Acetate Production from Anaerobic Oxidation of Methane via Intracellular Storage Compounds

The Effects of Model Insoluble Copper Compounds in a Sedimentary Environment on Denitrifying Anaerobic Methane Oxidation (DAMO) Enrichment

The contribution of denitrifying anaerobic methane oxidation (DAMO) as a methane sink across different habitats, especially those affected by anthropogenic activities, remains unclear. Mining and industrial and domestic use of metals/metal-containing compounds can all cause metal contamination in freshwater ecosystems. Precipitation of metal ions often limits their toxicity to local microorganisms, yet microbial activity may also cause the redissolution of various precipitates. In contrast to most other studies that apply soluble metal compounds, this study investigated the responses of enriched DAMO culture to model insoluble copper compounds, malachite and covellite, in simulated sedimentary environments. Copper ≤ 0.22 µm from covellite appeared to cause immediate inhibition in 10 h. Long-term tests (54 days) showed that apparent methane consumption was less impacted by various levels of malachite and covellite than soluble copper. However, the medium-/high-level malachite and covellite caused a 46.6-77.4% decline in denitrification and also induced significant death of the representative DAMO microorganisms. Some enriched species, such as Methylobacter tundripaludum, may have conducted DAMO or they may have oxidized methane aerobically using oxygen released by DAMO bacteria. Quantitative polymerase chain reaction analysis suggests that Candidatus Methanoperedens spp. were less affected by covellite as compared to malachite while Candidatus Methylomirabilis spp. responded similarly to the two compounds. Under the stress induced by copper, DAMO archaea, Planctomycetes spp. or Phenylobacterium spp. synthesized PHA/PHB-like compounds, rendering incomplete methane oxidation. Overall, the findings suggest that while DAMO activity may persist in ecosystems previously exposed to copper pollution, long-term methane abatement capability may be impaired due to a shift of the microbial community or the inhibition of representative DAMO microorganisms.

Toward the Use of Methyl-Coenzyme M Reductase for Methane Bioconversion Applications

ConspectusAs the main component of natural gas and renewable biogas, methane is an abundant, affordable fuel. Thus, there is interest in converting these methane reserves into liquid fuels and commodity chemicals, which would contribute toward mitigating climate change, as well as provide potentially sustainable routes to chemical production. Unfortunately, specific activation of methane for conversion into other molecules is a difficult process due to the unreactive nature of methane C-H bonds. The use of methane activating enzymes, such as methyl-coenzyme M reductase (MCR), may offer a solution. MCR catalyzes the methane-forming step of methanogenesis in methanogenic archaea (methanogens), as well as the initial methane oxidation step during the anaerobic oxidation of methane (AOM) in anaerobic methanotrophic archaea (ANME). In this Account, we highlight our contributions toward understanding MCR catalysis and structure, focusing on features that may tune the catalytic activity. Additionally, we discuss some key considerations for biomanufacturing approaches to MCR-based production of useful compounds.MCR is a complex enzyme consisting of a dimer of heterotrimers with several post-translational modifications, as well as the nickel-hydrocorphin prosthetic group, known as coenzyme F430. Since MCR is difficult to study in vitro, little information is available regarding which MCRs have ideal catalytic properties. To investigate the role of the MCR active site electronic environment in promoting methane synthesis, we performed electric field calculations based on molecular dynamics simulations with a MCR from Methanosarcina acetivorans and an ANME-1 MCR. Interestingly, the ANME-1 MCR active site better optimizes the electric field with methane formation substrates, indicating that it may have enhanced catalytic efficiency. Our lab has also worked toward understanding the structures and functions of modified F430 coenzymes, some of which we have discovered in methanogens. We found that methanogens produce modified F430s under specific growth conditions, and we hypothesize that these modifications serve to fine-tune the activity of MCR.Due to the complexity of MCR, a methanogen host is likely the best near-term option for biomanufacturing platforms using methane as a C1 feedstock. M. acetivorans has well-established genetic tools and has already been used in pilot methane oxidation studies. To make methane oxidation energetically favorable, extracellular electron acceptors are employed. This electron transfer can be facilitated by carbon-based materials. Interestingly, our analyses of AOM enrichment cultures and pure methanogen cultures revealed the biogenic production of an amorphous carbon material with similar characteristics to activated carbon, thus highlighting the potential use of such materials as conductive elements to enhance extracellular electron transfer.In summary, the possibilities for sustainable MCR-based methane conversions are exciting, but there are still some challenges to tackle toward understanding and utilizing this complex enzyme in efficient methane oxidation biomanufacturing processes. Additionally, further work is necessary to optimize bioengineered MCR-containing host organisms to produce large quantities of desired chemicals.

Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA

We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.

Microbial interactions facilitating efficient methane driven denitrification via in-situ utilization of short chain fatty acids

High nitrate pollution in agriculture and industry poses a challenge to emerging methane oxidation coupled denitrification. In this study, an efficient nitrate removal efficiency of 100 % was achieved at an influent loading rate of 400 mg-N/L·d, accompanied by the production of short chain fatty acids (SCFAs) with a maximum value of 80.9 mg/L. Batch tests confirmed that methane was initially converted to acetate, which then served as a carbon source for denitrification. Microbial community characterization revealed the dominance of heterotrophic denitrifiers, including Simplicispira (22.8 %), Stappia (4.9 %), and the high‑nitrogen-tolerant heterotrophic denitrifier Diaphorobacter (19.0 %), at the nitrate removal rate of 400 mg-N/L·d. Notably, the low abundance of methanotrophs ranging from 0.24 % to 3.75 % across all operational stages does not fully align with the abundance of pmoA genes, suggesting the presence of other functional microorganisms capable of methane oxidation and SCFAs production. These findings could facilitate highly efficient denitrification driven by methane and contributed to the development of denitrification using methane as an electron donor.

