Ammonia-oxidizing Bacteria amoA Gene Research Articles

Long-term effects of film mulching and fertilization regimes on gross N transformations in calcareous dryland soils

Plastic film mulching (PM) and nitrogen (N) fertilization regimes significantly affect crop yield, N supply capacity, and N losses. However, the long-term effects and the underlying mechanisms, like the belowground N transformations, call for in-depth investigation. Here, a 15N tracing study was conducted to quantify the gross N transformation rates of the calcareous soil subjected to 12 years of PM and various fertilization regimes. We found that autotrophic nitrification (ONH4) and mineralization (M) were the predominant soil N conversion processes, while dissimilatory nitrate reduction to ammonium (DNRA) and nitrate immobilization (INO3) were negligible in the calcareous soil, leading to the accumulation of nitrate. Long-term PM significantly decreased the rates of M, recalcitrant organic-N mineralization (MNrec), ONH4, and NH4+ immobilization to labile organic-N (INH4_Nlab) due to the negative effect on the abundances of fungi and ammonia-oxidizing bacteria (AOB) amoA gene compared to control soil. Relative to no N control, different fertilization regimes significantly increased the AOB amoA gene abundance, decreased fungal abundance and ITS:16S ratio, thus increasing ONH4 and M, decreasing NH4+ immobilization rates to labile and recalcitrant organic-N. Compared to normal N rate (F225), high N rate (F380) and normal N plus manure (F225+M) markedly increased ONH4 and INO3. Regression analyses revealed that M and AOB amoA gene abundance affected ONH4, and in turn N2O production. The findings provide an improved understanding of the long-term effects of PM and N managements on soil N supply capacity and potential N losses based on internal N cycling and molecular biology.

Maize–peanut intercropping and N fertilization changed the potential nitrification rate by regulating the ratio of AOB to AOA in soils

Maize–peanut intercropping could potentially mitigate nitrogen (N) loss from the soil, a process primarily governed by the net nitrification rate. However, the impact of maize–peanut intercropping on the potential nitrification rate (PNR) and its relationships with key players, such as ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), are not well understood. Herein, we conducted a field experiment involving two management systems and two crops, namely, maize (MPm) and peanut (MPp) intercropping, maize monoculture (MM), and peanut monoculture (PM), under three N fertilization rates (no N fertilization, 150 ​kg ​N ​ha−1, and 300 ​kg ​N ​ha−1). Under intercropping (MPm and MPp), the abundance of AOA amoA gene increased by 64.8 ​% and 60.3 ​% and the abundance of AOB amoA gene increased by 63.2 ​% and 68.2 ​% compared to the MM and PM monoculture systems, respectively. Furthermore, the abundances of AOA and AOB decreased in MPp and MM, while AOB increased in MPm and PM across the N fertilization gradient. The PNR increased corresponding to the N fertilization rates, with intercropping enhancing the PNR in peanut-planted soil but reducing the PNR in maize-planted soil compared to monocropping. Notably, no significant positive relationship between the abundances of AOA or AOB and the PNR. Random forest analysis indicated that the AOB/AOA ratio was an important predictor of the PNR. N fertilization and intercropping regulated the AOB/AOA ratio mainly through controlling the ammonia content and the soil C/N, respectively. These findings highlight the substantial impacts of N fertilization and intercropping on PNR, with the AOB/AOA ratio emerging as a valuable predictive indicator for the PNR.

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea.

This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 102 to 2.17 × 106 copies per gram of sediment and from 6.6 × 101 to 7.65 × 104 copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50°C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

Polyaspartic calcium improved soil quality and altered nitrification process in saline‐sodic paddy soils

AbstractSaline‐sodic paddy soils in the Songnen Plain suffer from nitrogen loss due to nitrification. The purpose of the study is to explore soil saline improvement and nitrification mitigation effects of polyaspartic calcium (PASP‐Ca) by evaluating changes of soil quality, nitrification, and microbial communities. Four PASP‐Ca application treatments (additions of 0, 500, 1000, and 1500 kg hm−2) were studied in an experiment in saline‐sodic paddy soils of the Songnen Plain, China. Results showed that PASP‐Ca application significantly decreased soil pH, electrical conductivity (EC), and water‐soluble salt ions, and significantly increased soil total carbon (TC), total nitrogen (TN), urease activity (UA), and sucrase activity (SA). PASP‐Ca application significantly slowed down soil nitrification, which was manifested in a significant increase in ammonium nitrogen () and a significant decrease in nitrate nitrogen () and ammonia monooxygenase activity (AMO). The composition and distribution of soil nitrifying microbial communities were affected by soil salinity, nutrient, and enzyme activities. Ammonia‐oxidizing bacteria (AOB) plays an important role in the nitrification process of saline‐sodic paddy soils, while PASP‐Ca application significantly inhibited nitrification by suppressing AOB amoA gene abundance. This study shows that PASP‐Ca, as an effective amendment, can improve soil salinization and slow down nitrification, which has an important role and significance in improving nitrogen utilization and reducing nitrogen loss of saline‐sodic soils.

