Ammonium sorption and ammonia inhibition of nitrite-oxidizing bacteria explain contrasting soil N2O production

The spatiotemporal heterogeneity of fertosphere hotspots impacted by biochar addition and the implications for NH3 and N2O emissions

The fertosphere, as the interfaces between fertilizer granular and soil particles, represents a key hotspot for nitrogen transformation processes, particularly for ammonia (NH3) and nitrous oxide (N2O) emissions. Understanding the heterogeneity of the fertosphere, especially when incorporating organic amendments like biochars, is crucial for predicting NH3 and N2O emissions after soil fertilization. In this study, we investigated the effects of three types of biochar (pristine, aged, and acid-washed biochar) on heterogeneity of fertosphere induced by localized urea application. pH-specific planar optodes were employed to visualize pH gradients in fertosphere hotspots with high spatial and temporal resolution. In addition, we conducted thorough measurements of the gradient distribution of electric conductivity (EC), mineral N, aqueous NH3 in soil and enzyme activities relevant to nitrification. Concurrently, NH3 and N2O emissions from the soil were continuously monitored at a high temporal resolution. Initially, urea-induced fertosphere exhibited significant NH3 emissions, primarily attributed to the pH elevation resulting from urea hydrolysis. However, after 6 days, NH3 emissions subsided, and there was a notable sharp increase in N2O emissions. Importantly, compared to urea application alone, the inclusion of pristine biochar led to a delay in soil pH decline with a 19% rise in NH3 emission. Aged biochar, characterized by a higher content of oxygen functional groups, demonstrated increased NH4+/NH3 adsorption capacity and enhanced ammonia monooxygenase (AMO) activity in soil, resulting in an 18% reduction in NH3 emission. While a slight decrease of 5% in NH3 cumulative emission was observed in the acid-washed biochar treatment. Notably, biochar could potentially promote nitrification-derived N2O emissions due to the accumulation of NH3 oxidation products (NH2OH). These findings could contribute to refining N transformation models for fertilized soils, and optimizing N fertilizer application strategies.

Urea amendment decouples nitrification in hydrocarbon contaminated Antarctic soil

Hydrocarbon contaminated soils resulting from human activities pose a risk to the natural environment, including in the Arctic and Antarctic. Engineered biopiles constructed at Casey Station, Antarctica, have proven to be an effective strategy for remediating hydrocarbon contaminated soils, with active ex-situ remediation resulting in significant reductions in hydrocarbons, even in the extreme Antarctic climate. However, the use of urea-based fertilisers, whilst providing a nitrogen source for bioremediation, has also altered the natural soil chemistry leading to increases in pH, ammonium and nitrite. Monitoring of the urea amended biopiles identified rising levels of nitrite to be of particular interest, which misaligns with the long term goal of reducing contaminant levels and returning soil communities to a 'healthy' state. Here, we combine amplicon sequencing, microfluidic qPCR on field samples and laboratory soil microcosms to assess the impact of persistent nitrite accumulation (up to 60 months) on nitrifier abundances observed within the Antarctic biopiles. Differential inhibition of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) Nitrobacter and Nitrospira in the cold, urea treated, alkaline soils (pH 8.1) was associated with extensive nitrite accumulation (76 ± 57 mg N/kg at 60 months). When the ratio of Nitrospira:AOB dropped below ∼1:1, Nitrobacter was completely inhibited or absent from the biopiles, and nitrite accumulated. Laboratory soil microcosms (incubated at 7 °C and 15 °C for 9 weeks) reproduced the pattern of nitrite accumulation in urea fertilized soil at the lower temperature, consistent with our longer-term observations from the Antarctic biopiles, and with other temperature-controlled microcosm studies. Diammonium phosphate amended soil did not exhibit nitrite accumulation, and could be a suitable alternative biostimulant to avoid excessive nitrite build-up.

Synergistic benefits of lime and 3,4-dimethylpyrazole phosphate application to mitigate the nitrous oxide emissions from acidic soils

Acidic soils cover approximately 50 % of the arable land with high N2O emission potential. 3,4-dimethylpyrazole phosphate (DMPP) inhibits N2O emission from soils; however, its efficiency is affected by acidity. Liming is used for soil conditioning to ameliorate the effects of acidity. In the present study, we investigated the effects of liming on the efficiency of DMPP in inhibiting N2O emission in acidic soils and the mechanisms involved. We evaluated the impact of liming, DMPP, and combined application and its microbial responses in two acidic soils from Zengcheng (ZC) and Shaoguan (SG) City, Guangdong Province, China. Soils were subjected to four treatments: un-limed soil (low soil pH) + urea (LU), un-limed soil + urea + DMPP (LD), limed soil (high soil pH) + urea (HU), and limed soil + urea + DMPP (HD) for analyses of the mineral N, N2O emissions, and full-length 16S and metagenome sequencing. The results revealed that, HU significantly decreased and increased the N2O emission by 17.8 % and 235.0 % in ZC and SG, respectively, compared with LU. This was caused by a trade-off between N2O production and consumption after liming, where microbial communities and N-cycling functional genes show various compositions in different acidic soils. LD reduced N2O emission by 23.5 % in ZC, whereas decreased 1.5 % was observed in SG. Interestingly, DMPP efficiency considerably improved after liming in two acidic soils. Compared with LU, HD significantly reduced N2O emissions by 61.2 % and 48.5 % in ZC and SG, respectively. Synergy of mitigation efficiency was observed by lime and DMPP application, which was attributed to the changes in the dominant nitrifiers and the increase in N2O consumption by denitrifiers. The combined application of lime and DMPP is a high-efficiency strategy for N2O mitigation can ensure agricultural sustainability in acidic arable soils with minimal environmental damage.

Integration of MFC reduces CH4, N2O and NH3 emissions in batch-fed wetland systems

The combination of microbial fuel cells (MFCs) with constructed wetlands (CWs) for enhancing water purification efficiency and generating bioelectricity has attracted extensive attention. However, the other benefits of MFC-CWs are seldom reported, especially the potential for controlling gaseous emissions. In this study, we have quantitatively compared the pollutant removal efficiency and the emission of multiple gases between MFC-CWs and batch-fed wetland systems (BF CWs). MFC-CWs exhibited significantly (p < 0.01) higher COD, NH₄⁺-N, TN, and TP removal efficiencies and significantly (p < 0.01) lower global warming potential (GWP) than BF CWs. The integration of MFC decreased GWP by 23.88% due to the reduction of CH₄ and N₂O fluxes, whereas the CO₂ fluxes were slightly promoted. The quantitative PCR results indicate that the reduced N₂O fluxes in MFC-CWs were driven by the reduced transcription of the nosZ gene and enhanced the ratio of nosZ/(nirS + nirK); the reduced CH₄ fluxes were related to pomA and mcrA. Additionally, the NH₃ fluxes were reduced by 52.20% in MFC-CWs compared to BF CWs. The integration of MFC promoted the diversity of microbial community, especially Anaerolineaceae, Saprospiraceae and Clostridiacea. This study highlights a further benefit of MFC-CWs and provides a new strategy for simultaneously removing pollutants and abating multiple gas emissions in BF CWs.

