Abundance Of Denitrifying Genes Research Articles

Effects of soil water content at freezing, thaw temperature, and snowmelt infiltration on N2O emissions and denitrifier gene and transcript abundance during a single freeze-thaw event

Climate change-related warming and increased precipitation may alter winter snow cover and thawing events, and therefore, may carry significant consequences for nitrous oxide (N2O) production pathways such as denitrification, and the abundance and expression of denitrifying microorganisms. We used a soil microcosm study to investigate the combined effect of soil thaw temperature, initial water filled pore space (WFPS) prior to soil freezing, and snowmelt infiltration simulated by the addition of water on N2O emission and denitrification rates, soil respiration rate, and the abundance and transcription of denitrifying (nirK, nirS, and nosZ) bacteria during a single freeze-thaw event. Soil respiration rate was primarily controlled by an increase in soil thaw temperature, whereas soil N2O emission and denitrification rates were generally greater in soils with a higher initial WFPS and soil thaw temperature. In contrast, snowmelt infiltration generally had a negligible effect on these rates, which may be related to pre-existing soil conditions that were already conducive to denitrification. Unexpectedly, the nosZ transcript/nosZ gene abundance ratio was lower in soils thawed at 8.0 °C compared to 1.5 °C; however, this may have resulted in a lower N2O reduction, thus explaining the greater levels of N2O emitted from soils thawed at 8.0 °C. Overall, this study demonstrated that increased N2O production during a single freeze-thaw event was primarily linked to antecedent conditions of high initial WFPS, soil thaw temperature, and a synergistic interplay between these two environmental parameters, and provides evidence that an increase in annual temperature and precipitation, along with the timing of precipitation, may further stimulate N2O production pathways.

Pollution abatement reducing the river N2O emissions although it is partially offset by a warming climate: Insights from an urbanized watershed study

Global nitrogen (N) pollution has resulted in increased river nitrous oxide (N2O) emissions, which contribute to climate change. However, little is known about how pollution abatement conversely reduces river N2O production in a warming climate. Here, field observations and microcosmic experiments were conducted in a coastal urbanized watershed (S.E. China) to explore the interactive effect of changing nitrate and temperature on river sediment denitrification (DNF) and N2O production. The results showed that urban river reaches (UR) with higher organic carbon content and denitrifying gene abundance in sediments have a greater DNF rate, nitrate removal efficiency (NRE), and N2O concentration than agricultural river reaches (AR). Microcosmic incubation suggested that the DNF rate and associated N2O production decreased under low nitrate addition, wherein the NRE increased. The scenario simulation illustrated a nonlinear response of N2O production to nitrate removal (i.e., ΔN2O/ΔNO3-N) from both UR and AR sediments at a given temperature, and the DNF rate and N2O production increased with increasing temperature. An increase in temperature by 1 degree Celsius would offset 18.75% of the N2O reduction by nitrate removal via DNF. These findings implied that watershed pollution abatement undoubtedly contributes to the reduction in global river N2O emissions although it is partially offset by extra N2O production caused by global warming.

Stimulating effects of snow cover on gaseous nitrogen emissions are intensified by biological soil crusts

Winter weather patterns are changing due to global climate change, which impacts the soil nitrogen cycle and greenhouse gas flux in these ecosystems, particularly the snow cover in temperate deserts. Biological soil crusts are important soil communities of the desert ecosystem and are sensitive to environmental changes. However, knowledge of the responses of gaseous nitrogen emissions from biological soil crusts to changes in snow cover is limited. In this study, the effects of snow cover on gaseous nitrogen emissions and the abundance of nitrifier (amoA) and denitrifier (narG, nirS, nirK, nosZ) genes were investigated in three snow cover treatments (snow removal, ambient snow, and increased snow depth). Snow cover significantly affected N2O and NO emissions from bare sand and biological soil crusts in winter. The abundance of denitrifier genes in bare sand and biological soil crusts and the abundance of nitrifier genes in moss crust increased with the depths of snow addition. N2O emissions increased with the successional stages of biological soil crusts during the winter. Both N2O and NO emissions from bare sand and biological soil crusts peaked in the freeze–thaw period (March) and were lowest in mid-winter (January). The emissions of N2O increased with increasing the abundance of amoA, nirK and nosZ genes. Our findings show that N2O emissions generally increased with increasing snow cover through their effects on nitrogen cycle related functional microbial groups. These effects were regulated by the types of biological soil crust, which can increase the effect of snow cover in winter.

