Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils

Greenhouse gas mitigation and soil carbon stabilization potential of forest biochar varied with biochar type and characteristics

Biochar is increasingly used in climate-smart agriculture, yet its impact on greenhouse gas (GHG) emissions and soil carbon (C) sequestration remains poorly understood. This study examined biochar-mediated changes in soil properties and their contribution to C stabilization and GHG mitigation by evaluating four types of biochar. Soil carbon dioxide (CO2) and nitrous oxide (N2O) emissions, soil chemical and biological properties, and soil organic carbon (SOC) mineralization kinetics were monitored using greenhouse, laboratory, and modeling experiments. Three pine wood biochars pyrolyzed at 460 °C (PB-460), 500 °C (PB-500), 700 °C (PB-700), and one pine bark biochar from gasification at 760 °C (GB-760) were added into soil at 1 % w/w basis. Soils amended with biochar were used to cultivate sorghum for three months in a greenhouse, followed by three months of laboratory incubation. Data obtained from laboratory incubation was modeled using various statistical approaches. The PB-500 and PB-700 reduced cumulative N2O-N emissions by 68.5 % and 73.9 % and CO2 equivalent C emissions by 66.9 % and 72.4 %, respectively, compared to unamended control. The N2O emissions were positively associated with soil nitrate N, available P, and biochar ash content while negatively associated with SOC. The CO2 emission was negatively related to biochar C:N ratio and volatile matter content. Biochar amended soils had 49.2 % (PB-500) to 87.7 % (PB-700) greater SOC and 22.9 % (PB-700) to 48.1 % (GB-760) greater sorghum yield than the control. While PB-700 had more saprophytes than the control, the GB-760 yielded a greater yield than biochars prepared by pyrolysis. Microbial biomass C was 7.23 to 23.3 % greater in biochar amended soils than in control. The double exponential decay model best explained the dynamics of C mineralization, which was associated with initial soil nitrate N and available P positively and total fungi and protozoa biomass negatively. Biochar amendment could be a climate smart agricultural strategy. Pyrolysis pine wood biochar showed the greatest potential to reduce GHG emissions and enhance SOC storage and stability, and gasification biochar contributed more to SOC storage and increased crop yield.

The effect of nitrogen input on N2O emission depends on precipitation in a temperate desert steppe

Nitrous oxide (N2O) is the third most important greenhouse gas, and can damage the atmospheric ozone layer, with associated threats to terrestrial ecosystems. However, to date it is unclear how extreme precipitation and nitrogen (N) input will affect N2O emissions in temperate desert steppe ecosystems. Therefore, we conducted an in-situ in a temperate desert steppe in the northwest of Inner Mongolia, China between 2018 and 2021, in which N inputs were combined with natural extreme precipitation events, with the aim of better understanding the mechanism of any interactive effects on N2O emission. The study result showed that N2O emission in this desert steppe was relatively small and did not show significant seasonal change. The annual N2O emission increased in a non-linear trend with increasing N input, with a much greater effect of N input in a wet year (2019) than in a dry year (2021). This was mainly due to the fact that the boost effect of high N input (on June 17th 2019) on N2O emission was greatly amplified by nearly 17-46 times by an extreme precipitation event on June 24th 2019. In contrast, this greatly promoting effect of high N input on N2O emission was not observed on September 26th 2019 by a similar extreme precipitation event. Further analysis showed that soil NH4+-N content and the abundance of ammonia oxidizing bacteria (amoA (AOB)) were the most critical factors affecting N2O emission. Soil moisture played an important indirect role in regulating N2O emission, mainly by influencing the abundance of amoA (AOB) and de-nitrification functional microorganisms (nosZ gene). In conclusion, the effect of extreme precipitation events on N2O emission was greatly increased by high N input. Furthermore, in this desert steppe, annual N2O flux is co-managed through soil nitrification substrate concentration (NH4+-N), the abundance of soil N transformation functional microorganisms and soil moisture. Overall, it was worth noting that an increase in extreme precipitation coupled with increasing N input may significantly increase future N2O emissions from desert steppes.

