further investigation.

On the evolution of coenzyme biosynthesis

Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD⁺) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.

Strategy of optimizing anaerobic digestion of cassava distiller wastewater using a novel automatic biological incubation system

Due to the drawbacks of using fossil fuels and the need to mitigate global warming caused by increasing greenhouse gas emissions, agricultural biomass for bioenergy production is gaining great interest around the world. This work presented a study at a biochemical plant in Lianyungang, Jiangsu Province, China to maximize methane production from cassava distiller wastewater. The plant's annual production of cassava distiller wastewater is more than 3 million tons and currently was treated using a series of 5000 m³ Internal Circulation (IC) reactors. Modification was applied at No.19 IC reactor by connecting it to two 1 m³ automatic biological incubators called Information Bio-Booster (IBB). The effluent of the IC reactor was fed into the IBBs and iron, cobalt and nickel were added directly in the IBBs. The function of the IBBs was to regulate the microbial community. Afterwards, the microorganisms in the IBBs were pumped back into the IC reactor to participate in the methane production reaction. Daily net increase of methane content and COD removal reached 8.02% and 33% respectively in No.19 IC reactor comparing to the unadjusted reactors. Preliminary lab experiments found that improvements of biogas production, enhanced COD removal and VS removal was closely related to the enhancement of anaerobic microbial communities' diversity and the promotion of enzyme activity through the addition of the metal salts. Daily economic value could be estimated to be $218 which indicated the application potential of using the proposed system to enhance anaerobic digestion at industrial plants for bioenergy production.

Quasi-Simultaneous Sensitive Detection of Two Gas Species by Cavity-Ringdown Spectroscopy with Two Lasers

We developed a cavity ringdown spectrometer by utilizing a step-scanning and dithering method for matching laser wavelengths to optical resonances of an optical cavity. Our approach is capable of working with two and more lasers for quasi-simultaneous measurements of multiple gas species. The developed system was tested with two lasers operating around 1654 nm and 1658 nm for spectral detections of 12CH4 and its isotope 13CH4 in air, respectively. The ringdown time of the empty cavity was about 340 µs. The achieved high detection sensitivity of a noise-equivalent absorption coefficient was 2.8 × 10-11 cm-1 Hz-1/2 or 1 × 10-11 cm-1 by averaging for 30 s. The uncertainty of the high precision determination of δ13CH4 in air is about 1.3‰. Such a system will be useful for future applications such as environmental monitoring.

Past, Present and Near Future: An Overview of Closed, Running and Planned Biomethanation Facilities in Europe

The power-to-methane technology is promising for long-term, high-capacity energy storage. Currently, there are two different industrial-scale methanation methods: the chemical one (based on the Sabatier reaction) and the biological one (using microorganisms for the conversion). The second method can be used not only to methanize the mixture of pure hydrogen and carbon dioxide but also to methanize the hydrogen and carbon dioxide content of low-quality gases, such as biogas or deponia gas, enriching them to natural gas quality; therefore, the applicability of biomethanation is very wide. In this paper, we present an overview of the existing and planned industrial-scale biomethanation facilities in Europe, as well as review the facilities closed in recent years after successful operation in the light of the scientific and socioeconomic context. To outline key directions for further developments, this paper interconnects biomethanation projects with the competitiveness of the energy sector in Europe for the first time in the literature. The results show that future projects should have an integrative view of electrolysis and biomethanation, as well as hydrogen storage and utilization with carbon capture and utilization (HSU&CCU) to increase sectoral competitiveness by enhanced decarbonization.

The rumen microbiome: balancing food security and environmental impacts

Ruminants produce edible products and contribute to food security. They house a complex rumen microbial community that enables the host to digest their plant feed through microbial-mediated fermentation. However, the rumen microbiome is also responsible for the production of one of the most potent greenhouse gases, methane, and contributes about 18% of its total anthropogenic emissions. Conventional methods to lower methane production by ruminants have proved successful, but to a limited and often temporary extent. An increased understanding of the host-microbiome interactions has led to the development of new mitigation strategies. In this Review we describe the composition, ecology and metabolism of the rumen microbiome, and the impact on host physiology and the environment. We also discuss the most pertinent methane mitigation strategies that emerged to balance food security and environmental impacts.

