Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils

Conversion of coastal wetlands to paddy fields substantially decreases methane oxidation potential and methanotrophic abundance on the eastern coast of China

Coastal wetland ecosystems play a key role in the global carbon cycle and climate mitigation. The land conversion of coastal wetlands to paddy fields, an increasingly common practice to feed the growing population, has been shown to dramatically stimulate the methane emissions of (CH4). However, the knowledge about how such wetland conversion affects the methane oxidation, a key process regulating methane emissions from coastal wetlands, is nearly unknown. In this study, a space-for-time substitution method was employed to investigate the impact of the conversion of coastal wetlands (dominated by Phragmites or mangrove (Kandelia and Bruguiera)) to paddy fields on the methane oxidation process on the eastern coast of China. Our results showed that the average CH4 oxidation potential in the converted paddy soils significantly reduced by 28.4 % and 29.3 %, respectively, and the average abundance of methanotrophic pmoA gene decreased by 77.1 % and 81.9 %, respectively, compared to the original Phragmites and mangrove soils. Significant changes in the methanotrophic community composition were also found after converting Phragmites and mangrove wetlands to paddy fields. Structural equation modeling analysis suggested that the land conversion significantly affected the CH4 oxidation potential by changing the soil physicochemical properties (pH, ammonium content, and nitrate content) and methanotrophic abundance. Overall this study showed significant alterations in CH4 oxidation potential and community composition and abundance of methanotrophs caused by conversion of coastal wetlands to paddy fields, improving the knowledge of the underlying microbial mechanisms of land conversion on methane emissions.

Variations in the N2 Fixation and CH4 Oxidation Activities of Type I Methanotrophs in the Rice Roots in Saline-Alkali Paddy Field Under Nitrogen Fertilization

The root-associated methanotrophs contribute to N2 fixation and CH4 oxidation in paddy fields under N-limited conditions. However, the impact of nitrogen inputs on N₂ fixation and CH₄ oxidation by methanotrophs is largely unknown, especially in saline-alkali paddy fields with higher nitrogen application. This study explored the impact of nitrogen fertilization on N₂ fixation and CH₄ oxidation by root-associated active diazotrophic and methanotrophic communities in a saline-alkali paddy field using 15N-N2 and 13C-CH4 isotope feeding experiments along with RNA-based sequencing. The 15N and 13C isotope feeding experiments showed that the CH₄ oxidation-dependent nitrogen fixation rate of methanotrophs (15N and 13C) in the roots of two rice cultivars was significantly higher than the CH₄ oxidation-independent nitrogen fixation rate of heterotrophic diazotrophs (only 15N) under nitrogen fertilization (SN) in a saline-alkali environment (P < 0.05). For Kongyu131 rice, the CH₄ oxidation-dependent nitrogen fixation rate ranged from 1.17 to 4.15 μmol/h/g, while the CH₄ oxidation-independent nitrogen fixation rate was determined to be 1.10 to 3.17 μmol/h/g. In J3 rice, these rates were 7.30 to 9.22 μmol/h/g and 5.76 to 4.85 μmol/h/g, respectively (P < 0.05). Moreover, both N2 fixation and CH4 oxidation rates of methanotrophs in the roots of salt-alkali tolerant J3 cultivar (9.22 μmol/h/g for N2 fixation; 0.09 μmol/h/g for CH4 oxidation) were significantly higher than those in the roots of the common rice cultivar Kongyu131 (4.15 μmol/h/g for N₂ fixation; 0.03 μmol/h/g for CH₄ oxidation) under nitrogen fertilization (P < 0.01). Thus, methanotrophs associated with J3 rice roots demonstrated improved N2 fixation and CH4 oxidation activities under saline-alkali stress in the presence of nitrogen fertilizer. Even heterotrophic diazotrophs in J3 rice roots showed enhanced N2 fixation with (SN) or without (LN) nitrogen inputs. The RNA-based amplicon sequencing showed that nitrogen fertilizer had a greater influence on diazotrophic and methanotrophic communities than the differences between rice cultivars. Further, active Methylomonas (type I methanotrophs) dominated the root-associated diazotrophic (9.8-20.9%) and methanotrophic (46.8-80.3%) communities. Within these, Methylomonas methanica (13.3 vs. 3.8%) and Methylomonas paludis (8.8 vs. 27.4%) were determined as the common genera in the diazotrophic and methanotrophic communities, respectively, with both proportions undergoing significant shifts under SN conditions. Whereas the LN condition led to high CH4 oxidation activity and a relatively high abundance of Methylocystis (26.0%) in the roots of Kongyu131 rice, which sharply decreased under the SN condition (0.3%). The findings revealed that CH4 oxidation-dependent N2 fixation and CH4 oxidation activities of root-associated type I methanotrophs were significantly affected under nitrogen fertilization, with a more pronounced effect in the salt-alkali tolerant J3 rice cultivar compared to Kongyu131. This study highlights the potential of aerobic diazotrophic methanotrophs in enhancing symbiotic diversity and environmental adaptability while contributing to CH4 emission reduction and bioavailable nitrogen accumulation in saline-alkali paddy fields.

Methane cycling in temperate forests

Temperate forest soils are considered significant methane (CH4) sinks, but other methane sources and sinks within these forests, such as trees, litter, deadwood, and the production of volatile organic compounds are not well understood. Improved understanding of all CH4 fluxes in temperate forests could help mitigate CH4 emissions from other sources and improve the accuracy of global greenhouse gas budgets. This review highlights the characteristics of temperate forests that influence CH4 flux and assesses the current understanding of the CH4 cycle in temperate forests, with a focus on those managed for specific purposes. Methane fluxes from trees, litter, deadwood, and soil, as well as the interaction of canopy-released volatile organic compounds on atmospheric methane chemistry are quantified, the processes involved and factors (biological, climatic, management) affecting the magnitude and variance of these fluxes are discussed. Temperate forests are unique in that they are extremely variable due to strong seasonality and significant human intervention. These features control CH4 flux and need to be considered in CH4 budgets. The literature confirmed that temperate planted forest soils are a significant CH4 sink, but tree stems are a small CH4 source. CH4 fluxes from foliage and deadwood vary, and litter fluxes are negligible. The production of volatile organic compounds could increase CH4's lifetime in the atmosphere, but current in-forest measurements are insufficient to determine the magnitude of any effect. For all sources and sinks more research is required into the mechanisms and microbial community driving CH4 fluxes. The variability in CH4 fluxes within each component of the forest, is also not well understood and has led to overestimation of CH4 fluxes when scaling up measurements to a forest or global scale. A roadmap for sampling and scaling is required to ensure that all CH4 sinks and sources within temperate forests are accurately accounted for and able to be included in CH4 budgets and models to ensure accurate estimates of the contribution of temperate planted forests to the global CH4 cycle.

