Soil Denitrification Research Articles

Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach

Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.

Lower soil nitrogen-oxide emissions associated with enhanced denitrification under replacing mineral fertilizer with manure in orchard soils

Emerging evidence suggests that replacing mineral fertilizers with organic livestock manure can effectively suppress reactive gaseous nitrogen (N) emissions from soils. However, the extent of this mitigation potential and the underlying microbial mechanisms in orchards remain unclear. To address this knowledge gap, we measured nitrous and nitric oxide (N2O and NO) emissions, microbial N cycling gene abundance, and N2O isotopomer ratios in pear and citrus orchards under three different fertilization regimes: no fertilization, mineral fertilizer, and manure plus mineral fertilizer. The results showed that although manure application caused large transient peaks of N2O, it reduced cumulative emissions of N2O and NO by an average of 20 % and 17 %, respectively, compared to the mineral fertilizer treatment. Partial replacement of mineral fertilizers with manure enhanced the contribution of AOA to nitrification and reduced the contribution of AOB, thus reducing N2O emissions from nitrification. Isotope analysis suggested that the pathway for N2O production in the soils of both orchards was dominated by bacterial denitrification and nitrifier denitrification. The manure treatment reduced the ratio of denitrification products. Additionally, the dual isotope mixing model results indicated that partially replacing mineral fertilizers with manure could promote soil denitrification, resulting in more N2O being reduced. N-oxide emissions were on average 67 % higher in the pear orchard than in the citrus orchard, probably due to the differences in soil physicochemical properties and growth habits between the two orchards. These findings underscore the potential of partially replacing mineral fertilizers with organic manure in orchards to reduce gaseous N emissions, contributing to the transition towards environmentally sustainable and climate-smart agricultural practices.

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

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

The microbial community, nutrient supply and crop yields differ along a potassium fertilizer gradient under wheat–maize double-cropping systems

Soil microorganisms play critical roles in ecosystem function. However, the relative impact of the potassium (K) fertilizer gradient on the microbial community in wheat-maize double-cropping systems remains unclear. In this long-term field experiment (2008–2019), we researched bacterial and fungal diversity, composition, and community assemblage in the soil along a K fertilizer gradient in the wheat season (K0, no K fertilizer; K1, 45 kg ha−1 K2O; K2, 90 kg ha−1 K2O; K3, 135 kg ha−1 K2O) and in the maize season (K0, no K fertilizer; K1, 150 kg ha−1 K2O; K2, 300 kg ha−1 K2O; K3, 450 kg ha−1 K2O) using bacterial 16S rRNA and fungal internally transcribed spacer (ITS) data. We observed that environmental variables, such as mean annual soil temperature (MAT) and precipitation, available K, ammonium, nitrate, and organic matter, impacted the soil bacterial and fungal communities, and their impacts varied with fertilizer treatments and crop species. Furthermore, the relative abundance of bacteria involved in soil nutrient transformation (phylum Actinobacteria and class Alphaproteobacteria) in the wheat season was significantly increased compared to the maize season, and the optimal K fertilizer dosage (K2 treatment) boosted the relative bacterial abundance of soil nutrient transformation (genus Lactobacillus) and soil denitrification (phylum Proteobacteria) bacteria in the wheat season. The abundance of the soil bacterial community promoting root growth and nutrient absorption (genus Herbaspirillum) in the maize season was improved compared to the wheat season, and the K2 treatment enhanced the bacterial abundance of soil nutrient transformation (genus MND1) and soil nitrogen cycling (genus Nitrospira) genera in the maize season. The results indicated that the bacterial and fungal communities in the double-cropping system exhibited variable sensitivities and assembly mechanisms along a K fertilizer gradient, and microhabitats explained the largest amount of the variation in crop yields, and improved wheat-maize yields by 11.2–22.6 and 9.2–23.8% with K addition, respectively. These modes are shaped contemporaneously by the different meteorological factors and soil nutrient changes in the K fertilizer gradients.