Nitrate-dependent anaerobic methane oxidation coupled to Fe(III) reduction as a source of ammonium and nitrous oxide

'Candidatus Methanoperedens nitroreducens' is an archaeal methanotroph with global importance that links carbon and nitrogen cycles and great potential for sustainable operation of wastewater treatment. It has been reported to mediate the anaerobic oxidation of methane through a reverse methanogenesis pathway while reducing nitrate to nitrite. Here, we demonstrate that 'Ca. M. nitroreducens' reduces ferric iron forming ammonium (23.1 %) and nitrous oxide (N2O, 46.5 %) from nitrate. These results are supported with the upregulation of genes coding for proteins responsible for dissimilatory nitrate reduction to ammonium (nrfA), N2O formation (norV, cyt P460), and multiple multiheme c-type cytochromes for ferric iron reduction. Concomitantly, an increase in the N2O-reducing SJA-28 lineage and a decrease in the nitrite-reducing 'Candidatus Methylomirabilis oxyfera' are consistent with the changes in 'Ca. M. nitroreducens' end products. These findings demonstrate the highly flexible physiology of 'Ca. M. nitroreducens' in anaerobic ecosystems with diverse electron acceptor conditions, and further reveals its roles in linking methane oxidation to global biogeochemical cycles. 'Ca. M. nitroreducens' could significantly affect the bioavailability of nitrogen sources as well as the emission of greenhouse gas in natural ecosystems and wastewater treatment plants.

Insights into feasibility and microbial characterizations on simultaneous elimination of dissolved methane from anaerobic effluents and nitrate/nitrite reduction in a conventional anoxic reactor with magnetite

Discovery of nitrate/nitrite-dependent anaerobic methane oxidation (DAMO) challenges the conventional biological treatment processes, since it provides a possibility of simultaneously mitigating dissolved methane emissions from anaerobic effluents and reducing additional carbon sources for denitrification. Due to the slow growth of specialized DAMO microbes, this possibility has been just practiced with biofilms in membrane biofilm reactors or granular sludge in membrane bioreactors. In this study, simultaneous elimination of dissolved methane from anaerobic effluents and nitrate/nitrite reduction was achieved in a conventional anoxic reactor with magnetite. Calculations of electron flow balance showed that, with magnetite the eliminated dissolved methane was almost entirely used for nitrate/nitrite reduction, while without magnetite approximately 52 % of eliminated dissolved methane was converted to unknown organics. Metagenomic sequencing showed that, when dissolved methane served as an electron donor, the abundance of genes for reverse methanogenesis and denitrification dramatically increased, indicating that anaerobic oxidation of methane (AOM) coupled to nitrate/nitrite reduction occurred. Magnetite increased the abundance of genes encoding the key enzymes involved in whole reverse methanogenesis and Nir and Nor involved in denitrification, compared to that without magnetite. Analysis of microbial communities showed that, AOM coupled to nitrate/nitrite reduction was proceeded by syntrophic consortia comprised of methane oxidizers, Methanolinea and Methanobacterium, and nitrate/nitrite reducers, Armatimonadetes_gp5 and Thauera. With magnetite syntrophic consortia exchanged electrons more effectively than that without magnetite, further supporting the microbial growth.

Coupling Partial Nitritation, Anammox and n-DAMO in a membrane aerated biofilm reactor for simultaneous dissolved methane and nitrogen removal

Anaerobic technologies with downstream autotrophic nitrogen removal have been proposed to enhance bioenergy recovery and transform a wastewater treatment plant from an energy consumer to an energy exporter. However, approximately 20-50 % of the produced methane is dissolved in the anaerobically treated effluent and is easily stripped into the atmosphere in the downstream aerobic process, contributing to the release of greenhouse gas emissions. This study aims to develop a solution to beneficially utilize dissolved methane to support high-level nitrogen removal from anaerobically treated mainstream wastewater. A novel technology, integrating Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction (i.e. PNAM) was demonstrated in a membrane-aerated biofilm reactor (MABR). With the feeding of ∼50 mg NH4+-N/L and ∼20 mg/L dissolved methane at a hydraulic retention time of 15 h, around 90 % of nitrogen and ∼100 % of dissolved methane can be removed together in the MABR. Microbial community characterization revealed that ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), anammox bacteria, nitrite/nitrate-dependent anaerobic methane oxidation microorganisms (n-DAMO bacteria and archaea) and aerobic methanotrophs co-existed in the established biofilm. Batch tests confirmed the active microbial pathways and showed that AOB, anammox bacteria and n-DAMO microbes were jointly responsible for the nitrogen removal, and dissolved methane was mainly removed by the n-DAMO process, with aerobic methane oxidation making a minor contribution. In addition, the established system was robust against dynamic changes in influent composition. The study provides a promising technology for the simultaneous removal of dissolved methane and nitrogen from domestic wastewater, which can support the transformation of wastewater treatment from an energy- and carbon-intensive process, to one that is energy- and carbon-neutral.

Livestock dung rather than biochar enhances the anaerobic methane oxidation in grassland soils

The terrestrial anaerobic methane oxidation (AOM) coupled with denitrification is considered to be an important link in the "cryptic cycle of methane". However, it remains uncertain how land use activity such as biochar and livestock dung amendments regulate the AOM in grassland. Here, we incubated soils with biochar and dung amendments in microcosms to monitor the AOM activity and quantified the maker genes of anaerobic methanotrophs and their potential syntrophs. Dung enhanced the AOM mediated by Candidatus Methylomirabilis oxyfera and stimulated denitrifying bacteria and anammox growths as well. The biochar amendment inhibited AOM due to the trapping of NO3- and NO2-. Our study raised the possibility that anthropogenic activity can regulate AOM through porosity alteration and substrate limitation.

Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress

Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.

Long-term effect of acetate and biochar addition on enrichment and activity of denitrifying anaerobic methane oxidation microbes

The denitrifying anaerobic methane oxidation (DAMO) process plays a crucial role in the global carbon/nitrogen cycles and methane emission control, and also has application potential in biological wastewater treatment. However, given that DAMO microbes are susceptible to external conditions such as additional carbon source in the system, it is essential to evaluate the effect of alternative carbon substance on the enrichment efficiency and metabolic activity of DAMO microbes. To this end, this study investigated the effect of acetate (0.1 mmol/L-R2, 0.5 mmol/L-R3) and biochar addition (R4) on the enrichment and activity of DAMO microbes. The long-term operation showed that the NO2--N and CH4 consumption rates in the reactors almost presented the sequence of R4>R2>R3>R1. However, the short-term activity test with isotope labelling showed the sequence of R2>R4>R1>R3. Furthermore, the addition of acetate and biochar improved the electrochemical activity and extracellular polymeric substance (EPS) secretion in the systems. In R4 reactor, the proportion of DAMO bacteria was the highest (7.20%), indicating that the addition of biochar could promote the enrichment of DAMO bacteria, and Thauera was co-enriched with the proportion increasing from 0.26% to 6.73%. While in R1, R2 and R3 reactors, DAMO bacteria were enriched with relatively low abundances (0.10%, 0.23%, 0.15%, respectively), together with methanogens and denitrifiers. This study showed that biochar and acetate with appropriate concentration could enhance the enrichment and activity of DAMO bacteria, the results can provide reference for the enrichment of DAMO microbes and its application in the biological nitrogen removal of wastewater.

