A Review of 3-Nitrooxypropanol for Enteric Methane Mitigation from Ruminant Livestock

Methane (CH4) from enteric fermentation accounts for 3 to 5% of global anthropogenic greenhouse gas emissions, which contribute to climate change. Cost-effective strategies are needed to reduce feed energy losses as enteric CH4 while improving ruminant production efficiency. Mitigation strategies need to be environmentally friendly, easily adopted by producers and accepted by consumers. However, few sustainable CH4 mitigation approaches are available. Recent studies show that the chemically synthesized CH4 inhibitor 3-nitrooxypropanol is one of the most effective approaches for enteric CH4 abatement. 3-nitrooxypropanol specifically targets the methyl-coenzyme M reductase and inhibits the final catalytic step in methanogenesis in rumen archaea. Providing 3-nitrooxypropanol to dairy and beef cattle in research studies has consistently decreased enteric CH4 production by 30% on average, with reductions as high as 82% in some cases. Efficacy is positively related to 3-NOP dose and negatively affected by neutral detergent fiber concentration of the diet, with greater responses in dairy compared with beef cattle when compared at the same dose. This review collates the current literature on 3-nitrooxypropanol and examines the overall findings of meta-analyses and individual studies to provide a synthesis of science-based information on the use of 3-nitrooxypropanol for CH4 abatement. The intent is to help guide commercial adoption at the farm level in the future. There is a significant body of peer-reviewed scientific literature to indicate that 3-nitrooxypropanol is effective and safe when incorporated into total mixed rations, but further research is required to fully understand the long-term effects and the interactions with other CH4 mitigating compounds.

Assessment of Temporal Effects of a Mud Volcanic Eruption on the Bacterial Community and Their Predicted Metabolic Functions in the Mud Volcanic Sites of Niaosong, Southern Taiwan

The microbial communities inhabiting mud volcanoes have received more attention due to their noteworthy impact on the global methane cycle. However, the impact of temporal effects of volcanic eruptions on the microbial community’s diversity and functions remain poorly characterized. This study aimed to underpin the temporal variations in the bacterial community’s diversity and PICRUSt-predicted functional profile changes of mud volcanic sites located in southern Taiwan using 16S rRNA gene sequencing. The physicochemical analysis showed that the samples were slightly alkaline and had elevated levels of Na⁺, Cl⁻, and SO₄²⁻. Comparatively, the major and trace element contents were distinctly higher, and tended to be increased in the long-period samples. Alpha diversity metrics revealed that the bacterial diversity and abundance were lesser in the initial period, but increased over time. Instead, day 96 and 418 samples showed reduced bacterial abundance, which may have been due to the dry spell that occurred before each sampling. The initial-period samples were significantly abundant in haloalkaliphilic marine-inhabiting, hydrocarbon-degrading bacterial genera such as Marinobacter, Halomonas, Marinobacterium, and Oceanimonas. Sulfur-reducing bacteria such as Desulfurispirillum and Desulfofarcimen were found dominant in the mid-period samples, whereas the methanogenic archaeon Methanosarcina was abundant in the long-period samples. Unfortunately, heavy precipitation encountered during the mid and long periods may have polluted the volcanic site with animal pathogens such as Desulfofarcimen and Erysipelothrix. The functional prediction results showed that lipid biosynthesis and ubiquinol pathways were significantly abundant in the initial days, and the super pathway of glucose and xylose degradation was rich in the long-period samples. The findings of this study highlighted that the temporal effects of a mud volcanic eruption highly influenced the bacterial diversity, abundance, and functional profiles in our study site.

Enceladus as a Potential Niche for Methanogens and Estimation of Its Biomass

Enceladus is a potential target for future astrobiological missions. NASA's Cassini spacecraft demonstrated that the Saturnian moon harbors a salty ocean beneath its icy crust and the existence and analysis of the plume suggest water-rock reactions, consistent with the possible presence of hydrothermal vents. Particularly, the plume analysis revealed the presence of molecular hydrogen, which may be used as an energy source by microorganisms ( e.g., methanogens). This could support the possibility that populations of methanogens could establish in such environments if they exist on Enceladus. We took a macroscale approximation using ecological niche modeling to evaluate whether conditions suitable for methanogenic archaea on Earth are expected in Enceladus. In addition, we employed a new approach for computing the biomass using the Monod growth model. The response curves for the environmental variables performed well statistically, indicating that simple correlative models may be used to approximate large-scale distributions of these genera on Earth. We found that the potential hydrothermal conditions on Enceladus fit within the macroscale conditions identified as suitable for methanogens on Earth, and estimated a concentration of 1010-1011 cells/cm3.

