Contribution of methanotrophic and nitrifying bacteria to CH4 and NH4+ oxidation in the rhizosphere of rice plants as determined by new methods of discrimination

Greenhouse gas emissions from on-site sanitation systems: A systematic review and meta-analysis of emission rates, formation pathways and influencing factors

Onsite sanitation systems (OSS) are significant sources of greenhouse gases (GHG) including carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). While a handful of studies have been conducted on GHG emissions from OSS, systematic evaluation of literature on this subject is limited. Our systematic review and meta-analysis provides state-of-the- art information on GHG emissions from OSS and identifies novel areas for investigation. The paper analyzes GHG emission rates from different OSS, the influence of various design, operational, and environmental factors on emission rates and proffers mitigation measures. Following the Preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA) guidelines, we identified 16 articles which quantified GHG emissions from OSS. Septic tanks emit substantial amounts of CO2 and CH4 ranging from 1.74 to 398.30 g CO2/cap/day and 0.06-110.13 g CH4/cap/day, respectively, but have low N2O emissions (0.01-0.06 g N₂O/cap/day). CH4 emissions from pit latrines range from 0.77 to 20.30 g CH4/cap/day N2O emissions range from 0.76 to 1.20 gN2O/cap/day. We observed statistically significant correlations (p < 0.05) between temperature, biochemical oxygen demand, chemical oxygen demand, dissolved oxygen, storage period, and GHG emissions from OSS. However, no significant correlation (p > 0.05) was observed between soil volumetric water content and CO2 emissions. CH4 emissions (expressed as CO2 equivalents) from OSS estimated following Intergovernmental Panel for Climate Change (IPCC) guidelines were found to be seven times lower (90.99 g CO2e/cap/day) than in-situ field emission measurements (704.7 g CO2e/cap/day), implying that relying solely on IPCC guidelines may lead to underestimation of GHG emission from OSS. Our findings underscore the importance of considering local contexts and environmental factors when estimating GHG emissions from OSS. Plausible mitigation measures for GHG emissions from OSS include converting waste to biogas in anaerobic systems (e.g. biogas), applying biochar, and implementing mitigation policies that equally address inequalities in sanitation service access. Future research on GHG from OSS should focus on in-situ measurements of GHGs from pit latrines and other common OSS in developing countries, understanding the fate and transport of dissolved organics like CH4 in OSS effluents and impacts of microbial communities in OSS on GHG emissions. Addressing these gaps will enable more holistic and effective management of GHG emissions from OSS.

Soil Enzyme Activity Regulates the Response of Soil C Fluxes to N Fertilization in a Temperate Cultivated Grassland

Exogenous nitrogen (N) inputs greatly change the emission and uptake of carbon dioxide (CO2) and methane (CH4) from temperate grassland soils, thereby affecting the carbon (C) budget of regional terrestrial ecosystems. Relevant research focused on natural grassland, but the effects of N fertilization on C exchange fluxes from different forage soils and the driving mechanisms were poorly understood. Here, a three-year N addition experiment was conducted on cultivated grassland planted with alfalfa (Medicago sativa) and bromegrass (Bromus inermis) in Inner Mongolia. The fluxes of soil-atmospheric CO2 and CH4; the content of the total dissolved N (TDN); the dissolved organic N (DON); the dissolved organic C (DOC); NH4+–N and NO3−–N in soil; enzyme activity; and auxiliary variables (soil temperature and moisture) were simultaneously measured. The results showed that N fertilization (>75 kg N ha−1 year−1) caused more serious soil acidification for alfalfa planting than for brome planting. N fertilization stimulated P-acquiring hydrolase (AP) in soil for growing Bromus inermis but did not affect C- and N-acquiring hydrolases (AG, BG, CBH, BX, LAP, and NAG). The oxidase activities (PHO and PER) of soil for planting Bromus inermis were higher than soil for planting Medicago sativa, regardless of N, whether fertilization was applied or not. Forage species and N fertilization did not affect soil CO2 flux, whereas a high rate of N fertilization (150 kg N ha−1 year−1) significantly inhibited CH4 uptake in soil for planting Medicago sativa. A synergistic effect between CO2 emission and CH4 uptake in soil was found over the short term. Our findings highlight that forage species affect soil enzyme activity in response to N fertilization. Soil enzyme activity may be an important regulatory factor for C exchange from temperate artificial grassland soil in response to N fertilization.

Methanotrophic denitrification in wastewater treatment: microbial aspects and engineering strategies

Anaerobic technologies are consolidated for sewage treatment and are the core processes for mining marketable products from waste streams. However, anaerobic effluents are supersaturated with methane, which represents a liability regarding greenhouse gas emissions. Meanwhile, anaerobic technologies are not capable of nitrogen removal, which is required to ensure environmental protection. Methane oxidation and denitrification processes can be combined to address both issues concurrently. Aerobic methane oxidizers can release intermediate organic compounds that can be used by conventional denitrifiers as electron donors. Alternatively, anoxic methanotrophic species combine methane oxidation with either nitrate or nitrite reduction in the same metabolism. Engineered systems need to overcome the long doubling times and low NO_x consumption rates of anoxic methanotrophic microorganisms. Another commonly reported bottleneck of methanotrophic denitrification relates to gas-liquid mass transfer limitations. Although anaerobic effluents are supersaturated with methane, experimental setups usually rely on methane supply in a gaseous mode. Hence, possibilities for the application of methane-oxidation coupled to denitrification in full scale might be overlooked. Moreover, syntrophic relationships among methane oxidizers, denitrifiers, nitrifiers, and other microorganisms (such as anammox) are not well understood. Integrating mixed populations with various metabolic abilities could allow for more robust methane-driven wastewater denitrification systems. This review presents an overview of the metabolic capabilities of methane oxidation and denitrification and discusses technological aspects that allow for the application of methanotrophic denitrification at larger scales.