Salinity effect on an anaerobic methane- and ammonium-oxidising consortium: Shifts in activity, morphology, osmoregulation and syntrophic relationship

Nitrate-dependent anaerobic methane oxidation (AOM) is a microbial process of both ecological significance for global methane mitigation and application potential for wastewater treatment. It is mediated by organisms belonging to the archaeal family 'Candidatus Methanoperedenaceae', which have so far mainly been found in freshwater environments. Their potential distribution in saline environments and their physiological responses to salinity variation were still poorly understood. In this study, the responses of the freshwater 'Candidatus Methanoperedens nitroreducens'-dominated consortium to different salinities were investigated using short- and long-term setups. Short-term exposure to salt stress significantly affected nitrate reduction and methane oxidation activities over the tested concentration range of 15-200‰ NaCl, and 'Ca. M. nitroreducens' showed the higher tolerance to high salinity stress than its partner of anammox bacteria. At high salinity concentration, near marine conditions of 37‰, the target organism 'Ca. M. nitroreducens' showed stabilized nitrate reduction activity of 208.5 µmol day-1 gCDW-1 in long-term bioreactors over 300 days, in comparison to 362.9 and 334.3 µmol day-1 gCDW-1 under low-salinity conditions (1.7‰ NaCl) and control conditions (∼15‰ NaCl). Different partners of 'Ca.  M. nitroreducens' evolved in the consortia with three different salinity conditions, suggesting the different syntrophic mechanisms shaped by changes in salinity. A new syntrophic relationship between 'Ca. M. nitroreducens' and Fimicutes and/or Chloroflexi denitrifying populations was identified under the marine salinity condition. Metaproteomic analysis shows that the salinity changes lead to higher expression of response regulators and selective ion (Na+/H+) channeling proteins that can regulate the osmotic pressure between the cell and its environment. The reverse methanogenesis pathway was, however, not impacted. The finding of this study has important implications for the ecological distribution of the nitrate-dependent AOM process in marine environments and the potential of this biotechnological process for the treatment of high-salinity industrial wastewater.

Combining biological denitrification and electricity generation in methane-powered microbial fuel cells

Methane has been demonstrated to be a feasible substrate for electricity generation in microbial fuel cells (MFCs) and denitrifying anaerobic methane oxidation (DAMO). However, these two processes were evaluated separately in previous studies and it has remained unknown whether methane is able to simultaneously drive these processes. Here we investigated the co-occurrence and performance of these two processes in the anodic chamber of MFCs. The results showed that methane successfully fueled both electrogenesis and denitrification. Importantly, the maximum nitrate removal rate was significantly enhanced from (1.4 ± 0.8) to (18.4 ± 1.2) mg N/(L·day) by an electrogenic process. In the presence of DAMO, the MFCs achieved a maximum voltage of 610 mV and a maximum power density of 143 ± 12 mW/m². Electrochemical analyses demonstrated that some redox substances (e.g. riboflavin) were likely involved in electrogenesis and also in the denitrification process. High-throughput sequencing indicated that the methanogen Methanobacterium, a close relative of Methanobacterium espanolae, catalyzed methane oxidation and cooperated with both exoelectrogens and denitrifiers (e.g., Azoarcus). This work provides an effective strategy for improving DAMO in methane-powered MFCs, and suggests that methanogens and denitrifiers may jointly be able to provide an alternative to archaeal DAMO for methane-dependent denitrification.

Acetate and Acetyl-CoA Metabolism of ANME-2 Anaerobic Archaeal Methanotrophs

Acetyl-CoA synthetase (ACS) and acetate ligase (ACD) are widespread among microorganisms, including archaea, and play an important role in their carbon metabolism, although only a few of these enzymes have been characterized. Anaerobic methanotrophs (ANMEs) have been reported to convert methane anaerobically into CO2, polyhydroxyalkanoate, and acetate. Furthermore, it has been suggested that they might be able to use acetate for anabolism or aceticlastic methanogenesis. To better understand the potential acetate metabolism of ANMEs, we characterized an ACS from ANME-2a as well as an ACS and an ACD from ANME-2d. The conversion of acetate into acetyl-CoA (Vmax of 8.4 μmol mg-1 min-1 and Km of 0.7 mM acetate) by the monomeric 73.8-kDa ACS enzyme from ANME-2a was more favorable than the formation of acetate from acetyl-CoA (Vmax of 0.4 μmol mg-1 min-1 and Km of 0.2 mM acetyl-CoA). The monomeric 73.4-kDa ACS enzyme from ANME-2d had similar Vmax values for both directions (Vmax,acetate of 0.9 μmol mg-1 min-1 versus Vmax,acetyl-CoA of 0.3 μmol mg-1 min-1). The heterotetrameric ACD enzyme from ANME-2d was active solely in the acetate-producing direction. Batch incubations of an enrichment culture dominated by ANME-2d fed with 13C2-labeled acetate produced 3 μmol of [13C]methane in 7 days, suggesting that this anaerobic methanotroph might have the potential to reverse its metabolism and perform aceticlastic methanogenesis using ACS to activate acetate albeit at low rates (2 nmol g [dry weight]-1 min-1). Together, these results show that ANMEs may have the potential to use acetate for assimilation as well as to use part of the surplus acetate for methane production. IMPORTANCE Acetyl-CoA plays a key role in carbon metabolism and is found at the junction of many anabolic and catabolic reactions. This work describes the biochemical properties of ACS and ACD enzymes from ANME-2 archaea. This adds to our knowledge of archaeal ACS and ACD enzymes, only a few of which have been characterized to date. Furthermore, we validated the in situ activity of ACS in ANME-2d, showing the conversion of acetate into methane by an enrichment culture dominated by ANME-2d.

Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings

The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m3/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs ("Candidatus Methanoperedens" and "Candidatus Methylomirabilis"), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to "Ca. Methylomirabilis" are recovered, while one surprisingly expresses nitrate reductases, which we designate as "Ca. Methylomirabilis nitratireducens" representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of "Ca. Methylomirabilis" bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.

Anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens' has a pleomorphic life cycle

'Candidatus Methanoperedens' are anaerobic methanotrophic (ANME) archaea with global importance to methane cycling. Here meta-omics and fluorescence in situ hybridization (FISH) were applied to characterize a bioreactor dominated by 'Candidatus Methanoperedens nitroreducens' performing anaerobic methane oxidation coupled to nitrate reduction. Unexpectedly, FISH revealed the stable co-existence of two 'Ca. M. nitroreducens' morphotypes: the archetypal coccobacilli microcolonies and previously unreported planktonic rods. Metagenomic analysis showed that the 'Ca. M. nitroreducens' morphotypes were genomically identical but had distinct gene expression profiles for proteins associated with carbon metabolism, motility and cell division. In addition, a third distinct phenotype was observed, with some coccobacilli 'Ca. M. nitroreducens' storing carbon as polyhydroxyalkanoates. The phenotypic variation of 'Ca. M. nitroreducens' probably aids their survival and dispersal in the face of sub-optimal environmental conditions. These findings further demonstrate the remarkable ability of members of the 'Ca. Methanoperedens' to adapt to their environment.

Heterotrophic denitrification: An overlooked factor that contributes to nitrogen removal in n-DAMO mixed culture

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) has been recognized as a sustainable process for simultaneous removal of nitrogen and methane. The metabolisms of denitrifying anaerobic methanotrophs, including Candidatus Methanoperedens and Candidatus Methylomirabilis, have been well studied. However, potential roles of heterotrophs co-existing with these anaerobic methanotrophs are generally overlooked. In this study, we pulse-fed methane and nitrate into an anaerobic laboratory sequencing batch bioreactor and enriched a mixed culture with stable nitrate removal rate (NRR) of ∼28 mg NO₃^--N L^-1 d^-1. Microbial community analysis indicates abundant heterotrophs, e.g., Arenimonas (5.3%-18.9%) and Fimbriimonadales ATM1 (6.4%), were enriched together with denitrifying anaerobic methanotrophs Ca. Methanoperedens (10.8%-13.2%) and Ca. Methylomirabilis (27.4%-34.3%). The results of metagenomics and batch tests suggested that the denitrifying anaerobic methanotrophs were capable of generating methane-derived intermediates (i.e., formate and acetate), which were employed by non-methanotrophic heterotrophs for denitrification and biomass growth. These findings offer new insights into the roles of heterotrophs in n-DAMO mixed culture, which may help to optimize n-DAMO process for nitrogen removal from wastewater.

Polyhydroxyalkanoate-driven current generation via acetate by an anaerobic methanotrophic consortium

Anaerobic oxidation of methane (AOM) is an important microbial process mitigating methane (CH₄) emission from natural sediments. Anaerobic methanotrophic archaea (ANME) have been shown to mediate AOM coupled to the reduction of several compounds, either directly (i.e. nitrate, metal oxides) or in consortia with syntrophic bacterial partners (i.e. sulfate). However, the mechanisms underlying extracellular electron transfer (EET) between ANME and their bacterial partners or external electron acceptors are poorly understood. In this study, we investigated electron and carbon flow for an anaerobic methanotrophic consortium dominated by 'Candidatus Methanoperedens nitroreducens' in a CH₄-fed microbial electrolysis cell (MEC). Acetate was identified as a likely intermediate for the methanotrophic consortium, which stimulated the growth of the known electroactive genus Geobacter. Electrochemical characterization, stoichiometric calculations of the system, along with stable isotope-based assays, revealed that acetate was not produced from CH₄ directly. In the absence of CH₄, current was still generated and the microbial community remained largely unchanged. A substantial portion of the generated current in the absence of CH₄ was linked to the oxidation of the intracellular polyhydroxybutyrate (PHB) and the breakdown of extracellular polymeric substances (EPSs). The ability of 'Ca. M. nitroreducens' to use stored PHB as a carbon and energy source, and its ability to donate acetate as a diffusible electron carrier expands the known metabolic diversity of this lineage that likely underpins its success in natural systems.

The Potential of Sequential Fermentations in Converting C1 Substrates to Higher-Value Products

Today production of (bulk) chemicals and fuels almost exclusively relies on petroleum-based sources, which are connected to greenhouse gas release, fueling climate change. This increases the urgence to develop alternative bio-based technologies and processes. Gaseous and liquid C1 compounds are available at low cost and often occur as waste streams. Acetogenic bacteria can directly use C1 compounds like CO, CO₂, formate or methanol anaerobically, converting them into acetate and ethanol for higher-value biotechnological products. However, these microorganisms possess strict energetic limitations, which in turn pose limitations to their potential for biotechnological applications. Moreover, efficient genetic tools for strain improvement are often missing. However, focusing on the metabolic abilities acetogens provide, they can prodigiously ease these technological disadvantages. Producing acetate and ethanol from C1 compounds can fuel via bio-based intermediates conversion into more energy-demanding, higher-value products, by deploying aerobic organisms that are able to grow with acetate/ethanol as carbon and energy source. Promising new approaches have become available combining these two fermentation steps in sequential approaches, either as separate fermentations or as integrated two-stage fermentation processes. This review aims at introducing, comparing, and evaluating the published approaches of sequential C1 fermentations, delivering a list of promising organisms for the individual fermentation steps and giving an overview of the existing broad spectrum of products based on acetate and ethanol. Understanding of these pioneering approaches allows collecting ideas for new products and may open avenues toward making full use of the technological potential of these concepts for establishment of a sustainable biotechnology.