In situ nitrous oxide and dinitrogen fluxes from a grazed pasture soil following cow urine application at two nitrogen rates

Cattle grazing of pastures deposits urine onto the pasture soil at high nitrogen (N) rates that exceed the pasture's immediate N demands, increasing the risk of N loss. Nitrous oxide (N₂O), a greenhouse gas, and dinitrogen (N₂) are lost from the cattle urine patches. There is limited information on the in situ loss of N₂ from grazed-pasture systems which is needed for understanding pasture soil N dynamics and balances. The ¹⁵N flux method was used to determine N₂ and N₂O fluxes over time following synthetic urine-¹⁵N application at either 400 or 800 kg N ha^-1 to a grazed perennial pasture soil. Results showed that daily N₂O fluxes were higher under 800 kg N ha^-1 than under 400 kg N ha^-1, but there was no significant difference in N₂ fluxes. Cumulative N₂O emissions from soil with 400 kg N ha^-1 and 800 kg N ha^-1 applied represented 0.16 ± 0.08% and 0.43 ± 0.08% of deposited N, respectively, while emitted N₂ accounted for 32.1 ± 4.1% and 14.4 ± 1.7%, respectively, over 95 days after urine application. Codenitrification and denitrification co-occurred, with denitrification accounting for 97.9 to 98.5% of total N₂ production. Recovery of urine-¹⁵N in pasture decreased with increasing N rate with 14.7 ± 0.5% and 9.9 ± 0.8% recovered at 400 and 800 kg N ha^-1, respectively after 95 days. The N₂O/(N₂ + N₂O) product ratio was generally higher during periods of nitrification of urine-N (the first month after urine application) but with no clear relationship to other measured variables. Contrary to our hypothesis, an elevated urine-N rate did not enhance N₂ loss. This is speculated to be due to enhanced ammonia volatilisation and transfer of N as nitrate, to deeper soil layers. Soil relative gas diffusivity indicated that high N₂ fluxes resulted from entrapped N₂ diffusing from the draining soil.

Continuous monitoring of dissolved inorganic nitrogen (DIN) transformations along the waste-vadose zone - groundwater path of an uncontrolled landfill, using multiple N-species isotopic analysis

Landfill leachates contain a heavy load of dissolved inorganic nitrogen (DIN), posing a threat to water resources. Therefore, it is highly important to understand the processes that control its evolution (speciation, accumulation, or attenuation) during the percolation of leachates through the unsaturated zone, finally affecting the groundwater. However, tracking DIN transformations in this complex and inaccessible environment is challenging, and knowledge concerning this important topic under field conditions is scarce. The presented study used a unique monitoring system that allows sampling of repetitive samples from within the waste and the unsaturated zone. An array of 8 wells penetrating the underlying aquifer completed the spatial observation. Multiple N-species isotopic approach was applied to discern the dominating N-involving processes over the continuum - from the waste mound through the unsaturated zone and the underlying aquifer. Despite the considerable heterogeneity observed throughout the profile, the results provided a cohesive and valuable reflection of the evolution of the inorganic nitrogen pool in this highly contaminated environment. Leachates inside the waste had reducing characteristics with high accumulation of ammonium (up to 360 mg/l NH₄⁺-N), and a distinct δ¹⁵N-NH₄⁺ range (-3‰ to +10‰). The upper layers of the unsaturated zone underneath the landfill margins found to be aerated, promoting N oxidation which resulted in the accumulation of nitrate in the leachates (up to 490 mg/l NO₃^-N). Exceptionally high concentrations of nitrite (up to 126 mg/l NO₂^-N) were found as oxygen levels decreased in deeper sections of the vadose zone. Enrichment of δ¹⁵N-NO₂^- compared to δ¹⁵N-NO₃^- indicated the significance of autotropic nitrite reduction, controlling the DIN composition, correlated with NO₂^- accumulation and net DIN attenuation. The δ¹⁵N: δ¹⁸O ratio implied co-occurrence of denitrification in the leachates, even in the more oxidized sections, further contributing to N-attenuation in the unsaturated zone. In the aquifer, δ¹⁵N-NH₄⁺ values and δ¹⁵N: δ¹⁸O ratio linked N contamination to the leachates source. The encounter with the oxidized groundwater promoted intensive nitrification. δ¹⁵N-NO₂^- values in the groundwater were lighter than both δ¹⁵N-NH₄⁺ and δ¹⁵N-NO₃^- by 22‰ to 62‰, implying the co-occurrence of nitrification-denitrification processes. The effect of denitrification grew with decreasing dissolved oxygen (DO) levels below 0.5 mg/l towards the center of the plume, contributing to net DIN attenuation in the plume. The findings are significant for any consideration of the risk posed by DIN, as well as remediation measures, in a landfill environment and other sites with a heavy load of degrading organic matter.

Impacts of corn stover management and fertilizer application on soil nutrient availability and enzymatic activity

Corn stover is a global resource used in many industrial sectors including bioenergy, fuel, and livestock operations. However, stover removal can negatively impact soil nutrient availability, especially nitrogen (N) and phosphorus (P), biological activity, and soil health. We evaluated the effects of corn stover management combined with N and P fertilization on soil quality, using soil chemical (nitrate, ammonium and Bray-1 P) and biological parameters (β-glucosidase, alkaline phosphatase, arylsulfatase activities and fluorescein diacetate hydrolysis—FDA). The experiment was performed on a Mollisol (Typic Endoaquoll) in a continuous corn system from 2013 to 2015 in Minnesota, USA. The treatments tested included six N rates (0 to 200 kg N ha⁻¹), five P rates (0 to 100 kg P₂O₅ ha⁻¹), and two residue management strategies (residue removed or incorporated) totalling 60 treatments. Corn stover management significantly impacted soil mineral-N forms and enzyme activity. In general, plots where residue was incorporated were found to have high NH₄⁺ and enzyme activity compared to plots where residue was removed. In contrast, fields where residue was removed showed higher NO₃⁻ than plots where residue was incorporated. Residue management had little effect on soil available P. Soil enzyme activity was affected by both nutrient and residue management. In most cases, activity of the enzymes measured in plots where residue was removed frequently showed a positive response to added N and P. In contrast, soil enzyme responses to applied N and P in plots where residue was incorporated were less evident. Soil available nutrients tended to decrease in plots where residue was removed compared with plots where residue was incorporated. In conclusion, stover removal was found to have significant potential to change soil chemical and biological properties and caution should be taken when significant amounts of stover are removed from continuous corn fields. The residue removal could decrease different enzymes related to C-cycle (β-glucosidase) and soil microbial activity (FDA) over continuous cropping seasons, impairing soil health.

