Bypassing the methane cycle

Mechanism of microbial regulation on methane metabolism in saline-alkali soils based on metagenomics analysis

Saline-alkali soils constitute a globally important carbon pool that plays a critical role in soil carbon dioxide (CO2) and methane (CH4) fluxes. However, the relative importance of microorganisms in the regulation of CH4 emissions under elevated salinity remains unclear. Here, we report the composition of CH4 production and oxidation microbial communities under five different salinity levels in the Yellow River Delta, China. This study also obtained the gene number of microbial CH4 metabolism via testing the soil metagenomes, and further investigated the key soil factors to determine the regulation mechanism. Spearman correlation analysis showed that the soil electrical conductivity, salt content, and Na+, and SO42- concentrations showed significantly negative correlations with the CO2 and CH4 emission rates, while the NO2--N concentration and NO2-/NO3- ratio showed significantly positive correlations with the CO2 and CH4 emission rates. Metabolic pathway analysis showed that the mcrA gene for CH4 production was highest in low-salinity soils. By contrast, the relative abundances of the fwdA, ftr, mch, and mer genes related to the CO2 pathway increased significantly with rising salinity. Regarding CH4 oxidation processes, the relative abundances of the pmoA, mmoB, and mdh1 genes transferred from CH4 to formaldehyde decreased significantly from the control to the extreme-salinity plot. The greater abundance and rapid increase of methanotrophic bacteria compared with the lower abundance and slow increase in methanogenic archaea communities in saline-alkali soils may have increased CH4 oxidation and reduced CH4 production in this study. Only CO2 emissions positively affected CH4 emissions from low- to medium-salinity soils, while the diversities of CH4 production and oxidation jointly influenced CH4 emissions from medium- to extreme-salinity plots. Hence, future investigations will also explore more metabolic pathways for CH4 emissions from different types of saline-alkali lands and combine the key soil enzymes and regulated biotic or abiotic factors to enrich the CH4 metabolism pathway in saline-alkali soils.

Mechanism and Kinetics of Methane Combustion. Part II: Potential Energy Surface for Hydrogen-Abstraction Reaction of CH4 + O(3P)

Methane combustion plays an important role in various fields such as combustion chemistry and atmospheric chemistry of the stratosphere. Highly accurate study of its initial reaction remains a key challenge. Here, through extensive studies with a state-of-the-art ab initio and neural network method, we present a potential energy surface of the O(³P) + CH₄ → OH + CH₃ reaction on the ground state 1³A and the first excited state 2³A. In this work, the energies of 10 167 points covering all important regions are obtained with state-averaged complete active space self-consistent field calculations and then fitted using the Levenberg-Marquardt algorithm with a root-mean-square error of 0.391 and 0.442 kcal/mol for the 1³A and 2³A states, respectively. This study explores the characteristics of the radical van der Waals (VdW) complex and reveals a detailed mechanism of the methane combustion initial reaction. Within the scope of this mechanism, this surface gives a fairly accurate description of the regions around the saddle point, conical intersection, and vdW wells in the entrance for efficient computational simulations. As a theoretical study on a prototypical polyatomic reaction, it is hopeful that this work will modify our understanding of the primary process in hydrocarbon combustion.

Regulating CH4, N2O, and NO emissions from an alkaline paddy field under rice-wheat rotation with controlled release N fertilizer

Controlled release fertilizer (CRF) has been shown to increase crop yield and N use efficiency (NUE) compared with traditional chemical fertilizer (TF). However, few studies examined the effects of CRF on CH₄, N₂O, and NO emissions simultaneously in alkaline paddy fields under rice-wheat rotation. In the present study, we conducted a 2-year field experiment to compare the effects of different CRF application strategies on these gas emissions with those of TF and explored the effects of CRF on global warming potential (GWP), crop yields, and greenhouse gas emission intensity (GHGI). Results showed that CRF can reduce 0.98-14.3%, 13.3-21.1%, and 8.22-16.3% of CH₄, N₂O, and NO emissions, respectively, in the studied alkaline paddy field. CRF reduce CH₄ emission probably by regulating soil NH₄⁺ concentration. CRF reduce N₂O and NO emissions probably by regulating inorganic N content in the studied alkaline paddy soil. CRF had the same effect on annual crop yield as TF, especially when CRF was applied twice in each season and had the same N application rate as TF. Annual crop yields and the agronomic efficiency of N (AE_N) increased by 8.24% and 21.6%, respectively. On the average of the two rice-wheat rotation cycles, GHGI significantly decreased by up to 14.1% after the application of CRF as relative to that after the application of TF (P < 0.05). These results suggest that CRF is an environment-friendly N fertilization strategy for mitigating GWP and ensuring high crop yield in an alkaline paddy field under rice-wheat rotation.