Response of Methanogen Communities to the Elevation of Cathode Potentials in Bioelectrochemical Reactors Amended with Magnetite

Electromethanogenesis refers to the process whereby methanogens utilize current for the reduction of CO₂ to CH₄. Setting low cathode potentials is essential for this process. In this study, we tested if magnetite, an iron oxide mineral widespread in the environment, can facilitate the adaptation of methanogen communities to the elevation of cathode potentials in electrochemical reactors. Two-chamber electrochemical reactors were constructed with inoculants obtained from paddy field soil. We elevated cathode potentials stepwise from the initial -0.6 V versus the standard hydrogen electrode (SHE) to -0.5 V and then to -0.4 V over the 130 days of acclimation. Only weak current consumption and CH₄ production were observed in the bioreactors without magnetite. However, significant current consumption and CH₄ production were recorded in the magnetite bioreactors. The robustness of electroactivity of the magnetite bioreactors was not affected by the elevation of cathode potentials from -0.6 V to -0.4 V. However, the current consumption and CH₄ production were halted in the bioreactors without magnetite when the cathode potentials were elevated to -0.4 V. Methanogens related to Methanospirillum were enriched on the cathode surfaces of magnetite bioreactors at -0.4 V, while Methanosarcina relatively dominated in the bioreactors without magnetite. Methanobacterium also increased in the magnetite bioreactors but stayed off electrodes at -0.4 V. Apparently, the magnetite greatly facilitates the development of biocathodes, and it appears that with the aid of magnetite, Methanospirillum spp. can adapt to the high cathode potentials, performing efficient electromethanogenesis. IMPORTANCE Converting CO₂ to CH₄ through bioelectrochemistry is a promising approach to the development of green energy biotechnology. This process, however, requires low cathode potentials, which entails a cost. In this study, we tested if magnetite, a conductive iron mineral, can facilitate the adaptation of methanogens to the elevation of cathode potentials. In two-chamber reactors constructed by using inoculants obtained from paddy field soil, biocathodes developed robustly in the presence of magnetite, whereas only weak activities in CH₄ production and current consumption were observed in the bioreactors without magnetite. The elevation of cathode potentials did not affect the robustness of electroactivity of the magnetite bioreactors over the 130 days of acclimation. Methanospirillum strains were identified as the key methanogens associated with the cathode surfaces during the operation at high potentials. The findings reported in this study shed new light on the adaptation of methanogen communities to the elevated cathode potentials in the presence of magnetite.

Growth Coordination Between Butyrate-Oxidizing Syntrophs and Hydrogenotrophic Methanogens

Syntrophy is a thermodynamically required mutualistic cooperation between fatty acid-oxidizing bacteria and methanogens that plays the important role in organic decomposition and methanogenesis in anoxic environments. In this study, three experiments were conducted to evaluate the cell-to-cell interaction in a thermophilic coculture consisting of Syntrophothermus lipocalidus and Methanocella conradii and a mesophilic coculture consisting of Syntrophomonas wolfei and Methanococcus maripaludis. First, syntrophs and methanogens were inoculated at different initial cell ratios to evaluate the growth synchronization. The quantitative PCR analysis revealed that the organism with a lower relative abundance at the beginning always grew faster, and the cell ratio converged over time to relative constant values in both the thermophilic and mesophilic cocultures. Next, intermittent ultrasound and constant shaking treatments were used to evaluate the influence of physical disturbance on microbial aggregation in the mesophilic coculture. The fluorescence in situ hybridization and scanning electron microscopy revealed that the tendency of syntrophic aggregation was not affected by the physical disturbances, although the activity was slightly depressed. Syntrophomonas dominated in the initial microbial aggregates, which, however, did not grow until Methanococcus was attached and increased to a significant extent, indicating the local growth synchronization during the formation and maturation of syntrophic aggregates. Last, microfluidic experiments revealed that whether or not Syntrophomonas or Methanococcus was loaded first, the second organism preferred moving to the place where the first organism was located, suggesting the cell-to-cell attraction between Syntrophomonas and Methanococcus. Collectively, our study demonstrated the growth synchronization and cell-to-cell attraction between the butyrate-oxidizing bacteria and methanogens for optimizing the syntrophic cooperation.

