Soil Nitrification Potential Research Articles

Optimization of an N2O Emission Flux Model Based on a Variable-Step Drosophila Algorithm

The application of intelligent process-based crop model parameter optimization algorithms can effectively improve both the model simulation accuracy and applicability. Based on measured values of soil N2O emission flux in wheat fields from 2020 to 2022, and meteorological data from 1971 to 2022, five parameters of the N2O emission flux module in the APSIM model were optimized using the variable step Fruit Fly algorithm (VSS-FOA). The optimized parameters were the soil nitrification potential, the range of concentrated KNH4 of ammonia and nitrogen at semi-maximum utilization efficiency, the proportion of nitrogen loss to N2O during the nitrification process, the denitrification coefficient, and the Power term P for calculating the denitrification water coefficient. Contrasting the optimized parameters using the VSS-FOA algorithm versus the default values supplied with the model substantially improved the goodness-of-fit to field measurements with the overall R2 increasing from 0.41 to 0.74, and a decrease in NRMSE from 17.1% to 11.4%. This work demonstrates that the VSS-FOA algorithm affords a straightforward mechanism for the optimization of parameters in models such as APSIM to enhance the accuracy of model N2O emission flux estimates.

Straw Returning Alleviates the Inhibition of Soil Nitrification Medicated by Ammonia-Oxidizing Archaea under Low Nitrogen Fertilization

Straw returning may stimulate soil microbial activity, thereby influencing microbial-mediated soil nitrification, which can lead to nitrate leaching and nitrogen (N) loss. However, its effects under long-term nitrogen fertilization remain unclear. At an experimental station with 34 years of fertilizer application (0, 135, and 270 kg ha−1 N), we investigated how nitrogen fertilization and straw returning affected the soil potential nitrification rate (PNR) and ammonia-oxidizing microorganisms (AOM). Our results suggest that N fertilization concurrently inhibits soil PNR, but this inhibition can be alleviated by straw returning, particularly with low nitrogen fertilization (p < 0.05). Long-term N fertilization significantly decreased the abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia-oxidizing bacteria cladeB (CAOB-cladeB). Straw returning increased AOA abundance and diversity, especially with low or no fertilization (p < 0.05). Furthermore, the partial least squares path model demonstrated that AOA abundance affected soil PNR by altering the AOA community. According to random forest analysis, soil pH and AOA beta diversity were the primary factors affecting soil PNR (explaining 10.76% and 10.03% of the variation, respectively). Overall, our findings highlight the importance of straw returning and AOA in soil nitrification under long-term nitrogen fertilization, emphasizing the need to consider these interactions for sustainable agriculture.

Wheat straw and microbial inoculants have an additive effect on N2O emissions by changing microbial functional groups

AbstractStraw‐decomposing microbial inoculants (MIs) have been increasingly applied to straw‐amended soils. However, the interactive effects and underlying microbial mechanisms of straw and decomposing MIs on nitrous oxide (N2O) emissions remain unclear. Here, a pot experiment with an Aquic Inceptisol was conducted to determine soil N2O emissions and the abundance and composition of microbial functional genes under six amendments: wheat straw (W), Bacillus subtilis MI (B), Streptomyces rochei MI (S), a combination of straw and B. subtilis MI (WB), a combination of straw and S. rochei MI (WS), and a control without wheat straw or MI (C). Compared with the control, the amendments of straw, decomposing MIs, and their combinations decreased soil N2O emissions by 43%, 22–30%, and 46–60%, respectively. Mechanistically, the positive relationship between ammonia‐oxidizing bacteria (AOB) and soil potential nitrification rate (PNR), along with decreased AOB abundance (−36%) following straw and decomposing MI amendments, further suggested that AOB predominated soil nitrification and was responsible for the suppressed nitrification. In addition, straw amendment increased nirK gene abundance (by 48%) and potential denitrification rate (by 11%), while the increase in nosZI gene abundance (+25%) involved in N2O consumption contributed to the decrease in N2O emissions. Overall, the additive effect of straw and decomposing MIs on soil N2O emissions was associated with two amendment‐induced changes in the abundance and composition of AOB and straw‐stimulated the abundance of the nosZI gene. Our results revealed the potential for mitigating N2O emissions following the amendments of straw and MI by influencing soil N2O‐related microbial groups.