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

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

Greenhouse gas emissions from Baltic coastal lakes

Coastal lakes (CL) act as limnetic-β-oligohaline systems located on non-tidal coastlines in fresh and salt water mixing zone. Owing to considerable terrestrial nutrient input and a high autochthonous productivity CLs release greenhouse gases (GHG) to the ambient atmosphere, however, neither emission from the system was assessed nor controls on the emission were recognized so far. In this study we attempted to quantify diffusive emissions of CH₄, CO₂ and N₂O from CLs based on data collected from seven lakes located on a south coast of the Baltic Sea in Poland. Lake water samples were collected with quarterly resolution along salinity, water depth and wind fetch gradients. From our data it emerged that the concentrations of GHGs were determined by temperature. CH₄ showed dependence on salinity, lake water depth and wind fetch. N₂O was controlled by dissolved O₂ and NO₃^- and CO₂ was largely related to wind fetch. It also appeared that concentrations of N₂O and CO₂ were influenced by terrestrial nutrient input. The mean fluxes of CH₄, CO₂ and N₂O for the whole system were 21.7 mg·m^-2·d^-1, 12.7 g·m^-2·d^-1 and 0.74 mg·m^-2·d^-1, respectively which was equivalent to 7.9 g CH₄·m^-2·y^-1, 4.6 kg CO₂·m^-2·y^-1 and 269 mg N₂O·m^-2·y^-1. CH₄ and N₂O were released throughout the year and CO₂ was predominantly emitted during winter. We showed that diffusive emissions of the GHGs showed relationships to the surface area of the lakes as well as the ratio of catchment area to lake area (CA/LA). The study would benefit from further extension with higher resolution analyses of the lakes over longer timescales and quantification of ebullitive GHG emission (CH₄ in particular).

Multiheme hydroxylamine oxidoreductases produce NO during ammonia oxidation in methanotrophs

Aerobic and nitrite-dependent methanotrophs make a living from oxidizing methane via methanol to carbon dioxide. In addition, these microorganisms cometabolize ammonia due to its structural similarities to methane. The first step in both of these processes is catalyzed by methane monooxygenase, which converts methane or ammonia into methanol or hydroxylamine, respectively. Methanotrophs use methanol for energy conservation, whereas toxic hydroxylamine is a potent inhibitor that needs to be rapidly removed. It is suggested that many methanotrophs encode a hydroxylamine oxidoreductase (mHAO) in their genome to remove hydroxylamine, although biochemical evidence for this is lacking. HAOs also play a crucial role in the metabolism of aerobic and anaerobic ammonia oxidizers by converting hydroxylamine to nitric oxide (NO). Here, we purified an HAO from the thermophilic verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV and characterized its kinetic properties. This mHAO possesses the characteristic P460 chromophore and is active up to at least 80 °C. It catalyzes the rapid oxidation of hydroxylamine to NO. In methanotrophs, mHAO efficiently removes hydroxylamine, which severely inhibits calcium-dependent, and as we show here, lanthanide-dependent methanol dehydrogenases, which are more prevalent in the environment. Our results indicate that mHAO allows methanotrophs to thrive under high ammonia concentrations in natural and engineered ecosystems, such as those observed in rice paddy fields, landfills, or volcanic mud pots, by preventing the accumulation of inhibitory hydroxylamine. Under oxic conditions, methanotrophs mainly oxidize ammonia to nitrite, whereas in hypoxic and anoxic environments reduction of both ammonia-derived nitrite and NO could lead to nitrous oxide (N2O) production.

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations

Coastal zones are transitional areas between land and sea where large amounts of organic and inorganic carbon compounds are recycled by microbes. Especially shallow zones near land have been shown to be the main source for oceanic methane (CH4) emissions. Water depth has been predicted as the best explanatory variable, which is related to CH4 ebullition, but exactly how sediment methanotrophs mediates these emissions along water depth is unknown. Here, we investigated the relative abundance and RNA transcripts attributed to methane oxidation proteins of aerobic methanotrophs in the sediment of shallow coastal zones with high CH4 concentrations within a depth gradient from 10-45 m. Field sampling consisted of collecting sediment (top 0-2 cm layer) from eight stations along this depth gradient in the coastal Baltic Sea. The relative abundance and RNA transcripts attributed to the CH4 oxidizing protein (pMMO; particulate methane monooxygenase) of the dominant methanotroph Methylococcales was significantly higher in deeper costal offshore areas (36-45 m water depth) compared to adjacent shallow zones (10-28 m). This was in accordance with the shallow zones having higher CH4 concentrations in the surface water, as well as more CH4 seeps from the sediment. Furthermore, our findings indicate that the low prevalence of Methylococcales and RNA transcripts attributed to pMMO was restrained to the euphotic zone (indicated by Photosynthetically active radiation (PAR) data, photosynthesis proteins, and 18S rRNA data of benthic diatoms). This was also indicated by a positive relationship between water depth and the relative abundance of Methylococcales and pMMO. How these processes are affected by light availability requires further studies. CH4 ebullition potentially bypasses aerobic methanotrophs in shallow coastal areas, reducing CH4 availability and limiting their growth. Such mechanism could help explain their reduced relative abundance and related RNA transcripts for pMMO. These findings can partly explain the difference in CH4 concentrations between shallow and deep coastal areas, and the relationship between CH4 concentrations and water depth.

