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Reactive oxygen species (ROS) are ubiquitous in O2-perturbed aquifers, but their role in shaping ammonia-oxidizing microbial communities is not clear. This study examined the dynamic responses of ammonia-oxidizing microorganisms (AOMs) in redox-fluctuating aquifers to ROS via field investigation and in-lab verification using transcriptomes/ metatranscriptome and RT-qPCR. Ammonia-oxidizing archaea (AOA) dominated recharge aquifers with lower ROS levels, whereas ammonia-oxidizing bacteria (AOB) and heterotrophic nitrifying aerobic bacteria (HNB) predominated in discharge areas with higher ROS levels. Similar succession in AOM enrichments was found in that the dominant AOMs changed from AOA Nitrosopumilus to AOB Nitrosomonas with increasing ROS. Ammonia oxidation and antioxidant capacity differed significantly among three AOM isolates exposed to ROS. ROS decreased the amoA gene expression of AOA strain Nitrososphaera viennensis PLX03, accompanied by inhibited ammonia oxidation capacity. By contrast, the catalase and superoxide dismutase activities of the AOB strain Nitrosomonas oligotropha PLL12 and HNB strain Pseudomonas aeruginosa PLL01 increased, and the antioxidant genes katG, sodA, ahpC, and ahpF were significantly upregulated. These results demonstrate that ROS exert an important influence on AOMs in redox-fluctuating aquifers. This study improves our understanding of the ecological niches of AOMs in surface/subsurface environments.

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Biological nitrification inhibitors are exudates from plant roots that can inhibit nitrification, and have advantages over traditional synthetic nitrification inhibitors. However, our understanding of the effects of biological nitrification inhibitors on nitrogen (N) loss and fertilizer N recovery efficiency in staple food crops is limited. In this study, acidic and calcareous soils were selected, and rice growth pot experiments were conducted to investigate the effects of the biological nitrification inhibitor, methyl 3-(4-hydroxyphenyl) propionate (MHPP) and/or a urease inhibitor (N-[n-butyl], thiophosphoric triamide [NBPT]) on NH3 volatilization, N leaching, fertilizer N recovery efficiency under a 20% reduction of the conventional N application rate. Our results show that rice yield and fertilizer N recovery efficiency were more sensitive to reduced N application in the calcareous soil than in the acidic soil. MHPP stimulated NH3 volatilization by 13.2% in acidic soil and 9.06% in calcareous soil but these results were not significant. In the calcareous soil, fertilizer N recovery efficiency significantly increased by 19.3% and 44.4% in the MHPP and NBPT+MHPP groups, respectively, relative to the reduced N treatment, and the rice yield increased by 16.7% in the NBPT+MHPP treatment (P < 0.05). However, such effects were not significant in the acidic soil. MHPP exerted a significant effect on soil ammonia oxidizers, and the response of abundance and community structure of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and total bacteria to MHPP depended on the soil type. MHPP+NBPT reduced NH3 volatilization, N leaching, and maintaining rice yield for a 20% reduction in conventional N fertilizer application rate. This could represent a viable strategy for more sustainable rice production, despite the inevitable increase in cost for famers.

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Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha-1 yr-1) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha-1 (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 107 to 1.05 × 107 copies g-1 dry soil, while AOB abundance increased from 3.63 × 107 up to a maximum of 8.24 × 107 copies g-1 dry soil with the N105 treatment (105 kg N ha-1 yr-1). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha-1 yr-1 was optimum for the AOB community and wheat yield in the semi-arid area.

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Anaerobic ammonium oxidation (anammox) process has been acknowledged as an environmentally friendly and time-saving technique capable of achieving efficient nitrogen removal. However, the community of nitrification process in anammox-inoculated wastewater treatment plants (WWTPs) has not been elucidated. In this study, ammonia oxidation (AO) and nitrite oxidation (NO) rates were analyzed with the incubation of activated sludge from Xinfeng WWTPs (Taiwan, China), and the community composition of nitrification communities were investigated by high-throughput sequencing. Results showed that both AO and NO had strong activity in the activated sludge. The average rates of AO and NO in sample A were 6.51 µmol L-1 h-1 and 6.52 µmol L-1 h-1, respectively, while the rates in sample B were 14.48 µmol L-1 h-1 and 14.59 µmol L-1 h-1, respectively. The abundance of the nitrite-oxidizing bacteria (NOB) Nitrospira was 0.89-4.95 × 1011 copies/g in both samples A and B, the abundance of ammonia-oxidizing bacteria (AOB) was 1.01-9.74 × 109 copies/g. In contrast, the abundance of ammonia-oxidizing archaea (AOA) was much lower than AOB, only with 1.28-1.53 × 105 copies/g in samples A and B. The AOA community was dominated by Nitrosotenuis, Nitrosocosmicus, and Nitrososphaera, while the AOB community mainly consisted of Nitrosomonas and Nitrosococcus. The dominant species of Nitrospira were Candidatus Nitrospira defluvii, Candidatus Nitrospira Ecomare2 and Nitrospira inopinata. In summary, the strong nitrification activity was mainly catalyzed by AOB and Nitrospira, maintaining high efficiency in nitrogen removal in the anammox-inoculated WWTPs by providing the substrates required for denitrification and anammox processes.