Mechanisms of mitigating nitrous oxide emission during composting by biochar and calcium carbonate addition

To investigate the mechanisms underlying effects of biochar and calcium carbonate (CaCO3) addition on nitrous oxide (N2O) emissions during composting, this paper conducted a systematic study on mineral nitrogen (N), dissolved organic carbon (C) and N, sources of N2O, and functional genes. Biochar and CaCO3 addition decreased N2O emissions by 26.5–47.8% (9.5–96.9 mg N kg−1 dw) and 13.9–37.4% (12.0–121.0 mg N kg−1 dw) compared to the control (14.3–179.7 mg N kg−1 dw), respectively. The mitigation of N2O emission was caused by decreased contribution of ammonia-oxidizing bacteria (AOB) and fungi to N2O production due to diminished AOB amoA, fungal nirK and P450 gene abundances, or by stimulated N2O reduction to N2 owing to increased abundances of nosZⅠ and nosZⅠⅠ genes under biochar and CaCO3 addition. The findings suggest that the addition of biochar or CaCO3 is effective in mitigating N2O emission during composting.

Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China

Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg−1 N ha−1) was 23.35 % higher than that at the intermediate rate (100–150 kg−1 N ha−1) and 20.77 % higher than that at the low rate (< 100 kg−1 N ha−1). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4+ content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.

Accelerated nitrification and altered community structure of ammonia-oxidizing microorganisms in the saline-alkali tolerant rice rhizosphere of coastal solonchaks

Plantations of saline-alkali tolerant rice in coastal areas are proposed as a strategy to improve rice yield and ensure global food security. The soil nitrification process driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is an integral part of the soil nitrogen cycle and correlates with the quality of coastal solonchak. However, little is known about the effects of saline-alkali tolerant rice cultivation on the soil nitrification process in coastal solonchaks. In this study, we investigated the community structures of AOA/AOB and the nitrification rate in the rice rhizosphere along salinity gradients. The abundance and nitrification rates of AOA and AOB declined with increasing salinity. Saline-alkali-tolerant rice cultivation significantly increased the abundance of AOA and AOB amoA genes from (3.09–11.5) × 106 and (7.76–52.0) × 105 copies g−1 in soils to (16.2–50.9) × 106 and (69.2–423) × 105 copies g−1 in the rhizosphere, respectively. Compared with bulk soils, the nitrification rate of AOA and AOB in the rhizosphere increased significantly with salinity. Saline-alkali-tolerant rice cultivation enhanced the nitrification process of saline-alkali tolerant soil by increasing the nitrification contribution of AOB. Our findings offer new clues on the accelerated nitrification process in the saline-alkali tolerant rice rhizosphere in coastal solonchaks and reveal its roles in shaping AOA/AOB communities, providing suggestions for saline-alkali tolerant rice plantations in coastal solonchaks.

Comparison of Biochar- and Lime-Adjusted pH Changes in N2O Emissions and Associated Microbial Communities in a Tropical Tea Plantation Soil

