Organic acids and ethanol inhibit the oxidation of methane by mire methanotrophs

Nutrient enrichment by high aquaculture effluent input exacerbates imbalances between methane production and oxidation in mangrove sediments

Frequent aquaculture activities introduce substantial nutrients into mangrove ecosystems; however, the impact of this nutrient enrichment on methane (CH4) emissions and the associated microbial communities remains largely unexplored. In this study, we used the static chamber method, combined with 16S rRNA-based, metagenomic sequencing and binning techniques, to investigate the emission patterns of greenhouse gases (GHGs), with a particular focus on CH4, in mangroves subjected to different levels of effluents. The results showed that the effluent input decreased the mineral protection of sediment carbon (C) pools and increased C loss by more than double. In particular, high effluent input increased CH4 emissions by 243.3 %. Random forest analysis revealed that changes in methanogens were an important factor in explaining the variation of CH4 emissions. Amplicon data showed that the proportion of methylotrophic methanogens increased after effluent input, and metagenomic binning further attributed this change to the adaptability of methylotrophic methanogens to the substances transporting by the effluent. The enhanced hypoxia in sediments resulting from effluent input promoted the transition of methanotrophic communities from aerobic to anaerobic types and made anaerobic oxidation of CH4 more reliant on sulfur reduction rather than nitrate reduction. The PLS model further revealed that the nutrients brought by effluent input stimulated an increase in DOC content which induced an imbalance between CH4 production and oxidation in sediments by facilitating methanogens but inhibiting methanotrophs, ultimately resulting in an increase in CH4 fluxes. These findings underscore the significance of mangroves receiving effluent input as critical consequent reactors, highlighting the necessity to consider effects of high nutrient enrichment by aquaculture effluent input on GHG emissions and blue C potential in mangroves.

Transformation of organic matter under anoxic conditions in soils

The transformation of organic matter under anoxic conditions is mediated by hydrolysis and fermentation processes resulting in products such as acetate and hydrogen which are then utilized by microorganisms in respiration. Respiring microorganisms employ an array of electron acceptors in soils, including nitrate, manganese(IV), iron(III), and sulfate, which are consumed depending on availability and decreasing Gibbs free energy yield. The classical view is that respiration is more rapid than fermentation and these two processes do not co-occur, however, evidence has mounted to challenge this view. In addition, it is unclear how the production of ammonium during ammonification of soil organic nitrogen is intertwined with fermentation and respiration. Accordingly, stirred-batch microcosms were incubated to quantify relevant chemical species over time (acetate, nitrate, iron(II), manganese(II), and ammonium) using native terminal electron acceptors (TEAs) and soil organic matter in four soils varying in drainage status under anoxic conditions. The net rate of acetate production in one of the moderately well-drained (Sadler) soils was 1.1 ± 0.07 μmol g-1 d-1, which was similar to Mn(II) accumulation rates (0.95 ± 0.3 μmol g-1 d-1, P = 0.57). A similar trend was observed in the well-drained (Feliciana) soil, indicating that Mn(IV) respiration and fermentation can co-occur in certain soils. In the other moderately well drained and the poorly drained soil, acetate production was suppressed due in part to elevated native nitrate levels, which raised the redox potential and acted as a competitive electron acceptor. Across all four soils, ammonification rates were positively correlated with acetate formation rates (r = 0.88, P < 0.001), suggesting the possibility of amino acid fermentation during these anoxic incubations. These results challenge the current paradigm that the fermentation step in anoxic organic matter decomposition is slow and Mn(IV) respiration is rapid, with implications for organic matter transformations and nutrient cycling.

A Study of the Community Relationships Between Methanotrophs and Their Satellites Using Constraint-Based Modeling Approach