Disproportionate microbial responses to decadal drainage on a Siberian floodplain

Permafrost thaw induces soil hydrological changes which in turn affects carbon cycle processes in the Arctic terrestrial ecosystems. However, hydrological impacts of thawing permafrost on microbial processes and greenhouse gas (GHG) dynamics are poorly understood. This study examined changes in microbial communities using gene and genome-centric metagenomics on an Arctic floodplain subject to decadal drainage, and linked them to CO₂ and CH₄ flux and soil chemistry. Decadal drainage led to significant changes in the abundance, taxonomy, and functional potential of microbial communities, and these modifications well explained the changes in CO₂ and CH₄ fluxes between ecosystem and atmosphere-increased fungal abundances potentially increased net CO₂ emission rates and highly reduced CH₄ emissions in drained sites corroborated the marked decrease in the abundance of methanogens and methanotrophs. Interestingly, various microbial taxa disproportionately responded to drainage: Methanoregula, one of the key players in methanogenesis under saturated conditions, almost disappeared, and also Methylococcales methanotrophs were markedly reduced in response to drainage. Seven novel methanogen population genomes were recovered, and the metabolic reconstruction of highly correlated population genomes revealed novel syntrophic relationships between methanogenic archaea and syntrophic partners. These results provide a mechanistic view of microbial processes regulating GHG dynamics in the terrestrial carbon cycle, and disproportionate microbial responses to long-term drainage provide key information for understanding the effects of warming-induced soil drying on microbial processes in Arctic wetland ecosystems.

The Effect of Different Concentrations of Total Polyphenols from Paulownia Hybrid Leaves on Ruminal Fermentation, Methane Production and Microorganisms

This experiment was conducted to study the effects of different concentrations of polyphenols of Paulownia Clon In Vitro 112^® leaves or their particular parts on in vitro ruminal fermentation, methane production and microbial population. Paulownia leaves with high (PLH; 31.35 mg/g dry matter (DM)), medium (PLM; 26.94 mg/g DM), and low level of polyphenols (PLL; 11.90 mg/g DM) were used from three plantation areas. Lamina (PLLA; 33.63 mg/g DM) and twigs (PLT; 2.53 mg/g DM) of leaves were also collected from the PLM plantation. The chemical analyses of Paulownia leaves indicated that the content of the most basic nutrients (e.g., crude protein concentration of 185 g/kg of DM) were similar to dehydrated alfalfa. The in vitro results showed that the use of Paulownia leaves with the highest content of total polyphenols (PLH and PLLA) decreased methane production, methanogens numbers, and acetate to propionate ratio. In PLT, lowered methane production was followed by reduced substrate degradability and volatile fatty acid (VFA) concentration along with higher acetate to propionate ratio. Therefore, reduction of methane production in PLH and PLLA was attributed to the lowered methanogen population, whereas in PLT it was caused by decreased substrate degradability with the resultant of limited hydrogen availability to the methanogens.

Presence of Adult Companion Goats Favors the Rumen Microbial and Functional Development in Artificially Reared Kids

Newborn dairy ruminants are usually separated from their dams after birth and fed on milk replacer. This lack of contact with adult animals may hinder the rumen microbiological and physiological development. This study evaluates the effects of rearing newborn goat kids in contact with adult companions on the rumen development. Thirty-two newborn goat kids were randomly allocated to two experimental groups which were reared either in the absence (CTL) or in the presence of non-lactating adult goats (CMP) and weaned at 7 weeks of age. Blood and rumen samples were taken at 5, 7, and 9 weeks of age to evaluate blood metabolites and rumen microbial fermentation. Next-generation sequencing was carried out on rumen samples collected at 7 weeks of age. Results showed that CTL kids lacked rumen protozoa, whereas CMP kids had an abundant and complex protozoal community as well as higher methanogen abundance which positively correlated with the body weight and blood β-hydroxybutyrate as indicators of the physiological development. CMP kids also had a more diverse bacterial community (+132 ASVs) and a different structure of the bacterial and methanogen communities than CTL kids. The core rumen bacterial community in CMP animals had 53 more ASVs than that of CTL animals. Furthermore, the number of ASVs shared with the adult companions was over 4-fold higher in CMP kids than in CTL kids. Greater levels of early rumen colonizers Proteobacteria and Spirochaetes were found in CTL kids, while CMP kids had higher levels of Bacteroidetes and other less abundant taxa (Veillonellaceae, Cyanobacteria, and Selenomonas). These findings suggest that the presence of adult companions facilitated the rumen microbial development prior to weaning. This accelerated microbial development had no effect on the animal growth, but CMP animals presented higher rumen pH and butyrate (+45%) and ammonia concentrations than CTL kids, suggesting higher fibrolytic and proteolytic activities. CMP kids also had higher blood β-hydroxybutyrate (+79%) and lower blood glucose concentrations (-23%) at weaning, indicating an earlier metabolic development which could favor the transition from pre-ruminant to ruminant after the weaning process. Further research is needed to determine the effects of this intervention in more challenging farm conditions.

