End Product Of Denitrification Research Articles

The ratio of denitrification end-products were influenced by soil pH and clay content across different texture classes in Oklahoma soils

Nitrous oxide (N2O) is a potent greenhouse gas that contributes to stratospheric ozone depletion and global climate change. Soil denitrification has two potential end-products, N2O and dinitrogen (N2), and the ratio of these end-products (N2O:(N2O+N2) or the N2O ratio) is controlled by various factors. This study aims to quantify the influence of soil pH on the ratio of denitrification end-products in Oklahoma soils with different soil textures. Six natural grassland soils encompassing three distinct soil textures were incubated in the laboratory under natural and modified pH with an overall tested pH ranging from 2 to 10. Denitrification end-products were measured in the laboratory using the acetylene inhibition technique and further estimated using a process-based biogeochemical model. Both the laboratory and model results showed that soil pH and texture influenced the ratio of the denitrification end-products. Generally, as soil pH increased the N2O ratio decreased, although both lab and model results indicated that this relationship was not linear. Soil texture may have an indirect effect on the N2O ratio, as two soils of the same texture could have different N2O ratios. However, clay percentage of the soil did show a linear positive correlation with the N2O ratio, suggesting components of soil texture may be more influential than others. Overall, soil pH was a controlling factor in the ratio of denitrification end-products and the newly observed nonlinear relationship warrants further study, particularly when considering its effects in different soil textures.

The effect of antecedent soil moisture conditions on soil nitrous oxide and dinitrogen dynamics after wetting: An intact soil core study

Ruminant excreta urinary‑nitrogen (N) deposited onto pasture soil generates inorganic-N concentrations in excess of the pasture's immediate requirements. Consequently, nitrous oxide (N2O) and dinitrogen (N2) may be emitted from the urine-affected soil via denitrification. Soil moisture plays a key role in determining the end-product of denitrification. Although the effects of soil moisture and drying-wetting cycles on soil N2O production have been widely studied using sieved soils in a controlled environment, these experiments may not reflect the actual conditions in the field due to the lack of plant cover and the disturbed soil structure. To address this an experiment was performed using intact soil cores (7.5 cm depth), with pasture plants present, under controlled environmental conditions (20 °C, 8 h of light per day). The 15N flux method was used to investigate how antecedent soil moisture affected soil N2O production and consumption in a pasture soil after wetting with a nitrate (NO3−) solution. The results showed that the antecedent dry condition (25 % WFPS, Dp/Do = 0.1783) increased the magnitude of the N2O flux peak after the soil was wetted (75 % WFPS, Dp/Do = 0.006) when compared to antecedent wet conditions (50 % WFPS, Dp/Do = 0.0503). There were no differences in the denitrification and nitrification related functional gene abundances between the two antecedent conditions post-wetting, indicating that the effect was not regulated by microbial changes but by the intensity of the “Birch effect” induced by soil wetting. The N2O reduction related gene (nosZII) abundance decreased after wetting with the NO3− solution, indicating a suppression effect on N2O consumption from the NO3− applied that overrode the potential “Birch effect” on N2 emission. The results of the study indicate that rewetting of antecedent dry soil increase N2O emissions but not N2 emissions when the soil NO3− concentration is high.

Contradictory Impacts of Nitrate on the Dissimilatory Arsenate-Respiring Prokaryotes-Induced Reductive Mobilization of Arsenic from Contaminated Sediments: Mechanism Insight from Metagenomic and Functional Analyses.

Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be a key impetus of the reductive dissolution of solid-phase arsenic. However, little is known about the interaction between nitrate and DARPs so far. In this study, we showed that nitrate either inhibited or promoted the DARP population-catalyzed reductive mobilization of As in sediments. Metagenomic analysis of the microbial communities in the microcosms after seven days of As release assays suggested that microbes mainly consisted of: Type-I DARPs having potential to reduce NO3- into NO2- and Type-II DARPs having potential to reduce NO3- to NH4+. We further isolated two cultivable DARPs, Neobacillus sp. A01 and Paenibacillus sp. A02, which represent Type-I and -II DARPs, respectively. We observed that nitrate suppressed A01-mediated release of As(III) but promoted A02-mediated release of As(III). Furthermore, we demonstrated that this observation was due to the fact that nitrite, the end product of incomplete denitrification by Type-I DARPs, suppressed the arrA gene expression per cell and growth of all DARPs, whereas ammonium, the end product of dissimilatory nitrate reduction to ammonium (DNRA) by Type-II DARPs, enhanced the arrA gene expression per cell and significantly promoted the growth of all DARPs. These findings suggest that the actual effects of nitrate on DARP population-catalyzed reductive mobilization of arsenic, largely depend on the ratio of Type-I to Type-II DARPs in sediments.

Denitrification contributes to N2O emission in paddy soils.

Denitrification is vital to nitrogen removal and N2O release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying mechanism of N2O emission from denitrification in paddy soils is yet to be elucidated. In this study, the potential N2O emission rate, enzymatic activity for N2O production and reduction, gene abundance, and community composition during denitrification were investigated using the 15N isotope tracer technique combined with slurry incubation, enzymatic activity detection, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. Results of incubation experiments showed that the average potential N2O emission rates were 0.51 ± 0.20 μmol⋅N⋅kg-1⋅h-1, which constituted 2.16 ± 0.85% of the denitrification end-products. The enzymatic activity for N2O production was 2.77-8.94 times than that for N2O reduction, indicating an imbalance between N2O production and reduction. The gene abundance ratio of nir to nosZ from qPCR results further supported the imbalance. Results of metagenomic analysis showed that, although Proteobacteria was the common phylum for denitrification genes, other dominant community compositions varied for different denitrification genes. Gammaproteobacteria and other phyla containing the norB gene without nosZ genes, including Actinobacteria, Planctomycetes, Desulfobacterota, Cyanobacteria, Acidobacteria, Bacteroidetes, and Myxococcus, may contribute to N2O emission from paddy soils. Our results suggest that denitrification is highly modular, with different microbial communities collaborating to complete the denitrification process, thus resulting in an emission estimation of 13.67 ± 5.44 g N2O⋅m-2⋅yr-1 in surface paddy soils.

Autochthonous organic matter promotes DNRA and suppresses N2O production in sediments of the coastal Baltic Sea

Coastal environments are nitrogen (N) removal hot spots, which regulate the amount of land-derived N reaching the open sea. However, mixing between freshwater and seawater creates gradients of inorganic N and bioavailable organic matter, which affect N cycling. In this study, we compare nitrate reduction processes between estuary and offshore archipelago environments in the coastal Baltic Sea. Denitrification rates were similar in both environments, despite lower nitrate and carbon concentrations in the offshore archipelago. However, DNRA (dissimilatory nitrate reduction to ammonium) rates were higher at the offshore archipelago stations, with a higher proportion of autochthonous carbon. The production rate and concentrations of the greenhouse gas nitrous oxide (N2O) were higher in the estuary, where nitrate concentrations and allochthonous carbon inputs are higher. These results indicate that the ratio between nitrate and autochthonous organic carbon governs the balance between N-removing denitrification and N-recycling DNRA, as well as the end-product of denitrification. As a result, a significant amount of the N removed in the estuary is released as N2O, while the offshore archipelago areas are characterized by efficient internal recycling of N. Our results challenge the current understanding of the role of these regions as filters of land-to-sea transfer of N.

Inundation time mediates denitrification end products and carbon limitation in constructed floodplains of an agricultural stream

Inundation time mediates denitrification end products and carbon limitation in constructed floodplains of an agricultural stream

Looking back to look ahead: a vision for soil denitrification research.