Fertilizer stabilizers reduce nitrous oxide emissions from agricultural soil by targeting microbial nitrogen transformations

Nitrous oxide (N₂O) is a pollutant released from agriculture soils following N fertilizer application. N stabilizers, such as N-(n-butyl) thiophosphoric triamide (NBPT) and 3,4-dimethylpyrazole phosphate (DMPP) could mitigate these N₂O emissions when applied with fertilizer. Here, field experiments were conducted to investigate the microbial mechanisms by which NBPT and DMPP mitigate N₂O emissions following urea application. We determined dynamic N₂O emissions and inorganic N concentrations for two wheat seasons and combined this with metagenomic sequencing. Application of NBPT, DMPP, and both NBPT and DMPP together with urea decreased mean N₂O accumulative emissions by 77.8, 91.4 and 90.7%, respectively, compared with urea application alone, mainly via repressing the increase in NO₂^- concentration after N fertilization. Sequencing results indicated that urea application enriched microorganisms that were positively correlated with N₂O production, whereas N stabilizers enriched microorganisms that were negatively correlated with N₂O production. Furthermore, compared to urea application alone, NBPT with urea reduced the abundances of genes related to denitrification, including napA/nasA, nirS/nirK, and norBC, resulting in a higher soil NO₃^- pool. Conversely, DMPP application, either alone or together with NBPT, decreased the abundance of genes involved in ammonia oxidation and denitrification, including amoCAB, hao, napA/nasA, nirS/nirK, and norBC, and maintained a greater soil NH₄⁺ pool. Both N stabilizers resulted in similar abundances of nirABD-which is related to NO₂^- reducers-as when no N fertilizer was applied, which could prevent NO₂^- accumulation, consequently mitigating N₂O emissions. These findings suggest that the high effectiveness of N stabilizers on mitigating N₂O emissions could be attributed to changes to soil microbial communities and N-cycling functional genes to control the by-product or intermediate products of microbial N-cycling processes in agricultural soils.

Remediation of soil contaminated with a commercial diesel-biodiesel blend (B12): A microcosm evaluation on the effects of (in)organic amendments

Bioremediation of fuel-contaminated soils largely depends on microbial activities, which might be stimulated using (in)organic amendments. Attenuation of a diesel-biodiesel blend (B12) was investigated in microcosms during 93 days. Soil was spiked with B12 (5%, m m^-1) and, in addition to contaminated Controls (unamended), soils received compost (COB), soybean hulls (SHB), or NPK fertilizer (IB) to reach a ~20:1 carbon-to-nitrogen (C:N) ratio regarding B12-carbon content. Effects of treatments on B12 attenuation, soil respiration, heterotrophic and B12-utilizing bacteria, pH, organic-C, nitrogen contents, and phytotoxicity, were evaluated. After 20 days, diesel range organics analysis indicated 58, 48, 45, and 43% attenuation in Controls, SHB, IB, and COB, respectively. Final dissipation reached 90, 86, 72, and 60% in Controls, COB, IB, and SHB. Compost and soybean hulls appeared as preferential substrates for microorganisms. Although microbial activity (soil respiration) was 39 and 22% higher than Controls in COB and SHB, amendments postponed attenuation. Amendments transiently affected bacterial numbers as compared to Controls; however, these effects were not related to attenuation levels. pH of the contaminated soils (~7.0) dropped to 6.1 in IB, whereas pH values were between 6.7 and 7.6 in other treatments. Organic-N and Kjeldahl-N decreased during incubations, indicating net N mineralization and subsequent nitrification, although N losses could occur. Organic-C, initially higher in SHB and COB, decreased in all treatments; however, more prominent losses in COB and SHB suggest amendments were preferentially used by microorganisms. Phytotoxicity was improved in Controls; however, it was not associated with attenuation levels in amended treatments, possibly owing to formation of toxic products and B12 sorption/desorption. In IB, decreased microbial activity, delayed attenuation, and remarkable phytotoxicity were due to excessive fertilization. Therefore, intrinsic soil conditions were adequate for B12 attenuation, without the need for nutritional inputs. Results also demonstrate that toxicity bioindicators are relevant to monitor remediation.

Microbial community analysis of biopiles in Antarctica provides evidence of successful hydrocarbon biodegradation and initial soil ecosystem recovery

Microorganisms comprise the bulk of biodiversity and biomass in Antarctic terrestrial ecosystems. To effectively protect and manage the Antarctic environment from anthropogenic impacts including contamination, the response and recovery of microbial communities should be included in soil remediation efficacy and environmental risk assessments. This is the first investigation into the microbial dynamics associated with large scale bioremediation of hydrocarbon contaminated soil in Antarctica. Over five years of active management, two significant shifts in the microbial community were observed. The initial shift at 12-24 months was significantly correlated with the highest hydrocarbon degradation rates, increased microbial loads, and significant increases in alkB gene abundances. ANCOM analysis identified bacterial genera most likely responsible for the bulk of degradation including Alkanindiges, Arthrobacter, Dietzia and Rhodococcus. The second microbial community shift occurring from 36 to 60 months was associated with further reductions in hydrocarbons and a recovery of amoA nitrification genes, but also increasing pH, accumulation of nitrite and a reduction of oligotrophic bacterial species. Over time, the addition of inorganic fertilisers altered the soil chemistry and led to a disruption of the nitrogen cycle, most likely decoupling ammonia oxidisers from nitrite oxidisers, resulting in nitrite accumulation. The results from this study provide key insights to the long-term management of hydrocarbon bioremediation in Antarctic soils.

Nitrification is a minor source of nitrous oxide (N2 O) in an agricultural landscape and declines with increasing management intensity

The long-term contribution of nitrification to nitrous oxide (N₂ O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N₂ O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N₂ O, we test the relative importance of nitrification-derived N₂ O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N₂ O fluxes was 13%-17% in a conventionally fertilized annual cropping system, 27%-42% in a low-input cover-cropped annual cropping system, and 52%-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be <10% of these values because of low N₂ O yields in cultured nitrifiers (typically 0.04%-8% of NH₃ oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N₂ O was produced by ammonia-oxidizing bacteria rather than archaea, who appeared responsible for no more than 30% of nitrification-derived N₂ O production in all but one ecosystem. Although the proportion of nitrification-derived N₂ O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N₂ O (higher V_max ) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N₂ O in all ecosystems examined.

Biochar amendment mitigated N2O emissions from paddy field during the wheat growing season

Biochar may variably impact nitrogen (N) transformation and N-cycle-related microbial activities. Yet the mechanism of biochar amendment on nitrous oxide (N₂O) emissions from agricultural ecosystems remains unclear. Based on a 6-year long-term biochar amendment experiment, we applied a dual isotope (¹⁵N-¹⁸O) labeling technique with tracing transcriptional genes to differentiate the contribution of nitrifier nitrification (NN), nitrifier denitrification (ND), nitrification-coupled denitrification (NCD) and heterotrophic denitrification (HD) pathway to N₂O production. Then the field experiment provided quantitative data on dynamic N₂O emissions, soil mineral N and key functional marker gene abundances during the wheat growing season. By using ¹⁵N-¹⁸O isotope, biochar decreased N₂O emission derived from ND (by 45-94%), HD (by 35-46%) and NCD (by 30-64%) compared to the values under N application. Biochar increased the relative contribution of NN to total N₂O production as evidenced by the increase in ammonia-oxidizing bacteria, but did not influence the cumulative NN-derived N₂O. The field experiment found that the majority of the N₂O emissions peaked following fertilization, in parallel with soil NH₄⁺ and nitrite dynamics. Soil N₂O emissions during the wheat growing stage were effectively decreased (by 38-48%) by biochar amendment. Based on the correlation analyses and random forest analysis in both microcosm and field experiments, the decrease in nitrite concentration (by 62-65%) and increase in N₂O consumption were mainly responsible for net N₂O mitigation, as evidenced by the decrease in the ratios of nitrite reductase genes/transcripts (nirS, nirK and fungal nirK) and N₂O reductase gene/transcripts (nosZI and nosZII). Based on the extrapolation from microcosm to field, biochar significantly mitigated N₂O emissions by weakening the ND processes, since NCD and HD contributed little during the N₂O emission "peaks" following urea fertilization. Therefore, emphasis should be put on the ND process and nitrite accumulation during N₂O emission peaks and extrapolated to all agroecosystems.