Hydrogen Economy Development Opportunities by Inter-Organizational Digital Knowledge Networks

Innovative power-to-X (P2X) technologies, as a set of emerging new solutions, could play a crucial role in creating sustainable, carbon-neutral economies, such as the hydrogen economy. These technologies, however, are generally not yet implemented on a commercial scale. This research focuses on how innovative, digital inter-organizational knowledge networks of industry representatives and universities could contribute to the commercial implementation of P2X technologies and increase the pace of sustainable hydrogen-based development. The findings of an extended case study with a hybrid (qualitative–quantitative) methodology and a five-year time horizon, suggest the need for a digital knowledge platform, where universities and industry representatives add and combine their knowledge. In contrast with expectations, however, the empirical results show that academia would, not only be capable of supporting the exploration of new solutions, but foster the exploitation of more mature technologies as well. Similarly, large energy companies could also drive exploratory activities, not only exploitative ones. The findings highlight the possible central role of the “system builder” actor, who integrates exploitative-explorative learning and facilitates the formation of a (digital) innovation ecosystem. By exceeding the dominant techno-economic and environmental aspects, this research contributes to the literature by highlighting the applicability of network-based innovation management theory for hydrogen economy research.

TWO-STAGE DEGRADATION OF SOLID ORGANIC WASTE AND LIQUID FILTRATE

The accumulation of solid and liquid organic waste requires their treatment to develop energy biotechnologies and prevent environment pollution. Aim. The goal of the work was to study the efficiency of the purification of the filtrate from dissolved organic compounds by aerobic oxidation and methane fermentation. Methods. The standard methods were used to determine рН and redox potential (Eh), the gas composition, the content of short-chain fatty acids, the concentration of dissolved organic compounds counting to the total сarbon. The efficiency of two types of microbial metabolism for the degradation of soluble organic compounds of filtrate was compared. Results. The aerobic oxidation was established to provide 1.9 times more efficient removal of dissolved organic compounds, compared with the anaerobic methane fermentation. However, it provided CH4 yield 1 L/dm3 of filtrate (сarbon concentration — 1071 mg/L). The necessity to optimize the methods for purifying filtrate to increase the efficiency of the process was determined. Conclusions. The obtained results will be the basis to develop complex biotechnology providing not only the production of environmentally friendly energy H2 via the fermentation of solid food waste, but also the purification of filtrate to solve the ecological and energy (CH4 production) problem of society.

Effects of granular activated carbon and temperature on the viscosity and methane yield of anaerobically digested of corn straw with different dry matter concentrations

Anaerobic digestion (AD) systems with high substrate concentrations are characterized by high viscosity, which affects material and energy transfer efficiencies, thereby influencing methane production efficiency. In this study, adding granular activated carbon (GAC) and increasing the temperature decreased the viscosity by 4.56-10.19% and 27.13-28.85%, respectively, and improved AD efficiency. Adding GAC and increasing the temperature enhanced the methane yields by 34.37-38.15% and 25.60-28.31%, respectively. Distance-based redundancy analysis showed that the viscosity, temperature, and GAC had the greatest effects on the composition of the microbial community. The dominant bacteria in the medium-temperature AD system at the phylum level belonged to Firmicutes, Bacteroidetes, and Euryarchaeota. In addition to the dominant bacteria in the medium-temperature AD system, the thermophilic phylum Thermotogae was abundant in the high-temperature AD system. Moreover, the relative abundance of Euryarchaeota, which contained most of the methanogens, was higher in the high-temperature AD system than in the medium-temperature AD system.

Anaerobic microbial methanol conversion in marine sediments

Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.

Transcriptional regulation of methanogenic metabolism in archaea

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

Microbially induced carbonate precipitation via methanogenesis pathway by a microbial consortium enriched from activated anaerobic sludge

AIMS

Various applications of microbially induced carbonate precipitation (MICP) has been proposed. However, most studies use cultured pure strains to obtain MICP, ignoring advantages of microbial consortia. The aims of this study were to: (i) test the feasibility of a microbial consortium to produce MICP; (ii) identify functional micro-organisms and their relationship; (iii) explain the MICP mechanism; (iv) propose a way of applying the MICP technique to soil media.