Biotechnology continues to drive innovation in the production of pharmaceuticals, biofuels, and other valuable compounds, leveraging the power of microbial systems for enhanced yield and sustainability. Genome-scale metabolic (GSM) modeling has become an essential approach in this field, which enables a guide for targeting genetic modifications and the optimization of metabolic pathways for various industrial applications. While single-species GSM models have traditionally been employed to optimize strains like Escherichia coli and Lactococcus lactis, the integration of these models into community-based approaches is gaining momentum. Herein, we present a pipeline for community metabolic modeling with a user-friendly GUI, applying it to analyze interactions between Methylococcus capsulatus, a biotechnologically important methanotroph, and Escherichia coli W3110 under oxygen- and nitrogen-limited conditions. We constructed models with unmodified and homoserine-producing E. coli strains using the pipeline implemented in the original BioUML platform. The E. coli strain primarily utilized acetate from M. capsulatus under oxygen limitation. However, homoserine produced by E. coli significantly reduced acetate secretion and the community growth rate. This homoserine was taken up by M. capsulatus, converted to threonine, and further exchanged as amino acids. In nitrogen-limited modeling conditions, nitrate and ammonium exchanges supported the nitrogen needs, while carbon metabolism shifted to fumarate and malate, enhancing E. coli TCA cycle activity in both cases, with and without modifications. The presence of homoserine altered cross-feeding dynamics, boosting amino acid exchanges and increasing pyruvate availability for M. capsulatus. These findings suggest that homoserine production by E. coli optimizes resource use and has potential for enhancing microbial consortia productivity.

Probing Denitrifying Anaerobic Methane Oxidation via Antimicrobial Intervention: Implications for Innovative Wastewater Management

Methane emissions present a significant environmental challenge in both natural and engineered aquatic environments. Denitrifying anaerobic methane oxidation (N-DAMO) has the potential for application in wastewater treatment plants. However, our understanding of the N-DAMO process is primarily based on studies conducted on environmental samples or enrichment cultures using metagenomic approaches. To gain deeper insights into N-DAMO, we used antimicrobial compounds to study the function and physiology of 'Candidatus Methanoperedens nitroreducens' and 'Candidatus Methylomirabilis oxyfera' in N-DAMO enrichment cultures. We explored the effects of inhibitors and antibiotics and investigated the potential application of N-DAMO in wastewater contaminated with ammonium and heavy metals. Our results showed that 'Ca. M. nitroreducens' was susceptible to puromycin and 2-bromoethanesulfonate, while the novel methanogen inhibitor 3-nitrooxypropanol had no effect on N-DAMO. Furthermore, 'Ca. M. oxyfera' was shown to be susceptible to the particulate methane monooxygenase inhibitor 1,7-octadiyne and a bacteria-suppressing antibiotic cocktail. The N-DAMO activity was not affected by ammonium concentrations below 10 mM. Finally, the N-DAMO community appeared to be remarkably resistant to lead (Pb) but susceptible to nickel (Ni) and cadmium (Cd). This study provides insights into microbial functions in N-DAMO communities, facilitating further investigation of their application in methanogenic, nitrogen-polluted water systems.

Three decades of shade trees improve soil organic carbon pools but not methane uptake in coffee systems

The rapid expansion of coffee plantations in tropical area at the cost of natural forest may suppress the methane (CH4) uptake and change the soil fertility. However, observations on soil CH4 uptake rates and the ecological consequence studies on coffee-based plantations are sparse. The objectives of this study were to characterize the dynamics of CH4 uptake among natural forest, coffee monoculture (CM), and coffee intercropping with shade tree (CI), and to evaluate the key drivers of soil CH4 uptake. Results showed that the conversion of forest into 25-year and 34-year CM plantations significantly reduced the soil organic carbon (SOC) content by 57% and 76%, respectively, whereas CI plantation profoundly increased the SOC by 20%-76% compared with CM plantation. Although soils of forest, CM and CI functioned exclusively as CH4 sinks, the CM and CI plantations significantly decreased the ambient CH4 uptake rates by 64%-83% due to soil moisture shift and soil nitrate availability by using chemical fertilizer. Interestingly, the potential CH4 uptake of CM and CI plantations did not decrease and in some treatments, was even higher than that of the natural forest. Potential CH4 uptake showed a negative correlation with soil pH and SOC content, but a positive correlation with soil available phosphorus (AP). Collectively, although the SOC and soil pH were increased through intercropping with shade trees for decades, the inhibition of atmospheric CH4 uptake was still difficult to alleviate.

Product analog binding identifies the copper active site of particulate methane monooxygenase

Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of structural and spectroscopic studies have sought to identify the active site among three candidates: the CuB, CuC, and CuD sites. Challenges associated with the isolation of active pMMO have hindered progress toward locating its catalytic center. However, reconstituting pMMO into native lipid nanodiscs stabilizes its structure and recovers its activity. Here, these active samples were incubated with 2,2,2,-trifluoroethanol (TFE), a product analog that serves as a readily visualized active-site probe. Interactions of TFE with the CuD site were observed by both pulsed ENDOR spectroscopy and cryoEM, implicating CuD and the surrounding hydrophobic pocket as the likely site of methane oxidation. Use of these orthogonal techniques on parallel samples is a powerful approach that can circumvent difficulties in interpreting metalloenzyme cryoEM maps.

