Nitrous oxide production and methane oxidation by different ammonia-oxidizing bacteria

Low Bacterial Diversity and Nitrate Levels in Cores from Deep Boreholes in Pristine Karst

This study investigates the nitrate gradients within the deep biosphere of karst carbonate rocks and their resident microbiota. Samples were taken from borehole cores at depths down to 350 m below the surface, collected during geological site investigations for proposed railway tunnels and analysed using 16S rRNA amplicon sequencing. 16S rRNA amplicon sequencing analysis revealed relatively low microbial diversity, which can serve as a reliable indicator of the pristine nature of deep karst. However, some local hotspots of diversity are independent of depth. Pseudomonadota dominated the samples, with Gammaproteobacteria dominating at the class level. The low nitrate content in deep karst, in contrast to higher values closer to the surface, serves as an additional marker of its undisturbed and unpolluted status. Based on the prediction of functional profiles from 16S rRNA sequencing data, nitrates remain low due to indigenous microbial denitrification and assimilatory nitrate reduction. Pathways related to nitrogen fixation, ammonia assimilation, and nitrification were not confirmed. When elevated nitrate levels are observed in karst, they are most probably related to anthropogenic activities. Environmental factors other than depth and nitrate content play an important role in shaping bacterial communities.

Nitrous Oxide Emissions from Nitritation Reactors under Hypersaline Conditions

This study focuses on nitrous oxide (N2O) emissions during hypersaline (4 % salinity) nitritation in continuously fed and mixed fixed bed reactors. In the presence of high concentrations of nitrite and ammonium, the percent yield of N2O emissions from ammonium removed decreased with increasing dissolved oxygen (DO). However, N2O production continued even at a high DO of 15 mg/L. Bulk ammonium concentration (not ammonia) was found to be the main controlling factor for N2O emissions under high and low DO during both nitritation and nitrification. Reducing bulk ammonium concentrations below 1 mg N/L in the nitritation reactor under both high and low DO conditions resulted in a reduction of N2O emissions of approximately 90 %. Under full nitrification and low DO, reducing nitrite concentrations below 0.3 mg N/L resulted in a 60 % reduction in N2O emissions. Similar results were observed in a low salinity reactor.

Isotopic assessment of soil N2O emission from a sub-tropical agricultural soil under varying N-inputs

Nitrogen fertilizers result in high crop productivity but also enhance the emission of N₂O, an environmentally harmful greenhouse gas. Only approximately a half of the applied nitrogen is utilized by crops and the rest is either vaporized, leached, or lost as NO, N₂O and N₂ via soil microbial activity. Thus, improving the nitrogen use efficiency of cropping systems has become a global concern. Factors such as types and rates of fertilizer application, soil texture, moisture level, pH, and microbial activity/diversity play important roles in N₂O production. Here, we report the results of N₂O production from a set of chamber experiments on an acidic sandy-loam agricultural soil under varying levels of an inorganic N-fertilizer, urea. Stable isotope technique was employed to determine the effect of increasing N-fertilizer levels on N₂O emissions and identify the microbial processes involved in fertilizer N-transformation that give rise to N₂O. We monitored the isotopic changes in both substrate (ammonium and nitrate) and the product N₂O during the entire course of the incubation experiments. Peak N₂O emissions of 122 ± 98 μg N₂O-N m^-2 h^-1, 338 ± 49 μg N₂O-N m^-2 h^-1 and 739 ± 296 μg N₂O-N m^-2 h^-1 were observed for urea application rate of 40, 80, and 120 μg N g^-1. The duration of emissions also increased with urea levels. The concentration and isotopic compositions of the substrates and product showed time-bound variation. Combining the observations of isotopic effects in δ¹⁵N, δ¹⁸O, and ¹⁵N site preference, we inferred co-occurrence of several microbial N₂O production pathways with nitrification and/or fungal denitrification as the dominant processes responsible for N₂O emissions. Besides this, dominant signatures of bacterial denitrification were observed in a second N₂O emission pulse in intermediate urea-N levels. Signature of N₂O consumption by reduction could be traced during declining emissions in treatment with high urea level.

N2O Emissions from Two Austrian Agricultural Catchments Simulated with an N2O Submodule Developed for the SWAT Model

Nitrous oxide (N2O) is a potent greenhouse gas stemming mainly from nitrogen (N)-fertilizer application. It is challenging to quantify N2O emissions from agroecosystems because of the dearth of measured data and high spatial variability of the emissions. The eco-hydrological model SWAT (Soil and Water Assessment Tool) simulates hydrological processes and N fluxes in a catchment. However, the routine for simulating N2O emissions is still missing in the SWAT model. A submodule was developed based on the outputs of the SWAT model to partition N2O from the simulated nitrification by applying a coefficient (K2) and also to isolate N2O from the simulated denitrification (N2O + N2) with a modified semi-empirical equation. The submodule was applied to quantify N2O emissions and N2O emission factors from selected crops in two agricultural catchments by using NH4NO3 fertilizer and the combination of organic N and NO3− fertilizer as N input data. The setup with the combination of organic N and NO3− fertilizer simulated lower N2O emissions than the setup with NH4NO3 fertilizer. When the water balance was simulated well (absolute percentage error <11%), the impact of N fertilizer application on the simulated N2O emissions was captured. More research to test the submodule with measured data is needed.

Identification of primary effecters of N2O emissions from full-scale biological nitrogen removal systems using random forest approach

Wastewater treatment plants (WWTPs) have long been recognized as point sources of N₂O, a potent greenhouse gas and ozone-depleting agent. Multiple mechanisms, both biotic and abiotic, have been suggested to be responsible for N₂O production from WWTPs, with basis on extrapolation from laboratory results and statistical analyses of metadata collected from operational full-scale plants. In this study, random forest (RF) analysis, a machine-learning approach for feature selection from highly multivariate datasets, was adopted to investigate N₂O production mechanism in activated sludge tanks of WWTPs from a novel perspective. Standardized measurements of N₂O effluxes coupled with exhaustive metadata collection were performed at activated sludge tanks of three biological nitrogen removal WWTPs at different times of the year. The multivariate datasets were used as inputs for RF analyses. Computation of the permutation variable importance measures returned biomass-normalized dissolved inorganic carbon concentration (DIC·VSS^-1) and specific ammonia oxidation activity (sOUR_AOB) as the most influential parameters determining N₂O emissions from the aerated zones (or phases) of activated sludge bioreactors. For the anoxic tanks, dissolved-organic-carbon-to-NO₂^-/NO₃^- ratio (DOC·(NO₂^--N + NO₃^--N)^-1) was singled out as the most influential. These data analysis results clearly indicate disparate mechanisms for N₂O generation in the oxic and anoxic activated sludge bioreactors, and provide evidences against significant contributions of N₂O carryover across different zones or phases or niche-specific microbial reactions, with aerobic NH₃/NH₄⁺ oxidation to NO₂^- and anoxic denitrification predominantly responsible from aerated and anoxic zones or phases of activated sludge bioreactors, respectively.

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N₂ O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N₂ O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N₂ O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N₂ O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N₂ O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N₂ O emissions.

