Kinetics of inhibition of methane oxidation by nitrate, nitrite, and ammonium in a humisol

Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin

In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6 mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.

Imbalanced metabolism induced NH4+ accumulation and its effect on the central metabolism of Methylomonas sp. ZR1

Nitrogen and carbon are the two most essential nutrient elements, and their metabolism is tightly coupled in single carbon metabolic microorganisms. However, the nitrogen metabolism and the nitrogen/carbon (N/C) metabolic balance in single-carbon metabolism is poorly studied. In this study, the nitrogen metabolism pattern of the fast growing methanotrophs Methylomonas sp. ZR1 grown in methane and methanol was studied. Effect study of different nitrogen sources on the cell growth of ZR1 indicates that nitrate salts are the best nitrogen source supporting the growth of ZR1 using methane and methanol as carbon source. However, its metabolic intermediate ammonium was found to accumulate with high N/C ratio in the medium and consequently inhibit the growth of ZR1. Studies of carbon and nitrogen metabolic kinetic under different N/C ratio conditions indicate that the accumulation of NH4+ is caused by the imbalanced nitrogen and carbon metabolism in ZR1. Feeding carbon skeleton α-ketoglutaric acid could effectively relieve the inhibition effect of NH4+ on the growth of ZR1, which further confirms this assumption. qPCR analysis of the expression level of the central metabolic key enzyme gene indicates that the nitrogen metabolic intermediate ammonium has strong regulation effect on the central nitrogen and carbon metabolism in ZR1. qPCR-combined genomic analysis confirms that a third ammonium assimilation pathway glycine synthesis system is operated in ZR1 to balance the nitrogen and carbon metabolism. Based on the qPCR result, it was also found that ZR1 employs two strategies to relieve ammonium stress in the presence of ammonium: assimilating excess ammonium or cutting off the nitrogen reduction reactions according to the available C1 substrate. Validating the connections between single-carbon and nitrogen metabolism and studying the accumulation and assimilation mechanism of ammonium will contribute to understand how nitrogen regulates cellular growth in single-carbon metabolic microorganisms.

Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient

Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH4). While sulfate loading from seawater intrusion may reduce CH4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH4 fluxes observed in oligohaline sediments.IMPORTANCELow-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.

Urban landscapes and legacy industry provide hotspots for riverine greenhouse gases: A source-to-sea study of the River Clyde

There is growing global concern that greenhouse gas (GHG) emissions from water bodies are increasing because of interactions between nutrient levels and climate warming. This paper investigates key land-cover, seasonal and hydrological controls of GHGs by comparison of the semi-natural, agricultural and urban environments in a detailed source-to-sea study of the River Clyde, Scotland. Riverine GHG concentrations were consistently oversaturated with respect to the atmosphere. High riverine concentrations of methane (CH₄) were primarily associated with point source inflows from urban wastewater treatment, abandoned coal mines and lakes, with CH₄-C concentrations between 0.1 - 44 µg l^-1. Concentrations of carbon dioxide (CO₂) and nitrous oxide (N₂O) were mainly driven by nitrogen concentrations, dominated by diffuse agricultural inputs in the upper catchment and supplemented by point source inputs from urban wastewater in the lower urban catchment, with CO₂-C concentrations between 0.1 - 2.6 mg l^-1 and N₂O-N concentrations between 0.3 - 3.4 µg l^-1. A significant and disproportionate increase in all GHGs occurred in the lower urban riverine environment in the summer, compared to the semi-natural environment, where GHG concentrations were higher in winter. This increase and change in GHG seasonal patterns points to anthropogenic impacts on microbial communities. The loss of total dissolved carbon, to the estuary is approximately 48.4 ± 3.6 Gg C yr^-1, with the annual inorganic carbon export approximately double that of organic carbon and four times that of CO_2, with CH₄ accounting for 0.03%, with the anthropogenic impact of disused coal mines accelerating DIC loss. The annual loss of total dissolved nitrogen to the estuary is approximately 4.03 ± 0.38 Gg N yr^-1 of which N₂O represents 0.06%. This study improves our understanding of riverine GHG generation and dynamics which can contribute to our knowledge of their release to the atmosphere. It identifies where action could support reductions in aquatic GHG generation and emission.

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.

Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N₂-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.

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 K_m 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.

Prospecting the significance of methane-utilizing bacteria in agriculture

Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.

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.

Anthropogenic-estuarine interactions cause disproportionate greenhouse gas production: A review of the evidence base

Biologically productive regions such as estuaries and coastal areas, even though they only cover a small percentage of the world's oceans, contribute significantly to methane and nitrous oxide emissions. This paper synthesises greenhouse gas data measured in UK estuary studies, highlighting that urban wastewater loading is significantly correlated with both methane (P < 0.001) and nitrous oxide (P < 0.005) concentrations. It demonstrates that specific estuary typologies render them more sensitive to anthropogenic influences on greenhouse gas production, particularly estuaries that experience low oxygen levels due to reduced mixing and stratification or high sediment oxygen demand. Significantly, we find that estuaries with high urban wastewater loading may be hidden sources of greenhouse gases globally. Synthesising available information, a conceptual model for greenhouse gas concentrations in estuaries with different morphologies and mixing regimes is presented. Applications of this model should help identification of estuaries susceptible to anthropogenic impacts and potential hotspots for greenhouse gas emissions.

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.