The effect of long-term biochar amendment on N2O emissions: Experiments with N15-O18 isotopes combined with specific inhibition approaches

Numerous studies reporting a transient decrease in soil nitrous oxide (N₂O) emissions after biochar amendment have mainly used short-term experiments. Thus, long-term field trials are needed to clarify the actual impact of biochar on N₂O emissions and the underlying mechanisms. To address this, both a ¹⁵N¹⁸O labeling technique and gene analyses were applied to investigate how N₂O production pathways and microbial mediation were affected by long term biochar amendment in field. Then, 1-octyne and 2-phenyl l-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) were used in combination with potassium chlorate to evaluate the relative contribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to potential ammonia oxidation (PAO) and the associated N₂O production. Acidic and alkaline greenhouse vegetable soils that had each received two separate treatments were collected (control, no biochar amendment; biochar, biochar amended in the field after 2 or 7 years). The results showed that biochar decreased N₂O emissions by 48% in acidic soils and by 22% in alkaline soils compared to those in control. These results were explained by decreases in nitrifier denitrification- (by 74%) and heterotrophic denitrification-derived N₂O production (by 58%), as further evidenced by a decrease in NO₂^- (by 87%) and the (nirK+nirS+fungal nirK):(nosZ-I + nosZ-II) ratio (by 5%) in both greenhouse vegetable soils. However, biochar increased nitrifier nitrification-derived N₂O in both soils because of increases in pH and PAO, which were attributed to an increased abundance of AOB rather than AOA. The contribution of AOB to PAO (or N₂O) exceeded 69% (or 68%) of the total in acidic soil and 88% (or 85%) of the total in alkaline soil after biochar amendment. Our findings demonstrated that the mitigation of N₂O by biochar is linked to specific N₂O production pathways.

Comparison of Novel and Established Nitrification Inhibitors Relevant to Agriculture on Soil Ammonia- and Nitrite-Oxidizing Isolates

Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; "Candidatus Nitrosocosmicus franklandus," "Candidatus Nitrosotalea sinensis"), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3-0.7 μM) compared to EQ (EC50 = 1-1.4 μM) and EQNL (EC50 = 26.6-129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9-248.7 μM vs EC50 = 0.6-2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8-2.1 and 1.0-6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.

Enhanced N2O Production Induced by Soil Salinity at a Specific Range

Nitrous oxide (N₂O) as a by-product of soil nitrogen (N) cylces, its production may be affected by soil salinity which have been proved to have significant negative effect on soil N transformation processes. The response of N₂O production across a range of different soil salinities is poorly documented; accordingly, we conducted a laboratory incubation experiment using an array of soils bearing six different salinity levels ranging from 0.25 to 6.17 dS m⁻¹. With ammonium-rich organic fertilizer as their N source, the soils were incubated at three soil moisture (θ) levels—50%, 75% and 100% of field capacity (θfc)—for six weeks. Both N₂O fluxes and concentrations of ammonium, nitrite and nitrate (NH₄⁺-N, NO₂⁻-N and NO₃⁻-N) were measured throughout the incubation period. The rates of NH₄⁺-N consumption and NO₃⁻-N accumulation increased with increasing soil moisture and decreased with increasing soil salinity, while the accumulation of NO₂⁻-N increased first then decreased with increasing soil salinity. N₂O emissions were significantly promoted by greater soil moisture. As soil salinity increased from 0.25 to 6.17 dS m⁻¹, N₂O emissions from soil first increased then decreased at all three soil moisture levels, with N₂O emissions peaking at electric conductivity (EC) values of 1.01 and 2.02 dS m⁻¹. N₂O emissions form saline soil were found significantly positively correlated to soil NO₂⁻-N accumulation. The present results suggest that greater soil salinity inhibits both steps of nitrification, but that its inhibition of nitrite oxidation is stronger than that on ammonia oxidation, which leads to higher NO₂⁻-N accumulation and enhanced N₂O emissions in soil with a specific salinity range.

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.

New Bidirectional Ammonia Flux Model in an Air Quality Model Coupled With an Agricultural Model

Ammonia surface flux is bidirectional; that is, net flux can be either upward or downward. In fertilized agricultural croplands and grasslands there is usually more emission than deposition especially in midday during warmer seasons. In North America, most of the ammonia emissions are from agriculture with a significant fraction of that coming from fertilizer. A new bidirectional ammonia flux modeling system has been developed in the Community Multiscale Air Quality (CMAQ) model, which has close linkages with the Environmental Policy Integrated Climate (EPIC) agricultural ecosystem model. Daily inputs from EPIC are used to calculate soil ammonia concentrations that are combined with air concentrations in CMAQ to calculate bidirectional surface flux. The model is evaluated against surface measurements of NH₃ concentrations, NH₄ ⁺ and SO₄ ^2- aerosol concentrations, NH₄ ⁺ wet deposition measurements, and satellite retrievals of NH₃ concentrations. The evaluation shows significant improvement over the base model without bidirectional ammonia flux. Comparisons to monthly average satellite retrievals show similar spatial distribution with the highest ammonia concentrations in the Central Valley of California (CA), the Snake River valley in Idaho, and the western High Plains. In most areas the model underestimates, but in the Central Valley of CA, it generally overestimates ammonia concentration. Case study analyses indicate that modeled high fluxes of ammonia in CA are often caused by anomalous high soil ammonia loading from EPIC for particular crop types. While further improvements to parameterizations in EPIC and CMAQ are recommended, this system is a significant advance over previous ammonia bidirectional surface flux models.

Impact of nitrogen compounds on fungal and bacterial contributions to codenitrification in a pasture soil

Ruminant urine patches on grazed grassland are a significant source of agricultural nitrous oxide (N₂O) emissions. Of the many biotic and abiotic N₂O production mechanisms initiated following urine-urea deposition, codenitrification resulting in the formation of hybrid N₂O, is one of the least understood. Codenitrification forms hybrid N₂O via biotic N-nitrosation, co-metabolising organic and inorganic N compounds (N substrates) to produce N₂O. The objective of this study was to assess the relative significance of different N substrates on codenitrification and to determine the contributions of fungi and bacteria to codenitrification. ¹⁵N-labelled ammonium, hydroxylamine (NH₂OH) and two amino acids (phenylalanine or glycine) were applied, separately, to sieved soil mesocosms eight days after a simulated urine event, in the absence or presence of bacterial and fungal inhibitors. Soil chemical variables and N₂O fluxes were monitored and the codenitrified N₂O fluxes determined. Fungal inhibition decreased N₂O fluxes by ca. 40% for both amino acid treatments, while bacterial inhibition only decreased the N₂O flux of the glycine treatment, by 14%. Hydroxylamine (NH₂OH) generated the highest N₂O fluxes which declined with either fungal or bacterial inhibition alone, while combined inhibition resulted in a 60% decrease in the N₂O flux. All the N substrates examined participated to some extent in codenitrification. Trends for codenitrification under the NH₂OH substrate treatment followed those of total N₂O fluxes (85.7% of total N₂O flux). Codenitrification fluxes under non-NH₂OH substrate treatments (0.7-1.2% of total N₂O flux) were two orders of magnitude lower, and significant decreases in these treatments only occurred with fungal inhibition in the amino acid substrate treatments. These results demonstrate that in situ studies are required to better understand the dynamics of codenitrification substrates in grazed pasture soils and the associated role that fungi have with respect to codenitrification.