Gross N transformation rates and related N2O emissions in Chinese and UK agricultural soils

The properties of agricultural soils in various regions of the world are variable and can have a significant but poorly understood impact on soil nitrogen (N) transformations and nitrous oxide (N₂O) emissions. For this reason, we undertook a study of gross N transformations and related N₂O emissions in contrasting agricultural soils from China and the UK. Seven Chinese and three UK agricultural soils were collected for study using a ¹⁵N tracing approach. The soil pH ranged from 5.4 to 8.7, with three acidic soils collected from Jinjing, Lishu and Boghall; one neutral soil collected from Changshu, and the other six alkaline soils collected from Quzhou, Zhangye, Changwu, Jinzhong, Boxworth and Stetchworth. Our results showed that the main N transformation processes were oxidation of ammonium (NH₄⁺) to nitrate (NO₃^-) (O_NH4), and mineralization of organic N to NH₄⁺. The gross autotrophic nitrification rates calculated in the three acidic soils were between 0.25 and 4.15 mg N kg^-1 d^-1, which were significantly lower (p < 0.05) than those in the remaining neutral and alkaline soils ranging from 6.94 to 14.43 mg N kg^-1 d^-1. Generally, soil pH was positively correlated (p < 0.001) with gross autotrophic nitrification rate and cumulative N₂O emissions, indicating that soil pH was an important factor regulating autotrophic nitrification and N₂O emissions. There was also a significant positive correlation between the gross autotrophic nitrification rate and cumulative N₂O emissions, highlighting the importance of this process for producing N₂O emissions in these agricultural soils under aerobic conditions. Gross NH₄⁺ immobilization rates were very low in most soils except for the Jinjing soil with the lowest pH. In conclusion, the gross autotrophic nitrification rates and related N₂O emissions were controlled by soil pH irrespectively of the soil's origin in these agricultural soils.

Arbuscular mycorrhizal fungi reduce nitrous oxide emissions from N2 O hotspots

Nitrous oxide (N2 O) is a potent, globally important, greenhouse gas, predominantly released from agricultural soils during nitrogen (N) cycling. Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with two-thirds of land plants, providing phosphorus and/or N in exchange for carbon. As AMF acquire N, it was hypothesized that AMF hyphae may reduce N2 O production. AMF hyphae were either allowed (AMF) or prevented (nonAMF) access to a compartment containing an organic matter and soil patch in two independent microcosm experiments. Compartment and patch N2 O production was measured both before and after addition of ammonium and nitrate. In both experiments, N2 O production decreased when AMF hyphae were present before inorganic N addition. In the presence of AMF hyphae, N2 O production remained low following ammonium application, but increased in the nonAMF controls. By contrast, negligible N2 O was produced following nitrate application to either AMF treatment. Thus, the main N2 O source in this system appeared to be via nitrification, and the production of N2 O was reduced in the presence of AMF hyphae. It is hypothesized that AMF hyphae may be outcompeting slow-growing nitrifiers for ammonium. This has significant global implications for our understanding of soil N cycling pathways and N2 O production.

The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions

High and low rates of ammonium supply are believed to favour ammonia-oxidising bacteria (AOB) and archaea (AOA), respectively. Although their contrasting affinities for ammonium are suggested to account for these differences, the influence of ammonia concentration on AOA and AOB has not been tested under environmental conditions. In addition, while both AOB and AOA contribute to nitrous oxide (N₂O) emissions from soil, N₂O yields (N₂O-N produced per NO₂^--N generated from ammonia oxidation) of AOA are lower, suggesting lower emissions when AOA dominate ammonia oxidation. This study tested the hypothesis that ammonium supplied continuously at low rates is preferentially oxidised by AOA, with lower N₂O yield than expected for AOB-dominated processes. Soil microcosms were supplied with water, urea or a slow release, urea-based fertiliser and 1-octyne (inhibiting only AOB) was applied to distinguish AOA and AOB activity and associated N₂O production. Low ammonium supply, from mineralisation of organic matter, or of the fertiliser, led to growth, ammonia oxidation and N₂O production by AOA only, with low N₂O yield. High ammonium supply, from free urea within the fertiliser or after urea addition, led to growth of both groups, but AOB-dominated ammonia oxidation was associated with twofold greater N₂O yield than that dominated by AOA. This study therefore demonstrates growth of both AOA and AOB at high ammonium concentration, confirms AOA dominance during low ammonium supply and suggests that slow release or organic fertilisers potentially mitigate N₂O emissions through differences in niche specialisation and N₂O production mechanisms in AOA and AOB.

Greenhouse gases emission from the sewage draining rivers

Carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) concentration, saturation and fluxes in rivers (Beitang drainage river, Dagu drainage rive, Duliujianhe river, Yongdingxinhe river and Nanyunhe river) of Tianjin city (Haihe watershed) were investigated during July and October in 2014, and January and April in 2015 by static headspace gas chromatography method and the two-layer model of diffusive gas exchange. The influence of environmental variables on greenhouse gases (GHGs) concentration under the disturbance of anthropogenic activities was discussed by Spearman correlative analysis and multiple stepwise regression analysis. The results showed that the concentration and fluxes of CO₂, CH₄ and N₂O were seasonally variable with >winter>fall>summer, spring>summer>winter>fall and summer>spring>winter>fall for concentrations and spring>summer>fall>winter, spring>summer>winter>fall and summer>spring>fall>winter for fluxes respectively. The GHGs concentration and saturation were higher in comprehensively polluted river sites and lower in lightly polluted river sites. The three GHGs emission fluxes in two sewage draining rivers of Tianjin were clearly higher than those of other rivers (natural rivers) and the spatial variation of CH₄ was more obvious than the others. CO₂ and N₂O air-water interface emission fluxes of the sewage draining rivers in four seasons were about 1.20-2.41 times and 1.13-3.12 times of those in the natural rivers. The CH₄ emission fluxes of the sewage draining rivers were 3.09 times in fall to 10.87 times in spring of those in the natural rivers in different season. The wind speed, water temperature and air temperature were related to GHGs concentrations. Nitrate and nitrite (NO₃^-+NO₂^--N) and ammonia (NH₄⁺-N) were positively correlated with CO₂ concentration and CH₄ concentration; and dissolved oxygen (DO) concentration was negatively correlated with CH₄ concentration and N₂O concentration. The effect of human activities on carbon and nitrogen cycling in river is great.

Abiotic Conversion of Extracellular NH2OH Contributes to N2O Emission during Ammonia Oxidation

Abiotic processes involving the reactive ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NH₂OH) for N₂O production have been indicated recently. The latter process would require the availability of substantial amounts of free NH₂OH for chemical reactions during ammonia (NH₃) oxidation, but little is known about extracellular NH₂OH formation by the different clades of ammonia-oxidizing microbes. Here we determined extracellular NH₂OH concentrations in culture media of several ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete ammonia oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation under standard cultivation conditions. NH₂OH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NH₂OH was also formed by the comammox enrichment during NH₃ oxidation. This enrichment exhibited the largest NH₂OH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%). The maximum proportions of NH₄⁺ converted to N₂O via extracellular NH₂OH during incubation, estimated on the basis of NH₂OH abiotic conversion rates, were 0.12%, 0.08%, and 0.14% for AOB, AOA, and Ca. Nitrospira inopinata, respectively, and were consistent with published NH₄⁺:N₂O conversion ratios for AOB and AOA.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO₂ that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO₂ leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO₂ levels (sample groups I and II) and one control site with low CO₂ content (group III). Samples from sites with elevated CO₂ had pH ranging from 6.2 to 4.5 and samples from the low-CO₂ control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO₂ content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO₂ conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO₂ leakage from geologic storage sites.