Straw addition promotes the nitrification process and the wheat yield linked to trophic interactions among microbes

AbstractStraw return with nitrogen (N) fertilizer can generally regulate soil N cycling by affecting the microbial community, thereby influencing crop productivity. Bacteria and fungi play a key role in nitrification, while the effects of soil microbial interactions that include protists under the condition of straw return and N fertilizer remain uncertain. Here, we evaluated the importance of the soil microbiome, particularly protists and ammonia‐oxidizing bacteria (AOB), in regulating the soil N transformation potential and wheat yields under different fertilization practices. The results showed that the activity of β‐1,4‐N‐acetylglucosaminidase (NAG) and the potential nitrification rate (PNR) increased significantly by 156.4% ~ 312.3% and 183.1% ~ 402.6% with the addition of N fertilizer and straw, respectively. The effect on PNR was greater for straw than fertilizer addition. The fertilization practices changed the microbial community structure, and there were stronger responses from the protists and AOB. The soil microbiome formed three closely co‐occurring modules (Modules 0, 1 and 2). Among them, Module 0 showed strong positive correlations with the soil total N, NAG, PNR and crop yield and may be the key ecological cluster. Moreover, the predatory protists Cercozoa, Conosa and Ochrophyta in Module 0 were significantly positively associated with the activity of NAG and the PNR, yields and AOB. The predatory protists in Module 0 may change the soil potential nitrification rate and enhance the yield of wheat by preying on the competitors of AOB. The results suggest that the incorporation of straw promotes the N transformation potential and wheat yields linked to trophic interactions between predatory protists and AOB in fluvo‐aquic soil.

Effects of Nitrogen Fertilizer on Nitrospira- and Nitrobacter-like Nitrite-Oxidizing Bacterial Microbial Communities under Mulched Fertigation System in Semi-Arid Area of Northeast China

The accumulation of nitrite is frequently overlooked, despite the fact that nitrification is the most essential phase of the entire nitrogen (N) cycle and that nitrifying bacteria play a significant role in nitrification. At present, the effects of different N application rates on soil nitrite-oxidizing bacteria (NOB) abundance, community composition, diversity, and its main influencing factors are still unclear. In this study, five N fertilizer application rates under film mulching and a drip irrigation system were studied in the semi-arid area of Northeast China. The treatments were 0 kg ha−1 (N0), 90 kg ha−1 (N1), 150 kg ha−1 (N2), 210 kg ha−1 (N3), and 270 kg ha−1 (N4). Fluorescent quantitative PCR and Illumina Miseq sequencing were used to analyze the abundance and community structure of NOB under different amounts of N application. The results showed that the increase in amounts of N application was strongly accompanied by an increase in the content of soil organic matter (SOM), total nitrogen (TN), nitrate nitrogen (NO3−-N), and ammonium nitrogen (NH4+-N), while the pH significantly reduced with an increase in N fertilization. N fertilization significantly increased soil nitrite oxidoreductase (NXR) activity, soil nitrification potential (PNR), and soil nitrite oxidation potential (PNO). A high N application rate significantly heightened the abundance of Nitrospira- and Nitrobacter-like NOB. N fertilizer considerably raised the Shannon index of Nitrospira-like NOB. The N application amount was the key factor affecting the community structure of Nitrospira-like NOB, and available nitrogen (AN) had the dominant influence on the community structure of Nitrospira-like NOB. N fertilizer can cause soil acidification, which affects NOB abundance and diversity. Nitrospira-like NOB may promote nitrite oxidation in different N application rates under a mulched fertigation system. The findings offered a crucial scientific foundation for further investigation into how nitrite-oxidizing bacteria respond to N fertilizer management strategies in farmland soil under film mulching drip irrigation in Northeast China.