Response of gene abundance of ammonia-oxidizing microorganisms and denitrifying microorganisms to nitrogen and phosphorus addition in subtropical forest.

We conducted a nitrogen (N) and phosphorus (P) addition experiment in Qianjiangyuan National Park in 2015, to investigate the response of ammonia-oxidizing microorganisms and denitrifying microorganisms. There were four treatments, including N addition (N), P addition (P), NP, and control (CK). Soil samples were collected in April (wet season) and November (dry season) of 2021. The abundance of amoA gene of ammonia-oxidizing microorganisms (i.e., ammonia-oxidizing archaea, AOA; ammonia-oxidizing bacteria, AOB; comammox) and denitrifying microbial genes (i.e., nirS, nirK, and nosZ) were determined using quantitative PCR approach. The results showed that soil pH was significantly decreased by long-term N addition, while soil ammonium and nitrate contents were significantly increased. Soil available P and total P contents were significantly increased with the long-term P addition. The addition of N (N and NP treatments) significantly increased the abundance of AOB-amoA gene in both seasons, and reached the highest in the N treatment around 8.30×107 copies·g-1 dry soil. The abundance of AOA-amoA gene was significantly higher in the NP treatment than that in CK, with the highest value around 1.17×109 copies·g-1 dry soil. There was no significant difference in N-related gene abundances between two seasons except for the abundance of comammox-amoA. Nitrogen addition exerted significant effect on the abundance of AOB-amoA, nirK and nosZ genes, especially in wet season. Phosphorus addition exerted significant effect on the abundance of AOA-amoA and AOB-amoA genes in both seasons, but did not affect denitrifying gene abundances. Soil pH, ammonium, nitrate, available P, and soil water contents were the main factors affecting the abundance of soil N-related functional genes. In summary, the response of soil ammonia-oxidizing microorganisms and denitrifying microorganisms was more sensitive to N addition than to P addition. These findings shed new light for evaluating soil nutrient availability as well as their response mechanism to global change in subtropical forests.

Salinity and high pH reduce denitrification rates by inhibiting denitrifying gene abundance in a saline-alkali soil

Denitrification, as the main nitrogen (N) removal process in farmland drainage ditches in coastal areas, is significantly affected by saline-alkali conditions. To elucidate the effects of saline-alkali conditions on denitrification, incubation experiments with five salt and salt-alkali gradients and three nitrogen addition levels were conducted in a saline-alkali soil followed by determination of denitrification rates and the associated functional genes (i.e., nirK/nirS and nosZ Clade I) via N2/Ar technique in combination with qPCR. The results showed that denitrification rates were significantly decreased by 23.83–50.08%, 20.64–57.31% and 6.12–54.61% with salt gradient increasing from 1 to 3‰, 8‰, and 15‰ under 0.05‰, 0.10‰ and 0.15‰ urea addition conditions, respectively. Similarly, denitrification rates were significantly decreased by 44.57–63.24% with an increase of the salt-alkali gradient from 0.5 to 8‰. The abundance of nosZ decreased sharply in the saline condition, while a high salt level significantly decreased the abundance of nirK and nirS. In addition, the increase of nitrogen concentration attenuated the reduction of nirK, nirS and nosZ gene abundance. Partial least squares regression (PLSR) models demonstrated that salinity, dissolved oxygen (DO) in the overlying water, N concentration, and denitrifying gene abundance were key determinants of the denitrification rate in the saline environment, while pH was an additional determinant in the saline-alkali environment. Taken together, our results suggest that salinity and high pH levels decreased the denitrification rates by significantly inhibiting the abundance of the denitrifying genes nirK, nirS, and nosZ, whereas increasing nitrogen concentration could alleviate this effect. Our study provides helpful information on better understanding of reactive N removal and fertilizer application in the coastal areas.

Soil nitrification and denitrification in Cunninghamia lanceolata plantations with different stand ages.