Kinetics of NH3 -oxidation, NO-turnover, N2 O-production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers

Ammonia oxidising bacteria (AOB) are thought to emit more nitrous oxide (N₂ O) than ammonia oxidising archaea (AOA), due to their higher N₂ O yield under oxic conditions and denitrification in response to oxygen (O₂ ) limitation. We determined the kinetics of growth and turnover of nitric oxide (NO) and N₂ O at low cell densities of Nitrosomonas europaea (AOB) and Nitrosopumilus maritimus (AOA) during gradual depletion of TAN (NH₃  + NH4+) and O₂ . Half-saturation constants for O₂ and TAN were similar to those determined by others, except for the half-saturation constant for ammonium in N. maritimus (0.2 mM), which is orders of magnitudes higher than previously reported. For both strains, cell-specific rates of NO turnover and N₂ O production reached maxima near O₂ half-saturation constant concentration (2-10 μM O₂ ) and decreased to zero in response to complete O₂ -depletion. Modelling of the electron flow in N. europaea demonstrated low electron flow to denitrification (≤1.2% of the total electron flow), even at sub-micromolar O₂ concentrations. The results corroborate current understanding of the role of NO in the metabolism of AOA and suggest that denitrification is inconsequential for the energy metabolism of AOB, but possibly important as a route for dissipation of electrons at high ammonium concentration.

Acidification Enhances Hybrid N2O Production Associated with Aquatic Ammonia-Oxidizing Microorganisms

Ammonia-oxidizing microorganisms are an important source of the greenhouse gas nitrous oxide (N₂O) in aquatic environments. Identifying the impact of pH on N₂O production by ammonia oxidizers is key to understanding how aquatic greenhouse gas fluxes will respond to naturally occurring pH changes, as well as acidification driven by anthropogenic CO₂. We assessed N₂O production rates and formation mechanisms by communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in a lake and a marine environment, using incubation-based nitrogen (N) stable isotope tracer methods with ¹⁵N-labeled ammonium (¹⁵NH4+) and nitrite (¹⁵NO2−), and also measurements of the natural abundance N and O isotopic composition of dissolved N₂O. N₂O production during incubations of water from the shallow hypolimnion of Lake Lugano (Switzerland) was significantly higher when the pH was reduced from 7.54 (untreated pH) to 7.20 (reduced pH), while ammonia oxidation rates were similar between treatments. In all incubations, added NH4+ was the source of most of the N incorporated into N₂O, suggesting that the main N₂O production pathway involved hydroxylamine (NH₂OH) and/or NO2− produced by ammonia oxidation during the incubation period. A small but significant amount of N derived from exogenous/added ¹⁵NO2− was also incorporated into N₂O, but only during the reduced-pH incubations. Mass spectra of this N₂O revealed that NH4+ and ¹⁵NO2− each contributed N equally to N₂O by a “hybrid-N₂O” mechanism consistent with a reaction between NH₂OH and NO2−, or compounds derived from these two molecules. Nitrifier denitrification was not an important source of N₂O. Isotopomeric N₂O analyses in Lake Lugano were consistent with incubation results, as ¹⁵N enrichment of the internal N vs. external N atoms produced site preferences (25.0–34.4‰) consistent with NH₂OH-dependent hybrid-N₂O production. Hybrid-N₂O formation was also observed during incubations of seawater from coastal Namibia with ¹⁵NH4+ and NO2−. However, the site preference of dissolved N₂O here was low (4.9‰), indicating that another mechanism, not captured during the incubations, was important. Multiplex sequencing of 16S rRNA revealed distinct ammonia oxidizer communities: AOB dominated numerically in Lake Lugano, and AOA dominated in the seawater. Potential for hybrid N₂O formation exists among both communities, and at least in AOB-dominated environments, acidification may accelerate this mechanism.

Nitrous Oxide Production at a Fully Covered Wastewater Treatment Plant: Results of a Long-Term Online Monitoring Campaign

The nitrous oxide emissions of the Viikinmäki wastewater treatment plant were measured in a 12 month online monitoring campaign. The measurements, which were conducted with a continuous gas analyzer, covered all of the unit operations of the advanced wastewater-treatment process. The relation between the nitrous oxide emissions and certain process parameters, such as the wastewater temperature, influent biological oxygen demand, and ammonium nitrogen load, was investigated by applying online data obtained from the process-control system at 1 min intervals. Although seasonal variations in the measured nitrous oxide emissions were remarkable, the measurement data indicated no clear relationship between these emissions and seasonal changes in the wastewater temperature. The diurnal variations of the nitrous oxide emissions did, however, strongly correlate with the alternation of the influent biological oxygen demand and ammonium nitrogen load to the aerated zones of the activated sludge process. Overall, the annual nitrous oxide emissions of 168 g/PE/year and the emission factor of 1.9% of the influent nitrogen load are in the high range of values reported in the literature but in very good agreement with the results of other long-term online monitoring campaigns implemented at full-scale wastewater-treatment plants.

Diversity, structure, and size of N(2)O-producing microbial communities in soils--what matters for their functioning?

Nitrous oxide (N(2)O) is mainly generated via nitrification and denitrification processes in soils and subsequently emitted into the atmosphere where it causes well-known radiative effects. How nitrification and denitrification are affected by proximal and distal controls has been studied extensively in the past. The importance of the underlying microbial communities, however, has been acknowledged only recently. Particularly, the application of molecular methods to study nitrifiers and denitrifiers directly in their habitats enabled addressing how environmental factors influence the diversity, community composition, and size of these functional groups in soils and whether this is of relevance for their functioning and N(2)O production. In this review, we summarize the current knowledge on community-function interrelationships. Aerobic nitrification (ammonia oxidation) and anaerobic denitrification are clearly under different controls. While N(2)O is an obligatory intermediate in denitrification, its production during ammonia oxidation depends on whether nitrite, the end product, is further reduced. Moreover, individual strains vary strongly in their responses to environmental cues, and so does N(2)O production. We therefore conclude that size and structure of both functional groups are relevant with regard to production and emission of N(2)O from soils. Diversity affects on function, however, are much more difficult to assess, as it is not resolved as yet how individual nitrification or denitrification genotypes are related to N(2)O production. More research is needed for further insights into the relation of microbial communities to ecosystem functions, for instance, how the actively nitrifying or denitrifying part of the community may be related to N(2)O emission.

From the affinity constant to the half-saturation index: understanding conventional modeling concepts in novel wastewater treatment processes

The "affinity constant" (KS) concept is applied in wastewater treatment models to incorporate the effect of substrate limitation on process performance. As an increasing number of wastewater treatment processes rely on low substrate concentrations, a proper understanding of these so-called constants is critical in order to soundly model and evaluate emerging treatment systems. In this paper, an in-depth analysis of the KS concept has been carried out, focusing on the different physical and biological phenomena that affect its observed value. By structuring the factors influencing half-saturation indices (newly proposed nomenclature) into advectional, diffusional and biological, light has been shed onto some of the apparent inconsistencies present in the literature. Particularly, the importance of non-ideal mixing as a source of variability between observed KS values in different systems has been illustrated. Additionally, discussion on the differences existent between substrates that affect half-saturation indices has been carried out; it has been shown that the observed KS for some substrates will reflect transport or biological limitations more than others. Finally, potential modeling strategies that could alleviate the shortcomings of the KS concept have been provided. These could be of special importance when considering the evaluation and design of emerging wastewater treatment processes.