Understanding vermicompost and organic manure interactions: impact on toxic elements, nitrification activity, comammox Nitrospira inopinata, and archaea/bacteria

Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB), and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p < 0.05) in fresh cow-dung vermicompost (stored for 40 days) as compared with other organic manure. The level of PTEs (Cu2+, Fe2+, Pb2+, Cd2+, and Zn2+) was significantly lower (p < 0.05) in vermicompost as compared with compost of waste material with Trichoderma and cow dung. Comammox N. inopinata, NOB, AOB, and AOA were significantly higher (p < 0.05) in stored cow-dung vermicompost (more than 1 year) as compared with other organic manure. The results of the scatterplot matrix analysis suggested that Fe2+, total nitrogen (TN), soil organic carbon (SOC), and total carbon (TC) were linearly correlated (p < 0.001) with NNRs and NPs in vermicompost and organic manure. Similarly, comammox N. inopinata bacteria, NOB, AOB, and AOA were linearly correlated (p < 0.001) with NNR and NP. These results indicated that vermicompost promoted nitrification activity by increasing microbial diversity and abundance, supplying nutrients and organic matter for microbial growth, and facilitating complex microbial interactions. It may be concluded that the influence of vermicompost, which played a great role in PTE concentration reduction, increased chemical, and biological properties, increased the growth rate of nitrifying bacteria/archaea and the nitrogen cycle.

Shifts in soil ammonia-oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions

Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize 68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.

Effects of environmental and housing system factors on ammonia and greenhouse gas emissions from cattle barns: A meta-analysis of a global data collation

This study provides a meta-analysis on the relationships between cattle barn CH4, NH3 and N2O emission rates and their key drivers (i.e., housing type, floor type, environmental conditions). Understanding these relationships is essential to reduce uncertainties in emission inventories and suggest targeted mitigation measures. The total number of daily emission rates included in the analysis was 139 for CH4, 293 for NH3 and 100 for N2O emissions. Emission rates in the database showed a large variation with 45-803.5 g/LU d-1 for CH4, 0.036-146.7 gN LU-1 d-1 for NH3, and 0.002-18 gN LU-1 d-1 for N2O emissions. Despite the high emission variability, significant effects were identified·NH3 showed positive correlation with air temperature; NH3 emissions differed between housing types but not between floor types·NH3 emissions from tied stalls were lower than the ones from cubicle housing regardless of the floor type. Additionally, NH3 emissions from loose housings were lower than the ones from cubicle housing·NH3 and N2O emission rates from temperate wet zones were lower than the ones from temperate dry zones. CH4 emission rates were affected by environmental factors only and not by housing and floor type, showing negative correlation with air temperature and humidity. The factors investigated can be suggested as ancillary variables and descriptors when cattle barn emissions are measured, in order to make best use of emission data. Country-specific data of these key drivers can be included into national inventories to adapt them to different agroecosystems and support targeted policies.

Hydrological connectivity affects nitrogen migration and retention in the land‒river continuum

Land use change and excessive nitrogen (N) loading threaten the health of receiving water bodies worldwide. However, the role of hydrological connectivity in linking watershed land use, N biogeochemistry and river water quality remain unclear. In this study, we investigated 15 subwatersheds in the Jiulong River watershed (southeastern China) during a dry baseflow period in 2018, combined with 3‒year (2017-2019) nutrient monitoring in 5 subwatersheds to explore river N dynamics (dissolved nutrients, dissolved gases and functional genes) and their controlling factors at three hydrological connectivity scales, i.e., watershed, hydrologically sensitive areas (HSAs) and riparian zone. The results show that land use at HSAs (less than 20% of watershed area) and watershed scales contributed similarly to river N variation, indicating that HSAs are hotspots for transporting land N into river channels. In particular, the agricultural land was the main factor affecting river nitrate and nitrous oxide (N₂O) concentrations, while the built-up land significantly affected river ammonium and nitrite. At the riparian zone scale, soils and sediments substantially influenced river N retention processes (i.e., nitrification and denitrification). Management and protection measures targeting HSAs and riparian zones are expected to efficiently reduce river N loading and improve water quality.