Screening methane-oxidizing bacteria from municipal solid waste landfills and simulating their effects on methane and ammonia reduction

Municipal solid waste landfills are not only a crucial source of global greenhouse gas emissions; they also produce large amounts of ammonia (NH₃), hydrogen sulfide, and other odorous gases that negatively affect the regional environment. Several types of methane-oxidizing bacteria (MOB) were proved to be effective in mitigating methane emission from landfills. Nevertheless, more MOB species and their technical parameters for best mitigating methane still need to be explored. In landfills, methane is simultaneously generated with ammonia, which may impede the CH₄ bio-oxidizing process of MOB. However, very limited studies examined the enhancement of methane reduction by introducing ammonia-oxidizing bacteria (AOB) in landfills. In this study, two enriched MOB cultures were gained from a typical municipal solid waste landfill, and then were cultured with three strains of ammonia-oxidizing bacteria (AOB). The MOB enrichment culture used in this work includes Methylocaldum, Methylocystaceae, and Methyloversatilis, with a methane oxidation capacity of 43.6-65.0%, and the AOB includes Candida ethanolica, Bacillus cereus, and Alcaligenes faecalis. The effects on the emission reduction of both NH₃ and CH₄ were measured using self-made landfill-simulating equipment, as MOB, AOB, and a MOB-AOB mixture were added to the soil cover of the simulation equipment. The concentrations of CH₄ and NH₃ in the MOB-AOB mixture group decreased sharply, and the CH₄ and NH₃ concentration was 76.4% and 83.7% of the control group level. We also found that addition of AOB can help MOB oxidize CH₄ and improve the emission reduction effect.

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.

Optimisation of bioscrubber systems to simultaneously remove methane and purify wastewater from intensive pig farms

The use of bioscrubber is attracting increasing attention for exhaust gas treatment in intensive pig farming. However, the challenge is to improve the methane (CH₄) removal efficiency as well as the possibility of pig house wastewater treatment. Three laboratory-scale bioscrubbers, each equipped with different recirculation water types, livestock wastewater (10-times-diluted pig house wastewater supernatant), a methanotroph growth medium (10-times-diluted), and tap water, were established to evaluate the performance of CH₄ removal and wastewater treatment. The results showed that enhanced CH₄ removal efficiency (25%) can be rapidly achieved with improved methanotrophic activity due to extra nutrient support from the wastewater. The majority of the CH₄ was removed in the middle to end part of the bioscrubbers, which indicated that CH₄ removal could be potentially optimised by extending the length of the reactor. Moreover, 52-86% of the ammonium (NH₄⁺-N), total organic carbon (TOC), and phosphate (PO₄^3--P) removal were simultaneously achieved with CH₄ removal in the present study. Based on these results, this study introduces a low-cost and simple-to-operate method to improve CH₄ removal and simultaneously treat pig farm wastewater in bioscrubbers.

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.

Resistance and Recovery of Methane-Oxidizing Communities Depends on Stress Regime and History; A Microcosm Study

Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors.

Relationship of nutrient dynamics and bacterial community structure at the water-sediment interface using a benthic chamber experiment

The relationships between nutrient dynamics and the bacterial community at the water-sediment interface were investigated using the results of nutrient release fluxes, bacterial communities examined by 16S rRNA pyrosequencing and canonical correlation analysis (CCA) accompanied by lab-scale benthic chamber experiment. The nutrient release fluxes from the sediments into the water were as follows: -3.832 to 12.157 mg m^-2 d^-1 for total phosphorus, 0.049 to 9.993 mg m^-2 d^-1 for PO₄-P, -2.011 to 41.699 mg m^-2 d^-1 for total nitrogen, -7.915 to -0.074 mg m^-2 d^-1 for NH₃-N, and -17.940 to 1.209 mg m^-2 d^-1 for NO₃-N. To evaluate the relationship between the bacterial communities and environmental variables, CCA was conducted in three representative conditions: in the overlying water, in the sediment at a depth of 0-5 cm, and in the sediment at a depth of 5-15 cm. CCA results showed that environmental variables such as nutrient release fluxes (TN, NH₄, NO₃, TP, and PO₄) and water chemical parameters (pH, DO, COD, and temperature) were highly correlated with the bacterial communities. From the results of the nutrient release fluxes and the bacterial community, this study proposed the hypothesis for bacteria involved in the nutrient dynamics at the interface between water and sediment. In the sediment, sulfate-reducing bacteria (SRB) such as Desulfatibacillum, Desulfobacterium, Desulfomicrobium, and Desulfosalsimonas are expected to contribute to the decomposition of organic matter, and release of ammonia (NH₄⁺) and phosphate (PO₄^3-). The PO₄^3- released into the water layer was observed by the positive fluxes of PO₄^3-. The NH₄⁺ released from the sediment was rapidly oxidized by the methane-oxidizing bacteria (MOB). This study observed in the water layer dominantly abundant MOB of Methylobacillus, Methylobacter, Methylocaldum, and Methylophilus. The nitrate (NO₃^-) accumulation caused by the oxidation environment of the water layer moved back to the sediment, which led to the relatively large negative fluxes of NO₃^-, compared to the small negative fluxes of NH₄⁺.