Effect of aeration regime on N₂O emission from partial nitritation-anammox in a full-scale granular sludge reactor

N₂O emission from wastewater treatment plants is high of concern due to the strong environmental impact of this greenhouse gas. Good understanding of the factors affecting the emission and formation of this gas is crucial to minimize its impact. This study addressed the investigation of the N₂O emission dynamics in a full-scale one-stage granular sludge reactor performing partial nitritation-anammox (PNA) operated at a N-loading of 1.75 kg NH₄⁺-N m⁻³ d⁻¹. A monitoring campaign was conducted, gathering on-line data of the N₂O concentration in the off-gas of the reactor as well as of the ammonium and nitrite concentrations in the liquid phase. The N₂O formation rate and the liquid N₂O concentration profile were calculated from the gas phase measurements. The mean (gaseous) N₂O-N emission obtained was 2.0% of the total incoming nitrogen during normal reactor operation. During normal operation of the reactor under variable aeration rate, intense aeration resulted in higher N₂O emission and formation than during low aeration periods (mean N₂O formation rate of 0.050 kg N m⁻³ d⁻¹ for high aeration and 0.029 kg N m⁻³ d⁻¹ for low aeration). Accumulation of N₂O in the liquid phase was detected during low aeration periods and was accompanied by a relatively lower ammonium conversion rate, while N₂O stripping was observed once the aeration was increased. During a dedicated experiment, gas recirculation without fresh air addition into the reactor led to the consumption of N₂O, while accumulation of N₂O was not detected. The transition from a prolonged period without fresh air addition and with little recirculation to enhanced aeration with fresh air addition resulted in the highest N₂O formation (0.064 kg N m⁻³ d⁻¹). The results indicate that adequate aeration control may be used to minimize N₂O emissions from PNA reactors.

Bacteria on leaves: a previously unrecognised source of N2O in grazed pastures

Nitrous oxide (N2O) emissions from grazed pastures are a product of microbial transformations of nitrogen and the prevailing view is that these only occur in the soil. Here we show this is not the case. We have found ammonia-oxidising bacteria (AOB) are present on plant leaves where they produce N2O just as in soil. AOB (Nitrosospira sp. predominantly) on the pasture grass Lolium perenne converted 0.02-0.42% (mean 0.12%) of the oxidised ammonia to N2O. As we have found AOB to be ubiquitous on grasses sampled from urine patches, we propose a 'plant' source of N2O may be a feature of grazed grassland.

Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea

Soil emissions are largely responsible for the increase of the potent greenhouse gas nitrous oxide (N2O) in the atmosphere and are generally attributed to the activity of nitrifying and denitrifying bacteria. However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N2O production from soil is unclear as is the mechanism by which they produce it. Here we investigate the potential of Nitrososphaera viennensis, the first pure culture of AOA from soil, to produce N2O and compare its activity with that of a marine AOA and an ammonia-oxidizing bacterium (AOB) from soil. N. viennensis produced N2O at a maximum yield of 0.09% N2O per molecule of nitrite under oxic growth conditions. N2O production rates of 4.6±0.6 amol N2O cell(-1) h(-1) and nitrification rates of 2.6±0.5 fmol NO2(-) cell(-1) h(-1) were in the same range as those of the AOB Nitrosospira multiformis and the marine AOA Nitrosopumilus maritimus grown under comparable conditions. In contrast to AOB, however, N2O production of the two archaeal strains did not increase when the oxygen concentration was reduced, suggesting that they are not capable of denitrification. In (15)N-labeling experiments we provide evidence that both ammonium and nitrite contribute equally via hybrid N2O formation to the N2O produced by N. viennensis under all conditions tested. Our results suggest that archaea may contribute to N2O production in terrestrial ecosystems, however, they are not capable of nitrifier-denitrification and thus do not produce increasing amounts of the greenhouse gas when oxygen becomes limiting.

N2O emission from nitrogen removal via nitrite in oxic-anoxic granular sludge sequencing batch reactor

Bionitrification is considered to be a potential source of nitrous oxide (N2O) emissions, which are produced as a by-product during the nitrogen removal process. To investigate the production of N2O during the process of nitrogen removal via nitrite, a granular sludge was studied using a lab-scale sequence batch reactor operated with real-time control. The total production of N2O generated during the nitrification and denitrification processes were 1.724 mg/L and 0.125 mg/L, respectively, demonstrating that N2O is produced during both processes, with the nitrification phase generating larger amount. In addition, due to the N2O-N mass/oxidized ammonia mass ratio, it can be concluded that nitrite accumulation has a positive influence on N2O emissions. Results obtained from PCR-DGGE analysis demonstrate that a specific Nitrosomonas microorganism is related to N2O emission.

Sensitivity of methanotrophic community structure, abundance, and gene expression to CH4 and O2 in simulated landfill biocover soil

Pressure on mitigating CH4 emission in landfill requires better understanding of methanotrophs in landfill biocovers. Most previous studies focused on CH4 as the sole substrate. This study aims to understand the sensitivity of methanotrophs to both substrates CH4 and O2 concentrations in landfill biocovers. The estimated CH4 oxidation rates (4.66-98.7 × 10(-16) mol cell(-1) h(-1)) were evidently higher than the previous reports, suggesting that activity of methanotrophs was enhanced with both the increasing of O2 and CH4 concentrations. Denaturing gradient gel electrophoresis based on the amplification of pmoA genes suggested that methanotrophs were more sensitive to CH4 than O2. Quantification of methanotrophs using pmoA- and mmoX-targeted real-time polymerase chain reaction showed that Mbac and Mcoc as well as Mcys groups were significantly dominant. Mbac group with pmoA gene transcription was dominant. Results indicate that CH4 mitigation would have higher potential by increasing O2 at appropriate CH4 concentrations.

Trait-based representation of biological nitrification: model development, testing, and predicted community composition

Trait-based microbial models show clear promise as tools to represent the diversity and activity of microorganisms across ecosystem gradients. These models parameterize specific traits that determine the relative fitness of an "organism" in a given environment, and represent the complexity of biological systems across temporal and spatial scales. In this study we introduce a microbial community trait-based modeling framework (MicroTrait) focused on nitrification (MicroTrait-N) that represents the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) using traits related to enzyme kinetics and physiological properties. We used this model to predict nitrifier diversity, ammonia (NH(3)) oxidation rates, and nitrous oxide (N(2)O) production across pH, temperature, and substrate gradients. Predicted nitrifier diversity was predominantly determined by temperature and substrate availability, the latter was strongly influenced by pH. The model predicted that transient N(2)O production rates are maximized by a decoupling of the AOB and NOB communities, resulting in an accumulation and detoxification of nitrite to N(2)O by AOB. However, cumulative N(2)O production (over 6 month simulations) is maximized in a system where the relationship between AOB and NOB is maintained. When the reactions uncouple, the AOB become unstable and biomass declines rapidly, resulting in decreased NH(3) oxidation and N(2)O production. We evaluated this model against site level chemical datasets from the interior of Alaska and accurately simulated NH(3) oxidation rates and the relative ratio of AOA:AOB biomass. The predicted community structure and activity indicate (a) parameterization of a small number of traits may be sufficient to broadly characterize nitrifying community structure and (b) changing decadal trends in climate and edaphic conditions could impact nitrification rates in ways that are not captured by extant biogeochemical models.