Water and Nitrogen Balance under Various Water and Fertilizer Regulation Modes

A experiment was conducted at the Jiangxi Province Center Station of Irrigation Experiment from 2019 to 2021 to study the water and nitrogen balance under water and fertilizer regulation modes. The study aimed to propose a recommended mode for paddy fields that could save water, control pollution, reduce gas emission, and improve fertilizer use efficiency. This study examined the impact of different irrigation methods and nitrogen application levels on water saving and emission reduction in paddy fields. The experiment included six treatments, which involved two irrigation methods (intermittent irrigation and flooding irrigation, referred to as W1 and W0, respectively) and three application rates of nitrogen fertilizer (0 kg/ha, 135 kg/ha, 180 kg/ha, referred to as N0, N1 and N2, respectively). The study found that irrigation methods had a significant effect on the amount of irrigation, drainage, leakage, nitrogen load from drainage, soil nitrification potential, and ammonia volatilization. The results showed that compared to flooding irrigation, intermittent irrigation reduced the amount of irrigation, drainage, leakage and nitrogen load from drainage by an average of 25.98%, 16.03%, 8.43% and 10.86%, respectively. However, the study also found that the nitrification potential and ammonia volatilization increased by an average of 6.45% and 4.32%, respectively. Fertilization levels had a significant effect on drainage nitrogen load, early soil nitrification potential and ammonia volatilization. Compared with the treatment of N2 (180 kg N/ha), the drainage nitrogen load under the treatment of N1 (135 kg N/ha) decreased by 10.86% on average, while nitrification potential and ammonia volatilization increased by 38.74% and 3.33%, respectively. In terms of nitrogen output, the amount of nitrogen absorbed by crops was the largest, followed by the nitrogen load from field drainage, then ammonia volatilization, and then denitrification. Considering the goals of water saving, emission reduction, and the efficient utilization of water and fertilizer in paddy fields, the optimal water and fertilizer regulation mode was the W1N1 mode (intermittent irrigation combined with reduced nitrogen fertilizer application rate, 135 kg N/ha).

Response of Nitrification Potential and Ammonia Oxidation Microbial Community in Purple Soils to the Application of Biochar Combined with Chemical Fertilizer and Manure

The effects of manure and chemical fertilizer combined with biochar on nitrification potential and ammonia oxidation microbial change characteristics of purple soils were studied to explore the effects of fertilization measures and soil environmental factors on nitrification potential and ammonia oxidation microbial change characteristics. In this study, purple soil was taken as the research object, and five treatments were set up:no fertilizer(CK), chemical fertilizer(F), manure(P), chemical fertilizer plus biochar(FP), and manure plus biochar(PP). PCR and T-RFLP methods were used to study the characteristics of soil AOA and AOB communities, and soil nitrification potential and environmental factors were measured at the same time to determine the effect of manure combined with biochar on the nitrification potential of purple soil. The results showed that:① compared with that in the CK treatment, the FP and PP treatments significantly increased soil nitrification potential(P<0.05). ② Compared with that in the CK treatment, the F, P, FP, and PP treatments significantly increased the number of copies of the AOA amoA gene in the soil by 78.17%-162.22%(P<0.05), and the F, FP, and PP treatments significantly increased the number of copies of the AOB amoA gene by 21.56%-78.32%(P<0.05). ③ Compared with that in the CK treatment, the PP treatment significantly improved the Shannon, richness, and evenness indices of the soil AOA community(P<0.05), and the combination of biochar(FP and PP treatments) could change the community structure of the soil AOB. ④ The chemical fertilizer and manure affected the AOA and AOB community structure by changing soil properties such as pH, TP, AP, C/N, SOM, NO3--N, and NH4+-N. ⑤ Stepwise regression analysis further showed that AOB amoA gene abundance was the main factor affecting soil nitrification potential. Therefore, under the condition that chemical fertilizer and manure were applied together with biochar, the AOB community was the main driver of the ammonia oxidation process in acidic purple soil, and fertilization affected the ammonia oxidation process by regulating C/N and NO3--N.

Effects of enrofloxacin on soil nitrification and denitrification: A microbiological study

Extensive use of enrofloxacin (ENR) leads to its widespread presence in soil, which seriously threatens the soil ecological environment and biogeochemical cycles. Thus, it is very important to comprehend the fate of ENR and its effect on nitrogen cycling in farmland soil. In this investigation, quantitative real-time PCR and 16 S rRNA genes amplicon sequencing were used to analyze the microbiological mechanism of the effects of ENR on the soil nitrification and denitrification processes of farmland. The results showed that the addition of ENR suppressed the ammoniation process, leading to a decline in NH4+-N content. Additionally, ENR led to a decrease in the soil nitrification potential by decreasing the relative abundance of Nitrosomonas and Nitrosospira. However, ENR inhibited the relative abundance of narG , as well as the activity of nitrate reductase, which led to the accumulation of NO3--N. Furthermore, ENR increased the possibility of nitrous oxide emissions by increasing the relative abundances of Flavobacterium, Bacillus and Aeromonas, as well as those of nirS and nosZ. This study provided data to support for the ecological impact and risk assessment of ENR on nitrogen cycling in farmland soil.