Millennial‐Scale Changes in Atmospheric Nitrous Oxide During the Holocene

AbstractNitrous oxide (N2O) is an important greenhouse gas which destroys the ozone in the stratosphere. Primary sources of atmospheric N2O are nitrification and denitrification in terrestrial soils and the ocean, and the main sink is photolysis in the stratosphere. Studies have mostly focused on the climate‐related response of N2O during glacial‐interglacial periods. However, its mechanism of variation during the Holocene remains unclear. We present a high‐resolution N2O record from the South Pole Ice (SPICE) core covering the Holocene epoch. The millennial‐scale N2O trend agrees with existing records. We constructed a Holocene composite consisting of the new N2O measurements in SPICE and existing records from other ice core sites. The N2O composite reveals four distinct periods of N2O variation during 11.5–10.0 ka, 10.0–6.2 ka, 6.2–2.2 ka, and 2.2–1.4 ka, including two maxima in 11.0–10.0 ka and 3.0–2.2 ka and minima in 8.8–6.2 ka and approximately 1.4 ka. Apart from these, our new high‐resolution record from SPICE shows a short‐term N2O decrease around 2.8 ka which is not observed in other records possibly due to lower sample resolution and/or higher age smoothing. Comparison of our new Holocene N2O composite with the paleo‐proxy records suggests the plausible linkage of major monsoon (Asian, North African, South and North American, and Australian‐Indonesian monsoon) and upwelling (Arabian Sea and Eastern Tropical South Pacific) regions in regulating the atmospheric N2O during the Holocene.

Nitrate reduction coupling with As(III) oxidation in neutral As-contaminated paddy soil preserves nitrogen, reduces N2O emissions and alleviates As toxicity

In arsenic (As)-contaminated paddy soil, microbial-driven nitrate (NO3−) reduction coupled with arsenite (As(III)) oxidation can reduce As toxicity, but the whereabouts of NO3− remain unclear. In this study, the experiments were established using selective streptomycin (STP) and cyclohexylamine to inhibit bacterial and fungal functional responses, respectively, and metagenomic sequencing techniques were used to explain the biological mechanisms of NO3− reduction coupled with As(III) oxidation in neutral As-contaminated paddy soil. The results indicated that fungal denitrification resulted in stronger nitrous oxide (N2O) emissions (321.6 μg kg−1) than bacterial denitrification (175.9 μg kg−1) in neutral As-contaminated paddy soil, but NO3− reduction coupled with As(III) oxidation reduced the N2O emissions. Only adding STP led to ammonium (NH4+) generation (17.7 mg kg−1), and simultaneously more NH4+ appeared in NO3− reduction coupled with As(III) oxidation; this may be because it improved the electron transfer efficiency by 18.2 %. Achromobacter was involved in denitrification coupled with As(III) oxidation. Burkholderiales was responsible for NO3− reduction to NH4+ coupled with As(III) oxidation. This study provided a theoretical basis for NO3− reduction coupled with As(III) oxidation reducing N2O emissions, promoting the reduction of NO3− to NH4+, and reducing As toxicity in paddy soil.

Elevated temperature and nutrients lead to increased N2O emissions from salt marsh soils from cold and warm climates

Salt marshes can attenuate nutrient pollution and store large amounts of ‘blue carbon’ in their soils, however, the value of sequestered carbon may be partially offset by nitrous oxide (N2O) emissions. Global climate and land use changes result in higher temperatures and inputs of reactive nitrogen (Nr) into coastal zones. Here, we investigated the combined effects of elevated temperature (ambient + 5℃) and Nr (double ambient concentrations) on nitrogen processing in marsh soils from two climatic regions (Quebec, Canada and Louisiana, U.S.) with two vegetation types, Sporobolus alterniflorus (= Spartina alterniflora) and Sporobolus pumilus (= Spartina patens), using 24-h laboratory incubation experiments. Potential N2O fluxes increased from minor sinks to major sources following elevated treatments across all four marsh sites. One day of potential N2O emissions under elevated treatments (representing either long-term sea surface warming or short-term ocean heatwaves effects on coastal marsh soil temperatures alongside pulses of N loading) offset 15–60% of the potential annual ambient N2O sink, depending on marsh site and vegetation type. Rates of potential denitrification were generally higher in high latitude than in low latitude marsh soils under ambient treatments, with low ratios of N2O:N2 indicating complete denitrification in high latitude marsh soils. Under elevated temperature and Nr treatments, potential denitrification was lower in high latitude soil but higher in low latitude soil as compared to ambient conditions, with incomplete denitrification observed except in Louisiana S. pumilus. Overall, our findings suggest that a combined increase in temperature and Nr has the potential to reduce salt marsh greenhouse gas (GHG) sinks under future global change scenarios.