Methylotrophic bacteria from rice paddy soils: mineral-nitrogen-utilizing isolates richness in bulk soil and rhizosphere

Methanol, the second most abundant volatile organic compound, primarily released from plants, is a major culprit disturbing atmospheric chemistry. Interestingly, ubiquitously found methanol-utilizing bacteria, play a vital role in mitigating atmospheric methanol effects. Despite being extensively characterized, the effect of nitrogen sources on the richness of methanol-utilizers in the bulk soil and rhizosphere is largely unknown. Therefore, the current study was planned to isolate, characterize and explore the richness of cultivable methylotrophs from the bulk soil and rhizosphere of a paddy field using media with varying nitrogen sources. Our data revealed that more genera of methylotrophs, including Methylobacterium, Ancylobacter, Achromobacter, Xanthobacter, Moraxella, and Klebsiella were enriched with the nitrate-based medium compared to only two genera, Hyphomicrobium and Methylobacterium, enriched with the ammonium-based medium. The richness of methylotrophic bacteria also differed substantially in the bulk soil as compared to the rhizosphere. Growth characterization revealed that majority of the newly isolated methanol-utilizing strains in this study exhibited better growth at 37 °C instead of 30 or 45 °C. Moreover, Hyphomicrobium sp. FSA2 was the only strain capable of utilizing methanol even at elevated temperature 45 °C, showing its adaptability to a wide range of temperatures. Differential carbon substrate utilization profiling revealed the facultative nature of all isolated methanol-utilizer strains with Xanthobacter sp. TS3, being an important methanol-utilizer capable of degrading toxic compounds such as acetone and ethylene glycol. Overall, our study suggests the role of nutrients and plant-microbial interaction in shaping the composition of methanol-utilizers in terrestrial environment.

Methanotrophic Communities and Cultivation of Methanotrophs from Rice Paddy Fields Fertilized with Pig-livestock Biogas Digestive Effluent and Synthetic Fertilizer in the Vietnamese Mekong Delta

Biogas digestive effluent (BDE) has been applied to rice fields in the Vietnamese Mekong Delta (VMD). However, limited information is available on the community composition and isolation of methanotrophs in these fields. Therefore, the present study aimed (i) to clarify the responses of the methanotrophic community in paddy fields fertilized with BDE or synthetic fertilizer (SF) and (ii) to isolate methanotrophs from these fields. Methanotrophic communities were detected in rhizospheric soil at the rice ripening stage throughout 2 cropping seasons, winter-spring (dry) and summer-autumn (wet). Methanotrophs were isolated from dry-season soil samples. Although the continued application of BDE markedly reduced net methane oxidation potential and the copy number of pmoA genes, a dissimilarity ordination ana-lysis revealed no significant difference in the methanotrophic community between BDE and SF fields (P=0.167). Eleven methanotrophic genera were identified in the methanotrophic community, and Methylosinus and Methylomicrobium were the most abundant, accounting for 32.3-36.7 and 45.7-47.3%, respectively. Type-I methanotrophs (69.4-73.7%) were more abundant than type-II methanotrophs (26.3-30.6%). Six methanotrophic strains belonging to 3 genera were successfully isolated, which included type I (Methylococcus sp. strain BE1 and Methylococcus sp. strain SF3) and type II (Methylocystis sp. strain BE2, Methylosinus sp. strain SF1, Methylosinus sp. strain SF2, and Methylosinus sp. strain SF4). This is the first study to examine the methanotrophic community structure in and isolate several methanotrophic strains from BDE-fertilized fields in VMD.

Application of nitrogen-rich sunflower husks biochar promotes methane oxidation and increases abundance of Methylobacter in nitrogen-poor soil

The area of sunflower crops is steadily increasing. A beneficial way of managing sunflower waste biomass could be its use as a feedstock for biochar production. Biochar is currently being considered as an additive for improving soil parameters, including the ability to oxidise methane (CH4) - one of the key greenhouse gases (GHG). Despite the high production of sunflower husk, there is still insufficient information on the impact of sunflower husk biochar on the soil environment, especially on the methanotrophy process. To fill this knowledge gap, an experiment was designed to evaluate the effects of addition of sunflower husk biochar (produced at 450-550 °C) at a wide range of doses (1-100 Mg ha-1) to Haplic Luvisol. In the presented study, the CH4 oxidation potential of soil with and without sunflower husk biochar was investigated at 60 and 100% water holding capacity (WHC), and with the addition of 1% CH4 (v/v). The comprehensive study included GHG exchange (CH4 and CO2), physicochemical properties of soil (pH, soil organic carbon (SOC), dissolved organic carbon (DOC), nitrate nitrogen (NO3--N), WHC), and the structure of soil microbial communities. That study showed that even low biochar doses (5 and 10 Mg ha-1) were sufficient to enhance pH, SOC, DOC and NO3--N content. Importantly, sunflower husk biochar was significant source of NO3--N, which soil concentration increased from 9.40 ± 0.09 mg NO3--N kg-1 for the control to even 19.40 ± 0.26 mg NO3--N kg-1 (for 100 Mg ha-1). Significant improvement of WHC (by 11.0-12.4%) was observed after biochar addition at doses of 60 Mg ha-1 and higher. At 60% WHC, application of biochar at a dose of 40 Mg ha-1 brought significant improvements in CH4 oxidation rate, which was 4.89 ± 0.37 mg CH4-C kg-1 d-1. Higher biochar doses were correlated with further improvement of CH4 oxidation rates, which at 100 Mg ha-1 was seventeen-fold higher (8.36 ± 0.84 mg CH4-C kg-1 d-1) than in the biochar-free control (0.48 ± 0.28 mg CH4-C kg-1 d-1). CO2 emissions were not proportional to biochar doses and only grew circa (ca.) twofold from 3.16 to 6.90 mg CO2-C kg-1 d-1 at 100 Mg ha-1. Above 60 Mg ha-1, the diversity of methanotrophic communities increased, with Methylobacter becoming the most abundant genus, which was as high as 7.45%. This is the first, such advanced and multifaceted study of the wide range of sunflower husk biochar doses on Haplic Luvisol. The positive correlation between soil conditions, methanotroph abundance and CH4 oxidation confirmed the multifaceted, positive effect of sunflower husk biochar on Haplic Luvisol. Sunflower husk biochar can be successfully used for Haplic Luvisol supplementation. This additive facilitates soil protection against degradation and has the potential to mitigate GHG emissions.

Soil organic carbon is a key determinant of CH4 sink in global forest soils

Soil organic carbon (SOC) is a primary regulator of the forest-climate feedback. However, its indicative capability for the soil CH₄ sink is poorly understood due to the incomplete knowledge of the underlying mechanisms. Therefore, SOC is not explicitly included in the current model estimation of the global forest CH₄ sink. Here, using in-situ observations, global meta-analysis, and process-based modeling, we provide evidence that SOC constitutes an important variable that governs the forest CH₄ sink. We find that a CH₄ sink is enhanced with increasing SOC content on regional and global scales. The revised model with SOC function better reproduces the field observation and estimates a 39% larger global forest CH₄ sink (24.27 Tg CH₄ yr^-1) than the model without considering SOC effects (17.46 Tg CH₄ yr^-1). This study highlights the role of SOC in the forest CH₄ sink, which shall be factored into future global CH₄ budget quantification.

