Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil

Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments

Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.

Hydrogenotrophic Methanogenesis Under Alkaline Conditions

A cement-based geological disposal facility (GDF) is one potential option for the disposal of intermediate level radioactive wastes. The presence of both organic and metallic materials within a GDF provides the opportunity for both acetoclastic and hydrogenotrophic methanogenesis. However, for these processes to proceed, they need to adapt to the alkaline environment generated by the cementitious materials employed in backfilling and construction. Within the present study, a range of alkaline and neutral pH sediments were investigated to determine the upper pH limit and the preferred route of methane generation. In all cases, the acetoclastic route did not proceed above pH 9.0, and the hydrogenotrophic route dominated methane generation under alkaline conditions. In some alkaline sediments, acetate metabolism was coupled to hydrogenotrophic methanogenesis via syntrophic acetate oxidation, which was confirmed through inhibition studies employing fluoromethane. The absence of acetoclastic methanogenesis at alkaline pH values (>pH 9.0) is attributed to the dominance of the acetate anion over the uncharged, undissociated acid. Under these conditions, acetoclastic methanogens require an active transport system to access their substrate. The data indicate that hydrogenotrophic methanogenesis is the dominant methanogenic pathway under alkaline conditions (>pH 9.0).

Ex Situ Culturing Experiments Revealed Psychrophilic Hydrogentrophic Methanogenesis Being the Potential Dominant Methane-Producing Pathway in Subglacial Sediment in Larsemann Hills, Antarctic

It was recognized only recently that subglacial ecosystems support considerable methanogenic activity, thus significantly contributing the global methane production. However, only limited knowledge is available on the physiological characteristics of this kind of methanogenic community because of the technical constraints associated with sampling and cultivation under corresponding environmental conditions. To elucidate methanogenesis beneath the glacial margin in East Antarctic Ice Sheet, we took an integrated approach that included cultivation of microbes associated with the sediment samples in the lab and analysis of mcrA gene therein. After 7 months of incubation, the highest rate of methanogenesis [398 (pmol/day)/gram] was observed at 1°C on a supply of H₂. The rates of methanogenesis were lower on acetate or unamended substrate than on H₂. The rates on these two substrates increased when the temperature was raised. Methanomicrobiales predominated before and after prolonged incubation, regardless whether H₂, acetate, or unamended substrate were the energy source. Therefore, it was inferred that psychrophilic hydrogenotrophic methanogenesis was the primary methane-producing pathway in the subglacial ecosystem we sampled. These findings highlight the effects of temperature and substrate on potential methanogenesis in the subglacial sediment of this area, and may help us for a better estimation on the Antarctica methane production in a changing climate.

Hydrogenotrophic methanogenesis is the dominant methanogenic pathway in neotropical tank bromeliad wetlands

Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that emits substantial amounts of CH₄ . Tank bromeliads growing in the forest canopy (functional type-II tank bromeliads) were found to emit more CH₄ than tank bromeliads growing on the forest floor (functional type-I tank bromeliads) but the reasons for this difference and the underlying microbial CH₄ -cycling processes have not been studied. Therefore, we characterized archaeal communities in bromeliad tanks of the two different functional types in a neotropical montane forest of southern Ecuador using terminal-restriction fragment length polymorphism (T-RFLP) and performed tank-slurry incubations to measure CH₄ production potential, stable carbon isotope fractionation and pathway of CH₄ formation. The archaeal community composition was dominated by methanogens and differed between bromeliad functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens and hydrogenotrophic methanogenesis was the dominant methanogenic pathway among all bromeliads. The relative abundance of aceticlastic Methanosaetaceae and the relative contribution of aceticlastic methanogenesis increased in type-I tank bromeliads probably due to more oxic conditions in type-I than in type-II bromeliads leading to the previously observed lower in situ CH₄ emissions from type-I tank bromeliads but to higher CH₄ production potentials in type-I tank bromeliad slurries.

Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil

In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy fields are heavily fertilized with nitrite and nitrate, which can be used as electron acceptors by anaerobic methanotrophs. Here we show that slurry incubations of Italian paddy field soil with nitrate and ¹³C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9 nmol g^-1_dw d^-1). Community analysis based on 16S rRNA amplicon sequencing and qPCR of the water-logged soil and the rhizosphere showed that anaerobic oxidation of methane-associated archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads. The NC10 phylum bacteria made up less than 1% of all bacterial sequences. The phylogenetic analysis was complemented by qPCR showing that AAA ranged from 0.28 × 10⁶ to 3.9 × 10⁶ 16S rRNA gene copies g^-1_dw in bulk soil and 0.27 × 10⁶ to 2.8 × 10⁶ in the rhizosphere. The abundance of NC10 phylum bacteria was an order of magnitude lower. Revisiting published diversity studies, we found that AAA have been detected, but not linked to methane oxidation, in several paddy fields. Our data suggest an important role of AAA in methane cycling in paddy fields.

Carbon Isotope Fractionation during Catabolism and Anabolism in Acetogenic Bacteria Growing on Different Substrates

Homoacetogenic bacteria are versatile microbes that use the acetyl coenzyme A (acetyl-CoA) pathway to synthesize acetate from CO2 and hydrogen. Likewise, the acetyl-CoA pathway may be used to incorporate other 1-carbon substrates (e.g., methanol or formate) into acetate or to homoferment monosaccharides completely to acetate. In this study, we analyzed the fractionation of pure acetogenic cultures grown on different carbon substrates. While the fractionation of Sporomusa sphaeroides grown on C1 compounds was strong (εC1, -49‰ to -64‰), the fractionation of Moorella thermoacetica and Thermoanaerobacter kivui using glucose (εGlu= -14.1‰) was roughly one-third as strong, suggesting a contribution of less-depleted acetate from fermentative processes. ForM. thermoacetica, this could indeed be validated by the addition of nitrate, which inhibited the acetyl-CoA pathway, resulting in fractionation during fermentation (εferm= -0.4‰). In addition, we determined the fractionation into microbial biomass of T. kivui grown on H2/CO2(εanabol.= -28.6‰) as well as on glucose (εanabol.= +2.9‰).