Biochar mitigates N2O emissions by promoting complete denitrification in acidic and alkaline paddy soils

AbstractBiochar is an efficacious amendment for mitigating nitrous oxide (N2O) emissions in soils. Nevertheless, the underlying mechanisms responsible for reduced N2O emissions by biochar in paddy soils remain inadequately elucidated. Here, using two typical paddy soils with contrasting pH values (5.40 and 7.56), the N2 and N2O fluxes and the associated functional genes were investigated in soil amended with varying amounts of biochar (0%, 0.5%, and 5%, weight/weight) via soil slurry incubation integrated with the N2/Ar technique and qPCR analysis. The results showed that N2O fluxes were significantly (p < 0.05) reduced by 0.65–3.64 times following biochar amendment, concomitant with a significant (p < 0.05) increase in N2 fluxes (5.47–46.14%) in both acidic and alkaline paddy soils. As a result, the N2O/(N2O + N2) ratios were significantly (p < 0.05) reduced by 1.53–4.65 fold in both soil types. In acidic paddy soils, the enhanced denitrification rates and the decreased N2O/(N2O + N2) ratios exhibited a strong correlation with increased pH values. In alkaline paddy soil, these changes were ascribed to the enhanced nosZ Clade I gene abundance and nosZ/(nirS + nirK) ratio. Our findings reveal that biochar primarily mitigates N2O emissions in paddy soils by promoting its reduction to N2.

Incubation study on remediation of nitrate-contaminated soil by Chroococcus sp.

The possibility of using the non-nitrogen-fixing cyanobacterium (Chroococcus sp.) for the reduction of soil nitrate contamination was tested through Petri dish experiments. The application of 0.03, 0.05 and 0.08mg/cm2 Chroococcus sp. efficiently removed NO3--N from the soil through assimilation of nitrate nutrient and promotion of soil denitrification. At the optimal application dose of 0.05mg/cm2, 44.06%, 36.89% and 36.17% of NO3--N were removed at initial NO3--N concentrations of 60, 90 and 120mg/kg, respectively. The polysaccharides released by Chroococcus sp. acted as carbon sources for bacterial denitrification and facilitated the reduction of soil salinity, which significantly (p < 0.05) stimulated the growth of denitrifying bacteria (Hyphomicrobium denitrificans and Hyphomicrobium sp.) as well as significantly (p < 0.05) elevated the activities of nitrate reductase and nitrite reductase by 1.07-1.23 and 1.15-1.22 times, respectively. The application of Chroococcus sp. promoted the dominance of Nocardioides maradonensis in soil microbial community, which resulted in elevated phosphatase activity and increased available phosphorus content. The application of Chroococcus sp. positively regulated the growth of soil bacteria belonging to the genera Chitinophaga, Prevotella and Tumebacillus, which may contribute to increased soil fertility through the production of beneficial enzymes such as invertase, urease and catalase. To date, this is the first study verifying the remediation effect of non-nitrogen-fixing cyanobacteria on nitrate-contaminated soil.

Earthworm effect on rhizosphere N-cycle microbial genes depends on soil properties

Earthworms are known to improve plant growth in a soil-dependent way, notably via modifications of the rhizosphere microbiota and its functions. We tested the hypothesis that earthworms influence the abundance of microbial genes involved in N cycle according to the type of soil. In three soils with contrasting texture, we quantified five N-cycling genes in different microsites (bulk, rhizosphere or earthworm casts) of microcosms containing (i) neither plants nor eathworms, (ii) plants, (iii) earthworms, (iv) both plant and earthworms. In the presence of earthworms, rhizophere was enriched in nifH (N2 fixation) and depressed in nosZ or narG (denitrification) in sandy soil, suggesting a shift in N balance towards immobilization; rhizosphere was enriched in nifH but also nosZ and narG in loamy soil; no effect was detected in clayey soil. The pattern of gene abundance across the different soils and microsites suggests that earthworms could favor microorganisms with a potential beneficial effect on plants specifically in sandy soils.

