Soil pH as the chief modifier for regional nitrous oxide emissions: New evidence and implications for global estimates and mitigation

Nitrous oxide (N₂O) is a greenhouse gas that also plays the primary role in stratospheric ozone depletion. The use of nitrogen fertilizers is known as the major reason for atmospheric N₂O increase. Empirical bottom‐up models therefore estimate agricultural N₂O inventories using N loading as the sole predictor, disregarding the regional heterogeneities in soil inherent response to external N loading. Several environmental factors have been found to influence the response in soil N₂O emission to N fertilization, but their interdependence and relative importance have not been addressed properly. Here, we show that soil pH is the chief factor explaining regional disparities in N₂O emission, using a global meta‐analysis of 1,104 field measurements. The emission factor (EF) of N₂O increases significantly (p < .001) with soil pH decrease. The default EF value of 1.0%, according to IPCC (Intergovernmental Panel on Climate Change) for agricultural soils, occurs at soil pH 6.76. Moreover, changes in EF with N fertilization (i.e. ΔEF) is also negatively correlated (p < .001) with soil pH. This indicates that N₂O emission in acidic soils is more sensitive to changing N fertilization than that in alkaline soils. Incorporating our findings into bottom‐up models has significant consequences for regional and global N₂O emission inventories and reconciling them with those from top‐down models. Moreover, our results allow region‐specific development of tailor‐made N₂O mitigation measures in agriculture.     

Excessive use of nitrogen in Chinese agriculture results in high N2O/(N2O+N2) product ratio of denitrification,primarily due to acidification of the soils

China is the world's largest producer and consumer of fertilizer N, and decades of overuse has caused nitrate leaching and possibly soil acidification. We hypothesized that this would enhance the soils' propensity to emit N₂O from denitrification by reducing the expression of the enzyme N₂O reductase. We investigated this by standardized oxic/anoxic incubations of soils from five long‐term fertilization experiments in different regions of China. After adjusting the nitrate concentration to 2 mM, we measured oxic respiration (R), potential denitrification (D), substrate‐induced denitrification, and the denitrification product stoichiometry (NO, N₂O, N₂). Soils with a history of high fertilizer N levels had high N₂O/(N₂O+N₂) ratios, but only in those field experiments where soil pH had been lowered by N fertilization. By comparing all soils, we found a strong negative correlation between pH and the N₂O/(N₂O+N₂) product ratio (r² = 0.759, P < 0.001). In contrast, the potential denitrification (D) was found to be a linear function of oxic respiration (R), and the ratio D/R was largely unaffected by soil pH. The immediate effect of liming acidified soils was lowered N₂O/(N₂O+N₂) ratios. The results provide evidence that soil pH has a marginal direct effect on potential denitrification, but that it is the master variable controlling the percentage of denitrified N emitted as N₂O. It has been known for long that low pH may result in high N₂O/(N₂O+N₂) product ratios of denitrification, but our documentation of a pervasive pH‐control of this ratio across soil types and management practices is new. The results are in good agreement with new understanding of how pH may interfere with the expression of N₂O reductase. We argue that the management of soil pH should be high on the agenda for mitigating N₂O emissions in the future, particularly for countries where ongoing intensification of plant production is likely to acidify the soils.     