Effective Suppression of Methane Emission by 2-Bromoethanesulfonate during Rice Cultivation

2-bromoethanesulfonate (BES) is a structural analogue of coenzyme M (Co-M) and potent inhibitor of methanogenesis. Several studies confirmed, BES can inhibit CH₄ prodcution in rice soil, but the suppressing effectiveness of BES application on CH₄ emission under rice cultivation has not been studied. In this pot experiment, different levels of BES (0, 20, 40 and 80 mg kg^-1) were applied to study its effect on CH₄ emission and plant growth during rice cultivation. Application of BES effectively suppressed CH₄ emission when compared with control soil during rice cultivation. The CH₄ emission rates were significantly (P<0.001) decreased by BES application possibly due to significant (P<0.001) reduction of methnaogenic biomarkers like Co-M concentration and mcrA gene copy number (i.e. methanogenic abunadance). BES significantly (P<0.001) reduced methanogen activity, while it did not affect soil dehydrogenase activity during rice cultivation. A rice plant growth and yield parameters were not affected by BES application. The maximum CH₄ reduction (49% reduction over control) was found at 80 mg kg^-1 BES application during rice cultivation. It is, therefore, concluded that BES could be a suitable soil amendment for reducing CH₄ emission without affecting rice plant growth and productivity during rice cultivation.

Potential for direct interspecies electron transfer in an electric-anaerobic system to increase methane production from sludge digestion

Direct interspecies electron transfer (DIET) between Geobacter species and Methanosaeta species is an alternative to interspecies hydrogen transfer (IHT) in anaerobic digester, which however has not been established in anaerobic sludge digestion as well as in bioelectrochemical systems yet. In this study, it was found that over 50% of methane production of an electric-anaerobic sludge digester was resulted from unknown pathway. Pyrosequencing analysis revealed that Geobacter species were significantly enriched with electrodes. Fluorescence in situ hybridization (FISH) further confirmed that the dominant Geobacter species enriched belonged to Geobacter metallireducens. Together with Methanosaeta species prevailing in the microbial communities, the direct electron exchange between Geobacter species and Methanosaeta species might be an important reason for the "unknown" increase of methane production. Conductivity of the sludge in this electric-anaerobic digester was about 30% higher than that of the sludge in a control digester without electrodes. This study not only revealed for the first time that DIET might be the important mechanism on the methanogenesis of bioelectrochemical system, but also provided a new method to enhance DIET by means of bioelectric enrichment of Geobacter species.

Methane production potentials, pathways, and communities of methanogens in vertical sediment profiles of river Sitka

Biological methanogenesis is linked to permanent water logged systems, e.g., rice field soils or lake sediments. In these systems the methanogenic community as well as the pathway of methane formation are well-described. By contrast, the methanogenic potential of river sediments is so far not well-investigated. Therefore, we analyzed (a) the methanogenic potential (incubation experiments), (b) the pathway of methane production (stable carbon isotopes and inhibitor studies), and (c) the methanogenic community composition (terminal restriction length polymorphism of mcrA) in depth profiles of sediment cores of River Sitka, Czech Republic. We found two depth-related distinct maxima for the methanogenic potentials (a) The pathway of methane production was dominated by hydrogenotrophic methanogenesis (b) The methanogenic community composition was similar in all depth layers (c) The main TRFs were representative for Methanosarcina, Methanosaeta, Methanobacterium, and Methanomicrobium species. The isotopic signals of acetate indicated a relative high contribution of chemolithotrophic acetogenesis to the acetate pool.

Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming

Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH4) in a future warmer climate. How warming affects the complex microbial network decomposing SOC is not understood. We studied CH4 production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH4 production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH4 production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H2-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae. Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH4 is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa.

High concentrations of methyl fluoride affect the bacterial community in a thermophilic methanogenic sludge

To precisely control the application of methyl fluoride (CH₃F) for analysis of methanogenic pathways, the influence of 0–10% CH₃F on bacterial and archaeal communities in a thermophilic methanogenic sludge was investigated. The results suggested that CH₃F acts specifically on acetoclastic methanogenesis. The inhibitory effect stabilized at an initial concentration of 3–5%, with around 90% of the total methanogenic activity being suppressed, and a characteristic of hydrogenotrophic pathway in isotope fractionation was demonstrated under this condition. However, extended exposure (12 days) to high concentrations of CH₃F (>3%) altered the bacterial community structure significantly, resulting in increased diversity and decreased evenness, which can be related to acetate oxidation and CH₃F degradation. Bacterial clone library analysis showed that syntrophic acetate oxidizing bacteria Thermacetogenium phaeum were highly enriched under the suppression of 10% CH₃F. However, the methanogenic community did not change obviously. Thus, excessive usage of CH₃F over the long term can change the composition of the bacterial community. Therefore, data from studies involving the use of CH₃F as an acetoclast inhibitor should be interpreted with care. Conversely, CH₃F has been suggested as a factor to stimulate the enrichment of syntrophic acetate oxidizing bacteria.