METHODS AND RESULTS

Anaerobic sludge was used as the source of the microbial consortium. A laboratory anaerobic sequencing batch reactor and beaker were used to perform precipitation experiment. The microbial consortium produced MICP with an efficiency of 96·6%. XRD and SEM analysis showed that the precipitation composed of different-size calcite crystals. According to high-throughput 16S rRNA gene sequencing, the functional micro-organisms included acetogenic bacteria, acetate-oxidizing bacteria and archaea Methanosaeta and Methanobacterium beijingense. The methanogenesis acetate degradation provides dissolved inorganic carbon and increases pH for MICP. A series of reactions catalysed by many enzymes and cofactors of methanogens and acetate-oxidizers are involved in the acetate degradation.

CONCLUSION

This work demonstrates the feasibility of using the microbial consortium to achieve MICP from an experimental and theoretical perspective.

SIGNIFICANCE AND IMPACT OF THE STUDY

A method of applying the microbial-consortium MICP to soil media is proposed. It has the advantages of low cost, low environmental impact, treatment uniformity and less limitations from natural soils. This method could be used to improve mechanical properties, plug pores and fix harmful elements of soil media, etc.

Methanosarcina acetivorans contains a functional ISC system for iron-sulfur cluster biogenesis

BACKGROUND

The production of methane by methanogens is dependent on numerous iron-sulfur (Fe-S) cluster proteins; yet, the machinery involved in Fe-S cluster biogenesis in methanogens remains largely unknown. Methanogen genomes encode uncharacterized homologs of the core components of the ISC (IscS and IscU) and SUF (SufBC) Fe-S cluster biogenesis systems found in bacteria and eukaryotes. Methanosarcina acetivorans contains three iscSU and two sufCB gene clusters. Here, we report genetic and biochemical characterization of M. acetivorans iscSU2.

RESULTS

Purified IscS2 exhibited pyridoxal 5'- phosphate-dependent release of sulfur from L-cysteine. Incubation of purified IscU2 with IscS2, cysteine, and iron (Fe²⁺) resulted in the formation of [4Fe-4S] clusters in IscU2. IscU2 transferred a [4Fe-4S] cluster to purified M. acetivorans apo-aconitase. IscU2 also restored the aconitase activity in air-exposed M. acetivorans cell lysate. These biochemical results demonstrate that IscS2 is a cysteine desulfurase and that IscU2 is a Fe-S cluster scaffold. M. acetivorans strain DJL60 deleted of iscSU2 was generated to ascertain the in vivo importance of IscSU2. Strain DJL60 had Fe-S cluster content and growth similar to the parent strain but lower cysteine desulfurase activity. Strain DJL60 also had lower intracellular persulfide content compared to the parent strain when cysteine was an exogenous sulfur source, linking IscSU2 to sulfur metabolism.

CONCLUSIONS

This study establishes that M. acetivorans contains functional IscS and IscU, the core components of the ISC Fe-S cluster biogenesis system and provides the first evidence that ISC operates in methanogens.

Seasonal Energy Storage Potential Assessment of WWTPs with Power-to-Methane Technology

Power-to-methane technology (P2M) deployment at wastewater treatment plants (WWTPs) for seasonal energy storage might land on the agenda of decision-makers across EU countries, since large WWTPs produce a notable volume of biogas that could be injected into the natural gas grid with remarkable storage capacities. Because of the recent rapid increase of local photovoltaics (PV), it is essential to explore the role of WWTPs in energy storage and the conditions under which this potential can be realized. This study integrates a techno-economic assessment of P2M technology with commercial/investment attractiveness of seasonal energy storage at large WWTPs. Findings show that a standardized 1 MWel P2M technology would fit with most potential sites. This is in line with the current technology readiness level of P2M, but increasing electricity prices and limited financial resources of WWTPs would decrease the commercial attractiveness of P2M technology deployment. Based on a Hungarian case study, public funding, biomethane feed-in tariff and minimized or compensated surplus electricity sourcing costs are essential to realize the energy storage potential at WWTPs.