Mitigation of methane emission in a rice paddy field amended with biochar-based slow-release fertilizer

Despite improving soil quality and reducing nitrogen (N) loss in paddy soil, replacing chemical fertilizer with organic fertilizer would significantly accelerate greenhouse gas emission in terms of methane (CH₄). The application of slow-release fertilizer has been proposed an effective approach to control CH₄ emissions, in addition to reducing N loss. Yet, the understanding of CH₄ emissions from paddy fields with the additions of different fertilizers is still less known. Therefore, the effects of different fertilizer treatments, including chemical fertilizer treatment (CF), mixed chemical and organic fertilizer treatment (OF), biochar-based slow-release fertilizer treatment (SF), and no fertilizer control treatment (CK) on CH₄ emissions and methanogenic community structure in paddy soils were investigated through a field experiment. Results showed that slow-release fertilizer addition significantly decreased CH₄ emissions by 33.4%, during the whole rice growing season compared to those in OF. The cumulative CH₄ emissions were in a significantly positive relation to soil NH₄⁺-N. Slow-release fertilizer amendment decreased the relative abundances of Methanosarcina and Methanoregula and increased the relative abundances of hydrogenotrophic Methanocella and Rice Cluster I. Reduced CH₄ emissions with slow-release fertilizer amendment might be mainly attributed to the different forms of N in the fertilizer and available potassium (K) in the paddy soil. Our findings produce novel insights into the application of slow-release fertilizer in controlling CH₄ emissions from rice fields.

Inoculation of plant growth promoting-methane utilizing bacteria in different N-fertilizer regime influences methane emission and crop growth of flooded paddy

Methane (CH₄) emission in rice fields is greatly influenced by the type and quantity of nitrogenous fertilizer used. The net methane emission from paddy fields is also influenced by the activity of methane utilizing bacteria, which inhabit the flooded paddy ecosystem. Efficient methane utilizing and plant growth promoting bacteria Methylobacterium oryzae MNL7 and Paenibacillus polymyxa MaAL70, respectively were co-inoculated along with different nitrogenous fertilizer combinations in flooded paddy to assess their impact on cumulative methane emission and crop growth promotion. Co-inoculation significantly influenced the plant growth parameters of paddy, resulting in an increase in grain yield by 14.04, 11.08, and 12.38% in treatments receiving Urea, Di-ammonium Phosphate (DAP) + Urea, or farm yard manure (FYM), over their respective un-inoculated plots. Significant improvement in the rice grain nutrient quality in term of crude protein, Fe and Zn content was observed as a result of bacterial co-inoculation in FYM fertilized plots as compared to Urea and DAP+ Urea fertilized plots. Significantly higher cumulative methane emission of 63.39 kg ha^-1 was observed in uninoculated plots fertilized with FYM treatment as compared to Urea (33.83 kg ha^-1) and DAP+Urea (31.66 kg ha^-1) treatments. Bacterial co-inoculation significantly reduced the cumulative methane emission by 12.03, 11.47 and 6.92% in Urea, DAP+Urea, and FYM fertilized plots over their respective uninoculated treatments. Among the different fertilizer treatments, bacterial co-inoculation with urea application performed significantly better in reducing cumulative methane emission. These findings suggest that methane utilizing bacteria which also possess plant growth promoting trait can be explored for developing a novel biofertilizer for flooded paddies, as they can aid in managing both the overall methane emission and enhancing crop yield.

Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum

The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient availability. Aerobic methanotrophs synthesize a variety of lipids important for cell functions. However, culture-based experiments studying the influence of environmental parameters on lipid production by aerobic methanotrophs are scarce. Such information is crucial to interpret lipid patterns of methanotrophic bacteria in the environment. In this study, the alkaliphilic strain Methylotuvimicrobium alcaliphilum was cultivated under different salinities and different nitrate concentrations to assess the effect of changing conditions on the inventory of pentacyclic triterpenoids. The results indicate that hopanoid abundance is enhanced at lower salinity and higher nitrate concentration. The production of most pentacyclic triterpenoids was favored at low salinity, especially for aminotriol. Interestingly, 3-methyl-aminotetrol and tetrahymanol were favored at higher salinity. Bacteriohopanepolyols (BHPs), particularly aminotriol and 3-methyl-aminotriol, increased considerably at higher nitrate concentrations. Four novel N-containing BHPs—aminodiol, 3-methyl-aminodiol, and isomers of aminotriol and 3-methyl-aminotriol—were identified. This study highlights the significance of environmental factors for bacterial lipid production and documents the need for cultivation studies under variable conditions to utilize the full potential of the biomarker concept.

Nitrogen fertilizer application in the rice-growing season can stimulate methane emissions during the subsequent flooded fallow period

Winter-flooded rice paddy field (FR), characterized by water conserved in the field during the fallow period, is a typical cropping system in southwest China, leading to considerable methane (CH₄) emissions. The effect of nitrogen (N) fertilization on CH₄ emissions during rice-growing seasons is well studied in FR, further studies covering N fertilizer applied in the rice-growing seasons affects CH₄ emissions during the subsequent fallow period is needed. Therefore, a field experiment was conducted in an FR of Sichuan province, China, with conventional N fertilized (CN) and N unfertilized (NN) treatments. The cumulative CH₄ emission from CN treatment during the rice-growing season and the subsequent fallow period was 389 ± 29.4 and 158 ± 31.2 kg C ha^-1, which were increased by 29.5% and 395% in comparison with the NN treatment, indicting N applied during the rice growing-season significantly facilitated CH₄ emission during the subsequent fallow period. During the rice-growing season, higher CH₄ emission from CN treatment could be attributed to elevated soil dissolved organic carbon (DOC) content that might have provided sufficient substrates for CH₄ production. During the fallow period, as compared to NN treatment, higher CH₄ emissions from CN treatment could be explained by greater linear regression slopes between CH₄ fluxes, soil temperature and DOC to dissolved inorganic N (DIN) (DOC/DIN) ratio. Moreover, the structural equation model (SEM) described that the soil temperature exhibited the most significant effects on CH₄ emissions for both treatments during the rice-growing season and subsequent fallow period. These findings are a major step forward to showing that N fertilizer applied in the rice-growing season could also affect CH₄ emission during the subsequent fallow period, accompanying other soil parameters controlling CH₄ emission.