Denitrification plays a critical role in regulating ecosystem nutrient availability and anthropogenic reactive nitrogen (N) production. Its importance has inspired an increasing number of studies, yet it remains the most poorly constrained term in terrestrial ecosystem N budgets. We censused the peer-reviewed soil denitrification literature (1975-2015) to identify opportunities for future studies to advance our understanding despite the inherent challenges in studying the process. We found that only one-third of studies reported estimates of both nitrous oxide (N2 O) and dinitrogen (N2 ) production fluxes, often the dominant end products of denitrification, while the majority of studies reported only net N2 O fluxes or denitrification potential. Of the 236 studies that measured complete denitrification to N2 , 49% used the acetylene inhibition method, 84% were conducted in the laboratory, 81% were performed on surface soils (0-20cm depth), 75% were located in North America and Europe, and 78% performed treatment manipulations, mostly of N, carbon, or water. To improve understanding of soil denitrification, we recommend broadening access to technologies for new methodologies to measure soil N2 production rates, conducting more studies in the tropics and on subsoils, performing standardized experiments on unmanipulated soils, and using more precise terminology to refer to measured process rates (e.g., net N2 O flux or denitrification potential). To overcome the greater challenges in studying soil denitrification, we envision coordinated research efforts based on standard reporting of metadata for all soil denitrification studies, standard protocols for studies contributing to a Global Denitrification Research Network, and a global consortium of denitrification researchers to facilitate sharing ideas, resources, and to provide mentorship for researchers new to the field.

Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils.

Antibiotics in soils may affect the structure and function of microbial communities. In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N2O) and dinitrogen (N2) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N2O and N2 production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing. Abundance and taxonomic composition of bacteria carrying two genotypes of N2O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR and metabolic inference. Soil samples treated with tetracycline generated 12 times more N2O, but N2 production was reduced by 84% compared to the control. In parallel with greater N2O production, we observed an increase in the fungi:bacteria ratio and a significant decrease in the abundance of nosZ-II carrying bacteria; nosZ-I abundance was not affected. NosZ-II-carrying Bacillus spp. (Firmicutes) and Anaeromyxobacter spp. (Deltaproteobacteria) were particularly susceptible to tetracycline and may serve as a crucial N2O sink in grassland soils. Our study indicates that the introduction of antibiotics to agroecosystems may promote higher N2O production due to the inhibitory effects on nosZ-II-carrying communities.

Open-channel measurement of denitrification in a large lowland river

Denitrification is considered to be the most important pathway removing nitrogen from terrestrial and freshwater ecosystems. However, field studies that quantify this process under in situ conditions are sparse, especially in large rivers. Here, we measured N2, the end product of denitrification, directly in the water column of a large 8th order lowland river (Elbe, Germany) using N2/Ar ratios measured by Membrane Inlet Mass Spectrometry (MIMS). Denitrification was calculated according to the open-channel two-station approach based on Lagrangian sampling along a 580 km long, mostly free flowing river section. Gas exchange was computed by several empirical equations to bound uncertainty in air–water exchange and the resulting fluxes were used to estimate ranges in N2-production. In summer 2011 and spring 2012, we found slight but distinct N2 super saturations in the river water averaging 2.8 and 3.5 µM, respectively. Denitrification rates averaged 18 and 13 mg N m− 2 h− 1 for summer 2011 and spring 2012, respectively. On an annual cycle this corresponds to a nitrogen removal of 10,000 t N year− 1 that is 10% of the total N inputs along the studied river section. These results show that large rivers can remove large amounts of nitrogen during downstream transport and demonstrate that the open-channel N2 method provides a valuable tool to study in situ denitrification not only in small, but also in large rivers.

