Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production

Competitive partitioning of denitrification pathways during arrested methanogenesis: Implications in ammonium recovery, N2O emission, and volatile fatty acid production

The complex interaction between nitrate (NO3-) reduction and fermentation is poorly understood when high levels of NO3- are introduced into anaerobic systems. This study investigated the competitive distribution between conventional denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA) during simultaneous denitrification and fermentation in arrested methanogenesis. Up to 62% of initial NO3- (200 mg-N/L) was retained as ammonium through DNRA at a chemical oxygen demand (COD)/N ratio of 25. Significant N2O emission occurred (1.7 - 8.0% of the initial NO3-) with limited carbon supply (≤1600 mg COD/L) and sludge concentration (≤3000 mg COD/L). VFA composition shifted predominantly towards acetic acid (>50%) in the presence of nitrate. A novel kinetic model was developed to predict DNRA vs. DEN partitioning and NO2- accumulation. Overall, NO3- input, organic loading, and carbon source characteristics independently and collectively controlled competitive DNRA vs. DEN partitioning.

Portable IC system enabled with dual LED-based absorbance detectors and 3D-printed post-column heated micro-reactor for the simultaneous determination of ammonium, nitrite and nitrate

BACKGROUND

The on-site and simultaneous determination of anionic nitrite (NO2-) and nitrate (NO3-), and cationic ammonium (NH4+), in industrial and natural waters, presents a significant analytical challenge. Toward this end, herein a 3D-printed micro-reactor with an integrated heater chip was designed and optimised for the post-column colorimetric detection of NH4+ using a modified Berthelot reaction. The system was integrated within a portable and field deployable ion chromatograph (Aquamonitrix) designed to separate and detect NO2- and NO3-, but here enabled with dual LED-based absorbance detectors, with the aim to provide the first system capable of simultaneous determination of both anions and NH4+ in industrial and natural waters.

RESULTS

Incorporating a 0.750 mm I.D. 3D-printed serpentine-based microchannel for sample-reagent mixing and heating, the resultant micro-reactor had a total reactor channel length of 1.26 m, which provided for a reaction time of 1.42 min based upon a total flow rate of 0.27 mL min-1, within a 40 mm2 printed area. The colorimetric reaction was performed within the micro-reactor, which was then coupled to a dedicated 660 nm LED-based absorbance detector. By rapidly delivering a reactor temperature of 70 °C in just 40 s, the optimal conditions to improve reaction kinetics were achieved to provide for limits of detection of 0.1 mg L-1 for NH4+, based upon an injection volume of just 10 μL. Linearity for NH4+ was observed over the range 0-50 mg L-1, n = 3, R2 = 0.9987. The reactor was found to deliver excellent reproducibility when included as a post-column reactor within the Aquamonitrix analyser, with an overall relative standard deviation below 1.2 % for peak height and 0.3 % for peak residence time, based upon 6 repeat injections.

SIGNIFICANCE

The printed post-column reactor assembly was integrated into a commercial portable ion chromatograph developed for the separation and detection of NO2- and NO3-, thus providing a fully automated system for the remote and simultaneous analysis of NO2-, NO3-, and NH4+ in natural and industrial waters. The fully automated system was deployed externally within a greenhouse facility to demonstrate this capability.

Effects of Long-Term Controlled-Release Urea on Soil Greenhouse Gas Emissions in an Open-Field Lettuce System

Controlled-release urea (CRU) fertilizers are widely used in agricultural production to reduce conventional nitrogen (N) fertilization-induced agricultural greenhouse gas emissions (GHGs) and improve N use efficiency (NUE). However, the long-term effects of different CRU fertilizers on GHGs and crop yields in vegetable fields remain relatively unexplored. This study investigated the variations in GHG emissions at four growth stages of lettuce in the spring and autumn seasons based on a five-year field experiment in the North China Plain. Four treatments were setup: CK (without N application), U (conventional urea-N application), ON (20% reduction in urea-N application), CRU (20% reduction in polyurethane-coated urea without topdressing), and DCRU (20% reduction in polyurethane-coated urea containing dicyandiamide [DCD] without topdressing). The results show that N application treatments significantly increased the GHG emissions and the lettuce yield and net yield, and DCRU exhibited the lowest N2O and CO2 emissions, the highest lettuce yield and net yield, and the highest lettuce N content of the N application treatments. When compared to U, the N2O emission peak under CRU and DCRU treatments was notably decreased and delayed, and their average N2O emission fluxes were significantly reduced by 10.20-20.72% and 17.51-29.35%, respectively, leading to a significant reduction in mean cumulative N2O emissions during the 2017-2021 period. When compared to U, the CO2 fluxes of DCRU significantly decreased by 8.0-16.54% in the seedling period, and mean cumulative CO2 emission decreased by 9.28%. Moreover, compared to U, the global warming potential (GWP) and greenhouse gas intensity (GHGI) of the DCRU treatment was significantly alleviated by 9.02-17.13% and 16.68-20.36%, respectively. Compared to U, the N content of lettuce under DCRU was significantly increased by 6.48-17.25%, and the lettuce net yield was also significantly increased by 5.41-7.71%. These observations indicated that the simple and efficient N management strategy to strike a balance between enhancing lettuce yields and reduce GHG emissions in open-field lettuce fields could be obtained by applying controlled-release urea containing DCD without topdressing.

Denitrification dominates dissimilatory nitrate reduction across global natural ecosystems

Denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) are three competing processes of microbial nitrate reduction that determine the degree of ecosystem nitrogen (N) loss versus recycling. However, the global patterns and drivers of relative contributions of these N cycling processes to soil or sediment nitrate reduction remain unknown, limiting our understanding of the global N balance and management. Here, we compiled a global dataset of 1570 observations from a wide range of terrestrial and aquatic ecosystems. We found that denitrification contributed up to 66.1% of total nitrate reduction globally, being significantly greater in estuarine and coastal ecosystems. Anammox and DNRA could account for 12.7% and 21.2% of total nitrate reduction, respectively. The contribution of denitrification to nitrate reduction increased with longitude, while the contribution of anammox and DNRA decreased. The local environmental factors controlling the relative contributions of the three N cycling processes to nitrate reduction included the concentrations of soil organic carbon, ammonium, nitrate, and ferrous iron. Our results underline the dominant role of denitrification over anammox and DNRA in ecosystem nitrate transformation, which is crucial to improving the current global soil N cycle model and achieving sustainable N management.

Effects of stand density on the structure of soil microbial functional groups in Robinia pseudoacacia plantations in the hilly and gully region of the Loess Plateau, China

Elucidating the responses of soil microbial functional groups to changes in stand density is crucial for understanding the sustainability of forest development. In this study, we obtained soil samples from Robinia pseudoacacia plantations of three different stand densities (low, middle, and high densities of 750, 1125, and 1550 trees ha-1, respectively) in the hilly and gully region of the Loess Plateau, China. We sought to determine the effects of stand density on the structure of soil microbial functional groups. Stand density had no significant effects on species diversity indices of fungal trophic modes or bacterial functional groups involved in carbon (C) cycling and nitrogen (N) cycling. However, differences in stand density substantially altered the composition of fungal functional groups. In low-density plantations, saprophytic fungi were the main trophic mode, with a high relative abundance of ∼62 %, whereas the fungal communities associated with middle- and high-density plantations were dominated by other fungi with a combined trophic mode, which accounted for ∼43 % and ∼41 % of the fungal trophic modes, respectively. Furthermore, we detected increases in the relative abundance of plant pathogens, nitrifiers, and nitrous oxide-denitrifying bacteria with increasing stand density. Results of the Monte Carlo test showed that soil pH influenced the composition of soil fungal (but not bacterial) groups. These findings suggested that a high density of trees might inhibit the decomposition of recalcitrant organic material and stimulate nitrous oxide emission, consequently decreasing soil nutrient availability and stimulating soil N loss. Moreover, high-density stands might increase the potential risk for plant disease. Overall, the present study suggested that reducing stand density to coverage between 750 and 1125 trees ha-1 would increase soil nutrient availability and prevent N loss from the soil. To verify these suppositions, further research is needed to determine the links between microbial functional groups composition and soil biogeochemistry.