Variation in methane uptake by grassland soils in the context of climate change - A review of effects and mechanisms

Grassland soils are climate-dependent ecosystems that have a significant greenhouse gas mitigating function through their ability to store large amounts of carbon (C). However, what is often not recognized is that they can also exhibit a high methane (CH₄) uptake capacity that could be influenced by future increases in atmospheric carbon dioxide (CO₂) concentration and variations in temperature and water availability. While there is a wealth of information on C sequestration in grasslands there is less consensus on how climate change impacts on CH₄ uptake or the underlying mechanisms involved. To address this, we assessed existing knowledge on the impact of climate change components on CH₄ uptake by grassland soils. Increases in precipitation associated with soils with a high background soil moisture content generally resulted in a reduction in CH₄ uptake or even net emissions, while the effect was opposite in soils with a relatively low background moisture content. Initially wet grasslands subject to the combined effects of warming and water deficits may absorb more CH₄, mainly due to increased gas diffusivity. However, in the longer-term heat and drought stress may reduce the activity of methanotrophs when the mean soil moisture content is below the optimum for their survival. Enhanced plant productivity and growth under elevated CO₂, increased soil moisture and changed nutrient concentrations, can differentially affect methanotrophic activity, which is often reduced by increasing N deposition. Our estimations showed that CH₄ uptake in grassland soils can change from -57.7 % to +6.1 % by increased precipitation, from -37.3 % to +85.3 % by elevated temperatures, from +0.87 % to +92.4 % by decreased precipitation, and from -66.7 % to +27.3 % by elevated CO₂. In conclusion, the analysis suggests that grasslands under the influence of warming and drought may absorb even more CH₄, mainly because of reduced soil water contents and increased gas diffusivity.

Effects of abrupt and gradual increase of atmospheric CO2 concentration on methanotrophs in paddy fields

The simulation of abrupt atmospheric CO₂ increase is a common way to examine the response of soil methanotrophs to future climate change. However, atmosphere is undergoing a gradual CO₂ increase, and it is unknown whether the previously reported response of methanotrophs to abrupt CO₂ increase can well represent their response to the gradual increase. To improve the understanding of the effect of elevated CO₂ (eCO₂) on methanotrophs in paddy ecosystems, the methane oxidation potential and communities of methanotrophs were examined via open top chambers under the three following CO₂ treatments: an ambient CO₂ concentration (AC); an abrupt CO₂ increase by 200 ppm above AC (AI); a gradual CO₂ increase by 40 ppm each year until 200 ppm above AC (GI). Relative to AC treatment, AI and GI treatments significantly (p < 0.05) increased the methane oxidation rate by 43.8% and 36.7%, respectively, during rice growth period. Furthermore, the abundance of pmoA genes was significantly (p < 0.05) increased by 62.4% and 32.5%, respectively, under AI and GI treatments. However, there were no significant variations in oxidation rate or gene abundance between the two eCO₂ treatments. In addition, no obvious change of overall community composition of methanotrophs was observed among treatments, while the proportions of Methylosarcina and Methylocystis significantly (p < 0.05) changed. Taken together, our results indicate similar response of methanotrophs to abrupt and gradual CO₂ increase, although the magnitude of response under gradual increase was smaller and the abrupt increase may somewhat overestimate the response.

Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems

Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH₄). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH₄ emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH₄ emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH₄ sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH₄ mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.

Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils

CH₄ emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH₄ oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH₄ produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH₄ oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH₄ oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH₄ emissions via the reduction of CH₄ oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO₃^- is responsible for the decrease in CH₄ oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH₄ oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH₄ emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH₄ dynamics in Arctic regions.

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.

The Effects of N Enrichment on Microbial Cycling of Non-CO2 Greenhouse Gases in Soils-a Review and a Meta-analysis

Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH₄) and nitrous oxide (N₂O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH₄ at the global scale. We also address the effects of N enrichment on N₂O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH₄ oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH₄⁺ enrichment, inhibits CH₄ oxidation, resulting in higher CH₄ emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N₂O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.

Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition

A high NH4+ load is known to inhibit bacterial methane oxidation. This is due to a competition between CH4 and NH3 for the active site of particulate methane monooxygenase (pMMO), which converts CH4 to CH3OH. Here, we combined global proteomics with amino acid profiling and nitrogen oxides measurements to elucidate the cellular acclimatization response of Methylocystis sp. strain SC2 to high NH4+ levels. Relative to 1 mM NH4+, a high (50 mM and 75 mM) NH4+ load under CH4-replete conditions significantly increased the lag phase duration required for proteome adjustment. The number of differentially regulated proteins was highly significantly correlated with an increasing NH4+ load. The cellular responses to increasing ionic and osmotic stress involved a significant upregulation of stress-responsive proteins, the K+ "salt-in" strategy, the synthesis of compatible solutes (glutamate and proline), and the induction of the glutathione metabolism pathway. A significant increase in the apparent Km value for CH4 oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH3 to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO2- and, upon decreasing O2 tension, N2O. Nitric oxide reductase and hybrid cluster proteins (Hcps) were the candidate enzymes for the production of N2O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition in response to increasing NH4+ exposure, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+. IMPORTANCE In addition to reducing CH4 emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH4+ concentrations. This is due to the competition of CH4 and NH3 for the active site of particulate methane monooxygenase, thereby resulting in the production of toxic hydroxylamine with an increasing NH4+ load. An understanding of the physiological and molecular response mechanisms of Methylocystis spp. is therefore of great importance. Here, we combined global proteomics with amino acid profiling and NOx measurements to disentangle the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to an increasing NH4+ load.

Variations in Concentration and Carbon Isotope Composition of Methanotroph Biomarkers in Sedge Peatlands Along the Altitude Gradient in the Changbai Mountain, China

Northern peatlands are one of the largest natural sources of atmospheric methane globally. As the only biological sink of methane, different groups of methanotrophs use different carbon sources. However, the variations in microbial biomass and metabolism of different methanotrophic groups in peatlands along the altitude gradient are uncertain. We measured the concentrations and metabolic characteristics of type I (16:1ω7c and 16:1ω5c) and type II (18:1ω7c) methanotroph biomarkers using biomarkers and stable isotopes in eight Carex peatlands along an altitude gradient from 300 to 1,500 m in the Changbai Mountain, China. We found that the trends with altitude in concentrations of the type I and type II methanotroph biomarkers were different. The dominating microbial group changed from type I to type II methanotroph with increasing altitude. The concentrations of type I and type II methanotroph biomarkers were significantly affected by the total phosphorus, total nitrogen, and dissolved organic carbon, respectively. The δ¹³C values of type II methanotroph biomarkers changed significantly along the altitude gradient, and they were more depleted than type II methanotroph biomarkers, which indicates the difference in carbon source preference between type I and type II methanotrophs. This study highlights the difference in the concentration and carbon source utilization of type I and type II methanotrophic groups along the altitude gradient, and enhances our understanding of the metabolic process of methane mediated by methanotrophs and its impact on carbon-sink function in northern peatlands.