Pathways of Iron and Sulfur Acquisition, Cofactor Assembly, Destination, and Storage in Diverse Archaeal Methanogens and Alkanotrophs

Archaeal methanogens, methanotrophs, and alkanotrophs have a high demand for iron (Fe) and sulfur (S); however, little is known of how they acquire, traffic, deploy, and store these elements. Here, we examined the distribution of homologs of proteins mediating key steps in Fe/S metabolism in model microorganisms, including iron(II) sensing/uptake (FeoAB), sulfide extraction from cysteine (SufS), and the biosynthesis of iron-sulfur [Fe-S] clusters (SufBCDE), siroheme (Pch2 dehydrogenase), protoheme (AhbABCD), cytochrome c (Cyt c) (CcmCF), and iron storage/detoxification (Bfr, FtrA, and IssA), among 326 publicly available, complete or metagenome-assembled genomes of archaeal methanogens/methanotrophs/alkanotrophs. The results indicate several prevalent but nonuniversal features, including FeoB, SufBC, and the biosynthetic apparatus for the basic tetrapyrrole scaffold, as well as its siroheme (and F₄₃₀) derivatives. However, several early-diverging genomes lacked SufS and pathways to synthesize and deploy heme. Genomes encoding complete versus incomplete heme biosynthetic pathways exhibited equivalent prevalences of [Fe-S] cluster binding proteins, suggesting an expansion of catalytic capabilities rather than substitution of heme for [Fe-S] in the former group. Several strains with heme binding proteins lacked heme biosynthesis capabilities, while other strains with siroheme biosynthesis capability lacked homologs of known siroheme binding proteins, indicating heme auxotrophy and unknown siroheme biochemistry, respectively. While ferritin proteins involved in ferric oxide storage were widespread, those involved in storing Fe as thioferrate were unevenly distributed. Collectively, the results suggest that differences in the mechanisms of Fe and S acquisition, deployment, and storage have accompanied the diversification of methanogens/methanotrophs/alkanotrophs, possibly in response to differential availability of these elements as these organisms evolved.

IMPORTANCE Archaeal methanogens, methanotrophs, and alkanotrophs, argued to be among the most ancient forms of life, have a high demand for iron (Fe) and sulfur (S) for cofactor biosynthesis, among other uses. Here, using comparative bioinformatic approaches applied to 326 genomes, we show that major differences in Fe/S acquisition, trafficking, deployment, and storage exist in this group. Variation in these characters was generally congruent with the phylogenetic placement of these genomes, indicating that variation in Fe/S usage and deployment has contributed to the diversification and ecology of these organisms. However, incongruency was observed among the distribution of cofactor biosynthesis pathways and known protein destinations for those cofactors, suggesting auxotrophy or yet-to-be-discovered pathways for cofactor biosynthesis.