Effects of amino-modified biofilm carriers on biogas production in the anaerobic digestion of corn straw

This paper studied the property of three different biofilm carriers added into the anaerobic digestion systems, a granular activated carbon, a polyacrylonitrile, and a polyacrylonitrile modified with diethylenetriamine (PAN-NH₂). The PAN-NH₂ system kept the maximum biogas and methane production, which were 42.69% and 37.29% higher than the control system, respectively. The value of pH and chemical oxygen demand, the content of total solid and volatile solid, volatile fatty acids concentration, coenzyme F₄₂₀ concentration, and microbial community analysis were investigated during the anaerobic digestion process. The PAN-NH₂ system had the highest removal efficiency of the pollutants and regulated the pH of the system better than other systems. The result of high-throughput sequencing analysis showed that the addition of biofilm carriers and mediation with amino-groups adjusted system pH and improved biogas and CH₄ production by reducing the relative abundance of bacteria in the hydrolysis/acidogenesis stages. Methanosarcina gradually replaced other methanogens during the experimental runs and was the dominant methanogen at the end of the anaerobic digestion process.

Mercury methylation potential in a sand dune on Lake Michigan's eastern shoreline

Lake Michigan hosts the largest freshwater sand dune system in the world and is economically important for the fishery industry and tourism. Due to industrial pollution and atmospheric mercury (Hg) deposition, toxic levels of methylmercury (MeHg) have been found in the Lake biota, but little information is known regarding MeHg sources and Hg methylation potential in the shoreline sand dunes. We conducted anaerobic incubation experiments with beach sands collected from Ludington, Michigan, and examined the effects of organic carbon substrate addition, inorganic nitrogen, and mineral magnetite on Hg methylation. Despite nutrient poor and low-organic carbon conditions, appreciable Hg methylation activity coupled with carbon degradation was observed in the sands. Addition of acetate as a carbon source substantially increased MeHg production from 2 to 380 ng/kg sediment while acetate was rapidly degraded in the first 19 days of incubation. Ammonium addition showed little influence on carbon degradation or Hg methylation, whereas iron oxide addition (~1% dry weight) significantly inhibited both carbon degradation and MeHg production (by up to 90%), highlighting strongly coupled interactions between microbes, carbon substrates, and minerals. This research demonstrates the potential of microbial Hg methylation in the sand dunes, which may play a role in MeHg input and bioaccumulation in the Lake Michigan ecosystem.

Nonenzymatic Metabolic Reactions and Life's Origins

Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.

Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea

The Sansha Yongle Blue Hole is the world’s deepest (301 m) underwater cave and has a sharp redox gradient, with oligotrophic, anoxic, and sulfidic bottom seawater. In order to discover the microbial communities and their special biogeochemical pathways in the blue hole, we analyzed the 16S ribosomal RNA amplicons and metagenomes of microbials from seawater depths with prominent physical, chemical, and biological features. Redundancy analysis showed that dissolved oxygen was the most important factor affecting the microbial assemblages of the blue hole and surrounding open sea waters, and significantly explained 44.7% of the total variation, followed by silicate, temperature, sulfide, ammonium, methane, nitrous oxide, nitrate, dissolved organic carbon, salinity, particulate organic carbon, and chlorophyll a. We identified a bloom of Alteromonas (34.9%) at the primary nitrite maximum occurring in close proximity to the chlorophyll a peak in the blue hole. Genomic potential for nitrate reduction of Alteromonas might contribute to this maximum under oxygen decrease. Genes that would allow for aerobic ammonium oxidation, complete denitrification, and sulfur-oxidization were enriched at nitrate/nitrite-sulfide transition zone (90 and 100 m) of the blue hole, but not anammox pathways. Moreover, γ-Proteobacterial clade SUP05, ε-Proteobacterial genera Sulfurimonas and Arcobacter, and Chlorobi harbored genes for sulfur-driven denitrification process that mediated nitrogen loss and sulfide removal. In the anoxic bottom seawater (100-300 m), high levels of sulfate reducers and dissimilatory sulfite reductase gene (dsrA) potentially created a sulfidic zone of ~200 m thickness. Our findings suggest that in the oligotrophic Sansha Yongle Blue Hole, O₂ deficiency promotes nitrogen- and sulfur-cycling processes mediated by metabolically versatile microbials.