Droplet Microfluidic-Based In Situ Analyzer for Monitoring Free Nitrate in Soil

Monitoring nutrients in the soil can provide valuable information for understanding their spatiotemporal variability and informing precise soil management. Here, we describe an autonomous in situ analyzer for the real-time monitoring of nitrate in soil. The analyzer can sample soil nitrate using either microdialysis or ultrafiltration probes placed within the soil and quantify soil nitrate using droplet microfluidics and colorimetric measurement. Compared with traditional manual sampling and lab analysis, the analyzer features low reagent consumption (96 μL per measurement), low maintenance requirement (monthly), and high measurement frequency (2 or 4 measurements per day), providing nondrifting lab-quality data with errors of less than 10% using a microdialysis probe and 2-3% for ultrafiltration. The analyzer was deployed at both the campus garden and forest for different periods of time, being able to capture changes in free nitrate levels in response to manual perturbation by the addition of nitrate standard solutions and natural perturbation by rainfall events.

Modeling denitrification nitrogen losses in China's rice fields based on multiscale field-experiment constraints

Denitrification plays a critical role in soil nitrogen (N) cycling, affecting N availability in agroecosystems. However, the challenges in direct measurement of denitrification products (NO, N2 O, and N2 ) hinder our understanding of denitrification N losses patterns across the spatial scale. To address this gap, we constructed a data-model fusion method to map the county-scale denitrification N losses from China's rice fields over the past decade. The estimated denitrification N losses as a percentage of N application from 2009 to 2018 were 11.8 ± 4.0% for single rice, 12.4 ± 3.7% for early rice, and 11.6 ± 3.1% for late rice. The model results showed that the spatial heterogeneity of denitrification N losses is primarily driven by edaphic and climatic factors rather than by management practices. In particular, diffusion and production rates emerged as key contributors to the variation of denitrification N losses. These findings humanize a 38.9 ± 4.8 kg N ha-1  N loss by denitrification and challenge the common hypothesis that substrate availability drives the pattern of N losses by denitrification in rice fields.

Role of Soil Microbiota Enzymes in Soil Health and Activity Changes Depending on Climate Change and the Type of Soil Ecosystem

The extracellular enzymes secreted by soil microorganisms play a pivotal role in the decomposition of organic matter and the global cycles of carbon (C), phosphorus (P), and nitrogen (N), also serving as indicators of soil health and fertility. Current research is extensively analyzing these microbial populations and enzyme activities in diverse soil ecosystems and climatic regions, such as forests, grasslands, tropics, arctic regions and deserts. Climate change, global warming, and intensive agriculture are altering soil enzyme activities. Yet, few reviews have thoroughly explored the key enzymes required for soil fertility and the effects of abiotic factors on their functionality. A comprehensive review is thus essential to better understand the role of soil microbial enzymes in C, P, and N cycles, and their response to climate changes, soil ecosystems, organic farming, and fertilization. Studies indicate that the soil temperature, moisture, water content, pH, substrate availability, and average annual temperature and precipitation significantly impact enzyme activities. Additionally, climate change has shown ambiguous effects on these activities, causing both reductions and enhancements in enzyme catalytic functions.

In situ 15 N-N2 O site preference and O2 concentration dynamics disclose the complexity of N2 O production processes in agricultural soil

Arable soil continues to be the dominant anthropogenic source of nitrous oxide (N2 O) emissions owing to application of nitrogen (N) fertilizers and manures across the world. Using laboratory and in situ studies to elucidate the key factors controlling soil N2 O emissions remains challenging due to the potential importance of multiple complex processes. We examined soil surface N2 O fluxes in an arable soil, combined with in situ high-frequency measurements of soil matrix oxygen (O2 ) and N2 O concentrations, in situ 15 N labeling, and N2 O 15 N site preference (SP). The in situ O2 concentration and further microcosm visualized spatiotemporal distribution of O2 both suggested that O2 dynamics were the proximal determining factor to matrix N2 O concentration and fluxes due to quick O2 depletion after N fertilization. Further SP analysis and in situ 15 N labeling experiment revealed that the main source for N2 O emissions was bacterial denitrification during the hot-wet summer with lower soil O2 concentration, while nitrification or fungal denitrification contributed about 50.0% to total emissions during the cold-dry winter with higher soil O2 concentration. The robust positive correlation between O2 concentration and SP values underpinned that the O2 dynamics were the key factor to differentiate the composite processes of N2 O production in in situ structured soil. Our findings deciphered the complexity of N2 O production processes in real field conditions, and suggest that O2 dynamics rather than stimulation of functional gene abundances play a key role in controlling soil N2 O production processes in undisturbed structure soils. Our results help to develop targeted N2 O mitigation measures and to improve process models for constraining global N2 O budget.

Different types of land use influence soil physiochemical properties, the abundance of nitrifying bacteria, and microbial interactions in tropical urban soil

Anthropogenic activities have led to unexpected changes in microbial community composition and structure, resulting in an interruption of soil ecological roles in urban environments. We questioned the impact of the different land use (e.g., agricultural, industrial, recreational, coastal, and residential areas) on the distribution of nitrifying bacteria and microbial interaction in tropical soil. The dominant nitrifying bacteria were ammonia-oxidizing archaea (AOA) in tropical soils up to 10⁷ copies/g of soil, while the abundance of ammonia-oxidizing bacteria (AOB) was significantly higher in agricultural soil only. Comammox (CMX) was ubiquitous up to 10⁵ copies/g of tropical soil, indicating that CMX might share ecological niches with AOA and considerably contribute to nitrification in urban areas. The most abundant phylum is Actinobacteria, accounting for 27-34 % relative abundance among most land-use types, but Proteobacteria was observed as the most prevalent phylum in agricultural soil. The physicochemical properties (e.g., soil pH and nutrient contents) of different types of land use influenced microbial richness and diversities associated with nitrogen cycling. Multivariate analysis disclosed that agricultural soils were distinct from other land uses because of the concentrations of nutrients and heavy metals and the abundance of microorganisms associated with nitrogen cycles. Also, the microbial co-occurrence network revealed that agricultural soils were a highly interconnected network of the microbial community. In this study, C: N ratio might have a significant impact on ecological networks and the abundance of nitrogen-related taxa, which could influence microbial interactions and complexity in tropical soils. Thus, the impact of anthropogenic land use induced changes in microbial composition and diversity, co-occurrence network, and nitrifying bacteria, leading to potential transformation in ecological services of tropical soils and nitrogen cycling in urban environments.

Carbon-sink potential of continuous alfalfa agriculture lowered by short-term nitrous oxide emission events

Alfalfa is the most widely grown forage crop worldwide and is thought to be a significant carbon sink due to high productivity, extensive root systems, and nitrogen-fixation. However, these conditions may increase nitrous oxide (N₂O) emissions thus lowering the climate change mitigation potential. We used a suite of long-term automated instrumentation and satellite imagery to quantify patterns and drivers of greenhouse gas fluxes in a continuous alfalfa agroecosystem in California. We show that this continuous alfalfa system was a large N₂O source (624 ± 28 mg N₂O m² y^-1), offsetting the ecosystem carbon (carbon dioxide (CO₂) and methane (CH₄)) sink by up to 14% annually. Short-term N₂O emissions events (i.e., hot moments) accounted for ≤1% of measurements but up to 57% of annual emissions. Seasonal and daily trends in rainfall and irrigation were the primary drivers of hot moments of N₂O emissions. Significant coherence between satellite-derived photosynthetic activity and N₂O fluxes suggested plant activity was an important driver of background emissions. Combined data show annual N₂O emissions can significantly lower the carbon-sink potential of continuous alfalfa agriculture.