Influence of two agroforestry systems on the nitrification potential in temperate pastures in Brittany, France

Background and aimsAgroforestry, whereby trees are associated with crops and/or livestock, is expected to mitigate nitrogen (N) losses from agriculture. However, little is known about how nitrification potential, an important process that drives N losses, is affected by agroforestry systems. This study aimed to investigate the effect of different silvopastoral agroforestry systems on soil nitrification potential.MethodsNitrification potential was evaluated in two agroforestry systems (hedgerow and alley cropping) associated with temporary grasslands in Brittany, France. In each system, soil was sampled along a transect spanning from the center of the tree row into the grass alley. Soil nitrification potential was determined ex situ and was explained by univariate and multivariate analysis of variables describing vegetation, physicochemical soil properties, and soil organisms.ResultsNitrification potential differed between the two agroforestry systems and among the positions in relation to the trees. In the alley cropping system, nitrification potential was on average 1.5 times higher in the tree row than at 1.5 and 10 m into the grass alley, while in the hedgerow system, nitrification potential at 1.5 m into the grass alley was on average 40% lower than at 10 m into the grass alley. Nitrification potential was strongly correlated with soil pH, whereas no correlation was observed between nitrification potential and community size of soil nitrifiers.ConclusionOur results point out the diverse effects of agroforestry systems on nitrification, a key soil process that is involved in the regulation of N losses.

Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains

Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.

Comammox dominate soil nitrification under different N fertilization regimes in semi-arid areas of Northeast China

The newly identified complete ammonia oxidation (Comammox), which is capable of oxidizing ammonia directly to nitrate, has complemented the knowledge of nitrification in the global nitrogen (N) cycle. Knowledge of the community compositions and contributions to nitrification of autotrophic ammonia-oxidizing archaea (AOA) and bacteria (AOB) and Comammox remain void. In this study, the abundance, community compositions, and contributions to nitrification of AOA, AOB, and Comammox were observed in five N gradients (0, 90, 150, 210, and 270 kg ha−1) in a semi-arid area of Northeast China. The results indicated that, compared with low N application rates, higher N application rates significantly improved the soil ammonia monooxygenase (AMO) and the hydroxylamine oxidase (HAO) activities while total nitrogen (TN) was noted to be the main factor driving AMO and HAO activities. Soil potential nitrification rate (PNR) significantly increased with the increase in N application rate, and soil PNR was positively correlated with TN, nitrate nitrogen (NO3−-N), soil organic matter (SOM), and ammonium nitrogen (NH4+-N). The structural equation model (SEM) showed that TN was the main factor driving the community composition of Comammox; SOM had a greatest effect on the community composition of AOA while NH4+-N had a greatest effect on the community composition of AOB. The soil PNR had a direct effect on the yield. Overall, the findings of this study highlighted that N application was more conducive to the reproduction of soil nitrifying microorganisms while Comammox was the dominant contributor to nitrification under N fertilization regimes in the semi-arid area of Northeast China.

Relationships between nitrogen-specific genes and soil potentials are more complex than single linear ones

Linkages between soil potentials and microbial functional genes are central in microbial ecology, though conflicting results have been obtained. Here, we investigated such linkages for log-transformed abundances of nitrogen (N) genes from grassland soils. The soil nitrification potential increased with rising A-amoA abundance only after it reaching 8.49 × e10 copy numbers g−1 soil, while the denitrification potential was positively correlated with narG and nirS after 8.44 × e10 and 8.12 × e10 copy numbers g−1 soil, respectively. Moreover, nitrification potential increased with rising ratio of A-amoA/B-amoA more strongly with a higher R2 after a threshold of 5.94, indicating that A-amoA controlled corresponding potential when it was abundant enough to overwhelm B-amoA. Our evaluation revealed the complexity between specific N genes and soil potentials, which were far from single linear relationships and abundant enough genes are necessary to correlate positively with corresponding functional potentials.