The variations in soil nitrification and denitrification processes, together with the abundances of functional microbes were investigated in Cunninghamia lanceolata plantations with different stand ages of 5, 8, 21, 27, and 40 years old. The results showed that the net nitrification rate fluctuated with increasing forest ages, with that of 8-year- and 27-year-old C. lanceolata plantations being significantly lower than other stand ages. The abundance of ammonia-oxidizing archaea (AOA) amoA in the 27-year-old plantation was significantly lower than that of the 40-year-old plantation, while there was no significant difference among the other stand ages. There was no significant difference in the abundance of AOB amoA gene, denitrifying functional genes or soil denitrification potential among different stand ages. The results of stepwise regression analysis showed that the abundance of AOA amoA gene was not significantly affected by soil physical and chemical properties. In addition, the abundance of AOB was positively associated with soil total carbon content and soil pH. The abundance of denitrifying functional genes including narG, nirK and nosZ increased with increasing soil pH. The abundance of nirK and nirS was influenced by soil total carbon. Stand age influenced soil net nitrification rate through the AOA amoA abundance. Moreover, soil denitrification potential was directly affected by stand age, or indirectly affected by stand age through soil microbial biomass carbon, soil pH and denitrifying gene abundance of narG and nirK. Compared with the denitrification process, soil nitrification and associated AOA amoA gene abundance were more sensitive to the development of C. lanceolata plantations. The rotation period sould be appropriately extended to reduce the risk of nitrogen losses resulting from soil nitrification.

Trade-offs on carbon and nitrogen availability lead to only a minor effect of elevated CO2 on potential denitrification in soil

The global surplus of reactive nitrogen (Nr) and elevated atmospheric CO2 are both major threats to current and future ecosystem integrity. Denitrification is the primary sink for Nr by the conversion to inert N2 and is also the predominant source of N2O emission. Yet, it is unclear how and to what extent soil denitrification would respond to elevated CO2 (eCO2), which is a major part of the uncertainties on the estimation of terrestrial nitrogen (N) cycle budget under the influence of climate changes. Herein, we provided quantitative results of a global meta-analysis with 127 observations that included data on soil potential denitrification rates (PDR) and denitrifying gene abundance, and 305 observations that included data on N2O emission and soil available N content under eCO2. Averaged across all studies, we found that globally eCO2 had an overall minor effect on soil PDR, but showed a large variation with different edaphic and environmental factors. The response was primarily explained by soil organic carbon (SOC) and mean annual precipitation (MAP), i.e., the higher SOC content or MAP, the lower response of soil PDR to eCO2. Further, eCO2 significantly decreased soil NO3- content (-15.3%) and denitrifying bacteria (-31.3%), but increased nirS (14.7%), napA (24.4%) genes and N2O emission (34.1%). We speculate that eCO2 has both positive and negative effects on soil potential denitrification, i.e., a higher soil C input induced by eCO2 supplies more energy for denitrifiers and thus increases denitrification in N-rich ecosystems, while unbalanced C:N input decreases soil NO3- content, causing substrate deficiency in N-limiting ecosystems under eCO2. Whilst the response of soil PDR to eCO2 is governed by trade-offs on soil C and N availability, this may serve as a buffer on soil available N content in terrestrial ecosystems under eCO2. Collectively, based on our findings, we built a comprehensive conceptual model defining the key regulators, which has significant implications for expanding the understanding and predicting the responses of the terrestrial N cycle to eCO2 in future scenario evaluation.

Nitrogen optimization coupled with alternate wetting and drying practice enhances rhizospheric nitrifier and denitrifier abundance and rice productivity.

Optimizing nitrogen (N) fertilization without sacrificing grain yield is a major concern of rice production system because most of the applied N has been depleted from the soil and creating environmental consequences. Hence, limited information is available about nutrient management (NM) performance at a specific site under alternate wetting and drying (AWD) irrigation compared to conventional permanent flooding (PF). We aimed to inquire about the performance of NM practices compared to the farmer’s fertilizer practice (FFP) under PF and AWD on rhizospheric nitrifier and denitrifier abundance, rice yield, plant growth, and photosynthetic parameters. Two improved NM practices; nutrient management by pig manure (NMPM); 40% chemical N replaced by pig manure (organic N), and nutrient management by organic slow-release fertilizer (NMSR); 40% chemical N replaced by organic slow-release N were compared. The results showed an increased total grain yield (16.06%) during AWD compared to PF. Compared to conventional FFP, NMPM, and NMSR significantly increased the yields by 53.84 and 29.67%, respectively, during AWD. Meanwhile, PF prompted a yield increase of 45.07 and 28.75% for NMPM and NMSR, respectively, (p < 0.05) compared to FFP. Besides, a significant correlation was observed between grain yield and nitrogen content during AWD (R2 = 0.58, p < 0.01), but no significant correlation was observed during PF. The NMPM contributed to photosynthetic attributes and the relative chlorophyll content under both watering events. Moreover, relatively higher abundances of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were observed during AWD, and the highest value was found after the late panicle stage. Our results suggest that the AWD–NMPM model is the best option to stimulate nitrifier and denitrifier gene abundance and promote rice production.

