Nitrifier-induced denitrification is an important source of soil nitrous oxide and can be inhibited by a nitrification inhibitor 3,4-dimethylpyrazole phosphate

The regulation effect of preventing soil nitrogen loss using microbial quorum sensing inhibitors

Preventing soil nitrogen (N) losses driven by microbial nitrification and denitrification contributes to improving global environmental concerns caused by NO3--N leaching and N2O emission. Quorum sensing (QS) signals regulate nitrification and denitrification of N-cycling bacteria in pure culture and water treatment systems, and mediate the composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in activated sludge. However, whether disrupting QS could prevent soil N losses remains unclear. This study explored the feasibility of applying quorum sensing inhibitors (QSIs) as an innovative strategy to reduce N losses from agricultural soils. The two QSIs, penicillic acid and 4-iodo-N-[(3S)-tetrahydro-2-oxo-3-furanyl]-benzeneacetamide (4-iodo PHL), were more effective in reducing N losses than traditional inhibitors, including N-(n-butyl) thiophosphoric triamide and 3,4-dimethylpyrazole phosphate. After 36 days of aerobic incubation, penicillic acid and 4-iodo PHL inhibited nitrification by 39% and 68%, respectively. The inhibitory effects are attributed to the fact that 4-iodo PHL decreased the abundance of archaeal and bacterial amoA genes, as well as the relative abundance of Candidatus Nitrocosmicus (AOA), Candidatus Nitrososphaera (AOA), and Nitrospira (nitrite-oxidizing bacteria/comammox), while penicillic acid reduced archaeal amoA abundance and the relative abundance of Nitrosospira (AOB) and the microbes listed above. Penicillic acid also strongly inhibited denitrification (33%) and N2O emissions (61%) at the peak of N2O production (day 4 of anaerobic incubation) via decreasing nitrate reductase gene (narG) abundance and increasing N2O reductase gene (nosZ) abundance, respectively. Furthermore, the environmental risks of QSIs to microbial community structure and network stability, CO2 emissions, and soil animals were acceptable. Overall, QSIs have application potential in agriculture to reduce soil N losses and the associated effect on climate change. This study established a new method to mitigate N losses from the perspective of QS, and can serve as important basis of decreasing the environmental risks of agricultural non-point source pollution.

AOB Nitrosospira cluster 3a.2 (D11) dominates N2O emissions in fertilised agricultural soils

Ammonia-oxidation process directly contribute to soil nitrous oxide (N2O) emissions in agricultural soils. However, taxonomy of the key nitrifiers (within ammonia oxidising bacteria (AOB), archaea (AOA) and complete ammonia oxidisers (comammox Nitrospira)) responsible for substantial N2O emissions in agricultural soils is unknown, as is their regulation by soil biotic and abiotic factors. In this study, cumulative N2O emissions, nitrification rates, abundance and community structure of nitrifiers were investigated in 16 agricultural soils from major crop production regions of China using microcosm experiments with amended nitrogen (N) supplemented or not with a nitrification inhibitor (nitrapyrin). Key nitrifier groups involved in N2O emissions were identified by comparative analyses of the different treatments, combining sequencing and random forest analyses. Soil cumulative N2O emissions significantly increased with soil pH in all agricultural soils. However, they decreased with soil organic carbon (SOC) in alkaline soils. Nitrapyrin significantly inhibited soil cumulative N2O emissions and AOB growth, with a significant inhibition of the AOB Nitrosospira cluster 3a.2 (D11) abundance. One Nitrosospira multiformis-like OTU phylotype (OTU34), which was classified within the AOB Nitrosospira cluster 3a.2 (D11), had the greatest importance on cumulative N2O emissions and its growth significantly depended on soil pH and SOC contents, with higher growth at high pH and low SOC conditions. Collectively, our results demonstrate that alkaline soils with low SOC contents have high N2O emissions, which were mainly driven by AOB Nitrosospira cluster 3a.2 (D11). Nitrapyrin can efficiently reduce nitrification-related N2O emissions by inhibiting the activity of AOB Nitrosospira cluster 3a.2 (D11). This study advances our understanding of key nitrifiers responsible for high N2O emissions in agricultural soils and their controlling factors, and provides vital knowledge for N2O emission mitigation in agricultural ecosystems.