Methane-Dependent Extracellular Electron Transfer at the Bioanode by the Anaerobic Archaeal Methanotroph "Candidatus Methanoperedens"

Anaerobic methanotrophic (ANME) archaea have recently been reported to be capable of using insoluble extracellular electron acceptors via extracellular electron transfer (EET). In this study, we investigated EET by a microbial community dominated by "Candidatus Methanoperedens" archaea at the anode of a bioelectrochemical system (BES) poised at 0 V vs. standard hydrogen electrode (SHE), in this way measuring current as a direct proxy of EET by this community. After inoculation of the BES, the maximum current density was 274 mA m^-2 (stable current up to 39 mA m^-2). Concomitant conversion of ¹³CH₄ into ¹³CO₂ demonstrated that current production was methane-dependent, with 38% of the current attributed directly to methane supply. Based on the current production and methane uptake in a closed system, the Coulombic efficiency was about 17%. Polarization curves demonstrated that the current was limited by microbial activity at potentials above 0 V. The metatranscriptome of the inoculum was mined for the expression of c-type cytochromes potentially used for EET, which led to the identification of several multiheme c-type cytochrome-encoding genes among the most abundant transcripts in "Ca. Methanoperedens." Our study provides strong indications of EET in ANME archaea and describes a system in which ANME-mediated EET can be investigated under laboratory conditions, which provides new research opportunities for mechanistic studies and possibly the generation of axenic ANME cultures.

Response of the Anaerobic Methanotrophic Archaeon Candidatus "Methanoperedens nitroreducens" to the Long-Term Ferrihydrite Amendment

Anaerobic methanotrophic (ANME) archaea can drive anaerobic oxidation of methane (AOM) using solid iron or manganese oxides as the electron acceptors, hypothetically via direct extracellular electron transfer (EET). This study investigated the response of Candidatus "Methanoperedens nitroreducens TS" (type strain), an ANME archaeon previously characterized to perform nitrate-dependent AOM, to an Fe(III)-amended condition over a prolonged period. Simultaneous consumption of methane and production of dissolved Fe(II) were observed for more than 500 days in the presence of Ca. "M. nitroreducens TS," indicating that this archaeon can carry out Fe(III)-dependent AOM for a long period. Ca. "M. nitroreducens TS" possesses multiple multiheme c-type cytochromes (MHCs), suggesting that it may have the capability to reduce Fe(III) via EET. Intriguingly, most of these MHCs are orthologous to those identified in Candidatus "Methanoperedens ferrireducens," an Fe(III)-reducing ANME archaeon. In contrast, the population of Ca. "M. nitroreducens TS" declined and was eventually replaced by Ca. "M. ferrireducens," implying niche differentiation between these two ANME archaea in the environment.

Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors

Methane (CH₄) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an important role in the global CH₄ cycle that is controlled by the balance between anaerobic production via methanogenesis and CH₄ removal via methanotrophic oxidation. Research in recent decades advanced our understanding of CH₄ oxidation, which until 1976 was believed to be a strictly aerobic process. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is now known to be an important sink of CH₄ in marine ecosystems. Furthermore, in 2006 it was discovered that anaerobic CH₄ oxidation can also be coupled to nitrate reduction (N-DAMO), demonstrating that AOM may be much more versatile than previously thought and linked to other electron acceptors. In consequence, an increasing number of studies in recent years showed or suggested that alternative electron acceptors can be used in the AOM process including Fe^III, Mn^IV, As^V, Cr^VI, Se^VI, Sb^V, V^V, and Br^V. In addition, humic substances as well as biochar and perchlorate (ClO₄^-) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whether ANME archaea can oxidize CH₄ and reduce metallic electron acceptors independently or via electron transfer to syntrophic partners, interspecies electron transfer, nanowires or conductive pili. Therefore, the aim of this review is to summarize and discuss the current state of knowledge about ANME archaea, focusing on their physiology, metabolic flexibility and potential to use various electron acceptors.

Ventilation induced evolution pattern of archaea, fungi, bacteria and their potential roles during co-bioevaporation treatment of concentrated landfill leachate and food waste

To obtain a favorable aeration type in co-bioevaporation treatment of concentrated landfill leachate and food waste, and to deeply understand the co-bioevaporation mechanisms, the temporal evolution differences of archaea, fungi and bacteria as well as the related microbial metabolism genes and functional enzymes under intermittent ventilation (IV) and continuous ventilation (CV) were investigated. Results through metagenomics analysis showed that the less sufficient oxygen and longer thermophilic phase in IV stimulated the vigorous growth of archaea, while CV was beneficial for fungal growth. Even genes of carbohydrates and lipids metabolism and ATP-associated enzymes (enzyme 2.7.13.3 and 3.6.4.12), as well as peptidoglycan biosynthesis enzyme (enzyme 3.4.16.4), were more abundant in CV, IV hold better DNA repair ability, higher microbial viability, and less dehydrogenase sensitivity to temperatures due to the critical contribution of Pseudomonas (3.1-45.9%). Furthermore, IV consumed a similar amount of heat for water evaporation with nearly half of the ventilation of CV and was a favorable aeration type in the practical application of co-bioevaporation.

Acetate and electricity generation from methane in conductive fiber membrane- microbial fuel cells

Microbial conversion of methane to electricity, fuels, and liquid chemicals has attracted much attention. However, due to the low solubility of methane, it is not considered a suitable substrate for microbial fuel cells (MFCs). In this study, a conductive fiber membrane (CFM) module was constructed as the bioanode of methane-driven MFCs, directly delivering methane. After biofilm formation on the CFM surface, a steady voltage output of 0.6 to 0.7 V was recorded, and the CFM-MFCs obtained a maximum power density of 64 ± 2 mW/m². Moreover, methane oxidation produced a high concentration of intermediate acetate (up to 7.1 mM). High-throughput 16S rRNA gene sequencing suggests that the microbial community was significantly changed after electricity generation. Methane-related archaea formed a symbiotic consortium with characterized electroactive bacteria and fermentative bacteria, suggesting a combination of three types of microorganisms for methane conversion into acetate and electricity.

Efficient nitrogen removal from mainstream wastewater through coupling Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction (PNAM)

The application of partial nitritation and anammox to remove nitrogen from mainstream wastewater is of great interest because of the potential to reduce energy cost and carbon dosage. However, this process confronts a dilemma of relatively high effluent nitrogen concentration (>10 mg N/L), owning to the unwanted prevalence of nitrite-oxidizing bacteria (NOB) and the intrinsic nitrate production by anammox bacteria. Here, a novel technology, named the one-stage PNAM, that integrates Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction reactions, was developed in a single membrane biofilm reactor (MBfR). With feeding of synthetic mainstream wastewater containing ∼50 mg NH₄⁺-N/L at a hydraulic retention time of 12 h, more than 95% nitrogen was removed in the established one-stage PNAM process at a practically useful rate of 0.1 kg N/m³/d. Microbial community characterization and in-situ batch tests revealed a sophisticated microbial structure consisting of ammonia-oxidizing bacteria (AOB), anammox bacteria, nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) bacteria and archaea, and a small fraction of NOB and aerobic methanotrophs. The role of methane in removing nitrate was confirmed by switching on/off the methane supply, which relaxed the requirement for NOB suppression. In addition, the established system was relatively robust against temperature variations, evidenced by a total nitrogen removal efficiency above 80% at temperature as low as 14 ℃. The results provide a promising alternative for efficient nitrogen removal from domestic wastewater using methane as the sole carbon source.