Controls and Adaptive Management of Nitrification in Agricultural Soils

Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.

Strategic grazing management and nitrous oxide fluxes from pasture soils in tropical dairy systems

Greenhouse gases emissions are considered one of the most important environmental issues of dairy farming systems. Nitrous oxide (N₂O) has particular importance owing to its global warming potential and stratospheric ozone depletion. The objective of this study was to investigate the influence of two rotational grazing strategies characterized by two pre-grazing targets (95% and maximum canopy light interception; LI_95% and LI_Max, respectively) on milk production efficiency and N₂O fluxes from soil in a tropical dairy farming system based on elephant grass (Pennisetum purpureum Schum. cv. Cameroon). Results indicated that LI_95% pre-grazing target provided more frequent defoliations than LI_Max. Water-filled pore space, soil and chamber temperatures were affected by sampling periods (P₁ and P₂). There was a significant pre-grazing target treatment × sampling period interaction effect on soil NH₄⁺ concentration, which was most likely associated with urinary-N discharge. During P₁, there was a greater urinary-N discharge for LI_95% than LI_Max (26.3 vs. 20.9 kg of urinary-N/paddock) caused by higher stocking rate, which resulted in greater N₂O fluxes for LI_95%. Inversely, during P₂, the soil NH₄⁺ and N₂O fluxes were greater for LI_Max than LI_95%. During this period, the greater urinary-N discharge (46.8 vs. 44.8 kg of urinary-N/paddock) was likely associated with longer stocking period for LI_Max relative to LI_95%, since both treatments had similar stocking rate. Converting hourly N₂O fluxes to daily basis and relating to milk production efficiency, LI_95% was 40% more efficient than LI_Max (0.34 vs. 0.57 g N-N₂O/kg milk·ha). In addition, LI_95% pre-grazing target decreased urea-N loading per milk production by 34%. Strategic grazing management represented by the LI_95% pre-grazing target allows for intensification of tropical pasture-based dairy systems, enhanced milk production efficiency and decreased N-N₂O emission intensity.

Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling

The new discovery of complete ammonia oxidizers (comammox), single organisms capable of oxidizing ammonia into nitrate, redefined the traditional view of nitrification. However, little is known about the relative contributions of comammox and other nitrifiers to nitrification, particularly in agricultural soils with long-term intensive input of nutrients. Herein, we investigated the communities of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and comammox Nitrospira in agricultural soils under nutrients input gradient of nitrogen (0-675 kg N ha^-1 year^-1), phosphorus (0-405 kg P₂O₅ ha^-1 year^-1), and potassium (0-675 kg K₂O ha^-1 year^-1) fertilizers for 19 years. The results showed that N and K fertilizers input significantly (P < 0.05) increased the AOB-amoA gene abundance, while AOA were not as sensitive as AOB. The comammox-amoA gene copies were increased in all fertilizer treatments and was significantly correlated (P < 0.05) with the amount of N fertilizer added. Terminal restriction fragment length polymorphism (T-RFLP) combined with clone-library assays of comammox-amoA gene showed that increasing gradient of nutrients input increased the relative abundance of 73 bp T-RF (assigned to Clade A) but decreased the relative abundance of 198 bp T-RF (representing Clade B). Correlation analyses and stepwise linear regression analyses demonstrated that AOB were the dominate contributors to soil potential nitrification, while comammox Nitrospira did not play a significant role (P > 0.05). This study provided insights into the adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations and their relative contributions to potential nitrification in arable soils.

Intense rainfalls trigger nitrite leaching in agricultural soils depleted in organic matter

Nitrate and ammonium are common inorganic contaminants of anthropogenic origin in many shallow aquifers around the world, while nitrite is less common, but it is most harmful than nitrate and ammonium due to its high reactivity. This paper presents evidence of nitrite accumulation after intense rainfalls in soil samples collected in an agricultural field characterized by organic matter chronic depletion. Moreover, an intact core from the same site was also collected to perform an unsaturated column experiment (60 cm long and 20 cm outer diameter) mimicking heavy rainfalls (230 mm in 2 days). Results from the field site showed nitrite accumulation (up to 0.45 mmol/kg) at 50-70 cm depth, just below the plough layer. The column experiment showed very high initial concentrations of nitrate and nitrite in the leachate and a progressive decrease of nitrate due to denitrification. The numerical flow model was calibrated versus the observed volumetric water contents and leachate flow rates. The numerical reactive transport model was calibrated versus the leachate concentrations of six dissolved species (ammonium, nitrate, nitrite, dissolved organic carbon, chloride and bromide). The optimized model resulted to be robustly calibrated providing insights on the kinetic rates driving the production, accumulation and leakage of nitrite, showing that incomplete denitrification is the source of nitrite. As far as the authors are aware, this is the first study reporting a clear link between high nitrite leaching rates and extreme rainfall events in lowland agricultural soils depleted in organic matter. The proposed methodology could be applied to quantify nitrite cycling processes in many other agricultural areas of the world affected by extreme rainfall events.

Cobalt-dependent inhibition of nitrite oxidation in Nitrobacter winogradskyi

Nitrobacter winogradskyi is an abundant, intensively studied autotrophic nitrite-oxidizing bacterium, which is frequently used as a model strain in the two-step nitrification of ammonia (NH₃) to nitrate (NO₃^-) via nitrite (NO₂^-), either in activated sludge, agricultural field studies or more recently in artificial microbial consortia for organic hydroponics. We observed a hitherto unknown cobalt ion-dependent inhibition of cell growth and NO₂^- oxidation activity of N. winogradskyi in a mineral medium, which strongly depended on accompanying Ca²⁺ and Mg²⁺ concentrations. This inhibition was bacteriostatic, but susceptible to natural chelators. l-Histidine effectively restored cell growth and NO₂^- oxidation activity of N. winogradskyi in mineral media containing Co²⁺ with >90% recovery. Our results suggest that Co²⁺ competed with alkaline earth metals during uptake and that its toxicity was significantly reduced by complexation.