Lower soil nitrous oxide emissions by a high lipid genetically modified perennial ryegrass line compared to its wild type

AbstractWe describe an experiment where cattle urine was applied at a rate of 420 kg N ha−1, equivalent to 10 L m−2, to mesocosm swards of a high lipid genetically modified perennial ryegrass line (HME) and its wild type (WT). We measured N pools and fluxes in the plant and soil, soil microbial populations and N2O production. HME plants produced 21% greater biomass than WT (p = .02), resulting in greater N uptake (27% higher in HME, p = .05). Urine N recovery in total plant biomass during the experiment in HME and WT swards were 54.7% and 33.9% respectively. The nitrification potential of soil was significantly lower (p = .01) in HME than WT. Partial least square‐discriminant analysis using microbial gene abundance data indicated that HME and WT plant growth induced distinct microbial populations in the soil. These differences in plant soil microbial interactions between HME and WT swards resulted in significantly lower N2O emissions from the HME sward. Total N2O emissions over the 4 weeks after urine application was 38% lower (p &lt; .03) in HME swards than in WT swards. The next step in this work is to identify the specific changes in HME traits that drive the reduction in N2O.

Effects of sulfadiazine and Cu on soil potential nitrification and ammonia-oxidizing archaea and bacteria communities across different soils.

Sulfadiazine (SDZ) and copper (Cu) are frequently detected in agricultural soils, but little is known on their single or combined impact on ammonia oxidizing microbial community and function across different soils. In this study, a microcosm was conducted to distinguish the microbial ecotoxicity of SDZ and Cu across different soils by analyzing soil potential nitrification rate (PNR) and the amoA gene sequences. The results showed that the single spiking of SDZ caused a consistent decrease of soil PNR among three tested soils, but no consistent synergistic inhibition of SDZ and Cu was observed across these soils. Moreover, across three tested soils, the distinct responses to the single or joint exposure of SDZ and Cu were found in amoA gene abundance, and diversity as well as the identified genus taxa of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Meanwhile, only the specific genus taxa of AOA or AOB consistently corresponded to the variation of soil PNR across different treated soils. The further principal component analysis (PCA) exhibited that the variable influence of SDZ and Cu on ammonia oxidizing microbial community and function was greatly dependent on soil type. Therefore, in addition to ecological functionality and the specific prokaryotic taxa, soil microbial ecotoxicity of SDZ and Cu also was dependent on edaphic factors derived from soil types. This study proposes an integrative assessment of soil properties and multiple microbial targets to soil contamination management.

Insight into the microbial nitrogen cycle in riparian soils in an agricultural region

Riparian zones are considered as an effective measure on preventing agricultural non-point source nitrogen (N) pollution. However, the mechanism underlying microbial N removal and the characteristics of N-cycle in riparian soils remain elusive. In this study, we systematically monitored the soil potential nitrification rate (PNR), denitrification potential (DP), as well as net N2O production rate, and further used metagenomic sequencing to elucidate the mechanism underlying microbial N removal. As a whole, the riparian soil had a very strong denitrification, with the DP 3.17 times higher than the PNR and 13.82 times higher than the net N2O production rate. This was closely related to the high soil NO3−-N content. In different profiles, due to the influence of extensive agricultural activities, the soil DP, PNR, and net N2O production rate near the farmland edge were relatively low. In terms of N-cycling microbial community composition, the taxa of denitrification, dissimilatory nitrate reduction, and assimilatory nitrate reduction accounted for a large proportion, all related to NO3−-N reduction. The N-cycling microbial community in waterside zone showed obvious differences to the landside zone. The abundances of N-fixation and anammox genes were significantly higher in the waterside zone, while the abundances of nitrification (amoA&B&C) and urease genes were significantly higher in the landside zone. Furthermore, the groundwater table was an important biogeochemical hotspot in the waterside zone, the abundance of N-cycle genes near the groundwater table was at a relative higher level. In addition, compared to different soil depths, greater variation in N-cycling microbial community composition was observed between different profiles. These results reveal some characteristics of the soil microbial N-cycle in the riparian zone in an agricultural region and are helpful for restoration and management of the riparian zone.