Ecological drivers of methanotrophic communities in paddy soils around mercury mining areas

Methanotrophs play a crucial role in mitigating methane (CH₄) emission by oxidizing produced CH₄ in paddy soils; however, ecological drivers of methanotrophic community in the soils around heavy metal contaminated areas remain unclear. In this study, we evaluated the effects of heavy metal pollution and soil properties on the abundance, diversity and composition of methanotrophic community in paddy soils from two typical mercury (Hg) mining regions in southwest China. The results of random forest and structure equation models suggest that both heavy metal content and soil nutrients greatly influenced the attributes of methanotrophic community. In general, the abundance and diversity of methanotrophs were negatively related to soil Hg content, but showed positive correlation with soil organic carbon content. However, the other metals (cadmium (Cd), nickel (Ni), lead (Pb), arsenic (As), zinc (Zn)) had inconsistent associations with the microbial indexes of methanotrophic community in the soil. Elevated levels of heavy metal and nutrients in the soils shifted the community composition of methanotrophs. For example, Pb, As and Zn contents had negative associations with the relative abundance of Methylocaldum. In addition, changes in the relative abundance of ecological clusters within the co-occurrence network of methanotrophs were related to metal contents and soil properties. Together, our findings provide novel insights into understanding ecological drivers of methanotrophic community in paddy soils around Hg mining regions, with important implications for mitigating CH₄ emissions in terrestrial ecosystems.

Manure amendment increased the abundance of methanogens and methanotrophs but suppressed the type I methanotrophs in rice paddies

Methane (CH₄) emission is the consequence of CH₄ production and consumption performed by methanogens and methanotrophs, respectively. Fertilization is an important factor that regulates the behavior of methanogens and methanotrophs; however, the effect of manure and rice straw addition combined with inorganic fertilizers on these communities is not well understood. This study aimed to explore how manure and rice straw amendments together with inorganic fertilizers influenced the methanogenic and methanotrophic communities in a 31-year fertilized rice paddy. Manure amendment significantly increased the abundance of mcrA and pmoA genes by 61.2% and 63.3% compared with the unfertilized control, whereas inorganic NPK fertilization alone or rice straw addition did not affect their abundances. Manure and rice straw amendments greatly decreased the Shannon index and ACE index of the methanogenic communities, whereas inorganic NPK fertilization alone increased the ACE index of the methanotrophic communities compared with the unfertilized control. Methanosarcinaceae and Methylococcaceae dominated at the family level, representing 23.1-35.0% and 48.7-67.2% of the total reads, for the methanogenic and methanotrophic communities, respectively. Application of manure together with inorganic fertilizers suppressed the Methanocellales methanogens and the type I methanotrophs (Methylococcus and Methylobacter). Fertilization greatly altered the community structure of methanogens and methanotrophs, and manure addition had more apparent effects than rice straw. Moreover, total nitrogen, soil organic carbon, available phosphorus, and available potassium correlated significantly to the abundance, composition, and community structure of methanogens and methanotrophs. In conclusion, our study revealed that long-term manure amendment in combination with inorganic fertilizers significantly increased the abundance of methanogens and methanotrophs, but suppressed the type I methanotrophs in rice paddies.