Inhibitory Effects of 3,4-Dimethylpyrazole Phosphate on CH4 and N2O Emissions in Paddy Fields of Subtropical China

3,4-Dimethylpyrazole phosphate (DMPP) has been widely employed to reduce nitrogen leaching and greenhouse gas emissions in the soils of dry farmlands. However, the effects of DMPP on the dynamics of nitrogen in paddy fields remain unclear. For this study, treatments with 0%, 0.25%, 0.5%, 1%, or 1.5% DMPP levels of nitrogen fertilization plus urea were designed to determine the effects on greenhouse gas emissions in paddy fields of subtropical China. All DMPP treatments significantly reduced CH4 and N2O emissions, from 54% to 34%, and 94% to 39%, respectively, compared with a urea fertilizer treatment alone. The soil NH4+ content decreased and NO3- increased more slowly with the application of DMPP. The crop yields under the various DMPP treatments showed no significant difference (p < 0.05). We concluded that the application of 0.5% and 1% DMPP may significantly reduce CH4 and N2O emissions in contrast to other treatments. This has important implications for the maintenance of rice yields, while reducing greenhouse gas emissions in paddy fields.

Elevational characteristics of the archaeal community in full-scale activated sludge wastewater treatment plants at a 3,660-meter elevational scale

Due to the important roles of archaea in wastewater treatment processes, archaeal communities have been studied extensively in various anaerobic reactors, but the knowledge of archaeal communities in full-scale activated sludge wastewater treatment plants (WWTPs) remains quite poor. In this study, 454-pyrosequencing was for the first time employed to investigate archaeal communities from 20 full-scale activated sludge WWTPs distributed at a 3,660-meter elevational scale in China. Results showed that archaeal communities from WWTPs were dominated by Methanosarcinales (84.6%). A core archaeal population (94.5%) composed of Methanosaeta, Methanosarcina, Methanogenium and Methanobrevibacter was shared among WWTPs. The elevational pattern of archaeal communities was observed in WWTPs, with an elevational threshold associated with archaeal community richness and structures at approximately 1,500 meters above sea level (masl). A declining trend in community richness with increasing elevation was observed at higher elevations, whereas no trend was presented at lower elevations. Spearman correlation analysis indicated that the archaeal community richness at higher elevations was associated with more environmental variables than that at lower elevations. Redundancy analysis indicated that wastewater variables were the dominant contributors to the variation of community structures at higher elevations, followed by operational variables and elevation.

Biological nitrification inhibition by rice root exudates and its relationship with nitrogen-use efficiency

Microbial nitrification in soils is a major contributor to nitrogen (N) loss in agricultural systems. Some plants can secrete organic substances that act as biological nitrification inhibitors (BNIs), and a small number of BNIs have been identified and characterized. However, virtually no research has focused on the important food crop, rice (Oryza sativa). Here, 19 rice varieties were explored for BNI potential on the key nitrifying bacterium Nitrosomonas europaea. Exudates from both indica and japonica genotypes were found to possess strong BNI potential. Older seedlings had higher BNI abilities than younger ones; Zhongjiu25 (ZJ25) and Wuyunjing7 (WYJ7) were the most effective genotypes among indica and japonica varieties, respectively. A new nitrification inhibitor, 1,9-decanediol, was identified, shown to block the ammonia monooxygenase (AMO) pathway of ammonia oxidation and to possess an 80% effective dose (ED₈₀ ) of 90 ng μl^-1 . Plant N-use efficiency (NUE) was determined using a ¹⁵ N-labeling method. Correlation analyses indicated that both BNI abilities and 1,9-decanediol amounts of root exudates were positively correlated with plant ammonium-use efficiency and ammonium preference. These findings provide important new insights into the plant-bacterial interactions involved in the soil N cycle, and improve our understanding of the BNI capacity of rice in the context of NUE.

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

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

Effects of water-saving irrigation on emissions of greenhouse gases and prokaryotic communities in rice paddy soil

The effects of water-saving irrigation on emissions of greenhouse gases and soil prokaryotic communities were investigated in an experimental rice field. The water layer was kept at 1-2 cm in the water-saving (WS) irrigation treatment and at 6 cm in the continuous flooding (CF) irrigation treatment. WS irrigation decreased CH(4) emissions by 78 % and increased N(2)O emissions by 533 %, resulting in 78 % reduction of global warming potential compared to the CF irrigation. WS irrigation did not affect the abundance or phylogenetic distribution of bacterial/archaeal 16S rRNA genes and the abundance of bacterial/archaeal 16S rRNAs. The transcript abundance of CH(4) emission-related genes generally followed CH(4) emission patterns, but the difference in abundance between mcrA transcripts and amoA/pmoA transcripts best described the differences in CH(4) emissions between the two irrigation practices. WS irrigation increased the relative abundance of 16S rRNAs and functional gene transcripts associated with Anaeromyxobacter and Methylocystis spp., suggesting that their activities might be important in emissions of the greenhouse gases. The N(2)O emission patterns were not reflected in the abundance of N(2)O emission-related genes and transcripts. We showed that the alternative irrigation practice was effective for mitigating greenhouse gas emissions from rice fields and that it did not affect the overall size and structure of the soil prokaryotic community but did affect the activity of some groups.

Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only

Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.

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

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

Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil

Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α-subunit (amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia.

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

The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH₃F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH₃F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH₃F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH₃F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH₃F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.

Structural and functional response of methane-consuming microbial communities to different flooding regimes in riparian soils

Climate change will lead to more extreme precipitation and associated increase of flooding events of soils. This can turn these soils from a sink into a source of atmospheric methane. The latter will depend on the balance of microbial methane production and oxidation. In the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. Four sites differing in flooding frequency were sampled and soil-physico-chemistry as well as methane oxidizing activities, numbers and community composition were assessed. Next to this, the active community members were determined by stable isotope probing of lipids. Methane consumption as well as population size distinctly increased with flooding frequency. All methane consumption parameters (activity, numbers, lipids) correlated with soil moisture, organic matter content, and conductivity. Methane oxidizing bacteria were present and activated quickly even in seldom flooded soils. However, the active species comprised only a few representatives belonging to the genera Methylobacter, Methylosarcina, and Methylocystis, the latter being active only in permanently or regularly flooded soils.

This study demonstrates that soils exposed to irregular flooding harbor a very responsive methane oxidizing community that has the potential to mitigate methane produced in these soils. The number of active species is limited and dominated by one methane oxidizing lineage. Knowledge on the characteristics of these microbes is necessary to assess the effects of flooding of soils and subsequent methane cycling therein.

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.

Methane source strength and energy flow shape methanotrophic communities in oxygen-methane counter-gradients

The role of microbial diversity for ecosystem functioning has become an important subject in microbial ecology. Recent work indicates that microbial communities and microbial processes can be very sensitive to anthropogenic disturbances. However, to what extent microbial communities may change upon, resist to, or overcome disturbances might differ depending on substrate availability. We used soil from an Italian rice field in gradient microcosms, and analysed the response of methanotrophic communities to an NH4 (+) pulse as a potential disturbance under two different CH4 source strengths. We found a significant influence of source strength, i.e. the energy flow through the methanotrophic community, while NH4 (+) had no effect. Our data suggest that historical contingencies, i.e. nitrogen fertilization, led to an ammonium-tolerant MOB community. Methanotrophs were able to oxidize virtually all CH4 diffusing into the oxic-anoxic boundary layer regardless of NH4 (+) addition. Total and active methanotrophic communities were assessed by a pmoA-specific microarray. From the reservoir of dormant methanotrophs, different species became active with Methylobacter and an environmental cluster affiliated with paddy soils being indicative for high CH4 source strength. Thus, a microbial seed bank is an important prerequisite to maintain functioning in a fluctuating environment.

Oxygen distribution and potential ammonia oxidation in floating, liquid manure crusts

Floating, organic crusts on liquid manure, stored as a result of animal production, reduce emission of ammonia (NH3) and other volatile compounds during storage. The occurrence of NO2- and NO3- in the crusts indicate the presence of actively metabolizing NH3-oxidizing bacteria (AOB) which may be partly responsible for this mitigation effect. Six manure tanks with organic covers (straw and natural) were surveyed to investigate the prevalence and potential activity ofAOB and its dependence on the O2 availability in the crust matrix as studied by electrochemical profiling. Oxygen penetration varied from <1 mm in young, poorly developed natural crusts and old straw crusts, to several centimeters in the old natural crusts. The AOB were ubiquitously present in all crusts investigated, but nitrifying activity could only be detected in old natural crusts and young straw crust with high O2 availability. In old natural crusts, total potential NH3 oxidation rates were similar to reported fluxes of NH3 from slurry without surface crust. These results indicate that old, natural surface crusts may develop into a porous matrix with high O2 availability that harbors an active population of aerobic microorganisms, including AOB. The microbial activity may thus contribute to a considerable reduction of ammonia emissions from slurry tanks with well-developed crusts.

Effects of oxygenation on ammonia oxidation potential and microbial diversity in sediment from surface-flow wetland mesocosms

Addition of oxygen to surface-flow wetland mesocosms treating synthetic secondary effluent resulted in a significant increase in ammonia oxidation potential in sediment compared to non-oxygenated controls. Ammonia oxidation potential in oxygenated wetland sediment (1.2-3.5 mg N g dw(-1) d(-1)) was 2-3 orders of magnitude higher than those measured in sediment and soil systems reported in the literature. Phylogenic analysis of sediment from the two treatments revealed substantial differences in microbial diversity including the presence of ammonia-oxidizing bacteria (Nitrosomonas oligotropha) and denitrifying bacteria only in oxygenated sediment, and an increase in the diversity of aerobic phototrophs and methanotrophs in control sediment. These observations supported the contention by Palmer et al. (2009) that oxygenation 'activated' nitrifying bacteria in wetland sediment leading to high rates of biological ammonia oxidation.