Effect of pesticides on nitrification activity and its interaction with chemical fertilizer and manure in long-term paddy soils

Effect of pesticides on nitrification activity and its interaction among heavy metal concentrations (HMCs), antibiotic resistance genes (ARGs), and ammonia monooxygenase (amoA) genes of long-term paddy soils is little known. The aim was to study the effect of pesticides on net nitrification rate (NR), potential nitrification rate (NP), HMCs, ARGs (sulI, sulII, tetO, and tetQ), and amoA (amoA-AOA, amoA-AOB, and amoA-NOB) genes in long-term treated paddy soils. NR and NP were significantly decreased (p < 0.05), whereas HMCs (Pb²⁺, Cu²⁺, Zn²⁺, and Fe³⁺) were a significantly increased (p < 0.05) in chemical fertilizer with pesticide treated paddy soils as compared with chemical fertilizer treated paddy soils. The scatter plot matrix indicated that total carbon (TC), soil organic carbon (SOC), total nitrogen (TN), and Fe were linearly correlated with NR and NP in long-term treated paddy soils. ARGs and amoA genes were significantly decreased (p < 0.05) in chemical fertilizer and manure with pesticide treated paddy soils. Overall, the result indicated the response of pesticide and their combination of manure with pesticide interaction present in long-term paddy soils, which will play a great role in the control uses of pesticides, manure, and chemical fertilizers in paddy soils and protect the nitrogen cycle as well as environment.

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.

Nitrogen-Induced Changes in Soil Environmental Factors Are More Important Than Nitrification and Denitrification Gene Abundance in Regulating N2O Emissions in Subtropical Forest Soils

Subtropical regions are currently experiencing a dramatic increase in nitrogen (N) deposition; however, the contributions of nitrification and denitrification processes to soil N₂O emissions and the underlying mechanisms under increasing N deposition remain unclear. Therefore, a ¹⁵N-tracing laboratory experiment with four N application rates (0, 12.5, 25, and 50 μg ¹⁵N g^-1 soil) was conducted to investigate the response of nitrification- and denitrification-derived N₂O to N additions in an evergreen broad-leaved forest (BF) and a Pinus forest (PF) in the Wuyi Mountains in southeastern China. Moreover, the abundance of functional genes related to nitrification (amoA), denitrification (nirK, nirS, and nosZ), and soil properties were measured to clarify the underlying mechanisms. Results showed that nitrification-derived N₂O emissions were generally decreased with increasing N input. However, denitrification-derived N₂O emissions were a non-linear response to N additions, with maximum N₂O emissions at the middle N application rate. Denitrification-derived N₂O was the dominant pathway of N₂O production, accounting for 64 to 100% of the total N₂O fluxes. Soil NH₄ ⁺-N content and pH were the predominant factors in regulating nitrification-derived N₂O emissions in BF and PF, respectively. Soil pH and the nirS abundance contributed the most to the variations of denitrification-derived N₂O emissions in BF and PF, respectively. Our results suggest that N application has the potential to increase the contribution of denitrification to N₂O production in subtropical forest soils. Changes in soil chemical properties induced by N addition are more important than the abundance of nitrification and denitrification functional genes in regulating soil nitrification- and denitrification-derived N₂O emissions.

Responses of soil nitrification activities to copper after a moisture stress

Some steps of the soil nitrogen (N) cycle are sensitive to environmental pressures like soil moisture or contamination, which are expected to evolve during the next decades. Individual stresses have been well studied, but their combination is not yet documented. In this work, we aimed at assessing the importance of the soil moisture on the impact of copper (Cu) contaminations on the N cycling soil function using the potential nitrification activities (PNA) as bioindicator. A two-step experiment was performed. First, a loamy soil was incubated 5 weeks in either 30, 60, or 90% of its water holding capacity (WHC) or alternating drought and rewetting periods. Thereafter, soil samples were exposed to a gradient of Cu concentrations through a bioassay involving nitrification. The dose-response curves of PNA in function of added Cu were modeled to calculate the effective Cu concentrations, namely ECx with x being the percentage of PNA inhibition. These values were then compared between experimental conditions to highlight differences in threshold values. The preincubation moisture treatments significantly affected the PNA responses to the secondary Cu stress with, for instance, hormetic responses in all cases except for the dry-rewetting treatment. Small PNA inhibitions were estimated for high Cu doses in the soils with low water contents (30% WHC) or submitted to dry-rewetting cycles, contrarily to the patterns observed for the soils with high water contents (90% WHC) or submitted to a single period of drought. Overall, significant differences were found in estimated ECx values between moisture treatments.