Modeling coupled nitrification–denitrification in soil with an organic hotspot

Abstract. The emission of nitrous oxide (N2O) from agricultural soils to the atmosphere is a significant contributor to anthropogenic greenhouse gas emissions. The recycling of organic nitrogen (N) in manure and crop residues may result in spatiotemporal variability in N2O production and soil efflux which is difficult to capture by process-based models. We propose a multi-species, reactive transport model to provide detailed insight into the spatiotemporal variability in nitrogen (N) transformations around such N2O hotspots, which consists of kinetic reactions of soil respiration, nitrification, nitrifier denitrification, and denitrification represented by a system of coupled partial differential equations. The model was tested with results from an incubation experiment at two different soil moisture levels (−30 and −100 hPa) and was shown to reproduce the recorded N2O and dinitrogen (N2) emissions and the dynamics of important carbon (C) and N components in soil reasonably well. The simulation indicated that the four different microbial populations developed in closely connected but separate layers, with denitrifying bacteria growing within the manure-dominated zone and nitrifying bacteria in the well-aerated soil outside the manure zone and with time also within the manure layer. The modeled N2O production within the manure zone was greatly enhanced by the combined effect of oxygen deficit, abundant carbon source, and supply of nitrogenous substrates. In the wetter soil treatment with a water potential of −30 hPa, the diffusive flux of nitrate (NO3-) across the manure–soil interface was the main source of NO3- for denitrification in the manure zone, while at a soil water potential of −100 hPa, diffusion became less dominant and overtaken by the co-occurrence of nitrification and denitrification in the manure zone. Scenarios were analyzed where the diffusive transport of dissolved organic carbon or different mineral N species was switched off, and they showed that the simultaneous diffusion of NO3-, ammonium (NH4+), and nitrite (NO2-) was crucial to simulate the dynamics of N transformations and N2O emissions in the model. Without considering solute diffusion in process-based N2O models, the rapid turnover of C and N associated with organic hotspots can not be accounted for, and it may result in the underestimation of N2O emissions from soil after manure application. The model and its parameters allow for new detailed insights into the interactions between transport and microbial transformations associated with N2O emissions in heterogeneous soil environments.

Nitrogen fertilization promoted microbial growth and N2O emissions by increasing the abundance of nirS and nosZ denitrifiers in semiarid maize field.

Nitrous oxide (N2O) emissions are a major source of gaseous nitrogen loss, causing environmental pollution. The low organic content in the Loess Plateau region, coupled with the high fertilizer demand of maize, further exacerbates these N losses. N fertilizers play a primary role in N2O emissions by influencing soil denitrifying bacteria, however, the underlying microbial mechanisms that contribute to N2O emissions have not been fully explored. Therefore, the research aimed to gain insights into the intricate relationships between N fertilization, soil denitrification, N2O emissions, potential denitrification activity (PDA), and maize nitrogen use efficiency (NUE) in semi-arid regions. Four nitrogen (N) fertilizer rates, namely N0, N1, N2, and N3 (representing 0, 100, 200, and 300 kg ha-1 yr.-1, respectively) were applied to maize field. The cumulative N2O emissions were 32 and 33% higher under N2 and 37 and 39% higher under N3 in the 2020 and 2021, respectively, than the N0 treatment. N fertilization rates impacted the abundance, composition, and network of soil denitrifying communities (nirS and nosZ) in the bulk and rhizosphere soil. Additionally, within the nirS community, the genera Cupriavidus and Rhodanobacter were associated with N2O emissions. Conversely, in the nosZ denitrifier, the genera Azospirillum, Mesorhizobium, and Microvirga in the bulk and rhizosphere soil reduced N2O emissions. Further analysis using both random forest and structural equation model (SEM) revealed that specific soil properties (pH, NO3--N, SOC, SWC, and DON), and the presence of nirS-harboring denitrification, were positively associated with PDA activities, respectively, and exhibited a significant association to N2O emissions and PDA activities but expressed a negative effect on maize NUE. However, nosZ-harboring denitrification showed an opposite trend, suggesting different effects on these variables. Our findings suggest that N fertilization promoted microbial growth and N2O emissions by increasing the abundance of nirS and nosZ denitrifiers and altering the composition of their communities. This study provides new insights into the relationships among soil microbiome, maize productivity, NUE, and soil N2O emissions in semi-arid regions.