Algal Organic Matter Drives Methanogen-Mediated Methylmercury Production in Water from Eutrophic Shallow Lakes

Algal blooms bring massive amounts of algal organic matter (AOM) into eutrophic lakes, which influences microbial methylmercury (MeHg) production. However, because of the complexity of AOM and its dynamic changes during algal decomposition, the relationship between AOM and microbial Hg methylators remains poorly understood, which hinders predicting MeHg production and its bioaccumulation in eutrophic shallow lakes. To address that, we explored the impacts of AOM on microbial Hg methylators and MeHg production by characterizing dissolved organic matter with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy and quantifying the microbial Hg methylation gene hgcA. We first reveal that the predominance of methanogens, facilitated by eutrophication-induced carbon input, could drive MeHg production in lake water. Specifically, bioavailable components of AOM (i.e., CHONs such as aromatic proteins and soluble microbial byproduct-like materials) increased the abundances (Archaea-hgcA gene: 438-2240% higher) and activities (net CH₄ production: 16.0-44.4% higher) of Archaea (e.g., methanogens). These in turn led to enhanced dissolved MeHg levels (24.3-15,918% higher) for three major eutrophic shallow lakes in China. Nevertheless, our model results indicate that AOM-facilitated MeHg production could be offset by AOM-induced MeHg biodilution under eutrophication. Our study would help reduce uncertainties in predicting MeHg production, providing a basis for mitigating the MeHg risk in eutrophic lakes.

Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China

Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla-Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.

Methanogenic Community, CH4 Production Potential and Its Determinants in the Active Layer and Permafrost Deposits on the Tibetan Plateau

Permafrost thaw could increase methane (CH4) emissions, which largely depends on CH4 production driven by methanogenic archaea. However, large-scale evidence regarding key methanogenic taxa and their relative importance to abiotic factors in mediating methanogenesis remains limited. Here, we explored the methanogenic community, potential CH4 production and its determinants in the active layer and permafrost deposits based on soil samples acquired from 12 swamp meadow sites along a ∼1000 km permafrost transect on the Tibetan Plateau. Our results revealed lower CH4 production potential, mcrA gene abundance, and richness in the permafrost layer than those in the active layer. CH4 production potential in both soil layers was regulated by microbial and abiotic factors. Of the microbial properties, marker OTUs, rather than the abundance and diversity of methanogens, stimulated CH4 production potential. Marker OTUs differed between the two soil layers with hydrogenotrophic Methanocellales and facultative acetoclastic Methanosarcina predominant in regulating CH4 production potential in the permafrost and active layer, respectively. Besides microbial drivers, CH4 production potential increased with the carbon/nitrogen (C/N) ratio in both soil layers and was also stimulated by soil moisture in the permafrost layer. These results provide empirical evidence for model improvements to better predict permafrost carbon feedback to climate warming.

[Community Characteristics of Methanogens and Methanogenic Pathways in Salt-tolerant Rice Soil]

It is known that methanogens play a critical role in the carbon cycle in soil, while methanogen community characteristics and their environmental influencing factors in the soil planted with salt-tolerant rice remain unclear. In this study, methanogen abundance, community composition, and relationships with environmental factors in soils planted with the salt-tolerant rice (YC1703) and ordinary rice (Lindao 10) were evaluated in the rice improvement demonstration base of Qingdao Wisdom Agricultural Industry using real-time fluorescence quantitative PCR and Illumina high-throughput sequencing. The results indicated that the abundance and community richness of methanogens in Lindao 10 soil were significantly higher than those in YC1703 soil, and methanogens in YC1703 soil exhibited higher diversity. The combined effects of rice varieties, rice growth period, and environmental factors had impacts on the methanogen community. The hydrogenotrophic methanogens were dominant in the YC1703 and Lindao 10 soils; thus, we speculated that the dominant pathway of methane production in these soils was hydrogenotrophic methanogenesis.

Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin

Tropical peatlands are hotspots of methane (CH₄) production but present high variation and emission uncertainties in the Amazon region. This is because the controlling factors of methane production in tropical peats are not yet well documented. Although inhibitory effects of nitrogen oxides (NO_x) on methanogenic activity are known from pure culture studies, the role of NO_x in the methane cycling of peatlands remains unexplored. Here, we investigated the CH₄ content, soil geochemistry and microbial communities along 1-m-soil profiles and assessed the effects of soil NO_x and nitrous oxide (N₂O) on methanogenic abundance and activity in three peatlands of the Pastaza-Marañón foreland basin. The peatlands were distinct in pH, DOC, nitrate pore water concentrations, C/N ratios of shallow soils, redox potential, and ¹³C enrichment in dissolved inorganic carbon and CH₄ pools, which are primarily contingent on H₂-dependent methanogenesis. Molecular 16S rRNA and mcrA gene data revealed diverse and novel methanogens varying across sites. Importantly, we also observed a strong stratification in relative abundances of microbial groups involved in NO_x cycling, along with a concordant stratification of methanogens. The higher relative abundance of ammonia-oxidizing archaea (Thaumarchaeota) in acidic oligotrophic peat than ammonia-oxidizing bacteria (Nitrospira) is noteworthy as putative sources of NO_x. Experiments testing the interaction of NO_x species and methanogenesis found that the latter showed differential sensitivity to nitrite (up to 85% reduction) and N₂O (complete inhibition), which would act as an unaccounted CH₄ control in these ecosystems. Overall, we present evidence of diverse peatlands likely differently affected by inhibitory effects of nitrogen species on methanogens as another contributor to variable CH₄ fluxes.