Degradation of biogas in a simulated landfill cover soil at laboratory scale: Compositional changes of main components and volatile organic compounds

A laboratory experiment lasting 28 days was run to simulate a typical landfill system and to investigate the compositional changes affecting the main components (CH₄, CO₂, and H₂) and nonmethane volatile organic compounds from biogas generated by anaerobic digestion of food waste and passing through a soil column. Gas samples were periodically collected from both the digester headspace and the soil column at increasing distances from the biogas source. CH₄ and H₂ were efficiently degraded along the soil column. The isotopic values of δ¹³C measured in CH₄ and CO₂ from the soil column were relatively enriched in ¹³C compared to the biogas. Aromatics and alkanes were the most abundant groups in the biogas samples. Among these compounds, alkylated benzenes and long-chain C₃₊ alkanes were significantly degraded within the soil column, whereas benzene and short-chain alkanes were recalcitrant. Terpene and O-substituted compounds were relatively stable under oxidising conditions. Cyclic, alkene, S-substituted, and halogenated compounds, which exhibited minor amounts in the digester headspace, were virtually absent in the soil column. These results pointed out how many recalcitrant potentially toxic and polluting compounds tend to be relatively enriched along the soil column, claiming action to minimise diffuse landfill gas (LFG) emissions. The proposed experimental approach represents a reliable tool for investigating the attenuation capacities of landfill cover soils for LFG components and developing optimised covers by adopting proper soil treatments and operating conditions to improve their degradation efficiencies.

Alfalfa-grass mixtures reduce greenhouse gas emissions and net global warming potential while maintaining yield advantages over monocultures

Improving forage productivity with lower greenhouse gas (GHG) emissions from limited grassland has been a hotspot of interest in global agricultural production. In this study, we analyzed the effects of grasses (tall fescue, smooth bromegrass), legume (alfalfa), and alfalfa-grass (alfalfa + smooth bromegrass and alfalfa + tall fescue) mixtures on GHG emissions, net global warming potential (Net GWP), yield-based greenhouse gas intensity (GHGI), soil chemical properties and forage productivity in cultivated grassland in northwest China during 2020-2021. Our results demonstrated that alfalfa-grass mixtures significantly improved forage productivity. The highest total dry matter yield (DMY) during 2020 and 2021 was obtained from alfalfa-tall fescue (11,311 and 13,338 kg ha^-1) and alfalfa-smooth bromegrass mixtures (10,781 and 12,467 kg ha^-1). The annual cumulative GHG emissions from mixtures were lower than alfalfa monoculture. Alfalfa-grass mixtures significantly reduced GHGI compared with the grass or alfalfa monocultures. Furthermore, results indicated that grass, alfalfa and alfalfa-grass mixtures differentially affected soil chemical properties. Lower soil pH and C/N ratio were recorded in alfalfa monoculture. Alfalfa and mixtures increased soil organic carbon (SOC) and soil total nitrogen (STN) contents. Importantly, alfalfa-grass mixtures are necessary for improving forage productivity and mitigating the GHG emissions in this region. In conclusion, the alfalfa-tall fescue mixture lowered net GWP and GHGI in cultivated grassland while maintaining high forage productivity. These advanced agricultural practices could contribute to the development of climate-sustainable grassland production in China.

Linking transcriptional dynamics of CH4-cycling grassland soil microbiomes to seasonal gas fluxes

Soil CH₄ fluxes are driven by CH₄-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. To date, a comprehensive understanding of underlying microbiome dynamics has rarely been obtained in situ. Using quantitative metatranscriptomics, we aimed to link CH₄-cycling microbiomes to net surface CH₄ fluxes throughout a year in two grassland soils. CH₄ fluxes were highly dynamic: both soils were net CH₄ sources in autumn and winter and sinks in spring and summer, respectively. Correspondingly, methanogen mRNA abundances per gram soil correlated well with CH₄ fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer, when the soils acted as net CH₄ sinks. CH₄ uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH₄ emissions from grassland soils. High methanotroph to methanogen ratios would indicate CH₄ sink properties. Our study links for the first time the seasonal transcriptional dynamics of CH₄-cycling soil microbiomes to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.