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The long-term contribution of nitrification to nitrous oxide (N2 O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N2 O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N2 O, we test the relative importance of nitrification-derived N2 O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N2 O fluxes was 13%-17% in a conventionally fertilized annual cropping system, 27%-42% in a low-input cover-cropped annual cropping system, and 52%-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be <10% of these values because of low N2 O yields in cultured nitrifiers (typically 0.04%-8% of NH3 oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N2 O was produced by ammonia-oxidizing bacteria rather than archaea, who appeared responsible for no more than 30% of nitrification-derived N2 O production in all but one ecosystem. Although the proportion of nitrification-derived N2 O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N2 O (higher Vmax ) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N2 O in all ecosystems examined.

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Mangrove ecosystems are natural nitrogen removal systems that are primarily mediated by nitrogen cycle microorganisms, but their relative contributions to nitrogen transformation and removal in mangrove sediments under anthropogenic nitrogen input needs further resolution and characterization. Here, we investigated the responses and the relative contributions of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidizing (anammox) bacteria and denitrifying bacteria after spiking urea into mangrove sediments incubated in a laboratory microcosm experiment for four weeks. During incubation, the diversity, abundances and transcription levels of the hzo genes for anammox bacteria, amoA genes for AOA and AOB, and nirS genes for denitrifying bacteria were monitored using targeted gene clone library analyses and quantitative PCR assays at the DNA and RNA levels. The results showed that mangrove sediments harbour habitat-specific anammox bacteria which related to Candidatus Scalindua and Candidatus Kuenenia clades. Mangrove specific AOA related to deep branched clades within Candidatus Nitrososphaera and Candidatus Nitrosotalea, and AOB related to Nitrosomonas and Nitrosospira were also detected in the collected sediment samples. Growth and activity of AOA were detected at all levels of amendment of nitrogen input, whereas AOB growth was detectable only at the high-level nitrogen input (1.5 mg urea per gram of dry sediment) with no amoA transcripts and lower abundance than AOA. The abundance and transcription levels of the nirS gene were higher (~1000 times) than those of the hzo gene in all groups. Pearson correlation analysis demonstrated that the abundance of both AOA and AOB amoA genes had a significant positive correlation with the nirS gene (p < 0.01). These results indicated that nitrification (primarily mediated by the AOA)-denitrification process played the most important role in nitrogen removal from the amendment of nitrogen short-term input in the mangrove sediments.

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Ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as complete ammonia oxidizers (comammox) aerobically catalyze ammonia oxidation which plays essential roles in riverine nitrogen cycle. However, performances of these ammonia oxidizers in high-elevation river sediments have rarely been documented. This study investigated the abundance, community, and activity of ammonia oxidizers in five high-elevation rivers of the Qinghai-Tibet Plateau (QTP). Comammox were dominant ammonia oxidizers in 23% of studied samples and the clade B was principal comammox type. amoA gene abundances of AOA and AOB in these high-elevation rivers were comparable to those in low-elevation rivers. However, in contrast to most studied low-elevation rivers, AOB amoA gene abundance outnumbered AOA in 92% samples, which might be caused by the lower temperature and more intense solar radiation of the QTP. Potential nitrification rates (PNRs) ranged from 0.02 to 2.95 nmol-N h-1 g-1 dry sediment. Ammonia concentration was the limiting factor to PNRs at some sites, and when ammonia was not limiting, the PNR: ammonia ratio was greater at higher temperatures. There was no apparent variation in ammonia oxidizer community compositions along the elevation gradient due to the high elevation (2687 to 4223 m) of our entire study area. However, compared with low-elevation rivers, the lower temperature, huge diurnal temperature change, and lower nutrient conditions in the QTP rivers shaped distinctive communities for ammonia oxidizers; the unique community characteristics were significantly correlated to PNRs. These results suggest that ammonia oxidizers in the five high-elevation rivers have adapted to high-elevation conditions; more research should be conducted to study their adaptation mechanisms and their roles in riverine nitrogen cycle.