Divergent responses of soil microbial functional groups to long-term high nitrogen presence in the tropical forests

A massive rise in atmospheric nitrogen deposition (ND) has threatened ecosystem health through accelerating soil nitrogen (N) cycling rates. While soil microbes serve a crucial function in soil N transformation, it remains poorly understood on how excess ND affects microbial functional populations regulating soil N transformation in tropical forests. To address this gap, we conducted 13-year N (as NH₄NO₃) addition experiments in one N-rich tropical primary forest (PF) and two N-poor tropical reforested forests (rehabilitated and disturbed) in South China. Based on our data, 13-year N introduction markedly enhanced soil N₂O generation in all forests, regardless of soil N status, but microbial functional groups showed divergent responses to excess N addition among the studied forests. In the PF, long-term N introduction markedly decreased presence of bacterial 16S rRNA gene, nitrifier (amoA) and denitrifier genes (nirK, nirS and nosZ) and bacteria/fungi ratio, which could be attributed to the decreases in soil pH, dissolved organic carbon to N ratio and understory plant richness. In the two reforested forests, however, long-term N introduction generally did neither alter soil properties nor the abundance of most microbial groups. We further found that the elevated N₂O generation was related to the increased soil N availability and decreased nosZ abundance, and the PF has the highest N₂O generation than the other two forests. Overall, our data indicates that the baseline soil N status may dominate response of microbial functional groups to ND in tropical forests, and N-rich forests are more responsive to excess N inputs, compared to those with low-N status. Forests with high soil N status can produce more N₂O than those with low-N status. With the spread of elevated ND from temperate to tropical zones, tropical forests should merit more attention because ecosystem N saturation may be common and high N₂O emission will occur.

Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N2 O emission

Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N₂ O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N₂ O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N₂ O emission by 261%, whereas there was no clear relationship between changes in soil N₂ O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N₂ O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N₂ O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N₂ O emission.

Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N2 O emission

Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N₂ O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N₂ O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N₂ O emission by 261%, whereas there was no clear relationship between changes in soil N₂ O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N₂ O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N₂ O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N₂ O emission.

Patterns and Drivers of nirK-Type and nirS-Type Denitrifier Community Assembly along an Elevation Gradient

nirK-type and nirS-type denitrifier communities mediate the conversion of nitrite to nitric oxide, which is the key step in denitrification. Results of previous studies have indicated that nirK-type and nirS-type denitrifiers may occupy different niches; however, the mechanisms and drivers of their responses to environmental changes within community assembly are poorly understood. In this study, we evaluated the distribution and assembly of nirK-type and nirS-type denitrifier communities along an elevation gradient from 1,800 to 4,100 m at Mount Gongga, China. Results showed that elevational patterns of alpha diversity in nirK-type and nirS-type denitrifier communities followed hump-backed patterns along the elevation gradient. However, nirK-type denitrifier communities formed two distinct clusters that were primarily separated by elevation, whereas nirS-type denitrifier communities formed three distinct clusters that were primarily separated by forest type along the elevation gradient. Moreover, deterministic processes were dominant in governing the assemblages of nirK-type and nirS-type denitrifiers. Soil pH was a key factor influencing the alpha and beta diversity of the nirK-type denitrifier communities, whereas plant richness was a primary variable influencing nirS-type denitrifiers. Additionally, our work revealed that soil denitrification potential was mainly explained by the variation in the beta diversity of denitrifier communities rather than the alpha diversity of denitrifier communities or denitrifier abundances over a large elevation gradient, and nirK-type denitrifiers played more important roles in soil denitrification. These results may contribute to predicting the consequences of global changes on denitrifier communities and their ecological services. IMPORTANCE Mount Gongga is the highest peak in the Hengduan Mountain region and is located at the southeastern fringe of the Tibetan Plateau, Sichuan Province, southwest China. As a transitional zone between the Tibetan Plateau and Sichuan Basin, Gongga Mountain features particularly diverse topography, geology, climate, and biodiversity and is a globally significant hot spot of biodiversity. In this contribution, we comprehensively describe the diversity and assembly of denitrifier communities along an elevation gradient on Gongga Mountain. Our findings established for the first time that the distribution patterns of beta diversity and driving factors differed between nirK-type and nirS-type denitrifier communities, and deterministic processes were dominant in shaping communities of denitrifiers. Moreover, the beta diversity of denitrifier communities rather than alpha diversity or denitrifier abundance played an important role in explaining denitrification potential, and the beta diversity of nirK-type denitrifier communities was more important than nirS-type denitrifier communities in soil denitrification. This work provides crucial insights into the spatial distribution of denitrifier communities and their ecological function and increases our understanding of the mechanisms underlying spatial distribution of community assembly along large elevation gradients.