Deciphering biochar compost co-application impact on microbial communities mediating carbon and nitrogen transformation across different stages of corn development

Under current climatic conditions, developing eco-friendly and climate-smart fertilizers has become increasingly important.The co-application of biochar and compost on agricultural soils has received considerable attention recently.Unfortunately, little is known about its effects on specific microbial taxa involved in carbon and nitrogen transformation in the soil.Herein, we report the efficacy of applying biochar-based amendments on soil physicochemical indices, enzymatic activity, functional genes, bacterial community, and their network patterns in corn rhizosphere at seedling (SS), flowering (FS), and maturity (MS) stages.The applied treatments were: compost alone (COM), biochar alone (BIOC), composted biochar (CMB), fortified compost (CMWB), and the control (no fertilizer (CNTRL).The non-metric multidimensional scaling (NMDS) indicated total nitrogen (TN), pH, NO₃^--N, urease, protease, and microbial biomass C (MBC) as the dominant environmental factors driving soil bacteria in this study.The dominant N mediating genes belonged to nitrate reductase (narG) and nitronate monooxygenase (amo), while beta-galactosidase, catalase, and alpha-amylase were the dominant genes observed relating to C cycling.Interestingly, the abundance of these genes was higher in COM, CMWB, and CMB compared with the CNTRL and BIOC treatments.The bacteria network properties of CWMB and CMB indicated robust niche overlap associated with high cross-feeding between bacterial communities compared to other treatments.Path and stepwise regression analyses revealed norank_Reyranellaceae and Sphingopyxis in CMWB as the major bacterial genera and the major predictive indices mediating soil organic C (SOC), NH₄⁺-N, NO₃^--N, and TN transformation.Overall, biochar with compost amendments improved soil nutrient conditions, regulated the composition of the bacterial community, and benefited C/N cycling in the soil ecosystem.

Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils

CH₄ emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH₄ oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH₄ produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH₄ oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH₄ oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH₄ emissions via the reduction of CH₄ oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO₃^- is responsible for the decrease in CH₄ oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH₄ oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH₄ emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH₄ dynamics in Arctic regions.

Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea

The desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches. IMPORTANCE The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. Here, we investigated bacterial and archaeal communities in the rhizosphere of pioneer plants by combining classic molecular methods with amplicon sequencing as well as metagenomics for functional insights. By implementing a desiccation gradient, we observed (i) remarkable differences in the archaeon-bacterium ratio of plant rhizosphere samples, (ii) replacement of archaeal indicator taxa during succession, and (iii) the presence of specific, potentially plant-beneficial biosynthetic pathways in archaea present during the early stages. In addition, our results provide hitherto-undescribed insights into the functional redundancy between plant-associated archaea and bacteria.

Conversion from rice fields to vegetable fields alters product stoichiometry of denitrification and increases N2O emission

Information about effects of conversion from rice fields to vegetable fields on denitrification process is still limited. In this study, denitrification rate and product ratio (i.e., N₂O/(N₂O + N₂) ratio) were investigated by soil-core incubation based N₂/Ar technique in one rice paddy field (RP) and two vegetable fields (VF4 and VF7, 4 and 7 years vegetable cultivating after conversion from rice fields, respectively). Genes related to denitrification and bacterial community composition were quantified to investigate the microbial mechanisms behind the effects of land-use conversion. The results showed that conversion of rice fields to vegetable fields did not significantly change denitrification rate although the abundance of denitrification related genes was significantly reduced by 79.22%-99.84% in the vegetable soils. Whereas, compared with the RP soil, N₂O emission rate was significantly (P < 0.05) increased by 53.5 and 1.6 times in the VF4 and VF7 soils, respectively. Correspondingly, the N₂O/(N₂O + N₂) ratio increased from 0.18% (RP soil) to 5.65% and 0.65% in the VF4 and VF7 soils, respectively. These changes were mainly attributed to the lower pH, higher nitrate content, and the altered bacterial community composition in the vegetable soils. Overall, our results showed that conversion of rice fields to vegetable fields increased the N₂O emission rate and altered the product ratio of denitrification. This may increase the contribution of land-use conversion to global warming and stratospheric ozone depletion.

Response of Wheat Cultivars to Organic and Inorganic Nutrition: Effect on the Yield and Soil Biological Properties

The deterioration of soil biological health is the most important aspect associated with the sustainability of cereal-based food production systems. The application of organic nutrient sources is widely accepted and recommended for sustaining crop productivity and preserving soil fertility. Therefore, a study was carried out to assess the effects of different levels of farmyard manure (FYM10: 10 t ha−1, FYM20: 20 t ha−1, FYM30: 30 t ha−1), including inorganic fertilizer (NPK) on the soil and the biological properties of five high-yielding wheat cultivars (HD 2967, DPW 621-50, PBW 550, and WH 1105) over a three-year period (2014–2015 to 2016–2017). The results showed that the application of NPK produced significantly higher yields compared to different levels of FYM and the control during all the study years. The continuous addition of a higher rate of FYM at 30 t ha−1 was found to be beneficial in terms of enhancing crop yield gain, thereby bridging the yield gap to only 7.2% in the third year; the gap was 69.1% in the first year with NPK application. The microbial population and microbial biomass carbon were significantly higher in the FYM treatments compared to the NPK treatment. The activities of different soil enzymes were observed to be significantly maximum in the FYM30 treatment. Similarly, the addition of FYM significantly improved the soil respiration and microbial activity over the NPK and control treatments. Based on the principal component analysis, fluorescein diacetate, bacteria, fungi, and actinomycetes were observed as sensitive biological parameters for the assessing of soil biological health. The soil biological index (SBI) determined with the sensitive parameters was in the decreasing order of FYM30 (0.70), FYM20 (0.61), FYM10 (0.55), NPK (0.18), and control (0.15). Considering both the SBI and the sustainability yield index together, the performance of WH 1105 was found to be better compared to the rest of the wheat cultivars. Our results conclude that the application of FYM in the long run increases the crop yield (24.3 to 38.9%) and improves the soil biological process, leading to the improved biological index of the soil.

The influences of soil sulfate content on the transformations of nitrate and sulfate during the reductive soil disinfestation (RSD) process

The transformations and products of sulfate (SO₄^2-) and nitrate (NO₃^-), especially the influences of SO₄^2- content on the transformations during RSD process, are unclear. In this study, a series of soil SO₄^2- contents (from 333 to 3000 mg S kg^-1) were prepared before RSD treatment. The results indicated that nearly all the cumulative NO₃^- (>98.6%) was removed and not affected by the soil SO₄^2- content. The ¹⁵N recovery results showed that 0.57-1.24% and 2.94-4.59% of NO₃^- translated into ammonium (NH₄⁺) and organic N, respectively, and high SO₄^2- contents stimulated the processes of NO₃^- dissimilatory reduction and NO₃^- immobilization. The soluble SO₄^2- contents decreased by 397-922 mg S kg^-1, but the contents of total sulfur, sulfide, and sulfate precipitation varied slightly after RSD, indicating that the decreased SO₄^2- was mainly immobilized into organic sulfur in all soils. In addition, a fraction of decreased SO₄^2- was adsorbed to the soil with a relatively high SO₄^2- content. The leaching of SO₄^2- was high (42.9-602 mg S kg^-1) during the RSD process, and the leaching amounts increased with increasing soil SO₄^2- content. In terms of the gases emitted from the transformations of NO₃^- and SO₄^2-, the cumulative emissions of nitrous oxide (N₂O) and six sulfurous gases (hydrogen sulfide, carbonyl sulfide, carbon disulfide, methyl mercaptan, dimethyl sulfide, and dimethyl disulfide) were in the ranges of 17.1-21.2 mg N kg^-1 and 7.78-23.5 μg S kg^-1, respectively, during the whole RSD process. The emissions of sulfurous gases were inhibited by high soil SO₄^2- content, but the N₂O emissions were unaffected. In conclusion, the soil SO₄^2- content influenced the transformations of NO₃^- and SO₄^2- during RSD process, and the SO₄^2- leaching and N₂O emissions might threaten the environment which should be concerned.

