Contribution Of Ammonia-oxidizing Archaea Research Articles

Impact of salinity and organic matter on the ammonia-oxidizing archaea and bacteria in treating hypersaline industrial wastewater: amoA gene abundance and ammonia removal contributions.

Studies publishedrecently proposed that ammonia-oxidizing archaea (AOA) may bebeneficial for hypersaline (salinity > 50g NaCl L-1) industrial wastewater treatment. However, knowledge of AOA activity in hypersaline bioreactors is limited. This study investigated the effects of salinity, organic matter, and practical pickled mustard tuber wastewater (PMTW) on AOA and ammonia-oxidizing bacteria (AOB) in two sequencing batch biofilm reactors (SBBRs). Results showed that despite observed salinity inhibition (p < 0.05), both AOA and AOB contributed to high ammonia removal efficiency at a salinity of 70 g NaCl L-1 in the two SBBRs. The ammonia removal efficiency of SBBR2 did not significantly differ from that of SBBR1 in the absence of organic matter (p > 0.05). Batch tests and quantitative real-time PCR (qPCR) reveal that salinity and organic matter inhibition resulted in a sharp decline in specific ammonia oxidation rates and amoA gene copy numbers of AOA and AOB (p < 0.05). AOA demonstrated higher abundance and more active ammonia oxidation activity in hypersaline and high organic matter environments. Salinity was positively correlated with the potential ammonia oxidation contribution of AOA (p < 0.05), resulting in a potential transition from AOB dominance to AOA dominance in SBBR1 as salinity levels rose. Moreover, autochthonous AOA in PMTW promoted the abundance and ammonia oxidation activities of AOA in SBBR2, further elevating the nitrification removal efficiency after feeding the practical PMTW. AOA demonstrates greater tolerance tothe challenging hypersaline environment, making it a valuable candidate for the treatment of practical industrial wastewater with high salinity and organic content.

Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate.

Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments

The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3−-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.

Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge

In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.

Ammonia-oxidizing archaea bacteria (AOB) and comammox drive the nitrification in alkaline soil under long-term biochar and N fertilizer applications

Ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia oxidizers (comammox) take an essential part in soil nitrogen (N) cycling. In case of 8 years biochar and N fertilizer application, nevertheless, the comparative contribution of comammox, AOA and AOB to nitrification is unclear. Our long-term field study on alkaline soil (pHwater 8.49) investigated the impact of biochar and N fertilizer on nitrification rate and potential ammonia oxidation in terms of the soil properties, both physical and chemical, together with the abundance and diversity of AOA, AOB and comammox. The findings revealed that biochar and N fertilizer did not affect the amoA abundance of AOA but increased it in AOB and commamox clade A and clade B, but decreased the diversity of AOA and comammox. Nitrogen fertilization significantly declined the diversity of AOB. The AOB abundance was controlled mainly by pH, whereas the AOA, AOB and comammox Chao1 index were governed by soil microbial biomass carbon (MBC). Additionally, biochar increased the soil nitrification rate with or without N fertilizer, but N fertilizer decreased the soil nitrification rate and potential ammonia oxidation (with nitrite oxidation inhibited) under the same biochar application. Biochar and/or N fertilizer increased the corresponding contribution of AOA and comammox to ammonia oxidation by 143–156 % and 33–395 %, respectively, but suppressed the contribution of AOB. Although the abundance of AOA amoA was obviously greater than that of AOB and comammox, the highest contribution to ammonia oxidation was by AOB in soil not fertilized by N and by comammox in the N-fertilized soil. Our findings suggest that changes in soil properties brought about by biochar and N fertilizer addition can influence the diversity of AOA, AOB and comammox, affecting potential ammonia oxidation and the nitrification rate. The AOB and comammox make a bigger contribution to nitrification than AOA in the alkaline soil.

Comammox plays a functionally important role in the nitrification of rice paddy soil with different nitrogen fertilization levels

Chemoautotrophic ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizers (comammox) catalyze ammonia oxidation; however, quantifying their individual gross ammonia oxidation activities in complex soil ecosystems remains elusive. In this study, we investigated the nitrifying population and community dynamics in response to fertilization in paddy soil under long-term treatment with different urea concentrations (0, 100, 200, and 300 kg N ha−1; designated N0, N100, N200, and N300, respectively). The community structure of nitrifiers, including comammox, was changed by long-term N fertilizers input, which also enhanced AOB abundance and comammox clade A/B abundance ratio, whereas it did not affect AOA abundance. Nevertheless, the microbial population sizes and community compositions remained largely similar following short-term fertilization throughout one rice-growing season. Furthermore, by employing a 15NO3− pool dilution technique in combination with chlorate and 1-octyne inhibition, we conducted a soil microcosm incubation without substrate supplementation to distinguish the relative contribution of comammox to gross ammonia oxidation from those of AOA and AOB. Comammox exhibited higher nitrification activity in soils treated with more N fertilizers, with the contribution increasing from 34 % (N0) to 75 % (N300), although its abundance was not dominant. This could be attributed to the repeated N-based fertilization, which reduced the soil pH, thereby decreasing the soil-free ammonia concentration. In contrast, the contribution of AOA declined from 57 % (N0) to 19 % (N300), while that of AOB only accounted for a minor fraction (<25 %) despite being in high abundance. Altogether, our findings provide evidence that the activity of nitrifying guilds is more valuable than their abundance and provide insights into the potential functional significance of comammox in the nitrification process in rice paddy systems.