The driving effect of nitrogen-related functional microorganisms under water and nitrogen addition on N2O emission in a temperate desert

Nitrous oxide (N₂O) is an important greenhouse gas and a precursor of ozone depletion in the upper atmosphere, thus contributing to climate change and biological safety. The mechanisms and response characteristics of N₂O emission in desert soils to precipitation and nitrogen (N) deposition are still unclear. To further elucidate this, an in-situ experiment was conducted in the Gurbantunggut Desert, a temperate desert in China, between June and September 2015 and 2016. The response in N₂O flux to water addition (equivalent to 5 mm precipitation) was very transient in summer, only lasting one to two days. This was attributed to the rapid decrease in soil moisture following the water addition, due to the high temperature and drought conditions, and there was no significant change in N₂O emission or in the abundance of N-related key functional genes. In contrast, N₂O emissions increased significantly in response to N addition. This was associated with an increase in functional gene abundances of amoA (ammonia oxidizing bacteria (AOB)) and ammonia-oxidizing archaea (AOA), which responded positively to increasing soil NH₄⁺-N content, but were inhibited by increasing soil NO₃^--N content. The abundance of the nirS (nitrate reductase) gene was significantly increased by increasing soil NO₃^--N content. Interestingly, the indirect effect of increased soil moisture in enhancing N₂O emission by increasing the abundance of AOA was offset by a direct effect of soil moisture in inhibiting soil N₂O emission. Overall, N₂O emissions were mainly controlled by AOA rather than AOB in summer, and were more sensitive to soil available N than to soil moisture in this temperate desert.

Higher Sensitivity of Microbial Network Than Community Structure under Acid Rain

Acid rain (AR), as a global environmental threat, has profoundly adverse effects on natural soil ecosystems. Microorganisms involved in the nitrogen (N) cycle regulate the global N balance and climate stabilization, but little is known whether and how AR influences the structure and complexity of these microbial communities. Herein, we conducted an intact soil core experiment by manipulating the acidity of simulated rain (pH 7.5 (control, CK) vs. pH 4.0 (AR)) in subtropical agricultural soil, to reveal the differences in the structure and complexity of soil nitrifying and denitrifying microbiota using Illumina amplicon sequencing of functional genes (amoA, nirS, and nosZ). Networks of ammonia-oxidizing archaea (AOA) and nirS-carrying denitrifiers in AR treatment were less complex with fewer nodes and lower connectivity, while network of nosZ-carrying denitrifiers in AR treatment had higher complexity and connectivity relative to CK. Supporting this, AR reduced the abundance of keystone taxa in networks of AOA and nirS-carrying denitrifiers, but increased the abundance of keystone taxa in nosZ-carrying denitrifiers network. However, AR did not alter the community structure of AOA, ammonia-oxidizing bacteria (AOB), nirS-, and nosZ-carrying denitrifiers. Moreover, AR did not change soil N₂O emissions during the experimental period. AOB community structure significantly correlated with content of soil available phosphorus (P), while the community structures of nirS- and nosZ-carrying denitrifiers both correlated with soil pH and available P content. Soil N₂O emission was mainly driven by the nirS-carrying denitrifiers. Our results present new perspective on the impacts of AR on soil N-cycle microbial network complexity and keystone taxa in the context of global changes.