Arbuscular mycorrhizal fungi drive soil nitrogen transformation under wheat varieties with different nitrogen utilization efficiencies

Arbuscular mycorrhizal fungi (AMF) can play important roles in plant nitrogen (N) uptake and use. However, it is still not well explored how AMF interact with host plants representing different N use types and thereby affect soil N transformation. A pot experiment was conducted to test the effects of AMF on N mineralization, nitrification, denitrification and nitrous oxide (N2O) reduction in soils under wheat varieties with high and low pre-anthesis N utilization efficiency (also called grain-specific N efficiency). Our results showed that AMF can increase N mineralization potential, with a greater effect for varieties with high N utilization efficiency. AMF also increased nitrification potential, ammonium oxidation potential, but did not nitrite oxidation potential, suggesting that AMF only act on the first nitrification step (ammonium oxidation). AMF increased NO3− but decreased NH4+ concentrations irrespective of the N use type of host plant. Moreover, AMF significantly increased denitrifying enzyme activity of the varieties with low N utilization efficiency, but decreased it for the varieties with high N utilization efficiency. N2O emission during soil incubation was in tandem with denitrification. Finally, AMF significantly increased N2O reductase activity irrespective of the N utilization efficiency of the host plant. The findings suggest that an interaction between the N utilization efficiency of wheat plants and AMF can modulate the N uptake of the host plant, and also regulate soil N transformation; a mechanism which may greatly affect the sustainability of wheat cropping systems.

Field soil properties and experimental nutrient additions drive the nitrous oxide ratio in laboratory denitrification experiments: a systematic review

Nitrous oxide (N2O), which contributes to global climate change and stratospheric ozone destruction, can be produced during denitrification. Although the N2O ratio, a measure of denitrification completion, is influenced by various properties, studies have largely been limited to site- or treatment-specific conclusions. The primary objective of this study was to identify important factors driving N2O ratios and their relationships in soils by systematically reviewing and quantitatively evaluating results from published laboratory denitrification studies. A database with 60 studies (657 observations) was compiled, including studies meeting the minimum criteria: (i) laboratory experiments on soils, (ii) nutrient (carbon and/or nitrogen) addition, and (iii) N2O and dinitrogen gas measurements. Of these, 14 studies (100 observations) had sufficient data for inclusion in the meta-analysis to assess the effect of added nutrients on the N2O ratio. Furthermore, we modeled the effect of moderators on treatment effect by fitting a meta-regression model with both quantitative and categorical variables. Close review of studies in the database identified soil pH, carbon addition, and nitrogen addition as important variables for the N2O ratio, but trends varied across studies. Correlation analysis of all studies clarified that soil pH was significantly correlated with the N2O ratio, where soils with higher pH had lower N2O ratios. The meta-analysis further revealed that nutrient addition had an overall significant, positive treatment effect (0.30 ± 0.03, P&amp;lt;.0001), indicating that experimentally adding nutrients increased the N2O ratio. The model was most significantly improved when soil texture was used as a moderator. The significance of soil texture for the N2O ratio was a major finding of this study, especially since the assays were usually conducted with soil slurries. Overall, this study highlights the importance of field soil properties (i.e., pH, texture) and laboratory conditions (i.e., nutrient addition) in driving the N2O ratio and N2O production from denitrification in soils.