Environmental Factors Affecting the Community of Methane-oxidizing Bacteria

Methane-oxidizing bacteria (MOB) are ubiquitous and play an important role in the mitigation of global warming by reducing methane. MOB are commonly classified into Type I and Type II, belonging to Gammaproteobacteria and Alphaproteobacteria, respectively, and the diversity of MOB has been examined. However, limited information is currently available on favorable environments for the respective MOB. To investigate the environmental factors affecting the dominant type in the MOB community, we performed MOB enrichment using down-flow hanging sponge reactors under 38 different environmental conditions with a wide range of methane (0.01–80%) and ammonium concentrations (0.001–2,000‍ ‍mg N L^–1) and pH 4–7. Enrichment results revealed that pH was a crucial factor influencing the MOB type enriched. Type II was dominantly enriched at low pH (4–5), whereas Type I was dominant around neutral pH (6–7). However, there were some unusual cultivated biomass samples. Even though high methane oxidation activity was observed, very few or zero conventional MOB were detected using common FISH probes and primer sets for the 16S rRNA gene and pmoA gene amplification. Mycobacterium mostly dominated the microbial community in the biomass cultivated at very high NH₄⁺ concentrations, strongly implying that it exhibits methane oxidation activity. Collectively, the present results revealed the presence of many unknown phylogenetic groups with the capacity for methane oxidation other than the reported MOB.

Novel QTL Associated with Aerenchyma-Mediated Radial Oxygen Loss (ROL) in Rice (Oryza sativa L.) under Iron (II) Sulfide

In rice, high radial oxygen loss (ROL) has been associated with the reduction in the activity of methanogens, therefore reducing the formation of methane (CH₄) due to the abundance in application of nitrogen (N)-rich fertilizers. In this study, we evaluated the root growth behavior and ROL rate of a doubled haploid (DH) population (n = 117) and parental lines 93-11 (P1, indica) and Milyang352 (P2, japonica) in response to iron (II) sulfide (FeS). In addition, we performed a linkage mapping and quantitative trait locus (QTL) analysis on the same population for the target traits. The results of the phenotypic evaluation revealed that parental lines had distinctive root growth and ROL patterns, with 93-11 (indica) and Milyang352 (japonica) showing low and high ROL rates, respectively. This was also reflected in their derived population, indicating that 93.2% of the DH lines exhibited a high ROL rate and about 6.8% had a low ROL pattern. Furthermore, the QTL and linkage map analysis detected two QTLs associated with the control of ROL and root area on chromosomes 2 (qROL-2-1, 127 cM, logarithm of the odds (LOD) 3.04, phenotypic variation explained (PVE) 11.61%) and 8 (qRA-8-1, 97 cM, LOD 4.394, PVE 15.95%), respectively. The positive additive effect (2.532) of qROL-2-1 indicates that the allele from 93-11 contributed to the observed phenotypic variation for ROL. The breakthrough is that the qROL-2-1 harbors genes proposed to be involved in stress signaling, defense response mechanisms, and transcriptional regulation, among others. The qPCR results revealed that the majority of genes harbored by the qROL-2-1 recorded a higher transcript accumulation level in Milyang352 over time compared to 93-11. Another set of genes exhibited a high transcript abundance in P1 compared to P2, while a few were differentially regulated between both parents. Therefore, OsTCP7 and OsMYB21, OsARF8 genes encoding transcription factors (TFs), coupled with OsTRX, OsWBC8, and OsLRR2 are suggested to play important roles in the positive regulation of ROL in rice. However, the recorded differential expression of OsDEF7 and OsEXPA, and the decrease in OsNIP2, Oscb5, and OsPLIM2a TF expression between parental lines proposes them as being involved in the control of oxygen flux level in rice roots.

Changes in Soil Chemical Properties Due to Long-Term Compost Fertilization Regulate Methane Turnover Related Gene Abundances in Rice Paddy

Maintaining rice yield, soil function, and fertility are essential components of long-term compost fertilization. However, paddy fields are major sources of anthropogenic methane emissions. The aim of the study is to evaluate the changes in soil chemical properties and their concurrent impact on the abundance of methanogenesis (mcrA) and methane oxidation (pmoA) related genes among compost (Com), NPK+Compost (NPKCom), and unfertilized (NF) fallow paddy fields under long-term compost fertilization. Results showed that compost and NPK+Compost fertilization altered the soil chemical properties of paddy fields with a significant increase in the functional gene abundance potentially associated with Methanobacteriaceae for mcrA (1.23 × 106 to 3.84 × 106 copy number g−1 dry soil) and methane oxidizing bacteria such as Methylomonas and Methylobacter for pmoA (1.65 × 106 to 4.3 × 106 copy number g−1 dry soil). Ordination plots visualized these changes, where treatments clustered distinctly indicating that Com and NPKCom treatments were characterized by paddy soils with elevated OM, TN, K and P content and higher abundances of methanogenesis and methane oxidation related genes. The study showed that long-term compost fertilization resulted in paddy fields with high nutrient content and high gene abundance, attributed to methanogens and methane oxidizing bacteria that responded well with compost fertilization. These results indicated the potential of these fallow paddy fields for methane emission and methane oxidation and that they are ‘primed’, potentially influencing subsequent paddy field responses to long-term compost application.

The impacts of nitrogen addition on upland soil methane uptake: A global meta-analysis

Elevated nitrogen (N) addition from anthropogenic activities has great impacts on soil methane (CH₄) uptake, which could interrupt the existing global CH₄ balance and cause feedbacks to climate and biogeochemical processes. Previous studies have come to inconsistent conclusions on both the quantification of the response of CH₄ uptake to N addition and understanding of its underlying mechanisms, probably due to the lack of experimental data. Here, we conduct a broad meta-analysis of 90 papers to quantify the responses of CH₄ uptake to N addition in upland soil. The results show that N addition has a significant negative impact on soil CH₄ uptake (-19.25%), which is termed the N inhibition effect. Soil pH is identified as the dominant factor, with the other factors affecting the CH₄ uptake through the alteration of soil pH. The N inhibition effect is observed to be large and significant in forest and grassland, but small and insignificant in farmland, because of the distinct composition of their methanotrophic communities. A threshold of the N addition level is identified at about 68 kg N ha^-1 year^-1, which indicates the lowest N inhibition effect. Furthermore, the convex relationship between response ratio of CH₄ uptake (negative) and N addition duration indicates that a medium level of N addition duration has the largest N inhibition effect, and longer or shorter durations will both reduce the effect. Our analysis of the N inhibition effect implies that controlling the N addition level could effectively reduce the CH₄ concentration in the atmosphere and thus relieve global warming.