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Biological nitrogen removal (BNR) is a critical process in wastewater treatment. Recently, there have new microbial communities been discovered to be capable of performing BNR with novel metabolic pathways. This review presents the up-to-date status on these microorganisms, including ammonia oxidizing archaea (AOA), complete ammonia oxidation (COMAMMOX) bacteria, anaerobic ammonium oxidation coupled to iron reduction (FEAMMOX) bacteria, anaerobic ammonium oxidation (ANAMMOX) bacteria and denitrifying anaerobic methane oxidation (DAMO) microorganism. Their metabolic pathways and enzymatic reactions in nitrogen cycle are demonstrated. Generally, these novel microbial communities have advantages over canonical nitrifiers or denitrifiers, such as higher substrate affinities, better physicochemical tolerances and/or less greenhouse gas emission. Also, their recent development and/or implementation in BNR is discussed and outlook. Finally, the key implications of coupling these microbial communities for BNR are identified. Overall, this review illustrates novel microbial communities that could provide new possibilities for high-performance and energy-saving nitrogen removal from wastewater.

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The abundance of ammonia-oxidizing bacteria and archaea and their amoA genes from the aerobic activated sludge tanks, recycled sludge and anaerobic digesters of a full-scale wastewater treatment plant (WWTP) was determined. Polymerase chain reaction and denaturing gradient gel electrophoresis were used to generate diversity profiles, which showed that each population had a consistent profile although the abundance of individual members varied. In the aerobic tanks, the ammonia-oxidizing bacterial (AOB) population was more than 350 times more abundant than the ammonia-oxidizing archaeal (AOA) population, however in the digesters, the AOA population was more than 10 times more abundant. Measuring the activity of the amoA gene expression of the two populations using RT-PCR also showed that the AOA amoA gene was more active in the digesters than in the activated sludge tanks. Using batch reactors and ddPCR, amoA activity could be measured and it was found that when the AOB amoA activity was inhibited in the anoxic reactors, the expression of the AOA amoA gene increased fourfold. This suggests that these two populations may have a cooperative relationship for the oxidation of ammonia.

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Ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as comammox catalyze ammonia oxidation. The distribution and biogeography of these ammonia oxidizers might be distinctive in high-elevation rivers, which are generally characterized by low temperature and low ammonium concentration but strong solar radiation; however, these characteristics have rarely been documented. This study explored the abundance, community, and activity of ammonia oxidizers in the overlying water of five rivers in the Qinghai-Tibet Plateau (QTP). Potential nitrification rates in these rivers ranged from 5.4 to 38.4 nmol N liter-1 h-1, and they were significantly correlated with ammonium concentration rather than temperature. Comammox were found in 25 of the total 28 samples, and they outnumbered AOA in three samples. Contrary to most studied low-elevation rivers, average AOB amoA gene abundance was significantly higher than that of AOA, and AOB/AOA ratios increased with decreasing water temperature. The Simpson index of the AOA community increased with elevation (P < 0.05), and AOA and AOB communities exhibited high dissimilarities with low-elevation rivers. Cold-adapted (Nitrosospira amoA cluster 1, 33.6%) and oligotrophic (Nitrosomonas amoA cluster 6a, 31.7%) groups accounted for large proportions in the AOB community. Suspended sediment concentration exerted significant effects on ammonia oxidizer abundance (r > 0.56), and owing to their elevational variations in source and concentration, suspended sediments facilitated distance-decay patterns for AOA and AOB community similarities. This study demonstrates distinctive biogeography and distribution patterns for ammonia oxidizers in high-elevation rivers of the QTP. Extensive research should be conducted to explore the role of these microbes in the nitrogen cycle of this zone.IMPORTANCE Ammonia-oxidizing archaea (AOA) and bacteria (AOB) as well as comammox contribute to ammonia oxidation, which plays significant roles in riverine nitrogen cycle and N2O production. Source regions of numerous rivers in the world lie in high-elevation zones, but the abundance, community, and activity of ammonia oxidizers in rivers in high-elevation regions have rarely been investigated. This study revealed distinctive distribution patterns and community structures for ammonia oxidizers in five high-elevation rivers of the Qinghai-Tibet Plateau, and the individual and combined effects of low temperature, low nutrients, and strong solar radiation on ammonia oxidizers were elucidated. The findings of this study are helpful to broaden our knowledge on the biogeography and distribution pattern of ammonia oxidizers in river systems. Moreover, this study provides some implications to predict the performance of ammonia oxidizers in high-elevation rivers and its variations under global climate warming.