Mitigation of greenhouse gas emissions and reduced irrigation water use in rice production through water-saving irrigation scheduling, reduced tillage and fertiliser application strategies

Rice production systems are the largest anthropogenic wetlands on earth and feed more than half of the world's population. However, they are also a major source of global anthropogenic greenhouse gas (GHG) emissions. Several agronomic strategies have been proposed to improve water-use efficiency and reduce GHG emissions. The aim of this study was to evaluate the impact of water-saving irrigation (alternate wetting and drying (AWD) vs. soil water potential (SWP)), contrasting land establishment (puddling vs. reduced tillage) and fertiliser application methods (broadcast vs. liquid fertilisation) on water-use efficiency, GHG emissions and rice yield. The experiment was laid out in a randomised complete block design with eight treatments (all combinations of the three factors) and four replicates. AWD combined with broadcasting fertilisation was superior to SWP in terms of maintaining yield. However, seasonal nitrous oxide (N₂O) emissions were significantly reduced by 64% and 66% in the Broadcast-SWP and Liquid fertiliser-SWP treatments, respectively, compared to corresponding treatments in AWD. The SWP also significantly reduced seasonal methane (CH₄) emissions by 34 and 30% in the broadcast and liquid fertilisation treatments, respectively. Area-scaled GWPs were reduced by 48% and 54% in Broadcast-SWP and Liquid fertiliser-SWP treatments respectively compared to the corresponding treatments in AWD. Compared to AWD, the broadcast and liquid fertilisation in SWP irrigation treatments reduced yield-scaled GWPs by 46% and 37%, respectively. In terms of suitability, based on yield-scaled GWPs, the treatments can be ordered as follows: Broadcast-SWP < Broadcast-AWD = Liquid fertiliser-SWP < Liquid fertiliser-AWD. Growing-season water use was 15% lower in the SWP treatments compared with the water-saving AWD. Reduced tillage reduced additional water use during land preparation. The conclusions of this study are that improved water management and timely coordination of N fertiliser with crop demand can reduce water use, N loss via N₂O emissions, and CH₄ emissions.

Microbial Communities Associated with Methylmercury Degradation in Paddy Soils

Bioaccumulation of the neurotoxin methylmercury (MeHg) in rice has raised worldwide concerns because of its risks to human health. Certain microorganisms are able to degrade MeHg in pure cultures, but the roles and diversities of the microbial communities in MeHg degradation in rice paddy soils are unknown. Using a series of microcosms, we investigated MeHg degradation in paddy soils from Hunan, Guizhou, and Hubei provinces, representing three major rice production regions in China, and further characterized one of the soils from the Hunan Province for microbial communities associated with MeHg degradation. Microbial demethylation was observed in all three soils, demonstrated by significantly more MeHg degraded in the unsterilized soils than in the sterilized controls. More demethylation occurred in water-saturated soils than in unsaturated soils, but the addition of molybdate and bromoethanesulfonic acid as the respective inhibitors of sulfate reducing bacteria and methanogens showed insignificant effects on MeHg degradation. However, the addition of Cu enhanced MeHg degradation and the enrichment of Xanthomonadaceae in the unsaturated soil. 16S rRNA Illumina sequencing and metatranscriptomic analyses of the Hunan soil consistently revealed that Catenulisporaceae, Frankiaceae, Mycobacteriaceae, and Thermomonosporaceae were among the most likely microbial taxa in influencing MeHg degradation in the paddy soil, and they were confirmed by combined analyses of the co-occurrence network, random forest modeling, and linear discriminant analysis of the effect size. Our results shed additional light onto the roles of microbial communities in MeHg degradation in paddy soils and its subsequent bioaccumulation in rice grains.

Impact of Electron Acceptor Availability on Methane-Influenced Microorganisms in an Enrichment Culture Obtained From a Stratified Lake

Methanotrophs are of major importance in limiting methane emissions from lakes. They are known to preferably inhabit the oxycline of stratified water columns, often assumed due to an intolerance to atmospheric oxygen concentrations, but little is known on the response of methanotrophs to different oxygen concentrations as well as their preference for different electron acceptors. In this study, we enriched a methanotroph of the Methylobacter genus from the oxycline and the anoxic water column of a stratified lake, which was also present in the oxic water column in the winter. We tested the response of this Methylobacter-dominated enrichment culture to different electron acceptors, i.e., oxygen, nitrate, sulfate, and humic substances, and found that, in contrast to earlier results with water column incubations, oxygen was the preferred electron acceptor, leading to methane oxidation rates of 45–72 pmol cell⁻¹ day⁻¹. Despite the general assumption of methanotrophs preferring microaerobic conditions, methane oxidation was most efficient under high oxygen concentrations (>600 μM). Low (<30 μM) oxygen concentrations still supported methane oxidation, but no methane oxidation was observed with trace oxygen concentrations (<9 μM) or under anoxic conditions. Remarkably, the presence of nitrate stimulated methane oxidation rates under oxic conditions, raising the methane oxidation rates by 50% when compared to oxic incubations with ammonium. Under anoxic conditions, no net methane consumption was observed; however, methanotroph abundances were two to three times higher in incubations with nitrate and sulfate compared to anoxic incubations with ammonium as the nitrogen source. Metagenomic sequencing revealed the absence of a complete denitrification pathway in the dominant methanotroph Methylobacter, but the most abundant methylotroph Methylotenera seemed capable of denitrification, which can possibly play a role in the enhanced methane oxidation rates under nitrate-rich conditions.

Elucidating the influence of environmental factors on biogas-based polyhydroxybutyrate production by Methylocystis hirsuta CSC1

The valorization of biogas as a feedstock for the generation of added-value bioproducts will play a key role on the sustainability of anaerobic digestion. The present work assessed the influence of key environmental parameters (O₂:CH₄ ratio, temperature and nitrogen source) on the growth and polyhydroxybutyrate (PHB) synthesis under nitrogen limiting conditions of the type II methanotroph Methylocystis hirsuta CSC1 using biogas as a feedstock. The O₂:CH₄ ratios tested (1:1, 1.5:1 and 2:1) did not affect significantly M. hirsuta CSC1 growth yields (~5 g TSS mol^-1 CH₄), although lower CH₄ removal rates were reached under O₂-limiting conditions (ratio 1:1). The highest PHB content (45 wt%) was achieved at a ratio 2:1 and was threefold higher than those obtained at lower ratios (~15 wt%). The increase in temperature from 15 to 25 °C resulted in increases in the growth yield (from 5 to 6 g TSS mol^-1 CH₄) and PHB content (from 32 to 40 wt%). Conversely, the lowest PHB content (30 wt%) was reached at 37 °C, together with a negligible growth under nutrient sufficient conditions. The nitrogen source also played a key role on both M. hirsuta CSC1 growth and PHB synthesis. Thus, ammonium resulted in the highest growth yield (7 g TSS mol^-1 CH₄), although the maximum PHB content was achieved when biomass was previously grown in nitrate as the nitrogen source (41 wt%). Nitrite exerted an inhibitory effect on M. hirsuta CSC1 growth.