Isolation of an Obligate Mixotrophic Methanogen That Represents the Major Population in Thermophilic Fixed-Bed Anaerobic Digesters

Methanothermobacter Met2 is a metagenome-assembled genome (MAG) that encodes a putative mixotrophic methanogen constituting the major populations in thermophilic fixed-bed anaerobic digesters. In order to characterize its physiology, the present work isolated an archaeon (strain Met2-1) that represents Met2-type methanogens by using a combination of enrichments under a nitrogen atmosphere, colony formation on solid media and limiting dilution under high partial pressures of hydrogen. Strain Met2-1 utilizes hydrogen and carbon dioxide for methanogenesis, while the growth is observed only when culture media are additionally supplemented with acetate. It does not grow on acetate in the absence of hydrogen. The results demonstrate that Methanothermobacter sp. strain Met2-1 is a novel methanogen that exhibits obligate mixotrophy.

Influence of nanoscale zero-valent iron and magnetite nanoparticles on anaerobic digestion performance and macrolide, aminoglycoside, β-lactam resistance genes reduction

The effect of nanoscale zero-valent iron (NZVI) and magnetite nanoparticles (Fe₃O₄ NPs) on anaerobic digestion (AD) performance was investigated through a series of 100-day semi-continuous mesophilic anaerobic digestions. The results indicated that biogas production had increased by 24.44% and 21.66% with the addition of 0.5 g/L Fe₃O₄ NPs and 1.0 g/L NZVI, respectively. Besides, the abundance of five widespread antibiotic resistance genes (ARGs) (ermF, ermA, ermT, aac(6')-IB, blaOXA-1) was also studied. The decrease in abundance of aac(6')-IB and blaOXA-1 was observed during the AD process with an average removal rate of 95.69% and 44.82%, respectively. Most of the ARGs, especially ermA and ermT, were less abundant in NZVI group compared with control group. The overall results suggested that the addition of NZVI and Fe₃O₄ NPs contributed to a better sludge anaerobic digestion performance, and NZVI was beneficial to the removal of some ARGs.

Biochar triggering multipath methanogenesis and subdued propionic acid accumulation during semi-continuous anaerobic digestion

The semi-continuous anaerobic digestion (AD) performances of dry chicken manure (DCM) were investigated at the temperature of 35 ± 1 °C with and without biochar. The average specific methane productions of 0.18 L/g VS_added and 0.17 L/g VS_added were achieved without biochar at the organic loading rate (OLR) of 3.125 and 6.25 g VS/L/d, respectively. An increase of 12% in methane production was obtained in the presence of biochar at the two operational OLRs. Accumulation of propionic acid was observed associating with AD of DCM, which was substantially alleviated by biochar supplement. The buffer capacity of biochar was supposed to develop through strengthening the buffer system established by NH₄⁺ and volatile fatty acids. Methanosarcina that can utilize multiple nutrients for methanogenesis was the dominant archaea in the presence of biochar, while the strictly aceticlastic Methanosaeta was dominant in control digester. These results suggest that biochar enhanced methanogenesis through intensifying its available pathway.

Evaluation of bacterial association in methane generation pathways of an anaerobic digesting sludge via metagenomic sequencing

Anaerobic digestion, a recently hot technology to produce biogases especially methane generation for biofuel from wastewater, is considered an effective explanation for energy crisis and global pollution threat. A complex microbiome population is present in sludge, which plays an important role in the digestion of complex polymer into simple monomers. 16S rRNA approaches simply are not enough for amplification due to the involvement of extreme complex population. However, Illumina sequencing is a recent powerful technology to reveal the entire microbiome structure and methane generation pathways in anaerobic digestion. Metagenomic sequencing was tested to reveal the microbial structure of a digested sludge from a local wastewater treatment plant in Beijing. The Illumina HiSeq program was used to extract about 5 GB of data for metagenomic analysis. The classification investigation revealed about 97.64% dominancy of bacteria while 1.78% were detected to be archaea using MG-RAST server. The most abundant bacterial communities were reported to be Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. Furthermore, the important microbiome involved in methane generation was revealed. The dominant methanogens were detected (Methanosaeta and Methanosarcina), with affiliation of dominant genes involved in acetoclastic methanogenesis in a digesting sludge. The metagenomic analysis showed that microbial structure and methane generation pathways were successfully dissected in an anaerobic digester.