Soil denitrification rates are more sensitive to hydrological changes than restoration approaches in a unique riparian zone

Abstract Riparian zones, an aquatic‐terrestrial interface, can intercept more than half of nitrogen (N) exported from terrestrial ecosystems to adjacent rivers, primarily by denitrification processes. However, damming has disrupted natural patterns and processes of flooding and vegetation community assemblages, and yet little is known about how hydrological changes and ecosystem restoration affect the biogeochemical functioning in the riparian ecosystems. We conducted an in situ experiment to evaluate the effects of hydrological change (e.g. altering flooding intensity and frequency) and restoration approaches (e.g. natural regeneration and active revegetation) on denitrification rates and the abundance of denitrifier genes in the riparian zone of the Three Gorges Reservoir, China. Our results showed that active revegetation did not significantly increase denitrification rates compared to the natural regeneration, but their underlying mechanism was different. At the natural regeneration area, the denitrification rate was primarily regulated by soil properties and abundance of nosZ gene, while at the active revegetation area, it was controlled merely by the abundance of nosZ gene. In addition, vegetation types showed little effect on the soil denitrification process, and the denitrification rate decreased with flooding intensity by reducing denitrifier gene abundance. The periodic flooding treatment doubled the denitrification rate compared with the no flooding treatment, which might be attributed to the enhancement of soil carbon availability. Our results suggest that in terms of N removal via denitrification processes, natural regeneration is a priority approach to restoring degraded riparian ecosystems. Read the free Plain Language Summary for this article on the Journal blog.

Mineralizable nitrogen and denitrification enzyme activity drive nitrate concentrations in well-drained stony subsoil under lucerne (Medicago sativa L.)

Nitrogen (N) inputs to agricultural systems contribute substantially to soil nitrate (NO3−) concentrations, which increase NO3− leaching and contamination of groundwater. The influence of soil microbes in regulating NO3− concentrations in the topsoil are well studied but it is often assumed that microbial regulation of NO3− concentrations in the subsoil is negligible. The aim of this study was to test this assumption by determining the relationships between microbial properties and NO3− concentrations in both the subsoil and the topsoil. We measured the size of the mineralizable N (Nm) pool, microbial properties (microbial biomass, bacterial richness), nitrifier gene abundance (amoA gene copy number), denitrifier gene abundance (nirK and nirS gene copy number), denitrifier enzyme activity and NO3− concentrations in the topsoil and the subsoil in a well-drained stony soil under an established lucerne crop. We used structural equation modelling (SEM) to identify and compare the linkages of microbial properties with NO3− concentrations at each depth. In the topsoil, we found higher Nm, gene abundance, denitrification enzyme activity, bacterial richness, and microbial biomass than those in the subsoil, but there were no relationships between these variables and NO3− concentrations in the topsoil (the SEM model explained 0.06% of the variability in NO3− concentrations). In contrast, in the subsoil, NO3− concentrations were strongly correlated with bacterial amoA abundance and denitrification enzyme activity, with both variables associated significantly with Nm. We found that bacterial richness was also associated with Nm in the subsoil. Our findings highlight that microbial properties are associated with NO3− concentrations in the subsoil (the SEM model explained 82% the variability in NO3− concentrations) and this suggest that nitrification and denitrification may contribute to regulating NO3− concentrations in the subsoil. Our findings also suggest that denitrification contributes to reducing NO3− concentrations in the subsoil. We conclude that studies addressing drivers of NO3− leaching need to consider the potential for microbially-mediated attenuation (or an increase) in NO3− concentrations throughout the soil profile.