Phosphorus alleviation of nitrogen-suppressed methane sink in global grasslands

Grassland ecosystems account for more than 10% of the global CH₄ sink in soils. A 4-year field experiment found that addition of P alone did not affect CH₄ uptake and experimental addition of N alone significantly suppressed CH₄ uptake, whereas concurrent N and P additions suppressed CH₄ uptake to a lesser degree. A meta-analysis including 382 data points in global grasslands corroborated these findings. Global extrapolation with an empirical modelling approach estimated that contemporary N addition suppresses CH₄ sink in global grassland by 11.4% and concurrent N and P deposition alleviates this suppression to 5.8%. The P alleviation of N-suppressed CH₄ sink is primarily attributed to substrate competition, defined as the competition between ammonium and CH₄ for the methane mono-oxygenase enzyme. The N and P impacts on CH₄ uptake indicate that projected increases in N and P depositions might substantially affect CH₄ uptake and alter the global CH₄ cycle.

Effect of soil types and ammonia concentrations on the contribution of ammonia-oxidizing bacteria to CH4 oxidation

Irrigation of stabilized landfill leachate to landfill cover soil is a cost-effective operation for leachate treatment. The contribution of ammonia-oxidizing bacteria (AOB) in the cover soil to CH₄ oxidation, however, is unclear, because AOB and methane-oxidizing bacteria (MOB) can co-oxidize CH₄ and NH₄⁺-N. Thus, the contribution of AOB and the inhibitory effect of NH₄⁺-N to CH₄ oxidation were determined by using an acetylene pretreatment discrimination method. The results showed that the contributions of AOB to CH₄ oxidation varied with the soil type and the concentration of NH₄⁺-N addition. The relative contribution of AOB to CH₄ oxidation for compost without NH₄⁺-N addition was the highest (65.0%), and was 2.5 and 3.4 times higher than the corresponding values for aged refuse and landfill cover soil, respectively. The inhibitory effect of NH₄⁺-N was enhanced by increasing the concentration of NH₄⁺-N addition for all the soil samples. At equal NH₄⁺-N addition concentrations, the inhibitory effect was always the lowest for the compost sample. The abundances of particulate methane monooxygenase (pmoA) and ammonia monooxygenase (amoA) genes were key factors influencing the CH₄ oxidation rate and contribution of AOB to CH₄ oxidation. The higher abundance of pmoA and lower abundance of amoA in landfill cover soil could explain the higher CH₄ oxidation rate and lower contribution of AOB to CH₄ oxidation in this soil type. Meanwhile, the higher contribution of AOB to CH₄ oxidation for compost could be attributed to the higher abundance of the amoA gene and lower abundance of pmoA.

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.

Impact of vegetation on the methane budget of a temperate forest

Upland forest soils are known to be the main biological sink for methane, but studies have shown that net methane uptake of a forest ecosystem can be reduced when methane emissions by vegetation are considered. We estimated the methane budget of a young oak plantation by considering tree stems but also the understorey vegetation. Automated chambers connected to a laser-based gas analyser, on tree stems, bare soil and soil covered with understorey vegetation, recorded CH₄ fluxes for 7 months at 3 h intervals. Tree stem emissions were low and equated to only 0.1% of the soil sink. Conversely, the presence of understorey vegetation increased soil methane uptake. This plant-driven enhancement of CH₄ uptake occurred when the soil was consuming methane. At the stand level, the methane budget shifted from -1.4 ± 0.4 kg C ha^-1 when we upscaled data obtained only on bare soil, to -2.9 ± 0.6 kg C ha^-1 when we considered soil area that was covered with understorey vegetation. These results indicate that aerenchymatous plant species, which are known to reduce the methane sink in wetlands, actually increase soil methane uptake two-fold in an upland forest by enhancing methane and oxygen transport and/or by promoting growth of methanotrophic populations.

Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil

The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO₂ flux in peat bog and net CH₄ flux in bog forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH₄ cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH₄ fluxes (r = 0.46, p < 0.0001). Phylotype functional assignments were supported by metatranscriptomic analysis. We propose that active microbial populations respond primarily to changes in hydrology, pH, and nutrient availability. The increased microbial carbon export observed over winter may have ramifications for climate-soil feedbacks in the PCTR.

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.

A modular approach for high-flux lactic acid production from methane in an industrial medium using engineered Methylomicrobium buryatense 5GB1

Convergence of market drivers such as abundant availability of inexpensive natural gas and increasing awareness of its global warming effects have created new opportunities for the development of small-scale gas-to-liquid (GTL) conversion technologies that can efficiently utilize methane, the primary component of natural gas. Leveraging the unique ability of methanotrophs that use methane as carbon and energy source, biological GTL platforms can be envisioned that are readily deployable at remote petroleum drilling sites where large chemical GTL infrastructure is uneconomical to set-up. Methylomicrobium buryatense, an obligate methanotroph, has gained traction as a potential industrial methanotrophic host because of availability of genetic tools and recent advances in its metabolic engineering. However, progress is impeded by low strain performance and lack of an industrial medium. In this study, we first established a small-scale cultivation platform using Hungate tubes for growth of M. buryatense at medium-to-high-throughput that also enabled 2X faster growth compared to that obtained in traditional glass serum bottles. Then, employing a synthetic biology approach we engineered M. buryatense with varying promoter (inducible and constitutive) and ribosome-binding site combinations, and obtained a strain capable of producing L-lactate from methane at a flux 14-fold higher than previously reported. Finally, we demonstrated L-lactate production in an industrial medium by replacing nitrate with less-expensive ammonium as the nitrogen source. Under these conditions, L-lactate was synthesized at a flux approximately 50-fold higher than that reported previously in a bioreactor system while achieving a titer of 0.6 g/L. These findings position M. buryatense closer to becoming an industrial host strain of choice, and pave new avenues for accelerating methane-to-chemical conversion using synthetic biology.

