Soil Potential Nitrification Rate Research Articles

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.

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.

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.

Changes in soil ammonia oxidizers and potential nitrification after clear-cutting of boreal forests in China.

The Korean pine and broad-leaved mixed forests are the most typical and complete ecosystem among the global boreal forests, with extremely important ecological functions. However, few studies on the changes of soil ammonia oxidizers and potential nitrification after clear-cutting of forests are reported. In this study, in contrast to primary Korean pine forests, nitrate (NO3-) was significantly higher in secondary broad-leaved forests, while ammonium (NH4+) was on the contrary. The abundance of ammonia-oxidizing bacteria (AOB) was greatly higher in secondary broad-leaved forests, while levels of ammonia-oxidizing archaea (AOA) were not significantly different between them. The significant differences of community structure of AOA and AOB were observed in different forest types and soil layers. Compared with AOA, community compositions of AOB was more sensitive to forest type. The dominant groups of AOA were Nitrososphaera and Nitrosotalea, and the dominant group of AOB was Nitrosospira, of which Nitrosospira cluster 2 and 4 were functional groups with highly activity. Soil potential nitrification rate (PNR) was higher in secondary broad-leaved forests. Furthermore, PNR and AOB abundance had a significant positive correlation, but no significant correlation with AOA abundance. These results provide insights into the soil nitrogen balance and effects on forest restoration after clear-cutting.

Responses of Ammonia-Oxidizing Microorganisms to Intercropping Systems in Different Seasons

Intercropping plays an essential role in agricultural production, impacting the soil’s physical and chemical properties and microbial communities. However, the responses of ammonia-oxidizing microorganisms in the continuous-cropping soil to different intercropping systems in different growing seasons are still insufficiently studied. Here, we investigated the effects of seven intercropping systems (alfalfa (Medicago sativa L.)/cucumber, trifolium (Trifolium repens L.)/cucumber, wheat (Triticum aestivum L.)/cucumber, rye (Secale cereale L.)/cucumber, chrysanthemum (Chrysanthemum coronrium L.)/cucumber, rape (Brassica campestris L.)/cucumber, mustard (Brassica juncea L.)/cucumber) on soil physical and chemical properties, potential nitrification rate (PNR), soil ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) communities in the greenhouse in spring and autumn. The results showed that, compared with cucumber monoculture, intercropping increased the soil NH4+-N and NO3−-N. The chrysanthemum–cucumber, rape–cucumber, and mustard–cucumber treatments increased soil PNR. Intercropping increased the AOA and AOB abundances in two seasons, especially in rape–cucumber, wheat–cucumber, chrysanthemum–cucumber, and trifolium–cucumber treatments. The ratio of AOA and AOB decreased with seasonal variation. The wheat–cucumber and rape–cucumber treatments increased soil AOA community diversity. Seasonal variation had a significant effect on the relative abundance of the AOB community. Nonmetric multidimensional scaling analysis showed that the AOA and AOB community structures were obviously different from spring to autumn. Redundancy analysis showed that the AOA community was significantly regulated by moisture, NO3−–N, and available potassium (AK), while the AOB community was significantly regulated by moisture, available phosphorus (AP), AK, NO3−-N, and pH. Network analysis showed that the co-occurrence relationship and complexity of AOA and AOB communities were different in two growing seasons. The AOB community may play a critical role in ammonia oxidation in autumn. Taken together, intercropping improved soil physicochemical state, increased soil PNR and significantly altered soil AOA and AOB communities. Seasonal variation significantly altered the AOA and AOB communities’ structure and interaction between them. The effect of seasonal variation on AOA and AOB communities was greater than intercropping.

Long-term mineral fertilizer substitution by organic fertilizer and the effect on the abundance and community structure of ammonia-oxidizing archaea and bacteria in paddy soil of south China

Ammonia oxidation in the soil is related to nitrogen (N) availability for plants, nitrate loss, and N fertilizer use efficiency, which is important for studies on the N cycle of paddy field ecosystems. Substitution of partial mineral N fertilizer with organic amendments is commonly considered to optimize fertilization practices and reduce the application of mineral N fertilizer in the paddy fields. However, little is known about the effects of this type of fertilization on the relative contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to soil nitrification. Therefore, a 34-year field trial including five fertilization regimes (CK, without fertilizer; NPK, mineral NPK fertilizer; NPKM1, 70% inorganic N + 30% organic N + PK; NPKM2, 50% inorganic N + 50% organic N + PK; NPKM3, 30% inorganic N + 70% organic N + PK; P: phosphorus, K: potassium) was conducted. AOA and AOB abundance and community structures were determined by quantitative PCR and high-throughput sequencing analyses. Although the abundance of AOA and AOB increased with the increase in the percentage (30%–70%) of organic N substitution, the abundance ratio of AOA to AOB (133.9–84.7) decreased. Soil potential nitrification rate (PNR) increased dramatically (p < 0.05) after replacing chemical N with organic N, and with the increase in the substitution ratio of organic N in paddy soils. AOA and AOB both correlated significantly (p < 0.05) with PNR, but the contribution of AOB to PNR exceeded that of AOA. Soil carbon (C) to N ratio was the best predictor (43.0%) for AOA abundance, while total N and NH4+-N incorporating models were the best predictors (90.3%) for AOB abundance. Variations in AOA composition correlated strongly with fertilizer-induced changes in soil pH and ammonia concentration, whereas the AOB community was only markedly correlated with pH (p = 0.004). The substitution of 30%–70% of mineral N with organic N could increase the soil pH to 5.54–5.87, and that of ammonia concentration to 8.37–24.1 μM, which was the main reason that AOB contributed more to PNR than AOA. These results indicate that the organic substitution fertilizer regime had much stronger effects on the abundance and composition of AOB than AOA, and the potential contribution of AOB to ammonia oxidation in paddy soils should not be ignored after mineral N partial substitution by organic N.

Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils.

The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg-1), which showed an antagonistic effect between Cu and SDZ (5 mg · kg-1), while the combined toxicity of high-concentration SDZ (10 mg · kg-1) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg-1 Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg-1 SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg-1 Cu combined with 5 mg · kg-1 SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.

Dynamics of ammonia oxidizers in response to different fertilization inputs in intensively managed agricultural soils

Ammonia oxidation, the rate-limiting step of autotrophic nitrification, is carried out by ammonia-oxidizing archaea (AOA) and bacteria (AOB) that differ in their physiology and metabolic pathways. However, there has been little field investigations on the dynamic responses of ammonia oxidizers to different fertilizer inputs in intensive crop rotations. Here, we examine the soil potential nitrification rates (PNR), abundance and communities of AOB and AOA across different growth stages of wheat and maize at two soil depths (0–20 and 20–40 cm) under three fertilization regimes, namely zero fertilization (CK), chemical fertilizer (NPK) and partial replacement of the chemical fertilizer nutrients with organic manure (NPKM). Soil PNR was higher in the surface soil than in the subsoil in the wheat season, but no significant difference was observed in the maize season. Fertilization especially NPK treatment increased soil PNR, and the effect was more pronounced in the surface soil in the wheat season. The influence of soil depth on the abundance and communities of AOA and AOB was greater than that of fertilizer regime or plant growth stage across wheat and maize growth stages. The differences of ammonia oxidizers communities were mainly attributable to soil total nitrogen, organic carbon and soil moisture contents in the two depths. The abundance of AOB decreased more sharply than that of AOA with increasing soil depth. In general, application of NPK only increased AOB abundance in both wheat and maize seasons, whereas NPKM treatment increased AOB abundance only in the maize season (except in the subsoil at harvest). Generally, soil PNR was correlated with AOB and AOA abundances except for AOB in the subsoil in the wheat season and AOA in the surface soil during maize growth. Fertilization regime did not increase AOA abundance or alter AOA communities across all soil depths and plant growth stages. Our results indicate that the ammonia oxidizers differ greatly in responses to fertilization regimes and the changes are associated with soil depth and crop growth stage. The dynamics of soil microorganisms should be integrated into fertilizer and crop management to achieve sustainable agricultural systems.

Effects of reducing chemical fertilizer combined with organic amendments on ammonia-oxidizing bacteria and archaea communities in a low-fertility red paddy field.

Ammonia oxidation process in soil has a great contribution to the emission of nitrous oxide, which is a hot issue in the study of N cycle of rice field ecosystem. Organic amendments which partially substitute chemical nitrogen fertilizer are widely adopted to optimizing N management and reduce the use of chemical nitrogen fertilizers in the paddy ecosystem, but their long-term effects on ammonia-oxidizing archaea (AOA) and bacteria (AOB) were not well understood. Thus, based on a 6-year field trial that comprised four fertilization strategies (CF, chemical fertilizer; PM, pig manure substituting for 20% chemical N; BF, biogas slurry substituting for 20% chemical N; and GM, milk vetch substituting for 20% chemical N) and no N fertilizer application as CK, the abundance and community structure of ammonia oxidizers were examined by using qPCR and Illumina Miseq sequencing approaches based on the functional marker genes (amoA) in a low-fertility paddy field. The results revealed that 6 years of organic-substitute fertilization significantly increased AOA abundance in comparison with NF and CF. However, only CF and PM had a higher AOB abundance than those in NF and no significant difference between CF and organic-substitute treatments was observed. Both AOA and AOB were significantly correlated with soil potential nitrification rate (PNR). Moreover, organic-substitute treatments showed the evident changes in the AOA community, while little were observed in the AOB community. Soil pH was the main predictor for AOA abundance, while NH4+-N and NO3--N were the main predictors for AOB abundance. This study suggests that both AOA and AOB were jointly contributed to the variation of soil potential nitrification rate, while the AOA community was shown to be more responsive to organic-substitute fertilization strategies than AOB in the tested soils.

The Structure and Diversity of Nitrogen Functional Groups from Different Cropping Systems in Yellow River Delta.