二氧化钛纳米颗粒对沼泽土壤反硝化和N2O排放的影响

近年来,二氧化钛纳米颗粒（TiO₂NPs）环境释放量不断增加,并通过多种途径进入湿地生态系统,不可避免地影响到湿地生态系统环境和功能。然而,关于TiO₂NPs对沼泽土壤反硝化作用和氧化亚氮（N₂O）排放的影响机及制尚不明确。选择典型沼泽土壤,通过室内培养实验研究土壤理化性质、反硝化酶活性、反硝化速率（DNR）和N₂O排放对不同剂量TiO₂NPs 0 mg/kg （CK）、10 mg/kg （A10）、100 mg/kg （A100）、1000 mg/kg （A1000）输入的响应,探讨TiO₂NPs输入对沼泽土壤反硝化作用和N₂O排放影响的内在机制。结果表明：不同剂量TiO₂NPs处理显著降低了土壤pH （P<0.05）,A10处理显著降低土壤总有机碳（TOC）含量（P<0.01）,A1000处理显著降低硝态氮（NO₃^--N）和亚硝态氮（NO₂^--N）含量（P<0.05）。TiO₂NPs处理抑制硝酸盐还原酶（NAR）活性,促进一氧化氮还原酶（NOR）和氧化亚氮还原酶（NOS）活性（P<0.01）,A1000处理先促进后抑制了亚硝酸盐还原酶（NIR）活性（P<0.05）。不同剂量TiO₂NPs处理抑制了土壤DNR,促进了N₂O排放,TiO₂NPs处理通过抑制NIR活性,降低土壤DNR,同时通过促进NOR活性,提高N₂O排放。综上,TiO₂NPs输入通过影响反硝化还原酶活性改变沼泽土壤反硝化过程,导致沼泽土壤N₂O排放增加,改变湿地氮的源、汇功能,影响全球气候变化。为TiO₂NPs输入的湿地环境风险评估研究提供理论基础。     

Forest streams are important sources for nitrous oxide emissions

Streams and river networks are increasingly recognized as significant sources for the greenhouse gas nitrous oxide (N₂O). N₂O is a transformation product of nitrogenous compounds in soil, sediment and water. Agricultural areas are considered a particular hotspot for emissions because of the large input of nitrogen (N) fertilizers applied on arable land. However, there is little information on N₂O emissions from forest streams although they constitute a major part of the total stream network globally. Here, we compiled N₂O concentration data from low‐order streams (~1,000 observations from 172 stream sites) covering a large geographical gradient in Sweden from the temperate to the boreal zone and representing catchments with various degrees of agriculture and forest coverage. Our results showed that agricultural and forest streams had comparable N₂O concentrations of 1.6 ± 2.1 and 1.3 ± 1.8 µg N/L, respectively (mean ± SD) despite higher total N (TN) concentrations in agricultural streams (1,520 ± 1,640 vs. 780 ± 600 µg N/L). Although clear patterns linking N₂O concentrations and environmental variables were difficult to discern, the percent saturation of N₂O in the streams was positively correlated with stream concentration of TN and negatively correlated with pH. We speculate that the apparent contradiction between lower TN concentration but similar N₂O concentrations in forest streams than in agricultural streams is due to the low pH (<6) in forest soils and streams which affects denitrification and yields higher N₂O emissions. An estimate of the N₂O emission from low‐order streams at the national scale revealed that ~1.8 × 10⁹ g N₂O‐N are emitted annually in Sweden, with forest streams contributing about 80% of the total stream emission. Hence, our results provide evidence that forest streams can act as substantial N₂O sources in the landscape with 800 × 10⁹ g CO₂‐eq emitted annually in Sweden, equivalent to 25% of the total N₂O emissions from the Swedish agricultural sector.     

Structures of reduced and ligand‐bound nitric oxide reductase provide insights into functional differences in respiratory enzymes

Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N₂O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non‐heme Fe center. We report herein on the structures of the reduced and ligand‐bound forms of cytochrome c‐dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3–2.7 Å, to elucidate structure‐function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO‐bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH₃‐CH=N‐OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ～0.5 Å increase in the heme/non‐heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton‐pumping activity in cNOR, because redox‐coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non‐heme Fe distance even in the bulky ligand‐bound form of cNOR (～4.5 Å) than the heme/Cu distance in CCO (～5 Å) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N‐N coupling to produce a hyponitrite intermediate for the generation of N₂O. Proteins 2014; 82:1258–1271. © 2013 Wiley Periodicals, Inc.     