Recent trends in methane to bioproduct conversion by methanotrophs

Methane is an abundant and low-cost gas with high global warming potential and its use as a feedstock can help mitigate climate change. Variety of valuable products can be produced from methane by methanotrophs in gas fermentation processes. By using methane as a sole carbon source, methanotrophic bacteria can produce bioplastics, biofuels, feed additives, ectoine and variety of other high-value chemical compounds. A lot of studies have been conducted through the years for natural methanotrophs and engineered strains as well as methanotrophic consortia. These have focused on increasing yields of native products as well as proof of concept for the synthesis of new range of chemicals by metabolic engineering. This review shows trends in the research on key methanotrophic bioproducts since 2015. Despite certain limitations of the known production strategies that makes commercialization of methane-based products challenging, there is currently much attention placed on the promising further development.

Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site

During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.

Interactions of functional microorganisms and their contributions to methane bioconversion to short-chain fatty acids

Methane bioconversion to value-added liquid chemicals has been proposed as a promising solution to augment the petroleum-dominated chemical market. Recent investigations have reported that various electron acceptors (e.g., nitrite and nitrate) are available to drive methane bioconversion to short-chain fatty acids (SCFAs). However, little is known about effects of the rate electron acceptor supplied on liquid chemical production from methane. Herein, three independent membrane biofilm reactors (MBfRs) feeding with respective nitrate, nitrite, combined nitrate and nitrite were operated under high and low rate condition in succession, to study whether feeding rate of electron acceptors could impact the methane bioconversion to SCFAs and the associated microbiological features. Long-term operation showed that all tested electron acceptors with a high supply rate were favorable for methane bioconversion to SCFAs (990.9 mg L^-1d^-1, 1695.7 mg L^-1d^-1, and 2425.7 mg L^-1d^-1), while under a low electron acceptor feeding rate, the SCFA production rate decreased to 8.9 mg L^-1d^-1, 16.8 mg L^-1d^-1, and 260.1 mg L^-1d^-1, respectively. Microbial community characterization showed that the biofilm was predominated by Methanosarcina, Methanobacterium, Propionispora and Clostridium. On the basis of the known metabolism characteristics of these microorganisms, it was assumed that these methanogens and fermenters contributed jointly to methane bioconversion to SCFAs. The findings could be helpful to understand the role of electron acceptor rate in methane bioconversion to liquid chemicals.

Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community

In recent years, the externalization of electrons as part of respiratory metabolic processes has been discovered in many different bacteria and some archaea. Microbial extracellular electron transfer (EET) plays an important role in many anoxic natural or engineered ecosystems. In this study, an anaerobic methane-converting microbial community was investigated with regard to its potential to perform EET. At this point, it is not well-known if or how EET confers a competitive advantage to certain species in methane-converting communities. EET was investigated in a two-chamber electrochemical system, sparged with methane and with an applied potential of +400 mV versus standard hydrogen electrode. A biofilm developed on the working electrode and stable low-density current was produced, confirming that EET indeed did occur. The appearance and presence of redox centers at −140 to −160 mV and at −230 mV in the biofilm was confirmed by cyclic voltammetry scans. Metagenomic analysis and fluorescence in situ hybridization of the biofilm showed that the anaerobic methanotroph ‘Candidatus Methanoperedens BLZ2’ was a significant member of the biofilm community, but its relative abundance did not increase compared to the inoculum. On the contrary, the relative abundance of other members of the microbial community significantly increased (up to 720-fold, 7.2% of mapped reads), placing these microorganisms among the dominant species in the bioanode community. This group included Zoogloea sp., Dechloromonas sp., two members of the Bacteroidetes phylum, and the spirochete Leptonema sp. Genes encoding proteins putatively involved in EET were identified in Zoogloea sp., Dechloromonas sp. and one member of the Bacteroidetes phylum. We suggest that instead of methane, alternative carbon sources such as acetate were the substrate for EET. Hence, EET in a methane-driven chemolithoautotrophic microbial community seems a complex process in which interactions within the microbial community are driving extracellular electron transfer to the electrode.

Methane in wastewater treatment plants: status, characteristics, and bioconversion feasibility by methane oxidizing bacteria for high value-added chemicals production and wastewater treatment

Methane is a type of renewable fuel that can generate many types of high value-added chemicals, however, besides heat and power production, there is little methane utilization in most of the wastewater treatment plants (WWTPs) all round the world currently. In this review, the status of methane production performance from WWTPs was firstly investigated. Subsequently, based on the identification and classification of methane oxidizing bacteria (MOB), the key enzymes and metabolic pathway of MOB were presented in depth. Then the production, extraction and purification process of high value-added chemicals, including methanol, ectoine, biofuel, bioplastic, methane protein and extracellular polysaccharides, were introduced in detail, which was conducive to understand the bioconversion process of methane. Finally, the use of methane in wastewater treatment process, including nitrogen removal, emerging contaminants removal as well as resource recovery was extensively explored. These findings could provide guidance in the development of sustainable economy and environment, and facilitate biological methane conversion by using MOB in further attempts.

Making good use of methane to remove oxidized contaminants from wastewater

Being an energetic fuel, methane is able to support microbial growth and drive the reduction of various electron acceptors. These acceptors include a broad range of oxidized contaminants (e.g., nitrate, nitrite, perchlorate, bromate, selenate, chromate, antimonate and vanadate) that are ubiquitously detected in water environments and pose threats to human and ecological health. Using methane as electron donor to biologically reduce these contaminants into nontoxic forms is a promising solution to remediate polluted water, considering that methane is a widely available and inexpensive electron donor. The understanding of methane-based biological reduction processes and the responsible microorganisms has grown in the past decade. This review summarizes the fundamentals of metabolic pathways and microorganisms mediating microbial methane oxidation. Experimental demonstrations of methane as an electron donor to remove oxidized contaminants are summarized, compared, and evaluated. Finally, the review identifies opportunities and unsolved questions that deserve future explorations for broadening understanding of methane oxidation and promoting its practical applications.