Methanobrevibacter smithii tonsillar phlegmon: a case report

Untreated tonsillar phlegmon is a life-threatening condition commonly caused by Streptococcus pyogenes and Fusobacterium necrophorum, among other pathogens. Here, using specific laboratory tools, we detected Methanobrevibacter smithii in addition to S. pyogenes. This unprecedented observation questions the role of methanogens in phlegmon and the optimal treatment of this mixed infection.

Benefits of Age-Improved Resistance of Mature Electroactive Biofilm Anodes in Anaerobic Digestion

Anaerobic digestion (AD) and microbial electrochemical technologies (MET) can be combined in manifold ways. Recent studies show negative influences of AD effluents on the performance of pre-grown Geobacter spp.-dominated biofilm anodes. In this study, it was investigated how such biofilm anodes are affected by AD effluents. Therefore, experiments using AD effluents in different concentrations (0-100%) in combination with biofilms of different ages were performed. Furthermore, the activity of methanogens was inhibited and minimized by application of 2-bromoethanesulfonate (2-BES) and microfiltration, respectively. Biofilms pre-grown for 5 weeks show higher resistance against AD effluents compared to biofilms pre-grown for only 3 weeks. Nevertheless, adaptation of biofilms to AD effluents was not successful. Biofilm activity in terms of coulombic efficiency and maximum current density (j_max) dropped by factor 32.2 ± 3.2 and 38.9 ± 8.4, respectively. The application of 2-BES and microfiltration had positive effects on the biofilm activity. The results support the assumption that methanogens or further compounds not studied here, for example, protozoans, which may have been inhibited or removed by 2-BES application or microfiltration, have an immediate influence on the stability of Geobacter spp.-dominated biofilms and may limit their practical application in AD environments.

Decreased Methane Emissions Associated with Methanogenic and Methanotrophic Communities in a Pig Manure Windrow Composting System under Calcium Superphosphate Amendment

With the rapid growth of livestock breeding, manure composting has evolved to be an important source of atmospheric methane (CH4) which accelerates global warming. Calcium superphosphate (CaSSP), as a commonly used fertilizer, was proposed to be effective in reducing CH4 emissions from manure composting, but the intrinsic biological mechanism remains unknown. Methanogens and methanotrophs both play a key role in mediating CH4 fluxes, therefore we hypothesized that the CaSSP-mediated reduction in CH4 emissions was attributed to the shift of methanogens and methanotrophs, which was regulated by physicochemical parameter changes. To test this hypothesis, a 60-day pig manure windrow composting experiment was conducted to investigate the response of CH4 emissions to CaSSP amendment, with a close linkage to methanogenic and methanotrophic communities. Results showed that CaSSP amendment significantly reduced CH4 emissions by 49.5% compared with the control over the whole composting period. The decreased mcrA gene (encodes the α-subunit of methyl-coenzyme M reductase) abundance in response to CaSSP amendment suggested that the CH4 emissions were reduced primarily due to the suppressed microbial CH4 production. Illumina MiSeq sequencing analysis showed that the overall distribution pattern of methanogenic and methanotrophic communities were significantly affected by CaSSP amendment. Particularly, the relative abundance of Methanosarcina that is known to be a dominant group for CH4 production, significantly decreased by up to 25.3% accompanied with CaSSP addition. Only Type I methanotrophs was detected in our study and Methylocaldum was the dominant methanotrophs in this composting system; in detail, CaSSP amendment increased the relative abundance of OTUs belong to Methylocaldum and Methylobacter. Moreover, the increased SO42- concentration and decreased pH acted as two key factors influencing the methanogenic and methanotrophic composition, with the former has a negative effect on methanogenesis growth and can later promote CH4 oxidation at a low level. This study deepens our understanding of the interaction between abiotic factors, function microbiota and greenhouse gas (GHG) emissions, as well as provides implication for practically reducing composting GHG emissions.