Weakened growth of cropland‐N2O emissions in China associated with nationwide policy interventions

China has experienced rapid agricultural development over recent decades, accompanied by increased fertilizer consumption in croplands; yet, the trend and drivers of the associated nitrous oxide (N₂O) emissions remain uncertain. The primary sources of this uncertainty are the coarse spatial variation of activity data and the incomplete model representation of N₂O emissions in response to agricultural management. Here, we provide new data‐driven estimates of cropland‐N₂O emissions across China in 1990–2014, compiled using a global cropland‐N₂O flux observation dataset, nationwide survey‐based reconstruction of N‐fertilization and irrigation, and an updated nonlinear model. In addition, we have evaluated the drivers behind changing cropland‐N₂O patterns using an index decomposition analysis approach. We find that China's annual cropland‐N₂O emissions increased on average by 11.2 Gg N/year² (p < .001) from 1990 to 2003, after which emissions plateaued until 2014 (2.8 Gg N/year², p = .02), consistent with the output from an ensemble of process‐based terrestrial biosphere models. The slowdown of the increase in cropland‐N₂O emissions after 2003 was pervasive across two thirds of China's sowing areas. This change was mainly driven by the nationwide reduction in N‐fertilizer applied per area, partially due to the prevalence of nationwide technological adoptions. This reduction has almost offset the N₂O emissions induced by policy‐driven expansion of sowing areas, particularly in the Northeast Plain and the lower Yangtze River Basin. Our results underline the importance of high‐resolution activity data and adoption of nonlinear model of N₂O emission for capturing cropland‐N₂O emission changes. Improving the representation of policy interventions is also recommended for future projections.     

NO and N2O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains

Fungal denitrification is claimed to produce non-negligible amounts of N₂O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with . Enzymatic reduction of (NIR) and NO (NOR) was assessed by correcting measured NO- and N₂O-kinetics for abiotic NO- and N₂O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N₂O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N₂O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N₂O as a response to an abiotic NO production from the medium.     

Denitrification and N2O effluxes in the Bothnian Bay (northern Baltic Sea) river sediments as affected by temperature under different oxygen concentrations

Denitrification rates and nitrous oxide (N₂O) effluxes were measured at different temperatures and for different oxygen concentrations in the sediments of a eutrophied river entering the Bothnian Bay. The experiments were made in a laboratory microcosm with intact sediment samples. ¹⁵N-labelling was used to measure denitrification rates (Dw). The rates were measured at four temperatures (5, 10, 15 and 20°C) and with three oxygen inputs (<0.2, 5, and 10 mg O₂ l⁻¹). The temperature response was highly affected by oxygen concentration. At higher O₂ concentrations (5 and 10 mg O₂ l⁻¹) a saturation over 10°C was observed, whereas the anoxic treatment (<0.2 mg O₂ l⁻¹) showed an exponential increase in the temperature interval with a Q ₁₀ value of 3.1. The result is described with a combined statistical model. In contrast with overall denitrification, the N₂O effluxes from sediments decreased with increasing temperature. The N₂O effluxes had a lower response to oxygen than denitrification rates. The N₂O/N₂ ratio was always below 0.02. Increased temperatures in the future could enhance denitrification rates in boreal river sediments but would not increase the amount of N₂O produced.     

The production and emission of nitrous oxide from headwater streams in the Midwestern United States

The emission of nitrous oxide (N₂O) from streams draining agricultural landscapes is estimated by the Intergovernmental Panel on Climate Change (IPCC) to constitute a globally significant source of this gas to the atmosphere, although there is considerable uncertainty in the magnitude of this source. We measured N₂O emission rates and potential controlling variables in 12 headwater streams draining a predominantly agricultural basin on glacial terrain in southwestern Michigan. The study sites were nearly always supersaturated with N₂O and emission rates ranged from ?8.9 to 266.8 μg N₂O‐N m^?2 h^?1 with an overall mean of 35.2 μg N₂O‐N m^?2 h^?1. Stream water NO₃^? concentrations best‐predicted N₂O emission rates. Although streams and agricultural soils in the basin had similar areal emission rates, emissions from streams were equivalent to 6% of the anthropogenic emissions from soils because of the vastly greater surface area of soils. We found that the default value of the N₂O emission factor for streams and groundwater as defined by the IPCC (EF5‐g) was similar to the value observed in this study lending support to the recent downward revision to EF5‐g. However, the EF5‐g spanned four orders of magnitude across our study sites suggesting that the IPCC's methodology of applying one emission factor to all streams may be inappropriate.     

Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil

Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N₂O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N₂O emissions increased when the size of inoculated C58 population in the soils was in the same range as the indigenous nosZ community. However, in two of the three soils, the increase in potential denitrification in inoculated microcosms compared with the noninoculated microcosms was higher than the increase in N₂O emissions. This suggests that the indigenous denitrifier community was capable of acting as a sink for the N₂O produced by A. tumefaciens. The relative amount of N₂O emitted also increased in two soils with the number of inoculated C58 cells, establishing a direct causal link between the denitrifier community composition and potential N₂O emissions by manipulating the proportion of denitrifiers having the nosZ gene. However, the number of denitrifiers which do not possess a nitrous oxide reductase might not be as important for N₂O emissions in soils having a high N₂O uptake capacity compared with those with lower. In conclusion, we provide a proof of principle that the inability of some denitrifiers to synthesize the nitrous oxide reductase can influence the nature of the denitrification end products, indicating that the extent of the reduction of N₂O to N₂ by the denitrifying community can have a genetic basis.     

A study of the impacts of Zn and Cu on two rhizobial species in soils of a long-term field experiment

Two agriculturally important species of rhizobia, Rhizobium leguminosarum biovar viciae (pea rhizobia) and R. leguminosarum bv. trifolii (white clover rhizobia), were enumerated in soils of a long-term field experiment to which sewage sludges contaminated predominantly with Zn or Cu, or Zn plus Cu, were added in the past. In addition to total soil Zn and Cu concentrations, soil pore water soluble Zn and free Zn²⁺, and soluble Cu concentrations are reported. Pea and white clover rhizobia were greatly reduced in soils containing ≥200 mg Zn kg^-1, and soil pore water soluble Zn and free Zn²⁺ concentrations ≥7 and ≥3 mg l^-1, respectively, in soils of pH 5.9–6. Copper also reduced rhizobial numbers, but only at high total soil concentrations (>250 mg kg^-1) and not to the same extent as Zn. Yields of field grown peas decreased significantly as total soil Zn, soil pore water soluble Zn and free Zn⁺² increased (R² = 0.79, 0.75 and 0.75, respectively; P < 0.001). A 50% reduction in seed yield occurred at a total soil Zn concentration of about 290 mg kg^-1, in soils of pH 5.9–6. The corresponding soil pore water soluble Zn and free Zn²⁺ concentrations were about 9 and 4 mg l^-1, respectively. Pea seed yields were not significantly correlated with total soil Cu (R² = 0.33) or soil pore water soluble Cu (R² = 0.39). Yield reductions were due to a combination of greatly reduced numbers of free-living rhizobia in the soil due to Zn toxicity, thus indirectly affecting N₂-fixation, and Zn phytotoxicity. These effects were exacerbated in slightly acidic soils due to increased solubility of Zn, and to some extent Cu, and an increase in the free Zn²⁺ fraction in soil pore water. The current United Kingdom, German and United States limits for Zn and Cu in soils are discussed in view of the current study. None of these limits are based on toxicity thresholds in soil pore water, which may have wider validity for different soil types and at different pH values than total soil concentrations. This revised version was published online in June 2006 with corrections to the Cover Date.     