Understanding how reed-biochar application mitigates nitrogen losses in paddy soil: Insight into microbially-driven nitrogen dynamics

Biochar application to chemical-amended paddy soils has been proposed as a potential strategy to enhance nitrogen (N) retention and nitrogen use efficiency (NUE) by crops. However, optimal concentrations for these enhancements and the potential drivers are not well understood. Herein, a column-based pot experiment was carried out to investigate the impacts of reed-biochar application rate on N losses and dynamics in paddy soils treated by chemical fertilizer, and particularly, to explore the dominant factors of the processes. The addition of 2–4% reed-biochar had the most significant effects on mitigating N loss by leaching. Reed-biochar amendment increased soil total N and mineral N (NH4+-N and NO3−-N) content, and denitrifying gene abundance, and the increments of those variables were positively related to the application rate. Soil treated with 1–4% reed-biochar at harvest period showed higher gene abundances of ammonia-oxidizing and dissimilatory nitrate reduction to ammonium (DNRA) and higher activity of β-1,4-N-acetyl-glucosaminidase (NAG) and leucine aminopeptidase compared with the 4–8% application rate. The amoA-AOA gene abundance, NAG activity, and total carbon (C) content were the main predictors of total N and mineral N accumulated leakage. Total C content was the main predictor of soil total N and mineral N content, followed by the pH and NAG activity. These results suggest that adding 2–4% reed-biochar was more beneficial to mitigate N loss and thus enhance soil N storage and availability. This study highlights the importance of understanding how microbial populations mediate N transformation to decipher biochar-driven NUE enhancement in paddy soils.

Influence of chemical fumigation and biofumigation on soil nitrogen cycling processes and nitrifier and denitrifier abundance

Chemical fumigation and biofumigation are used to reduce soil-borne diseases in agricultural production systems; however, other essential soil processes such as the soil nitrogen (N) cycle may also be affected. This study compared the effects of chemical fumigation and biofumigation on soil net N mineralization, nitrification, denitrification, and soil nitrifier and denitrifier abundance. Six treatments were compared using soil microcosms over a 160-day incubation period: fumigation with chloropicrin; fumigation with metam sodium used alone (MS) or combined with barley plant residues (MSBR); biofumigation with mustard residues; addition of non-biofumigant barley residues; and an untreated control. Biofumigation did not inhibit soil nitrification, whereas chemical fumigation with MS (with or without barley) and chloropicrin inhibited nitrification for 16 and 64 days, respectively. Biofumigation, barley residues, and MSBR increased soil respiration, N2O emission, and denitrification rates. However, biofumigation had lower denitrification and N2O cumulative emissions and rates compared to barley residues, suggesting that biofumigation may reduce N2O production pathways. All chemical fumigation treatments significantly decreased nitrifier gene abundance compared to biofumigation; however, only chloropicrin decreased the abundance of denitrifying genes. After 160 days, 22% of the added plant residue dry matter remained in the MSBR-treated soil, which was ∼2-fold greater than the barley-treated soil, indicating chemical fumigation may also affect the carbon cycle. Overall, these results suggest that chemical fumigation, especially with chloropicrin, has a greater impact on nitrification and nitrifier and denitrifier gene abundance than biofumigation with mustard residues.

Long-term effects of imbalanced fertilization with lime and gypsum additions on denitrifying functional genes of an Ultisol at Yingtan, Jiangxi, China

The abundance of denitrifying functional genes plays a key role in driving the soil nitrous oxide (N2O) emission potential. Nitrite reductase genes (nirK and nirS) and nitrous oxide reductase genes (nosZ I and nosZ II) are the dominant denitrifying funtional genes. In this study, real-time quantitative PCR was conducted to evaluate the effects of 32-year imbalanced fertilization and lime and gypsum additions on the abundances of nirK, nirS, nosZ I and nosZ II genes in an Ultisol at Yingtan, Jiangxi Province. We further explored the underlying driving factors. The results showed that, compared with the balanced fertilization treatment, fertilization without phosphorus (P) signifi-cantly decreased the abundances of nirK, nirS, nosZ I and nosZ II genes. Fertilization without nitrogen (N) significantly reduced the abundances of nirK, nosZ I and nosZ II, but did not affect the abundance of nirS. Fertilization without potassium (K) did not affect the abundances of all denitri-fying functional genes. Results of stepwise regression analysis and random forest analysis showed that soil pH was a key environmental factor affecting the abundances of nosZ I and nosZ II. The application of lime or lime + gypsum significantly increased soil pH, which subsequently increased the abundances of nosZ II and nosZ II/nosZ I by 150%-231% and 127%-155%, respectively. Our results suggested that application of lime or lime + gypsum favored nosZ II more than nosZ I in upland Ultisols, which might enhance the relative importance of nosZ II in N2O reduction. Overall, fertilization without P would reduce denitrifying gene abundances, while the application of lime or lime + gypsum enriched nosZ II and increased ratio of nosZ II/nosZ I, which might be beneficial for reducing N2O emission potential in the Ultisols.