Effect of gradual increase of atmospheric CO2 concentration on nitrification potential and communities of ammonia oxidizers in paddy fields

Currently, the influence of elevated atmospheric CO2 concentration (eCO2) on ammonia oxidation to nitrite, the rate-limiting step of nitrification in paddy soil, is poorly known. Previous studies that simulate the effect of eCO2 on nitrification are primarily based on an abrupt increase of atmospheric CO2 concentration. However, paddy ecosystems are experiencing a gradual increase of CO2 concentration. To better understand how the nitrification potential, abundance and communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) respond to eCO2 in paddy ecosystems, a field experiment was conducted using the following two treatments: a gradual increase of CO2 (EC, increase of 40 ppm per year until 200 ppm above ambient) and ambient CO2 (CK). The results demonstrated that the EC treatment significantly (P < 0.05) stimulated the soil potential nitrification rate (PNR) at the jointing and milky stages, which increased by 127.83% and 27.35%, respectively, compared with CK. Furthermore, the EC treatment significantly (P < 0.05) stimulated the AOA and AOB abundance by 56.60% and 133.84%, respectively, at the jointing stage. Correlation analysis showed that the PNR correlated well with the abundance of AOB (R2 = 0.7389, P < 0.001). In addition, the EC treatment significantly (P < 0.05) altered the community structure of AOB, while it had little effect on that of AOA. A significant difference in the proportion of Nitrosospira was observed between CO2 treatments. In conclusion, the gradual increase of CO2 positively influenced the PNR and abundance of ammonia oxidizers, and AOB could be more important than AOA in nitrification under eCO2.

The active functional microbes contribute differently to soil nitrification and denitrification potential under long-term fertilizer regimes in North-East China.

Nitrogen (N) cycling microorganisms mediate soil nitrogen transformation processes, thereby affecting agricultural production and environment quality. However, it is not fully understood how active N-cycling microbial community in soil respond to long-term fertilization, as well as which microorganisms regulate soil nitrogen cycling in agricultural ecosystem. Here, we collected the soils from different depths and seasons at a 29-year fertilization experimental field (organic/chemical fertilizer), and investigated the transcriptions of N-cycling functional genes and their contribution to potential nitrification and denitrification. We found that long-term fertilization exerted significant impacts on the transcript abundances of nitrifiers (AOA amoA, AOB amoA and hao) and denitrifiers (narG and nosZ), which was also notably influenced by season variation. The transcriptions of AOA amoA, hao, and narG genes were lowest in autumn, and AOB amoA and nosZ transcript abundances were highest in autumn. Compared to no fertilization, soil potential nitrification rate (PNR) was reduced in fertilization treatments, while soil potential denitrification rate (PDR) was significantly enhanced in organic combined chemical fertilizer treatment. Both PNR and PDR were highest in 0–20 cm among the tested soil depths. Path model indicated active nitrifiers and denitrifiers had significant impact on soil PNR and PDR, respectively. The transcriptions of AOA amoA and nxr genes were significantly correlated with soil PNR (Pearson correlation, r > 0.174, p < 0.05). Significant correlation of napA and nosZ transcriptions with soil PDR (Pearson correlation, r > 0.234, p < 0.05) was also revealed. Random forest analysis showed that SOC content and soil pH were the important factors explaining the total variance of active nitrifers and denitrifiers, respectively. Taken together, long-term fertilization regimes reduced soil PNR and enhanced PDR, which could be attributed to the different responses of active N-cycling microorganisms to soil environment variations. This work provides new insight into the nitrogen cycle, particularly microbial indicators in nitrification and denitrification of long-term fertilized agricultural ecosystems.