Role of chemical reactions in the nitrogenous trace gas emissions and nitrogen retention: A meta-analysis

Increasing evidence has been found that chemical reactions affect significantly the terrestrial nitrogen (N) cycle, which was previously assumed to be mainly dominated by biological processes. Due to the limitation of knowledge and analytical techniques, it is currently challenging to discern the contribution of biotic and abiotic processes to the terrestrial N cycle for geobiologists and biogeochemists alike. To better understand the role of abiotic reactions in the terrestrial N cycle, it is necessary to comprehend the chemical controls on nitrogenous trace gas emissions and N retention in soil under various environmental conditions. In this manuscript, we assess the role of abiotic reactions in nitrous oxide (N₂O) and nitric oxide (NO) emissions as well as N retention through a meta-analysis using all related peer-reviewed publications before August 2020. Results show that abiotic reactions contributed 29.3-37.7% and 44.0-57.0% to the total N₂O emission and N retention, representing 3.7-4.7 and 4.0-6.0 Tg year^-1 of global terrestrial N₂O emission and N retention, respectively. Much higher NO production was observed in sterilized soils than that in unsterilized treatments indicating the major contribution of chemical reactions to NO emission and rapid microbial reduction of NO to N₂O and N₂. Chemical hydroxylamine oxidation accounts for the largest abiotic contribution to N₂O emission, while chemical nitrite reduction and fixation represent for the largest contribution to abiotic NO production and soil N retention, respectively. Factors influencing the abiotic processes include pH, total organic carbon (TOC), total nitrogen (TN), the ratio of carbon to nitrogen (C/N), and transition metals. These results broadened our knowledge about the mechanisms involved in chemical N reactions and provided a simplified estimation about their contribution to nitrogenous trace gas emission and N retention, which is meaningful to further study interactions of biologically and chemically mediated reactions in biogeochemical N cycle.

Delineation of Nitrate Reduction Hotspots in Artificially Drained Areas through Assessment of Small-Scale Spatial Variability of Electrical Conductivity Data

Identification of nitrate reduction hotspots (NRH) can be instrumental in implementing targeted strategies for reducing nitrate loading from agriculture. In this study, we aimed to delineate possible NRH areas from soil depths of 80 to 180 cm in an artificially drained catchment by utilizing electrical conductivity (EC) values derived by the inversion of apparent electrical conductivity data measured by an electromagnetic induction instrument. The NRH areas were derived from the subzones generated from clustering the EC values via two methods, unsupervised ISODATA clustering and the Optimized Hot Spot Analysis, that highly complement each other. The clustering of EC values generated three classes, wherein the classes with high EC values correspond to NRH areas as indicated by their low redox potential values and nitrate (NO₃⁻) concentrations. Nitrate concentrations in the NRH were equal to 13 to 17% of the concentrations in non-NRH areas and occupied 26% of the total area of the drainage catchments in the study. It is likely that, with the identification of NRH areas, the degree of nitrogen reduction in the vadose zone may be higher than initially estimated at the subcatchment scale.

How could simulated dewatering of slurry mitigate nitrous oxide emissions from fall and spring injections? - A modelling study in a Chernozem soil in Western Canada

Process-based ecosystem models, such as ecosys, can be useful tools to gain insights and accurately project nitrous oxide (N₂O) inventories in national, regional and global scales, and to explore potential emission reduction strategies. Our objectives are to investigate how the ecosys model simulate the effects of fall and spring slurry injections on N₂O production and if de-watering slurry could become a potential N₂O mitigation strategy for both fall and spring injections. The ecosys model was used to simulate hourly N₂O fluxes from 2014 to 2017 in a cropping system with and without slurry (fall and spring additions) in comparison with field measurements in Alberta, Canada. Furthermore, we performed simulations of de-watered fall and spring slurry applications in the same scenarios. Our results showed ecosys adequately simulated soil temperatures and moisture contents at 10 and 20 cm depths [correlation coefficients (r) ≥ 0.929 for temperatures; r ≥ 0.529 for moistures]. The divergences of modelled and measured soil water contents during spring thaws could be attributed to uncertainties in model inputs for soil hydrological parameters as well as uncertainties in field measurements. The model captured reasonably well the dynamics of N₂O fluxes from soils receiving fall and spring slurry (r = 0.356). However, the concurrent discrepancies of N₂O fluxes between modelled and measured values during the wetter spring thaw of 2017 might be a result of an unsatisfactory simulation of snowmelt infiltration and runoff. Compared to whole slurry, simulated de-watered slurry resulted in considerable reductions in cumulative N₂O emissions by 16-36 and 23-29% for fall and spring slurry injections, respectively. The model results indicate that de-watering slurry would potentially be an efficient emission mitigation strategy; however, there is still a paucity of studies addressing the feasibility of dewatering as a practice and further research can focus on this knowledge gap.

Quantitative analysis of soil sustainability after applying stabilizing amendments in long-term Cd-contaminated paddy soils

Considering the biomagnification in food chains, cadmium (Cd) contamination in paddy fields has become concerning. The remediation of soil cadmium by the addition of amendments is a common agricultural practice. However, it remains ambiguous whether amendment use decreases soil environmental quality (SEQ) and sustainability. In this study, five compound amendments with different pH were utilized in long-term Cd-contaminated paddy soils. The SEQ of all treatments was quantitatively assessed according to a comprehensive evaluation mathematical model (Criteria Importance Through Inter-criteria Correlation (CRITIC)-Technique for Order Preference by Similarity to Ideal Solution (TOPSIS)), and the indicators involved in microbial functional gene (MFG) abundance, soil physicochemical and microbiological properties (CMP) and soil microbial function (N-related enzyme and transformation rate, N-ET) were measured. The results show that the SQE and remediation effect (expressed by the decrease in available Cd (A_Cd), %) in our treatments were alkaline > natural > acidic except for D alkaline treatment. The significant contradiction between soil SQE and remediation effect in D treatment attribute to its dose effects, which inhibiting microbial nitrogen assimilation and dissimilation and therefore counteracts the promoting effect of the decrease in A_Cd. Based on this discussion, three alkaline amendments (A, B and D) with similar effective remediation effect were employed in four other Cd-contaminated soils. Results indicated that both negative effect (D treatment) and promoting effect (A and B treatment) existed in the next 3 years.

Combined effects of oxygen and temperature on nitrogen removal in a nitrate-rich ex-paddy wetland

Temperature is generally considered to be the primary factor controlling the nitrogen removal rate (NR) in nitrate (NO₃^-)-rich submerged sediments. Temperature stimulates both sediment oxygen (O₂) respiration, to create anaerobic conditions, and microbial photosynthetic activity, to provide the organic carbon required for denitrification and expand the uppermost aerobic layer, i.e., the O₂ penetration depth (OPD). The OPD serves as a diffusion barrier for NO₃^- to the underlying anaerobic layer for denitrification. The complex effects of O₂ and temperature on the NR are unclear under field conditions with a wide range of temperatures and O₂ suppliers. This study aimed to determine the combined effects of O₂ and temperature on the NR in an NO₃^--rich, riparian ex-paddy wetland ("yatsu" environment) under long-term bare soil conditions. We used three years of field monitoring with occasional O₂ microprofile measurements from undisturbed submerged soil cores. We observed vertical supersaturated O₂ concentration plateaus up to 4.2 mm depth, which confirmed the presence of underground O₂ producers, i.e., photosynthetic microorganisms forming habitat in the soil, and very large OPDs of up to 42.9 mm. A multiple regression analysis showed that temperature and dissolved O₂ concentration in the flooded water were the key positive and negative influences, respectively, on the NR (332 kg N ha^-1 year^-1 on average), in association with the total N input. Microbial photosynthesis appeared to remain active regardless of the season, providing O₂ to increase OPD and partly suppress the NR; however, photosynthesis has increased the soil C content and appears to have positively contributed to a sustained NR during the 20 years of bare soil conditions. Our results suggest that temporal no vegetation-shade (bare soil) conditions with periodic weed cutting is recommended to effectively remove N from the watershed, while maintaining high temperatures and soil organic C in yatsu environments.

Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling

The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N₂O) from the tropics. Toward closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N₂O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N₂O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ∼45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems. IMPORTANCE Tropical rainforests are the largest terrestrial sinks of atmospheric CO₂ and the largest natural source of N₂O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from three distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.

Effects of dry-wet cycles on nitrous oxide emissions in freshwater sediments: a synthesis

Background

Sediments frequently exposed to dry-wet cycles are potential biogeochemical hotspots for greenhouse gas (GHG) emissions during dry, wet and transitional phases. While the effects of drying and rewetting on carbon fluxes have been studied extensively in terrestrial and aquatic systems, less is known about the effects of dry-wet cycles on N₂O emissions from aquatic systems. As a notable part of lotic systems are temporary, and small lentic systems can substantially contribute to GHG emissions, dry-wet cycles in these ecosystems can play a major role on N₂O emissions.

Methodology

This study compiles literature focusing on the effects of drying, rewetting, flooding, and water level fluctuations on N₂O emissions and related biogeochemical processes in sediments of lentic and lotic ecosystems.

Results

N₂O pulses were observed following sediment drying and rewetting events. Moreover, exposed sediments during dry phases can be active spots for N₂O emissions. The general mechanisms behind N₂O emissions during dry-wet cycles are comparable to those of soils and are mainly related to physical mechanisms and enhanced microbial processing in lotic and lentic systems. Physical processes driving N₂O emissions are mainly regulated by water fluctuations in the sediment. The period of enhanced microbial activity is driven by increased nutrient availability. Higher processing rates and N₂O fluxes have been mainly observed when nitrification and denitrification are coupled, under conditions largely determined by O₂ availability.

Conclusions

The studies evidence the driving role of dry-wet cycles leading to temporarily high N₂O emissions in sediments from a wide array of aquatic habitats. Peak fluxes appear to be of short duration, however, their relevance for global emission estimates as well as N₂O emissions from dry inland waters has not been quantified. Future research should address the temporal development during drying-rewetting phases in more detail, capturing rapid flux changes at early stages, and further explore the functional impacts of the frequency and intensity of dry-wet cycles.

Using Different Forms of Nitrogen to Study Hypersensitive Response Elicited by Avirulent Pseudomonas syringae

Nitrate, ammonium, or a combination of both is the form of N available for nitrogen assimilation from soil by the plants. Nitrogen is an important and integral part of amino acids, nucleotides, and defense molecules. Hence it is very important to study the role of nitrate and ammonium nutrition in plant defense via hypersensitive response (HR). Shifting plants from ammonium nitrate Hoagland solution to nitrate Hoagland nutrition slightly enhances root length and leaf area. HR phenotype is different in nitrate and ammonium grown plants when challenged with avirulent Pseudomonas syringae DC3000 avrRpm1. HR is also associated with increased production of reactive oxygen species (ROS) and nitric oxide (NO). Hence to understand HR development it is essential to measure HR lesions, cell death, ROS, NO, and bacterial growth. Here we provide a stepwise protocol of various parameters to study HR in Arabidopsis in response to nitrate and ammonium nutrition.

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO₃^- occurs in two steps; in the first step, NO₃^- is reduced to NO₂^-; and in the second, unlike denitrification, NO₂^- is reduced to NH₄⁺ without intermediates. There are two sets of NO₃^-/NO₂^- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N₂O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N₂O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO₂^-/NO₃^- ratio, and concentrations of ferrous iron (Fe²⁺) and sulfide (S^2-). Under low-redox conditions, a high C/NO₃^- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO₃^- are equal, the NO₂^-/NO₃^- ratio modulates partitioning of NO₃^-, and a high NO₂^-/NO₃^- ratio favours DNRA. A high S^2-/NO₃^- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO₃^- to NH₄⁺, it is essential for protecting NO₃^- from leaching and gaseous (N₂O) losses and enriches soils with readily available NH₄⁺-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO₃^- pollution, enhance soil health and improve environmental quality.

Nitrous Oxide from Beef Cattle Manure: Effects of Temperature, Water Addition and Manure Properties on Denitrification and Nitrification

Beef feedyards produce nitrous oxide (N2O), a potent greenhouse gas. Limited research has evaluated the processes that produce feedyard N2O, and how rainfall and temperature impact N2O losses. Manure in feedyard pens develops into a complex ecosystem of microbes, extracellular enzymes, feces, and urine, with varying H2O content. This study aimed to improve understanding of feedyard N cycling under differing environmental conditions by incubation of manure in simulated feedyard pens using large chambers under laboratory conditions. We hypothesized that nitrification was the primary source of feedyard N2O, with interactions among temperature, H2O content, and manure properties. Emissions of N2O were monitored with a real–time N2O analyzer. Manure samples were taken at intervals for analyses of physicochemical properties, denitrification enzyme activity (DEA), and nitrification activity (NA). Due to equipment limitations, there was only one chamber per temperature tested. Correlation was poor among N2O emissions and rates of DEA and NA. However, significant relationships were found among key manure characteristics, such as ammonia/ammonium and nitrate/nitrite concentrations, manure dry matter, redox status, and temperature. These data suggest that most N2O was derived from denitrification in the top 5 cm of the manure pack. Further study is warranted to identify the processes involved in flushes of N2O emitted immediately after rainfall, possibly due to abiotic chemical reactions that release N2O sequestered in manure pores.

Finding the optimal fertilizer type and rate to balance yield and soil GHG emissions under reclaimed water irrigation

Water and inorganic nitrogen fertilizer have a notable impact on crop yield and greenhouse gas (GHG) emissions from soil. Reclaimed water (RW) is widely used for irrigation when there are shortages of water resources. It is very important to control yield and greenhouse gas emissions by fertilization under reclaimed water irrigation (RWI). The study consisted of a continuous test that evaluated three types of fertilizer treatments (urea, amine, and slow-release fertilizer) and a no-fertilizer treatment under three-year RWI and four fertilizer levels (150, 200, 250 and 300 kg.N.ha^-1) under one-year RWI to determine the best fertilizer to support maize production and reduce GHG (CO₂ and N₂O) emissions from soil; further, the applicability of RWI in the DNDC model was verified. For many years, GHG emissions under RWI showed an increasing trend, but the effect was not significant. A strong correlation was found between the GHG emissions flux and fertilizer amount, and a threshold fertilization amount existed between 220 and 260 kg.N.ha^-1 that minimized yield-scaled N₂O emissions and the ratio of GHG cumulative emission to yield (GHG/Y). The results indicated that the optimal amounts of SF and UF under RWI were 240 and 225 kg.N.ha^-1 by second-order equation and the DNDC model, respectively, and the rate better balanced the yield and GHG emissions.