Spatial distribution of ammonia oxidizers in marine sediments of the Bohai, Yellow and East China Seas

Ammonia oxidation, an essential process within the global nitrogen cycle, is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). To date, the current knowledge on the biogeography of AOA and AOB in the ocean across a large geographic distance remains poorly known. In this study, the abundance, microbial composition, and diversity of AOA and AOB in marine sediments collected from the Bohai Sea, Yellow Sea, and East China Sea were characterized by employing quantitative PCR and Illumina Miseq sequencing of both archaeal and bacterial amoA genes. qPCR analysis demonstrated significantly higher abundances of archaeal amoA genes than those of bacterial amoA genes with AOA/AOB ratios varying from 1.59 to 292.88, suggesting a greater contribution of AOA to nitrification in the seas. Nitrosopumilus and Nitrosospira were the predominant clusters of AOA and AOB respectively in all sediment samples. The distribution pattern of both AOA and AOB communities revealed by PCoA (principal coordinate analysis) showed distinct geographic separation of sediment samples from the three seas. Correlation analysis indicated that ammonia (NH4+-N) and nitrate (NO3−-N) content were the main selective forces leading to the distinct biogeography of the two ammonia oxidizers in the ocean. The results are of great significance in improving our understanding of the contribution of AOA and AOB in the nitrogen transformation in the marine ecosystem and providing insights into the environmental factors that shape the assembly of aerobic ammonium oxidizers.

Organic substitution stimulates ammonia oxidation-driven N2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils

Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N2O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N2O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N2O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N2O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N2O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N2O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N2O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N2O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.

Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands

Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N2O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N2O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N2O through lab-scale subsurface CWs. The N2O emission flux of CW at 8 °C was 1.23 mg m−2·h−1, significantly lower than that at 25 °C (1.92 mg m−2·h−1). The contribution of ammonia oxidation to N2O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N2O production from AOA increased from 1.91 ng N·g−1 at 25 °C to 4.11 ng N·g−1 soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N2O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N2O at low temperature.

Different contributions of ammonia oxidizing archaea and bacteria to nitrification in soils amended with equivalent amounts of either ammonium-N or organic-N

Although considerable knowledge exists on the impact of crop residues on soil N availability, information about their impact on nitrification specifically is lacking. The unique physiologies of ammonia oxidizing archaea (AOA) suggests their activities might respond differently to crop residue amendment compared to ammonia oxidizing bacteria (AOB). An incubation study was conducted on two widely distributed Oregon agricultural silt loam soils of the Walla Walla (WW) and Woodburn (CC) series, amended with a fertilizer rate of 70 μg N g−1 soil in the form of (1) NH4+-N, (2) clover stems (C:N ~ 25), or (3) clover leaves (C:N ~ 13). NH4+ accumulation in the presence of acetylene, and the relative amounts of AOA and AOB activities, in the presence of the selective AOB inhibitor, 1-octyne, were examined over a 28-31d incubation. Nitrifying activity in the crop residue-amended WW soil matched the rate of ammonification and was predominately octyne-resistant suggesting that nitrifying activity was dominated by AOA. In CC soil, the relative contributions of AOA and AOB to emergent activities was influenced by the nature of the residue and in a soil specific manner. In leaf amended CC soil, AOB contributed the majority of initial nitrifying activity over 0-7d, with the contribution of AOA activity increasing post 7d to represent 100% of the total rate. In stem amended CC soil, emergence of nitrifying and ammonifying activities were delayed, but after 7d incubation AOA activity emerged at a rate greater than the accompanying rate of ammonification. In NH4+-N amended soils, AOB activity emerged quickly at rates greater than when N was supplied by residues. The response of AOA activity to NH4+-N was soil specific being immediate and at a greater rate than leaf residue supported activity in WW soil, whereas in CC soil, AOA activity was temporally delayed (as with residue treatment) and emerged at a rate similar to that supported by leaf residue. From a practical perspective, the findings of this study show that an application of 70 μg N g−1 soil as crop residues can prevent AOB driven nitrifying activity from reaching its potential compared to an inorganic NH4+-N application, and also suggest the potential of AOA activity to be modified by residues in a soil specific manner.