Metatranscriptomic insights into the microbial metabolic activities during an Ulva prolifera green tide in coastal Qingdao areas

Green tide, a typical marine environmental disaster that profoundly influenced the coastal areas, has been occurred consecutively in the South Yellow Sea of China since 2007. Herein, the active microbial community structure and metabolic pathways in Qingdao offshore during an Ulva prolifera green tide were investigated by using metatranscriptomic approach. The dominant active microbial taxa at the outbreak phase were primarily a functional group that can utilize organic matters derived from U. prolifera, such as Lentibacter, Polaribacter and Planktomarina. While the taxa involved in biogeochemical cycles, including Phaeobacter, Pseudomonas and Marinobacterium, dominated the active microbial communities at the decline phase. The expression level of enzymes involved in U. prolifera polysaccharides degradation was significantly higher at the outbreak phase compared to the decline phase. At the same time, the main players Glaciecola and Polarbacter showed similar trends, suggesting that the low competitiveness for nutrients of related microorganisms at this phase made them degrade more U. prolifera polysaccharides to meet their own nutrient needs, thereby accelerating the degradation of U. prolifera. According to KEGG annotation, the biogeochemical pathways including nitrogen cycle, sulfur cycle and methane oxidation altered during the green tide, with thiosulfate oxidation and methane oxidation probably being the crucial pathways at the outbreak and the decline phase respectively. The coupling of sulfide oxidation and denitrification was also observed in this study. Furthermore, the green tide in Qingdao offshore might impact the greenhouse effects induced by CH4 and N2O through influencing the related microbial processes.

Metagenomic analysis insights into the influence of 3,4-dimethylpyrazole phosphate application on nitrous oxide mitigation efficiency across different climate zones in Eastern China

Excessive nitrogen (N) fertilization in agroecological systems increases nitrous oxide (N2O) emissions. 3,4-dimethylpyrazole phosphate (DMPP) is used to mitigate N2O losses. The influence of DMPP efficiency on N2O mitigation was clearly affected by spatiotemporal heterogeneity. Using field and incubation experiments combined with metagenomic sequencing, we aimed to investigate DMPP efficiency and the underlying microbial mechanisms in dark-brown (Siping, SP), fluvo-aquic (Cangzhou, CZ; Xinxiang, XX), and red soil (Wenzhou, WZ) from diverse climatic zones. In the field experiments, the DMPP efficiency in N2O mitigation ranged from 51.6% to 89.9%, in the order of XX, CZ, SP, and WZ. The DMPP efficiency in the incubation experiments ranged from 58.3% to 93.9%, and the order of efficiency from the highest to lowest was the same as that of the field experiments. Soil organic matter, total N, pH, texture, and taxonomic and functional α-diversity were important soil environment and microbial factors for DMPP efficiency. DMPP significantly enriched ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB), which promoted N-cycling with low N2O emissions. Random forest (RF) and regression analyses found that an AOA (Nitrosocosmicus) and NOB (Nitrospina) demonstrated important and positive correlation with DMPP efficiency. Moreover, genes associated with carbohydrate metabolism were important for DMPP efficiency and could influenced N-cycling and DMPP metabolism. The similar DMPP efficiency indicated that the variation in DMPP efficiency was significantly due to soil physicochemical and microbial variations. In conclusion, filling the knowledge gap regarding the response of DMPP efficiency to abiotic and biotic factors could be beneficial in DMPP applications, and in adapting more efficient strategies to improve DMPP efficiency and mitigate N2O emissions in multiple regions.

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

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

Niche Differentiation Among Canonical Nitrifiers and N2O Reducers Is Linked to Varying Effects of Nitrification Inhibitors DCD and DMPP in Two Arable Soils

The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N₂O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N₂O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N₂O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N₂O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N₂O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N₂O reducers in determining the varying efficacies of DCD and DMPP in different arable soils.