The use of biochar and lime (CaO) is a common approach to mitigating soil acidification. However, little is known about how biochar and lime amendments impact N2O emissions and potential microbial mechanisms. We conducted a 45-day microcosm incubation experiment to examine N2O emission and associated functional guilds to biochar and lime amendment in an acidic tea plantation soil. Results show that lime and biochar treatments significantly reduced cumulative N2O emissions by 49.69% and 63.01%, respectively, while significantly increasing cumulative CO2 emissions by 27.51% and 19.35%, respectively. Additionally, lime and biochar treatments significantly decreased the abundances of bacterial nirK, nirS, nosZ and fungal nirK genes, while increasing that of the ammonia-oxidizing bacteria (AOB) and the complete ammonia-oxidizing bacteria (comammox) amoA genes. The stimulated or inhibitory effects of biochar on functional genes abundances were higher than lime. The N2O emission rate was positively linked with the abundance of the fungal nirK gene but was negatively correlated with AOB and comammox amoA genes abundances. The random forest and linear regression analysis revealed that fungal denitrifiers were the most important predictors of N2O emissions. Lime and biochar amendments reduced the alpha diversity and altered the community composition of nirK-harboring fungal denitrifiers. Ascomycota was the dominant fungal denitrifiers belonging to the families Nectriaceae, Aspergillaceae, and Chaetomiaceae, and the relative abundances of genera Chaetomium, Penicillium and Fusarium were positively correlated with N2O emissions. Overall, our findings suggest that biochar is more effective than lime in reducing N2O emissions, and this is likely due to the powerful effects it has on community traits of nirK-harboring fungal denitrifiers.

Changes in the activities of key enzymes and the abundance of functional genes involved in nitrogen transformation in rice rhizosphere soil under different aerated conditions

Soil microorganisms play important roles in nitrogen transformation. The aim of this study was to characterize changes in the activity of nitrogen transformation enzymes and the abundance of nitrogen function genes in rhizosphere soil aerated using three different methods (continuous flooding (CF), continuous flooding and aeration (CFA), and alternate wetting and drying (AWD)). The abundances of amoA ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), nirS, nirK, and nifH genes; and the activities of urease, protease, ammonia oxidase, nitrate reductase, and nitrite reductase were measured at the tillering (S1), heading (S2), and ripening (S3) stages. We analyzed the relationships of the aforementioned microbial activity indices, in addition to soil microbial biomass carbon (MBC) and soil microbial biomass nitrogen (MBN), with the concentration of soil nitrate and ammonium nitrogen. The abundance of nitrogen function genes and the activities of nitrogen invertase in rice rhizosphere soil were higher at S2 compared with S1 and S3 in all treatments. AWD and CFA increased the abundance of amoA and nifH genes, and the activities of urease, protease, and ammonia oxidase, and decreased the abundance of nirS and nirK genes and the activities of nitrate reductase and nitrite reductase, with the effect of AWD being particularly strong. During the entire growth period, the mean abundances of the AOA amoA, AOB amoA, and nifH genes were 2.9, 5.8, and 3.0 higher in the AWD treatment than in the CF treatment, respectively, and the activities of urease, protease, and ammonia oxidase were 1.1, 0.5, and 0.7 higher in the AWD treatment than in the CF treatment, respectively. The abundances of the nirS and nirK genes, and the activities of nitrate reductase and nitrite reductase were 73.6, 84.8, 10.3 and 36.5% lower in the AWD treatment than in the CF treatment, respectively. The abundances of the AOA amoA, AOB amoA, and nifH genes were significantly and positively correlated with the activities of urease, protease, and ammonia oxidase, and the abundances of the nirS and nirK genes were significantly positively correlated with the activities of nitrate reductase. All the above indicators were positively correlated with soil MBC and MBN. In sum, microbial activity related to nitrogen transformation in rice rhizosphere soil was highest at S2. Aeration can effectively increase the activity of most nitrogen-converting microorganisms and MBN, and thus promote soil nitrogen transformation.

DMPP mitigates N2O and NO productions by inhibiting ammonia-oxidizing bacteria in an intensified vegetable field under different temperature and moisture regimes

Vegetable soils with high nitrogen input are major sources of nitrous oxide (N2O) and nitric oxide (NO), and incorporation of the nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) into soils has been documented to effectively reduce emissions. However, the efficiency of DMPP in terms of soil N2O and NO mitigations varies greatly depending on soil temperature and moisture levels. Thus, further evaluations of DMPP efficiency in diverse environments are required to encourage widespread application. A laboratory incubation study (28 d) was established to investigate the interactive effects of DMPP, temperature (15, 25, and 35 °C), and soil moisture (55% and 80% of water-holding capacity (WHC)) on net nitrification rate, N2O and NO productions, and gene abundances of nitrifiers and denitrifiers in an intensive vegetable soil. Results showed that incubating soil with 1% DMPP led to partial inhibition of the net nitrification rate and N2O and NO productions, and the reduction percentage of N2O production was higher than that of NO production (69.3% vs. 38.2%) regardless of temperature and soil moisture conditions. The increased temperatures promoted the net nitrification rate but decreased soil N2O and NO productions. Soil moisture influenced NO production more than N2O production, decreasing with the increased moisture level (80%). The inhibitory effect of DMPP on cumulative N2O and NO productions decreased with increased temperatures at 55% WHC. Conversely, the inhibitory effect of DMPP on cumulative N2O production increased with increased temperatures at 80% WHC. Based on the correlation analyses and automatic linear modeling, the mitigation of both N2O and NO productions from the soil induced by DMPP was attributed to the decreases in ammonia-oxidizing bacteria (AOB) amoA gene abundance and NO2--N concentration. Overall, our study indicated that DMPP reduced both N2O and NO productions by regulating the associated AOB amoA gene abundance and NO2--N concentration. These findings improve our insights regarding the implications of DMPP for N2O and NO mitigations in vegetable soils under various climate scenarios.

Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China.

The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0-20 cm, topsoil; 20-40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH4 +-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH4 +-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems.

Impacts of Biochar and Vermicompost Addition on Physicochemical Characteristics, Metal Availability, and Microbial Communities in Soil Contaminated with Potentially Toxic Elements

In the current work, the effects of biochar, vermicompost, as well as their combined application on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soils contaminated with potentially toxic elements (PTEs) were investigated. In this regard, four treatments were performed; among them, treatment A served as a control without additive, treatment B with vermicompost (2%), treatment C with biochar (2%), and treatment D with biochar (2%) plus vermicompost (2%). In addition, the abundance and structure of the AOA and AOB amoA gene were measured using quantitative PCR and high-throughput sequencing. The relationships between the microbial community, physicochemical parameters, and CaCl2-extractable PTEs were analyzed using the Pearson correlation method. We found that adding biochar and vermicompost promoted the immobilization of PTEs and nitrogen biotransformation. The rational use of biochar and vermicompost is beneficial for the growth of bacterial and fungal communities in soils polluted by PTEs. AOA and AOB amoA genes were stimulated by biochar, vermicompost, and their combination, but their structure was hardly affected.

Shifts of ammonia-oxidation process along salinity gradient in an estuarine wetland

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play an important role in nitrogen (N) cycling of the estuarine sediments. However, the shifts of potential ammonia oxidation rates (PARs) of AOA and AOB along different salinity gradients are not well understood. Here, salinity-treated (0, 5, 15, 25 and 35 ‰) incubation experiments of sediment from the Pearl River Estuary were performed to explore the influence of salinity on ammonia oxidation process, including the PARs and gene abundances of AOA and AOB. Significant shifts of PARs and amoA gene abundances of ammonia oxidation process along salinity gradient were observed during the incubation (0–60 d). After a long-term incubation, both PARtotal (4.61 ± 0.93 μg N g−1 d−1) and PARaob (3.05 ± 1.04 μg N g−1 d−1) reached their maximum values at 25 ‰ salinity, and PARaoa (1.96 ± 0.10 μg N g−1 d−1) reached its maximum values at 35 ‰ salinity, which showed that PARs had higher values under high salinity conditions. AOB amoA gene was more abundant than AOA under moderate and high salinity, and only a significant linear correlation was observed between PARaob and AOB abundances. In addition, the ammonia oxidation activities showed a wide range of salinity tolerance, which is worthy of further study on community structure and transcript richness. Our study illustrates that salinity plays a key role in regulating the ammonia oxidation process in estuarine sediments, and has guiding significance for N fixation and N loss associated with saltwater incursion.

Rhizospheric Microbiome Responses to Cover Crop Suppression Methods

Although winter cover crops (WCCs) have demonstrated positive effects on soil properties, relatively little is known about the responses of the soil and plant microbiomes to the introduction of WCCs and their associated management. Our objective was to evaluate the effects of WCC suppression methods on the rhizosphere microbiome of oats under field conditions. Rhizospheric soil was extracted to quantify the abundances of amoA gene of ammonia-oxidizing bacteria and archaea, and nitrite reductase genes (nirK and nirS), and to determine potential nitrification activity. The bacterial 16S rRNA V4 region and fungal ITS regions were sequenced with the Illumina MiSeq system. Overall, our results indicated that the composition of the bacterial and fungal communities of the rhizosphere were sensitive to the WCC suppression methods. Some bacterial genera, including fungal antagonists and chitin degraders, and two fungi associated with plant potential pathogens, were favored by both suppression methods, yet both methods negatively affected other genera associated with plant growth promotion characteristics. Our work contributes to a more complete understanding of the interactions between WCC management practices, soil properties, and microbial communities in the rhizosphere, which is essential for choosing management strategies that maintain soil health and promote environmental sustainability.