Exploring simultaneous nitrous oxide and methane sink in wetland sediments under anoxic conditions

Methane (CH₄) and nitrous oxide (N₂O) are the most powerful greenhouse gases globally; recent emissions exceed previous estimates. The potential link between N₂O reduction and CH₄ oxidation in anoxic wetland sediments would be a sink for both gases, which has attracted broad attention. To explore the simultaneous N₂O and CH₄ biotransformation, wetland sediments were used to inoculate an enrichment reactor, continuously fed with CH₄ and N₂O for 500 days. After enrichment, the CH₄ oxidation rate reached 2.8 μmol·g^-1_dw·d^-1, which was 800-fold higher than the rate of the wetland sediments used as inoculum. Moreover, stable isotopic tracing proved CH₄ oxidation was driven by N₂O consumption under anoxic conditions. Genomic sequencing showed that the microbial community was dominated by methanotrophs. Species of Methylocaldum genus, belonging to γ-Proteobacteria class, were significantly enriched, and became the predominant methanotrophs. Quantitative analysis indicated methane monooxygenase and nitrous oxide reductase increased by 38- and 8-fold compared to the inoculum. As to the potential mechanisms, we propose that N₂O-driven CH₄ oxidation was mediated by aerobic methanotrophs solely or along with denitrifying bacteria under hypoxia. Electrons and energy are generated and transferred in the oxidative phosphorylation pathway. Our findings expand the range of electron acceptors associated with CH₄ oxidation as well as elucidate the significant role of methanotrophs relative to both carbon and nitrogen cycles.

Organohalide-Respiring Bacteria at the Heart of Anaerobic Metabolism in Arctic Wet Tundra Soils

Recent work revealed an active biological chlorine cycle in coastal Arctic tundra of northern Alaska. This raised the question of whether chlorine cycling was restricted to coastal areas or if these processes extended to inland tundra. The anaerobic process of organohalide respiration, carried out by specialized bacteria like Dehalococcoides, consumes hydrogen gas and acetate using halogenated organic compounds as terminal electron acceptors, potentially competing with methanogens that produce the greenhouse gas methane. We measured microbial community composition and soil chemistry along an ∼262-km coastal-inland transect to test for the potential of organohalide respiration across the Arctic Coastal Plain and studied the microbial community associated with Dehalococcoides to explore the ecology of this group and its potential to impact C cycling in the Arctic. Concentrations of brominated organic compounds declined sharply with distance from the coast, but the decrease in organic chlorine pools was more subtle. The relative abundances of Dehalococcoides were similar across the transect, except for being lower at the most inland site. Dehalococcoides correlated with other strictly anaerobic genera, plus some facultative ones, that had the genetic potential to provide essential resources (hydrogen, acetate, corrinoids, or organic chlorine). This community included iron reducers, sulfate reducers, syntrophic bacteria, acetogens, and methanogens, some of which might also compete with Dehalococcoides for hydrogen and acetate. Throughout the Arctic Coastal Plain, Dehalococcoides is associated with the dominant anaerobes that control fluxes of hydrogen, acetate, methane, and carbon dioxide. Depending on seasonal electron acceptor availability, organohalide-respiring bacteria could impact carbon cycling in Arctic wet tundra soils.IMPORTANCE Once considered relevant only in contaminated sites, it is now recognized that biological chlorine cycling is widespread in natural environments. However, linkages between chlorine cycling and other ecosystem processes are not well established. Species in the genus Dehalococcoides are highly specialized, using hydrogen, acetate, vitamin B₁₂-like compounds, and organic chlorine produced by the surrounding community. We studied which neighbors might produce these essential resources for Dehalococcoides species. We found that Dehalococcoides species are ubiquitous across the Arctic Coastal Plain and are closely associated with a network of microbes that produce or consume hydrogen or acetate, including the most abundant anaerobic bacteria and methanogenic archaea. We also found organic chlorine and microbes that can produce these compounds throughout the study area. Therefore, Dehalococcoides could control the balance between carbon dioxide and methane (a more potent greenhouse gas) when suitable organic chlorine compounds are available to drive hydrogen and acetate uptake.

Biochar facilitates rapid restoration of methanogenesis by enhancing direct interspecies electron transfer after high organic loading shock

This study evaluated the effectiveness of biochar addition against high organic loading shock (OLS) of 80 kg COD/m³/d in up-flow anaerobic sludge blanket (UASB) reactors (R1 with biochar; R2 without biochar). After OLS of 24 h, R2 suffered the irreversible acidification (pH of 5.42 ± 0.07) with low biogas production of 0.08 ± 0.01 m³/kg COD/d. In contrast, the biogas production in R1 restored rapidly to 0.33 ± 0.04 m³/kg COD/d, and effluent pH in R1 returned to 7.01 ± 0.22. With addition of biochar, potential direct interspecies electron transfer (DIET) partners, including volatile fatty acids (VFAs)-oxidizing bacteria (Bacteroidetes, Smithella, Desulfovibrio, Geobacter) and methanogens (Methanosaeta, Methanosarcina) were enriched in R1, which were conductive to maintain the balance of acidogenesis and methanogenesis. Moreover, the retention of Methanosaeta and Methanosarcina coupled with biochar maintained the structural stability of granular sludge in R1 under the pressure of OLS and VFAs, which guaranteed the stability of anaerobic system.

Valorization of methane from environmental engineering applications: A critical review

Wastewater and waste management sectors alone account for 18% of the anthropogenic methane (CH₄) emissions. This study presents a critical overview of methanotrophs ("methane oxidizing microorganisms") for valorizing typically discarded CH₄ from environmental engineering applications, focusing on wastewater treatment plants. Methanotrophs can convert CH₄ into valuable bioproducts including chemicals, biodiesel, DC electricity, polymers, and S-layers, all under ambient conditions. As discarded CH₄ and its oxidation products can also be used as a carbon source in nitrification and annamox processes. Here we discuss modes of CH₄ assimilation by methanotrophs in both natural and engineered systems. We also highlight the technical challenges and technological breakthroughs needed to enable targeted CH₄ oxidation in wastewater treatment plants.