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities

Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO₂, N₂O, and CH₄. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

Response of methanotrophic activity to extracellular polymeric substance production and its influencing factors

The accumulation of extracellular polymeric substance (EPS) is speculated to be related with the decrease of CH₄ oxidation rate after a peak in long-term laboratory landfill covers and biofilters. However, few data have been reported about EPS production of methanotrophs and its feedback effects on methanotrophic activity. In this study, Methylosinus sporium was used asa model methanotroph to investigate EPS production and its influencing factors during CH₄ oxidation. The results showed that methanotrophs could secret EPS into the habits during CH₄ oxidation and had a negative feedback effect on CH₄ oxidation. The EPS amount fitted well with the CH₄ oxidation activity with the exponential model. The environmental factors such as pH, temperature, CH₄, O₂, NO₃^--N and NH₄⁺-N could affect the EPS production of methanotrophs. When pH, temperature, CH₄, O₂ and N concentrations (including NO₃^--N and NH₄⁺-N) were 6.5-7.5, 30-40°C, 10-15%, 10% and 20-140mgL^-1, respectively, the high cell growth rate and CH₄ oxidation activity of Methylosinus sporium occurred in the media with the low EPS production, which was beneficial to sustainable and efficient CH₄ oxidation. In practice, O₂-limited condition such as the O₂ concentration of 10% might be a good way to control EPS production and enhance CH₄ oxidation to mitigate CH₄ emission from landfills.

Activity of Type I Methanotrophs Dominates under High Methane Concentration: Methanotrophic Activity in Slurry Surface Crusts as Influenced by Methane, Oxygen, and Inorganic Nitrogen

Livestock slurry is a major source of atmospheric methane (CH), but surface crusts harboring methane-oxidizing bacteria (MOB) could mediate against CH emissions. This study examined conditions for CH oxidation by in situ measurements of oxygen (O) and nitrous oxide (NO), as a proxy for inorganic N transformations, in intact crusts using microsensors. This was combined with laboratory incubations of crust material to investigate the effects of O, CH, and inorganic N on CH oxidation, using CH to trace C incorporation into lipids of MOB. Oxygen penetration into the crust was 2 to 14 mm, confining the potential for aerobic CH oxidation to a shallow layer. Nitrous oxide accumulated within or below the zone of O depletion. With 10 ppmv CH there was no O limitation on CH oxidation at O concentrations as low as 2%, whereas CH oxidation at 10 ppmv CH was reduced at ≤5% O. As hypothesized, CH oxidation was in general inhibited by inorganic N, especially NO, and there was an interaction between N inhibition and O limitation at 10 ppmv CH, as indicated by consistently stronger inhibition of CH oxidation by NH and NO at 3% compared with 20% O. Recovery of C in phospholipid fatty acids suggested that both Type I and Type II MOB were active, with Type I dominating high-concentration CH oxidation. Given the structural heterogeneity of crusts, CH oxidation activity likely varies spatially as constrained by the combined effects of CH, O, and inorganic N availability in microsites.

Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System

Manure composting is a significant source of atmospheric methane (CH₄) and nitrous oxide (N₂O) that are two potent greenhouse gases. The CH₄ and N₂O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH₄ and N₂O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH₄ and N₂O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH₄-related functional genes (mcrA and pmoA genes) and N₂O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH₄ and N₂O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH₄⁺ together as the best predictors for CH₄ fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N₂O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH₄ and N₂O fluxes to elevated atmospheric CO₂ concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models.

The conversion of grassland to acacia forest as an effective option for net reduction in greenhouse gas emissions

This study aimed to evaluate the effect of forestation with leguminous Acacia mearnsii De Wild in native grasslands on the soil greenhouse (GHG) fluxes and their main driving factors. The experiment was conducted in the Brazilian Pampa over the period of one year in a six-year-old Acacia plantation, evaluating four treatments: Acacia (AM), Acacia with litter periodically removed (A-l), Acacia after harvest (AH) and native grassland (NG) (reference treatment). Air samples were obtained by the static chamber method, and gas concentrations were evaluated by gas chromatography. Soil and climate factors were monitored. The accumulated fluxes of methane (CH4) and nitrous oxide (N2O) were statistically similar between the soils in the AM and NG treatments, which tended to oxidize CH4 (-1445 and -1752 g C-CH4 ha(-1) yr(-1), respectively) and had low emission of N2O (242 and 316 g N-N2O ha(-1) yr(-1)), most likely influenced by the low water-filled pore space and the low content of mineral N in the soil. However, the soil in the AH treatment presented higher emissions of both gases, totaling 1889 g C-CH4 ha(-1) yr(-1) and 1250 g N-N2O ha(-1) yr(-1). Afforestation neither significantly affected the total organic C stocks nor their lability, keeping the C management index for the forested area similar to that in the NG treatment. The conversion from grassland to Acacia forest represents an effective option for mitigating the net reduction in greenhouse gas emissions, which is basically determined by C accumulation in biomass and wood products.

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites

This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils.

