Ammonia-oxidizing Bacteria amoA Research Articles

氮磷添加下典型温带、亚热带森林土壤氮循环功能基因丰度和微生物群落属性数据集

Nitrogen (N) and phosphorus (P) are essential nutrients for soil microbial growth and activities. There are notable differences in the concentrations of N and P and the characteristics of microbial communities observed between temperate and subtropical forests soils, and this is also true for soil vertical profiles. As a consequence of the rise in global atmospheric N deposition, soil nutrient imbalances and P limitation are increasingly aggravated in eastern China. However, there is a lack of systematic dataset showing how N deposition and P addition affect soil N cycling microbes and soil physicochemical properties in eastern China; hence a comprehensive dataset is needed to a better understanding of the impact of N deposition and P addition on soil nitrogen cycle. This dataset is constructed based on the field experimental setup in the forests of Chinese Ecosystem Research Network (CERN). To obtain a systematic dataset on N-cycling microbial communities, we conducted measurements and collected data of soil N-cycling functional genes abundance, N-cycling microbial community diversities and compositions and enzyme activities in three typical forests with N and/or P additions. We collected 0-10 cm top soils from a temperate forest (Changbai Mountain) and two subtropical forests (Qianyanzhou and Dinghu Mountain) with field N and/or P additions, and the soils along 0-80 cm vertical profiles without nutrient additions. The N-cycling functional genes involved in the datasets cover ammonia oxidizing archaea amoA, ammonia oxidizing bacteria amoA, nirK, nirS, nosZ, qnorB, narG, nir, nifH and chiA. The potential activities included in the datasets cover nitrification activity, denitrification activity, nitrogen fixation activity and organic nitrogen decomposition enzyme activity. The datasets also include soil physiochemical properties, including soil pH, moisture content, N2O emission, net nitrification rate and the concentrations of organic carbon, NH4+ , NO3− , available phosphorus, total nitrogen, total carbon, total phosphorus and dissolved organic carbon. The creation and sharing of the datasets can provide data and support for understanding the microbial mechanisms of soil N-cycling and the modelling processes under the scenario of aggravated N deposition and P addition. The datasets will also provide support for forest management efforts with regard to greenhouse gas N2O emission, N and nutrient loss in forest ecosystems.

Addition of cellulose and hemicellulose degrading microorganisms intensified nitrous oxide emission during composting

This study aims to clarify the mechanisms underlying effects of inoculating cellulose and hemicellulose-degrading microorganisms on nitrous oxide (N2O) emissions during composting with silkworm excrement and mulberry branches. Inoculation with cellulose and hemicellulose–degrading microorganisms resulted in significant increases of total N2O emission by 10.4 ± 2.0 % (349.1 ± 6.2 mg N kg−1 dw) and 26.7 ± 2.1 % (400.6 ± 6.8 mg N kg−1 dw), respectively, compared to the control (316.3 ± 3.6 mg N kg−1 dw). The stimulation of N2O emission was attributed to the enhanced contribution of ammonia-oxidizing bacteria (AOB) and denitrifying bacteria to N2O production, as evidenced by the increased AOB amoA and denitrifying nirK gene abundances. Moreover, microbial inoculation stimulated N2O reduction to N2 owing to increased abundances of nosZⅠ and nosZⅠⅠ genes. These findings highlight the necessity to develop cost-effective and environmentally friendly strategies to reduce N2O emissions when cellulose and hemicellulose-degrading microorganisms are inoculated during composting.

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.

Ubiquitous occurrence and functional dominance of comammox Nitrospira in full-scale wastewater treatment plants

The recent discovery of complete ammonia oxidation (comammox) bacteria has fundamentally upended the traditional two-step nitrification conception, but their functional importance in wastewater treatment plants (WWTPs) is still poorly understood. This study investigated distributions of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in activated sludge samples collected from 25 full-scale WWTPs. Using quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing, our results revealed that comammox Nitrospira ubiquitously occurred in all of 25 WWTPs and even outnumbered AOB and AOA with an average abundance of 1∼183 orders of magnitude higher in 19 WWTPs. Moreover, DNA-based stable isotope probing (DNA-SIP) assays validated that comammox Nitrospira actively participated in ammonia oxidation in the three microcosms seeding with activated sludge from three typical WWTPs, in which the ratios of comammox amoA to AOB amoA were at the range of 1∼10, 10∼100 and >100, respectively. Phylogenetic analysis in heavy fractions further indicated that Nitrospira nitrosa (N. nitrosa) was the dominant and active species. We quantified the contribution of ammonia oxidizers based on the currently available kinetic parameters of the representative species and found that comammox made major contributions to ammonia oxidation than other nitrifiers (5 ∼ 106 times that of AOB). The findings not only demonstrate the ubiquitous occurrence of comammox, but also highlight their functional dominance in ammonia oxidation in WWTPs.