Effects of dicyandiamide and Mg/P on the global warming potential of swine slurry and sawdust cocomposting

Composting is an emerging strategy for swine slurry treatment; nonetheless, significant greenhouse gases (GHG) emissions may occur during this process. We carried out two separate assays with increasing doses of dicyandiamide (DCD; up to 1.1% w/w) as a nitrification inhibitor and solutions of MgCl₂ and H₃PO₄ (Mg/P; up to 0.09/0.06 mol kg^-1) to promote struvite crystallization in order to assess their efficiencies as additives to decrease GHG emission during swine slurry cocomposting with sawdust (1:1v/v). We monitored the nitrous oxide (N₂O-N), methane (CH₄-C), and carbon dioxide (CO₂-C) emissions and the ammonia (NH₄⁺-N) and nitrate/nitrite (NOx-N) concentrations in compost reactors (35 L) during the first 4-5 weeks of composting. DCD had no effect on CH₄-C and CO₂-C emissions but decreased N₂O-N losses by up to 56% compared with control. However, DCD inactivation was favored by thermophilic conditions and N₂O-N emissions increased to same levels of control after 13 days. Mg/P was effective to decrease N₂O-N losses only at the highest dose, which also sustained higher [NH₄⁺-N] in the compost by the end of the assessment. Nonetheless, the use of 0.09/0.06 mol kg^-1 of Mg/P also decreased CH₄-C and CO₂-C emissions compared with lower doses of Mg/P and unamended treatments. Overall, DCD and Mg/P amendments decreased the global warming potential (GWP) of swine slurry composting by up to 46 and 28%, respectively. The Mg/P application may be also interesting to increase the compost quality by increasing its NH₄⁺-N availability. Graphical abstract.

Increased organic fertilizer application and reduced chemical fertilizer application affect the soil properties and bacterial communities of grape rhizosphere soil

Increasing organic fertilizer application can improve the sustainability of soil productivity, but the effects of increased organic fertilizer application with reduced chemical fertilizer application over different time periods on chemical properties and bacterial community of grape rhizosphere soil in an arid region are not clear. In this study, three years of fixed-point field tests were used to compare the effects of various fertilization treatments on the soil properties and bacterial community in the grape rhizosphere. The results showed that (1) T1 and T2 significantly increased SOM, AN, AP and AK contents in grape rhizosphere soil. TN, TP and TK contents in grape leaves of T2 were the highest of those in five fertilization treatments. (2) The abundances of Proteobacteria and Bacteroidetes phyla and especially of Arthrobacter, Pseudomonas, Nitrosopira and Bacillus genera were higher in T2 than in the other samples. (3) SOM, AP and AN contents in soil were the main factors affecting soil bacterial community and mineral element contents in grape leaves and roots according to an RDA analysis. In summary, the application of organic fertilizer with reduced chemical fertilizer for two years had the greatest impact on the soil properties and bacterial community of the grape rhizosphere soil.

Effect of Long-Term Pesticides and Chemical Fertilizers Application on the Microbial Community Specifically Anammox and Denitrifying Bacteria in Rice Field Soil of Jhenaidah and Kushtia District, Bangladesh

In this study, we investigated the effect of long-term pesticides and chemical fertilizers application on the microbial communities specifically anammox and denitrification bacteria in rice field soils. The abundances of microbial communities (16S rDNA), anammox (hszB), and denitrification (narG, nirK, nirS, and nosZ) genes were quantified by q-PCR. 10 pesticides (5 insecticides, 3 fungicides and 2 herbicides) and chemical fertilizers urea, potassium, phosphate, DAP (di-ammonium phosphate), gypsum, and boric acid were used by local farmers. Nitrate, SOC (ammonia, soil organic carbon), N and C content significantly (p < 0.05) decreased in the rice field soils as compared to the upland soils. Abundance of 16S rDNA, hszB, narG, nirK, nirS, and nosZ genes significantly (p < 0.05) decreased in the rice field soils and positively correlated with chemical properties of soils. Our results provide useful information and further maintenance should be instilled to the potential of chemical and biological factors decreased in rice field soils.

Abiotic Transient Nitrite Occurrences from Nitrate Reduction through Goethite-Mediated Fe(III)/Fe(II) Cycle with Labile Organic Materials and Ammonia

The abiotic reduction of NO3− to NO2−—coupled with the oxidation of labile organic materials such as citric acid, syringic acid and natural organic matter (NOM) and NH4+ through the goethite-mediated Fe(III)/Fe(II) cycle under anaerobic condition—was investigated at pH values of 4 and 7. The concentrations of the produced Fe2+ and NO2− were monitored. At a pH of 4, concentrations of Fe2+ increased, except for citric acid; no NO2− was detected. The reason why it was not detected is unclear. A possible reaction was the adsorption of NO2− onto goethite at pH < point of zero charge (pzc) of goethite (6.42) due to electrical attractive force. The maximum production of NO2− at a pH of 7 was in the order of citric acid >> syringic acid > NOM. However, Fe2+ was not detected at this pH even though Fe2+ should be required for NO2− production. To better understand of these phenomena, the adsorptive removal of Fe2+ and NO2− onto goethite was experimentally investigated. More than 90% of the produced Fe2+ and NO2− could be removed rapidly by adsorption onto the surface of goethite at pH 7 and 4, respectively. In addition, the reaction of Fe2+ with NO3− appeared to determine the overall reaction rate of the Fe(III)/Fe(II) cycle because of its relatively slow reaction rate. Using these results, we conclude that NO2− can be produced from NO3− reduction through Fe(III)/Fe(II) cycle with labile organic materials and ammonium at a pH of 7; especially, Fe(III)/Fe(II) cycle with citric acid results the maximum NO2− production higher than 600 μM for a long time (over 200 h) and then disappeared. But, the reasons for its disappearance were not addressed in this study.

Effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on N-turnover, the N2O reductase-gene nosZ and N2O:N2 partitioning from agricultural soils

Nitrification inhibitors (NIs) have been shown to reduce emissions of the greenhouse gas nitrous oxide (N₂O) from agricultural soils. However, their N₂O reduction efficacy varies widely across different agro-ecosystems, and underlying mechanisms remain poorly understood. To investigate effects of the NI 3,4-dimethylpyrazole-phosphate (DMPP) on N-turnover from a pasture and a horticultural soil, we combined the quantification of N₂ and N₂O emissions with ¹⁵N tracing analysis and the quantification of the N₂O-reductase gene (nosZ) in a soil microcosm study. Nitrogen fertilization suppressed nosZ abundance in both soils, showing that high nitrate availability and the preferential reduction of nitrate over N₂O is responsible for large pulses of N₂O after the fertilization of agricultural soils. DMPP attenuated this effect only in the horticultural soil, reducing nitrification while increasing nosZ abundance. DMPP reduced N₂O emissions from the horticultural soil by >50% but did not affect overall N₂ + N₂O losses, demonstrating the shift in the N₂O:N₂ ratio towards N₂ as a key mechanism of N₂O mitigation by NIs. Under non-limiting NO₃⁻ availability, the efficacy of NIs to mitigate N₂O emissions therefore depends on their ability to reduce the suppression of the N₂O reductase by high NO₃⁻ concentrations in the soil, enabling complete denitrification to N₂.

Comparison of Community and Function of Dissimilatory Nitrate Reduction to Ammonium (DNRA) Bacteria in Chinese Shallow Lakes with Different Eutrophication Degrees

Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in controlling nitrogen (N) loading in lake ecosystems. However, studies on the linkage between DNRA bacterial community structure and lake eutrophication remain unclear. We examined the community and abundance of DNRA bacteria at six basins of four shallow lakes with different degrees of eutrophication in China. Measurements of the different forms of N and phosphorus (P) in the water column and interstitial water as well as total organic carbon (TOC) and sulfide in the sediments in summer (July 2016) were performed. The nutritional status of Lake Chaohu was more serious than that of the lakes in Wuhan, including Lake Qingling, Lake Houguan, and Lake Zhiyin by comparing geochemical and physical parameters. We found a higher abundance of the nrfA gene, which is a function gene of DNRA bacteria in sediments with higher contents of TOC and sulfide. Moreover, nitrate was a significant factor influencing the DNRA bacterial community structure. A significant difference of the DNRA bacterial community structure between Lake Chaohu and the lakes in Wuhan was discovered. Furthermore, DNRA bacterial abundance and community positively correlated with NH4+ and Chl a concentrations in Lake Chaohu, in which a percent abundance of dominant populations varied along eutrophication gradients. Overall, the abundance and community structure of the DNRA bacteria might be important regulators of eutrophication and cyanobacteria bloom in Lake Chaohu.