Meta-analysis of the effect of nitrification inhibitors on the abundance and community structure of N2O-related functional genes in agricultural soils

Application of nitrification inhibitors (NIs) in agricultural systems is an important strategy to enhance fertilizer nitrogen use efficiency and mitigate soil nitrous oxide (N₂O) emissions. Here, we conducted a global meta-analysis of 88 published studies to assess the response of N₂O-related functional gene and transcript abundances, and community structure to NIs application. Application of NIs significantly reduced the abundance of ammonia-oxidizing bacteria ammonia monooxygenase (AOB amoA) genes, AOB amoA transcript and nitrite reductase (nirS and nirK) genes. The effectiveness of NIs on reducing the AOB amoA abundance was influenced by N form, soil texture, soil pH and the experimental type (field vs. laboratory). Specifically, NIs were more effective when a mixed inorganic and organic N source was applied to a medium-textured soils. The NIs effectiveness increased with increasing soil pH. The response of AOB amoA abundance to NIs application was not affected by NI type, N rate, soil moisture, soil temperature and soil organic carbon (SOC). The inhibitory effect of NIs on nirS abundance increased with increasing soil temperature. NIs decreased soil nitrifying enzyme activity (NEA) and denitrifying enzyme activity (DEA) by 34.5 % and 27.0 %, respectively, leading to an overall 63.6 % reduction of N₂O emissions. Soil NEA correlated positively with the abundance and community structure of AOB amoA but not with AOA amoA. Decrease in DEA with NIs application coincided with the decreasing nirS and nirK abundances. This global-scale assessment demonstrates that the effectiveness of NIs in reducing N₂O emissions was attributed to the inhibiting effects on AOB amoA, nirS and nirK genes. Our findings highlight that NIs' inhibition effects on bacterial ammonia-oxidizing community and the encode enzymes in transformation of nitrite to nitric oxide are the main mechanisms for mitigation of N fertilizer-induced N₂O emissions.

Impact of intercropping grass on the soil rhizosphere microbial community and soil ecosystem function in a walnut orchard

The intercropping of grass in orchards has beneficial effects on soil properties and soil microbial communities and is an important soil management measure for improving orchard productivity and land-use efficiency. However, few studies have explored the effects of grass intercropping on rhizosphere microorganisms in walnut orchards. In this study, we explored the microbial communities of clear tillage (CT), walnut/ryegrass (Lolium perenne L.) (Lp), and walnut/hairy vetch (Vicia villosa Roth.) (Vv) intercropping system using MiSeq sequencing and metagenomic sequencing. The results revealed that the composition and structure of the soil bacterial community changed significantly with walnut/Vv intercropping compared to CT and walnut/Lp intercropping. Moreover, the walnut/hairy vetch intercropping system had the most complex connections between bacterial taxa. In addition, we found that the soil microorganisms of walnut/Vv intercropping had a higher potential for nitrogen cycling and carbohydrate metabolism, which may be related to the functions of Burkholderia, Rhodopseudomonas, Pseudomonas, Agrobacterium, Paraburkholderia, and Flavobacterium. Overall, this study provided a theoretical basis for understanding the microbial communities associated with grass intercropping in walnut orchards, providing better guidance for the management of walnut orchards.

Contribution of Ammonium-Induced Nitrifier Denitrification to N2O in Paddy Fields

Paddy fields are one of the most important sources of nitrous oxide (N₂O), but biogeochemical N₂O production mechanisms in the soil profile remain unclear. Our study used incubation, dual-isotope (¹⁵N-¹⁸O) labeling methods, and molecular techniques to elucidate N₂O production characteristics and mechanisms in the soil profile (0-60 cm) during summer fallow, rice cropping, and winter fallow periods. The results pointed out that biotic processes dominated N₂O production (72.2-100%) and N₂O from the tillage layer accounted for 91.0-98.5% of total N₂O in the soil profile. Heterotrophic denitrification (HD) was the main process generating N₂O, contributing between 53.4 and 96.6%, the remainder being due to ammonia oxidation pathways, which was further confirmed by metagenomics and quantitative polymerase chain reaction (qPCR) assays. Nitrifier denitrification (ND) was an important N₂O production source, contributing 0-46.6% of total N₂O production, which showed similar trends with N₂O emissions. Among physicochemical and biological factors, ammonium content and the ratio of total organic matter to nitrate were the main driving factors affecting the contribution ratios of the ammonia oxidation pathways and HD pathway, respectively. Moisture content and pH affect norC-carrying Spirochetes and thus the N₂O production rate. These findings confirm the importance of ND to N₂O production and help to elucidate the impact of anthropogenic activities, including tillage, fertilization, and irrigation, on N₂O production.