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Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.

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Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their differential contribution to nitrous oxide (N2O) production, particularly in greenhouse based high N input vegetable soils. Six N treatments (N1, N2, N3, N4, N5 and N6 representing 0, 293, 587, 880, 1173 and 1760 kg N ha-1 yr-1, respectively) were continuously managed for three years in a typically intensified vegetable field in China. The aerobic incubation experiment involving these field-treated soils was designed to evaluate the relative contributions of AOA and AOB to N2O production by using acetylene or 1-octyne as inhibitors. The results showed that the soil pH and net nitrification rate gradually declined with increasing the fertilizer N application rates. The AOA were responsible for 44-71% of the N2O production with negligible N2O from AOB in urea unamended control soils. With urea amendment, the AOA were responsible for 48-53% of the N2O production in the excessively fertilized soils, namely the N5-N6 soils, while the AOB were responsible for 42-55% in the conventionally fertilized soils, namely the N1-N4 soils. Results indicated that overdose fertilization induced higher AOA-dependent N2O production than AOB, whereas urea supply led to higher AOB-dependent N2O production than AOA in conventionally fertilized soils. Additionally, a positive relationship existed between N2O production and NO2- accumulation during the incubation. Further mechanisms for NO2--dependent N2O production in intensive vegetable soils therefore deserve urgent attention.

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Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors. AOA were more abundant than AOB in both young and matured revegetated forest soils in both summer and winter seasons. In summer, however, the abundance of amoA-AOA decreased remarkably (p < 0.01), ranging from 1.90 (± 0.07) × 108 copies per gram dry soil in matured forest to 5.04 (± 0.43) × 108 copies per gram dry soil in young forest, and amoA-AOB was below detection limits to obtain any meaningful values. Moreover, exchangeable Al3+ and organic matter were found to regulate the physiologically functional nitrifiers, especially AOA abundance in acidic forest soils. AOB community in winter showed stronger correlation with the restoration status of revegetated forests and AOA community dominated by Nitrosotalea devanaterra, in contrast, was more sensitive to the seasonal and spatial variations of environmental factors. These results enrich the current knowledge of nitrification during re-forestry and provide valuable information to developmental status of revegetated forests for management through microbial analysis.

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Ammonia oxidation, performed by both ammonia oxidizing bacteria (AOB) and archaea (AOA), is an important step for nitrogen removal in constructed wetlands (CWs). However, little is known about the distribution of these ammonia oxidizing organisms in CWs and the associated wetland environmental variables. Their relative importance to nitrification in CWs remains still controversial. The present study investigated the seasonal dynamics of AOA and AOB communities in a free water surface flow CW (FWSF-CW) used to ameliorate the quality of polluted river water. Strong seasonality effects on potential nitrification rate (PNR) and the abundance, richness, diversity and structure of AOA and AOB communities were observed in the river water treatment FWSF-CW. PNR was positively correlated to AOB abundance. AOB (6.76×105-6.01×107 bacterial amoA gene copies per gram dry sediment/soil) tended to be much more abundant than AOA (from below quantitative PCR detection limit to 9.62×106 archaeal amoA gene copies per gram dry sediment/soil). Both AOA and AOB abundance were regulated by the levels of nitrogen, phosphorus and organic carbon. Different wetland environmental variables determined the diversity and structure of AOA and AOB communities. Wetland AOA communities were mainly composed of unknown species and Nitrosopumilus-like organisms, while AOB communities were mainly represented by both Nitrosospira and Nitrosomonas.

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Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al3+ species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4+ equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al3+. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.

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The discovery that acetylene inhibited ammonia oxidation by Nitrosomonas europeae came about by studying linkages of microbial Nitrogen cycling processes in laboratory soil columns. Continuous addition of ammonium chloride (25 µg N/ml) to the soil columns resulted in steady state nitrification of all of the ammonia to nitrate. Acetylene (10.1 kPa) was introduced to detect nitrous oxide, a product of denitrification of nitrate, however, nitrification was inhibited and washout and disappearance of nitrate in the column effluent was detected. Concomitantly, ammonium levels in the effluent rose. Nitrification of nitrite was not affected by acetylene. Summary Acetylene inhibited the metalloenzyme, ammonia monooxygenase in the obligate chemoautotrophic nitrifier, Nitrosomonas europeae.

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Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 104 to 2.94 × 105 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 105 and 1.05 × 106 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH4+-N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.