Manure combined with biochar reduces rhizosphere nitrification potential and amoA gene abundance of ammonia-oxidizing microorganisms in acid purple soil

Fertilization and soil environmental factors determine the niche differentiation of ammonia-oxidizing microorganisms, thereby affecting the ammonia-oxidation process. However, the characteristics of rhizosphere potential nitrification rate (PNR), ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) population under manure combined biochar are unclear. In this study, a pot experiment growing lemon was conducted, setting up six treatments, namely no fertilization (CK), chemical fertilizer (CF), manure (M), chemical fertilizer combined with biochar (CFBC), manure combined with biochar (MBC), fresh manure combined with biochar (FMBC). We investigated the effects of manure, chemical fertilizer and manure combined with biochar on soil physical-chemical properties, PNR, and the amoA gene abundance, diversity and structure of AOA and AOB in the rhizosphere. Our results showed that compared with CK treatment, CF and CFBC increases PNR by 19.3–34.7 % in the rhizosphere, M, MBC and FMBC decrease PNR about 60.0 %; CF and CFBC increased AOA amoA gene copies by 40.2–101.7 %, while M, MBC and FMBC treatments decreased it by 66.5–81.9 %, five fertilization treatments decreased the AOB amoA gene copy by 33.1–81.9 %. The redundancy analysis showed that chemical fertilizer and manure combined with biochar affects the population structure of AOA and AOB by pH, available phosphorus (AP), ratio of carbon to nitrogen (C/N), soil moisture content (SMC), nitrate nitrogen (NO3−-N) and ammonium nitrogen (NH4+-N) in the rhizosphere. The results of partial least squares indicated that pH, total nitrogen (TN), AOA amoA gene copy and AOA Shannon index were main factors affecting nitrification potential in the rhizosphere. Therefore, AOA dominates the ammonia oxidation process in the acid purple soil under the condition of chemical fertilizer and pig manure combined with rice husk biochar. Meanwhile, fertilization affected ammonia oxidation process by regulating soil pH and TN in lemon rhizosphere soil.

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

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

Responses of soil ammonia-oxidizing microorganisms to simulated nitrogen deposition in a natural Castanopsis carlesii forest

Subtropical region of China is one of the global hotspots receiving nitrogen deposition. Nitrogen deposition could affect the abundance and community structure of ammonia oxidizers including ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox Nitrospira), with consequences on soil nutrient cycling that are driven by microorganisms. There is limited understanding for the newly discovered comammox Nitrospira in the subtropical forest soils. Here, we investigated the effect of simulated N deposition on abundances of soil ammonia oxidizers in the Castanopsis fargesii Nature Reserve in Xinkou Town, Sanming City, Fujian Province, China. Soil samples were collected from the field plots which received long-term nitrogen deposition with different dosages, including: CK, no additional treatment; LN, low nitrogen deposition treatment, dosage of 40 kg N·hm-2·a-1; and HN, high nitrogen deposition treatment, dosage of 80 kg N·hm-2·a-1. After 8-year treatment, simulated N deposition decreased soil pH and organic matter content, and increased nitrate content. We failed to amplify the amoA gene of AOB in the tested soils. High nitrogen deposition increased the abundance of AOA, but did not affect the abundance of comammox Nitrospira clade A and clade B. The ratio of comammox Nitrospira to AOA decreased with N addition, indicating that N addition weakened the role of comammox Nitrospira in nitrification in the subtropical forest soils. However, there were strong non-specific amplifications for both comammox Nitrospira clades A and B, highlighting the demand for the development of high coverage and specificity primers for comammox Nitrospira investigations in the future. The abundance of comammox Nitrospira clade A was positively correlated with total nitrogen (TN) and NH4+ concentration, while that of clade B was positively associated with soil organic carbon (SOC), TN and NH4+ Concentration. Overall, our findings demonstrated that simulated N deposition increased the relative importance of AOA in nitrification in the natural Castanopsis carlesii forest soil. These findings could provide theoretical support in coping with global change and N deposition in these regions.