Influences of Chemical Fertilizers and a Nitrification Inhibitor on Greenhouse Gas Fluxes in a Corn (Zea mays L.) Field in Indonesia

The influences of chemical fertilizers and a nitrification inhibitor on greenhouse gas fluxes (N(2)O and CH(4)) in a corn field in Indonesia were investigated using a closed chamber. Plots received 45+45 kg-N ha(-1) of nitrogen fertilizer by split applications of urea, a single application of controlled-release fertilizer (CRF-LP30) or urea+dicyandiamide (DCD; a nitrification inhibitor), and no nitrogen application (control). Cumulative amounts of N(2)O emitted from the field were 1.87, 1.70, 1.06, and 0.42 kg N(2)O-N ha(-1) season(-1) for the urea, CRF-LP30, urea+DCD, and control plots, respectively. The application of urea+DCD reduced the emission of N(2)O by 55.8% compared with urea. On the other hand, the soil acted as a sink for CH(4) in the CRL-LP30, control, and urea+DCD plots with value of -0.09, -0.06 and -0.06 kg CH(4)-C ha(-1) season(-1), respectively. When the viability of AOB (ammonia-oxidizing bacteria) and NOB (nitrite-oxidizing bacteria) were monitored, AOB numbers were correlated with the N(2)O emission. These results suggest that 1) there is a potential for reducing emissions of N(2)O by applying DCD, and 2) corn fields treated with CRF or urea+DCD can act as a sink for CH(4) in a tropical humid climate.

N2O production pathways in the subtropical acid forest soils in China

To date, N(2)O production pathways are poorly understood in the humid subtropical and tropical forest soils. A (15)N-tracing experiment was carried out under controlled laboratory conditions to investigate the processes responsible for N(2)O production in four subtropical acid forest soils (pH<4.5) in China. The results showed that denitrification was the main source of N(2)O emission in the subtropical acid forest soils, being responsible for 56.1%, 53.5%, 54.4%, and 55.2% of N(2)O production, in the GC, GS, GB, and TC soils, respectively, under aerobic conditions (40%-52%WFPS). The heterotrophic nitrification (recalcitrant organic N oxidation) accounted for 27.3%-41.8% of N(2)O production, while the contribution of autotrophic nitrification was little in the studied subtropical acid forest soils. The ratios of N(2)O-N emission from total nitrification (heterotrophic+autotrophic nitrification) were higher than those in most previous references. The soil with the lowest pH and highest organic-C content (GB) had the highest ratio (1.63%), suggesting that soil pH-organic matter interactions may exist and affect N(2)O product ratios from nitrification. The ratio of N(2)O-N emission from heterotrophic nitrification varied from 0.02% to 25.4% due to soil pH and organic matter. Results are valuable in the accurate modeling of N2O production in the subtropical acid forest soils and global budget.

Turnover of carbohydrate-rich vegetal matter during microaerobic composting and after amendment in soil

We propose that microaerobic composting (MC) can be used to decompose vegetal matter with a short turnover time and large carbon (C) recycling potential. We used a novel method for measuring the degree of fragmentation of water-insoluble acid-soluble (WIAS) polysaccharides as a proxy in tracking their relative degree of degradation (i.e., fragmentation endpoint index). Oak leaves and food scrap processed by MC reached a fragmentation end point within 2 weeks. After amending the MC products into soil, the half-life of the polysaccharide residues was ~6-7 times longer (~100-110 days) than that measured during MC. The main products given up during MC were volatile organic acids (VOAs), alcohols and soluble carbohydrates in the compost tea, and CO(2). These products accounted for about 2% of the initial carbon in the feedstock. Very small amounts of VOAs, particularly butyric acid, were formed in the amended soil. Based on a residence time of materials in fermentors of 2 weeks, a ~100-m(3) capacity MC facility could process 2,000-4,000 metric tons of vegetable matter amended in ten hectares of arable land per year.

Field application of nitrogen and phenylacetylene to mitigate greenhouse gas emissions from landfill cover soils: effects on microbial community structure

Landfills are large sources of CH(4), but a considerable amount of CH(4) can be removed in situ by methanotrophs if their activity can be stimulated through the addition of nitrogen. Nitrogen can, however, lead to increased N(2)O production. To examine the effects of nitrogen and a selective inhibitor on CH(4) oxidation and N(2)O production in situ, 0.5 M of NH(4)Cl and 0.25 M of KNO(3), with and without 0.01% (w/v) phenylacetylene, were applied to test plots at a landfill in Kalamazoo, MI from 2007 November to 2009 July. Nitrogen amendments stimulated N(2)O production but had no effect on CH(4) oxidation. The addition of phenylacetylene stimulated CH(4) oxidation while reducing N(2)O production. Methanotrophs possessing particulate methane monooxygenase and archaeal ammonia-oxidizers (AOAs) were abundant. The addition of nitrogen reduced methanotrophic diversity, particularly for type I methanotrophs. The simultaneous addition of phenylacetylene increased methanotrophic diversity and the presence of type I methanotrophs. Clone libraries of the archaeal amoA gene showed that the addition of nitrogen increased AOAs affiliated with Crenarchaeal group 1.1b, while they decreased with the simultaneous addition of phenylacetylene. These results suggest that the addition of phenylacetylene with nitrogen reduces N(2)O production by selectively inhibiting AOAs and/or type II methanotrophs.

Phylogenetic diversity of gene sequences isolated from the rumen as analysed using a self-organizing map (SOM)

AIMS

To determine the origins of DNA sequences isolated from the rumen microbial ecosystem using a self-organizing map (SOM).

METHODS AND RESULTS

DNA sequences other than 16S small subunit ribosomal RNA (SSU rRNA) gene sequences that were detected from the rumen were analysed by the SOM method reported by Abe et al. [2000, Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene 365, 27-34]. Because query sequences positioned by SOM were scattered on the master drawing of SOM, it was suggested that many DNA sequences isolated from the rumen were collected from a broad range of micro-organisms. Although the results obtained by SOM were similar to those obtained by the neighbour-joining (NJ) method, SOM was able to presume the phylotypes of the query sequences without information about the 16S SSU rRNA gene sequences and homology searches, and to reveal existence of novel micro-organisms deduced to be cellulolytic bacteria, archaea and methanotrophic bacterium.

CONCLUSIONS

As the SOM method defined phylotypes of unreported rumen micro-organisms, it is presumed that these phylotypes would be involved in rumen fermentation in cooperation with known rumen micro-organisms. Moreover, it is demonstrated that SOM is a useful tool for affiliating DNA sequences, which have no matches in databases.

SIGNIFICANCE AND IMPACT OF STUDY

Through SOM analysis, a better means of identifying rumen micro-organisms and estimating their roles in rumen function was provided.

Mechanisms and specific directionality of autotrophic nitrous oxide and nitric oxide generation during transient anoxia

The overall goal of this study was to determine the molecular and metabolic responses of chemostat cultures of model nitrifying bacteria to imposition of and recovery from transient anoxic conditions. Based on the study, a specific directionality in nitrous oxide (N(2)O) and nitric oxide (NO) production was demonstrated. N(2)O production was only observed during recovery to aerobic conditions after a period of anoxia and correlated positively with the degree of ammonia accumulation during anoxia. NO, on the other hand, was emitted mainly under anoxia. The production of NO was linked to a major imbalance in the expression of the nitrite reductase gene, which was overexpressed during transient anoxia. In contrast, genes coding for ammonia and hydroxylamine oxidation and nitric oxide reduction were generally under-expressed during transient anoxia. These results are different from the observed parallel expression and activity of nitrite and nitric oxide reductase in heterotrophic bacteria subjected to transient oxygen cycling. Unlike NO, the production of N(2)O could not be solely correlated to gene expression patterns and likely involved responses at the enzyme activity or metabolic levels. Based on experimental data, the propensity of the nitrifying cultures for N(2)O production is related to a shift in their metabolism from a low specific activity (q < q(max)) toward the maximum specific activity (q(max)).

Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers

Methane and nitrous oxide are both potent greenhouse gasses, with global warming potentials approximately 25 and 298 times that of carbon dioxide. A matrix of soil microcosms was constructed with landfill cover soils collected from the King Highway Landfill in Kalamazoo, Michigan and exposed to geochemical parameters known to affect methane consumption by methanotrophs while also examining their impact on biogenic nitrous oxide production. It was found that relatively dry soils (5% moisture content) along with 15 mg NH (4) (+) (kg soil)(-1) and 0.1 mg phenylacetylene(kg soil)(-1) provided the greatest stimulation of methane oxidation while minimizing nitrous oxide production. Microarray analyses of pmoA showed that the methanotrophic community structure was dominated by Type II organisms, but Type I genera were more evident with the addition of ammonia. When phenylacetylene was added in conjunction with ammonia, the methanotrophic community structure was more similar to that observed in the presence of no amendments. PCR analyses showed the presence of amoA from both ammonia-oxidizing bacteria and archaea, and that the presence of key genes associated with these cells was reduced with the addition of phenylacetylene. Messenger RNA analyses found transcripts of pmoA, but not of mmoX, nirK, norB, or amoA from either ammonia-oxidizing bacteria or archaea. Pure culture analyses showed that methanotrophs could produce significant amounts of nitrous oxide, particularly when expressing the particulate methane monooxygenase (pMMO). Collectively, these data suggest that methanotrophs expressing pMMO played a role in nitrous oxide production in these microcosms.

Nitrogen as a regulatory factor of methane oxidation in soils and sediments

The oxidation of methane by methane-oxidising microorganisms is an important link in the global methane budget. Oxic soils are a net sink while wetland soils are a net source of atmospheric methane. It has generally been accepted that the consumption of methane in upland as well as lowland systems is inhibited by nitrogenous fertiliser additions. Hence, mineral nitrogen (i.e. ammonium/nitrate) has conceptually been treated as a component with the potential to enhance emission of methane from soils and sediments to the atmosphere, and results from numerous studies have been interpreted as such. Recently, ammonium-based fertilisation was demonstrated to stimulate methane consumption in rice paddies. Growth and activity of methane-consuming bacteria in microcosms as well as in natural rice paddies was N limited. Analysing the available literature revealed that indications for N limitation of methane consumption have been reported in a variety of lowland soils, upland soils, and sediments. Obviously, depriving methane-oxidising bacteria of a suitable source of N hampers their growth and activity. However, an almost instantaneous link between the presence of mineral nitrogen (i.e. ammonium, nitrate) and methane-oxidising activity, as found in rice soils and culture experiments, requires an alternative explanation. We propose that switching from mineral N assimilation to the fixation of molecular nitrogen may explain this phenomenon. However, there is as yet no experimental evidence for any mechanism of instantaneous stimulation, since most studies have assumed that nitrogenous fertiliser is inhibitory of methane oxidation in soils and have focused only on this aspect. Nitrogen as essential factor on the sink side of the global methane budget has been neglected, leading to erroneous interpretation of methane emission dynamics, especially from wetland environments. The purpose of this minireview is to summarise and balance the data on the regulatory role of nitrogen in the consumption of methane by soils and sediments, and thereby stimulate the scientific community to embark on experiments to close the existing gap in knowledge.

Impact of nitrate-enhanced leachate recirculation on gaseous releases from a landfill bioreactor cell

This study evaluates the impact of nitrate injection on a full scale landfill bioreactor through the monitoring of gaseous releases and particularly N(2)O emissions. During several weeks, we monitored gas concentrations in the landfill gas collection system as well as surface gas releases with a series of seven static chambers. These devices were directly connected to a gas chromatograph coupled to a flame ionisation detector and an electron capture detector (GC-FID/ECD) placed directly on the field. Measurements were performed before, during and after recirculation of raw leachate and nitrate-enhanced leachate. Raw leachate recirculation did not have a significant effect on the biogas concentrations (CO(2), CH(4) and N(2)O) in the gas extraction network. However, nitrate-enhanced leachate recirculation induced a marked increase of the N(2)O concentrations in the gas collected from the recirculation trench (100-fold increase from 0.2 ppm to 23 ppm). In the common gas collection system however, this N(2)O increase was no more detectable because of dilution by gas coming from other cells or ambient air intrusion. Surface releases through the temporary cover were characterized by a large spatial and temporal variability. One automated chamber gave limited standard errors over each experimental period for N(2)O releases: 8.1 +/- 0.16 mg m(-2) d(-1) (n = 384), 4.2 +/- 0.14 mg m(-2) d(-1) (n = 132) and 1.9 +/- 0.10 mg m(-2) d(-1) (n = 49), during, after raw leachate and nitrate-enhanced leachate recirculation, respectively. No clear correlation between N(2)O gaseous surface releases and recirculation events were evidenced. Estimated N(2)O fluxes remained in the lower range of what is reported in the literature for landfill covers, even after nitrate injection.

Electrons, life and the evolution of Earth's oxygen cycle

The biogeochemical cycles of H, C, N, O and S are coupled via biologically catalysed electron transfer (redox) reactions. The metabolic processes responsible for maintaining these cycles evolved over the first ca 2.3 Ga of Earth's history in prokaryotes and, through a sequence of events, led to the production of oxygen via the photobiologically catalysed oxidation of water. However, geochemical evidence suggests that there was a delay of several hundred million years before oxygen accumulated in Earth's atmosphere related to changes in the burial efficiency of organic matter and fundamental alterations in the nitrogen cycle. In the latter case, the presence of free molecular oxygen allowed ammonium to be oxidized to nitrate and subsequently denitrified. The interaction between the oxygen and nitrogen cycles in particular led to a negative feedback, in which increased production of oxygen led to decreased fixed inorganic nitrogen in the oceans. This feedback, which is supported by isotopic analyses of fixed nitrogen in sedimentary rocks from the Late Archaean, continues to the present. However, once sufficient oxygen accumulated in Earth's atmosphere to allow nitrification to out-compete denitrification, a new stable electron 'market' emerged in which oxygenic photosynthesis and aerobic respiration ultimately spread via endosymbiotic events and massive lateral gene transfer to eukaryotic host cells, allowing the evolution of complex (i.e. animal) life forms. The resulting network of electron transfers led a gas composition of Earth's atmosphere that is far from thermodynamic equilibrium (i.e. it is an emergent property), yet is relatively stable on geological time scales. The early coevolution of the C, N and O cycles, and the resulting non-equilibrium gaseous by-products can be used as a guide to search for the presence of life on terrestrial planets outside of our Solar System.