Black Plastic Film Mulching Increases Soil Nitrous Oxide Emissions in Arid Potato Fields

Black plastic film mulching is a common practice for potato production in the arid area of Northwest China. Many studies have reported the significant positive effect of black plastic film mulch on potato harvest, while the effect of black plastic film mulch treatment on soil nitrous oxide (N₂O) emissions is still unclear. As a consequence, this study aimed to examine the effect of black plastic film mulch treatment on N₂O emission from arid upland potato fields. With the static chamber-gas chromatography method, soil N₂O emissions were measured. The results showed that black plastic film mulching treatment significantly increased cumulative soil N₂O emissions by 21-26% compared with non-mulched treatment. Cumulative N₂O emission positively correlated with soil temperature, soil moisture, soil CO₂ concentration, and amoA-AOB abundance. This study indicated that black plastic film mulching, mainly through increasing soil temperature and soil moisture, increasing soil carbon dioxide (CO₂) concentration, and promoting the abundance of nitrification-related functional gene of amoA-AOB, regulated N₂O emissions. This study also highlighted that the specific soil environment under black plastic film mulch is conducive to N₂O emissions and lay the foundation for settling the contradiction between food production and greenhouse gas mitigation in upland soils. The negative effects of black plastic film mulching on the environment should be considered in future applications in food production.

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.

A meta-analysis to examine whether nitrification inhibitors work through selectively inhibiting ammonia-oxidizing bacteria

Nitrification inhibitor (NI) is often claimed to be efficient in mitigating nitrogen (N) losses from agricultural production systems by slowing down nitrification. Increasing evidence suggests that ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) have the genetic potential to produce nitrous oxide (N₂O) and perform the first step of nitrification, but their contribution to N₂O and nitrification remains unclear. Furthermore, both AOA and AOB are probably targets for NIs, but a quantitative synthesis is lacking to identify the “indicator microbe” as the best predictor of NI efficiency under different environmental conditions. In this present study, a meta-analysis to assess the response characteristics of AOB and AOA to NI application was conducted and the relationship between NI efficiency and the AOA and AOB amoA genes response under different conditions was evaluated. The dataset consisted of 48 papers (214 observations). This study showed that NIs on average reduced 58.1% of N₂O emissions and increased 71.4% of soil NH4+ concentrations, respectively. When 3, 4-dimethylpyrazole phosphate (DMPP) was applied with both organic and inorganic fertilizers in alkaline medium soils, it had higher efficacy of decreasing N₂O emissions than in acidic soils. The abundance of AOB amoA genes was dramatically reduced by about 50% with NI application in most soil types. Decrease in N₂O emissions with NI addition was significantly correlated with AOB changes (R² = 0.135, n = 110, P < 0.01) rather than changes in AOA, and there was an obvious correlation between the changes in NH4+ concentration and AOB amoA gene abundance after NI application (R² = 0.037, n = 136, P = 0.014). The results indicated the principal role of AOB in nitrification, furthermore, AOB would be the best predictor of NI efficiency.

Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox)

In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N₂O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.

Reduced fertilization mitigates N2O emission and drip irrigation has no impact on N2O and NO emissions in plastic-shed vegetable production in northern China