Characteristics and influencing factors of soil nitrification potential in coastal salinized farmland

Understanding the nitrification capacity of coastal saline farmland soils and its main drivers is of great significance to regulate soil nitrification and improve the utilization efficiency of nitrogen fertilization in farmland. Using a combination of field investigations and laboratory analyses, we examined farmland soil nitrification potential and soil physical, chemical, and biological properties in the coastal muddy tidal flat saline soil area (Dongying and Dongtai). We established the correlation between soil properties and soil nitrification potential with multiple stepwise regression analyses and structural equation modeling (SEM). The results showed that soil pH value was relatively stable and other soil properties and soil nitrification potential varied in coastal saline farmland. The soil nitrification potential ranged from 0.04 to 10.42 mg·kg-1·d-1 and decreased with the increases of soil salinization level. Soil nitrification potential had the strongest correlation with soil organic matter, cation exchange capacity, and Cl-, with the correlation coefficient being 0.409, 0.397 and -0.337, respectively. The results of multiple stepwise regression analysis showed that Na+, silt, cation exchange capacity, and CO32-+HCO3- were the main influencing factors of soil nitrification potential. The results from the SEM analysis suggested that Na+, silt, cation exchange capacity, and CO32-+HCO3- directly affected soil nitrification potential, and soil organic matter, clay, Cl- and SO42- had indirect effects. In all, soil Na+ and cation exchange capacity were the two main factors affecting nitrification. Adjusting soil NaCl content and cation exchange capacity was an effective means of regulating soil nitrification.

Nutrient status of integrated rice-crayfish system impacts the microbial nitrogen-transformation processes in paddy fields and rice yields.

Increasing rice yield is essential for alleviating global food crisis. High soil nutrient level guarantees high rice yields in conventional rice monoculture (RM) systems, but excessive unconsumed nutrients act as pollutants and can even threaten rice growth. The integrated rice-crayfish (IRC) system aims to transfer the excess nutrients from crayfish to paddy fields to improve the comprehensive utilization rate of nutrients and create additional profits, while the responding characteristics of IRC microbial communities in paddy fields and rice yields to the nutrient status remain unclear. Considering the crucial roles of microbiomes in promoting nutrient cycling for crop absorption in rice production progresses, the composition and functional characteristics of soil microbial communities from six IRC farms with variant nutrient statuses in the Yangtze River Delta were surveyed in this study. Compared with RM systems, IRC systems with appropriately improved (p < 0.05) soil quality created favorable nutrient (FN) status accompanied by 15% rice yields increase, while IRC systems with extremely high nutrients (HN) status (p < 0.01) accompanied by 14% rice yields reduction. Soil microbial diversity and network complexity were maintained in FN-IRC systems, but declined in HN-IRC systems, with the Shannon index significantly decreased by 9.2% and network density decreased from 0.135 (in RM) to 0.062. In the FN-IRC systems, the keystone taxa identified by co-occurrence networks displayed inextricably positive correlations with soil nitrification potential (calculated by normalization of amoA gene abundance) and rice yields. While in HN-IRC systems, the large loss of keystone taxa might limit soil nitrogen fixation potential (calculated by normalization of nifH gene abundance), and further rice yields. Our study indicates that soil nutrient management in IRC systems claim attention, and the improvement of nitrogen metabolism is the key to realize agricultural cleaner production.

The Responses of Ammonia-Oxidizing Microorganisms to Different Environmental Factors Determine Their Elevational Distribution and Assembly Patterns.

The assembly mechanisms shaping the elevational patterns of diversity and community structure in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are not well understood. We investigated the diversities, co-occurrence network patterns, key drivers, and potential activities of AOA and AOB communities along a large altitudinal gradient. The α-diversity of the AOA communities exhibited a monotonically decreasing pattern with increasing elevation, whereas a sinusoidal pattern was observed for the AOB communities. The mean annual temperature was the single factor that most strongly influenced the α-diversity of the AOA communities; however, the interactions of plant richness, soil conductivity, and total nitrogen made comparable contributions to the α-diversity of the AOB communities. Moreover, the β-diversities of the AOA and AOB communities were divided into two distinct clusters by elevation, i.e., low- (1800-2600m) and high-altitude (2800-4100m) sections. These patterns were attributed mainly to the soil pH, followed by variations in plant richness along the altitudinal gradient. In addition, the AOB communities were more important to the soil nitrification potential in the low-altitude section, whereas the AOA communities contributed more to the soil nitrification potential in the high-altitude section. Overall, this study revealed the key factors shaping the elevational patterns of ammonia-oxidizing communities and might predict the consequences of changes in ammonia-oxidizing communities.