Isotopic evidence for axial tree stem methane oxidation within subtropical lowland forests

Knowledge regarding mechanisms moderating methane (CH₄ ) sink/source behaviour along the soil-tree stem-atmosphere continuum remains incomplete. Here, we applied stable isotope analysis (δ¹³ C-CH₄ ) to gain insights into axial CH₄ transport and oxidation in two globally distributed subtropical lowland species (Melaleuca quinquenervia and Casuarina glauca). We found consistent trends in CH₄ flux (decreasing with height) and δ¹³ C-CH₄ enrichment (increasing with height) in relation to stem height from ground. The average lower tree stem δ¹³ C-CH₄ (0-40 cm) of Melaleuca and Casuarina (-53.96‰ and -65.89‰) were similar to adjacent flooded soil CH₄ ebullition (-52.87‰ and -62.98‰), suggesting that stem CH₄ is derived mainly by soil sources. Upper stems (81-200 cm) displayed distinct δ¹³ C-CH₄ enrichment (Melaleuca -44.6‰ and Casuarina -46.5‰, respectively). Coupled 3D-photogrammetry with novel 3D-stem measurements revealed distinct hotspots of CH₄ flux and isotopic fractionation on Melaleuca, which were likely due to bark anomalies in which preferential pathways of gas efflux were enhanced. Diel experiments revealed greater δ¹³ C-CH₄ enrichment and higher oxidation rates in the afternoon, compared with the morning. Overall, we estimated that c. 33% of the methane was oxidised between lower and upper stems during axial transport, therefore potentially representing a globally significant, yet previously unaccounted for, methane sink.

A Win-Loss Interaction on Fe0 Between Methanogens and Acetogens From a Climate Lake

Diverse physiological groups congregate into environmental corrosive biofilms, yet the interspecies interactions between these corrosive physiological groups are seldom examined. We, therefore, explored Fe⁰-dependent cross-group interactions between acetogens and methanogens from lake sediments. On Fe⁰, acetogens were more corrosive and metabolically active when decoupled from methanogens, whereas methanogens were more metabolically active when coupled with acetogens. This suggests an opportunistic (win-loss) interaction on Fe⁰ between acetogens (loss) and methanogens (win). Clostridia and Methanobacterium were the major candidates doing acetogenesis and methanogenesis after four transfers (metagenome sequencing) and the only groups detected after 11 transfers (amplicon sequencing) on Fe⁰. Since abiotic H₂ failed to explain the high metabolic rates on Fe⁰, we examined whether cell exudates (spent media filtrate) promoted the H₂-evolving reaction on Fe⁰ above abiotic controls. Undeniably, spent media filtrate generated three- to four-fold more H₂ than abiotic controls, which could be partly explained by thermolabile enzymes and partly by non-thermolabile constituents released by cells. Next, we examined the metagenome for candidate enzymes/shuttles that could catalyze H₂ evolution from Fe⁰ and found candidate H₂-evolving hydrogenases and an almost complete pathway for flavin biosynthesis in Clostridium. Clostridial ferredoxin-dependent [FeFe]-hydrogenases may be catalyzing the H₂-evolving reaction on Fe⁰, explaining the significant H₂ evolved by spent media exposed to Fe⁰. It is typical of Clostridia to secrete enzymes and other small molecules for lytic purposes. Here, they may secrete such molecules to enhance their own electron uptake from extracellular electron donors but indirectly make their H₂-consuming neighbors-Methanobacterium-fare five times better in their presence. The particular enzymes and constituents promoting H₂ evolution from Fe⁰ remain to be determined. However, we postulate that in a static environment like corrosive crust biofilms in lake sediments, less corrosive methanogens like Methanobacterium could extend corrosion long after acetogenesis ceased, by exploiting the constituents secreted by acetogens.

Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH₄ source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH₄ emissions across floodplain areas. Here, we report the in situ composition of CH₄ cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH₄ cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH₄ were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH₄ emissions in the region.

Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials

Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber-degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interactions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate metabolic pathways in the fungal hydrogenosome. The ability of co-cultures of anaerobic fungi and methanogens to degrade fiber and produce methane could potentially be a valuable method for the degradation of lignocellulosic materials and methane production.