Carbon gas production under different electron acceptors in a freshwater marsh soil

Dynamics of carbon (C) gas emission from wetlands influence global C cycling. In many freshwater systems such as Louisiana freshwater marsh, soil contents of NO3(-) and SO4(2-) have increased due to nutrient loading and saltwater intrusion. This could affect C mineralization and the emission of the major greenhouse gases carbon dioxide (CO2) and methane (CH4). In this investigation, a laboratory microcosm study was carried out to elucidate the effects of NO(3)(-) and SO4(2-) on CO2 and CH4 production from a freshwater marsh soil located in the Barataria Basin of Louisiana coast, which has been subjected to the Mississippi River diversion and seawater intrusion. Composite soil samples were collected from top 50 cm marsh profile, treated with different levels of NO3(-) (0, 3.2 and 5mM) or SO4(2-) (0, 2, and 5mM) concentrations, and incubated for 214d under anaerobic conditions. The results showed that the presence of NO3(-) (especially at 3.2mM) significantly decreased CO2 productions whereas SO4(2-) did not. On the other hand, both NO(3)(-) and SO4(2-) treatments decreased CH4 production but the NO3(-) almost completely inhibited CH4 production (>99%) whereas the SO4(2-) treatments reduced CH4 production by 78-90%. The overall C mineralization rate constant under the NO3(-) presence was also low. In addition, the results revealed that a large proportion (95%) of anaerobic carbon mineralization in the untreated freshwater soil was unexplained by the reduction of any of the measured major electron acceptors.

Effect of temperature on composition of the methanotrophic community in rice field and forest soil

Temperature change affects methane consumption in soil. However, there is no information on possible temperature control of methanotrophic bacterial populations. Therefore, we studied CH(4) consumption and populations of methanotrophs in an upland forest soil and a rice field soil incubated at different temperatures between 5 and 45 degrees C for up to 40 days. Potential methane consumption was measured at 4% CH(4). The temporal progress of CH(4) consumption indicated growth of methanotrophs. Both soils showed maximum CH(4) consumption at 25-35 degrees C, but no activity at >40 degrees C. In forest soil CH(4) was also consumed at 5 degrees C, but in rice soil only at 15 degrees C. Methanotroph populations were assessed by terminal restriction fragment length polymorphism (T-RFLP) targeting particulate methane monooxygenase (pmoA) genes. Eight T-RFs with relative abundance >1% were retrieved from both forest and rice soil. The individual T-RFs were tentatively assigned to different methanotrophic populations (e.g. Methylococcus/Methylocaldum, Methylomicrobium, Methylobacter, Methylocystis/Methylosinus) according to published sequence data. Two T-RFs were assigned to ammonium monooxygenase (amoA) gene sequences. Statistical tests showed that temperature affected the relative abundance of most T-RFs. Furthermore, the relative abundance of individual T-RFs differed between the two soils, and also exhibited different temperature dependence. We conclude that temperature can be an important factor regulating the community composition of methanotrophs in soil.

Animal–plant–microbe interactions: direct and indirect effects of swan foraging behaviour modulate methane cycling in temperate shallow wetlands

Wetlands are among the most important ecosystems on Earth both in terms of productivity and biodiversity, but also as a source of the greenhouse gas CH(4). Microbial processes catalyzing nutrient recycling and CH(4) production are controlled by sediment physico-chemistry, which is in turn affected by plant activity and the foraging behaviour of herbivores. We performed field and laboratory experiments to evaluate the direct effect of herbivores on soil microbial activity and their indirect effects as the consequence of reduced macrophyte density, using migratory Bewick's swans (Cygnus columbianus bewickii Yarrell) feeding on fennel pondweed (Potamogeton pectinatus L.) tubers as a model system. A controlled foraging experiment using field enclosures indicated that swan bioturbation decreases CH(4) production, through a decrease in the activity of methanogenic Archaea and an increased rate of CH(4) oxidation in the bioturbated sediment. We also found a positive correlation between tuber density (a surrogate of plant density during the previous growth season) and CH(4) production activity. A laboratory experiment showed that sediment sterilization enhances pondweed growth, probably due to elimination of the negative effects of microbial activity on plant growth. In summary, the bioturbation caused by swan grazing modulates CH(4) cycling by means of both direct and indirect (i.e. plant-mediated) effects with potential consequences for CH(4) emission from wetland systems.

Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils

The activity and abundance of methanotrophic bacteria were measured in an acidic and a neutral forest soil. The soils exhibited high uptake rates (>30 microg CH4 m(-2) h(-1)) of atmospheric CH4 at all measurement times throughout the vegetation period. The abundances of various phylogenetic groups of methanotrophs, including some uncultured putative ones, were measured using real-time polymerase chain reaction assays. Each assay specifically targeted the pmoA gene or mmoX gene of a particular group of methanotrophs, or the amoA gene of ammonia-oxidizing bacteria. As yet uncultured methanotrophs of a group previously named 'forest soil cluster' or 'USC alpha' were numerically dominant in the acidic soil, while cultured but taxonomically uncharacterized methanotrophs of a group 'Cluster I' were dominant in the neutral soil. Each group was detected in numbers equivalent to about 10(6) pmoA gene copies per gram dry weight of soil and comprised >90% of the detectable methanotrophic bacteria in the respective soil. As the numbers of ammonia-oxidizing bacteria were similar but not higher, they could not have accounted for the observed CH4 uptake rates due to their low cell-specific CH4 oxidation activity. Based on CH4 flux and bacterial abundance data, estimated cell-specific CH4 oxidation rates of the detected methanotrophic bacteria were 540-800 x 10(-18) mol cell(-1) h(-1), which is high compared with literature values of cultured methanotrophic bacteria. These estimated cell-specific CH4 oxidation rates are sufficiently high to allow not only maintenance but even growth on atmospheric CH4 alone. Transcripts of mRNA of the pmoA gene were detected in the acidic soil, demonstrating that USC alpha methanotrophs expressed pmoA under ambient methane mixing ratios. On the other hand, pmoA transcripts of Cluster I or of other methanotrophic groups were not detectable. Our study suggests that USC alpha and Cluster I methanotrophs are adapted to the low concentration of methane in forest soils by possessing high cell-specific CH4 oxidation activities.