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians

Sardinia, Italy, has a high prevalence of residents who live more than 100 years. The reasons for longevity in this isolated region are currently unknown. Gut microbiota may hold a clue. To explore the role gut microbiota may play in healthy aging and longevity, we used metagenomic sequencing to determine the compositional and functional differences in gut microbiota associated with populations of different ages in Sardinia. Our data revealed that the gut microbiota of both young and elderly Sardinians shared similar taxonomic and functional profiles. A different pattern was found in centenarians. Within the centenarian group, the gut microbiota was correlated with the functional independence measurement of the host. Centenarians had a higher diversity of core microbiota species and microbial genes than those in the young and elderly. We found that the gut microbiota in Sardinian centenarians displayed a rearranged taxonomic pattern compared with those of the young and elderly, featured by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enriched for Methanobrevibacter smithii and Bifidobacterium adolescentis Moreover, functional analysis revealed that the microbiota in centenarians had high capacity for central metabolism, especially glycolysis and fermentation to short-chain fatty acids (SCFAs), although the gut microbiota in centenarians was low in genes encoding enzymes involved in degradation of carbohydrates, including fibers and galactose.IMPORTANCE The gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment that is regarded as beneficial for host gut epithelium. The low abundance of genes encoding components of pathways involved in carbohydrate degradation was also found in the gut microbiota of Sardinian centenarians and is often associated with poor gut health. Overall, our study here represents an expansion of previous research investigating the age-related changes in gut microbiota. Furthermore, our study provides a new prospective for potential targets for gut microbiota intervention directed at limiting gut inflammation and pathology and enhancing a healthy gut barrier.

Revealing the correlation of biomethane generation, DOM fluorescence, and microbial community in the mesophilic co-digestion of chicken manure and sheep manure at different mixture ratio

Batch co-digestion tests of chicken manure (CM) and sheep manure (SM) at different ratio (R_s/c) were conducted under mesophilic condition (35 °C). Batch kinetic analysis of bioCH₄ production, excitation-emission matrix (EEM) fluorescence of dissolved organic matter (DOM), and microbial community were investigated. The well-fitted modified Gompertz model (R², 0.98-0.99) resulted that the co-digestion markedly improved the methane production rate and shortened the lag phase time. The highest bioCH₄ yield of 219.67 mL/gVS_add and maximum production rate of 0.378 mL/gVS_add/h were obtained at an optimum R_s/c of 0.4. Additionally, a significant variation of DOM was detected at the R_s/c of 0.4 with a consistent degradation of soluble microbial byproduct-like and protein-like organics. The positive synergy effects of co-digestion conspicuously enhanced the bioCH₄ production efficiency. FI₃₇₀ and NADH were significantly correlated to R_s/c (p < 0.05). Moreover, the correlations among process indicator, EEM-peaks and different environmental parameters were evaluated by Pearson correlation analysis. The high diversity of acetoclastic methanogens and hydrogenotrophic methanogens in the co-digestion improved the stability of process. Graphical Abstract.

The acetotrophic pathway dominates methane production in Zoige alpine wetland coexisting with hydrogenotrophic pathway