Nitrous oxide (N2O)-reducing denitrifier-inoculated organic fertilizer mitigates N2O emissions from agricultural soils

The only known sink for nitrous oxide (N2O) is biochemical reduction to dinitrogen (N2) by N2O reductase (N2OR). We hypothesized that the application of N2O-reducing denitrifier-inoculated organic fertilizer could enhance soil N2O consumption while the disruption of nosZ genes could result in inactivation of N2O consumption. To test such hypotheses, a denitrifier-inoculated granular organic fertilizer was applied to both soil microcosms and fields. Of 41 denitrifier strains, 38 generated 30N2 in the end products of denitrification (30N2 and 46N2O) after the addition of Na15NO3 in culture condition, indicating their high N2O reductase activities. Of these 41 strains, 18 were screened in soil microcosms after their inoculation into the organic fertilizer, most of which were affiliated with Azospirillum and Herbaspirillum. These 18 strains were nutritionally starved to improve their survival in soil, and 14 starved and/or non-starved strains significantly decreased N2O emissions in soil microcosms. However, the N2O emission had not been decreased in soil microcosms after inoculating with a nosZ gene-disruptive strain, suggesting that N2O reductase activity might be essential for N2O consumption. Although the decrease of N2O was not significant at field scales, the application of organic fertilizer inoculated with Azospirillum sp. TSH100 and Herbaspirillum sp. UKPF54 had decreased the N2O emissions by 36.7% in Fluvisol and 23.4% in Andosol in 2014, but by 21.6% in Andosol in 2015 (H. sp. UKPF54 only). These results suggest that the application of N2O-reducing denitrifier-inoculated organic fertilizer may enhance N2O consumption or decrease N2O emissions in agricultural soils.

Long term farming systems affect soils potential for N2O production and reduction processes under denitrifying conditions

N2O is a potent greenhouse gas with an atmospheric lifetime of 114 years which also contributes to ozone layer destruction. Mitigating N2O emissions is especially challenging to the agricultural sector that is responsible for the majority of anthropogenic N2O release. In order to develop effective mitigation strategies, a detailed understanding of drivers for N2O production and reduction in agriculturally managed soils is needed. Denitrification is recognized as one of the most important source processes for N2O emissions from soils. However, the last step in denitrification, the reduction of N2O to N2 is the only known sink for N2O in soil. Although the impact of single parameters on denitrification is quite well documented, there is still a knowledge gap when it comes to the impact of complex farming systems on N2O production and reduction. In this experiment, we incubated soil samples from the DOK long term field trial in Therwil/Switzerland comparing organic (BIOORG) and conventional (CONMIN) farming systems with an a non-fertilized control (NOFERT). Soil samples were incubated under 90% WFPS after fertilization with NH415NO3 equivalent to a moderate fertilization event in the field with 40 kg N ha−1. In order to assess soil's potential for N2O production and reduction, we combined direct measurements of denitrification end products N2O and N2 with molecular analysis of functional denitrifying communities involved in NO2− and N2O reduction on DNA and mRNA levels. In order to monitor N cycling processes under the chosen conditions, stable isotope tracing was employed to quantify nitrification and NO3− consumption rates. Results revealed increased NO3− consumption and greatest potential for N2O emissions in BIOORG as a result of increased soil organic carbon contents. Production of N2 was similar in BIOORG and CONMIN and significantly lower in NOFERT, most likely due to significantly decreased pH inhibiting N2O reduction. This caused the greatest N2O/(N2O + N2) ratios in NOFERT (0.88 ± 0.02) followed by BIOORG (0.79 ± 0.01) and CONMIN (0.68 ± 0.02) (p < 0.001). Lowest N2O/(N2O + N2) ratios in CONMIN were reflected by lowest N2O emissions and coincided with elevated nosZ transcript copies in the beginning of incubation. Although highest N2O emissions in BIOORG were detected, the incubation setup cannot directly be translated to field conditions. Nevertheless, our results emphasize that farming system induced changes on soil geochemical parameters like soil pH and soil organic carbon affect microbial N2O production and reduction processes during denitrification.

Irrigation of DOC-rich liquid promotes potential denitrification rate and decreases N2O/(N2O+N2) product ratio in a 0–2 m soil profile

Lack of dissolved organic carbon (DOC) is generally one of the key factors limiting denitrification in subsoil beneath the root zone. Despite a number of laboratory DOC amendment studies, the effects of in situ DOC infiltration on subsoil denitrification, and on subsequent end product composition, are less understood. Here, we report on the effects of in situ infiltration of a DOC-rich liquid, derived from decomposing straw, on potential denitrification rate (PDR), N2O/(N2O + N2) product ratio, and nitrate stock in a 0–2 m soil profile. The results showed that in situ infiltration with a DOC-rich liquid (100 mm, 2 ton DOC ha−1) significantly increased the DOC concentration and PDR, and significantly decreased the N2O/(N2O + N2) product ratio in the soil profile. Up to 70% of the nitrate accumulated in the 0–2 m soil profile disappeared within three weeks following the infiltration of the DOC-rich liquid. The majority of the nitrate removed could be accounted for by denitrification. The predominant end product of denitrification was N2. The mass ratio between the consumed DOC and nitrate-N was about 5. Our results demonstrate the significant potential for removing subsoil nitrate by in situ introduction of DOC generated from the above-ground crop biomass.

Vertical distribution of denitrification end-products in paddy soils

Knowledge of denitrification process and its end-product at various depths of paddy soil is very important for our understanding of its role in mitigating reactive N and indirect nitrous oxide (N2O) emission. In this study, the end-products of denitrification were determined at four depths in a long-term field lysimeter experiment in southeast China over a rice season. Three treatments were included: (1) chemical fertilizer (NPK); (2) NPK plus pig manure (NPKM); and (3) NPK plus straw (NPKS). The concentration of dissolved N2O increased with soil depth across all treatments and the highest concentration of excess dinitrogen (N2) was observed at 0.2m depth, as was the highest dissolved organic carbon (DOC) content. Denitrification reduced the amount of nitrate by 48–54% in the paddy soil profile, especially at 0.2m depth (68–88%), whereas the lower reduction of NO3− (17–44%) in the subsoil (at 0.6 and 0.8m depth) was accompanied by a higher concentration of NO3−. Our results demonstrated that DOC was the major limiting factor of denitrification in the subsoil. The application of pig manure markedly increased the amount of DOC in the surface soil, resulting in a high rate of denitrification, whereas the addition of straw had no effect on denitrification. The indirect emission factors for N2O (EF5-g, 0.001–0.006) were comparable with the default value (0.0025) reported by the Intergovernmental Panel on Climate Change. The low N2O production was probably caused by the complete reduction of N2O to N2, as reflected by the lower N2O/(N2O+N2) ratios in the paddy soil profile. Although the surface soil was identified as a hotspot for denitrification, a considerable amount of excess N2 was observed in the subsoil for all three treatments. We therefore conclude that the loss of N through denitrification may be significantly underestimated if only the surface soil is considered.

An improved (15) N tracer approach to study denitrification and nitrogen turnover in soil incubations.

Denitrification (the reduction of oxidized forms of inorganic nitrogen (N) to N2 O and N2 ) from upland soils is considered to be the least well-understood process in the global N cycle. The main reason for this lack of understanding is that the terminal product (N2 ) of denitrification is extremely difficult to measure against the large atmospheric background. We describe a system that combines the (15) N-tracer technique with a 40-fold reduced N2 (2% v/v) atmosphere in a fully automated incubation setup for direct quantification of N2 and N2 O emissions. The δ(15) N values of the emitted N2 and N2 O were determined using a custom-built gas preparation unit that was connected to a DELTA V Plus isotope ratio mass spectrometer. The system was tested on a pasture soil from sub-tropical Australia under different soil moisture conditions and combined with (15) N tracing in extractable soil N pools to establish a full N balance. The method proved to be highly sensitive for detecting N2 (1.12μgNh(-1) kg(-1) dry soil (ds)) and N2 O (0.36μgNh(-1) kg(-1) ds) emissions. The main end product of denitrification in the investigated soil was N2 O for both water contents, with N2 accounting for only 3% to 13% of the total denitrification losses. Between 90 and 95% of the added (15) N fertiliser could be recovered in N gases and extractable soil N pools. The high and N2 O-dominated denitrification rates found in this study are pointing at both the high ecological and the agronomic importance of denitrification in subtropical pasture soils. The new system allows for a direct and highly sensitive detection of N2 and N2 O fluxes from soils and may help to significantly improve our mechanistic understanding of N cycling and denitrification in terrestrial agro-ecosystems. Copyright © 2016 John Wiley & Sons, Ltd.