Spatiotemporal dynamics of ammonia-oxidizing archaea and bacteria contributing to nitrification in sediments from Bohai Sea and South Yellow Sea, China

Nitrification is a central process in nitrogen cycle in the ocean. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play significant roles in ammonia oxidation which is the first and rate-limiting step in nitrification, and their differential contribution to nitrification is an important issue, attracting extensive attention. In this study, based on the quantification of archaeal and bacterial amoA gene and the measurement of potential nitrification rate (PNR), we investigated the spatiotemporal dynamics of PNRs and the amoA gene abundance and transcript abundance of aerobic ammonia oxidizers in surface sediments collected in summer and spring across ~900 km of the Bohai Sea and Yellow Sea in China. The results revealed that the contribution of AOA to nitrification was greater than that of AOB in coastal sediments, probably due to salinity and ammonia concentration. Besides, seasons had significant effect on amoA gene abundance and transcript abundance, especially for AOA, while both seasons and sea areas had significant influence on PNR of AOA and AOB. Further analysis showed complex relationships among amoA gene abundances, transcript abundances and PNRs. More importantly, both spatial (geographic distance) and environmental factors were vital in explaining the variations of ammonia-oxidizing microorganism abundances and the PNRs.

Effect of Low Temperature on Contributions of Ammonia Oxidizing Archaea and Bacteria to Nitrous Oxide in Constructed Wetlands

Effect of Low Temperature on Contributions of Ammonia Oxidizing Archaea and Bacteria to Nitrous Oxide in Constructed Wetlands

Assessing the influence of environmental niche segregation in ammonia oxidizers on N2O fluxes from soil and sediments

Understanding the environmental niche segregation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and its impact on their relative contributions to nitrification and nitrous oxide (N2O) production is essential for predicting N2O dynamics within an ecosystem. Here, we used ammonia oxidizer-specific inhibitors to measure the differential contributions of AOA and AOB to potential ammonia oxidization (PAO) and N2O fluxes over pH (4.0–9.0) and temperature (10–45 °C) gradients in five soils and three wetland sediments. AOA and AOB activities were differentiated using PTIO (2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide), 1-octyne, and acetylene. We used square root growth (SQRT) and macromolecular rate theory (MMRT) models to estimate cardinal temperatures and thermodynamic characteristics for AOA- and AOB-dominated PAO and N2O fluxes. We found that AOA and AOB occupied different niches for PAO, and soil temperature was the major determinant of niche specialization. SQRT and MMRT models predicted a higher optimum temperature for AOA-dominated PAO and N2O fluxes compared with those of AOB. Additionally, PAO was dominated by AOA in acidic conditions, whereas both AOA- and AOB-dominated N2O fluxes decreased with increasing pH. Consequently, net N2O fluxes (AOA and AOB) under acidic conditions were approximately one to three-fold higher than those observed in alkaline conditions. Moreover, structural equation and linear regression modeling confirmed a significant positive correlation (R2 = 0.45, p < 0.01) between PAO and N2O fluxes. Collectively, these results show the influence of ammonia oxidizer responses to temperature and pH on nitrification-driven N2O fluxes, highlighting the potential for mitigating N2O emissions via pH manipulation.

Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils.

Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.

Dominance of archaeal ammonia-oxidizers in soil nitrification across different soil types and fertilities in North China plain

Microbially mediated soil nitrification process was largely limited by ammonia-oxidizing archaea (AOA) and bacteria (AOB), which further affect nitrogen (N) loss and retention with concomitant impacts on both crop productivity and environment. However, the spatial distribution of ammonia-oxidizers and their varying contributions to soil nitrification activity at provincial scale are poorly explored. 135 agricultural soils across different soil types and fertility conditions were collected from Henan province in North China Plain to draw the map of soil AOA and AOB abundance with quantitative PCR analysis. Soil nitrification potential (NP) and the relative contribution of AOA and AOB to NP that recovers after acetylene inactivation were essentially determined among the five major soil types. The abundance of ammonia-oxidizers, which was positively and significantly related with pH, was obviously predominated by AOA with AOA/AOB ranging 1.96–9.79 at provincial scale. AOA contributed more (at 60%–79%) to soil nitrification in acidic and neutral soils (Lime concretion black soil, Yellow-cinnamon soil, Paddy soil and Cinnamon soil) with significant relationships with its higher abundance, pH, soil organic carbon and ammonium nitrogen. On the contrary, the even contribution of AOB compared with AOA in alkaline Fulvo-aquic soil showed poor relationship with its abundance but was strongly affected by soil N availability. In summary, AOA even with lower abundance showed stronger function in acidic and ammonia-limited soil environments, but AOB with higher abundance tends to be the leader of soil nitrification in alkaline and substrate-rich soils of Henan province.