Organic carbon from graminoid roots as a driver of fermentation in a fen

Fen Schlöppnerbrunnen is a moderately acidic methane-emitting peatland overgrown by Molinia caerulea and other wetland graminoids (e.g. Carex rostrata). Recently, the accumulation of H2, an indicator for fermentation, was observed with anoxically incubated C. rostrata roots but not with root-free fen soil. Based on this finding, we hypothesized that root-derived organic carbon has a higher capacity to promote fermentation processes than peat organic carbon from root-free fen soil. To address this hypothesis, C. rostrata and M. caerulea roots were anoxically incubated with or without fen soil and the product profiles of root treatments were compared with those of root-free soil treatments. Ethanol, acetate, propionate, butyrate, H2 and CO2 accumulated in root treatments and collective amounts of carbon in accumulating products were 20-200 times higher than those in root-free soil treatments, in which mainly CO2 accumulated. Analyses of 16S rRNA and 16S rRNA gene sequences revealed that Clostridium, Propionispira and Rahnella, representatives of butyrate, propionate and mixed acid fermenters, respectively, were relatively enriched in root treatments. In contrast, differences of the microbial community before and after incubation were marginal in root-free soil treatments. Collectively, these findings supported the assumed stimulatory effect of root-derived organic carbon on fen fermenters.

Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.

Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review

Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.

Methanogens and Methanotrophs Show Nutrient-Dependent Community Assemblage Patterns Across Tropical Peatlands of the Pastaza-Marañón Basin, Peruvian Amazonia

Tropical peatlands are globally important carbon reservoirs that play a crucial role in fluxes of atmospheric greenhouse gases. Amazon peatlands are expected to be large source of atmospheric methane (CH₄) emissions, however little is understood about the rates of CH₄ flux or the microorganisms that mediate it in these environments. Here we studied a mineral nutrient gradient across peatlands in the Pastaza-Marañón Basin, the largest tropical peatland in South America, to describe CH₄ fluxes and environmental factors that regulate species assemblages of methanogenic and methanotrophic microorganisms. Peatlands were grouped as minerotrophic, mixed and ombrotrophic categories by their general water source leading to different mineral nutrient content (rich, mixed and poor) quantified by trace elements abundance. Microbial communities clustered dependent on nutrient content (ANOSIM p < 0.001). Higher CH₄ flux was associated with minerotrophic communities compared to the other categories. The most dominant methanogens and methanotrophs were represented by Methanobacteriaceae, and Methylocystaceae, respectively. Weighted network analysis demonstrated tight clustering of most methanogen families with minerotrophic-associated microbial families. Populations of Methylocystaceae were present across all peatlands. Null model testing for species assemblage patterns and species rank distributions confirmed non-random aggregations of Methylococcacae methanotroph and methanogen families (p < 0.05). We conclude that in studied amazon peatlands increasing mineral nutrient content provides favorable habitats for Methanobacteriaceae, while Methylocystaceae populations seem to broadly distribute independent of nutrient content.

Methane biofiltration in the presence of ethanol vapor under steady and transient state conditions: an experimental study

Methane (CH₄) removal in the presence of ethanol vapors was performed by a stone-based bed and a hybrid packing biofilter in parallel. In the absence of ethanol, a methane removal efficiency of 55 ± 1% was obtained for both biofilters under similar CH₄ inlet load (IL) of 13 ± 0.5 g_CH4 m^-3 h^-1 and an empty bed residence time (EBRT) of 6 min. The results proved the key role of the bottom section in both biofilters for simultaneous removal of CH₄ and ethanol. Ethanol vapor was completely eliminated in the bottom sections for an ethanol IL variation between 1 and 11 g_ethanol m^-3 h^-1. Ethanol absorption and accumulation in the biofilm phase as well as ethanol conversion to CO₂ contributed to ethanol removal efficiency of 100%. In the presence of ethanol vapor, CO₂ productions in the bottom section increased almost fourfold in both biofilters. The ethanol concentration in the leachate of the biofilter exceeding 2200 g_ethanol m^-3_leachate in both biofilters demonstrated the excess accumulation of ethanol in the biofilm phase. The biofilters responded quickly to an ethanol shock load followed by a starvation with 20% decrease of their performance. The return to normal operations in both biofilters after the transient conditions took less than 5 days. Unlike the hybrid packing biofilter, excess pressure drop (up to 1.9 cmH₂O m^-1) was an important concern for the stone bed biofilter. The biomass accumulation in the bottom section of the stone bed biofilter contributed to 80% of the total pressure drop. However, the 14-day starvation reduced the pressure drop to 0.25 cmH₂O m^-1.