Intensive management affects composition of betaproteobacterial ammonia oxidizers in turfgrass systems

Turfgrass is a highly managed ecosystem subject to frequent fertilization, mowing, irrigation, and application of pesticides. Turf management practices may create a perturbed environment for ammonia oxidizers, a key microbial group responsible for nitrification. To elucidate the long-term effects of turf management on these bacteria, we assessed the composition of betaproteobacterial ammonia oxidizers in a chronosequence of turfgrass systems (i.e., 1, 6, 23, and 95 years old) and the adjacent native pines by using both 16S rRNA and amoA gene fragments specific to ammonia oxidizers. Based on the Shannon-Wiener diversity index of denaturing gradient gel electrophoresis patterns and the rarefaction curves of amoA clones, turf management did not change the relative diversity and richness of ammonia oxidizers in turf soils as compared to native pine soils. Ammonia oxidizers in turfgrass systems comprised a suite of phylogenetic clusters common to other terrestrial ecosystems. Nitrosospira clusters 0, 2, 3, and 4; Nitrosospira sp. Nsp65-like sequences; and Nitrosomonas clusters 6 and 7 were detected in the turfgrass chronosequence with Nitrosospira clusters 3 and 4 being dominant. However, both turf age and land change (pine to turf) effected minor changes in ammonia oxidizer composition. Nitrosospira cluster 0 was observed only in older turfgrass systems (i.e., 23 and 95 years old); fine-scale differences within Nitrosospira cluster 3 were seen between native pines and turf. Further investigations are needed to elucidate the ecological implications of the compositional differences.

Functional robustness and gene pools of a wastewater nitrification reactor: comparison of dispersed and intact biofilms when stressed by low oxygen and low pH

The functional robustness of biofilms in a wastewater nitrification reactor, and the gene pools therein, were investigated. Nitrosomonas and Nitrosospira spp. were present in similar amounts (cloning-sequencing of ammonia-oxidizing bacteria 16S rRNA gene), and their estimated abundance (1.1 x 10(9) cells g(-1) carrier material, based on amoA gene real-time PCR) was sufficient to explain the observed nitrification rates. The biofilm also had a diverse community of heterotrophic denitrifying bacteria (cloning-sequencing of nirK). Anammox 16S rRNA genes were detected, but not archaeal amoA. Dispersed biofilms (DB) and intact biofilms (IB) were incubated in gas-tight reactors at different pH levels (4.5 and 5.5 vs. 6.5) while monitoring O(2) depletion and concentrations of NO, N(2)O and N(2) in the headspace. Nitrification was severely reduced by suboptimal O(2) concentrations (10-100 microM) and low pH (IB was more acid tolerant than DB), but the N(2)O/NO(3)(-) product ratio of nitrification remained low (<10(-3)). The NO(2)(-) concentrations during nitrification were generally 10 times higher in DB than in IB. Transient NO and N(2)O accumulation at the onset of denitrification was 10-10(3) times higher in DB than in IB (depending on the pH). The contrasting performance of DB and IB suggests that the biofilm structure, with anoxic/micro-oxic zones, helps to stabilize functions during anoxic spells and low pH.

A review of stable isotope techniques for N2O source partitioning in soils: recent progress, remaining challenges and future considerations

Nitrous oxide is produced in soil during several processes, which may occur simultaneously within different micro-sites of the same soil. Stable isotope techniques have a crucial role to play in the attribution of N(2)O emissions to different microbial processes, through estimation (natural abundance, site preference) or quantification (enrichment) of processes based on the (15)N and (18)O signatures of N(2)O determined by isotope ratio mass spectrometry. These approaches have the potential to become even more powerful when linked with recent developments in secondary isotope mass spectrometry, with microbial ecology, and with modelling approaches, enabling sources of N(2)O to be considered at a wide range of scales and related to the underlying microbiology. Such source partitioning of N(2)O is inherently challenging, but is vital to close the N(2)O budget and to better understand controls on the different processes, with a view to developing appropriate management practices for mitigation of N(2)O. In this respect, it is essential that as many of the contributing processes as possible are considered in any study aimed at source attribution, as mitigation strategies for one process may not be appropriate for another. To aid such an approach, here the current state of the art is critically examined, remaining challenges are highlighted, and recommendations are made for future direction.

Production of NO, N2O and N2 by extracted soil bacteria, regulation by NO2(-) and O2 concentrations

The oxygen control of denitrification and its emission of NO/N2O/N2 was investigated by incubation of Nycodenz-extracted soil bacteria in an incubation robot which monitors O2, NO, N2O and N2 concentrations (in He+O2 atmosphere). Two consecutive incubations were undertaken to determine (1) the regulation of denitrification by O2 and NO2(-) during respiratory O2 depletion and (2) the effects of re-exposure to O2 of cultures with fully expressed denitrification proteome. Early denitrification was only detected (as NO and N2O) at <or=80 microM O2 in treatments with NO2(-), and the rates were three orders of magnitude lower than the rates observed after oxygen depletion (with N2 as the primary product). When re-exposed to O2, the cultures continued to denitrify (8-55% of the rates during the foregoing anoxic phase), but its main product was N2O. The N2O reductase activity recovered as oxygen was being depleted. The results suggest that expression of the denitrifying proteome may result in significant subsequent aerobic denitrification, and this has profound implications for the understanding and modelling of denitrification and N2O emission. Short anoxic spells caused by transient flooding during rainfall, could lead to subsequent unbalanced aerobic denitrification, in which N2O is a major end product.

PCR profiling of ammonia-oxidizer communities in acidic soils subjected to nitrogen and sulphur deposition

Communities of ammonia-oxidizing bacteria (AOB) were characterized in two acidic soil sites experimentally subjected to varying levels of nitrogen and sulphur deposition. The sites were an acidic spruce forest soil in Deepsyke, Southern Scotland, with low background deposition, and a nitrogen-saturated upland grass heath in Pwllpeiran, North Wales. Betaproteobacterial ammonia-oxidizer 16S rRNA and ammonia monooxygenase (amoA) genes were analysed by cloning, sequencing and denaturing gradient gel electrophoresis (DGGE). DGGE profiles of amoA and 16S rRNA gene fragments from Deepsyke soil in 2002 indicated no effect of nitrogen deposition on AOB communities, which contained both Nitrosomonas europaea and Nitrosospira. In 2003, only Nitrosospira could be detected, and no amoA sequences could be retrieved. These results indicate a decrease in the relative abundance of AOB from the year 2002 to 2003 in Deepsyke soil, which may be the result of the exceptionally low rainfall in spring 2003. Nitrosospira-related sequences from Deepsyke soil grouped in all clusters, including cluster 1, which typically contains only sequences from marine environments. In Pwllpeiran soil, 16S rRNA gene libraries were dominated by nonammonia oxidizers and no amoA sequences were detectable. This indicates that autotrophic AOB play only a minor role in these soils even at high nitrogen deposition.

Long-term warming effects on root morphology, root mass distribution, and microbial activity in two dry tundra plant communities in northern Sweden

Effects of warming on root morphology, root mass distribution and microbial activity were studied in organic and mineral soil layers in two alpine ecosystems over>10 yr, using open-top chambers, in Swedish Lapland. Root mass was estimated using soil cores. Washed roots were scanned and sorted into four diameter classes, for which variables including root mass (g dry matter (g DM) m(-2)), root length density (RLD; cm cm(-3) soil), specific root length (SRL; m g DM(-1)), specific root area (SRA; m2 kg DM(-1)), and number of root tips m(-2) were determined. Nitrification (NEA) and denitrification enzyme activity (DEA) in the top 10 cm of soil were measured. Soil warming shifted the rooting zone towards the upper soil organic layer in both plant communities. In the dry heath, warming increased SRL and SRA of the finest roots in both soil layers, whereas the dry meadow was unaffected. Neither NEA nor DEA exhibited differences attributable to warming. Tundra plants may respond to climate change by altering their root morphology and mass while microbial activity may be unaffected. This suggests that carbon may be incorporated in tundra soils partly as a result of increases in the mass of the finer roots if temperatures rise.

Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707

The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H(+)-dependent F(0)F(1) type, one Na(+)-dependent V type).

Nitrogen removal in a wastewater treatment plant through biofilters: nitrous oxide emissions during nitrification and denitrification

In order to estimate N(2)O emissions from immersed biofilters during nitrogen removal in tertiary treatments at urban wastewater treatment plants (WWTPs), a fixed culture from the WWTP of "Seine Centre" (Paris conurbation) was subjected to lab-scale batch experiments under various conditions of oxygenation and a gradient of methanol addition. The results show that during nitrification, N(2)O emissions are positively related to oxygenation (R (2) = 0.99). However, compared to the rates of ammonium oxidation, the percentage of emitted N(2)O is greater when oxygenation is low (0.5-1 mgO(2) L(-1)), representing up to 1% of the oxidized ammonium (0.4% on average). During denitrification, the N(2)O emission reaches a significant peak when the quantity of methanol allows denitrification of between 66% and 88%. When methanol concentrations lead to a denitrification of close to 100%, the flows of N(2)O are much lower and represent on average 0.2% of the reduced nitrate. By considering these results, we can estimate, the emissions of N(2)O during nitrogen removal, at the "Seine Centre" WWTP, to approximately 38 kgN-N(2)O day(-1).

Transcriptome of a Nitrosomonas europaea mutant with a disrupted nitrite reductase gene (nirK)

Global gene expression was compared between the Nitrosomonas europaea wild type and a nitrite reductase-deficient mutant using a genomic microarray. Forty-one genes were differentially regulated between the wild type and the nirK mutant, including the nirK operon, genes for cytochrome c oxidase, and seven iron uptake genes. Relationships of differentially regulated genes to the nirK mutant phenotype are discussed.

Nitrous oxide emissions from secondary activated sludge in nitrifying conditions of urban wastewater treatment plants: effect of oxygenation level

In order to better understand the mechanisms of N(2)O emissions from nitrifying activated sludge of urban WWTPs, sludge from the Valenton plant (Paris conurbation) are subjected to lab-scale batch experiments under various conditions of oxygenation. The results show that the highest N(2)O emissions (7.1 microgN-N(2)OgSS(-1) h(-1) in average) occur at a dissolved oxygen (DO) concentration of around 1mgO(2)L(-1). These high emissions at low oxygenation (from 0.1 to 2 mg O(2)L(-1)) are due to two processes: autotrophic nitrifier denitrification and heterotrophic denitrification. Nitrifier denitrification always dominates, representing from 58% to 83% of the N(2)O production. This N(2)O production originating from nitrifying activated sludge becomes 8 times higher when nitrite is added at a DO of 1 mg O(2)L(-1); a decrease is observed both at higher and lower oxygenation. Heterotrophic denitrification represents less than 50% of the N(2)O production, decreasing from 42% to 17% when oxygenation increases from 0.1 to 2 mg O(2) L(-1). We show that ammonium oxidizing bacteria (AOB) can shift to nitrifier denitrification when oxygen is depleted in the environments including in the WWTPs, nitrite then plays the role of oxygen as the final electron acceptor. As opposed to what happens in nitrification, the end products of nitrifier denitrification are gaseous forms of nitrogen, where N(2)O is not negligible compared to N(2). Overall, N(2)O emissions represent 0.1-0.4% of oxidized NH(4)(+), depending on the oxygenation level. N(2)O emissions would range from 0.11 to 0.42 TN-N(2)O day(-1) for a tertiary treatment of the Paris wastewater effluents, consisting exclusively of activated sludge nitrification.

Role of nitrogen oxides in the metabolism of ammonia-oxidizing bacteria

Ammonia-oxidizing bacteria (AOB) can use oxygen and nitrite as electron acceptors. Nitrite reduction by Nitrosomonas is observed under three conditions: (i) hydrogen-dependent denitrification, (ii) anoxic ammonia oxidation with nitrogen dioxide (NO(2)) and (iii) NO(x)-induced aerobic ammonia oxidation. NO(x) molecules play an important role in the conversion of ammonia and nitrite by AOB. Absence of nitric oxide (NO), which is generally detectable during ammonia oxidation, severely impairs ammonia oxidation by AOB. The lag phase of recovery of aerobic ammonia oxidation was significantly reduced by NO(2) addition. Acetylene inhibition tests showed that NO(2)-dependent and oxygen-dependent ammonia oxidation can be distinguished. Addition of NO(x) increased specific activity of ammonia oxidation, growth rate and denitrification capacity. Together, these findings resulted in a hypothetical model on the role of NO(x) in ammonia oxidation: the NO(x) cycle.

Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway

Nitrous oxide (N(2)O) emission from soils is a major contributor to the atmospheric loading of this potent greenhouse gas. It is thought that autotrophic ammonia oxidizing bacteria (AOB) are a significant source of soil-derived N(2)O and a denitrification pathway (i.e. reduction of NO(2) (-) to NO and N(2)O), so-called nitrifier denitrification, has been demonstrated as a N(2)O production mechanism in Nitrosomonas europaea. It is thought that Nitrosospira spp. are the dominant AOB in soil, but little information is available on their ability to produce N(2)O or on the existence of a nitrifier denitrification pathway in this lineage. This study aims to characterize N(2)O production and nitrifier denitrification in seven strains of AOB representative of clusters 0, 2 and 3 in the cultured Nitrosospira lineage. Nitrosomonas europaea ATCC 19718 and ATCC 25978 were analysed for comparison. The aerobically incubated test strains produced significant (P < 0.001) amounts of N(2)O and total N(2)O production rates ranged from 2.0 amol cell(-1) h(-1), in Nitrosospira tenuis strain NV12, to 58.0 amol cell(-1) h(-1), in N. europaea ATCC 19718. Nitrosomonas europaea ATCC 19718 was atypical in that it produced four times more N(2)O than the next highest producing strain. All AOB tested were able to carry out nitrifier denitrification under aerobic conditions, as determined by production of (15)N-N(2)O from applied (15)N-NO(2) (-). Up to 13.5% of the N(2)O produced was derived from the exogenously applied (15)N-NO(2) (-). The results suggest that nitrifier denitrification could be a universal trait in the betaproteobacterial AOB and its potential ecological significance is discussed.

Distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundances

The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 +/- 1.2 per thousand, 32.5 +/- 0.6 per thousand, and 35.6 +/- 1.4 per thousand for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 +/- 4.2 per thousand) was similar to that produced during hydroxylamine oxidation (33.5 +/- 1.2 per thousand) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 +/- 1.7 per thousand), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens (-0.6 +/- 1.9 per thousand and -0.5 +/- 1.9 per thousand, respectively) were similar to those during nitrate reduction (-0.5 +/- 1.9 per thousand and -0.5 +/- 0.6 per thousand, respectively), indicating no influence of either substrate on site preference. Site preferences of approximately 33 per thousand and approximately 0 per thousand are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O.