Effect of Chemical Fertilizer and Manure Combined with Biochar on Denitrification Potential and Denitrifying Bacterial Community in Rhizosphere Soil

To clarify the effect of chemical fertilizer and manure combined with biochar on denitrifying microorganisms and denitrification potential of rhizosphere soil, a pot experiment growing lemon was conducted involving five treatments, namely no fertilization (CK), chemical fertilizer (CF), manure (M), chemical fertilizer combined with biochar (CFBC), and manure combined with biochar (MBC). We determined the characteristics of the rhizosphere soil nirS-, nirK-, and nosZ-type denitrifying bacteria populations; denitrification potential; and soil environmental factors to clarify the effects of chemical and manure combined with biochar on denitrification. Our results showed that compared with that in CK, the CF treatment reduced the rhizosphere soil denitrification potential by 47.7%, whereas the M and MBC treatments increased the denitrification potential by 2192.7% and 1989.9%, respectively. The M and MBC treatments increased the gene copy number of nirS and nosZ, the CF and CFBC treatments decreased the gene copy number of nirS and nosZ, and all four fertilization treatments increased the gene copy number of nirK. Stepwise regression analysis showed that pH was the main factor for the abundance of nirS-type denitrifying bacteria and SOM and NH+4-N were the main factors for the abundance of nirK-type denitrifying bacteria, whereas pH, NO-3-N, and N/P were main factors for the abundance of nosZ-type denitrifying bacteria. The results of partial least squares analysis indicated that the abundance of nirS-and nosZ-type denitrifying bacteria, pH, TN, and N/P were the main factors affecting rhizosphere denitrification potential. Therefore, in acidic purple soil, nirS- and nosZ-type denitrifying bacteria were the main drivers of the soil denitrification process in lemon rhizospheres under chemical fertilizer and pig manure combined with biochar, whereas fertilizer affected the rhizosphere soil denitrification process by regulating soil pH, TN, and N/P.

Irrigation rather than fertilization drives the abundance, community structure and assembly process of soil denitrifiers

Fertilization and irrigation have significant impacts on soil nitrogen cycling and associated microbes, yet we have limited understanding on community structure and assembly process of soil denitrifiers. Here, we examined the abundance, diversity, composition, and assembly process of soil denitrifier communities harboring the nirS, nirK, and nosZ genes in soils under long-term (11 years) fertilization and irrigation managements. Our results indicated that irrigation significantly increased the abundance of nirS, nirK, and nosZ genes by 6.10–18.85, 2.36–2.85, and 4.85–6.16 times in the chemical fertilizer (NPK) treatments and by 1.02–13.68, 0.95–1.45, and 1.49–2.28 times in the manure (M) treatments compared to the corresponding control without irrigation (I0), respectively. Principal co-ordinates analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) showed that fertilization had a more important role in altering the nosZ-type denitrifier community structure, while irrigation dominated in influencing the nirS- and nirK-type. Regardless of fertilization, irrigation shifted community assembly of the nirS-type denitrifier from deterministic process to stochastic process, while driving the nosZ-type from stochastic process to deterministic process. The nirK-type denitrifier was determined by stochastic process and was neither affected by fertilization nor irrigation. Network co-occurrence analysis showed that irrigation differently affected the community network complexity under NPK and M. One irrigation (I1) and two irrigations (I2) increased and decreased the network complexity, respectively, in the NPK treatments, while opposite results were found in M. Additionally, soil moisture and pH significantly (p < 0.05) correlated with the gene abundance, community structure, and assembly process of the denitrifiers. Overall, irrigation rather than fertilization greatly induced the changes in abundance, community structure, network structure, and assembly process of the denitrifiers via soil moisture and pH, highlighting the importance of irrigation in regulating soil denitrification associated microbes.