Nitrosospira cluster 3 lineage of AOB and nirK of Rhizobiales respectively dominated N2O emissions from nitrification and denitrification in organic and chemical N fertilizer treated soils

Agricultural soils are known as nitrous oxide (N2O) sources due to the input of nitrogen (N) fertilizer and livestock faecal excretion. However, few studies have explored the responses of N2O microbial emission pathways and their related functional guilds to long-term soil fertilization regimes. This study examined the effects of four 38-year long-term fertilization treatments (control with no-fertilizer (CK); inorganic N fertilizer (N); manure (M); inorganic N fertilizer with manure (MN)) on the N2O levels generated from nitrification and denitrification, as well as on the nitrifiers and heterotrophic denitrifiers. The acetylene inhibition method was used to determine the microbial pathways of the N2O emissions and molecular biological techniques (cloning, high-throughput sequencing and quantitative PCR) were performed to investigate the nitrifier and denitrifier responses. The organic fertilization demonstrably increased the N2O emissions from nitrification and the abundance of canonical ammonia oxidizers and complete ammonia oxidizers (clade B), but distinctly decreased the abundance of clade A. Combined with the results that strong and positive relationships were detected between the abundance of bacterial amoA genes and N2O content produced from nitrification. We proposed that organic fertilizer applications stimulated the generation of N2O from nitrification dominated by the Nitrosospira cluster 3 lineage of AOB. In contrast, the amount of N2O produced by denitrification was appreciably stimulated by chemical N fertilization, compared to organic fertilization. Strong and positive relationships were detected between the nirK-type denitrifying gene abundances and the N2O emissions generated from denitrification. This suggested that single N fertilizer additions appreciably stimulated N2O production from denitrification dominated by the nirK lineage of the Rhizobiales. These results indicated that chemical N and organic fertilizers stimulated N2O emissions from denitrification and nitrification, respectively, which were dominated by the Nitrosospira cluster 3 lineage of AOB and the nirK lineage of Rhizobiales, respectively.

Role of microbial communities in conferring resistance and resilience of soil carbon and nitrogen cycling following contrasting stresses

Soils frequently experience environmental stresses that may have transient or persistent impact on important ecosystem services, such as carbon (C) and nitrogen (N) cycling. Microbial communities underpin resistance (the ability to withstand a stress) and resilience (the ability to recover from a stress) of these functions. Whilst functional stability and resilience have been studied extensively, the link to genetic stability is missing. In this study, the resistance and resilience of C mineralization, ammonia oxidation and denitrification, their associated gene abundances (16S rRNA, bacterial amoA, nirK, nirS, nosZ-I and nosZ-II) and bacterial community structures (T-RFLP 16S rRNA) were compared in two managed soils for 28 days after stressing the soils with either a persistent (1 mg Cu soil g−1) or a transient (heat at 40 °C for 16 h) stress. The average resistance of C mineralization to Cu was 60%, which was significantly greater than the resistance of ammonia oxidation (25%) and denitrification (31%) to Cu. Similarly, the average resilience of C mineralization to Cu was 52%, which was significantly greater than the resilience of ammonia oxidation (12%) and denitrification (18%) to Cu. However, this pattern was not significant after heat stress, indicating the critical role of different stressors. Changes in total bacterial community structure rather than abundance of 16S rRNA reflected the responses of C mineralization to Cu and heat. Both Cu and heat significantly decreased functional gene abundance (amoA, nirK, nirS, nosZ-I and nosZ-II), however, a significant recovery of denitrifying gene abundance was observed after 28 days following heat. There were lack of constant relationships between functional and genetic stability, highlighting that soil physiochemical properties, the nature of the stressor, and microbial life history traits combine to confer functional resistance and resilience. Genetic responses on their own are therefore inadequate in predicating changes to soil functions following stresses.