Cultivation of Important Methanotrophs From Indian Rice Fields

Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10^–6–10^–8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.

Are CH4, CO2, and N2O Emissions from Soil Affected by the Sources and Doses of N in Warm-Season Pasture?

The intensification of pasture production has increased the use of N fertilizers—a practice that can alter soil greenhouse gas (GHG) fluxes. The objective of the present study was to evaluate the fluxes of CH4, CO2, and N2O in the soil of Urochloa brizantha ‘Marandu’ pastures fertilized with different sources and doses of N. Two field experiments were conducted to evaluate GHG fluxes following N fertilization with urea, ammonium nitrate, and ammonium sulfate at doses of 0, 90, 180, and 270 kg N ha−1. GHG fluxes were quantified using the static chamber technique and gas chromatography. In both experiments, the sources and doses of N did not significantly affect cumulative GHG emissions, while N fertilization significantly affected cumulative N2O and CO2 emissions compared to the control treatment. The N2O emission factor following fertilization with urea, ammonium nitrate, and ammonium sulfate was lower than the United Nations’ Intergovernmental Panel on Climate Change standard (0.35%, 0.24%, and 0.21%, respectively, with fractionation fertilization and 1.00%, 0.83%, and 1.03%, respectively, with single fertilization). These findings are important for integrating national inventories and improving GHG estimation in tropical regions.

Novel QTL Associated with Shoot Branching Identified in Doubled Haploid Rice (Oryza sativa L.) under Low Nitrogen Cultivation

Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica), grown under normal nitrogen and low nitrogen cultivation open field conditions. The results of the phenotypic evaluation indicated that parental lines 93-11 (P1, a high tillering indica cultivar) and Milyang352 (P2, a low tillering japonica cultivar) showed distinctive phenotypic responses, also reflected in their derived population. In addition, the linkage mapping and quantitative trait locus (QTL) analysis detected three QTLs associated with tiller number on chromosome 2 (qTNN2-1, 130 cM, logarithm of the odds (LOD) 4.14, PVE 14.5%; and qTNL2-1, 134 cM, LOD: 6.05, PVE: 20.5%) and chromosome 4 (qTN4-1, 134 cM, LOD 3.92, PVE 14.5%), with qTNL2-1 having the highest phenotypic variation explained, and the only QTL associated with tiller number under low nitrogen cultivation conditions, using Kompetitive Allele-Specific PCR (KASP) and Fluidigm markers. The additive effect (1.81) of qTNL2-1 indicates that the allele from 93-11 (P1) contributed to the observed phenotypic variation for tiller number under low nitrogen cultivation. The breakthrough is that the majority of the candidate genes harbored by the QTLs qTNL2-1 and qTNN4-1 (here associated with the control of shoot branching under low and normal nitrogen cultivation, respectively), were also proposed to be involved in plant stress signaling or response mechanisms, with regard to their annotations and previous reports. Therefore, put together, these results would suggest that a possible crosstalk exists between the control of plant growth and development and the stress response in rice.

Nitrogen addition decreases methane uptake caused by methanotroph and methanogen imbalances in a Moso bamboo forest

Forest soils play an important role in controlling global warming by reducing atmospheric methane (CH₄) concentrations. However, little attention has been paid to how nitrogen (N) deposition may alter microorganism communities that are related to the CH₄ cycle or CH₄ oxidation in subtropical forest soils. We investigated the effects of N addition (0, 30, 60, or 90 kg N ha⁻¹ yr⁻¹) on soil CH₄ flux and methanotroph and methanogen abundance, diversity, and community structure in a Moso bamboo (Phyllostachys edulis) forest in subtropical China. N addition significantly increased methanogen abundance but reduced both methanotroph and methanogen diversity. Methanotroph and methanogen community structures under the N deposition treatments were significantly different from those of the control. In N deposition treatments, the relative abundance of Methanoculleus was significantly lower than that in the control. Soil pH was the key factor regulating the changes in methanotroph and methanogen diversity and community structure. The CH₄ emission rate increased with N addition and was negatively correlated with both methanotroph and methanogen diversity but positively correlated with methanogen abundance. Overall, our results suggested that N deposition can suppress CH₄ uptake by altering methanotroph and methanogen abundance, diversity, and community structure in subtropical Moso bamboo forest soils.

Do methanotrophs drive phosphorus mineralization in soil ecosystem?

Experiments were carried out to elucidate linkage between methane consumption and mineralization of phosphorous (P) from different P sources. The treatments were (i) no CH₄ + no P amendment (absolute control), (ii) with CH₄ + no P amendment (control), (iii) with CH₄ + inorganic P as Ca₃(PO₄)₂, and (iv) with CH₄ + organic P as sodium phytate. P sources were added at 25 µg P·(g soil)^-1. Soils were incubated to undergo three repeated CH₄ feeding cycles, referred to as feeding cycle I, feeding cycle II, and feeding cycle III. CH₄ consumption rate k (µg CH₄ consumed·(g soil)^-1·day^-1) was 0.297 ± 0.028 in no P amendment control, 0.457 ± 0.016 in Ca₃(PO₄)₂, and 0.627 ± 0.013 in sodium phytate. Rate k was stimulated by 2 to 6 times over CH₄ feeding cycles and followed the trend of sodium phytate > Ca₃(PO₄)₂ > no P amendment control. CH₄ consumption stimulated P solubilization from Ca₃(PO₄)₂ by a factor of 2.86. Acid phosphatase (µg paranitrophenol released·(g soil)^-1·h^-1) was higher in sodium phytate than the no P amendment control. Abundance of 16S rRNA and pmoA genes increased with CH₄ consumption rates. The results of the study suggested that CH₄ consumption drives mineralization of unavailable inorganic and organic P sources in the soil ecosystem.

Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi

The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.

The response of methanotrophs to additions of either ammonium, nitrate or urea in alpine swamp meadow soil as revealed by stable isotope probing

Different forms of nitrogen (N) are deposited on the Qinghai-Tibetan plateau (QTP), while their differential effects on soil methanotrophs and their activity remain elusive. We constructed microcosms amended with different N fertilizers (ammonia, nitrate and urea) using the soils sampled from a swamp meadow on the QTP. The responses of active methanotrophs to different forms of nitrogen were determined by stable isotope probing with 5% 13C-methane. At the early stage of incubation, all N fertilizers, especially urea, suppressed methane oxidation compared with the control. The methane oxidation rate increased during the incubation, suggesting an adaptation and stimulation of some methanotrophs to elevated methane. At the onset of the incubation, the type II methanotrophs Methylocystis were most abundant, but decreased during the incubation and were replaced by the type Ia methanotrophs Methylomonas. Ammonia and urea had similar effects on the methanotroph communities, both characterized by an elevation in the proportion of Methylobacter and more diverse methanotroph communities. Nitrate had less effect on the methanotroph community. Our results uncovered the active methanotrophs responding to different nitrogen forms, and suggested that urea-N might have large effects on methanotroph diversity and activity in swamp meadow soils on the QTP.