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Acidic forest peat soil in Xiaoxing'an Mountain was used to investigate the type and key drivers of nitrification by carrying out nitrification incubation after adding 10 mL·L-1 C2H2 and different amounts of (NH4)2SO4(0, 1.2, 6.0 mmol N·kg-1). Results showed that strong mineralization (0.9-1.4 mg N·kg-1·d-1) and nitrification (0.4-0.6 mg N·kg-1·d-1) after 2 weeks of incubation were observed for both nitrogen and no nitrogen treatments, and no significant difference was observed for different (NH4)2SO4 application treatments. For C2H2 treatment, there was relatively stronger mineralization (0.8 mg N·kg-1·d-1), but no obvious nitrification (0 mg N·kg-1·d-1). These results indicated that the nitrification in acidic peat soil was mainly autotrophic, and inorganic nitrogen application did not affect nitrification rate significantly. Results also implied that the substrate (NH3) for nitrification was from the organic N mineralization, rather than the (NH4)2SO4 application. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) abundances increased significantly during 0-14 d regardless of nitrogen application. However, no significant difference in AOB and AOA abundances for different (NH4)2SO4 application treatments was observed, indicating that ammonia oxidizers did not respond positively to (NH4)2SO4 application. Compared with the treatments without C2H2, AOB and AOA abundances did not change significantly during the incubation in C2H2 treatment, suggesting that both AOA and AOB were likely the key players in nitrification in the acidic peat soil.

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In this study, the short-term effect of roxithromycin(ROX) on the abundance and diversity of ammonia-oxidizing archaea(AOA) and ammonia-oxidizing bacteria(AOB) based on amoA gene in activated sludge were investigated by high-throughput sequencing and quantitative real-time PCR(qPCR). High-throughput sequencing overcomes the drawbacks of low sequencing depth, significant randomness and great bias of traditional Sanger sequencing. This approach can provide enough sequencing depth to comprehensively investigate the sensitive and insensitive ammonia-oxidizing microorganisms under ROX selective pressure. Lab-scale reactors were operated under ten different ROX levels. The results indicated that the environmental(0.3-30 µg·L-1) and medium(300 µg·L-1and 3000 µg·L-1) levels of ROX did not affect ammonia oxidation, while the higher concentration(5000-12000 µg·L-1) of ROX showed a significant negative effect on ammonia oxidation. The environmental and medium levels of ROX stimulated the growth of AOA, however, the higher level of ROX decreased the abundance of AOA. In addition, different levels of ROX(except 0.3 µg·L-1) caused the decrease of the abundance of AOB, which suggested that AOA was less sensitive than AOB under ROX selective pressure. The results of high-throughput sequencing showed that ROX selective pressure caused the decrease of the numbers of OTUs for AOA and increase of that for AOB. The insensitive AOA, accounting for 57.70%-97.81% of the total sequences, were Candidatus Nitrososphaera gargensis and Candidatus Nitrosoarchaeum koreensis. The insensitive AOB were Nitrosomonas oligotropha, Nitrosospira multiformis, Nitrosomonas watsonii and Nitrosomonas halophilus, accounting for 0.76%-5.10% of the total sequences. These results also indicated that AOA was insensitive to ROX, but AOB was sensitive to ROX. RDA analyses showed that AOA Ca. Nitrososphaera gargensis, Ca. Nitrosoarchaeum koreensis and AOB N. oligotropha, N. watsonii, N. halophilus were positively correlated with ROX concentrations.

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Stream microbial communities and associated processes are influenced by environmental fluctuations that may ultimately dictate nutrient export. Discharge fluctuations caused by intermittent stream flow are increasing worldwide in response to global change. We examined the impact of flow cessation and drying on in-stream nitrogen cycling. We determined archaeal (AOA) and bacterial ammonia oxidizer (AOB) abundance and ammonia oxidation activity in surface and deep sediments from different sites along the Fuirosos stream (Spain) subjected to contrasting hydrological conditions (i.e., running water, isolated pools, and dry streambeds). AOA were more abundant than AOB, with no major changes across hydrological conditions or sediment layers. However, ammonia oxidation activity and sediment nitrate content increased with the degree of stream drying, especially in surface sediments. Upscaling of our results shows that ammonia oxidation in dry streambeds can contribute considerably (~50%) to the high nitrate export typically observed in intermittent streams during first-flush events following flow reconnection. Our study illustrates how the dry channels of intermittent streams can be potential hotspots of ammonia oxidation. Consequently, shifts in the duration, spatial extent and severity of intermittent flow can play a decisive role in shaping nitrogen cycling and export along fluvial networks in response to global change.

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