Effects of triclosan and triclocarban on denitrification and N2O emissions in paddy soil

Triclosan (TCS) and triclocarban (TCC) are two common antimicrobial compounds, which are widely used as ingredients in pharmaceuticals and personal care products. They occur ubiquitously in soil due to biosolid application as agricultural fertilizers, but their influence on microbially mediated soil biogeochemical processes is poorly understood. We tested the effects of varying concentrations of TCS and TCC applied both individually and together on denitrification and N₂O emissions in paddy soil. We also quantified denitrification functional gene abundances by q-PCR to elucidate the microbial mechanisms of TCS and TCC's effects. Our results showed that TCS and TCC exposure both individually and together significantly (p < 0.05) inhibited denitrification (7.0-36.7%) and N₂O emissions (15.4-86.4%) except for the 0.01 mg kg^-1 TCC treatment in which denitrification was slightly but significantly (p < 0.05) stimulated. The inhibitory effects of TCS and TCC exposure were mainly attributed to their negative net effects on denitrifying bacteria as suggested by the decrease in abundances of 16S rRNA, narG, nirK and clade I nosZ genes in the TCS and TCC treatments. Overall, we found that TCS and TCC exposure in paddy soil could substantially alter nitrogen cycling in rice paddy ecosystems by inhibiting denitrification and N₂O emissions. These effects should be taken into consideration when evaluating the environmental impacts of TCS and TCC.

Greenhouse gas emissions from intact riparian wetland soil columns continuously loaded with nitrate solution: a laboratory microcosm study

In this study, we aimed at determining greenhouse gas (GHG) (CO₂, CH₄, and N₂O) fluxes exchange between the soil collected from sites dominated by different vegetation types (Calamagrostis epigeios, Phragmites australis, and Carex schnimdtii) in nitrogenous loaded riparian wetland and the atmosphere. The intact soil columns collected from the wetland were incubated in laboratory and continuously treated with [Formula: see text]-enriched water simulating downward surface water percolating through the soil to become groundwater in a natural system. This study revealed that the soil collected from the site dominated by C. epigeios was net CO₂ and N₂O sources, whereas the soil from P. australis and C. schnimdtii were net sinks of CO₂ and N₂O, respectively. The soil from the site dominated by C. schnimdtii had the highest climate impact, as it had the highest global warming potential (GWP) compared with the other sites. Our study indicates that total organic carbon and [Formula: see text] concentration in the soil water has great influence on GHG fluxes. Carbon dioxide (CO₂) and N₂O fluxes were accelerated by the availability of higher [Formula: see text] concentration in soil water. On the other hand, higher [Formula: see text] concentration in soil water favors CH₄ oxidation, hence the low CH₄ production. Temporally, CO₂ fluxes were relatively higher in the first 15 days and reduced gradually likely due to a decline in organic carbon. The finding of this study implies that higher [Formula: see text] concentration in wetland soil, caused by human activities, could increase N₂O and CO₂ emissions from the soil. This therefore stresses the importance of controls of [Formula: see text] leaching in the mitigation of anthropogenic N₂O and CO₂ emissions.

Hypoxia and associated feedbacks at sediment-water interface as an early warning signal of resilience shift in an anthropogenically impacted river

Multiple human perturbations in the large rivers often cause habitat fragmentation creating patches of unpredictable structural and functional attributes. The resilience has been largely neglected in riverine studies, despite its pivotal importance in ecosystem recovery. We expect that a shift in sub-habitat conditions along a river transect subjected to frequent oxygen fluctuation and release of carbon, nutrients and other substances generate feedbacks to overstep the resilience and constrain ecosystem recovery. Because dissolved oxygen (DO) plays a regulatory role in ecosystem structure and functioning and feedbacks the denitrification and sediment-P release, we consider the mechanistic links among DO_sw, denitrification and sediment-P release to identify resilience level and to construct a dynamic fit model to uncover the level of resilience and critical transitions in the river. We investigated 180 sites downstream two point sources and two tributaries, each with a 1.4 km river segment, covering 630 km length of the Ganga River. The dynamic fit model intersecting the DO_sw at <1.5 mg L^-1, sediment-P release >7.03 mg m^-2 d^-1 and denitrification rate >1.0 mg N m^-2 hr^-1 at 25 m reach downstream point sources indicated a threat to natural/self-recovery of the Ganga River. The non-metric multidimensional scaling (NMDS) and neighbor-joining analysis indicated that locations up to 700 m downstream Wazidpur drain have overstepped the ecosystem resilience. We found almost similar results downstream Assi drain and study confluences. Our explicit incorporation of DO_sw, sediment-P release, and denitrification in an organized framework provides key insights to detect resilience and critical transitions in an anthropogenically impacted river ecosystem. Given the importance of the Ganga River for national water security and supply across several major states in India, research on the factors and status of resilience underpinning its recovery should be high on our national agenda.

Use of nitrogen and oxygen isotopes of dissolved nitrate to trace field-scale induced denitrification efficiency throughout an in-situ groundwater remediation strategy

In the framework of the Life+ InSiTrate project, a pilot-plant was established to demonstrate the viability of inducing in-situ heterotrophic denitrification to remediate nitrate (NO₃^-)-polluted groundwater. Two injection wells supplied acetic acid by pulses to an alluvial aquifer for 22months. The monitoring was performed by regular sampling at three piezometers and two wells located downstream. In the present work, the pilot-plant monitoring samples were used to test the usefulness of the isotopic tools to evaluate the efficiency of the treatment. The laboratory microcosm experiments determined an isotopic fractionation (ε) for N-NO₃^- of -12.6‰ and for O-NO₃^- of -13.3‰. These ε¹⁵N_NO3/N2 and ε¹⁸O_NO3/N2 values were modelled by using a Rayleigh distillation equation to estimate the percentage of the induced denitrification at the pilot-plant while avoiding a possible interference from dilution due to non-polluted water inputs. In some of the field samples, the induced NO₃^- reduction was higher than 50% with respect to the background concentration. The field samples showed a reduced slope between δ¹⁸O-NO₃^- and δ¹⁵N-NO₃^- (0.7) compared to the laboratory experiments (1.1). This finding was attributed to the reoxidation of NO₂^- to NO₃^- during the treatment. The NO₃^- isotopic characterization also permitted the recognition of a mixture between the denitrified and partially or non-denitrified groundwater in one of the sampling points. Therefore, the isotopic tools demonstrated usefulness in assessing the implementation of the field-scale induced denitrification strategy.

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop

Rising global air temperature and atmospheric CO₂ are expected to have considerable effects on soil nutrient cycling and plant productivity. Soil nitrification controlled by ammonia-oxidizing bacteria and archaea (AOB and AOA) communities plays a key role in contributing to plant nitrogen (N) availability; however, response of soil nitrification and functional microbial communities to climate change and subsequent consequences for crop yields remain largely unknown. Cotton productivity is a function of temperature and N availability under well-watered conditions. In general, cotton growth responds positively to elevated CO₂, but simultaneous warming may offset benefits of rising CO₂. In this study, cotton was used as a model system to elucidate the short-term response of soil nitrification and ammonia-oxidizing communities to elevated temperature and elevated CO₂ using field-based environmentally-controlled chambers. Elevated temperature (ambient + 1.1 °C) altered the AOA community, while elevated temperature and elevated CO₂ (ambient + 132 ppm) significantly increased soil nitrification rate and shifted AOB and AOA communities, but these effects depended on cotton developmental stages. Ammonia-oxidizing community abundance and structure were statistically correlated with nitrifying activity. Our findings suggest that climate change will positively affect soil nitrifying communities, leading to an increase in process rates and subsequent N availability, which is directly linked to crop productivity.

Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests

Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.

Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems

Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.