Ammonium Impacts Methane Oxidation and Methanotrophic Community in Freshwater Sediment

Lacustrine ecosystems are regarded as one of the important natural sources of greenhouse gas methane. Aerobic methane oxidation, carried out by methane-oxidizing bacteria, is a key process regulating methane emission. And ammonium is believed to greatly influence aerobic methane oxidation activity. To date, disagreement exists in the threshold of ammonium effect. Moreover, knowledge about how aerobic methanotrophic community composition and functional gene transcription respond to ammonium is still lacking. In the present study, microcosms with freshwater lake sediment were constructed to explore the effect of ammonium level on aerobic methanotrophs. Methane oxidation potential, and the density, diversity and composition of pmoA gene and its transcripts were examined during 2-week incubation. A negative impact of ammonium on aerobic methane oxidation potential and a positive impact on pmoA gene density were observed only at a very high level of ammonium. However, pmoA gene transcription increased notably at all ammonium levels. The composition of functional pmoA gene and transcripts were also influenced by ammonium. But a great shift was only observed in pmoA transcripts at the highest ammonium level.

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.

Enrichment of Type I Methanotrophs with nirS Genes of Three Emergent Macrophytes in a Eutrophic Wetland in China

The pmoA gene, encoding particulate methane monooxygenase in methanotrophs, and nirS and nirK genes, encoding bacterial nitrite reductases, were examined in the root and rhizosphere sediment of three common emergent macrophytes (Phragmites australis, Typha angustifolia, and Scirpus triqueter) and unvegetated sediment from eutrophic Wuliangsuhai Lake in China. Sequencing analyses indicated that 334 out of 351 cloned pmoA sequences were phylogenetically the most closely related to type I methanotrophs (Gammaproteobacteria), and Methylomonas denitrificans-like organisms accounted for 44.4% of the total community. In addition, 244 out of 250 cloned nirS gene sequences belonged to type I methanotrophs, and 31.2% of nirS genes were the most closely related to paddy rice soil clone SP-2-12 in Methylomonas of the total community. Three genera of type I methanotrophs, Methylomonas, Methylobacter, and Methylovulum, were common in both pmoA and nirS clone libraries in each sample. A quantitative PCR (qPCR) analysis demonstrated that the copy numbers of the nirS and nirK genes were significantly higher in rhizosphere sediments than in unvegetated sediments in P. australis and T. angustifolia plants. In the same sample, the nirS gene copy number was significantly higher than that of nirK. Furthermore, type I methanotrophs were localized in the root tissues according to catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Thus, nirS-carrying type I methanotrophs were enriched in macrophyte root and rhizosphere sediment and are expected to play important roles in carbon/nitrogen cycles in a eutrophic wetland.

Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands

Reed (Phragmites australis) is dominant vegetation in alkaline wetlands that is harvested annually due to its economic value. To reveal the effects of harvesting reeds on the emission of greenhouse gases (GHG), the annual soil physicochemical characteristics and flux of GHGs in a reed wetland without harvesting (NHRW) and with harvesting (HRW) were measured. The results showed that after the harvesting of reeds, the total organic carbon (TOC) and total nitrogen (TN) significantly decreased, and soil temperature significantly increased. The annual cumulative N₂O emissions decreased from 0.73 ± 0.20 kg ha^-1 to -0.57 ± 0.49 kg ha^-1 with the harvesting of reeds. The annual cumulative CH₄ emissions also decreased from 561.88 ± 18.61 kg ha^-1 to 183.13 ± 18.77 kg ha^-1 with the harvesting of reeds. However, harvesting of reeds had only a limited influence on the annual cumulative CO₂ emissions. A Pearson correlation analysis revealed that the CO₂ and N₂O emissions were more sensitive to temperature than the CH₄ emissions. Both structural equation modeling (SEM) analysis and slurry incubation confirmed that higher temperatures offset the reduction of CO₂ emissions after reed harvesting. Metagenomics showed that the abundance of functional genes involved in both GHG sink and source decreased with reed harvesting. This study presents a comprehensive view of reed harvesting on GHG emissions in alkaline wetlands, yielding new insight into the microbial response and offering a novel perspective on the potential impacts of wetland management.

Biochar can mitigate methane emissions by improving methanotrophs for prolonged period in fertilized paddy soils

Biochar application to fertilized paddy soils has been recommended as an effective countermeasure to mitigate methane (CH₄) emissions, but its mechanism and effective duration has not yet been adequately elucidated. A laboratory incubation experiment was performed to gain insight into the combined effects of fresh and six-year aged biochar on potential methane oxidation (PMO) in paddy soils with ammonium or nitrate-amendment. Results showed that both ammonium and nitrate were essential for CH₄ oxidation though high ammonium (4 mM) inhibited PMO as compared to low ammonium (1 mM and 2 mM), and that nitrate was better in promoting PMO than ammonium. Moreover, ammonium-amendment promoted type I pmoA, and nitrate-amendment enhanced type II pmoA abundance. Both fresh and aged biochar increased PMO as well as nitrification by enhancing the total, type I and type II methanotrophs as compared to the control. Increased soil PMO with mineral N input in both six-year aged biochar and fresh biochar amendment, indicating that biochar mitigated CH₄ by promoting PMO for prolonged period in fertilized paddy soils.

Effect of N dose on soil GHG emissions from a drip-fertigated olive (Olea europaea L.) orchard

Agronomic practices may mitigate greenhouse gas emissions (GHG) from crops. Appropriate nitrogen (N) and irrigation management provide the potential to reduce nitrous oxide (N₂O) and methane (CH₄) emissions. However, there is little information about the combination of both practices on the GHG emissions from olive orchards. This four-year study was conducted to qualitatively compare the effect of N doses applied through two drip irrigation strategies on N₂O and CH₄ emissions in a super-intensive (1010 trees ha^-1) olive orchard. The design (randomised blocks) was asymmetric: 0, 50 and 100 kg N ha^-1 yr^-1 were tested with full irrigation (FI; 2013 to 2016), but only 0 and 50 kg N ha^-1 yr^-1 were tested with regulated deficit irrigation (RDI; 2014 to 2016). The study shows that the soil acted as a main sink of N₂O and CH₄, regardless of the soil water content. Methane oxidation increased with N dose in the FI strategy (significant in 2013 and 2015). Overall, there was a tendency of yield to increase with the N dose without increasing emissions and without depending of the irrigation strategy. However, these results were not significant. Further confirmation of this tendency is necessary; particularly comparing FI + N100 (most promising treatment in terms of profitability) with the RDI + N100 (not available in this study) water-saving strategy.