Nitrification performance and bacterial community dynamics in a membrane bioreactor with elevated ammonia concentration: The combined inhibition effect of salinity, free ammonia and free nitrous acid on nitrification at high ammonia loading rates

The responses of the operational performance and bacterial community structure of a nitrification membrane bioreactor (MBR) to elevated ammonia loading rate (ALR) were investigated. Effective nitrification performance was achieved at high ALR up to 3.43 kg NH4+-N/m3·d, corresponding to influent NH4+-N concentration of 2000 mg/L. Further increasing influent NH4+-N concentration to 3000 mg/L, the MBR system finally became completely inefficient due to the combined inhibition effect of salinity, free ammonia and free nitrous acid on nitrification. Ammonia-oxidizing bacteria (AOB) Nitrosomonas were enriched with the increase of ALR. The relative abundance of Nitrosomonas in the sludge with ALR of 2.57 kg NH4+-N/m3·d was up to 14.82%, which were 9-fold and 53-fold higher than that in seed sludge and the sludge with ALR of 0.10 kg NH4+-N/m3·d, respectively. The phylogenetic analysis of AOB amoA genes showed that Nitrosomonas europaea/mobilis lineage are chiefly responsible for catalyzing ammonia oxidation at high ALRs.

Effects of aquatic nitrogen pollution on particle-attached ammonia-oxidizing bacteria in urban freshwater mesocosms.

Ammonia-oxidizing bacteria (AOB) attached to aquatic particles are important participants in ammonia oxidation within hypereutrophic urban river systems. To explore the effects of aquatic nitrogen pollution on particle-attached AOB in urban river, we utilized laboratory mesocosms to investigate the responses of abundances and community structure of particle-attached AOB to ammonium (NH4+) and glycine (C2H5NO2) amendments. The abundance and community structure of particle-attached AOB were determined with quantitative real-time polymerase chain reaction (qRT-PCR) analysis and high-throughput sequencing based on the AOB amoA gene, respectively. Most of the bacterial amoA sequences from different treatments were affiliated with uncultured Nitrosomonadaceae bacterium, uncultured Nitrosomonadales bacterium, and uncultured Nitrosomonas sp., which are closely associated with organic pollution. The species richness and diversity of particle-attached AOB communities increased with increasing NH4+ and glycine concentrations. Treatment effects contributed significantly to the variance in particle-attached AOB communities. Although, glycine was completely transformed to ammonium within a few days and ammonium amendments would change the community structure of particle-attached AOB, the effect of glycine on the particle-attached AOB community was regulated by both the resulting ammonium concentration, as well as organic matter availability to the heterotrophic bacteria. Results suggested that high anthropogenic nitrogen loadings appeared to promote higher particle-attached AOB richness and diversity in the hypereutrophic urban river, but the effect of organic nitrogen on the particle-attached AOB community was different from the effect of inorganic nitrogen. This study informs ammonia oxidization mechanisms in the hypereutrophic urban rivers, which contributes to remediation/restoration strategies.

Triclosan enriched resistance genes more easily than copper in the presence of environmental tetracycline in aerobic granular sludge system

Triclosan (TCS) and copper (Cu2+) were exposed to aerobic granular sludge (AGS) system treating wastewater containing environmental tetracycline, respectively, to explore the different biochemical responses, more importantly, the fates of resistance genes (RGs) in AGS system. The results showed that TCS and Cu2+ could significantly inhibit the N and P removal in AGS system by reducing several key functional genes, including amoA gene of ammonia-oxidizing bacteria, Nitrospira and phosphorus accumulating organisms 16S rRNA genes. TCS caused higher degree of RGs' enrichment than Cu2+, which made the average total relative abundance of RGs of 1.38 ± 0.73 and 0.78 ± 0.24 in TCS and Cu system, respectively. Cu2+ could induce a wider range of horizontal gene transfer than TCS, leading to the detections of more potential hosts harboring RGs in Cu system. Cu system seemed to have stronger repair, immunity and defense ability than TCS system, which enabled it to have sufficient ability to trigger protection mechanism to realize self-protection, eventually the RGs also were controlled. Integron (intI1 and intI3) and plasmids (trb-C and IncQ) might cooperate with microorganisms and water quality parameters to enhance the enrichment of RGs in TCS system, however this interaction among various environmental factors was not obvious in Cu system, which might be responsible for the lower abundance of RGs. The increasing levels of TCS and Cu2+ in wastewater should be paid more attentions during the treatment of wastewater containing environmental tetracycline by AGS system. Especially for TCS, it had the ability to enrich RGs more easily than Cu2+, which should be prevented from entering wastewater treatment plants as far as possible, to avoid more serious proliferation and dissemination of various RGs.