Steady state and dynamic behaviors of a methane biofilter under periodic addition of ethanol vapors

Ethanol was added to a methane (CH₄) biofilter with inorganic packing materials over three cycles based on increasing the gas flow rates from 3 to 6 and finally to 12 L min^-1 corresponding to empty bed residence times (EBRT) of 6, 3 and 1.5 min. The steady state performance of the CH₄ biofilter was studied for CH₄ inlet loads (ILs) of 33, 66 and 132 g_CH4 m^-3 h^-1 prior and after each ethanol cycle. In addition, the steady state removal of a mixture of CH₄ and ethanol for a CH₄/ethanol mass ratio of around 7.5 g_CH4 g ^-1_ethanol was evaluated over three cycles (EBRTs of 6, 3 and 1.5 min). In the absence of ethanol, the CH₄ removal efficiency (RE) dropped from 35 to 7% due to an EBRT decrease from 6 to 1.5 min. In addition, the presence of ethanol resulted in a CH₄ RE reduction at a constant EBRT in every cycle. The CH₄ REs dropped from 35 to 29%, 17 to 13% and 7 to 0% for corresponding ethanol ILs of 4.5, 9 and 18 g_ethanol m^-3 h^-1 over the cycles. Moreover, the periodic presence of ethanol in the CH₄ biofilter allowed the study of transient behaviors of the biofilter during ethanol addition and the biofilter recovery after each cycle. The CH₄ RE reduction as a result of ethanol addition in each cycle was instantaneous. However, the CH₄ RE recovery after completion of ethanol addition took 10, 14 and 25 days for ethanol ILs of 4.5, 9 and 18 g_ethanol m^-3 h^-1 respectively. The recovery time was related to the ethanol concentration in the leachate which were 1100 ± 200, 1100 ± 350 and 2500 ± 400 g_ethanol m^-3_leachate for corresponding ethanol ILs of 4.5, 9 and 18 g_ethanol m^-3 h^-1, respectively. Based on steady state and dynamic process conditions of the biofilter, the lowest gas flow rate of 3 L min^-1 (EBRT of 6 min) produced the best performance when both pollutants were present (CH₄ IL of 33 g_CH4 m^-3 h^-1 and ethanol IL of 4.5 g_ethanol m^-3 h^-1).

Effect of biomass concentration on methane oxidation activity using mature compost and graphite granules as substrata

Reported methane oxidation activity (MOA) varies widely for common landfill cover materials. Variation is expected due to differences in surface area, the composition of the substratum and culturing conditions. MOA per methanotrophic cell has been calculated in the study of natural systems such as lake sediments to examine the inherent conditions for methanotrophic activity. In this study, biomass normalised MOA (i.e., MOA per methanotophic cell) was measured on stabilised compost, a commonly used cover in landfills, and on graphite granules, an inert substratum widely used in microbial electrosynthesis studies. After initially enriching methanotrophs on both substrata, biomass normalised MOA was quantified under excess oxygen and limiting methane conditions in 160ml serum vials on both substrata and blends of the substrata. Biomass concentration was measured using the bicinchoninic acid assay for microbial protein. The biomass normalised MOA was consistent across all compost-to-graphite granules blends, but varied with time, reflecting the growth phase of the microorganisms. The biomass normalised MOA ranged from 0.069±0.006μmol CH4/mg dry biomass/h during active growth, to 0.024±0.001μmol CH4/mg dry biomass/h for established biofilms regardless of the substrata employed, indicating the substrata were equally effective in terms of inherent composition. The correlation of MOA with biomass is consistent with studies on methanotrophic activity in natural systems, but biomass normalised MOA varies by over 5 orders of magnitude between studies. This is partially due to different methods being used to quantify biomass, such as pmoA gene quantification and the culture dependent Most Probable Number method, but also indicates that long term exposure of materials to a supply of methane in an aerobic environment, as can occur in natural systems, leads to the enrichment and adaptation of types suitable for those conditions.