The Yellow River Delta (YRD) region is an important production base in Shandong Province. It encompasses an array of diversified crop systems, including the corn–wheat rotation system (Wheat–Corn), soybean–corn rotation system (Soybean–Corn), fruits or vegetables system (Fruit), cotton system (Cotton) and rice system (Rice). In this study, the communities of ammonia oxidizer–, denitrifier– and nitrogen (N)–fixing bacteria in those cropping systems were investigated by Illumina Miseq sequencing. We found that Rice soil exhibited significantly higher diversity indices of investigated N–cycling microbial communities than other crop soils, possibly due to its high soil water content. Wheat–Corn soils had higher abundances of nitrification gene amoA and denitrification genes nirK and nirS, and exhibited higher soil potential nitrification rate (PNR), compared with Soybean–Corn, Cotton and Fruit soils. Consistently, redundancy analysis (RDA) showed that soil water content (SWC), electrical conductivity (EC), and total nitrogen (TN) were the most important influencing factors of the diversity and structure of the investigated N–cycling microbial.

Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems

Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.

Responses of nitrification and denitrification to nitrogen and phosphorus fertilization: does the intrinsic soil fertility matter?

Nitrogen (N) is not only a major regulator of productivity in terrestrial systems but can also be a pollutant. While the effects of fertilizer addition to soil N cycling processes and the associated soil microbial groups have been extensively studied, little attention has been paid to the interaction of fertilizer amendment and the intrinsic fertility of the soil. We conducted a filed study on the Chinese Loess Plateau with soils of two fertility levels (low fertility and high fertility), amended with or without synthetic fertilizer (N and phosphorus, NP). Soil samples were collected three times in a continuous winter wheat cropping system and analyzed for soil potential nitrification (PNA) and denitrification (DEA) rates, nitrifiers and denitrifiers. Populations of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and the resulting PNA were increased by the NP application regardless of intrinsic soil fertility. The NP application increased DEA by 15–228% in the low fertility soil, but decreased DEA by 18–46% in the high fertility soil. Soil denitrifiers also showed divergent responses to NP application in low and high fertility soils, i.e., the abundance of nirS-nitrite reducers increased in the low fertility soil, while nirS- and nirK-nitrite reducers were unchanged in the high fertility soil. The narG-nitrate reducers, AOB and AOA were more responsive to the NP application in the tillering stage (BBCH 25–26) than in other periods, whereas PNA, DEA and denitrifier gene abundance (nirS and nirK) varied more in the flowering stage (BBCH 65). Our results suggest that the responses of soil nitrification/nitrifiers and denitrification /denitrifiers to NP application varied with intrinsic soil fertility levels. The contrasting responses of nitrification and denitrification to NP application in high fertility soil indicate a decoupling of both processes.

Chronic Nitrogen Fertilization Modulates Competitive Interactions Among Microbial Ammonia Oxidizers in a Loess Soil

Nitrogen (N) application may lead to niche segregation of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB), thereby reducing the competitive interactions between AOA and AOB due to higher ammonium substrate availability. However, the adaptive mechanisms of AOA and AOB under N enrichment remain poorly understood. Stable isotope probing (SIP) microcosm incubation was employed to reveal community changes of active AOA and AOB in a loess soil from a field experiment growing potatoes that received no N (control, CK), low N (LN, 75 kg N ha−1), and high N (HN, 375 kg N ha−1). The results showed that the soil potential nitrification rate (PNR) was measured by culturing of the soil samples from the field experiment. Soil PNR was significantly increased in HN by 87.5% and 67.5% compared with CK and LN, respectively. Compared with CK, the 13C-amoA genes of soil AOA and AOB in HN had 2.58 × 104 and 1.55 × 106 copies, representing 1.6- and 16.2-fold increase respectively. It was indicated that AOB dominated soil ammonia oxidation. A phylogenetic analysis of the 13C-amoA gene showed that N application significantly increased the proportion of 54d9-like AOA up to 90% in HN, while the Nitrososphaera gargensis-like and Nitrososphaera viennensis-like AOA were inhibited and completely disappeared. Nitrogen application also resulted in the community shift of active AOB-dominant group from Nitrosospira briensis-like to Nitrosospira sp. TCH711-like. Our study provides compelling evidence for the emergence and maintenance of active nitrifying communities under the intensified N input to an agricultural ecosystem.

Responses difference analysis of soil potential nitrification rates to Cu and sulfadiazine

ABSTRACTTo investigate responses difference of soil potential nitrification rates (PNR) to heavy metals and antibiotics, batch toxicity experiments of Cu and sulfadiazine (SDZ) were conducted in four typical soils which were collected from different locations of China. Toxic differences of Cu and SDZ to soil PNR were evaluated based on their values of EC20 and EC50 calculated with logistic model. It was found that soil nitrification was a good indicator of Cu contamination in soils except for paddy soil. For SDZ, their ECX values were significantly higher than its concentration level (0.002 ~ 0.760 mg·kg-1) in soils. Thus, it was concluded that soil nitrification might be more sensitive to Cu than SDZ in field soil. The further Pearson correlation analysis indicated that the response of soil PNR to Cu and SDZ contamination were significantly related with soil PNR0 and pH.