Unimodal Response of Soil Methane Consumption to Increasing Nitrogen Additions

Nitrogen (N) status has a great impact on methane (CH₄) consumption by soils. Modeling studies predicting soil CH₄ consumption assume a linear relationship between CH₄ uptake and N addition rate. Here, we present evidence that a nonlinear relationship may better characterize changes in soil CH₄ uptake with increasing N additions. By conducting a field experiment with eight N-input levels in a Tibetan alpine steppe, we observed a unimodal relationship; CH₄ uptake increased at low to medium N levels but declined at high N levels. Environmental and microbial properties jointly determined this response pattern. The generality of the unimodal trend was further validated by two independent analyses: (i) we examined soil CH₄ uptake across at least five N-input levels in upland ecosystems across China. A unimodal CH₄ uptake-N addition rate relationship was observed in 3 out of 4 cases; and (ii) we performed a meta-analysis to explore the N-induced changes in soil CH₄ uptake with increasing N additions across global upland ecosystems. Results showed that the changes in CH₄ uptake exhibited a quadratic correlation with N addition rate. Overall, we suggest that the unimodal relationship should be considered in biogeochemistry models for accurately predicting soil CH₄ consumption under global N enrichment.

Ammonium influences kinetics and structure of methanotrophic consortia

The literature is conflicted on the influence of ammonium on the kinetics and microbial ecology of methanotrophy. In this study, methanotrophic cultures were enriched, under ammonium concentrations ranging from 0 to 200 mM, from an inoculum comprising leachate and top-cover soil from a landfill. Specific CH₄ biodegradation rates were highest (7.8 × 10^-4 ± 6.0 × 10^-5 gCH₄ g_X^-1 h^-1) in cultures enriched at 4 mM NH₄⁺, which were mainly dominated by type II methanotrophs belonging to Methylocystis spp. Lower specific CH₄ oxidation rates (average values of 1.8-3.6 × 10^-4 gCH₄ g_X^-1 h^-1) were achieved by cultures enriched at higher NH₄⁺ concentrations (20 and 80 mM), and had higher affinity for CH₄ compared to 4 mM enrichments. These lower affinities were attributed to lower diversity dominated by type I methanotrophs, of the Methylosarcina, Methylobacter and Methylomicrobium genera, encountered with increasing concentrations of NH₄⁺. The study indicates that CH₄ oxidation biotechnologies applied at low NH₄⁺ concentrations can support efficient abatement of CH₄ and high diversity of methanotrophic consortia, whilst enriching type II methanotrophs.

Anaerobic Methane Oxidation in High-Arctic Alaskan Peatlands as a Significant Control on Net CH4 Fluxes

Terrestrial consumption of the potent greenhouse gas methane (CH4) is a critical aspect of the future climate, as CH4 concentrations in the atmosphere are projected to play an increasingly important role in global climate forcing. Anaerobic oxidation of methane (AOM) has only recently been considered a relevant control on methane fluxes from terrestrial systems. We performed in vitro anoxic incubations of intact peat from Utqiaġvik (Barrow), Alaska using stable isotope tracers. Our results showed an average potential AOM rate of 15.0 nmol cm3 h−1, surpassing the average rate of gross CH4 production (6.0 nmol cm3 h−1). AOM and CH4 production rates were positively correlated. While CH4 production was insensitive to additions of Fe(III), there was a depth:Fe(III) interaction in the kinetic reaction rate constant for AOM, suggestive of stimulation by Fe(III), particularly in shallow soils (<10 cm). We estimate AOM would consume 25–34% of CH4 produced under ambient conditions. Soil genetic surveys showed phylogenetic links between soil microbes and known anaerobic methanotrophs in ANME groups 2 and 3. These results suggest a prevalent role of AOM to net CH4 fluxes from Arctic peatland ecosystems, and a probable link with Fe(III)-reduction.

Biofiltration of methane

The on-going annual increase in global methane (CH₄) emissions can be largely attributed to anthropogenic activities. However, as more than half of these emissions are diffuse and possess a concentration less than 3% (v/v), physical-chemical treatments are inefficient as an abatement technology. In this regard, biotechnologies, such as biofiltration using methane-oxidizing bacteria, or methanotrophs, are a cost-effective and efficient means of combating diffuse CH₄ emissions. In this review, a number of abiotic factors including temperature, pH, water content, packing material, empty-bed residence time, inlet gas flow rate, CH₄ concentration, as well biotic factors, such as biomass development, are reviewed based on empirical findings on CH₄ biofiltration studies that have been performed in the last decades.

Biofiltration of methane using hybrid mixtures of biochar, lava rock and compost

Using hybrid packing materials in biofiltration systems takes advantage of both the inorganic and organic properties offered by the medium including structural stability and a source of available nutrients, respectively. In this study, hybrid mixtures of compost with either lava rock or biochar in four different mixture ratios were compared against 100% compost in a methane biofilter with active aeration at two ports along the height of the biofilter. Biochar outperformed lava rock as a packing material by providing the added benefit of participating in sorption reactions with CH₄. This study provides evidence that a 7:1 volumetric mixture of biochar and compost can successfully remove up to 877 g CH₄/m³·d with empty-bed residence times of 82.8 min. Low-affinity methanotrophs were responsible for the CH₄ removal in these systems (K_M(app) ranging from 5.7 to 42.7 µM CH₄). Sequencing of 16S rRNA gene amplicons indicated that Gammaproteobacteria methanotrophs, especially members of the genus Methylobacter, were responsible for most of the CH₄ removal. However, as the compost medium was replaced with more inert medium, there was a decline in CH₄ removal efficiency coinciding with an increased dominance of Alphaproteobacteria methanotrophs like Methylocystis and Methylocella. As a biologically-active material, compost served as the sole source of nutrients and inoculum for the biofilters which greatly simplified the operation of the system. Higher elimination capacities may be possible with higher compost content such as a 1:1 ratio of either biochar or lava rock, while maintaining the empty-bed residence time at 82.8 min.

The influence of cattle grazing on methane fluxes and engaged microbial communities in alpine forest soils

Recent dynamics and uncertainties in global methane budgets necessitate a dissemination of current knowledge on the controls of sources and sinks of atmospheric methane. Forest soils are considered to be efficient methane sinks; however, as they are microbially mediated they are sensitive to anthropogenic influences and tend to switch from being sinks to being methane sources. With regard to global changes in land use, the present study aimed at (i) investigating the influence of grazing on flux rates of methane in forest soils, (ii) deducing possible (a)biotic factors regulating these fluxes, and (iii) gaining an insight into the complex interactions between methane-cycling microorganisms and ecosystem functioning. Here we show that extensive grazing significantly mitigated the soil's sink strength for atmospheric methane through alterations of both microbial activity and community composition. In situ flux measurements revealed that all native, non-grazed areas were net methane consumers, while the adjacent, grazed areas were net methane producers. Whereas neither parent material nor soil properties including moisture and organic matter showed any correlation to the ascertained fluxes, significantly higher archaeal abundances at the grazed study sites indicated that small inputs of methanogens associated with cattle grazing may be sufficient to sustainably increase methane emissions.