As a typical alpine wetland on the Tibetan Plateau, the Zoige wetland processes a large carbon stock and is a hotspot of methane emission. To date, many studies have investigated the methane flux in this wetland; however, the research on the source of methane in the soils of Zoige wetland is not clear enough. In this study, we determined the dynamic characteristics of the stable carbon isotopes during the methanogenesis of Zoige wetland soil and the corresponding microbial changes. The results showed that the δ¹³CH₄ varied between −19.86‰ and −28.32‰ and the α_C ranged from 1.0029 to 1.0104 in the methanogenesis process, which suggests the dominance of acetotrophic methanogenesis. And among the increased methanogens, acetotrophic methanogens multiplied more obviously than hydrogenotrophic menthanogens. In addition, the results of structural equation models showed that the variations in stable carbon isotopes during the process were mainly affected by acetotrophic methanogens. Although the acetotrophic pathway was dominate, the varied isotope characteristics, increased methanogens and ratio of carbon dioxide to methane all showed that hydrogenotrophic and acetotrophic methanogenesis coexisted in the Zoige wetland. Overall, our study provided a detailed and definitive information to the source of methane in the soil of the Zoige wetland and laid a foundation of mechanism to the research of greenhouse gas in this alpine wetland.

Optimizing biomethane production of mesophilic chicken manure and sheep manure digestion: Mono-digestion and co-digestion kinetic investigation, autofluorescence analysis and microbial community assessment

Optimization of mesophilic methane production from Chicken manure (CM) and Sheep manure (SM) at total solid (TS) of 8% and 1.6% were obtained by sequence tests in mono-digestion. However, the positive synergy of co-digestion with an optimum CM/SM of 2.5 (310 mLCH₄/gVS_added) resulted in a high hydrolytic capacity and methane production. The modified Gompertz model (R² > 0.98) and modified Aiba model (R² > 0.88) illustrated co-digestion significantly improved the methane generation rate with strong ammonia tolerance. Dissolved Organic Matter (DOM) variation in response to the metabolic rate of microbial community illustrated that the SMP-like and protein-like components half-split by EEM-PARAFAC were significantly negative corresponded to bio-methane production. Moreover, the canonical correlation analysis (CCA) resulted a significant difference between the substrate and DOM composition. Potential functional metabolic illustrated statistically significance difference between mono and co-digestion, however, Methanosaeta and Syntrophobacter predominated the syntrophic methanogenesis. The constructed complex metabolic cooperation caused the co-digestion stable and high efficiency.

Trace elements effect on hydrolytic stage towards biogas production of model lignocellulosic substrates

The effect and the response of several trace elements (TE) addition to the anaerobic degradation of key compounds of lignocellulosic biomass were evaluated. Lignin, cellulose and xylose were selected as principal compounds of lignocellulosic biomass. Lignin degradation was only improved by the addition of 1000 mg Fe/L, which allowed an improvement on the methane yield coefficient of 28% compared to control. SEM images from an abiotic assay showed that this effect is more likely related with a chemical effect induced by the Fe solution, instead of an enzymatic response. Pre-treatments focused on breaking the recalcitrant structure of the lignin could be more promising than TE addition for rich lignin-content substrates. Unlike to the response observed with lignin, cellulose showed a clear effect of the TE addition on methane production rate, indicating a higher preponderance of the enzymatic activity compared to the lignin biomethanization. Experiments with xylose resulted in a strong accumulation of volatile fatty acids. TE addition should be adapted to the substrate composition given the different response of each lignocellulosic compound to the different TE addition.

Effects of the presence of nanoscale zero-valent iron on the degradation of polychlorinated biphenyls and total organic carbon by sediment microbial fuel cell

The degradation of polychlorinated biphenyls (PCBs) and total organic carbon (TOC) by sediment microbial fuel cell (SMFC) with/without nanoscale zero-valent iron (NZVI) addition was investigated. It was found that the combined application led to the highest removal efficiencies of PCBs (37.55 ± 1.11%) and TOC (49.72 ± 1.54%) in all circumstances and produced a higher power density (108.89 mW/m²) and a corresponding lower internal resistance (264 Ω) than operation employing SMFC only. The TOC removal efficiency and the total production of electricity were linear. High-throughput sequencing of anodic microbial communities indicated that the electrode participation can increase the abundance of electrogenic bacteria (Geobacter and Pseudomonas) and the NZVI addition can reduce the oxidation reduction potential of the system and therefore enrich some bacteria (Longilinea and Desulfofustis) beneficial to the degradation of organic matter.