Sulfur-driven autotrophic denitrification of nitric oxide for efficient nitrous oxide recovery

Nitrous oxide (N₂O) was previously deemed as a potent greenhouse gas but is actually an untapped energy source, which can accumulate during the microbial denitrification of nitric oxide (NO). Compared with the organic electron donor required in heterotrophic denitrification, elemental sulfur (S⁰) is a promising electron donor alternative due to its cheap cost and low biomass yield in sulfur-driven autotrophic denitrification. However, no effort has been made to test N₂O recovery from sulfur-driven denitrification of NO so far. Therefore, in this study, batch and continuous experiments were carried out to investigate the NO removal performance and N₂O recovery potential via sulfur-driven NO-based denitrification under various Fe(II)EDTA-NO concentrations. Efficient energy recovery was achieved, as up to 35.5%–40.9% of NO was converted to N₂O under various NO concentrations. N₂O recovery from Fe(II)EDTA-NO could be enhanced by the low bioavailability of sulfur and the acid environment caused by sulfur oxidation. The NO reductase (NOR) and N₂O reductase (N₂OR) were inhibited distinctively at relatively low NO levels, leading to efficient N₂O accumulation, but were suppressed irreversibly at NO level beyond 15 mM in continuous experiments. Such results indicated that the regulation of NO at a relatively low level would benefit the system stability and NO removal capacity during long-term system operation. The continuous operation of the sulfur-driven Fe(II)EDTA-NO-based denitrification reduced the overall microbial diversity but enriched several key microbial community. Thauera, Thermomonas, and Arenimonas that are able to carry out sulfur-driven autotrophic denitrification became the dominant organisms with their relative abundance increased from 25.8% to 68.3%, collectively.     

Peaks of in situ N2O emissions are influenced by N2O‐producing and reducing microbial communities across arable soils

Agriculture is the main source of terrestrial N₂O emissions, a potent greenhouse gas and the main cause of ozone depletion. The reduction of N₂O into N₂ by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N₂O‐reducers (nosZII) was related to the potential capacity of the soil to act as a N₂O sink. However, little is known about how this group responds to different agricultural practices. Here, we investigated how N₂O‐producers and N₂O‐reducers were affected by agricultural practices across a range of cropping systems in order to evaluate the consequences for N₂O emissions. The abundance of both ammonia‐oxidizers and denitrifiers was quantified by real‐time qPCR, and the diversity of nosZ clades was determined by 454 pyrosequencing. Denitrification and nitrification potential activities as well as in situ N₂O emissions were also assessed. Overall, greatest differences in microbial activity, diversity, and abundance were observed between sites rather than between agricultural practices at each site. To better understand the contribution of abiotic and biotic factors to the in situ N₂O emissions, we subdivided more than 59,000 field measurements into fractions from low to high rates. We found that the low N₂O emission rates were mainly explained by variation in soil properties (up to 59%), while the high rates were explained by variation in abundance and diversity of microbial communities (up to 68%). Notably, the diversity of the nosZII clade but not of the nosZI clade was important to explain the variation of in situ N₂O emissions. Altogether, these results lay the foundation for a better understanding of the response of N₂O‐reducing bacteria to agricultural practices and how it may ultimately affect N₂O emissions.     

Denitrification and nitrous oxide emissions from riparian forests soils exposed to prolonged nitrogen runoff

Compared to upland forests, riparian forest soils have greater potential to remove nitrate (NO₃) from agricultural runoff through denitrification. It is unclear, however, whether prolonged exposure of riparian soils to nitrogen (N) loading will affect the rate of denitrification and its end products. This research assesses the rate of denitrification and nitrous oxide (N₂O) emissions from riparian forest soils exposed to prolonged nutrient runoff from plant nurseries and compares these to similar forest soils not exposed to nutrient runoff. Nursery runoff also contains high levels of phosphate (PO₄). Since there are conflicting reports on the impact of PO₄ on the activity of denitrifying microbes, the impact of PO₄ on such activity was also investigated. Bulk and intact soil cores were collected from N-exposed and non-exposed forests to determine denitrification and N₂O emission rates, whereas denitrification potential was determined using soil slurries. Compared to the non-amended treatment, denitrification rate increased 2.7- and 3.4-fold when soil cores collected from both N-exposed and non-exposed sites were amended with 30 and 60 μg NO₃-N g⁻¹ soil, respectively. Net N₂O emissions were 1.5 and 1.7 times higher from the N-exposed sites compared to the non-exposed sites at 30 and 60 μg NO₃-N g⁻¹ soil amendment rates, respectively. Similarly, denitrification potential increased 17 times in response to addition of 15 μg NO₃-N g⁻¹ in soil slurries. The addition of PO₄ (5 μg PO₄-P g⁻¹) to soil slurries and intact cores did not affect denitrification rates. These observations suggest that prolonged N loading did not affect the denitrification potential of the riparian forest soils; however, it did result in higher N₂O emissions compared to emission rates from non-exposed forest soils.     