Soil extracellular enzyme activities and the abundance of nitrogen-cycling functional genes responded more to N addition than P addition in an Inner Mongolian meadow steppe

Nitrogen (N) and phosphorus (P) availability in soils commonly limit belowground biological processes in terrestrial ecosystems. Soil extracellular enzyme activities (EEAs) and microbial functional groups play critical roles in soil biological processes and nutrient cycling, yet their response to nutrient addition are poorly understood. To address this issue, we applied six fertilization treatments composed of combinations of N (0, 1.55, 13.95 g N m−2 yr−1) and P (0, 5.24 g P m−2 yr−1) for two years in a meadow steppe of Inner Mongolia. Soils were collected from each plot in July and August and analyzed for abundances of N-cycling genes and EEAs, and their relationships with treatments. The addition of N significantly increased C-acquisition enzyme activity and enzyme C:N and C:P ratios. Enzymatic stoichiometry indicated that N addition alleviated microbial demand for N, while it increased microbial C limitation. Microbial C and N limitation were significantly correlated with NH4+–N in July, yet they were correlated with soil water content (SWC) in August. The abundance of amoA significantly increased with N addition and was positively related to mineral-N accumulation. The abundance of denitrifier genes and gaseous N loss potential were accelerated by N addition in July, while a neutral effect was observed in August. Nitrate leaching potential was significantly increased by N addition, yet it declined with P addition in July. P addition also suppressed amoA abundance of ammonia oxidizing bacteria. Partial least squares path modelling indicated that N addition positively affected microbial-C limitation, soil N-loss potential and negatively affected microbial-N limitation. P addition negatively affected soil N-loss potential. Ultimately, this study highlights the importance of soil N availability in regulating microbial metabolism and soil N-loss potential, and enhances our understanding of the mechanisms responsible for variation in microbial nutrient cycling in meadow steppe soils.

Nitrification and urease inhibitors improve rice nitrogen uptake and prevent denitrification in alkaline paddy soil

Increasing evidence indicates that nitrification is a vital factor in crop growth and nitrous oxide emission. Nitrification and urease inhibitors have been demonstrated to be effective in inhibiting the nitrification process and are widely used as fertilizer additives in agricultural soils. However, the effects of these inhibitors on rice N uptake and N2O production through denitrification in paddy soils remain unclear. In the present work, we compared the influences of nitrification inhibitors dicyandiamide (DCD), nitrapyrin (2-chloro-6-(trichloromethyl) pyridine; NP) and N-(n-butyl) thiophosphoric triamide (NBPT) on rice growth, the fate of urea nitrogen (N), and the abundances and activities of ammonia oxidizers and denitrifiers. The fate of urea N was determined by the 15N isotope labeling technique, and the abundances of ammonia oxidizers and denitrifiers were determined using qPCR. All three inhibitors improved rice growth mainly due to the increase in urea N use efficiency. Urea N uptake was negatively correlated with nitrification. The growth of ammonia-oxidizing bacteria (AOB), important in nitrification, was directly blocked by DCD. Additionally, NP and NBPT impeded the growth of ammonia-oxidizing archaea (AOA). In addition, NP significantly increased the microbial biomass to promote more residual urea N in soil and increased soil N transformation. NBPT significantly inhibited urea hydrolysis indirectly affecting nitrification. All three inhibitors decreased the potential denitrification rate (PDR) at the rice heading stage but had little effect on the denitrifier gene abundance except for nitrapyrin, which decreased the nirK gene abundance. DCD and NBPT may reduce the denitrification activity by decreasing the denitrification substrate (NO3−) concentration. These results suggest that DCD, NP and NBPT have a beneficial effect on improving rice N uptake and have the potential to reduce N2O generation through denitrification.