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.

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.

Nitrification rate in dairy cattle urine patches can be inhibited by changing soil bioavailable Cu concentration

Ammonia oxidation to hydroxylamine is catalyzed by the ammonia monooxygenase enzyme and copper (Cu) is a key element for this process. We investigated the effect of soil bioavailable Cu changes induced through the application of Cu-complexing compounds on nitrification rate, ammonia-oxidizing bacteria (AOB) and archaea (AOA) amoA gene abundance, and mineral nitrogen (N) leaching in urine patches using the Manawatu Recent soil. Further, evaluated the combination of organic compound calcium lignosulphonate (LS) with a growth stimulant Gibberellic acid (GA). Treatments were applied in May 2021 as late-autumn treatments: control (no urine), urine-only at 600 kg N ha−1, urine + dicyandiamide (DCD), urine + co-poly-acrylic-maleic acid (PA-MA), urine + LS, urine + split-application of LS (2LS), and urine + combination of GA plus LS (GA + LS). In addition, another four treatments were applied in July 2021 as mid-winter treatments: control, urine-only at 600 kg N ha−1, urine + GA, and urine + GA + LS. Soil bioavailable Cu and mineral N leaching were examined during the experimental period. The AOB/AOA amoA genes were quantified using quantitative polymerase chain reaction. Changes in soil bioavailable Cu across treatments correlated with nitrification rate and AOB amoA abundance in late-autumn while the AOA amoA abundance did not change. The reduction in soil bioavailable Cu induced by the PA-MA and 2LS was linked to significant (P < 0.05) reduction in mineral N leaching of 16 and 30%, respectively, relative to the urine-only. The LS did not induce a significant effect on either bioavailable Cu or mineral N leaching relative to urine-only. The GA + LS reduced mineral N leaching by 10% relative to LS in late-autumn, however, there was no significant effect in mid-winter. This study demonstrated that reducing soil bioavailable Cu can be a potential strategy to reduce N leaching from urine patches.

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.

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 Nitrous Oxide Emission to Nitrogen Addition at Two Topographic Positions of a Subtropical Forest

AbstractTopography can influence nitrous oxide (N2O) emission via its influences on soil nutrient availability, moisture, and microbial communities. Nevertheless, it is still unclear whether topography modulates the responses of soil N2O emissions to elevated N deposition. Here the N addition experiment was conducted in the valley and on the slope of a subtropical karst forest in southwest China. Nitrogen was applied as NH4NO3 in two levels, that is, 50 (moderate N) and 100 (high N) kg N ha−1 yr−1 with no N addition plots as the control. Nitrogen addition consistently increased N2O emission in the valley, but only high N addition significantly increased N2O emission on the slope in 2017. The cumulative N2O fluxes across the 3 years were 1.16 ± 0.24 kg N ha−1 in the valley and 1.50 ± 0.06 kg N ha−1 on the slope under the control. Nitrogen addition stimulated N2O emission by 88.7%–113.3% in the valley due to increased ammonium, nitrate and dissolved organic carbon availabilities and ammonia‐oxidizing bacteria (AOB) amoA abundance. High N addition stimulated N2O emission by 84.3% on the slope owing to increased nitrate and carbon availabilities, AOB amoA, and nirK abundances. The stimulation of N2O emission by moderate N addition was more pronounced in the valley than on the slope largely owing to the lower N status in the valley. This work highlights the importance of N status in regulating the responses of soil N2O emissions to elevated N deposition.

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.