Contribution and Driving Mechanism of N2O Emission Bursts in a Chinese Vegetable Greenhouse after Manure Application and Irrigation

Solar greenhouse vegetable fields have been found to be hotspots of nitrous oxide (N2O) emissions in China, mainly due to excessive manure application and irrigation. Pulses of N2O emissions have been commonly reported by field monitoring works conducted in greenhouse fields, though their significance regarding total N2O emissions and the driving mechanism behind them remain poorly understood. N2O fluxes were monitored in situ using a static opaque chamber method in a typical greenhouse vegetable field. Then, laboratory incubations were conducted under different soil moisture and manure application gradients to monitor nitrous oxide emissions and related soil properties, using a robotized incubation system. Field monitoring showed that the occurrence of clear N2O emission bursts closely followed fertilization and irrigation events, accounting for 76.7% of the annual N2O efflux. The soil N2O flux increased exponentially with the water-filled pore space (WFPS), causing extremely high N2O emissions when the WFPS was higher than 60%. During the lab incubation, emission bursts led to N2O peaks within 40 h, synchronously changing with the transit soil NO2−. An integrated analysis of the variations in the gas emission and soil properties indicated that the denitrification of transit NO2− accumulation was the major explanation for N2O emission bursts in the greenhouse filed. Nitrous oxide emission bursts constituted the major portion of the N2O emissions in the Chinese greenhouse soils. Nitrite (NO2−) denitrification triggered by fertilization and irrigation was responsible for these N2O emission pulses. Our results clarified the significance and biogeochemical mechanisms of N2O burst emissions; this knowledge could help us to devise and enact sounder N2O mitigation measures, which would be conducive to sustainable development in vegetable greenhouse fields.

Overdose fertilization induced ammonia-oxidizing archaea producing nitrous oxide in intensive vegetable fields

Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their differential contribution to nitrous oxide (N₂O) production, particularly in greenhouse based high N input vegetable soils. Six N treatments (N1, N2, N3, N4, N5 and N6 representing 0, 293, 587, 880, 1173 and 1760 kg N ha^-1 yr^-1, respectively) were continuously managed for three years in a typically intensified vegetable field in China. The aerobic incubation experiment involving these field-treated soils was designed to evaluate the relative contributions of AOA and AOB to N₂O production by using acetylene or 1-octyne as inhibitors. The results showed that the soil pH and net nitrification rate gradually declined with increasing the fertilizer N application rates. The AOA were responsible for 44-71% of the N₂O production with negligible N₂O from AOB in urea unamended control soils. With urea amendment, the AOA were responsible for 48-53% of the N₂O production in the excessively fertilized soils, namely the N5-N6 soils, while the AOB were responsible for 42-55% in the conventionally fertilized soils, namely the N1-N4 soils. Results indicated that overdose fertilization induced higher AOA-dependent N₂O production than AOB, whereas urea supply led to higher AOB-dependent N₂O production than AOA in conventionally fertilized soils. Additionally, a positive relationship existed between N₂O production and NO₂^- accumulation during the incubation. Further mechanisms for NO₂^--dependent N₂O production in intensive vegetable soils therefore deserve urgent attention.

Assessing PM2.5 Model Performance for the Conterminous U.S. with Comparison to Model Performance Statistics from 2007-2015

Previous studies have proposed that model performance statistics from earlier photochemical grid model (PGM) applications can be used to benchmark performance in new PGM applications. A challenge in implementing this approach is that limited information is available on consistently calculated model performance statistics that vary spatially and temporally over the U.S. Here, a consistent set of model performance statistics are calculated by year, season, region, and monitoring network for PM2.5 and its major components using simulations from versions 4.7.1-5.2.1 of the Community Multiscale Air Quality (CMAQ) model for years 2007-2015. The multi-year set of statistics is then used to provide quantitative context for model performance results from the 2015 simulation. Model performance for PM2.5 organic carbon in the 2015 simulation ranked high (i.e., favorable performance) in the multi-year dataset, due to factors including recent improvements in biogenic secondary organic aerosol and atmospheric mixing parameterizations in CMAQ. Model performance statistics for the Northwest region in 2015 ranked low (i.e., unfavorable performance) for many species in comparison to the 2007-2015 dataset. This finding motivated additional investigation that suggests a need for improved speciation of wildfire PM2.5emissions and modeling of boundary layer dynamics near water bodies. Several limitations were identified in the approach of benchmarking new model performance results with previous results. Since performance statistics vary widely by region and season, a simple set of national performance benchmarks (e.g., one or two targets per species and statistic) as proposed previously are inadequate to assess model performance throughout the U.S. Also, trends in model performance statistics for sulfate over the 2007 to 2015 period suggest that model performance for earlier years may not be a useful reference for assessing model performance for recent years in some cases. Comparisons of results from the 2015 base case with results from five sensitivity simulations demonstrated the importance of parameterizations of NH3 surface exchange, organic aerosol volatility and production, and emissions of crustal cations for predicting PM2.5 species concentrations.

A Short-term Study to Compare Field Strategies for Ammonia Emission Mitigation

Abatement of NH emissions is crucial in calcareous soils under semiarid Mediterranean climates. The aim of the study was to compare NH emissions using different slurry application methods. An experiment was performed on a clay loam soil to evaluate NH emissions before sowing and at winter cereal tillering. Pig slurry was applied using two methods, one that applied slurry by splashing it over a plate (SP), and another that applied slurry in strips using trail hoses (TH). Emissions were measured using semi-static chambers at variable intervals for 12 to 13 d (315.5 h for sowing and 287 h for tillering). Maximum NH flux emissions were always observed during the earliest period of measurements after slurry spreading (3.5-5 h). Before sowing, regardless of the method, accumulated NH losses (during 315.5 h) ranged between 2 and 3 kg NH-N ha because of the low dry matter content of the slurry (<2%), which enhanced infiltration. Losses represented about 2 to 3% of the total N applied. At cereal tillering, average accumulated losses of NH (during 287 h) were 1.7 kg N ha using TH (1.1% of total N applied) and were as high as 5.4 kg N ha (3.2% of total N applied) using SP. Because N topdressing is recommended as a measure to increase its efficiency, TH is recommended over SP. Thus, this short-term study concludes that TH may reduce NH emissions in semiarid environments. Further study of these strategies is recommended under different climate and soil conditions.

Anoxic nitrogen cycling in a hydrocarbon and ammonium contaminated aquifer

Nitrogen fate and transport through contaminated groundwater systems, where N is both ubiquitous and commonly limits pollutant attenuation, must be re-evaluated given evidence for new potential microbial N pathways. We addressed this by measuring the isotopic composition of dissolved inorganic N (DIN = NH₄⁺, NO₂^-, and NO₃^-) and N functional gene abundances (amoA, nirK, nirS, hszA) from 20 to 38 wells across an NH₄⁺, hydrocarbon, and SO₄^2- contaminated aquifer. In-situ N attenuation was confirmed on three sampling dates (0, +6, +12 months) by the decreased [DIN] (4300 - 40 μM) and increased δ¹⁵N-DIN (5‰-33‰) over the flow path. However, the assumption of negligible N attenuation within the plume was complicated by the presence of alternative electron acceptors (SO₄^2-, Fe³⁺), both oxidizing and reducing functional genes, and N oxides within this anoxic zone. Active plume N cycling was corroborated using an NO₂^- dual isotope based model, which found the fastest (∼10 day) NO₂^- turnover within the N and electron donor rich central plume. Findings suggest that N cycling is not always O₂ limited within chemically complex contaminated aquifers, though this cycling may recycle the N species rather than attenuate N.