Laboratory study on nitrate removal and nitrous oxide emission in intact soil columns collected from nitrogenous loaded riparian wetland, Northeast China

Nitrate (NO3−) pollution of surface and groundwater systems is a major problem globally. For some time now wetlands have been considered potential systems for improving water quality. Nitrate dissolved in water moving through wetlands can be removed through different processes, such as the denitrification process, where heterotrophic facultative anaerobic bacteria use NO3− for respiration, leading to the production of nitrogen (N₂) and nitrous oxide (N₂O) gases. Nitrate removal and emission of N₂O in wetlands can vary spatially, depending on factors such as vegetation, hydrology and soil structure. This study intended to provide a better understanding of the spatial variability and processes involved in NO3− removal and emission of N₂O in riparian wetland soils. We designed a laboratory experiment simulating surface water flow through soil columns collected from different sites dominated by different plant species within a wetland. Water and gas samples for NO3−,NH4+ and N₂O analyses were collected every 5 days for a period of 30 days. The results revealed significant removal of NO3− in all the soil columns, supporting the role of riparian wetland soils in removing nitrogen from surface runoff. Nitrate removal at 0 and 10cm depths in sites dominated by Phragmites australis and Carex schnimdtii was significantly higher than in the site dominated by Calamagrostis epigeio. Nitrous oxide emissions varied spatially and temporally with negative flux observed in sites dominated by P. australis and C. schnimdtii. These results reveal that in addition to the ability of wetlands to remove NO3−, some sites within wetlands are also capable of consuming N₂O, hence mitigating not only agricultural nitrate pollution but also climate change.

Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum

Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO₂ respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N₂-N g^-1 h^-1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential.

Effect of urbanization on soil methane and nitrous oxide fluxes in subtropical Australia

Increasing population densities and urban sprawl are causing rapid land use change from natural and agricultural ecosystems into smaller, urban residential properties. However, there is still great uncertainty about the effect that urbanization will have on biogeochemical C and N cycles and associated greenhouse gas (GHG) budgets. We aimed to evaluate how typical urbanization related land use change in subtropical Australia affects soil GHG exchange (N₂ O and CH₄ ) and the associated global warming potential (GWP). Fluxes were measured from three land uses: native forest, a long-term pasture, and a turf grass lawn continuously over two years using a high-resolution automated chamber system. The fertilized turf grass had the highest N₂ O emissions, dominated by high fluxes >100 g N₂ O-N day^-1 immediately following establishment though decreased to just 0.6 kg N₂ O-N ha^-1 in the second year. Only minor fluxes occurred in the forest and pasture, with the high aeration of the sandy topsoil limiting N₂ O emissions while promoting substantial CH₄ uptake. Native forest was consistently the strongest CH₄ sink (-2.9 kg CH₄ -C ha^-1  year^-1 ), while the pasture became a short-term CH₄ source after heavy rainfall when the soil reached saturation. On a two-year average, land use change from native forest to turf grass increased the non-CO₂ GWP from a net annual GHG sink of -83 CO₂ -e ha^-1  year^-1 to a source of 245 kg CO₂ -e ha^-1  year^-1 . This study highlights that urbanization can substantially alter soil GHG exchange by altering plant soil water use and by increasing bulk density and inorganic N availability. However, on well-drained subtropical soils, the impact of urbanization on inter-annual non-CO₂ GWP of turf grass was low compared to urbanized ecosystems in temperate climates.

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle

Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO₄ ^2- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.

Tetracycline and sulfamethazine alter dissimilatory nitrate reduction processes and increase N2O release in rice fields

Effects of antibiotics on the transformation of nitrate and the associated N₂O release in paddy fields are obscure. Using soil slurry experiments combined with ¹⁵N tracer techniques, the influence of tetracycline and sulfamethazine (applied alone and in combination) on the denitrification, anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA) and N₂O release rates in the paddy soil were investigated, while genes related to nitrate reduction and antibiotic resistance were quantified to explore the microbial mechanisms behind the antibiotics' effects. The potential rates of denitrification, anammox, and DNRA were significantly (p < 0.05) reduced, which were mainly attributed to the inhibitory effects of the antibiotics on nitrate-reducing microbes. However, the N₂O release rates were significantly (p < 0.05) stimulated by the antibiotic treatments (0.6-6000 μg kg^-1 soil dry weight), which were caused by the different inhibition effects of antibiotics on N₂O production and N₂O reduction as suggest by the changes in abundance of nirS (nitrite reduction step) and nosZ (N₂O reduction to N₂ step) genes. Antibiotic resistance gene (tetA, tetG, sulI, and sulIII) abundances were significantly (p < 0.05) increased under high antibiotic exposure concentrations (>600 μg kg^-1 soil dry weight). Our results suggest that the widespread occurrence of antibiotics in paddy soils may pose significant eco-environmental risks (nitrate accumulation and greenhouse effects) by altering nitrate transformation processes.

Effects of long-term pig manure application on antibiotics, abundance of antibiotic resistance genes (ARGs), anammox and denitrification rates in paddy soils

Previous studies of long-term manure applications in paddy soil mostly focused on the effects on denitrification, occurrence of antibiotics and antibiotic resistance genes (ARGs) without considering the effects on anaerobic ammonium oxidation (anammox). Here, we investigated the potential rates of anammox and denitrification, occurrence of antibiotics and AGRs in response to three fertilization regimes (C, no fertilizer; N, mineral fertilizer; and NM, N plus pig manure) in six long-term paddy experiment sites across China. The potential rates of anammox (0.11-3.64 nmol N g^-1 h^-1) and denitrification (1.5-29.05 nmol N g^-1 h^-1) were correlated with the abundance of anammox genes (hzsB) and denitrification functional genes (narG, nirK, nirS and nosZ), respectively. The anammox and denitrification rates were affected by soil organic carbon (SOC) and significantly (p < 0.05) increased in NM treatments relative to those in N treatments. Although pig manure application increased antibiotic concentrations and abundance of ARGs compared with N treatments, the increased antibiotics did not directly affect the anammox and denitrification rates. Our results suggested that long-term pig manure application significantly increased antibiotic concentrations, abundance of ARGs, and rates of anammox and denitrification, and that the effects of pig manure-derived antibiotics on anammox and denitrification were marginal. This is the first report that investigates the effects of long-term pig manure application on anammox in paddy soils. More attention should be paid to the potential ecological risk of increased ARGs caused by pig manure application in paddy soils.

Treated and untreated wastewater effluents alter river sediment bacterial communities involved in nitrogen and sulphur cycling

Studying the dynamics of nitrogen and sulphur cycling bacteria in river surface sediments is essential to better understand their contribution to global biogeochemical cycles. Evaporitic rocks settled at the headwater of the Deba River catchment (northern Spain) lead to high values of sulphate concentration in its waters. Besides, the discharge of effluents from untreated and treated residual (urban and industrial) wastewaters increases the concentration of metals, nutrients and organic compounds in its mid- and low-water courses. The aim of this study was to assess the impact of anthropogenic contamination from untreated and treated residual and industrial wastewaters on the structure and function of bacterial communities present in surface sediments of the Deba River catchment. The application of a quantitative functional approach (qPCR) based on denitrification genes (nir: nirS+nirK; and nosZ), together with a 16S rRNA gene metabarcoding structural analysis, revealed (i) the high relevance of the sulphur cycle at headwater surface sediments (as reflected by the abundance of members of the Syntrophobacterales order, and the Sulfuricurvum and Thiobacillus genera) and (ii) the predominance of sulphide-driven autotrophic denitrification over heterotrophic denitrification. Incomplete heterotrophic denitrification appeared to be predominant in surface sediments strongly impacted by treated and untreated effluents, as reflected by the lower values of the nosZ/nir ratio, thus favouring N₂O emissions. Understanding nitrogen and sulphur cycling pathways has profound implications for the management of river ecosystems, since this knowledge can help us determine whether a specific river is acting or not as a source of greenhouse gases (i.e., N₂O).