Long-term nitrogen fertilization shaped the nifH, nirK, and nosZ gene community patterns in red paddy soil in south China

To understand the diversities of diazotrophs and denitrifiers in red paddy soil under long-term fertilization conditions, nifH, nirK, and nosZ libraries were constructed by PCR-RFLP. nirK gene diversity proved to be lower than that of nosZ and nifH, and nirK and nosZ genes were more sensitive to different fertilization treatments than the nifH gene was. The 3 libraries were dominated by diverse microbes, including the Alpha, Beta, Gamma, and Delta subclasses of the Proteobacteria. Long-term addition of urea with straw mulch and azophoska increased the abundance of nonsymbiotic diazotrophs, which indicated that nonsymbiotic diazotrophs were responsible for the majority of the nitrogen-fixing ability in paddy soil. In addition, a potential link between nifH and nosZ was found due to the existence of nitrogen fixers, such as Bradyrhizobium and Ralstonia, in the nosZ library. The main chemical factors affecting the 3 genes were identified: pH was the most important factor of the nifH community; the nirK gene was more affected by pH and organic matter; available potassium and the carbon-to-nitrogen ratio significantly influenced the community structure of the nosZ gene.

The responses of soil nitrogen transformation to nitrogen addition are mainly related to the changes in functional gene relative abundance in artificial Pinus tabulaeformis forests

The increase of soil nitrogen (N) availability may alter soil microbial community composition and the natural N cycle in forest ecosystems. However, the responses of soil microbial nitrogen functional genes (NFGs) to N addition and their consequent effect on the N-cycle processes are poorly understood. In this study, soil samples were collected from an artificial Pinus tabulaeformis forest located in Loess Plateau (China) to which N at four different concentrations was added (0 [N0], 3 [N3], 6 [N6], and 9 [N9] g N m^-2 y^-1) for 4 years. We quantified the relative abundance of NFGs using functional gene microarray GeoChip 5.0 and determined net N transformation and N₂O emission rates in a 14-day incubation experiment. The results showed that N3 and N6 treatments did not significantly affect the total relative abundance and diversity of NFGs assemblage but significantly increased the relative abundance of specific genes for the NH₃ cycle (ureC, nirA, and nrfA), and nitrification (amoA) and denitrification (norB). These positive effects were related to the increase in soil organic C, NO₃^--N, and microbial biomass C (MBC). N9 treatment significantly decreased the relative abundance of all NFGs, and this negative impact was correlated with reduced dissolved organic C and MBC. Moreover, N addition significantly changed net N nitrification, mineralization, and N₂O emission rates, and NFGs explained the higher variances in the N transformation processes than soil properties. Specifically, ammonia-oxidizing archaea (amoA-AOB) and MBC were the key factors related to net N nitrification; ureC, nirK, and MBC were the key factors related to net N mineralization; and narG and nirS were the key factors related to N₂O emission. Our results show that global N deposition may mainly influence N transformation processes by regulating the corresponding NFG relative abundance, thereby affecting the N cycle in forest soils.

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.

Effect of N dose on soil GHG emissions from a drip-fertigated olive (Olea europaea L.) orchard

Agronomic practices may mitigate greenhouse gas emissions (GHG) from crops. Appropriate nitrogen (N) and irrigation management provide the potential to reduce nitrous oxide (N₂O) and methane (CH₄) emissions. However, there is little information about the combination of both practices on the GHG emissions from olive orchards. This four-year study was conducted to qualitatively compare the effect of N doses applied through two drip irrigation strategies on N₂O and CH₄ emissions in a super-intensive (1010 trees ha^-1) olive orchard. The design (randomised blocks) was asymmetric: 0, 50 and 100 kg N ha^-1 yr^-1 were tested with full irrigation (FI; 2013 to 2016), but only 0 and 50 kg N ha^-1 yr^-1 were tested with regulated deficit irrigation (RDI; 2014 to 2016). The study shows that the soil acted as a main sink of N₂O and CH₄, regardless of the soil water content. Methane oxidation increased with N dose in the FI strategy (significant in 2013 and 2015). Overall, there was a tendency of yield to increase with the N dose without increasing emissions and without depending of the irrigation strategy. However, these results were not significant. Further confirmation of this tendency is necessary; particularly comparing FI + N100 (most promising treatment in terms of profitability) with the RDI + N100 (not available in this study) water-saving strategy.