Characteristics of a Novel Aerobic Denitrifying Bacterium, Enterobacter cloacae Strain HNR

A novel aerobic denitrifier strain HNR, isolated from activated sludge, was identified as Enterobacter cloacae by16S rRNA sequencing analysis. Glucose was considered as the most favorable C-source for strain HNR. The logistic equation well described the bacterial growth, yielding a maximum growth rate (μmax) of 0.283h(-1) with an initial NO3 (-)-N concentration of 110mg/L. Almost all NO3 (-)-N was removed aerobically within 30h with an average removal rate of 4.58mgNL(-1)h(-1). Nitrogen balance analysis revealed that proximately 70.8% of NO3 (-)-N was removed as gas products and only 20.7% was transformed into biomass. GC-MS result indicates that N2 was the end product of aerobic denitrification. The enzyme activities of nitrate reductase and nitrite reductase, which are related to the process of aerobic denitrification, were 0.0688 and 0.0054 U/mg protein, respectively. Thus, the aerobic denitrification of reducing NO3 (-) to N2 by strain HNR was demonstrated. The optimal conditions for nitrate removal were C/N ratio 13, pH value 8, shaking speed 127rpm and temperature 30°C. These findings show that E. cloacae strain HNR has a potential application on wastewater treatment to achieve nitrate removal under aerobic conditions.

Can pH amendments in grazed pastures help reduce N2O emissions from denitrification? – The effects of liming and urine addition on the completion of denitrification in fluvial and volcanic soils

Soil pH plays a critical role in determining the overall rate of several important processes in the agricultural nitrogen cycle. During denitrification, the activity of nitrous oxide reductase (N2O-R) is reduced at low pH. This effect has led to suggestions that soil pH adjustment via liming to enhance the activity of this enzyme might be a viable agricultural greenhouse gas mitigation strategy by enhancing the reduction of N2O in the soil to climatically inert N2. We assessed the effect of liming on the apparent activity of N2O-R by measuring the denitrification end products, N2O and N2, in a series of short-term anaerobic incubations. We compared a weakly-buffered fluvial soil and a well-buffered, volcanic soil under different incubation temperatures and in the presence or absence of a ∼600 kg ha−1 cow urine-N amendment. Our results indicated that the liming effect was heavily modulated by soil type, temperature, and urine amendment. Liming (at rates of 1.5 and 3.0 t ha−1 for the volcanic soil and at rates of 5 and 10 t ha−1 for the fluvial soil) caused pH increases of between 0.43 and 1.25 pH units. The highest reductions in N2O in the fluvial soil occurred when the 1.5 t ha−1 rate was used in the fluvial soils under urine addition and at the higher temperature. The combined flux of N2O + N2 did not change with liming. However, an interaction of soil type and urine amendment caused large differences in the partitioning of the denitrification end-products between N2O and N2 – an effect that overwhelmed the relatively modest effects of liming. When the soils were amended with urine-N, the resulting denitrification gases from the volcanic soil were mostly in the form of N2O (60–77%), whereas in the fluvial soil the denitrification products were mostly in the form of N2 and a much smaller portion were in the form of N2O (11–45%). Nevertheless, we found liming-induced enhancements of N2O-R of 15–20% (P < 0.05) in urine-amended, fluvial soil. We suggest some possible mechanisms that would explain such large differences in the N2O/(N2O + N2) product ratio.