Thermophilic methane production and oxidation in compost

Methane cycling within compost heaps has not yet been investigated in detail. We show that thermophilic methane oxidation occurred after a lag phase of up to one day in 4-week old, 8-week old and mature (>10-week old) compost material. The potential rate of methane oxidation was between 2.6 and 4.1 micromol CH4(gdw)(-1)h(-1). Profiles of methane concentrations within heaps of different ages indicated that 46-98% of the methane produced was oxidised by methanotrophic bacteria. The population size of thermophilic methanotrophs was estimated at 10(9) cells (gdw)(-1), based on methane oxidation rates. A methanotroph (strain KTM-1) was isolated from the highest positive step of a serial dilution series. This strain belonged to the genus Methylocaldum, which contains thermotolerant and thermophilic methanotrophs. The closest relative organism on the basis of 16S rRNA gene sequence identity was M. szegediense (>99%), a species originally isolated from hot springs. The temperature optimum (45-55 degrees C) for methane oxidation within the compost material was identical to that of strain KTM-1, suggesting that this strain was well adapted to the conditions in the compost material. The temperatures measured in the upper layer (0-40 cm) of the compost heaps were also in this range, so we assume that these organisms are capable of effectively reducing the potential methane emissions from compost.

Ammonium and hydroxylamine uptake and accumulation in Nitrosomonas

Starved cells of Nitrosomonas europaea and further ammonia oxidizers were able to rapidly accumulate ammonium and hydroxylamine to an internal concentration of about 1 and 0.8 M, respectively. In kinetic studies, the uptake/accumulation rates for ammonium [3.1 mmol (g protein)(-1) min(-1)] and hydroxylamine [4.39 mmol (g protein)(-1) min(-1)] were determined. The uptake and accumulation process of ammonium and hydroxylamine was not coupled to ammonia or hydroxylamine oxidation and nitrite was not produced. In the presence of uncouplers the ammonium accumulation was completely inhibited, indicating an active, membrane-potential-driven transport mechanism. When the external ammonium or hydroxylamine pool was depleted, the internal ammonium and hydroxylamine was consumed within 12 h or 20 min, respectively. The binding of ammonium/ammonia was correlated with an energized membrane system, and hydroxylamine may bind to the hydroxylamine oxidoredutase.

Nitrogen isotopomer site preference of N2O produced by Nitrosomonas europaea and Methylococcus capsulatus Bath

The relative importance of individual microbial pathways in nitrous oxide (N(2)O) production is not well known. The intramolecular distribution of (15)N in N(2)O provides a basis for distinguishing biological pathways. Concentrated cell suspensions of Methylococcus capsulatus Bath and Nitrosomonas europaea were used to investigate the site preference of N(2)O by microbial processes during nitrification. The average site preference of N(2)O formed during hydroxylamine oxidation by M. capsulatus Bath (5.5 +/- 3.5 per thousand) and N. europaea (-2.3 +/- 1.9 per thousand) and nitrite reduction by N. europaea (-8.3 +/- 3.6 per thousand) differed significantly (ANOVA, f((2,35)) = 247.9, p = 0). These results demonstrate that the mechanisms for hydroxylamine oxidation are distinct in M. capsulatus Bath and N. europaea. The average delta(18)O-N(2)O values of N(2)O formed during hydroxylamine oxidation for M. capsulatus Bath (53.1 +/- 2.9 per thousand) and N. europaea (-23.4 +/- 7.2 per thousand) and nitrite reduction by N. europaea (4.6 +/- 1.4 per thousand) were significantly different (ANOVA, f((2,35)) = 279.98, p = 0). Although the nitrogen isotope value of the substrate, hydroxylamine, was similar in both cultures, the observed fractionation (delta(15)N) associated with N(2)O production via hydroxylamine oxidation by M. capsulatus Bath and N. europaea (-2.3 and 26.0 per thousand, respectively) provided evidence that differences in isotopic fractionation were associated with these two organisms. The site preferences in this study are the first measured values for isolated microbial processes. The differences in site preference are significant and indicate that isotopomers provide a basis for apportioning biological processes producing N(2)O.

Diversity of the particulate methane monooxygenase gene in methanotrophic samples from different rice field soils in China and the Philippines

Methanotrophic bacteria play a crucial role in regulating the emission of CH4 from rice fields into the atmosphere. We investigated the CH4 oxidation activity together with the diversity of methanotrophic bacteria in ten rice field soils from different geographic locations. Upon incubation of aerated soil slurries under 7% CH4, rates of CH4 oxidation increased after a lag phase of 1-4 days and reached values of 3-10 micromol d(-1) g-dw(-1) soil. The methanotrophic community was assayed by retrieval of the pmoA gene which encodes the a subunit of the particulate methane monooxygenase. After extraction of DNA from actively CH4-oxidizing soil samples and PCR-amplification of the pmoA, the community was analyzed by Denaturant Gradient Gel Electrophoresis (DGGE) and Terminal Restriction Fragment Length Polymorphism (T-RFLP). DGGE bands were excised, the pmoA re-amplified, sequenced and the encoded amino acid sequence comparatively analyzed by phylogenetic treeing. The analyses allowed the detection of pmoA sequences related to the following methanotrophic genera: the type-I methanotrophs Methylobacter, Methylomicrobium, Methylococcus and Methylocaldum, and the type-II methanotrophs Methylocystis and Methylosinus. T-RFLP analysis detected a similar diversity, but type-II pmoA more frequently than DGGE. All soils but one contained type-II in addition to type-I methanotrophs. Type-I Methylomonas was not detected at all. Different combinations of methanotrophic genera were detected in the different soils. However, there was no obvious geographic pattern of the distribution of methanotrophs.