Plastic-shed vegetable production in China creates hotspots for emission of the potent greenhouse gas nitrous oxide (N₂O) and the atmospheric pollutant nitric oxide (NO). To mitigate N₂O and NO emissions, determination of the predominant processes of N₂O and NO generation in plastic-shed vegetable production is important. Here, we reported the findings of a 2-year experimental study on the effects of reduced fertilization and/or drip irrigation on N₂O and NO emissions during plastic-shed tomato production in northern China. Five treatments were applied: 1) over fertilization and flood irrigation (conventional practice); 2) fertilization reduced by 20% and flood irrigation; 3) fertilization reduced by 20% and drip irrigation; 4) fertilization reduced by 30% and drip irrigation, and 5) control (no fertilizer input and flood irrigation). Reduced both basal and top-dressed fertilization maintained tomato yields. Compared with conventional practices (mean annual N₂O and NO emissions: 18.1 ± 1.3 and 0.79 ± 0.02 kg N ha^-1 yr ^-1, respectively), fertilization reduction by 20%-30% decreased the annual N₂O emission by 21.2%-27.0% owing to lower soil inorganic nitrogen (SIN) contents under the reduced fertilization practices. Switching from flood to drip irrigation might weaken denitrification due to lower soil moisture and less wet soil area, but increased SIN contents, and thus had no significant impact on annual N₂O and NO emissions. Peak N₂O fluxes occurred at soil temperature 28 °C and water-filled pore space (WFPS) > 60%, were higher than those for NO, and peak NO fluxes appeared 4-6 days later than N₂O fluxes, consistent with the decline in WFPS. These observations indicated that N₂O and NO from alkaline plastic-shed soil may be mainly generated via heterotrophic denitrification and nitrification, respectively. Reduced fertilization and drip irrigation in plastic-shed tomato production maintained crop productivity and mitigated N₂O emission. These results could be integrated into the decision-making in sustainable plastic-shed production.

The end of hunger: fertilizers, microbes and plant productivity

It is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and biodiversity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil biodiversity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant-associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome-based innovations to promote plant productivity and contribute to the end of hunger.

Century-long changes and drivers of soil nitrous oxide (N2 O) emissions across the contiguous United States

The atmospheric concentration of nitrous oxide (N₂ O) has increased by 23% since the pre-industrial era, which substantially destructed the stratospheric ozone layer and changed the global climate. However, it remains uncertain about the reasons behind the increase and the spatiotemporal patterns of soil N₂ O emissions, a primary biogenic source. Here, we used an integrative land ecosystem model, Dynamic Land Ecosystem Model (DLEM), to quantify direct (i.e., emitted from local soil) and indirect (i.e., emissions related to local practices but occurring elsewhere) N₂ O emissions in the contiguous United States during 1900-2019. Newly developed geospatial data of land-use history and crop-specific agricultural management practices were used to force DLEM at a spatial resolution of 5 arc-min by 5 arc-min. The model simulation indicates that the U.S. soil N₂ O emissions totaled 0.97 ± 0.06 Tg N year^-1 during the 2010s, with 94% and 6% from direct and indirect emissions, respectively. Hot spots of soil N₂ O emission are found in the US Corn Belt and Rice Belt. We find a threefold increase in total soil N₂ O emission in the United States since 1900, 74% of which is from agricultural soil emissions, increasing by 12 times from 0.04 Tg N year^-1 in the 1900s to 0.51 Tg N year^-1 in the 2010s. More than 90% of soil N₂ O emission increase in agricultural soils is attributed to human land-use change and agricultural management practices, while increases in N deposition and climate warming are the dominant drivers for N₂ O emission increase from natural soils. Across the cropped acres, corn production stands out with a large amount of fertilizer consumption and high-emission factors, responsible for nearly two-thirds of direct agricultural soil N₂ O emission increase since 1900. Our study suggests a large N₂ O mitigation potential in cropland and the importance of exploring crop-specific mitigation strategies and prioritizing management alternatives for targeted crop types.

Greenhouse gas emissions of biosolid and cow manure during composting and vermicomposting and when applied to soil cultivated with wheat (Triticum sp. L.)