Effect of irrigation, nitrogen application, and a nitrification inhibitor on nitrous oxide, carbon dioxide and methane emissions from an olive (Olea europaea L.) orchard

Drip irrigation combined with nitrogen (N) fertigation is applied in order to save water and improve nutrient efficiency. Nitrification inhibitors reduce greenhouse gas emissions. A field study was conducted to compare the emissions of nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4) associated with the application of N fertiliser through fertigation (0 and 50kgNha(-1)), and 50kgNha(-1)+nitrification inhibitor in a high tree density Arbequina olive orchard. Spanish Arbequina is the most suited variety for super intensive olive groves. This system allows reducing production costs and increases crop yield. Moreover its oil has excellent sensorial features. Subsurface drip irrigation markedly reduced N2O and N2O+N2 emissions compared with surface drip irrigation. Fertiliser application significantly increased N2O+N2, but not N2O emissions. Denitrification was the main source of N2O. The N2O losses (calculated as emission factor) ranging from -0.03 to 0.14% of the N applied, were lower than the IPCC (2007) values. The N2O+N2 losses were the largest, equivalent to 1.80% of the N applied, from the 50kgNha(-1)+drip irrigation treatment which resulted in water filled pore space >60% most of the time (high moisture). Nitrogen fertilisation significantly reduced CO2 emissions in 2011, but only for the subsurface drip irrigation strategies in 2012. The olive orchard acted as a net CH4 sink for all the treatments. Applying a nitrification inhibitor (DMPP), the cumulative N2O and N2O+N2 emissions were significantly reduced with respect to the control. The DMPP also inhibited CO2 emissions and significantly increased CH4 oxidation. Considering global warming potential, greenhouse gas intensity, cumulative N2O emissions and oil production, it can be concluded that applying DMPP with 50kgNha(-1)+drip irrigation treatment was the best option combining productivity with keeping greenhouse gas emissions under control.

Methane oxidation potential of boreal landfill cover materials: The governing factors and enhancement by nutrient manipulation

Methanotrophs inhabiting landfill covers are in a crucial role in mitigating CH4 emissions, but the characteristics of the cover material or ambient temperature do not always enable the maximal CH4 oxidation potential (MOP). This study aimed at identifying the factors governing MOPs of different materials used for constructing biocovers and other cover structures. We also tested whether the activity of methanotrophs could be enhanced at cold temperature (4 and 12°C) by improving the nutrient content (NO3(-), PO4(3-), trace elements) of the cover material. Compost samples from biocovers designed to support CH4 oxidation were exhibiting the highest MOPs (4.16 μmol CH4 g dw(-1) h(-1)), but also the soil samples collected from other cover structures were oxidising CH4 (0.41 μmol CH4 g dw(-1) h(-1)). The best predictors for the MOPs were the NO3(-) content and activity of heterotrophic bacteria at 72.8%, which were higher in the compost samples than in the soil samples. The depletion of NO3(-) from the landfill cover material limiting the activity of methanotrophs could not be confirmed by the nutrient manipulation assay at 4°C as the addition of nitrogen decreased the MOPs from 0.090 μmol CH4 g dw(-1) h(-1) to <0.085 μmol CH4 g dw(-1) h(-1). At 12°C, all nutrient additions reduced the MOPs. The inhibition was believed to result from high ionic concentration caused by nutrient addition. At 4°C, the addition of trace elements increased the MOPs (>0.096 μmol CH4 g dw(-1)h(-1)) suggesting that this was attributable to stimulation of the enzymatic activity of the psychrotolerant methanotrophs.

Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8

Aerobic methane-oxidizing bacteria (MOB) are a diverse group of microorganisms that are ubiquitous in natural environments. Along with anaerobic MOB and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. Clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. Previous findings show that nitrite amendment inhibits the activity of some cultivated methanotrophs; however, the physiological pathways that allow some strains to transform nitrite, expression of gene inventories, as well as the electron sources that support this activity remain largely uncharacterized. Here we show that Methylomicrobium album strain BG8 utilizes methane, methanol, formaldehyde, formate, ethane, ethanol, and ammonia to support denitrification activity under hypoxia only in the presence of nitrite. We also demonstrate that transcript abundance of putative denitrification genes, nirS and one of two norB genes, increased in response to nitrite. Furthermore, we found that transcript abundance of pxmA, encoding the alpha subunit of a putative copper-containing monooxygenase, increased in response to both nitrite and hypoxia. Our results suggest that expression of denitrification genes, found widely within genomes of aerobic methanotrophs, allow the coupling of substrate oxidation to the reduction of nitrogen oxide terminal electron acceptors under oxygen limitation. The present study expands current knowledge of the metabolic flexibility of methanotrophs by revealing that a diverse array of electron donors support nitrite reduction to nitrous oxide under hypoxia.

Production of Nitrous Oxide from Nitrite in Stable Type II Methanotrophic Enrichments

The coupled aerobic-anoxic nitrous decomposition operation is a new process for wastewater treatment that removes nitrogen from wastewater and recovers energy from the nitrogen in three steps: (1) NH4(+) oxidation to NO2(-), (2) NO2(-) reduction to N2O, and (3) N2O conversion to N2 with energy production. Here, we demonstrate that type II methanotrophic enrichments can mediate step two by coupling oxidation of poly(3-hydroxybutyrate) (P3HB) to NO2(-) reduction. Enrichments grown with NH4(+) and NO2(-) were subject to alternating 48-h aerobic and anoxic periods, in which CH4 and NO2(-) were added together in a "coupled" mode of operation or separately in a "decoupled mode". Community structure was stable in both modes and dominated by Methylocystis. In the coupled mode, production of P3HB and N2O was low. In the decoupled mode, significant P3HB was produced, and oxidation of P3HB drove reduction of NO2(-) to N2O with ∼ 70% conversion for >30 cycles (120 d). In batch tests of wasted cells from the decoupled mode, N2O production rates increased at low O2 or high NO2(-) levels. The results are significant for the development of engineered processes that remove nitrogen from wastewater and for understanding of conditions that favor environmental production of N2O.