Positive diversity-functioning relationships in model communities of methanotrophic bacteria

Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH₄ at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH₄ consumption and community size were positively correlated. The temporal CH₄ consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.

Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments

Anaerobic oxidation of methane (AOM) is a biological process that plays an important role in reducing the CH₄ emissions from a wide range of ecosystems. Arctic and sub-Arctic lakes are recognized as significant contributors to global methane (CH₄) emission, since CH₄ production is increasing as permafrost thaws and provides fuels for methanogenesis. Methanotrophy, including AOM, is critical to reducing CH₄ emissions. The identity, activity, and metabolic processes of anaerobic methane oxidizers are poorly understood, yet this information is critical to understanding CH₄ cycling and ultimately to predicting future CH₄ emissions. This study sought to identify the microorganisms involved in AOM in sub-Arctic lake sediments using DNA- and phospholipid-fatty acid (PLFA)- based stable isotope probing. Results indicated that aerobic methanotrophs belonging to the genus Methylobacter assimilate carbon from CH₄, either directly or indirectly. Other organisms that were found, in minor proportions, to assimilate CH₄-derived carbon were methylotrophs and iron reducers, which might indicate the flow of CH₄-derived carbon from anaerobic methanotrophs into the broader microbial community. While various other taxa have been reported in the literature to anaerobically oxidize methane in various environments (e.g. ANME-type archaea and Methylomirabilis Oxyfera), this report directly suggest that Methylobacter can perform this function, expanding our understanding of CH₄ oxidation in anaerobic lake sediments.

Biochar amendment reduces paddy soil nitrogen leaching but increases net global warming potential in Ningxia irrigation, China

The efficacy of biochar as an environmentally friendly agent for non-point source and climate change mitigation remains uncertain. Our goal was to test the impact of biochar amendment on paddy rice nitrogen (N) uptake, soil N leaching, and soil CH4 and N2O fluxes in northwest China. Biochar was applied at four rates (0, 4.5, 9 and13.5 t ha-1 yr-1). Biochar amendment significantly increased rice N uptake, soil total N concentration and the abundance of soil ammonia-oxidizing archaea (AOA), but it significantly reduced the soil NO3--N concentration and soil bulk density. Biochar significantly reduced NO3--N and NH4+-N leaching. The C2 and C3 treatments significantly increased the soil CH4 flux and reduced the soil N2O flux, leading to significantly increased net global warming potential (GWP). Soil NO3--N rather than NH4+-N was the key integrator of the soil CH4 and N2O fluxes. Our results indicate that a shift in abundance of the AOA community and increased rice N uptake are closely linked to the reduced soil NO3--N concentration under biochar amendment. Furthermore, soil NO3--N availability plays an important role in regulating soil inorganic N leaching and net GWP in rice paddies in northwest China.

Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China

Changes in land-uses and fertilization are important factors regulating methane (CH₄) emissions from paddy soils. However, the responses of soil CH₄ emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH₄ fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH₄ fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH₄ fluxes, whereas fertilization did not distinctly affect soil CH₄ fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH₄ fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH₄ fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH₄ fluxes. Overall, our study shed insight on the underlying mechanisms of how land-use conversion from paddies to orchards decreased CH₄ emissions.

Effects of nitrogen and biochar amendment on soil methane concentration profiles and diffusion in a rice-wheat annual rotation system

The CH₄ emissions from soil were influenced by the changeable CH₄ concentrations and diffusions in soil profiles, but that have been subjected to nitrogen (N) and biochar amendment over seasonal and annual time frames. Accordingly, a two-year field experiment was conducted in southeastern China to determine the amendment effects on CH₄ concentrations and diffusive effluxes as measured by a multilevel sampling probe in paddy soil during two cycles of rice-wheat rotations. The results showed that the top 7-cm soil layers were the primary CH₄ production sites during the rice-growing seasons. This layer acted as the source of CH₄ generation and diffusion, and the deeper soil layers and the wheat season soil acted as the sink. N fertilization significantly increased the CH₄ concentration and diffusive effluxes in the top 7-cm layers during the 2013 and 2014 rice seasons. Following biochar amendment, the soil CH₄ concentrations significantly decreased during the rice season in 2014, relative to the single N treatment. Moreover, 40 t ha⁻¹ biochar significantly decreased the diffusive effluxes during the rice seasons in both years. Therefore, our results showed that biochar amendment is a good strategy for reducing the soil profile CH₄ concentrations and diffusive effluxes induced by N in paddy fields.

Methane production, oxidation and mitigation: A mechanistic understanding and comprehensive evaluation of influencing factors

Methane is one of the critical greenhouse gases, which absorb long wavelength radiation, affects the chemistry of atmosphere and contributes to global climate change. Rice ecosystem is one of the major anthropogenic sources of methane. The anaerobic waterlogged soil in rice field provides an ideal environment to methanogens for methanogenesis. However, the rate of methanogenesis differs according to rice cultivation regions due to a number of biological, environmental and physical factors like carbon sources, pH, Eh, temperature etc. The interplay between the different conditions and factors may also convert the rice fields into sink from source temporarily. Mechanistic understanding and comprehensive evaluation of these variations and responsible factors are urgently required for designing new mitigation options and evaluation of reported option in different climatic conditions. The objective of this review paper is to develop conclusive understanding on the methane production, oxidation, and emission and methane measurement techniques from rice field along with its mitigation/abatement mechanism to explore the possible reduction techniques from rice ecosystem.

Composition of microbial PLFAs and correlations with topsoil characteristics in the rare active travertine spring-fed fen

We studied soil PLFAs composition and specific soil properties among transect of small-scale fen in Stankovany, Slovakia. The aim of this study was to determine potential differences in the microbial community structure of the fen transect and reveal correlations among PLFAs and specific soil characteristics. PCA analyses of 43 PLFAs showed a separation of the samples along the axis largely influenced by i14:0, 16:1ω5, br17:0, 10Me16:0, cy17:0, cy17:1, br18:0 and 10Me17:0. We measured a high correlation of sample scores and distance from fen edge (Kendall’s test τ = 0.857, P < 0.01). Kendall’s test showed a negative correlation of PLFAs content (mol%) and distance from the fen border for Gram (+) bacteria, Actinomycetes, mid-chain branched saturated PLFAs and total PLFAs. The redundancy analysis of the PLFA data set for the eight samples using PLFAs as species and 21 environmental variables identified soil properties significantly associated with the PLFA variables, as tested by Monte Carlo permutation showing most significant environmental variables including dichlormethan extractables, water extractables, Klason lignin, acid-soluble lignin, holocellulose, total extractables, organic matter content, total PLFA amount, bacterial PLFA and total nitrogen negatively correlated to axis 1 and dry weight and carbonate carbon positively correlated to axis 1. The amounts of Klason lignin, acid-soluble lignin, holocellulose total extractables, total PLFA, bacterial PLFA and total nitrogen were significantly correlated positively to the distance from fen border while moisture and total carbonate carbon were correlated negatively.