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

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

Detection of Methanobrevobacter smithii and Methanobrevibacter oralis in Lower Respiratory Tract Microbiota

Methanogens, the sole microbes producing methane, are archaea commonly found in human anaerobic microbiota. Methanogens are emerging as opportunistic pathogens associated with dysbiosis and are also detected and cultured in anaerobic abscesses. Their presence in the respiratory tract is yet unknown. As a preliminary answer, prospective investigation of 908 respiratory tract samples using polyphasic approach combining PCR-sequencing, real-time PCR, fluorescent in situ hybridization (FISH), and methanogens culture was carried out. Methanobrevibacter smithii and Methanobrevibacter oralis DNA sequences, were detected in 21/527 (3.9%) sputum samples, 2/188 (1.06%) bronchoalveolar lavages, and none of 193 tracheo-bronchial aspirations. Further, fluorescence in situ hybridization detected methanogens in three sputum investigated specimens with stick morphology suggesting M. oralis and in another one bronchoalveolar lavage sample investigated, diplococal morphology suggesting M. smithii. These observations extend the known territory of methanogens to the respiratory tract and lay the foundations for further interpretation of their detection as pathogens in any future cases of isolation from bronchoalveolar lavages and the lungs.

Influence of Liquid-to-Gas Ratio on the Syngas Fermentation Efficiency: An Experimental Approach

Syngas fermentation by methanogens is a novel process to purify biogas. Methanogens are able to ferment non-desirable CO₂, H_2, and CO to methane. However, to use methanogens on an industrial scale, more research has to be done. There are studies that discuss the growth of methanogens on syngas in combination with acetate. In this research, growth of methanogens on syngas as sole carbon source is discussed. Effluent of an anaerobic fed-batch was selectively cultivated with syngas in 400 mL Eppendorf© bioreactors. After a period of 7 days, fifteen 120 mL flasks were filled with three different liquid-to-gas ratios (1:1, 1:3, 1:5). Results showed that different liquid-to-gas ratios change the metabolic preference of the anaerobic microbial community. Moreover, complete conversion in a four-to-eight-day period, via the carboxidotrophic pathway, was observed in all three liquid-to-gas ratios.

A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans

CRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. The Methanosarcina acetivorans CRISPR-Cas9 system was repurposed by replacing Cas9 with the catalytically dead Cas9 (dCas9) to generate a CRISPRi-dCas9 system for targeted gene repression. To test the utility of the system, genes involved in nitrogen (N₂) fixation were targeted for dCas9-mediated repression. First, the nif operon (nifHI ₁ I ₂ DKEN) that encodes molybdenum nitrogenase was targeted by separate guide RNAs (gRNAs), one targeting the promoter and the other targeting nifD Remarkably, growth of M. acetivorans with N₂ was abolished by dCas9-mediated repression of the nif operon with each gRNA. The abundance of nif transcripts was >90% reduced in both strains expressing the gRNAs, and NifD was not detected in cell lysate. Next, we targeted NifB, which is required for nitrogenase cofactor biogenesis. Expression of a gRNA targeting the coding sequence of NifB decreased nifB transcript abundance >85% and impaired but did not abolish growth of M. acetivorans with N₂ Finally, to ascertain the ability to study gene regulation using CRISPRi-dCas9, nrpR1, encoding a subunit of the repressor of the nif operon, was targeted. The nrpR1 repression strain grew normally with N₂ but had increased nif operon transcript abundance, consistent with NrpR1 acting as a repressor. These results highlight the utility of the system, whereby a single gRNA when expressed with dCas9 can block transcription of targeted genes and operons in M. acetivorans IMPORTANCE Genetic tools are needed to understand and manipulate the biology of archaea, which serve critical roles in the biosphere. Methanogenic archaea (methanogens) are essential for the biological production of methane, an intermediate in the global carbon cycle, an important greenhouse gas, and a biofuel. The CRISPRi-dCas9 system in the model methanogen Methanosarcina acetivorans is, to our knowledge, the first Cas9-based CRISPR interference system in archaea. Results demonstrate that the system is remarkably efficient in targeted gene repression and provide new insight into nitrogen fixation by methanogens, the only archaea with nitrogenase. Overall, the CRISPRi-dCas9 system provides a simple, yet powerful, genetic tool to control the expression of target genes and operons in methanogens.