Assessing the Impact of Non-Urea Ruminant Urine Nitrogen Compounds on Urine Patch Nitrous Oxide Emissions

Urea, the dominant form of N in ruminant urine, degrades in soil to produce NO emissions. However, the fate of non-urea urine N compounds (NUNCs) in soil and their contribution to urine patch NO emissions remain unclear. This study evaluated five NUNCs: allantoin (10%), creatinine (3%), creatine (3%), uric acid (1%), and (hypo)xanthine (0.6%), where numbers in parentheses represent the average percentage of total urine N. The fates of NUNCs in a pasture soil were determined using N-labeled NUNCs in a laboratory trial. Two NUNCs, hypoxanthine and creatine, were added to the soil with perennial ryegrass ( L.) present and sampled over time for soil inorganic N, NO emissions, and plant N dynamics. The N enrichments of soil inorganic N and plant N were significantly increased within 24 h of NUNC application, indicating rapid microbial degradation and plant uptake of NUNCs in pasture soil. An autumn field trial was also conducted to evaluate the in situ impact of varying concentrations of NUNCs on urine patch NO emissions. Increasing the proportion of urine N excreted as NUNCs did not alter the urine patch NO emission factor, soil inorganic N concentrations, or plant N uptake. It is concluded that NUNCs rapidly degrade in pasture soil and that an increased ruminant excretion of urine N as NUNCs does not significantly alter the urine patch NO emission factor.

Variable effects of biochar application to soils on nitrification-mediated N2O emissions

Although a meta-analysis on biochar's effects on N₂O emission reported an overall reduction in N₂O emission by adding biochar to the soils, there are still variations in the changes in N₂O emission, especially from field results. The objectives of this study are 1) to compare the effects of biochar addition on N₂O emission between three agricultural upland field experiments, where soil water status was dry favoring nitrification and 2) to identify main factors explaining biochar's variable effects on N₂O emission. Three field experiments were conducted: Exp A in the cultivated grassland treated with rice husk biochar at 2 ton ha^-1 + urea (CHAR) and with urea only (CON); Exp B in the cabbage field with CHAR and CON treatments; and Exp C in the pepper field with CHAR, CON, and CHAR + DCD (dicyandiamide, nitrification inhibitor) treatments. In Exp A and C, cumulative N₂O emissions significantly increased by 82.5% and 55.8% in the CHAR than CON treatments, respectively, while in Exp B, there was no difference in cumulative N₂O emission between the CHAR and CON. Based on results from using nitrification inhibitor and soil % water filled pore space (WFPS), we assumed that the main N₂O production mechanism was nitrification. Our results suggest that soil water status right after urea application is the primary determinant of different effects of biochar on N₂O emission in addition to soil C status and biochar's adsorption. Principal component analysis using the 25 compiled data also supported our results. This study identified the specific field conditions under which biochar could have stimulating effects on N₂O emission. Mitigation potential of biochar application should be reconsidered if biochar and urea were amended to dry soils with low C contents.

Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil

Nitrification is the two-step aerobic oxidation of ammonia to nitrate via nitrite in the nitrogen-cycle on earth. However, very limited information is available on how fertilizer regimes affect the distribution of nitrite oxidizers, which are involved in the second step of nitrification, across aggregate size classes in soil. In this study, the community compositions of nitrite oxidizers (Nitrobacter and Nitrospira) were characterized from a red soil amended with four types of fertilizer regimes over a 26-year fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/organic combined fertilization (MNPK). Our results showed that the addition of M and NPK significantly decreased Nitrobacter Shannon and Chao1 index, while M and MNPK remarkably increased Nitrospira Shannon and Chao1 index, and NPK considerably decreased Nitrospira Shannon and Chao1 index, with the greatest diversity achieved in soils amended with MNPK. However, the soil aggregate fractions had no impact on that alpha-diversity of Nitrobacter and Nitrospira under the fertilizer treatment. Soil carbon, nitrogen and phosphorus in the soil had a significant correlation with Nitrospira Shannon and Chao1 diversity index, while total potassium only had a significant correlation with Nitrospira Shannon diversity index. However, all of them had no significant correlation with Nitrobacter Shannon and Chao1 diversity index. The resistance indices for alpha-diversity indexes (Shannon and Chao1) of Nitrobacter were higher than those of Nitrospira in response to the fertilization regimes. Manure fertilizer is important in enhancing the Nitrospira Shannon and Chao1 index resistance. Principal co-ordinate analysis revealed that Nitrobacter- and Nitrospira-like NOB communities under four fertilizer regimes were differentiated from each other, but soil aggregate fractions had less effect on the nitrite oxidizers community. Redundancy analysis and Mantel test indicated that soil nitrogen, carbon, phosphorus, and available potassium content were important environmental attributes that control the Nitrobacter- and Nitrospira-like NOB community structure across different fertilization treatments under aggregate levels in the red soil. In general, nitrite-oxidizing bacteria community composition and alpha-diversity are depending on fertilizer regimes, but independent of the soil aggregate.

Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils

Application of nitrogen (N) fertilizers, predominantly as urea, is a major source of reactive N in the environment, with wide ranging effects including increased greenhouse gas accumulation in the atmosphere and aquatic eutrophication. The soil microbial community is the principal driver of soil N cycling; thus, improved understanding of microbial community responses to urea addition has widespread implications. We used next-generation amplicon sequencing of the 16S rRNA gene to characterize bacterial and archaeal communities in eight contrasting agricultural soil types amended with 0, 100, or 500 μg N g^-1 of urea and incubated for 21 days. We hypothesized that urea amendment would have common, direct effects on the abundance and diversity of members of the microbial community associated with nitrification, across all soils, and would further affect the broader heterotrophic community resulting in decreased diversity and variation in abundances of specific taxa. Significant (P < 0.001) differences in bacterial community diversity and composition were observed by site, but amendment with only the greatest urea concentration significantly decreased Shannon indices. Expansion in the abundances of members of the families Microbacteriaceae, Chitinophagaceae, Comamonadaceae, Xanthomonadaceae, and Nitrosomonadaceae were also consistently observed among all soils (linear discriminant analysis score ≥ 3.0). Analysis of nitrifier genera revealed diverse, soil-specific distributions of oligotypes (strains), but few were correlated with nitrification gene abundances that were reported in a previous study. Our results suggest that the majority of the bacterial and archaeal community are likely unassociated with N cycling, but are significantly negatively impacted by urea application. Furthermore, these results reveal that amendment with high concentrations of urea may reduce nitrifier diversity, favoring specific strains, specifically those within the nitrifying genera Nitrobacter, Nitrospira, and Nitrosospira, that may play significant roles related to N cycling in soils receiving intensive urea inputs.

Influence of soil moisture on codenitrification fluxes from a urea-affected pasture soil

Intensively managed agricultural pastures contribute to N₂O and N₂ fluxes resulting in detrimental environmental outcomes and poor N use efficiency, respectively. Besides nitrification, nitrifier-denitrification and heterotrophic denitrification, alternative pathways such as codenitrification also contribute to emissions under ruminant urine-affected soil. However, information on codenitrification is sparse. The objectives of this experiment were to assess the effects of soil moisture and soil inorganic-N dynamics on the relative contributions of codenitrification and denitrification (heterotrophic denitrification) to the N₂O and N₂ fluxes under a simulated ruminant urine event. Repacked soil cores were treated with ¹⁵N enriched urea and maintained at near saturation (−1 kPa) or field capacity (−10 kPa). Soil inorganic-N, pH, dissolved organic carbon, N₂O and N₂ fluxes were measured over 63 days. Fluxes of N₂, attributable to codenitrification, were at a maximum when soil nitrite (NO₂⁻) concentrations were elevated. Cumulative codenitrification was higher (P = 0.043) at −1 kPa. However, the ratio of codenitrification to denitrification did not differ significantly with soil moisture, 25.5 ± 15.8 and 12.9 ± 4.8% (stdev) at −1 and −10 kPa, respectively. Elevated soil NO₂⁻ concentrations are shown to contribute to codenitrification, particularly at −1 kPa.