Nitrous oxide emissions from a cropped soil in a semi-arid climate

Understanding nitrous oxide (N₂O) emissions from agricultural soils in semi‐arid regions is required to better understand global terrestrial N₂O losses. Nitrous oxide emissions were measured from a rain‐fed, cropped soil in a semi‐arid region of south‐western Australia for one year on a sub‐daily basis. The site included N‐fertilized (100 kg N ha^?1 yr^?1) and nonfertilized plots. Emissions were measured using soil chambers connected to a fully automated system that measured N₂O using gas chromatography. Daily N₂O emissions were low (?1.8 to 7.3 g N₂O‐N ha^?1 day^?1) and culminated in an annual loss of 0.11 kg N₂O‐N ha^?1 from N‐fertilized soil and 0.09 kg N₂O‐N ha^?1 from nonfertilized soil. Over half (55%) the annual N₂O emission occurred from both N treatments when the soil was fallow, following a series of summer rainfall events. At this time of the year, conditions were conducive for soil microbial N₂O production: elevated soil water content, available N, soil temperatures generally >25 °C and no active plant growth. The proportion of N fertilizer emitted as N₂O in 1 year, after correction for the ‘background’ emission (no N fertilizer applied), was 0.02%. The emission factor reported in this study was 60 times lower than the IPCC default value for the application of synthetic fertilizers to land (1.25%), suggesting that the default may not be suitable for cropped soils in semi‐arid regions. Applying N fertilizer did not significantly increase the annual N₂O emission, demonstrating that a proportion of N₂O emitted from agricultural soils may not be directly derived from the application of N fertilizer. ‘Background’ emissions, resulting from other agricultural practices, need to be accounted for if we are to fully assess the impact of agriculture in semi‐arid regions on global terrestrial N₂O emissions.     

Indirect N2O emissions from shallow groundwater in an agricultural catchment (Seine Basin, France)

Production and accumulation of nitrous oxide (N₂O), a major greenhouse gas, in shallow groundwater might contribute to indirect N₂O emissions to the atmosphere (e.g., when groundwater flows into a stream or a river). The Intergovernmental Panel on Climate Change (IPCC) has attributed an emission factor (EF_5g) for N₂O, associated with nitrate leaching in groundwater and drainage ditches—0.0025 (corresponding to 0.25% of N leached which is emitted as N₂O)—although this is the subject of considerable uncertainty. We investigated and quantified the transport and fate of nitrate (NO₃ ^?) and dissolved nitrous oxide from crop fields to groundwater and surface water over a 2-year period (monitoring from April 2008 to April 2010) in a transect from a plateau to the river with three piezometers. In groundwater, nitrate concentrations ranged from 1.0 to 22.7 mg NO₃ ^?–N l^?1 (from 2.8 to 37.5 mg NO₃ ^?–N l^?1 in the river) and dissolved N₂O from 0.2 to 101.0 μg N₂O–N l^?1 (and from 0.2 to 2.9 μg N₂O–N l^?1 in the river). From these measurements, we estimated an emission factor of EF_5g = 0.0026 (similar to the value currently used by the IPCC) and an annual indirect N₂O flux from groundwater of 0.035 kg N₂O–N ha^?1 year^?1, i.e., 1.8% of the previously measured direct N₂O flux from agricultural soils.     