Biosolids are a by-product of wastewater treatment, and their nutritional composition makes them ideal for fertilizing crops. However, pre-treatments, such as conditioning and/or (vermi)composting, are often required to stabilize the product and remove pathogens. Biosolids, cow manure, and a 50-50% mixture were conditioned for 21 days, composted or vermicomposted with Eisenia fetida (Savigny 1826) for 28 days, and applied to soil cultivated with wheat (Triticum sp. L.), while emissions of nitrous oxide (N₂O), methane (CH₄), and carbon dioxide (CO₂) were monitored. Emissions of CH₄ were large from the biosolid and N₂O from the cow manure during conditioning. Emissions of CH₄ remained high during (vermi)composting of the biosolids, while the emissions of N₂O from the cow manure dropped. The addition of E. fetida did not affect the emissions of greenhouse gases during (vermi)composting. The emission of N₂O was higher when (vermi)composted biosolid was applied to soil cultivated with wheat than when (vermi)composted cow manure was applied. The global warming potential (GWP) of the sum of the emitted greenhouse gases (GHG) during conditioning, (vermi)composting, and when the final product was applied to soil was 3 times larger from the cow manure than from the biosolid, but mixing biosolid with cow manure eliminated that difference. It was concluded that mixing biosolid with cow manure might be a simple way to reduce the GWP of the emitted GHG during storage, (vermi)composting, and when applied to soil.

Tea plantation intercropping green manure enhances soil functional microbial abundance and multifunctionality resistance to drying-rewetting cycles

Climate change leads to more serious drying-rewetting alternation disturbance, which furtherly affects soil ecosystem function and agriculture production. Intercropping green manure, as an ancient agricultural practice, can improve the physical, chemical, and biological fertility of soil in tea plantation. However, the effects of intercropping green manure on soil multifunctional resistance to drying-rewetting disturbance in tea plantation has not been reported. In this study, the effects of different green manure practices over four years (tea plant monoculture, tea plant and soybean intercropping, tea plant and soybean + milk vetch intercropping) on soil multifunctionality resistance to drying-rewetting cycles, and the pivotal influencing factors were investigated. We used quantitative PCR array and analysis of multiple enzyme activities to characterize the abundance of functional genes and ecosystem multifunctionality, respectively. Compared with tea plantation monoculture, tea plant intercropping soybean and soybean + milk vetch significantly increased multifunctionality resistance by 12.07% and 25.86%, respectively. Random forest analysis indicated that rather than the diversity, the abundance of functional genes was the major drive of multifunctionality resistance. The structure equation model further proved that tea plantation intercropping green manure could improve the abundance of C cycling related functional genes mediated by soil properties, and ultimately increased multifunctionality resistance to drying-rewetting disturbance. Therefore, tea plantation intercropping green manure is an effective approach to maintain the multifunctionality resistance, which is conducive to maintain the soil nutrient supply capacity and tea production under the disturbance of drying-rewetting alternation.

Dimethylpyrazole-based nitrification inhibitors have a dual role in N2O emissions mitigation in forage systems under Atlantic climate conditions

Nitrogen fertilization is the most important factor increasing nitrous oxide (N₂O) emissions from agriculture, which is a powerful greenhouse gas. These emissions are mainly produced by the soil microbial processes of nitrification and denitrification, and the application of nitrification inhibitors (NIs) together with an ammonium-based fertilizer has been proved as an efficient way to decrease them. In this work the NIs dimethylpyrazole phosphate (DMPP) and dimethylpyrazole succinic acid (DMPSA) were evaluated in a temperate grassland under environmental changing field conditions in terms of their efficiency reducing N₂O emissions and their effect on the amount of nitrifying and denitrifying bacterial populations responsible of these emissions. The stimulation of nitrifying bacteria induced by the application of ammonium sulphate as fertilizer was efficiently avoided by the application of both DMPP and DMPSA whatever the soil water content. The denitrifying bacteria population capable of reducing N₂O up to N₂ was also enhanced by both NIs provided that sufficiently high soil water conditions and low nitrate content were occurring. Therefore, both NIs showed the capacity to promote the denitrification process up to N₂ as a mechanism to mitigate N₂O emissions. DMPSA proved to be a promising NI, since it showed a more significant effect than DMPP in decreasing N₂O emissions and increasing ryegrass yield.