Enhancing methane oxidation in a bioelectrochemical membrane reactor using a soluble electron mediator

BACKGROUND

Bioelectrochemical methane oxidation catalysed by anaerobic methanotrophic archaea (ANME) is constrained by limited methane bioavailability as well as by slow kinetics of extracellular electron transfer (EET) of ANME. In this study, we tested a combination of two strategies to improve the performance of methane-driven bioelectrochemical systems that includes (1) the use of hollow fibre membranes (HFMs) for efficient methane delivery to the ANME organisms and (2) the amendment of ferricyanide, an effective soluble redox mediator, to the liquid medium to enable electrochemical bridging between the ANME organisms and the anode, as well as to promote EET kinetics of ANME.

RESULTS

The combined use of HFMs and the soluble mediator increased the performance of ANME-based bioelectrochemical methane oxidation, enabling the delivery of up to 196 mA m^-2, thereby outperforming the control system by 244 times when HFMs were pressurized at 1.6 bar.

CONCLUSIONS

Improving methane delivery and EET are critical to enhance the performance of bioelectrochemical methane oxidation. This work demonstrates that by process engineering optimization, energy recovery from methane through its direct oxidation at relevant rates is feasible.

From Acetate to Bio-Based Products: Underexploited Potential for Industrial Biotechnology

Currently, most biotechnological products are based on microbial conversion of carbohydrate substrates that are predominantly generated from sugar- or starch-containing plants. However, direct competitive uses of these feedstocks in the food and feed industry represent a dilemma, so using alternative carbon sources has become increasingly important in industrial biotechnology. A promising alternative carbon source that may be generated in substantial amounts from lignocellulosic biomass and C1 gases is acetate. This review discusses the underexploited potential of acetate to become a next-generation platform substrate in future industrial biotechnology and summarizes alternative sources and routes for acetate production. Furthermore, biotechnological aspects of microbial acetate utilization and the state of the art of biotechnological acetate conversion into value-added bioproducts are highlighted.

Investigation of central energy metabolism-related protein complexes of ANME-2d methanotrophic archaea by complexome profiling

The anaerobic oxidation of methane is important for mitigating emissions of this potent greenhouse gas to the atmosphere and is mediated by anaerobic methanotrophic archaea. In a 'Candidatus Methanoperedens BLZ2' enrichment culture used in this study, methane is oxidized to CO₂ with nitrate being the terminal electron acceptor of an anaerobic respiratory chain. Energy conservation mechanisms of anaerobic methanotrophs have mostly been studied at metagenomic level and hardly any protein data is available at this point. To close this gap, we used complexome profiling to investigate the presence and subunit composition of protein complexes involved in energy conservation processes. All enzyme complexes and their subunit composition involved in reverse methanogenesis were identified. The membrane-bound enzymes of the respiratory chain, such as F₄₂₀H₂:quinone oxidoreductase, membrane-bound heterodisulfide reductase, nitrate reductases and Rieske cytochrome bc₁ complex were all detected. Additional or putative subunits such as an octaheme subunit as part of the Rieske cytochrome bc₁ complex were discovered that will be interesting targets for future studies. Furthermore, several soluble proteins were identified, which are potentially involved in oxidation of reduced ferredoxin produced during reverse methanogenesis leading to formation of small organic molecules. Taken together these findings provide an updated, refined picture of the energy metabolism of the environmentally important group of anaerobic methanotrophic archaea.

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea

Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.

Ocean cold seeps are poorly understood relative to related systems like hydrothermal vents. Here the authors use high pressure bioreactors and microbial communities from a cold seep mud volcano and find a previously missing step of methane conversion to acetate that likely fuels heterotrophic communities.

Microbial Methane Conversion to Short-Chain Fatty Acids Using Various Electron Acceptors in Membrane Biofilm Reactors

Given our vast methane reserves and the forecasted shortage of crude oil in the not too distant future, the conversion of methane into value-added liquid chemicals or fuels would be beneficial. The generated chemicals or fuels could augment the petroleum-dominated chemical market, and also satisfy the increasing demand for transportation fuels. While methane bioconversion to liquid chemicals has just been reported recently, there is limited understanding of the process. This study aims to clarify the potential electron acceptors that could support the process. Here we operated four membrane biofilm reactors (MBfRs) fed with nitrate, nitrite, oxygen at a relatively low rate, and oxygen at a relatively high rate, respectively, to study if they can support methane bioconversion to short-chain fatty acids (SCFAs) and the associated microbiological features. All tested electron acceptors facilitated methane bioconversion to SCFAs (ranging from 1.1 to 36.7 mg acetate L^-1 d^-1, or 3.4 to 114.6 mg acetate d^-1 m^-2 of biofilm). The carbon efficiency was estimated to be 7.9 ± 1.4% to 148.5 ± 1.3%, with an efficiency higher than 100%, suggesting the assimilation of other carbon, very likely CO₂, into the products. A low oxygen supply rate of 46.4 ± 2.3 mg O₂ d^-1 m^-2 was found to be the most favorable among all the electron conditions provided according to the SCFAs production rate and also the carbon utilization efficiency. Microbial characterization revealed that completely different communities evolved in the respective reactors, suggesting diverse microbial pathways exist for methane bioconversion into value-added chemicals.

Optical Detection of Small Metabolites for Biological Gas Conversion by using Metal Nanoparticle Monolayers Produced by Capillary-Assisted Transfer

Detection of small metabolites is essential for monitoring and optimizing biological gas conversion. Currently, such detection is typically done by liquid chromatography with offline sampling. However, this method often requires large equipment with multiple separation columns and is at risk of serious microbial contamination during sampling. Here we propose real-time optical detection of small metabolites using uniform plasmonic nanoparticles monolayers produced by capillary-assisted transfer. We reproducibly fabricate metal nanoparticles monolayers with a diameter of ∼1 mm for the detection of acetate, butyrate, and glucose by a glass capillary tube. Metal nanoparticles monolayers are not only uniform in terms of average interparticle distance but also structurally stable under dynamic fluidic conditions. The monolayers resistant to fluid shear stress with surface-enhanced Raman scattering are able to reversibly monitor the concentration of acetate and sensitively detect acetate and glucose at levels as low as 10 μM, which is more than 2 orders of magnitude lower than the concentration range of typical biological gas conversion. In addition, structurally similar metabolites such as acetate and butyrate, when mixed, become distinguishable by our method.