Synergistic effects of dissolved organic carbon and inorganic nitrogen on methane uptake in forest soils without and with freezing treatment

There is limited knowledge about how the interaction of dissolved organic carbon (DOC) and inorganic nitrogen (N) released into the soil just after freezing can affect methane (CH₄) uptake in forest soils. Here, we present how freezing treatment and glucose, as a DOC source, can affect the roles of NH₄⁺-N and NO₃⁻-N in inhibiting soil CH₄ uptake, by using soil-core incubation experiments. A long-term freezing at low temperature reduced cumulative CH₄ uptake in the soils sampled from two temperate forest stands without carbon (C) and N addition. The inhibition effects of N addition as NH₄Cl and KNO₃ on the soil CH₄ uptake were much larger than C addition. Freezing treatment eliminated the inhibition effect of NH₄Cl and KNO₃ addition on CH₄ uptake, and this response was affected by glucose addition and forest types. The addition of glucose eliminated the inhibition effect of NO₃⁻-N on CH₄ uptake in the forest soils without and with freezing treatment, while the addition of NH₄⁺-N and glucose inhibited synergistically the soil CH₄ uptake. The results highlight the importance of synergistic effects of DOC and N inputs on the soil CH₄ uptake under forest stands during soil wetting and thawing periods.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

Discovery of a novel methanogen prevalent in thawing permafrost

Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.

Effects of Long-Term CO2 Enrichment on Soil-Atmosphere CH4 Fluxes and the Spatial Micro-Distribution of Methanotrophic Bacteria

Background

Effects of elevated atmospheric CO₂ concentrations on plant growth and associated C cycling have intensively been studied, but less is known about effects on the fluxes of radiatively active trace gases other than CO₂. Net soil-atmosphere CH₄ fluxes are determined by the balance of soil microbially-driven methane (CH₄) oxidation and methanogenesis, and both might change under elevated CO₂.

Methods and Results

Here, we studied CH₄ dynamics in a permanent grassland exposed to elevated CO₂ for 14 years. Soil-atmosphere fluxes of CH₄ were measured using large static chambers, over a period of four years. The ecosystem was a net sink for atmospheric CH₄ for most of the time except summer to fall when net CH₄ emissions occurred. We did not detect any elevated CO₂ effects on CH₄ fluxes, but emissions were difficult to quantify due to their discontinuous nature, most likely because of ebullition from the saturated zone. Potential methanotrophic activity, determined by incubation of fresh sieved soil under standardized conditions, also did not reveal any effect of the CO₂ treatment. Finally, we determined the spatial micro-distribution of methanotrophic activity at less than 5× atmospheric (10 ppm) and elevated (10000 ppm) CH₄ concentrations, using a novel auto-radiographic technique. These analyses indicated that domains of net CH₄ assimilation were distributed throughout the analyzed top 15 cm of soils, with no dependence on CH₄ concentration or CO₂ treatment.

Conclusions

Our investigations suggest that elevated CO₂ exerts no or only minor effects on CH₄ fluxes in the type of ecosystem we studied, at least as long as soil moisture differences are small or absent as was the case here. The autoradiographic analyses further indicate that the spatial niche of CH₄ oxidation does not shift in response to CO₂ enrichment or CH₄ concentration, and that the same type of methanotrophs may oxidize CH₄ from atmospheric and soil-internal sources.

Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate

Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.

Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost

The response of methanogens to thawing permafrost is an important factor for the global greenhouse gas budget. We tracked methanogenic community structure, activity, and abundance along the degradation of sub-Arctic palsa peatland permafrost. We observed the development of pronounced methane production, release, and abundance of functional (mcrA) methanogenic gene numbers following the transitions from permafrost (palsa) to thaw pond structures. This was associated with the establishment of a methanogenic community consisting both of hydrogenotrophic (Methanobacterium, Methanocellales), and potential acetoclastic (Methanosarcina) members and their activity. While peat bog development was not reflected in significant changes of mcrA copy numbers, potential methane production, and rates of methane release decreased. This was primarily linked to a decline of potential acetoclastic in favor of hydrogenotrophic methanogens. Although palsa peatland succession offers similarities with typical transitions from fen to bog ecosystems, the observed dynamics in methane fluxes and methanogenic communities are primarily attributed to changes within the dominant Bryophyta and Cyperaceae taxa rather than to changes in peat moss and sedge coverage, pH and nutrient regime. Overall, the palsa peatland methanogenic community was characterized by a few dominant operational taxonomic units (OTUs). These OTUs seem to be indicative for methanogenic species that thrive in terrestrial organic rich environments. In summary, our study shows that after an initial stage of high methane emissions following permafrost thaw, methane fluxes, and methanogenic communities establish that are typical for northern peat bogs.