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

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

Biological nitrification inhibitor co-application with urease inhibitor or biochar yield different synergistic interaction effects on NH3 volatilization, N leaching, and N use efficiency in a calcareous soil under rice cropping

Nitrogen management measures (NMMs) such as the application of urease inhibitors (UIs), synthetic nitrification inhibitors (SNIs), and biochar (BC) are commonly used in mitigating nitrogen (N) loss and increasing fertilizer recovery efficiency (FRE) in agriculture. Calcareous soil under rice cropping is characterized by high nitrification potential, N loss risk, and low FRE. Application of SNIs may stimulate NH₃ volatilization in high pH soils and the effects of SNIs on FRE are not always positive. BNIs have many advantages over SNIs. Whether combined application of BNI, UI, and BC that can result in a synergistic effect of improving FRE and decreasing N loss in a calcareous soil under rice cropping worth investigating. In this study, we conducted pot experiments to investigate the effects of single and co-application of BNI (methyl 3-(4-hydroxyphenyl) propionate or MHPP, 500 mg kg^-1 soil), UI (N-(n-butyl), thiophosphoric triamide or NBPT, 2% of urea-N), or BC (wheat straw, 0.5% (w/w)) with chemical fertilizer on NH₃ volatilization, N₂O emission, N leaching, crop N uptake, and FRE in a calcareous soil under rice cropping. Our results demonstrated that those NMMs could mitigate NH₃ volatilization by 12.5%-26.5%, N₂O emission by 62.7%-73.5%, and N leaching loss by 17.5%-49.0%. However, BNI might have a risk of increasing NH₃ (5.98%) volatilization loss. Among those NMMs, double inhibitors (BNI plus UI) yielded a synergistic effect that could mitigate N loss to the maximum extent and effectively improve FRE by 25.4%. The mechanisms of the above effects could be partly ascribed to the niche differentiation between the abundance of AOA and AOB and the changed community structure of AOB, which could further influence nitrification and N fate. Our results demonstrated that co-application of BNI and UI with urea is an effective strategy in reducing N loss and improving FRE in a calcareous soil under rice cropping.

DMPP reduces nitrogen fertilizer application rate, improves fruit quality, and reduces environmental cost of intensive apple production in China

In China, excessive application of nitrogen (N) fertilizer is common in intensive apple production. To resolve issues of benefit reduction and environmental pollution caused by excessive N, a two-year trial was conducted in an apple orchard with a split-plot design, in which the main factor was the N level (500, 400, 300, and 200 kg N ha^-1 year^-1, expressed as TN, TN80%, TN60%, and TN40%, respectively) and the deputy factor was whether or not to add 3,4-dimethylpyrazole phosphate (DMPP, expressed as +D). The effects of N reduction combined with DMPP on soil N transformation, fruit quality, economic benefits, and environmental effects were investigated. The results showed that DMPP reduced the production of nitrate and its vertical migration by inhibiting the abundance of AOB amoA and decreased N₂O emission by reducing nirKC1 levels. Moreover, N reduction combined with DMPP improved N use efficiency (26.67-49.35%) and reduced N loss rate (15.25-38.76%). Compared with TN, TN60% + D increased the content of anthocyanin and soluble sugar by 21.15% and 13.09%, respectively, and decreased environmental costs caused by NH₃ volatilization and N₂O emission by 33.84%, while maintaining yield and N utilization rate at relatively high levels. Considering the agronomic, economic and environmental benefits, on the basis of traditional N application rate, 40% N reduction combined with DMPP (TN60% + D) could ensure target yield, corresponding quality and economic benefits, maintain soil N fertility, and reduce the risk of N losses to the environment. The present research could provide references for green, efficient, and sustainable development of apple production.

The composition of antibiotic resistance genes is not affected by grazing but is determined by microorganisms in grassland soils

Grazing is expected to exert a substantial influence on antibiotic resistance genes (ARGs) in grassland ecosystems. However, the precise effects of grazing on the composition of ARGs in grassland soils remain unclear. This is especially the case for grassland soils subject to long-term grazing. Here, we investigated ARGs and bacterial community composition in soils subject to long-term historic grazing (13-39 years) and corresponding ungrazed samples. Using a combination of shotgun metagenomics, amplicon analyses and associated soil physicochemical data, we provide novel insights regarding the structure of ARGs in grassland soils. Interestingly, our analysis revealed that long-term historic grazing had no impacts on the composition of ARGs in grassland soils. An average of 378 ARGs, conferring resistance to 14 major categories of antibiotics (80%), were identified in both grazing and ungrazed sites. Actinobacteria, Proteobacteria and Acidobacteria were the most prevalent predicted hosts in these soils and were also shown to harbour genetic capacity for multiple-resistant ARGs. Our results suggested that positive effects of bacterial community composition on ARGs could potentially be controlled by affecting MGEs. Soil properties had direct effects on the composition of ARGs through affecting the frequency of horizontal gene transfer among bacteria. Twelve novel ARGs were found in S. grandis steppe grasslands, indicating that different vegetation types might induce shifts in soil ARGs. Collectively, these findings suggest that soil properties, plants and microorganisms play critical roles in shaping ARG patterns in grasslands. Together, these data establish a solid baseline for understanding environmental antibiotic resistance in grasslands.