Abundance and Structure Composition of nirK and nosZ Genes as Well as Denitrifying Activity in Heavy Metal-polluted Paddy Soils

Denitrification is an important microbial process in soils and leads to the emission of nitrous oxide (N₂O). However, studies about the microbial community involved in denitrification processes in polluted paddy fields are scarce. Here, we studied two rice paddies which had been polluted for more than three decades by metal mining and smelter activities. Abundance and community composition were determined using real-time polymerase chain reaction (PCR) assay and denaturing gradient gel electrophoresis of nitrite reductase and nitrous oxide reductase gene amplicons (nirK and nosZ), while denitrifying activities were assessed by measuring potential denitrifier enzyme activity. We found that the community structure of both nirK and nosZ containing denitrifiers shifted under pollution in the two rice paddies. All the retrieved nirK sequences did not group into either α- or β-proteobacteria, while most of the nosZ species were affiliated with α-proteobacteria. While the abundance of both nirK and nosZ was significantly reduced in the polluted soils at “Dexing” (with relatively higher Cu levels), these parameters did not change significantly at “Dabaoshan” (polluted with Cd, Pb, Cu, and Zn). Furthermore, total denitrifying activity and N₂O production and reduction rates also only decreased under pollution at “Dexing.” These findings suggest that nirK and nosZ containing denitrifier populations and their activities could be sensitive to considerable Cu pollution, which could potentially affect N₂O release from polluted paddy soils.     

A new CuZ active form in the catalytic reduction of N2O by nitrous oxide reductase from Pseudomonas nautica

The final step of bacterial denitrification, the two-electron reduction of N₂O to N₂, is catalyzed by a multi-copper enzyme named nitrous oxide reductase. The catalytic centre of this enzyme is a tetranuclear copper site called CuZ, unique in biological systems. The in vitro reconstruction of the activity requires a slow activation in the presence of the artificial electron donor, reduced methyl viologen, necessary to reduce CuZ from the resting non-active state (1Cu^II/3Cu^I) to the fully reduced state (4Cu^I), in contrast to the turnover cycle, which is very fast. In the present work, the direct reaction of the activated form of Pseudomonas nautica nitrous oxide reductase with stoichiometric amounts of N₂O allowed the identification of a new reactive intermediate of the catalytic centre, CuZ°, in the turnover cycle, characterized by an intense absorption band at 680 nm. Moreover, the first mediated electrochemical study of Ps. nautica nitrous oxide reductase with its physiological electron donor, cytochrome c-552, was performed. The intermolecular electron transfer was analysed by cyclic voltammetry, under catalytic conditions, and a second-order rate constant of (5.5 ± 0.9) × 10⁵ M⁻¹ s⁻¹ was determined. Both the reaction of stoichiometric amounts of substrate and the electrochemical studies show that the active CuZ° species, generated in the absence of reductants, can rearrange to the resting non-active CuZ state. In this light, new aspects of the catalytic and activation/inactivation mechanism of the enzyme are discussed.     

Cadmium-copper antagonism in the activation of periplasmic nitrous oxide reductase of copper-deficient cells fromPseudomonas stutzeri

Summary Copper-deficient cells ofPseudomonas stutzeri strain ZoBell synthesize catalytically inactive nitrous oxide (N₂O) reductase which is activated by added Cu(II) in the absence of de novo protein synthesis. The apparentK _m for the activation process is 0.13 M. Activation is temperature-dependent and is inhibited by Cd(II)(K _i 1.27 M) and less strongly by Zn(II), Ni(II), and Co(II). The same metal ions at 20 M have little or no effect on N₂O reduction of intact cells. Apo-N₂O reductase of transposon Tn5-inducednos ^– mutants with defective Cu-chromophore biosynthesis is not reactivated by Cu(II). N₂O reductase of Cu-sufficient and Cu-deficient wild type, and ofnos ^– mutants is localized in the periplasm, the latter providing the likely site of metal incorporation into the apoenzyme.