N2O and CH4 emissions from a fallow-wheat rotation with low N input in conservation and conventional tillage under a Mediterranean agroecosystem

Conservation agriculture that includes no tillage (NT) or minimum tillage (MT) and crop rotation is an effective practice to increase soil organic matter in Mediterranean semiarid agrosystems. But the impact of these agricultural practices on greenhouse gases (GHGs), such as nitrous oxide (N2O) and methane (CH4), is variable depending mainly on soil structure and short/long-term tillage. The main objective of this study was to assess the long-term effect of three tillage systems (NT, MT and conventional tillage (CT)) and land-covers (fallow/wheat) on the emissions of N2O and CH4 in a low N input agricultural system during one year. This was achieved by measuring crop yields, soil mineral N and dissolved organic C contents, and fluxes of N2O and CH4. Total cumulative N2O emissions were not significantly different (P>0.05) among the tillage systems or between fallow and wheat. The only difference was produced in spring, when N2O emissions were significantly higher (P<0.05) in fallow than in wheat subplots, and NT reduced N2O emissions (P<0.05) compared with MT and CT. Taking into account the water filled pore space (WFPS), both nitrification and denitrification could have occurred during the experimental period. Denitrification capacity in March was similar in all tillage systems, in spite of the higher DOC content maintained in the topsoil of NT. This could be due to the similar denitrifier densities, targeted by nirK copy numbers at that time. Cumulative CH4 fluxes resulted in small net uptake for all treatments, and no significant differences were found among tillage systems or between fallow and wheat land-covers. These results suggest that under a coarse-textured soil in low N agricultural systems, the impact of tillage on GHG is very low and that the fallow cycle within a crop rotation is not a useful strategy to reduce GHG emissions.

Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2

Nitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low-affinity pMMO1) and pmoCAB2 (high-affinity pMMO2). We used RNA-Seq to identify strain SC2 genes that respond to standard (10 mM) and high (30 mM) NH4(+) concentrations in the medium, compared with 10 mM NO3(-). While the expression of pmoCAB1 was unaffected, pmoCAB2 was significantly downregulated (log2 fold changes of -5.0 to -6.0). Among nitrogen metabolism-related processes, genes involved in hydroxylamine detoxification (haoAB) were highly upregulated, while those for assimilatory nitrate/nitrite reduction, high-affinity ammonium uptake and nitrogen regulatory protein PII were downregulated. Differential expression of pmoCAB2 and haoAB was independently validated by end-point reverse transcription polymerase chain reaction. Methane oxidation by SC2 cells exposed to 30 mM NH4(+) was inhibited at ≤ 400 ppmv CH4 , where pMMO2 but not pMMO1 is functional. When transferred back to standard nitrogen concentration, methane oxidation capability and pmoCAB2 expression were restored. Given that Methylocystis contributes to atmospheric methane oxidation in upland soils, differential expression of pmoCAB2 explains, at least to some extent, the strong inhibitory effect of ammonium fertilizers on this activity.

Do cover crops enhance N₂O, CO₂ or CH₄ emissions from soil in Mediterranean arable systems?

This study evaluates the effect of planting three cover crops (CCs) (barley, Hordeum vulgare L.; vetch, Vicia villosa L.; rape, Brassica napus L.) on the direct emission of N₂O, CO₂ and CH₄ in the intercrop period and the impact of incorporating these CCs on the emission of greenhouse gas (GHG) from the forthcoming irrigated maize (Zea mays L.) crop. Vetch and barley were the CCs with the highest N₂O and CO₂ losses (75 and 47% increase compared with the control, respectively) in the fallow period. In all cases, fluxes of N₂O were increased through N fertilization and the incorporation of barley and rape residues (40 and 17% increase, respectively). The combination of a high C:N ratio with the addition of an external source of mineral N increased the fluxes of N₂O compared with -Ba and -Rp. The direct emissions of N₂O were lower than expected for a fertilized crop (0.10% emission factor, EF) compared with other studies and the IPCC EF. These results are believed to be associated with a decreased NO₃(-) pool due to highly denitrifying conditions and increased drainage. The fluxes of CO₂ were in the range of other fertilized crops (i.e., 1118.71-1736.52 kg CO₂-Cha(-1)). The incorporation of CC residues enhanced soil respiration in the range of 21-28% for barley and rape although no significant differences between treatments were detected. Negative CH₄ fluxes were measured and displayed an overall sink effect for all incorporated CC (mean values of -0.12 and -0.10 kg CH₄-Cha(-1) for plots with and without incorporated CCs, respectively).

Environmental impacts on the diversity of methane-cycling microbes and their resultant function

Methane is an important anthropogenic greenhouse gas that is produced and consumed in soils by microorganisms responding to micro-environmental conditions. Current estimates show that soil consumption accounts for 5–15% of methane removed from the atmosphere on an annual basis. Recent variability in atmospheric methane concentrations has called into question the reliability of estimates of methane consumption and calls for novel approaches in order to predict future atmospheric methane trends. This review synthesizes the environmental and climatic factors influencing the consumption of methane from the atmosphere by non-wetland, terrestrial soil microorganisms. In particular, we focus on published efforts to connect community composition and diversity of methane-cycling microbial communities to observed rates of methane flux. We find abundant evidence for direct connections between shifts in the methane-cycling microbial community, due to climate and environmental changes, and observed methane flux levels. These responses vary by ecosystem and associated vegetation type. This information will be useful in process-based models of ecosystem methane flux responses to shifts in environmental and climatic parameters.