Gas emissions during cattle manure composting and stockpiling

Manure composting is a common management practice for cattle feedlots, but gaseous emissions from composting are poorly understood. The objective of this study was to quantify ammonia (NH₃ ), nitrous oxide (N₂ O), carbon dioxide (CO₂ ), and methane (CH₄ ) emissions from windrow composting (turning) and static stockpiling (nonturning) of manure at a commercial feedlot in Australia. An inverse-dispersion technique using an open-path Fourier transform infrared (OP-FTIR) spectrometer gas sensor was deployed to measure emissions of NH₃ , N₂ O, CO₂ , and CH₄ over a 165-d study period, and 29 and 15% of the total data intervals were actually used to calculate the fluxes for the windrow and stockpile, respectively. The nitrogen (N) lost as NH₃ and N₂ O emissions represented 26.4 and 3.8% of the initial N in windrow, and 5.3 and 0.8% of that in the stockpile, respectively. The carbon (C) lost as CO₂ and CH₄ emissions represented 44 and 0.3% of the initial C in windrow, and 54.8 and 0.7% of that in the stockpile, respectively. Total greenhouse gas (GHG) emissions from the manure windrow were 2.7 times higher than those of the stockpiled manure. This work highlights the value that could be accrued if one could reduce emissions of NH₃ -N and N₂ O-N from composting, which would retain manure N content while reducing GHG emissions.

Reduction of N2O emission by biochar and/or 3,4-dimethylpyrazole phosphate (DMPP) is closely linked to soil ammonia oxidizing bacteria and nosZI-N2O reducer populations

Biochar has been demonstrated to reduce nitrous oxide (N₂O) emissions from soils, but its effect is highly soil-dependent. In particular, in soils with strong nitrification potential, biochar addition may increase N₂O emissions. Thus, in soils with strong nitrification potential, the combination of biochar with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) may be more effective in reducing N₂O emissions than biochar alone. However, the combined use of biochar and DMPP on soil N₂O emissions is relatively unexplored, and underlying microbial mechanisms of how biochar and/or DMPP amendment affect N₂O emissions is still largely unknown. Here, a 30-day incubation experiment was established with four treatments: CK (control), BC (biochar), DMPP, and BD (biochar and DMPP), all at agronomically recommended rates, and N cycling assessed following addition of urea. Treatment of soil with BC, DMPP and BD reduced N₂O emissions (compared with urea alone) by 59.1%, 95.5% and 74.1%, respectively. Quantification of N cycling genes (amoA, nirS, nirK, and nosZ) indicated that biochar stimulated growth of ammonia oxidizing archaea (AOA) and bacteria (AOB), while DMPP alone inhibited the activity and growth of AOB. In the BD treatment, DMPP was absorbed onto biochar reducing its efficacy in inhibiting AOB growth. The response patterns of nirS/nirK nitrite-reducing denitrifiers to biochar and/or DMPP addition varied among clades. Notably, biochar and/or DMPP increased the abundance of nosZI and nosZII-N₂O reducers, but nosZI-clade taxa were more closely associated with reducing N₂O emission than nosZII taxa. Overall, our findings proved that the dynamics of AOB and nosZI-N₂O reducers resulting from the addition of biochar and/or DMPP played a key role in governing soil N₂O emissions.

Nitrification inhibitors effectively target N2 O-producing Nitrosospira spp. in tropical soil

The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3 - , NH4 + , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 - , NH4 + and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 + , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.

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.

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N₂O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N₂O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N₂O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N₂O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N₂O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.