Methane oxidation activity and diversity of aerobic methanotrophs in pH-neutral and semi-neutral thermal springs of the Kunashir Island, Russian Far East

Aerobic methane oxidation has been mostly studied in environments with moderate to low temperatures. However, the process also occurs in terrestrial thermal springs, where little research on the subject has been done to date. The potential activity of methane oxidation and diversity of aerobic methanotrophic bacteria were studied in sediments of thermal springs with various chemical and physical properties, sampled across the Kunashir Island, the Kuriles archipelago. Activity was measured by means of the radioisotope tracer technique utilizing (14)C-labeled methane. Biodiversity assessments were based on the particulate methane monooxygenase (pmoA) gene, which is found in all known thermophilic and thermotolerant methanotrophs. We demonstrated the possibility of methane oxidation in springs with temperature exceeding 74 °C, and the most intensive methane uptake was shown in springs with temperatures about 46 °C. PmoA was detected in 19 out of 30 springs investigated and the number of pmoA gene copies varied between 10(4) and 10(6) copies per ml of sediment. Phylogenetic analysis of PmoA sequences revealed the presence of methanotrophs from both the Alpha- and Gammaproteobacteria. Our results suggest that methanotrophs inhabiting thermal springs with temperature exceeding 50 °C may represent novel thermophilic and thermotolerant species of the genera Methylocystis and Methylothermus, as well as previously undescribed Gammaproteobacteria.

Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.

The (d)evolution of methanotrophy in the Beijerinckiaceae--a comparative genomics analysis

The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy.

Aerobic methanotroph diversity in Riganqiao peatlands on the Qinghai-Tibetan Plateau

The Zoige Plateau is characterized by its high altitude, low latitude and low annual mean temperature of approximately 1°C and is a major source of atmospheric methane in the Qinghai-Tibetan Plateau. Methanotrophs play an important role in the global cycling of CH4, but the diversity, identity and activity of methanotrophs in this region are poorly characterized. Soils were collected from hummocks and hollows in the Riganqiao peatland and the methanotroph community was analysed by qPCR and sequencing methane monooxygenase (pmoA and mmoX) genes. The pmoA genes ranged between 10(7) and 10(8) copies g(-1) fresh soil, with a somewhat greater abundance in hummocks than hollows. The pmoA genes were analysed by amplicon pyrosequencing and the mmoX genes by cloning and sequencing. Methylocystis species were found to be the most abundant methanotrophs, but numerous clades were present including three novel pmoA and three novel mmoX clusters. There were differences between the methanotroph communities in the hummocks and hollows, with the most significant being an increased abundance of uncultivated type Ib methanotrophs in the hollows. The results indicate that aerobic methanotrophs are abundant in Riganqiao peatland and include previously undetected clades in this geographically isolated and distinctive environment.

Does dissolved organic carbon regulate biological methane oxidation in semiarid soils?

In humid ecosystems, the rate of methane (CH4 ) oxidation by soil-dwelling methane-oxidizing bacteria (MOB) is controlled by soil texture and soil water holding capacity, both of which limit the diffusion of atmospheric CH4 into the soil. However, it remains unclear whether these same mechanisms control CH4 oxidation in more arid soils. This study was designed to measure the proximate controls of potential CH4 oxidation in semiarid soils during different seasons. Using a unique and well-constrained 3-million-year-old semiarid substrate age gradient, we were able to hold state factors constant while exploring the relationship between seasonal potential CH4 oxidation rates and soil texture, soil water holding capacity, and dissolved organic carbon (DOC). We measured unexpectedly higher rates of potential CH4 oxidation in the wet season than the dry season. Although other studies have attributed low CH4 oxidation rates in dry soils to desiccation of MOB, we present several lines of evidence that this may be inaccurate. We found that soil DOC concentration explained CH4 oxidation rates better than soil physical factors that regulate the diffusion of CH4 from the atmosphere into the soil. We show evidence that MOB facultatively incorporated isotopically labeled glucose into their cells, and MOB utilized glucose in a pattern among our study sites that was similar to wet-season CH4 oxidation rates. This evidence suggests that DOC, which is utilized by MOB in other environments with varying effects on CH4 oxidation rates, may be an important regulator of CH4 oxidation rates in semiarid soils. Our collective understanding of the facultative use of DOC by MOB is still in its infancy, but our results suggest it may be an important factor controlling CH4 oxidation in soils from dry ecosystems.

Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993

A novel species is proposed for two facultatively methanotrophic representatives of the genus Methylocystis, strains H2s(T) and S284, which were isolated from an acidic (pH 4.3) Sphagnum peat-bog lake (Teufelssee, Germany) and an acidic (pH 3.8) peat bog (European North Russia), respectively. Cells of strains H2s(T) and S284 are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. They possess both a soluble and a particulate methane monooxygenase (MMO); the latter is represented by two isozymes, pMMO1 and pMMO2. The preferred growth substrates are methane and methanol. In the absence of C1 substrates, however, these methanotrophs are capable of slow growth on acetate. Atmospheric nitrogen is fixed by means of an aerotolerant nitrogenase. Strains H2s(T) and S284 grow between pH 4.2 and 7.6 (optimum pH 6.0-6.5) and at 8-37 °C (optimum 25-30 °C). The major fatty acids are C18 : 1ω8c, C18 : 1ω7c and C16 : 1ω7c; the major quinone is Q-8. The DNA G+C content is 62.0-62.3 mol%. Strains H2s(T) and S284 share identical 16S rRNA gene sequences, which displayed 96.6-97.3 % similarity to sequences of other taxonomically characterized members of the genus Methylocystis. Therefore, strains H2s(T) and S284 are classified as members of a novel species, for which the name Methylocystis bryophila sp. nov. is proposed; strain H2s(T) ( = DSM 21852(T)  = VKM B-2545(T)) is the type strain.

Microbial CH(4) and N(2)O Consumption in Acidic Wetlands

Acidic wetlands are global sources of the atmospheric greenhouse gases methane (CH(4)), and nitrous oxide (N(2)O). Consumption of both atmospheric gases has been observed in various acidic wetlands, but information on the microbial mechanisms underlying these phenomena is scarce. A substantial amount of CH(4) is consumed in sub soil by aerobic methanotrophs at anoxic-oxic interfaces (e.g., tissues of Sphagnum mosses, rhizosphere of vascular plant roots). Methylocystis-related species are likely candidates that are involved in the consumption of atmospheric CH(4) in acidic wetlands. Oxygen availability regulates the activity of methanotrophs of acidic wetlands. Other parameters impacting on the methanotroph-mediated CH(4) consumption have not been systematically evaluated. N(2)O is produced and consumed by microbial denitrification, thus rendering acidic wetlands as temporary sources or sinks for N(2)O. Denitrifier communities in such ecosystems are diverse, and largely uncultured and/or new, and environmental factors that control their consumption activity are unresolved. Analyses of the composition of N(2)O reductase genes in acidic wetlands suggest that acid-tolerant Proteobacteria have the potential to mediate N(2)O consumption in such soils. Thus, the fragmented current state of knowledge raises open questions concerning methanotrophs and denitrifiers that consume atmospheric CH(4) and N(2)O in acidic wetlands.

Functionally redundant cellobiose-degrading soil bacteria respond differentially to oxygen

The availability of oxygen (O(2)) in aerated (i.e., water-unsaturated) soils affects the metabolic activities of aerobic and anaerobic soil prokaryotes that degrade plant-derived saccharides. Fluctuating availabilities of O(2) were imposed on agricultural soil slurries supplemented with cellobiose. Slurries were subjected to oxic conditions (48 h), followed by an anoxic period (120 h) and a final oxic period (24 h). Redox potential was stable at 500 mV during oxic periods but decreased rapidly (within 10 h) under anoxic conditions to -330 mV. The consumption of cellobiose occurred without apparent delay at all redox potentials. The metabolic activities of seven previously identified saccharolytic family-level taxa of the investigated soil were measured with newly designed quantitative PCR assays targeting the 16S rRNA. Four taxa responded to the experimental conditions. The amounts of rRNAs of Micrococcaceae and Cellulomonadaceae (Actinobacteria) increased under oxic conditions. In contrast, the RNA contents of Clostridiaceae (cluster I, Firmicutes) and two uncultured family-level-taxa, i.e., "Cellu" and "Sphingo" (both Bacteroidetes) increased under anoxic conditions. That the degradation of cellobiose was independent of the availability of O(2) and that redox potentials decreased in response to anaerobic activities indicated that the degradation of cellobiose was linked to functionally redundant cellobiose-degrading taxa capable of altering redox conditions.

Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses

Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With Sphagnum mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA, pmoA, pxmA, and mmoX gene sequences showed that the alphaproteobacterial isolates belonged to the Methylocystis and Methylosinus genera. The Methylosinus species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the Methylomonas genus, and the other strain, M200, may represent a novel genus, most closely related to the genera Methylosoma and Methylovulum. So far, no acidophilic or acid-tolerant methanotrophs in the Gammaproteobacteria class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from Sphagnum mosses.