The diversity of the N2O reducers matters for the N2O:N2 denitrification end-product ratio across an annual and a perennial cropping system

Agriculture is the main source of terrestrial emissions of N2O, a potent greenhouse gas and the main cause of ozone layer depletion. The reduction of N2O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only biological process known to eliminate this greenhouse gas. Recent studies showed that a previously unknown clade of N2O-reducers was related to the capacity of the soil to act as an N2O sink, opening the way for new strategies to mitigate emissions. Here, we investigated whether the agricultural practices could differently influence the two N2O reducer clades with consequences for denitrification end-products. The abundance of N2O-reducers and producers was quantified by real-time PCR, and the diversity of both nosZ clades was determined by 454 pyrosequencing. Potential N2O production and potential denitrification activity were used to calculate the denitrification gaseous end-product ratio. Overall, the results showed limited differences between management practices but there were significant differences between cropping systems in both the abundance and structure of the nosZII community, as well as in the [rN2O/r(N2O+N2)] ratio. More limited differences were observed in the nosZI community, suggesting that the newly identified nosZII clade is more sensitive than nosZI to environmental changes. Potential denitrification activity and potential N2O production were explained mainly by the soil properties while the diversity of the nosZII clade on its own explained 26% of the denitrification end-product ratio, which highlights the importance of understanding the ecology of this newly identified clade of N2O reducers for mitigation strategies.

Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils.

Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.

Temperature effects on N2O and N2 denitrification end-products for a New Zealand pasture soil

Denitrification results in the formation of two gaseous end-products: radiatively active greenhouse gas nitrous oxide (N2O) and radiatively inert di-nitrogen (N2). Measuring N2 produced by soil microorganisms has historically been difficult because of interference by high background concentrations (780,840 ppm) of atmospheric N2. Here, we applied a new automated technique for simultaneous measurement of the denitrification end-products N2O and N2. We tested the hypothesis that the temperature response function (defined here as Q10) for N2O was greater than for N2 under anaerobic conditions in the laboratory. The Q10 for N2O was 2.0 and the Q10 for N2 was 1.4, indicating differences in sensitivity to temperature. Denitrified-N shifted towards N2O as temperature increased. While moisture strongly controls the relative abundance of denitrification end-products, additional experiments are needed to determine how a wider range of temperatures may affect N2O and N2. Results could enhance understanding of temperature controls on N2O production and consumption processes.

Substrate induced denitrification over or under estimates shifts in soil N₂/N₂O ratios.

The increase in atmospheric nitrous oxide (N2O), a potent greenhouse and ozone depleting gas, is of serious global concern. Soils are large contributors to this increase through microbial processes that are enhanced in agricultural land due to nitrogenous fertilizer applications. Denitrification, a respiratory process using nitrogen oxides as electron acceptors in the absence of oxygen, is the main source of N2O. The end product of denitrification is benign dinitrogen (N2) and understanding what regulates the shift in ratio of N2O and N2 emission is crucial for mitigation strategies. The role of organic carbon in controlling N2O reduction is poorly understood, and mostly based on application of glucose. Here we investigated how a range of carbon compounds (succinate, butyrate, malic acid, acetate, glucose, sucrose and cysteine) affect denitrifier N2/N2O production stoichiometry under laboratory conditions. The results show that a soil's capability in efficiently reducing N2O to N2 is C substrate dependent and most compounds tested were different in regards to this efficiency compared to glucose. We challenge the concept of using glucose as a model soil C compound in furthering our understanding of denitrification and specifically the efficiency in the N2O reductase enzyme. Organic acids, commonly exuded by roots, increased N2/N2O ratios compared to glucose, and therefore mitigated net N2O release and we suggest provides better insights into soil regulatory aspects of N2O reduction. The widespread use of glucose in soil laboratory studies could lead to misleading knowledge on the functioning of denitrification in soils with regards to N2O reduction.