Interactive effects of MnO2, organic matter and pH on abiotic formation of N2O from hydroxylamine in artificial soil mixtures

Abiotic conversion of the reactive nitrification intermediate hydroxylamine (NH₂OH) to nitrous oxide (N₂O) is a possible mechanism of N₂O formation during nitrification. Previous research has demonstrated that manganese dioxide (MnO₂) and organic matter (OM) content of soil as well as soil pH are important control variables of N₂O formation in the soil. But until now, their combined effect on abiotic N₂O formation from NH₂OH has not been quantified. Here, we present results from a full-factorial experiment with artificial soil mixtures at five different levels of pH, MnO₂ and OM, respectively, and quantified the interactive effects of the three variables on the NH₂OH-to-N₂O conversion ratio (R_NH2OH-to-N2O). Furthermore, the effect of OM quality on R_NH2OH-to-N2O was determined by the addition of four different organic materials with different C/N ratios to the artificial soil mixtures. The experiments revealed a strong interactive effect of soil pH, MnO₂ and OM on R_NH2OH-to-N2O. In general, increasing MnO₂ and decreasing pH increased R_NH2OH-to-N2O, while increasing OM content was associated with a decrease in R_NH2OH-to-N2O. Organic matter quality also affected R_NH2OH-to-N2O. However, this effect was not a function of C/N ratio, but was rather related to differences in the dominating functional groups between the different organic materials.

Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question

Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N₂) gas. The greenhouse gas nitrous oxide (N₂O) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source to form N₂O. However, N₂ can be formed from two distinct N sources (known as hybrid N₂) through biologically mediated processes of anammox and codenitrification. We questioned if hybrid N₂ produced during fungal incubation at neutral pH could be attributed to abiotic nitrosation and if N₂O was consumed during N₂ formation. Experiments with gas chromatography indicated N₂ was formed in the presence of live and dead fungi and in the absence of fungi, while N₂O steadily increased. We used isotope pairing techniques and confirmed abiotic production of hybrid N₂ under both anoxic and 20% O₂ atmosphere conditions. Our findings question the assumptions that (1) N₂O is an intermediate required for N₂ formation, (2) production of N₂ and N₂O requires anaerobiosis, and (3) hybrid N₂ is evidence of codenitrification and/or anammox. The N cycle framework should include abiotic production of N₂.

A geostatistical approach to identify and mitigate agricultural nitrous oxide emission hotspots

Anthropogenic emissions of nitrous oxide (N₂O), a trace gas with severe environmental costs, are greatest from agricultural soils amended with nitrogen (N) fertilizer. However, accurate N₂O emission estimates at fine spatial scales are made difficult by their high variability, which represents a critical challenge for the management of N₂O emissions. Here, static chamber measurements (n=60) and soil samples (n=129) were collected at approximately weekly intervals (n=6) for 42-d immediately following the application of N in a southern Minnesota cornfield (15.6-ha), typical of the systems prevalent throughout the U.S. Corn Belt. These data were integrated into a geostatistical model that resolved N₂O emissions at a high spatial resolution (1-m). Field-scale N₂O emissions exhibited a high degree of spatial variability, and were partitioned into three classes of emission strength: hotspots, intermediate, and coldspots. Rates of emission from hotspots were 2-fold greater than non-hotspot locations. Consequently, 36% of the field-scale emissions could be attributed to hotspots, despite representing only 21% of the total field area. Variations in elevation caused hotspots to develop in predictable locations, which were prone to nutrient and moisture accumulation caused by terrain focusing. Because these features are relatively static, our data and analyses indicate that targeted management of hotspots could efficiently reduce field-scale emissions by as much 17%, a significant benefit considering the deleterious effects of atmospheric N₂O.

Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4(+)-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.

Evaluation of Intensive "4R" Strategies for Decreasing Nitrous Oxide Emissions and Nitrogen Surplus in Rainfed Corn

The "4R" approach of using the right rate, right source, right timing, and right placement is an accepted framework for increasing crop N use efficiency. However, modifying only one 4R component does not consistently reduce nitrous oxide (NO) emissions. Our objective was to determine if N fertilizer applied in three split applications (Sp), by itself or combined with changes in N source and rate, could improve N recovery efficiency (NRE) and N surplus (NS) and decrease NO emissions. Over two corn ( L.) growing seasons in Minnesota, NO emissions ranged from 0.6 to 0.9 kg N ha. None of the treatment combinations affected grain yield. Compared with urea applied in a single application at the recommended N rate, Sp by itself did not improve NRE or NS and did not decrease NO. Combining Sp with urease and nitrification inhibitors and/or a 15% reduction in N rate increased NRE from 57 to >73% and decreased NS by >20 kg N ha. The only treatment that decreased NO (by 20-53%) was Sp combined with inhibitors and reduced N rate. Emissions of NO were more strongly correlated with NS calculated from grain N uptake ( = 0.61) compared with whole-plant N uptake ( = 0.39), possibly because most N losses occurred before grain filling. Optimizing both application timing and N source can allow for a moderate reduction in N rate that does not affect grain yield but decreases NO. Grain-based NS may be a more useful indicator of NO emissions than whole-plant-based NS.

Clays Can Decrease Gaseous Nutrient Losses from Soil-Applied Livestock Manures

Clays could underpin a viable agricultural greenhouse gas (GHG) abatement technology given their affinity for nitrogen and carbon compounds. We provide the first investigation into the efficacy of clays to decrease agricultural nitrogen GHG emissions (i.e., NO and NH). Via laboratory experiments using an automated closed-vessel analysis system, we tested the capacity of two clays (vermiculite and bentonite) to decrease NO and NH emissions and organic carbon losses from livestock manures (beef, pig, poultry, and egg layer) incorporated into an agricultural soil. Clay addition levels varied, with a maximum of 1:1 to manure (dry weight). Cumulative gas emissions were modeled using the biological logistic function, with 15 of 16 treatments successfully fitted ( < 0.05) by this model. When assessing all of the manures together, NH emissions were lower (×2) at the highest clay addition level compared with no clay addition, but this difference was not significant ( = 0.17). Nitrous oxide emissions were significantly lower (×3; < 0.05) at the highest clay addition level compared with no clay addition. When assessing manures individually, we observed generally decreasing trends in NH and NO emissions with increasing clay addition, albeit with widely varying statistical significance between manure types. Most of the treatments also showed strong evidence of increased C retention with increasing clay additions, with up to 10 times more carbon retained in treatments containing clay compared with treatments containing no clay. This preliminary assessment of the efficacy of clays to mitigate agricultural GHG emissions indicates strong promise.