Effects of barium on the pathways of anaerobic digestion

The sufficient presence of trace elements (TE) is essential for anaerobic digestion. Barium (Ba) is considered a non-essential trace element that can be collaterally added to digesters as part of low-cost trace element sources or because of its presence in some feedstocks, such as crude glycerol. In the present study, the impact of Ba supplementation (2-2000 mg/L) on each stage of the anaerobic digestion (AD) process was evaluated using pure substrates (i.e., cellulose, glucose, a mixture of volatile fatty acids, sodium acetate and hydrogen) as well as a complex substrate (i.e., dried green fodder). Hydrolytic activity was affected at dosages higher than 200 mg Ba/L, whereas cellulose degradation was completely inhibited at 2000 mg Ba/L. The negative effects of the addition of Ba to methane production were observed only in the hydrolytic activity, and no effects were detected at any barium dosage in the subsequent anaerobic steps. Because Ba does not have a reported role as a cofactor of enzymes, this response could have been due to a direct inhibitory effect, a variation in the bioavailability of other trace elements, or even the availability of CO₂/SO₄ through precipitation as Ba-carbonates and sulphates. The results showed that the addition of Ba modified the chemical equilibrium of the studied system by varying the soluble concentration of some TEs and therefore their bioavailability. The highest variation was detected in the soluble concentration of zinc, which increased as the amount of Ba increased. Although little research has shown that Ba has some utility in anaerobic processes, its addition must be carefully monitored to avoid an undesirable modification of the chemical equilibrium in the system.

The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States

The rumen ecosystem represents a classic example of host-microbiome symbiosis. In this obligatory relationship, the host feeds on plant fibers that can only be degraded through a set of complex metabolic cascades, exclusively encoded in rumen-associated microbes. These various metabolic pathways are distributed across a multitude of microbial populations. Application of basic ecological principles to this ecosystem can contribute to profound understanding of the rules that shape it. Here, we discuss recent studies by examining the mapping between host attributes, rumen ecosystem composition, and functionality to propose simple, yet powerful concepts to guide the interpretation of microbiome data and enable a better understanding of how the system responds to perturbations.

The auto fluorescence characteristics, specific activity, and microbial community structure in batch tests of mono-chicken manure digestion

Batch tests inoculated with granular and suspended sludge of mono chicken manure (CM) digestion were conducted. Kinetic analysis showed a maximum bio-CH₄ generation (6 mL/gVS/d) at an optimal TS of 10-12%. At a TS of 25%, serious inhibition was found for granular sludge and even greater inhibition for the suspended sludge caused by free ammonia. The auto fluorescence of Excitation-mission matrix with parallel factor analysis (PARAFAC) showed that the dissolved organic matter (DOM) varied between the form C1, C2, C3 and C4. The split component of the SMP-like C2 and protein-like C4 significantly related to the bio-methane production in time series. The canonical correlation analysis (CCA) indicated that ammonia, pH, and TS influenced the PARAFAC component significantly. The aceticlastic methanogens of the genus Methanosaeta and acetogens of the genus Syntrophobacter predominated in the CM sludge. The methanogens and acetogens formed a metabolic cooperation, making the process a stable methane produced activity.

Methanogenesis on Early Stages of Life: Ancient but Not Primordial

Of the six known autotrophic pathways, the Wood-Ljungdahl pathway (WL) is the only one present in both the acetate producing Bacteria (homoacetogens) and the methane producing Archaea (hydrogenotrophic methanogens), and it has been suggested that WL is one of the oldest metabolic pathways. However, only the so-called carbonyl branch is shared by Archaea and Bacteria, while the methyl branch is different, both in the number of reactions and enzymes, which are not homologous among them. In this work we show that some parts of the methyl branch of archaeal Wood-Ljungdahl pathway (MBWL) are present in bacteria as well as in non-methanogen archaea, although the tangled evolutionary history of MBWL cannot be traced back to the Last Common Ancestor. We have also analyzed the different variants of methanogenesis (hydrogenotrophic, acetoclastic and methylotrophic pathways), and concluded that each of these pathways, and every different enzyme or subunit (in the case of multimeric enzymes), has their own intricate evolutionary history. Our study supports the scenario of hydrogenotrophic methanogenesis being older than the other variants, albeit not old enough to be present in the last archaeal common ancestor.

The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing

The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a “back-up” team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.