Occurrence and activity of Archaea in aerated activated sludge wastewater treatment plants

The occurrence, distribution and activity of archaeal populations within two aerated, activated sludge wastewater treatment systems, one treating domestic waste and the second treating mixed domestic and industrial wastewater, were investigated by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR)-amplified ribosomal RNA gene fragments and process measurements. In the plant receiving mixed industrial and domestic waste the archaeal populations found in the mixed liquor were very similar to those in the influent sewage, though a small number of DGGE bands specific to the mixed liquor were identified. In contrast, the activated sludge treating principally domestic waste harboured distinct archaeal populations associated with the mixed liquor that were not prevalent in the influent sewage. We deduce that the Archaea in the plant treating mixed wastewater were derived principally from the influent, whereas those in the plant treating solely domestic waste were actively growing in the treatment plant. Archaeal 16S rRNA gene sequences related to the Methanosarcinales, Methanomicrobiales and the Methanobacteriales were detected. Methanogenesis was measured in activated sludge samples incubated under oxic and anoxic conditions, demonstrating that the methanogens present in both activated sludge plants were active only in anoxic incubations. The relatively low rates of methanogenesis measured indicated that, although active, the methanogens play a minor role in carbon turnover in activated sludge.

Population dynamics of type I and II methanotrophic bacteria in rice soils

Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse-active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere. Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of type I and type II methanotrophs with depth and in relation to rice roots. Methanotroph population fluctuations occurred primarily within the top 0-2 cm of soil, where methanotroph cells increased by a factor of 3-5 over the flooded rice-growing season. The results indicate that rice roots and rhizospheres were less important than the soil-water interface in supporting methanotroph growth. Both type I and type II methanotrophs were abundant throughout the year. However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth.

Ammonia-oxidizing bacteria: a model for molecular microbial ecology

The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important in the global cycling of nitrogen. These organisms are unique in their ability to use the conversion of ammonia to nitrite as their sole energy source. Because of the importance of this functional group of bacteria, understanding of their ecology and physiology has become a subject of intense research over recent years. The monophyletic nature of these bacteria in terrestrial environments has facilitated molecular biological approaches in studying their ecology, and progress in this field has been rapid. The ammonia-oxidizing bacteria of the beta-subclass Proteobacteria have become somewhat of a model system within molecular microbial ecology, and this chapter reviews recent progress in our knowledge of their distribution, diversity, and ecology.

Methane production and oxidation in an anoxic rice soil as influenced by inorganic redox species

The effects of addition of inorganic redox substances (species of NO3-, Mn4+, Fe3+, and SO4(2-)) on methane production and oxidation in anoxic rice (Oryza sativa L.) soil samples were examined. Sulfate was the most inhibitory for methane production followed by Fe3+, NO3-, and Mn4+, in that order. Addition of rice straw at a rate of 1% (w/w) as a carbon source to increase the electron donor to the electron acceptor ratio did not completely alleviate the inhibitory effects of redox species on methane production. Interestingly, laboratory incubation studies showed that addition of MnO2 and K2SO4 enhanced aerobic methane oxidation in soil samples held at 60% water holding capacity. The suspensions of pretreated soil samples with different redox species, when tested for their ability to oxidize methane in soil solution equivalent medium supplemented with respective redox species under aerobic and anaerobic conditions showed differential effects of redox species. Nitrate and Fe3+ stimulated methane oxidation under anaerobic conditions and retarded it under aerobic conditions. Manganese(IV) ion retarded methane oxidation under anaerobic conditions, but enhanced it under aerobic conditions. However, SO4(2-) stimulated methane oxidation in soil solution equivalent medium under both aerobic and anaerobic conditions.

Methane oxidation and the competition for oxygen in the rice rhizosphere

A mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. In flooded rice paddies these methanotrophs compete for available O(2) with other types of bacteria. Soil incubation studies and most-probable-number (MPN) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. MPN counts of methanotrophs showed large spatial and temporal variability. The most abundant methanotrophs (a Methylocystis sp.) and heterotrophs (a Pseudomonas sp. and a Rhodococcus sp.) were isolated and characterized. Growth dynamics of these bacteria under carbon and oxygen limitations are presented. Theoretical calculations based on measured growth dynamics show that methanotrophs were only able to outcompete heterotrophs at low oxygen concentrations (frequently < 5 microM). The oxygen concentration at which methanotrophs won the competition from heterotrophs did not depend on methane concentration, but it was highly affected by organic carbon concentrations in the paddy soil. Methane oxidation was severely inhibited at high acetate concentrations. This is in accordance with competition experiments between Pseudomonas spp. and Methylocystis spp. carried out at different oxygen and carbon concentrations. Likely, methane oxidation mainly occurs at microaerophilic and low-acetate conditions and thus not directly at the root surface. Acetate and oxygen concentrations in the rice rhizosphere are in the critical range for methane oxidation, and a high variability in methane oxidation rates is thus expected.