Three-Source Partitioning of Methane Emissions from Paddy Soil: Linkage to Methanogenic Community Structure

Identification of the carbon (C) sources of methane (CH₄) and methanogenic community structures after organic fertilization may provide a better understanding of the mechanism that regulate CH₄ emissions from paddy soils. Based on our previous field study, a pot experiment with isotopic ¹³C labelling was designed in this study. The objective was to investigate the main C sources for CH₄ emissions and the key environmental factor with the application of organic fertilizer in paddies. Results indicated that 28.6%, 64.5%, 0.4%, and 6.5% of ¹³C was respectively distributed in CO₂, the plants, soil, and CH₄ at the rice tillering stage. In total, organically fertilized paddy soil emitted 3.51 kg·CH₄ ha⁻¹ vs. 2.00 kg·CH₄ ha⁻¹ for the no fertilizer treatment. Maximum CH₄ fluxes from organically fertilized (0.46 mg·m⁻²·h⁻¹) and non-fertilized (0.16 mg·m⁻²·h⁻¹) soils occurred on day 30 (tillering stage). The total percentage of CH₄ emissions derived from rice photosynthesis C was 49%, organic fertilizer C < 0.34%, and native soil C > 51%. Therefore, the increased CH₄ emissions from paddy soil after organic fertilization were mainly derived from native soil and photosynthesis. The 16S rRNA sequencing showed Methanosarcina (64%) was the dominant methanogen in paddy soil. Organic fertilization increased the relative abundance of Methanosarcina, especially in rhizosphere. Additionally, Methanosarcina sp. 795 and Methanosarcina sp. 1H1 co-occurred with Methanobrevibacter sp. AbM23, Methanoculleus sp. 25XMc2, Methanosaeta sp. HA, and Methanobacterium sp. MB1. The increased CH₄ fluxes and labile methanogenic community structure in organically fertilized rice soil were primarily due to the increased soil C, nitrogen, potassium, phosphate, and acetate. These results highlight the contributions of native soil- and photosynthesis-derived C in paddy soil CH₄ emissions, and provide basis for more complex investigations of the pathways involved in ecosystem CH₄ processes.

Limited potential of harvest index improvement to reduce methane emissions from rice paddies

Rice is a staple food for nearly half of the world's population, but rice paddies constitute a major source of anthropogenic CH₄ emissions. Root exudates from growing rice plants are an important substrate for methane-producing microorganisms. Therefore, breeding efforts optimizing rice plant photosynthate allocation to grains, i.e., increasing harvest index (HI), are widely expected to reduce CH₄ emissions with higher yield. Here we show, by combining a series of experiments, meta-analyses and an expert survey, that the potential of CH₄ mitigation from rice paddies through HI improvement is in fact small. Whereas HI improvement reduced CH₄ emissions under continuously flooded (CF) irrigation, it did not affect CH₄ emissions in systems with intermittent irrigation (II). We estimate that future plant breeding efforts aimed at HI improvement to the theoretical maximum value will reduce CH₄ emissions in CF systems by 4.4%. However, CF systems currently make up only a small fraction of the total rice growing area (i.e., 27% of the Chinese rice paddy area). Thus, to achieve substantial CH₄ mitigation from rice agriculture, alternative plant breeding strategies may be needed, along with alternative management.

Differentiated Mechanisms of Biochar Mitigating Straw-Induced Greenhouse Gas Emissions in Two Contrasting Paddy Soils

Straw returns to the soil is an effective way to improve soil organic carbon and reduce air pollution by straw burning, but this may increase CH₄ and N₂O emissions risks in paddy soils. Biochar has been used as a soil amendment to improve soil fertility and mitigate CH₄ and N₂O emissions. However, little is known about their interactive effect on CH₄ and N₂O emissions and the underlying microbial mechanisms. In this study, a 2-year pot experiment was conducted on two paddy soil types (an acidic Utisol, TY, and an alkaline Inceptisol, BH) to evaluate the influence of straw and biochar applications on CH₄ and N₂O emissions, and on related microbial functional genes. Results showed that straw addition markedly increased the cumulative CH₄ emissions in both soils by 4.7- to 9.1-fold and 23.8- to 72.4-fold at low (S1) and high (S2) straw input rate, respectively, and significantly increased mcrA gene abundance. Biochar amendment under the high straw input (BS2) significantly decreased CH₄ emissions by more than 50% in both soils, and increased both mcrA gene and pmoA gene abundances, with greatly enhanced pmoA gene and a decreased mcrA/pmoA gene ratio. Moreover, methanotrophs community changed distinctly in response to straw and biochar amendment in the alkaline BH soil, but showed slight change in the acidic TY soil. Straw had little effect on N₂O emissions at low input rate (S1) but significantly increased N₂O emissions at the high input rate (S2). Biochar amendment showed inconsistent effect on N₂O emissions, with a decreasing trend in the BH soil but an increasing trend in the TY soil in which high ammonia existed. Correspondingly, increased nirS and nosZ gene abundances and obvious community changes in nosZ gene containing denitrifiers in response to biochar amendment were observed in the BH soil but not in the TY soil. Overall, our results suggested that biochar amendment could markedly mitigate the CH₄ and N₂O emissions risks under a straw return practice via regulating functional microbes and soil physicochemical properties, while the performance of this practice will vary depending on soil parent material characteristics.

Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil

Paddy soil accounts for 10% of global atmospheric methane (CH₄) emissions. Many types of fertilizers may enhance CH₄ emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH₄ and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha^-1. Paddy CH₄, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH₄ emissions were significantly higher in OT (145.31 kg ha^-1) than MT (84.62 kg ha^-1), CT (77.88 kg ha^-1) or ctrl (32.19 kg ha^-1). Soil organic acids were also increased by organic fertilization. CH₄ effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH₄ production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH₄ emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha^-1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.

Mitigating Methane: Emerging Technologies To Combat Climate Change's Second Leading Contributor

Methane (CH₄) is the second greatest contributor to anthropogenic climate change. Emissions have tripled since preindustrial times and continue to rise rapidly, given the fact that the key sources of food production, energy generation and waste management, are inexorably tied to population growth. Until recently, the pursuit of CH₄ mitigation approaches has tended to align with opportunities for easy energy recovery through gas capture and flaring. Consequently, effective abatement has been largely restricted to confined high-concentration sources such as landfills and anaerobic digesters, which do not represent a major share of CH₄'s emission profile. However, in more recent years we have witnessed a quantum leap in the sophistication, diversity and affordability of CH₄ mitigation technologies on the back of rapid advances in molecular analytical techniques, developments in material sciences and increasingly efficient engineering processes. Here, we present some of the latest concepts, designs and applications in CH₄ mitigation, identifying a number of abatement synergies across multiple industries and sectors. We also propose novel ways to manipulate cutting-edge technology approaches for even more effective mitigation potential. The goal of this review is to stimulate the ongoing quest for and uptake of practicable CH₄ mitigation options; supplementing established and proven approaches with immature yet potentially high-impact technologies. There has arguably never been, and if we do not act soon nor will there be, a better opportunity to combat climate change's second most significant greenhouse gas.

Higher yields and lower methane emissions with new rice cultivars

Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH₄ ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH₄ emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH₄ emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH₄ oxidation by promoting O₂ transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH₄ emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH₄ emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH₄ emission in China and other rice growing regions.

Biologically derived fertilizer: A multifaceted bio-tool in methane mitigation

Methane emissions are affected by agricultural practices. Agriculture has increased in scale and intensity because of greater food, feed and energy demands. The application of chemical fertilizers in agriculture, particularly in paddy fields, has contributed to increased atmospheric methane emissions. Using organic fertilizers may improve crop yields and the methane sink potential within agricultural systems, which may be further improved when combined with beneficial microbes (i.e. biofertilizers) that improve the activity of methane oxidizing bacteria such as methanotrophs. Biofertilizers may be an effective tool for agriculture that is environmentally beneficial compared to conventional inorganic fertilizers. This review highlights and discusses the interplay between ammonia and methane oxidizing bacteria, the potential interactions of microbial communities with microbially-enriched organic amendments and the possible role of these biofertilizers in augmenting the methane sink potential of soils. It is suggested that biofertilizer applications should not only be investigated in terms of sustainable agriculture productivity and environmental management, but also in terms of their effects on methanogen and methanotroph populations.

Microbial Community Structure in the Rhizosphere of Rice Plants

The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth.