Nitrous oxide emission and denitrifier communities in drip-irrigated calcareous soil as affected by chemical and organic fertilizers

Greenhouse gas emissions and drivers of the global warming potential of vineyards under different irrigation and fertilizer management practices

In the context of global warming and low water and fertilizer utilization efficiency in vineyards, identifying the driving factors of global warming potential (GWP) and proper irrigation and fertilization management strategies are crucial for high grape yields and emission reduction. In this experiment, drip fertigation technology was used, including three irrigation levels (W3 (100% M, where M is the irrigation quota), W2 (75% M) and W1 (50% M)) and four fertilization levels (F3 (648 kg hm-2), F2 (486 kg hm-2), F1 (324 kg hm-2) and F0 (0 kg hm-2)). Traditional furrow irrigation and fertilization (CG) and rainfed (CK) treatments were used as control treatments. The results indicated that under the drip fertigation system, fertilization significantly increased the grape leaf chlorophyll relative content (SPAD) and leaf area index (LAI) within a fertilizer application of 0-486 kg hm-2. Irrigation primarily had a direct positive effect on the water-filled pore space (WFPS) in the 0-60 cm soil layer, and the residual soil nutrient content was mainly affected by fertilization. The vital stage for reducing greenhouse gas emissions was the fruit-inflating and fruit-rendering stages. The CG treatment not only failed to ensure high grape yield but also adversely affected the soil environment and the reduction of greenhouse gas emissions in the vineyard. Fertilization had a direct positive effect on the grape SPAD, LAI, yield, and soil residual nutrient content. GWP was primarily directly driven by SPAD, WFPS, and soil residual nutrient content, while grape yield was primarily directly driven by fertilization and SPAD. In conclusion, the W2F2 treatment (25 % reduced irrigation and 486 kg hm-2 of fertilization) of drip fertigation in the vineyard was the preferred irrigation and fertilizer management strategy for maintaining good vine vigor and balancing grape yield and environmental benefits.

Organic fertilizer application promotes the soil nitrogen cycle and plant starch and sucrose metabolism to improve the yield of Pinellia ternata

Pinellia ternata (Thunb.) Breit is a traditional Chinese medicine with important pharmacological effects. However, its cultivation is challenged by soil degradation following excessive use of chemical fertilizer. We conducted an experiment exploring the effects of replacing chemical fertilizers with organic fertilizers (OF) on the growth and yield of P. ternata, as well as on the soil physicochemical properties and microbial community composition using containerized plants. Six fertilization treatments were evaluated, including control (CK), chemical fertilizer (CF), different proportions of replacing chemical fertilizer with organic fertilizer (OM1-4). Containerized P. ternata plants in each OF treatment had greater growth and yield than the CK and CF treatments while maintaining alkaloid content. The OM3 treatment had the greatest yield among all treatments, with an increase of 42.35% and 44.93% compared to the CK and CF treatments, respectively. OF treatments improved soil quality and fertility by enhancing the activities of soil urease (S-UE) and sucrase (S-SC) enzymes while increasing soil organic matter and trace mineral elements. OF treatments increased bacterial abundance and changed soil community structure. In comparison to the CK microbial groups enriched in OM3 were OLB13, Vicinamibacteraceae, and Blrii41. There were also changes in the abundance of gene transcripts among treatments. The abundance of genes involved in the nitrogen cycle in the OM3 has increased, specifically promoting the transformation of N-NO3- into N-NH4+, a type of nitrogen more easily absorbed by P. ternata. Also, genes involved in "starch and sucrose metabolism" and "plant hormone signal transduction" pathways were positively correlated to P. ternata yield and were upregulated in the OM3 treatment. Overall, OF in P. ternata cultivation is a feasible practice in advancing sustainable agriculture and is potentially profitable in commercial production.

Soil nitrogen cycling gene abundances in response to organic amendments: A meta-analysis

Quantification of nitrogen (N) cycling genes contributes to our best understanding of N transformation processes. The application of organic amendment (OA) is widely recognized as an effective measure to improve N management and soil fertility in various ecosystems. However, our understanding of N-cycling gene abundances in response to OA application remains deficient. We performed a meta-analysis embracing 124 sets of observation data to study the impact of OA application on the main N-cycling gene abundances, including nifH, amoA, nirS, nirK and nosZ. We found that the significantly positive response of N-cycling gene abundances to OA application was attributed to the rotation cropping system (by 6.45 %-104.20 %) in the field experiment (by 19.43 %-52.56 %), OA application alone (by 8.29 %-111.70 %) especially manure addition (by 33.43 %-98.70 %), application dose of OAs within 10-20 t ha-1 (by 45.33 %-381.90 %), fertilization duration <5 years (by 43.69 %-112.63 %), C/N of OA <25 (by 37.87 %-160.90 %), SOC lower than 1.2 % (by 41.44 %-157.89 %) and application to alkaline soil (by 32.24 %-134.40 %). Moreover, soil organic carbon (SOC) and pH were the most essential regulators associated with N-cycling gene abundances with OA application. Identification of key driving factors of the abundance of N-cycling functional genes will help remedy strategies for managing OAs in ecosystems.

Soil salinity is the main factor influencing the soil bacterial community assembly process under long-term drip irrigation in Xinjiang, China

Identifying the potential factors associated with the impact of long-term drip irrigation (DI) on soil ecosystems is essential for responding to the environmental changes induced by extensive application of DI technology in arid regions. Herein, we examined the effects of the length of time that DI lasts in years (NDI) on soil bacterial diversity as well as the soil bacterial community assembly process and the factors influencing it. The results showed that long-term DI substantially reduced soil salinity and increased soil bacterial diversity while affecting the soil bacterial community structure distinctly. Null model results showed that the soil bacterial community assembly transitioned from stochastic processes to deterministic processes, as NDI increased. Homogeneous selection, a deterministic process, emerged as the dominant process when NDI exceeded 15 years. Both random forest and structural equation models showed that soil salinity was the primary factor affecting the bacterial community assembly process. In summary, this study suggested that soil bacteria respond differently to long-term DI and depends on the NDI, influencing the soil bacterial community assembly process under long-term DI.

The impact of fertilization on ammonia-oxidizing bacteria and comammox Nitrospira communities and the subsequent effect on N2O emission and maize yield in a semi-arid region

The control of nitrous oxide (N2O) emissions through nitrification and the optimization of maize yield are important in agricultural systems. However, within the semi-arid region, the impact of fertilization on the function of nitrification communities and its connection with N2O emissions in the rhizosphere soil is still unclear. Our study investigates the influence of fertilization treatments on the communities of ammonia-oxidizing bacteria (AOB) and the complete ammonia oxidizers of the Nitrospira known as comammox (CAOB) in a maize agroecosystem. Nitrous oxide production, potential nitrification activity (PNA), maize yield, and nitrogen use efficiency (NUE) were determined for the same samples. The fertilizer treatments included a control group without fertilization (NA), inorganic fertilizer (CF), organic fertilizer (SM), combined inorganic and organic fertilizer (SC), and maize straw (MS). The SC treatment indicated a lower cumulative N2O emission than the CF treatment in the 2020 and 2021 cropping seasons. The AOB community under the CF, MS, and SM treatments was predominantly composed of Nitrosospira cluster 3b, while the SC treatment was associated with the comammox Nitrospira clade A.1 lineage, related to key species such as Ca. Nitrospira inopinata and Ca. Nitrospira nitrificans. Network analysis demonstrated a positive potential for competitive interaction between hub taxonomy and distinct keystone taxa among AOB and comammox Nitrospira nitrifiers. The structural equation model further revealed a significant positive association between AOB nitrifiers and N2O emission, PNA, soil pH, SOC, NO 3 - -N, and DON under organic fertilization. The keystone taxa in the comammox Nitrospira nitrifier and network Module II exhibited a positive correlation with maize productivity and NUE, likely due to their functional activities stimulated by the SC treatment. It is noteworthy that the AOB community played a more significant role in driving nitrification compared to the composition of comammox Nitrospira. Collectively, combined inorganic and organic fertilizer (SC) treatment exhibits high potential for reducing N2O emissions, enhancing maize productivity, increasing NUE, and increasing the sustainability of the nitrogen dynamics of maize agroecosystems in the semi-arid Loess Plateau.

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.

Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield

Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.

Replacing chemical fertilizer with manure reduces N2O emissions in winter wheat - summer maize cropping system under limited irrigation

Nitrous oxide (N₂O) emissions from agroecosystems are a major contributor to global warming and stratospheric ozone depletion. However, knowledge concerning the hotspots and hot moments of soil N₂O emissions with manure application and irrigation, as well as the underlying mechanisms remain incomplete. Here, a 3-year field experiment was conducted with the combination of fertilization (no fertilizer, F0; 100% chemical fertilizer N, Fc; 50% chemical N + 50% manure N, Fc + m; and 100% manure N, Fm) and irrigation (with irrigation, W1; and without irrigation, W0; at wheat jointing stage) for winter wheat - summer maize cropping system in the North China Plain. Results showed that irrigation did not affect annual N₂O emissions of the wheat-maize system. Manure application (Fc + m and Fm) reduced annual N₂O emissions by 25-51% compared with Fc, which mainly occurred during 2 weeks after fertilization combined with irrigation (or heavy rainfall). In particular, Fc + m reduced the cumulative N₂O emissions during 2 weeks after winter wheat sowing and summer maize top dressing by 0.28 and 0.11 kg ha^-1, respectively, compared with Fc. Meanwhile, Fm maintained the grain N yield and Fc + m increased grain N yield by 8% compared with Fc under W1. Overall, Fm maintained the annual grain N yield and lower N₂O emissions compared to Fc under W0, and Fc + m increased the annual grain N yield and maintained N₂O emissions compared with Fc under W1, respectively. Our results provide scientific support for using manure to minimize N₂O emissions while maintaining crop N yield under optimal irrigation to support the green transition in agricultural production.

Incorporating straw into intensively farmed cropland soil can reduce N2O emission via inhibition of nitrification and denitrification pathways

Straw incorporation (SI) combined with N fertilizer has been shown to affect soil N₂O emission and N-related functional microbes in agriculture. However, the responses of N₂O emission, community structure of nitrifiers and denitrifiers and related microbial functional genes to straw management strategies in the winter wheat season in China remain unclear. Here, we conducted a two-season experiment in a winter wheat field in Ningjing County, northern China, to examine four treatments: no fertilizer with (N0S1) and without maize straw (N0S0); N fertilizer with (N1S1) and without maize straw (N1S0), and their effects on N₂O emissions, soil chemical parameters, crop yield, as well as the dynamics of nitrifying and denitrifying microbial communities. We found that seasonal N₂O emissions decreased by 7.1-11.1% (p < 0.05) in N1S1 as compared to N1S0, without significant difference between N0S1 and N0S0. In combination with N fertilization, SI increased the yield by 2.6-4.3%, altered the microbial community composition, increased Shannon and ACE indexes, and decreased the abundance of AOA (9.2%), AOB (32.2%; p < 0.05), nirS (35.2%; p < 0.05), nirK (21.6%; p < 0.05) and nosZ (19.2%). However, in the absence of N fertilizer, SI promoted the major genera of Nitrosavbrio (AOB), unclassifiied_Gammaproteobacteria, Rhodanobacter (nirS), Sinorhizobium (nirK), which strongly correlated positively with N₂O emissions. Thereby, a negative interaction effect between SI and N fertilizer on AOB and nirS emphasized that SI could offset the increase of N₂O emission caused by fertilization. Soil moisture and NO₃^- concentration were the major factors affecting N-related microbial community structure. Our study reveals that SI suppressed N₂O emission significantly and simultaneously decreased the abundance of N-related functional genes and altered denitrifying bacterial community composition. We conclude that SI helps to enhance yield and alleviate fertilizer-induced environmental costs in intensively farmed fields in northern China.

Proper organic substitution attenuated both N2O and NO emissions derived from AOB in vegetable soils by enhancing the proportion of Nitrosomonas

The ammonia oxidation process driven by microorganisms is an essential source of nitrous oxide (N₂O) and nitric oxide (NO) emissions. However, few evaluations have been performed on the changes in the community structure and abundance of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) under substituting portion of chemical fertilizers with organic manure (organic substitution) and their relative contribution to the ammonia oxidation process. Here, five long-term fertilization strategies were applied in field (SN: synthetic fertilizer application; OM: organic manure; M1N1: substituting 50 % of chemical N fertilizer with organic manure; M1N4: substituting 20 % of chemical N fertilizer with organic manure; and CK: no fertilizer). We investigated the response characteristics of AOB and AOA community structures by selective inhibitor shaking assays and high-throughput sequencing and further explained their relative contribution to the ammonia oxidation process during three consecutive years of vegetable production. Compared to SN and M1N4, the potential of ammonia oxidation (PAO) was significantly reduced by 26.4 % and 22.3 % in OM and 9.5 % and 4.4 % in M1N1, resulting in N₂O reductions of 38.9 % and 30.8 % (OM) and 31.2 % and 21.1 % (M1N1), respectively, and NO reductions of 45.0 % and 34.1 % (OM) and 40.1 % and 28.3 % (M1N1). RDA and correlation analyses showed that the soil organic carbon and ammonium nitrogen content increased while AOB gene abundance and diversity significantly decreased with increasing organic replacement ratio; however, the relative abundance of Nitrosomonas in AOB increased in OM and M1N1, which further demonstrates that AOB are the main driver in vegetable soils. Therefore, the appropriate proportion of organic substitution (OM and M1N1) could decrease the N₂O and NO emissions contributed by AOB by affecting the soil physicochemical properties and AOB community structure.

Hydrochar more effectively mitigated nitrous oxide emissions than pyrochar from a coastal soil of the Yellow River Delta, China

Application of char amendments (e.g., pyrochar or biochar, hydrochar) in degraded soils is proposed as a promising solution for mitigating climate change via carbon sequestration and greenhouse gases (GHGs) emission reduction. However, the hydrochar-mediated microbial modulation mechanisms underlying N₂O emissions from coastal salt-affected soils, one of essential blue C ecosystems, were poorly understood. Therefore, a wheat straw derived hydrochar (SHC) produced at 220 °C was prepared to investigate its effects on N₂O emissions from a coastal salt-affected soil in the Yellow River Delta and to distinguish the microbial regulation mechanisms in comparison with corresponding pyrochar pyrolyzed at 500 °C (SPC) using a 28-day soil microcosm experiment. Compared with SPC, the acidic SHC (pH 4.15) enriched in oxygenated functional groups, labile C and N constituents. SHC application more efficiently depressed cumulative soil N₂O emissions (48.4-61.1 % vs 5.57-45.2 %) than those of SPC. SHC-induced inhibition of ammonia-oxidizing gene (amoA)-mediated nitrification and promotion of full reduction of N₂O to N₂ by nitrous oxide reductase gene (nosZ) were the underlying microbial mechanisms. Structural equation models further revealed that SHC-modulated bacterial N-transformation responses, i.e., inhibited nitrification and promoted heterotrophic denitrification, mainly contributed to reduced N₂O emissions, whereas modification of soil properties (e.g., decreased pH, increased total C content) by SPC dominantly accounted for decreased N₂O emissions. These results address new insights into microbial regulation of N₂O emission reduction from the coastal salt-affected soils amended with hydrochar, and provide the promising strategies to enhance C sequestration and mitigate GHG emissions in the blue C ecosystems.

The Effects of N Enrichment on Microbial Cycling of Non-CO2 Greenhouse Gases in Soils-a Review and a Meta-analysis

Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH₄) and nitrous oxide (N₂O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH₄ at the global scale. We also address the effects of N enrichment on N₂O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH₄ oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH₄⁺ enrichment, inhibits CH₄ oxidation, resulting in higher CH₄ emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N₂O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.

Impact of soil amendments on nitrous oxide emissions and the associated denitrifying communities in a semi-arid environment

Denitrifying bacteria produce and utilize nitrous oxide (N2O), a potent greenhouse gas. However, there is little information on how organic fertilization treatments affect the denitrifying communities and N2O emissions in the semi-arid Loess Plateau. Here, we evaluated how the denitrifying communities are responsible for potential denitrification activity (PDA) and N2O emissions. A field experiment was conducted with five fertilization treatments, including no fertilization (CK), mineral fertilizer (MF), mineral fertilizer plus commercial organic fertilizer (MOF), commercial organic fertilizer (OFP), and maize straw (MSP). Our result showed that soil pH, soil organic carbon (SOC), and dissolved organic nitrogen (DON) were significantly increased under MSP treatment compared to MF treatment, while nitrate nitrogen (NO3−−N) followed the opposite trend. Organic fertilization treatments (MOF, OFP, and MSP treatments) significantly increased the abundance and diversity of nirS- and nosZ-harboring denitrifiers, and modified the community structure compared to CK treatment. The identified potential keystone taxa within the denitrifying bacterial networks belonged to the distinct genera. Denitrification potentials were significantly positively correlated with the abundance of nirS-harboring denitrifiers, rather than that of nirK- and nosZ-harboring denitrifiers. Random forest modeling and structural equation modeling consistently determined that the abundance, community composition, and network module I of nirS-harboring denitrifiers may contribute significantly to PDA and N2O emissions. Collectively, our findings highlight the ecological importance of the denitrifying communities in mediating denitrification potentials and the stimulatory impact of organic fertilization treatments on nitrogen dynamics in the semi-arid Loess Plateau.

Effect of thermophilic microbial agents on nitrogen transformation, nitrogen functional genes, and bacterial communities during bean dregs composting

This study explored how a thermophilic microbial agent altered nitrogen transformation, nitrogen functional genes, and bacterial communities during bean dregs composting with (T) and without (CK) a thermophilic microbial agent for 15 days. The results showed that the maximum temperature in T reached 73 °C and remained above 70 °C for 8 days, while that in CK was only 65 °C. The pH in T had essentially stabilized on day 7, while that in CK was still increasing. On day 15, the seed germination index (GI) of T (95%) reached maturity (defined by GI ≥ 85%), while the GI of CK was only 36%. The concentrations of total nitrogen, water-soluble nitrogen, ammonia nitrogen, and nitrate nitrogen in T (2.5%, 18.9 g/kg, 8.75 g/kg, and 1.69 g/kg) were all lower than those in CK (3.6%, 28.9 g/kg, 12.75 g/kg, and 6.82 g/kg). During composting, Bacillus played a major role in nitrogen reduction, nitrogen mineralization, denitrification, and the conversion between nitrite and nitrate. Weissella played a major role in nitrogen assimilation. Komagataeibacter and Bacillus played a major role in nitrogen fixation in CK and T, respectively. Nitrification was not observed during composting. The nosZ gene, which converts nitrous oxide to nitrogen, was found only in T. Network analysis suggested that the average number of neighbours in T was 3.30% higher than that in CK and the characteristic path length in T was 14.15% higher than that in CK. Therefore, the thermophilic microbial agents could cause nitrogen loss but promote the maturity of bean dregs, which have great potential application.

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.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Nitrogen and Sulfur Additions Improved the Diversity of nirK- and nirS-Type Denitrifying Bacterial Communities of Farmland Soil

Anthropogenic nitrogen (N) and sulfur (S) deposition can change above- and belowground biodiversity, including soil microbial diversity. The diversity of denitrifying microorganisms is of great significance to the calculation of the global nitrogen cycle and nitrogen flux. For a long time, nirK and nirS have been used as the functional genes to study denitrifying microorganisms, and have gradually become molecular markers for studying the composition and diversity of denitrifying bacteria. Here, three-time exposures to N and S applications (7, 30, and 60 days), were independently established. Additionally, the abundance, diversity, and structure of nirK- and nirS-type denitrifying communities were examined by sequencing analyses in response to three treatments, namely, N and S (T_N/S), sodium chloride (T_NaCl) and deionized water (pH = 7.0) (CK). Our results suggest that T_N/S led to higher electrical conductivity (EC), total nitrogen (TN), total organic carbon (TOC), nitrate nitrogen (NO₃^--N), ammonium nitrogen (NH₄⁺-N), and lower pH compared with T_NaCl and CK, which affected the diversity of nirK- and nirS-type denitrifying bacterial communities. We also observed that the nirK-type denitrifying community demonstrated a higher sensitivity to N and S additions. Overall, our results are important for the understanding of nitrogen in soil and N₂O emissions.

Saline and alkaline stresses alter soil properties and composition and structure of gene-based nitrifier and denitrifier communities in a calcareous desert soil

BACKGROUND

Saline and alkaline stresses damages the health of soil systems. Meanwhile, little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the responses of gene-based nitrifier and denitrifier communities to chloride (CS), sulfate (SS), and alkaline (AS) stresses with those in a no-stress control (CK) in pots with a calcareous desert soil.

RESULTS

Compared with CK, saline and alkaline stress decreased potential nitrification rate (PNR) and NO₃-N; increased pH, salinity, water content, and NH₄-N; and decreased copy numbers of amoA-AOA and amoA-AOB genes but increased those of denitrifier nirS and nosZ genes. Copies of nirK increased in SS and AS but decreased in CS. There were more copies of amoA-AOB than of amoA-AOA and of nirS than of nirK or nosZ. Compared with CK, SS and AS decreased operational taxonomic units (OTUs) of amoA-AOB but increased those of nirS and nosZ, whereas CS decreased nirK OTUs but increased those of nosZ. The numbers of OTUs and amoA-AOB genes were greater than those of amoA-AOA. There were positive linear relations between PNR and amoA-AOA and amoA-AOB copies. Compared with CK, the Chao 1 index of amoA-AOA and amoA-AOB decreased in AS, that of nirK increased in CS and SS, but that of nirS and nosZ increased in all treatments. The Shannon index of amoA-AOB decreased but that of nirS increased in CS and SS, whereas the index of nirK decreased in all treatments. Saline and alkaline stress greatly affected the structure of nitrifier and denitrifier communities and decreased potential biomarkers of nirS-type; however, AS increased those of nirK- and nosZ-type, and SS decreased those of nosZ-type. Soil water content, pH, and salinity were important in shaping amoA-AOA and denitrifier communities, whereas soil water and pH were important to amoA-AOB communities.

CONCLUSION

These results indicate that the nitrifier and denitrifier communities respond to saline and alkaline stresses conditions. Communities of amoA-AOA and amoA-AOB contribute to nitrification in alluvial gray desert soil, and those of nirS are more important in denitrification than those of nirK or nosZ.

A global meta-analysis of nitrous oxide emission from drip-irrigated cropping system

Drip irrigation is a useful practice to enhance water and fertilizer nitrogen (N) use efficiency. However, the use of drip irrigation to mitigate nitrous oxide (N₂ O) emissions in agricultural systems globally is uncertain. Here, we performed a global meta-analysis of 485 field measurements of N₂ O emissions from 74 peer-reviewed publications prior to March 2021, to quantify the fertilizer-induced N₂ O emission factor (EF) of drip irrigation and examine the influencing factors of climate, crop, soil properties, and source and rate of fertilizer N application. The results showed that drip irrigation reduced (p < 0.05) N₂ O emissions by 32% and 46% compared to furrow and sprinkler irrigation systems, respectively. The overall average EF with drip irrigation was 0.35%, being two-thirds lower than the IPCC Tier I default value of 1% (kg N₂ O-N/kg added fertilizer N). The EF was not significantly affected by climate, crop, soil texture, soil organic carbon content, and pH. The EF was also not significantly (p > 0.05) affected by synthetic N fertilizer source despite a lower numerical value with enhanced efficiency than conventional fertilizers. The EF increased significantly (p < 0.001) with N addition rate in a binomial distribution. Using the IPCC default EF overestimated N₂ O emissions inventories for drip-irrigated cropping systems by 7614 and 13,091 Mg per year for China and the globe, respectively. These results indicate that drip irrigation should be recommended as an essential N₂ O mitigation strategy for irrigated crop production.

Quantifying soil N2O emissions from soil and anaerobically digested swine manure, nitrification and denitrification using 15N isotope labeling method

Increasing use of anaerobically digested swine manure in the farmland makes it necessary to understand its impact on N2O emissions, regarding the source of N2O and the corresponding mechanism of action. We used a 15N-labeled sulfate modifying the soil in order to identify the sources of N2O and the pathways of nitrification and denitrification. Three soil moisture contents (50% WHC, 75% WHC, and 100% WHC) along with three levels of anaerobically digested swine manure (0 g·kg-1, 10 g·kg-1, and 25 g·kg-1) were tested using randomized block design. Although the combined effect of contents of anaerobically digested swine manure and the soil moisture contents added to the system stimulated the utilization of soil N and promoted denitrification, the process of nitrification dominated. In anaerobically digested swine manure-treated soils, the rate of contribution of anaerobically digested swine manure to N2O accounted for 68.6-99.8%. In the 25 g·kg-1 treatment, the maximum of N2O produced by denitrification and nitrification were 14.1% and 93.1%.

Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas

Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments: (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered and assigned to 527 operational taxonomic units. Members of the Ascomycota phylum were dominant in all samples and accounted for 94.41% of the total number of detected sequences, followed by the Basidiomycota (5.05%), and unidentified fungi (0.54%). Alpha and beta diversity analyses revealed significantly different fungal populations in the three fertilizer treatments over the two time periods. The fungal diversity and richness on the grape berry surface in the B.O and A.O treatments were higher than those in the CH treatment. Among the detected fungi, the B.O treatments were mainly Pichia, Aureobasidium, and Candida genera, while the CH treatments were Botrytis, Aspergillus, and Penicillium. Moreover, significant differences were revealed between the two assessment times (T0 and T1). The samples from the T0 timepoint had higher fungal richness and diversity than the samples from T1 timepoint. Increasing organic fertilizer usage in grape management could improve grape quality and went on to increase the fungal diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.

Greenhouse gas emissions from constructed wetlands are mitigated by biochar substrates and distinctly affected by tidal flow and intermittent aeration modes

Biochar substrates and tidal flow (TF) and intermittent aeration (IA) operation modes have recently been applied to improve the treatment performance of constructed wetlands (CWs), but their roles in regulating greenhouse gas (GHG) emissions from CWs are still unclear. In this preliminary study, CO₂, CH₄ and N₂O fluxes and associated microbial characteristics in four groups of subsurface-flow CWs, i.e., ceramsite CWs (C-CWs), biochar-amended CWs (B-CWs), intermittently aerated B-CWs (AB-CWs) and tide-flow B-CWs (TB-CWs), were comparatively investigated. The results showed that biochar amendment significantly mitigated CH₄ and N₂O fluxes from the CWs by supporting higher abundances of mcrA and nosZ genes and higher ratios of pmoA/mcrA and nosZ/(nirK + nirS), thus reducing global warming potential (GWP, a decrease of 55.8%), in addition to promoting total nitrogen (TN) removal by 41.3%, mainly by increasing the abundances and activities of nitrifiers and denitrifiers. The TF mode efficiently improved nitrogen removal, but it greatly increased GHG fluxes since large amounts of GHGs escaped from the empty CW matrix after water draining. IA abated GHG emissions from the CWs, mainly after aeration. TF and IA decreased the abundances of functional bacteria and archaea related to C and N transformation, except nitrifiers, and shaped the microbial community structures. The application of a biochar substrate and IA mode can facilitate the design and operation of CWs in a more ecologically sustainable way.

Effects of biochar on nitrification and denitrification-mediated N2O emissions and the associated microbial community in an agricultural soil

Nitrous oxide (N₂O) is a strong greenhouse gas, and it is of great significance for N₂O reduction to study the effects of biochar on its production pathway. In this research, the contributions and mechanisms of biochar on autotrophic nitrification (ANF), heterotrophic nitrification (HNF), and denitrification (DF) to N₂O emissions were studied by using ¹⁵N stable isotopes and high-throughput sequencing after laboratory incubation. The results showed that biochar addition at 2% (B2) significantly reduced the N₂O emissions from the ANF by an average of 20.6%, while adding 5% biochar (B5) had no significant effect on the ANF. Both B2 and B5 significantly reduced the N₂O emissions from the HNF by 15.7% and 13.2%, respectively, and reduced the N₂O emissions from the DF by 40.9% and 11.7%, respectively. B2 enhanced the relative contribution rate of the ANF to N₂O emissions by 6.3%, while B5 had little effect on it. Biochar addition significantly changed the copy numbers of the AOA and AOB, as well as the nirK, nirS, and nosZ genes, but it had no significant effect on the community composition of the AOA and had minimal effect on the AOB community. B2 significantly increased the abundance of the genus Rhodococcus of nirK type denitrifiers and had a significant effect on the relative abundance of Cupriavidus and Pseudomonas of the nosZ type denitrifiers. These results revealed that the inhibitory effects of biochar on N₂O emissions from nitrification might be attributed to the direct immobilization and adsorption of inorganic N by biochar and to its promotion of the genus Rhodococcus of nirK-type denitrifiers and the genera Cupriavidus and Pseudomonas of the nosZ-type denitrifiers. The soil exchangeable NH₄⁺-N and NO₃^--N concentrations were the primary factors affecting the N₂O emission rates. These results help to elucidate the effects and mechanisms of biochar on N₂O production pathways in agricultural soil.

Effects of phosphogypsum and medical stone on nitrogen transformation, nitrogen functional genes, and bacterial community during aerobic composting

This study explored the effects of adding phosphogypsum (PPG), medical stone (MS), and both (PPM) during composting on nitrogen transformation, nitrogen functional genes, the bacterial community, and their relationships with NH₃ and N₂O emissions. Adding MS and PPM reduced NH₃ emissions by 25.78-68.37% and N₂O emissions by 19.00-42.86%. PPG reduced NH₃ emissions by 59.74% but slightly increased N₂O emissions by 8.15%. MS was strongly correlated with the amoA-dominated nitrification process. PPG and PPM had strong correlations with nirS- and nirK-dominated, and nosZ-dominated denitrification processes, respectively. PPM promoted nitrification and denitrification processes more than PPG and MS. Different functional bacteria had key roles in nitrification and denitrification during different composting stages. Firmicutes probably contributed to the conversion and release of nitrogen in the thermophilic period, whereas Proteobacteria, Chloroflexi, Bacteroidetes, and other phyla might have played important roles in the cooling and maturation periods. PPM obtained the greatest reductions in NH₃ and N₂O release via the regulation of environmental variables, nitrogen functional genes, and the bacterial community. Overall, these results provide insights at a molecular level into the effects of PPG and MS on nitrogen transformation and NH₃ and N₂O emissions during composting.

Mitigating N2O emission by synthetic inhibitors mixed with urea and cattle manure application via inhibiting ammonia-oxidizing bacteria, but not archaea, in a calcareous soil

Synthetic inhibitors and organic amendment have been proposed for mitigating greenhouse gas N2O emissions. However, their combined effect on the N2O emissions and ammonia-oxidizer (ammonia-oxidizing bacteria and archaea, AOB and AOA) communities remains unclear in calcareous soils under climate warming. We conducted two incubation experiments (25 and 35 °C) to examine how N2O emissions and AOA and AOB communities responded to organic amendment (urea plus cattle manure, UCM), and in combination with urease (N-(n-butyl) thiophosphoric triamide, NBPT) and nitrification inhibitor (nitrapyrin). The treatments of UCM + nitrapyrin and UCM + nitrapyrin + NBPT significantly lowered total N2O emissions by average 64.5 and 71.05% at 25 and 35 °C, respectively, compared with UCM treatment. AOB gene abundance and α-diversity (Chao1 and Shannon indices) were significantly increased by the application of urea and manure (P < 0.05). However, relative to UCM treatment, nitrapyrin addition treatments decreased AOB gene abundance and Chao 1 index by average 115.4 and 30.4% at 25 and 35 °C, respectively. PCA analysis showed that UCM or UCM plus nitrapyrin notably shifted AOB structure at both temperatures. However, fertilization had little effects on AOA community (P > 0.05). Potential nitrification rate (PNR) was greatly decreased by nitrapyrin addition, and PNR significantly positively correlated with AOB gene abundance (P = 0.0179 at 25 °C and P = 0.0029 at 35 °C) rather than AOA (P > 0.05). Structural equation model analysis showed that temperature directly increased AOA abundance but decrease AOB abundance, while fertilization indirectly influenced AOB community by altering soil NH4+, pH and SOC. In conclusion, the combined application of organic amendment, NBPT and nitrapyrin significantly lowered N2O emissions via reducing AOB community in calcareous soil even at high temperature. Our findings provide a solid theoretical basis in mitigating N2O emissions from calcareous soil under climate warming.

Greenhouse gas emissions from inorganic and organic fertilizer production and use: A review of emission factors and their variability

Fertilizers have become an essential part of our global food supply chain and are necessary to sustain our growing population. However, fertilizers can also contribute to greenhouse gas (GHG) emissions, along with other potential nutrient losses in the environment, e.g. through leaching. To reduce this environmental impact, tools such as life cycle assessments and decision support systems are being used to aid in selecting sustainable fertilization scenarios. These scenarios often include organic waste-derived amendments, such as manures, composts and digestates. To produce an accurate assessment and comparison of potential fertilization scenarios, these tools require emission factors (EFs) that are used to estimate GHG emissions and that are an integral part of these analyses. However, such EFs seem to be very variable in nature, thereby often resulting in high uncertainty on the outcomes of the analyses. This review aims to identify ranges and sources of variability in EFs to provide a better understanding of the potential uncertainty on the outcomes, as well as to provide recommendations for selecting EFs for future studies. As such, an extensive review of the literature on GHG emissions from production, storage, transportation and application of synthetic fertilizers (N, P, K), composts, digestates and manures was performed. This paper highlights the high variability that is present in emissions data and confirms the great impact of this uncertainty on the quality and validity of GHG predictions related to fertilizers. Variability in EFs stem from the energy source used for production, operating conditions, storage systems, crop and soil type, soil nutrient content, amount and method of fertilizer application, soil bacterial community, irrigation method, among others. Furthermore, a knowledge gap exists related to EFs for potassium fertilizers and waste valorization (anaerobic digestion/composting) processes. Overall, based on this review, it is recommended to determine EFs on a case by case basis when possible and to use uncertainty analyses as a tool to better understand the impact of EF variability.

Effect of N fertilizer types on N2O and NO emissions under drip fertigation from an agricultural field in the North China Plain

N₂O and NO emissions from a winter wheat-summer maize rotation field in the North China Plain were comparably investigated under three different treatments: 1) flood irrigation (A-Flood treatment) plus fertilization of NH₄Cl, 2) drip fertigation (A-Drip treatment) plus fertilization of NH₄Cl and 3) drip fertigation (AN-Drip treatment) plus fertilization of a mixture of Ca(NO₃)₂ and NH₄Cl. The annual N₂O cumulative emissions from the A-Drip treatment and the A-Flood treatment were almost identical, whereas it from the AN-Drip treatment was significantly lower (33%) than that from the A-Flood treatment. Compared with the A-Flood treatment, the annual NO cumulative emission from the A-Drip treatment was significantly increased by 140% but it from the AN-Drip treatment was only slightly increased by 14%. Compared with drip fertigation with NH₄Cl, drip fertigation with the mixture of Ca(NO₃)₂ and NH₄Cl significantly reduced the cumulative emissions of N₂O (31%) and NO (52%) from the nitrification dominated fields by decreasing the supplement of NH₄⁺ substrate. Among the three fertilization treatments, the yields of the maize from the A-Drip and AN-Drip treatments were significantly increased, while the yields of the wheat were almost the same. Considering the benefit of increasing yields and reducing N fertilizer and water input, the application of nitrate-based fertilizer instead of partial ammonium-based fertilizer through drip fertigation could be a promising method for keeping agronomic productivity and environmental sustainability.

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China

Organic fertilizer application could have an impact on the nitrogen cycle mediated by microorganisms in arable soils. However, the dynamics of soil ammonia oxidizers and denitrifiers in response to compost addition are less understood. In this study, we examined the effect of four compost application rates (0, 11.25, 22.5 and 45 t/ha) on soil ammonia oxidizers and denitrifiers at soybean seedling, flowering and mature stage in a field experiment in Northeast China. As revealed by quantitative PCR, compost addition significantly enhanced the abundance of ammonia oxidizing bacteria (AOB) at seedling stage, while the abundance of ammonia oxidizing archaea was unaffected across the growing season. The abundance of genes involved in denitrification (nirS, nirK and nosZ) were generally increased along with compost rate at seedling and flowering stages, but not in mature stage. The non-metric multidimensional scaling analysis revealed that moderate and high level of compost addition consistently induced shift in AOB and nirS containing denitrifers community composition across the growing season. Among AOB lineages, Nitrosospira cluster 3a gradually decreased along with the compost rate across the growing season, while Nitrosomonas exhibited an opposite trend. Network analysis indicated that the complexity of AOB and nirS containing denitrifiers network gradually increased along with the compost rate. Our findings highlighted the positive effect of compost addition on the abundance of ammonia oxidizers and denitrifiers and emphasized that compost addition play crucial roles in shaping their community compositions and co-occurrence networks in black soil of Northeast China.

Nitrous oxide emission and the related denitrifier community: A short-term response to organic manure substituting chemical fertilizer

Partially substituting chemical fertilizer with organic manure can aid in the disposal of agricultural wastes via recycling into agricultural land, reduce chemical fertilizer application, and influence nitrogen (N) transformation. However, relatively few studies have investigated the association between soil physicochemical properties, denitrifier communities and N₂O emission after short-term substitution of organic manure in vegetable fields. We conducted a short-term vegetable field experiment which included one control treatment (CT, no fertilizer) and three fertilization treatments containing equal amount of total N, phosphorus and potassium (CF, chemical fertilizer only; CMR, chemical fertilizer plus mushroom residue; COM, chemical fertilizer plus cattle manure). The results showed that partial substitution of chemical fertilizer with organic manure greatly increased cumulative N₂O emissions, N₂O emission factors and yield-scaled N₂O emissions by 122-203%, 238-600% and 128-181%, respectively. Compared with the CF treatment, short-term substitution with organic manure reduced the abundance of nirS- and nosZ-type denitrifiers, and increased that of nirK-type denitrifiers. Modeling indicated that nirS abundance, together with soil available N, NIR activity, nirK abundance, SOC, NH₄⁺, and NO₃^- were the primary factors associated with cumulative N₂O emissions. The denitrifier community composition of the CF- treated soil was separated from that of soils treated with CMR and COM, and was primarily influenced by soil NH₄⁺ concentration. NIR activity showed a significant correlation with denitrifier community composition. Overall, short-term substitution of chemical fertilizer with cattle manure (lower C/N ratio) reduced the abundance of nirS- and nosZ-type denitrifiers, but stimulated N₂O emission.

Characterization of Denitrifying Community for Application in Reducing Nitrogen: a Comparison of nirK and nirS Gene Diversity and Abundance

Studies have shown that the addition of biochar to agricultural soils has the potential to mitigate climate change by decreasing nitrous oxide (N₂O) emissions resulting from denitrification. Rice paddy field soils have been known to have strong denitrifying activity, but the response of microbes to biochar for weakening denitrification in rice paddy field soils is not well known. In this work, compared with the chemical fertilizer alone, the chemical fertilizer + 20 t hm^-2 biochar fertilizer slightly decreased denitrifying the nitrite reductase activity (S-NiR) and N₂O emission without statistic difference, whereas the chemical fertilizer + 40 t hm^-2 biochar significantly boosted them. The abundance of nir-denitrifiers contributed to S-NiR and N₂O emission, especially nirS-denitrifiers, rather than the variation of community structure. Pearson correlation analysis showed that NO₂^--N was a key factor for controlling the abundance of nir-denitrifiers, S-NiR and N₂O emission. The biochar addition fertilization treatments strongly shaped the community structure of nirK-denitrifiers, while the community structure of nirS-denitrifiers remained relatively stable. In addition, Paracoccus and Sinorhizobium were revealed to be as the predominant lineage of nirS- and nirK-containing denitrifiers, respectively. Distance-based redundancy analysis (db-RDA) showed that changes in the nir-denitrifier community structure were significantly related to soil organic carbon, NO₃^--N, and total phosphorus. Our findings suggest that, although the nirS- and nirK-denitrifiers are both controlling nitrite reductase, their responses to biochar addition fertilization treatments showed significant discrepancies of diversity, abundance, and contribution to N₂O and S-NiR in a paddy soil.

Roles of nxrA-like oxidizers and nirS-like reducers in nitrite conversion during swine manure composting

Nitrite has a key role in nitrogen conversion during composting. In this study, the dynamic changes in the NO₂^- contents, abundances of nirS and nxrA, and the bacteria that harbored these genes were determined during composting. NO₂^- accumulated during the initial composting stage. The nirS gene was abundant throughout composting, whereas the nxrA gene was only abundant in the late composting phases. Ralstonia sp. and Thauera sp. were the dominant denitrifiers that harbored nirS, and Nitrobacter winogradskyi Nb-255 was the dominant nitrifier that harbored nxrA. Structural equation modeling showed that NO₂^- was mainly reduced by nirS in the early phases, and oxidized by nxrA in the late phases, but especially in the maturity phase. Network analysis showed that the dominant bacteria harboring nirS and nxrA were hubs in the modules related to the reduction and oxidation of NO₂^-, and they had competitive relationships during the cooling and maturity phases.

The effect of biochar amendment on N-cycling genes in soils: A meta-analysis

Nitrogen (N) cycling by soil microbes can be estimated by quantifying the abundance of microbial functional genes (MFG) involved in N-transformation processes. In agro-ecosystems, biochars are regularly applied for increasing soil fertility and stability. In turn, it has been shown that biochar amendment can alter soil N cycling by altering MFG abundance and richness. However, the general patterns and mechanisms of how biochar amendment modifies N-cycling gene abundance have not been synthesized to date. Here, we addressed this knowledge gap by performing a meta-analysis of existing literatures up to 2019. We included five main marker genes involved in N cycling: nifH, amoA, nirK, nirS and nosZ. We found that biochar addition significantly increased the abundance of ammonia-oxidizing archaea (AOA), nirK, nirS and nosZ by an average of 25.3%, 32.0%, 14.6% and 17.0%, respectively. Particularly, biochar amendment increased the abundances of most N-cycling genes when soil pH changed from very acidic (pH < 5) to acidic (pH: 5.5-6.5). Experimental conditions, cover plants, biochar pyrolysis temperature and fertilizer application were also important factors regulating the response of most N-cycling genes to biochar amendment. Moreover, soil pH significantly correlated with ammonia-oxidizing bacteria (AOB) abundance, while we found that most genes involved in nitrification and denitrification were not significantly correlated with each other across studies. Our results contribute to developing quantitative models of microbially-mediated N-transforming processes in response to biochar addition, and stimulate research on how to use biochar amendment for reducing reactive N gas emissions and enhancing N bioavailability to crop plants in agro-ecosystems.

Manure application increased denitrifying gene abundance in a drip-irrigated cotton field

Application of inorganic nitrogen (N) fertilizer and manure can increase nitrous oxide (N₂O) emissions. We tested the hypothesis that increased N₂O flux from soils amended with manure reflects a change in bacterial community structure and, specifically, an increase in the number of denitrifiers. To test this hypothesis, a field experiment was conducted in a drip-irrigated cotton field in an arid region of northwestern China. Treatments included plots that were not amended (Control), and plots amended with urea (Urea), animal manure (Manure) and a 50/50 mix of urea and manure (U+M). Manure was broadcast-incorporated into the soil before seeding while urea was split-applied with drip irrigation (fertigation) over the growing season. The addition treatments did not, as assessed by nextgen sequencing of PCR-amplicons generated from rRNA genes in soil, affect the alpha diversity of bacterial communities but did change the beta diversity. Compared to the Control, the addition of manure (U+M and Manure) significantly increased the abundance of genes associated with nitrate reduction (narG) and denitrfication (nirK and nosZ). Manure addition (U+M and Manure) did not affect the nitrifying enzyme activity (NEA) of soil but resulted in 39–59 times greater denitrifying enzyme activity (DEA). In contrast, urea application had no impact on the abundances of nitrifier and denitrifier genes, DEA and NEA; likely due to a limitation of C availability. DEA was highly correlated (r = 0.70–0.84, P < 0.01) with the abundance of genes narG, nirK and nosZ. An increase in the abundance of these functional genes was further correlated with soil NO₃⁻, dissolved organic carbon, total C, and total N concentrations, and soil C:N ratio. These results demonstrated a positive relationship between the abundances of denitrifying functional genes (narG, nirK and nosZ) and denitrification potential, suggesting that manure application increased N₂O emission by increasing denitrification and the population of bacteria that mediated that process.

Effects of combined biochar and organic fertilizer on nitrous oxide fluxes and the related nitrifier and denitrifier communities in a saline-alkali soil

This study intended to evaluate the combined effects of both biochar and organic fertilizer on nitrous oxide (N₂O) fluxes and composition of nitrifier and denitrifier of saline-alkali soil. Therefore, four different treatments such as CK (only chemical fertilizer), B (only biochar), M (only organic fertilizer), BM (B:M = 1:1) were used in this experiment. The results showed that N₂O emissions were decreased in B and BM treatments compare to the control. In contrast, N₂O emissions were highest before day 12 but lowest after day 19 in M treatment compare to the control. Application of biochar, organic fertilizer and biochar plus organic fertilizer decreased the nirS and nirK genes copies and enhanced the nosZ gene copies which resulting in the lower N₂O fluxes. The ammonia-oxidizing bacteria (AOB) amoA and nirK genes copies were significantly increased by organic fertilizer before day 12, leading to high N₂O emissions. The genera Nitrosospira (AOB) and Nitrososphaera (ammonia-oxidizing archaea, AOA) assumed absolute superiority. Additionally, Nitrosospira (AOB) was also appeared in nirK-type denitrifiers, illustrating denitrification was carried out by nitrifiers. The genera Azospirillum (nirS), Burkholderia (nosZ) and Polymorphum (nosZ) were dominant in CK. There was only one dominant genus, Mesorhizobium (nosZ) in the B treatment. The genera Mesorhizobium (nirK), Azoarcus (nirS), Kocuria (nirS) and Pseudomonas (nosZ) occupied the main status in the M treatment. The relative abundance of Rhodanobacter (nirS) and Azospirillum (nosZ) were higher in the BM treatment compared with other treatments. Soil water content (SWC), pH, NH₄⁺-N and NO₃^--N were the main factors affecting AOB and denitrifiers, which influencing N₂O emissions. Overall, combined application of biochar and organic fertilizer can reduce the N₂O emission where AOB and nirK-type denitrifier were the main contributors to the N₂O emission.

Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns

Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.

N2O emission contributions by different pathways and associated microbial community dynamics in a typical calcareous vegetable soil

Nitrous oxide, one of the powerful long-lived greenhouse gases, is emitted mainly through biological processes, especially from fertilized soil. It is critical to partition the contribution of different pathways to N₂O emissions and the relevant characteristics of microbial communities to identify the key N₂O processes. An microcosm was conducted to partition the N₂O emissions from different pathways, and the changes in soil mineral nitrogen and various nitrifiers (amoA bacteria and amoA archaea) and denitrifiers (nirS, nirK, and nosZ) were also determined using qPCR and high-throughput sequencing methods. Different gas inhibitor combinations (i.e., 0.06% acetylene, pure oxygen, 0.06% acetylene in pure oxygen, and pure helium) were used to partition the N₂O pathways. A 5% oxygen treatment, with and without acetylene, was also included so that the N₂O emissions could be measured under lower oxygen partial pressure. Results showed that ammonia-oxidation (AO) and successive nitrifier denitrification (NiD) were the main pathways contributing to N₂O emissions at the earlier period after ammonium sulfate application with the cumulative N₂O emissions accounting for 30.9% and 59.2% of the total N₂O emissions, respectively. The higher NiD N₂O contributions occurred when the soil nitrite concentration appeared higher, especially under the lower oxygen conditions. Higher N₂O emissions from AO and NiD were associated with the compositional proportion of some dominant AOB species. Denitrification contributed more N₂O (63.6%-69.3%) in the later period during incubation, coinciding with the following characteristics for denitrifiers: a) lower nosZ/(nirS + nirK) ratio, b) more diversity in nirS, and c) different proportions of some dominant species in nirK. Our results demonstrated that higher AO and successive NiD were the main N₂O emission pathways, suggesting that controlling the ammonium content and weakening the AO are critical in decreasing N₂O emissions.