Inhibition of methane oxidation in a slurry surface crust by inorganic nitrogen: an incubation study

Livestock slurry is an important source of methane (CH). However, depending on the dry matter content of the slurry, a floating crust may form where methane-oxidizing bacteria (MOB) and CH oxidation activity have been found, suggesting that surface crusts may reduce CH emissions from slurry. However, it is not known how MOB in this environment interact with inorganic nitrogen (N). We studied inhibitory effects of ammonium (NH), nitrate (NO), and nitrite (NO) on potential CH oxidation in a cattle slurry surface crust. At headspace concentrations of 100 and 10,000 ppmv, CH oxidation was assayed at salt concentrations up to 500 mM. First-order rate constants were used to evaluate the strength of inhibition. Nitrite was the most potent inhibitor, reducing methanotrophic activity by up to 70% at only 1 mM NO. Methane-oxidizing bacteria were least sensitive to NO, tolerating up to 30 mM NO at 100 ppmv CH and 50 mM NO at 10,000 ppmv CH without any decline in activity. The inhibition by NH increased progressively, and no range of tolerance was observed. Methane concentrations of 10,000 ppmv resulted in 50- to 100-fold higher specific CH uptake rates than 100 ppmv CH but did not change the inhibition patterns of N salts. In slurry surface crusts, MOB maintained activity at higher concentrations of NH and NO than reported for MOB in soils and sediments, possibly showing adaptation to high N concentrations in the slurry environment. Yet it appears that the effectiveness of surface crusts as CH sinks will depend on inorganic N concentrations.

The effect of nitrate on ethylene biofiltration

This study investigated the effects of filter media types and nitrate (NO(3)(-)) concentrations in nutrient solutions on C(2)H(4) biofiltration. A new nutrient solution with zero NO(3)(-) concentration was supplied to two perlite-bed biotrickling filters, two perlite-bed biofilters, and two GAC (Granular Activated Carbon)-bed biofilters, while the other with 2 g L(-1) of NO(3)(-) was used for the other two GAC biofilters. All reactors underwent a total test duration of over 175 days with an EBRT (Empty Bed Residence Time) of 30 s, inlet gas flow rate of 7 L min(-1), and inlet C(2)H(4) concentrations of 20-30 mg m(-3). NO(3)(-) concentration and media type significantly affected the C(2)H(4) removal efficiencies in all types of biofiltration. The perlite media with no NO(3)(-) achieved C(2)H(4) removal efficiencies 10-50% higher than the others. A NO(3)(-) concentration as high as 2 g L(-1) in the original nutrient solution may act as an inhibitor that suppresses the growth or activity of C(2)H(4) degraders. In addition, the perlite media resulted in higher C(2)H(4) removal efficiencies than GAC media, because the hydrophilic surface of the perlite leads to a higher moisture content and thus to favorable microbial growth.

Seasonal methane oxidation potential in manure crusts

Organic crusts on liquid manure storage tanks harbor ammonia- and nitrite-resistant methane oxidizers and may significantly reduce methane emissions. Methane oxidation potential (0.6 mol CH(4) m(-2) day(-1)) peaked during fall and winter, after 4 months of crust development. Consequences for methane mitigation potential of crusts are discussed.

Do nitrogen fertilizers stimulate or inhibit methane emissions from rice fields?

In rice cultivation, there are controversial reports on net impacts of nitrogen (N) fertilizers on methane (CH ₄ ) emissions. Nitrogen fertilizers increase crop growth as well as alter CH ₄ producing (Methanogens) and consuming (Methanotrophs) microbes, and thereby produce complex effects on CH ₄ emissions. Objectives of this study were to determine net impact of N fertilizers on CH ₄ emissions and to identify their underlying mechanisms in the rice soils. Database was obtained from 33 published papers that contained CH ₄ emissions observations from N fertilizer (28-406 kg N ha^-1 ) treatment and its control. Results have indicated that N fertilizers increased CH ₄ emissions in 98 of 155 data pairs in rice soils. Response of CH ₄ emissions per kg N fertilizer was significantly (P < 0.05) greater at < 140 kg N ha^-1 than > 140 kg N ha^-1 indicating that substrate switch from CH ₄ to ammonia by Methanotrophs may not be a dominant mechanism for increased CH ₄ emissions. On the contrary, decreased CH ₄ emission in intermittent drainage by N fertilizers has suggested the stimulation of Methanotrophs in rice soils. Effects of N fertilizer stimulated Methanotrophs in reducing CH ₄ emissions were modified by the continuous flood irrigation due to limitation of oxygen to Methanotrophs. Greater response of CH ₄ emissions per kg N fertilizer in urea than ammonia sulfate probably indicated the interference of sulfate in the CH ₄ production process. Overall, response of CH ₄ emissions to N fertilizers was correlated with N-induced crop yield (r = +0.39; P < 0.01), probably due to increased carbon substrates for Methanogens. Using CH ₄ emission observations, this meta-analysis has identified dominant microbial processes that control net effects of N fertilizers on CH ₄ emissions in rice soils. Finally, we have provided a conceptual model that included microbial processes and controlling factors to predict effects of N fertilizers on CH ₄ emissions in rice soils.

Inhibition of methane oxidation by nitrogenous fertilizers in a paddy soil

Nitrogenous fertilizers are generally thought to have an important role in regulating methane oxidation. In this study, the effect of ammonium on methane oxidation activity was investigated in a paddy soil using urea at concentrations of 0, 50, 100, 200, and 400 μg N per gram dry weight soil (N/g.d.w.s) and ammonium sulfate at concentrations of 0, 50, and 200 μg N/g.d.w.s. The results of this study demonstrate that urea concentrations of 200 μg N/g.d.w.s. and above significantly inhibit methane oxidation activity, whereas no statistically significant difference was observed in methane oxidation activity among soil microcosms with urea concentrations of less than 200 μg N/g.d.w.s after incubation for 27 days. Similar results were obtained in a sense that methane oxidation activity was inhibited only when the ammonium sulfate concentration was 200 μg N/g.d.w.s in soil microcosms in this study. Phylogenetic analysis of pmoA genes showed that nitrogen fertilization resulted in apparent changes in the community composition of methane-oxidizing bacteria (MOB). Type I MOB displayed an increased abundance in soil microcosms amended with nitrogenous fertilizers, whereas type II MOB dominated the native soil. Furthermore, although no statistically significant relationship was observed between pmoA gene and amoA gene abundances, methane oxidation activity was significantly negatively correlated with nitrification activity in the presence of urea or ammonium sulfate. Our results indicate that the methane oxidation activity in paddy soils might be inhibited when the concentration of ammonium fertilizers is high and that the interactions between ammonia and methane oxidizers need to be further investigated.