Influence of liming-induced pH changes on nitrous oxide emission, nirS, nirK and nosZ gene abundance from applied cattle urine in allophanic and fluvial grazed pasture soils

The influence of soil pH changes by liming on denitrification and denitrifier gene abundance under different biogeochemical conditions by amending two contrasting soils with water, cattle urine (600 mg N kg−1 soil) and urine + dicyandiamide (DCD) (10 mg kg−1 soil) and incubating at 10 °C and 15 °C was evaluated. Liming increased N2O emission, denitrification rate and denitrifier gene abundance in both soils. The increase in N2O and denitrification with liming was higher in fluvial soil (24% increase in N2O and 22% increase in denitrification) than in allophanic soil (16% in N2O and 19% increase in denitrification). There was more N2O coming from urine applied to limed soil than that from urine to un-limed soil. Addition of DCD with urine reduced both N2O emission and denitrification; the reduction was greater in limed soil than in un-limed soil. Results of quantitative polymerase chain reaction (qPCR) of bacterial denitrifier genes (nirS, nirK and nosZ genes) indicate that liming-induced soil pH changes increased denitrifier gene abundance and caused more complete bacterial denitrification in urine-amended soils. These results suggest that liming grazed pasture soils induces complete denitrification, which may mitigate N2O emissions.

Crop residue carbon-to-nitrogen ratio regulates denitrifier N2O production post flooding

The response of nitrifier and denitrifier populations and associated N2O emissions to different carbon-to-nitrogen (C/N = 17 or 45) straw amendments was monitored under flooding-drying and non-flooding conditions. A 10-week laboratory mesocosm study was conducted in two soils, (i) a paddy soil with a long history of managed flooding-drying (CN), and (ii) a wheat cropping soil with no previous history of flooding (UK). We measured N2O fluxes and the abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite reductase (nirK and nirS) genes, and nitrous oxide reductase (nosZI and nosZII) genes during flooding (4 weeks) and post-flooding (6 weeks). Straw addition enhanced N2O emissions, with higher fluxes apparent after incorporation of narrow C/N residues. Moreover, the impact of crop amendment on N2O emission was exacerbated when soil was under flooding-drying conditions. The abundances of nirS and nosZI genes in CN soil and AOA gene in UK soil were increased by straw amendment, with highest in narrow C/N straw amendments. Structural equation modeling showed that the impact of denitrifier gene abundance on the N2O flux was stronger than that of nitrifier gene abundance in the two soils, and significant correlations were observed between N2O fluxes and the consumption of DOC and NO3−, indicating that denitrification was the dominant N2O production pathway during the drying phase. The ratio of (nirS + nirK)/(nosZI + nosZII) in the narrow C/N amendment was greater than in the wide C/N treatment after flooding, suggesting that the straw C/N ratio had an effect on the capacity for N2O production via denitrification. We conclude that crop amendments with an appropriate C/N ratio could minimize N2O fluxes through regulating the denitrification process when soils are subjected to regular flooding and drying and also experiencing greater frequencies of flooding.

A comparison of nitrate removal and denitrifying bacteria populations among three wetland plant communities.

Reed canary grass (Phalaris arundinacea L.) is an invasive, cool-season grass commonly dominating wetlands with high nutrient loads. Its impact on nitrogen removal via denitrification in wetlands is unknown. Most studies of denitrification in treatment wetlands have focused on the effects of physical or chemical variables and not on the effects of plant roots on the soil environment. The purpose of this study was to measure effects of plant type on denitrification rates in typical wetland soils of the midwestern United States by comparing wet prairie mix, switchgrass-dominated, and reed canary grass plant communities. Nitrate (NO3 - ) removal and other parameters were measured in miniature wetlands, or mesocosms, containing each plant community transplanted from a small agricultural treatment wetland in southern Minnesota. Quantitative polymerase chain reaction analysis was used to quantify the total bacteria population (measured with 16S rRNA genes) and denitrifying gene abundance (measured with nosZ genes) from the rhizosphere of each plant community. The wet prairie mix mesocosms on average removed the most NO3 - in each test (p=.01 and .08). Whereas the wet prairie mix removed the most NO3 - from the surface water (p<.01), reed canary grass removed more from the subsurface (p<.01). Ratios of denitrifying to total bacteria were higher in the wet prairie mix than in the other communities' root zones (p<.05). Results suggest that reed canary grass invasion could reduce denitrification in wetlands, especially during the spring and fall when it is growing but other plants are dormant.