The contribution of ammonia-oxidizing archaea and bacteria to gross nitrification under different substrate availability

The first step of autotrophic nitrification is performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recent studies show that their relative contributions are determined by the substrate sources and availability, yet evidence provided by quantification of their respective gross activities in soil is lacking. Here, we conducted a microcosm study with agricultural soil with high (50 μg N g−1) and low (5 μg N g−1) ammonium application, and quantified gross nitrification rates using 15N-tracers. AOA and AOB activities were distinguished using the bacterial inhibitor 1-octyne and acetylene, which inhibits both AOA and AOB. Under low ammonium supply, AOA and AOB contributed equally to gross ammonia oxidation, but AOB outcompeted AOA under higher ammonium supply. These results provide the first direct evidence that substrate availability affects the relative contribution of AOA and AOB to gross nitrification.

Measuring Responses of Dicyandiamide-, 3,4-Dimethylpyrazole Phosphate-, and Allylthiourea-Induced Nitrification Inhibition to Soil Abiotic and Biotic Factors.

Nitrification inhibitors (NIs) such as dicyandiamide (DCD), 3,4-dimethylpyrazole phosphate (DMPP), and allylthiourea (AT) are commonly used to suppress ammonia oxidization at different time scales varying from a few hours to several months. Although the responses of NIs to edaphic and temperature conditions have been studied, the influence of the aforementioned factors on their inhibitory effect remains unknown. In this study, laboratory-scale experiments were conducted to assess the short-term (24 h) influence of eight abiotic and biotic factors on the inhibitory effects of DCD, DMPP, and AT across six cropped and non-cropped soils at two temperature conditions with three covariates of soil texture. Simultaneously, the dominant contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to potential ammonia oxidization (PAO) were distinguished using the specific inhibitor 2 phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). Our results revealed that AT demonstrated a considerably greater inhibitory effect (up to 94.9% for an application rate of 75 mg of NI/kg of dry soil) than DCD and DMPP. The inhibitory effect of AT was considerably affected by the relative proportions of silt, sand, and clay in the soil and total PAO. In contrast to previous studies, the inhibitory effects of all three NIs remained largely unaffected by the landcover type and temperature conditions for the incubation period of 24 h. Furthermore, the efficacy of all three tested NIs was not affected by the differential contributions of AOA and AOB to PAO. Collectively, our results suggested a limited influence of temperature on the inhibitory effects of all three NIs but a moderate dependence of AT on the soil texture and PAO. Our findings can enhance the estimation of the inhibitory effect in soil, and pure cultures targeting the AOA and AOB supported ammonia oxidization and, hence, nitrogen dynamics under NI applications.

Residual effects of four-year amendments of organic material on N2O production driven by ammonia-oxidizing archaea and bacteria in a tropical vegetable soil

Organic material (OM) applied to cropland not only enhances soil fertility but also profoundly affects soil nitrogen cycling. However, little is known about the relative contributions of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrous oxide (N2O) production during ammonia oxidation in response to the additions of diverse types of OMs in the tropical soil for vegetable production. Herein, the soils were sampled from a tropical vegetable field subjected to 4-year consecutive amendments of straw or manure. All the soils were amended with ammonium sulfate ((NH4)2SO4, applied at a dose of 150 mg N kg−1) and incubated aerobically for four weeks under 50% water holding capacity. 1-octyne or acetylene inhibition technique was used to differentiate the relative contributions of AOA and AOB to N2O production. Results showed that AOA dominated N2O production in soil managements of unfertilized control (CK), chemical fertilization (NPK), and NPK with straw (NPKS), whereas AOB contributed more in soil under NPK with manure (NPKM). Straw addition stimulated AOA-dependent N2O production by 94.8% despite the decreased AOA-amoA abundance. Moreover, manure incorporation triggered both AOA- and AOB-dependent N2O production by 147.2% and 233.7%, respectively, accompanied with increased AOA and AOB abundances. Those stimulating effects were stronger for AOB, owing to its sensitivity to the alleviated soil acidification and decreased soil C/N ratio. Our findings highlight the stimulated N2O emissions during ammonia oxidation by historical OM amendments in tropical vegetable soil, with the magnitude of those priming effects dependent on the types of OM, and appropriate measures need to be taken to counter this challenge in tropical agriculture ecosystems.

Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques.

In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.

A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea.

The continuous increase of nitrous oxide (N2O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N2O production, a clear understanding of the knowledge on archaeal N2O production is necessary for global N2O mitigation. Compared to bacterial N2O production by ammonia-oxidizing bacteria (AOB), AOA-driven N2O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N2O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N2O production pathways, discussed the relative contribution of AOA to N2O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N2O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N2O production. We, then, put forward perspectives for archaeal N2O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N2O mitigations.