Di-(2-ethylhexyl) phthalate (DEHP) exposure suppressed the community diversity and abundance of ammonia-oxidizers and mitigated N2O emissions in an alkaline soil

Phthalic acid esters (PAEs) pollution has become an increasing issue worldwide, but little is known about its effects on ammonia-oxidizers and nitrous oxide (N2O) in the soil environment. Here, a 50-day soil microcosm experiment was conducted using low and high doses bis (2-Ethylhexyl) phthalate (DEHP) to estimate the effect of DEHP exposure on soil N2O emissions and the nitrifying community in calcareous soil. The results showed that DEHP exposure at 10 and 100 mg kg-1 doses significantly reduced N2O by 67.5% and 73.6%, respectively, relative to the DEHP absent treatment. The microbial biomass carbon and nitrogen (MBC and MBN) were consistently and significantly decreased with DEHP exposure at 5, 22, and 50 days after incubation, especially with high-dose. The bipartite association networks showed that DEHP exposure changed the compositions of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. Moreover, the AOA and AOB amoA gene abundances were significantly decreased by DEHP addition to the soil (P < 0.05). Random forest modeling showed that the AOB Shannon index and pH were the most important biotic and abiotic factors affecting N2O emissions in the soil with DEHP exposure, respectively. Partial least squares path modeling (PLS-PM) demonstrated that the reduction of N2O emissions due to DEHP exposure was mainly ascribed to the changes of the AOB community. The results from this study highlight the toxicity of DEHP on the ammonia oxidizers, and its mitigating effect on N2O emissions in the soil where ammonia-oxidation is largely driven by AOB.

Soil Amendments Alter Ammonia-Oxidizing Archaea and Bacteria Communities in Rain-Fed Maize Field in Semi-Arid Loess Plateau

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are key drivers of nitrification in rainfed soil ecosystems. However, within a semi-arid region, the influence of different soil amendments on the composition of soil AOA and AOB communities and soil properties of rainfed maize is still unclear. Therefore, in this study, the abundance, diversity, and composition of AOA and AOB communities and the potential nitrification activity (PNA) was investigated across five soil treatments: no fertilization (NA), urea fertilizer (CF), cow manure (SM), corn stalk (MS), and cow manure + urea fertilizer (SC). The AOB amoA gene copy number was influenced significantly by fertilization treatments. The AOB community was dominated by Nitrosospira cluster 3b under the CF and SC treatments, and the AOA community was dominated by Nitrososphaera Group I.1b under the CF and NA amendments; however, manure treatments (SM, MS, and SC) did not exhibit such influence. Network analysis revealed the positive impact of some hub taxonomy on the abundance of ammonia oxidizers. Soil pH, NO3−-N, Module 3, biomass, and AOB abundance were the major variables that influenced the potential nitrification activity (PNA) within structural equation modeling. PNA increased by 142.98–226.5% under the treatments CF, SC, SM, and MS compared to NA. In contrast to AOA, AOB contributed dominantly to PNA. Our study highlights the crucial role of bacterial communities in promoting sustainable agricultural production in calcareous soils in semi-arid loess plateau environments.

PH and ammonium concentration are dominant predictors of the abundance and community composition of comammox bacteria in long-term fertilized Mollisol

The newly-discovered complete ammonia-oxidizing bacteria (comammox) doubts our inherent understanding of nitrification. Herein, we study communities of comammox, ammonia-oxidizing bacteria (AOB) and archaea (AOA) in Mollisol after a 30-year fertilization history with four treatments: chemical nitrogen (N) and potassium (K) fertilizers (NK); chemical N, phosphorus (P), and K fertilizers (NPK); chemical NPK fertilizers plus organic manure (NPKM); and a control without fertilizers (CK). Compared with CK, chemical fertilizer treatments (NK and NPK) significantly reduced AOA amoA gene abundance and increased AOB and comammox amoA gene abundances. The highest values of AOA and AOB amoA gene abundances were found in the NPKM treatment and the highest value of comammox amoA gene abundance was observed in the NK treatment. The application of combined NPK and organic manure (NPKM) significantly increased AOA, AOB, and comammox amoA gene abundances compared to CK. Long-term chemical fertilization decreased the diversity of comammox community; whereas, the application of combined NPK with organic manure (NPKM) restored it to levels comparable to CK. Long-term fertilization management altered the community structure of comammox based on principal coordinate analysis (PCoA). Soil pH and NH4+-N concentration were the key factors affecting soil abundance and community structure of comammox. This study demonstrates the different responses of comammox community and canonical ammonia oxidizers to long-term fertilization practices in Mollisol.