NirS and nosZII bacterial denitrifiers as well as fungal denitrifiers are coupled with N2O emissions in long-term fertilized soils

Fertilizer application plays a critical role in soil fertility and crop yield and has been reported to significantly affect soil denitrification. However, the mechanisms by which denitrifying bacteria (nirK, nirS, nosZI, and nosZII) and fungi (nirK and p450nor) affect soil denitrification are poorly understood. Therefore, in this study, we investigated the effect of different fertilization treatments on the abundance, community structure, and function of soil denitrifying microorganisms in an agricultural ecosystem with long-term fertilization using mineral fertilizer or manure and their combination. The results showed that the application of organic fertilizer significantly increased the abundance of nirK-, nirS-, nosZI-, and nosZII-type denitrifying bacteria as the soil pH and phosphorus content increased. However, only the community structure of nirS- and nosZII-type denitrifying bacteria was influenced by the application of organic fertilizer, which led to a higher contribution of bacteria to nitrous oxide (N2O) emissions than that observed after inorganic fertilizer application. The increase in soil pH reduced the abundance of nirK-type denitrifying fungi, which may have presented a competitive disadvantage relative to bacteria, resulting in a lower contribution of fungi to N2O emissions than that observed after inorganic fertilizer application. The results demonstrated that organic fertilization had a significant impact on the community structure and activity of soil denitrifying bacteria and fungi. Our results also highlighted that after organic fertilizer application, nirS- and nosZII-denitrifying bacteria communities represent likely hot spots of bacterial soil N2O emissions while nirK-type denitrifying fungi represent hot spots for fungal soil N2O emissions.

Denitrification contributes to N2O emission in paddy soils.

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

Improving an existing proxy-based approach for floodplain denitrification assessment to facilitate decision making on restoration

Excess nitrogen (N) from agricultural sources is a major contributor to the water pollution of rivers in Europe. Floodplains are of tremendous importance as they can permanently remove nitrate (NO3) from the environment by releasing reactive N to the atmosphere in its gaseous forms (N2O, N2) during denitrification. However, the quantitative assessment of this ecosystem function is still challenging, particularly on the national level. In this study, we modeled the potential of NO3-N removal through microbial denitrification in soils of the active floodplains of the river Elbe and river Rhine in Germany. We combined laboratory measurements of soil denitrification potentials with straightforward modelling data, covering the average inundation duration from six study areas, to improve an existing Germany-wide proxy-based approach (PBAe) on NO3-N retention potential. The PBAe estimates this potential to be 30–150 kg NO3-N ha−1 yr−1. However, with soil pH and Floodplain Status Category identified as essential parameters for the proxies, the improved PBA (PBAi) yields a removal potential of 5–480 kg N ha−1 yr−1. To account for these parameters, we applied scaling factors using a bonus-malus system with a base value of 10–120 N ha−1 yr−1. Upscaling the determined proxies of the PBAi to the entire active floodplains of the river Elbe and river Rhine results in similarly high NO3-N retention sums of ~7000 t yr−1 in spite of very different retention area sizes, strengthening the argument for area availability as the primary objective of restoration efforts. Although PBAs are always subject to uncertainty, the PBAi enables a more differentiated spatial quantification of denitrification because local key controlling parameters are included. Hence, the PBAi is an innovative and robust approach to quantify denitrification in floodplain soils, supporting a better assessment of ecosystem services for decision-making on floodplain restoration.

Overestimated nitrogen loss from denitrification for natural terrestrial ecosystems in CMIP6 Earth System Models

Denitrification and leaching nitrogen (N) losses are poorly constrained in Earth System Models (ESMs). Here, we produce a global map of natural soil 15N abundance and quantify soil denitrification N loss for global natural ecosystems using an isotope-benchmarking method. We show an overestimation of denitrification by almost two times in the 13 ESMs of the Sixth Phase Coupled Model Intercomparison Project (CMIP6, 73 ± 31 Tg N yr−1), compared with our estimate of 38 ± 11 Tg N yr−1, which is rooted in isotope mass balance. Moreover, we find a negative correlation between the sensitivity of plant production to rising carbon dioxide (CO2) concentration and denitrification in boreal regions, revealing that overestimated denitrification in ESMs would translate to an exaggeration of N limitation on the responses of plant growth to elevated CO2. Our study highlights the need of improving the representation of the denitrification in ESMs and better assessing the effects of terrestrial ecosystems on CO2 mitigation.