Search

Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

We lack empirical evidence for the relative importance of microbial functional attributes vs taxonomic attributes in regulating specified soil processes related to carbon (C) and nitrogen (N) cycling, which has hindered our ability to predict the responses of ecosystem multifunctionality to environmental changes. Here, we collected soil samples from a long-term experimental field with eight inorganic and organic fertilization treatments and evaluated the linkage between microbial functional attributes (abundance of functional genes), taxonomic attributes (microbial taxonomic composition), and soil processes including soil respiration, denitrification and nitrification. Long-term fertilization had no significant effect on the bacterial or fungal alpha-diversity. The treatments of chicken manure and sewage sludge addition significantly altered the rates of soil respiration, denitrification and nitrification, which were significantly correlated with the abundances of relevant functional genes. Random forest model indicated that the abundance of functional genes was the main diver for the rate of soil processes. The predominant effect of microbial functional attributes in driving soil processes was maintained when simultaneously accounting for multiple abiotic (total C, total N and soil pH) and biotic drivers (bacterial and fungal community structure), indicating that microbial functional attributes were the predominant driver predicting the rate of soil respiration, denitrification and nitrification. Our results suggested the importance of developing a functional gene-centric framework to incorporate microbial communities into biogeochemical models, which may provide new insights into the biodiversity-functions relationship and have implications for future management of the consequences of biodiversity loss for ecosystem multifunctionality., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Soil ecosystem represents the largest contributor to global nitrous oxide (N 2 O) production, which is regulated by a wide variety of microbial communities in multiple biological pathways. A mechanistic understanding of these N 2 O production biological pathways in complex soil environment is essential for improving model performance and developing innovative mitigation strategies. Here, combined approaches of the 15 N- 18 O labelling technique, transcriptome analysis, and Illumina MiSeq sequencing were used to identify the relative contributions of four N 2 O pathways including nitrification, nitrifier-induced denitrification (nitrifier denitrification and nitrification-coupled denitrification) and heterotrophic denitrification in six soils (alkaline vs. acid soils). In alkaline soils, nitrification and nitrifier-induced denitrification were the dominant pathways of N 2 O production, and application of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) significantly reduced the N 2 O production from these pathways; this is probably due to the observed reduction in the expression of the amoA gene in ammonia-oxidizing bacteria (AOB) in the DMPP-amended treatments. In acid soils, however, heterotrophic denitrification was the main source for N 2 O production, and was not impacted by the application of DMPP. Our results provide robust evidence that the nitrification inhibitor DMPP can inhibit the N 2 O production from nitrifier-induced denitrification, a potential significant source of N 2 O production in agricultural soils., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)

To investigate the effect of moisture change on nitrification and denitrification and their corresponding functional microbes, an acidic paddy soil from Taoyuan, Hunan Province was selected as the study object, and soil microcosm experiment containing 4 different water holding capacity (WHC) levels (30% WHC, 60% WHC, 90% WHC, and waterlog) was set up in this study. Results showed that no active nitrification and denitrification occurred in 30% WHC treatment as there were no obvious ammonia consumption and nitrate accumulation, while nitrification was active in 60% WHC and 90% WHC treatments as indicated by the obvious accumulation of nitrate in those two treatments. Meanwhile, significant ammonia consumption and N2O emission were only observed in 90% WHC treatment, implying that a much stronger nitrification in 90% WHC treatment than in 60% WHC treatment and the co-occurrence of nitrification and denitrification in 90% WHC treatment. In waterlog treatment, relatively lower N2O emission was detected and no obvious nitrification was detected, corresponding to a significant lower soil Eh in this treatment than in the other three non-waterlog treatments. Except the early stage of incubation (7 d), the abundance of nirS, nirK and ammonia-oxidizing bacteria (AOB) amoA genes showed similar responses to soil moisture change over time. Except the slight decrease in waterlog treatment, the abundances of the three genes increased significantly as the soil moisture increased, and the highest abundances of nirS, nirK, and amoA gene were observed in 90% WHC treatment in which the highest nitrification and denitrification activity was detected. T-RFLP analysis showed that the community composition of nirS gene-containing denitrifiers changed significantly in response to soil moisture change after two weeks, and soil Eh and C(w) were the main factors affecting the community composition of denitrifiers.

The low utilization efficiency of nitrogen fertilizer in agricultural ecosystem has caused serious economic and environmental issues. Dicyandiamide (DCD) is a widely used nitrification inhibitor, which can inhibit nitrification via affecting ammonia oxidizing microorganisms with minimal influence on other soil microorganisms, thereby reducing the leaching of nitrate and emission of greenhouse gases. The factors influencing the efficiency of DCD in soil include soil temperature, pH, texture, organic matter, moisture, etc. Recently, the application of molecular methods in agricultural systems has shed new light on the microbial mechanism underlying nitrification inhibition by DCD. In this review, the enzymatic inhibition mechanism, the application effects and their influence factors of DCD were summarized, and the prospects of its application were discussed as well.

Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. (13)CO(2)-DNA-stable isotope probing results showed significant assimilation of (13)C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO(2) fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active (13)CO(2)-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.

During the past decades, extensive nitrogen fertilization and acid deposition have greatly contributed to soil acidification in agroecosystems. Liming, the addition of calcium- and magnesium-rich material to soil, is an effective management strategy used to improve fertility and productivity of agricultural soils degraded by acidification. Nitrification plays a central role in nitrogen (N) availability in agroecosystems and contributes to soil acidification. However, little is known regarding the effects of liming on this process and microbial populations that drive it. Here, we investigated population dynamics and activity of ammonia oxidizers in response to a 2-year liming field trial in acidic soils received long-term fertilization with chemical N fertilizers and short-term lime amendment in microcosm incubations. Our results showed that activity, abundance and population structure of both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were sensitive to liming in fertilized acidic soils. AOB abundance and potential nitrification rates increased in field plots subjected to liming, whereas the opposite was observed for AOA. In microcosm incubations, AOA abundance increased progressively over 60 days, namely under low CaO levels, whereas AOB abundance was greatly stimulated only during the first week under high CaO levels. 13CO2-SIP-DNA experiments further supported that AOA were the most active ammonia oxidizers in fertilized field soils. However, in N-fertilized soils freshly amended with CaO, only autotrophic growth of AOB was observed after seven days, but not after 30 days when growth of AOA was observed. Taken together, our results indicated that both AOA and AOB play a role in nitrification following liming in fertilized acidic soils, likely through selection of better adapted clades of organisms. Although AOA were likely the main drivers of nitrification in these soils in the long-term, liming stimulated AOB activity in the short-term.

The discovery of complete ammonia oxidizers, comammox Nitrospira, represents a breakthrough in the history of nitrification research. Nitrospira inopinata, which was obtained from an aquatic ecosystem, is the only pure comammox bacterial isolate reported so far. Ammonia oxidation kinetics of N. inopinata indicated that they prefer an oligotrophic lifestyle and may directly compete with ammonia-oxidizing archaea (AOA), but representatives of comammox Nitrospira from terrestrial ecosystems are lacking. Current studies demonstrate that the functionally dominant comammox Nitrospira in terrestrial ecosystems are separated from most sequences obtained from aquatic and engineering systems. Clades A and B of comammox Nitrospira seemingly have different ecological preferences in soils, possibly due to their different ammonium uptake systems. Analyses of the evolutionary history indicate that some genes of comammox Nitrospira involved in ammonia oxidation could be laterally transferred from β-ammonia-oxidizing bacteria (AOB). Some comammox Nitrospira species may have similar ecological preferences with AOB and be functionally active in the niches where nitrification was previously considered to be dominated by AOB. Taken together, this review summarizes the recent findings of the biogeographical distribution and ecological preference of comammox Nitrospira in large-scale soil surveys, the responses of comammox Nitrospira to nitrogen application in soil, and the putative mechanisms underpinning the ecological niche of terrestrial comammox Nitrospira. These studies from terrestrial ecosystems suggest that comammox Nitrospira are not strictly oligotrophic but both oligotrophic and copiotrophic with a broader ecological niche breadth. Comammox Nitrospira in terrestrial ecosystems are abundant and active in both oligotrophic and copiotrophic environments. These findings have profoundly expanded our knowledge of the environmental niches of comammox Nitrospira and their relative contribution to nitrification in soils. [ABSTRACT FROM AUTHOR]

Purpose: The discovery of comammox Nitrospira being capable of complete oxidising ammonia to nitrate radically challenged the conventional concept of two-step nitrification. However, the response of comammox Nitrospira to nitrification inhibitors (NIs) and their role in soil nitrification remain largely unknown, which has hindered our ability to predict the efficiency of NIs in agroecosystems. Materials and methods: We evaluated the effect of four NIs, 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin), 3,4-dimethylpyrazole phosphate (DMPP), allylthiourea (ATU) and dicyandiamide (DCD) on the growth of comammox Nitrospira, ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in two pasture and arable soils. Results and discussion: The amendment of nitrogen fertiliser significantly increased soil nitrate concentrations over time, indicating a sustaining nitrification activity in both soils. The addition of all the four NIs effectively reduced the production of nitrate in both soils, but to varying degrees during incubation. The abundances of comammox Nitrospira clade A were significantly increased by addition of nitrogen fertilisers and significantly impeded by the four NIs in the pasture soil, but their abundances were only remarkably hindered by nitrapyrin in the arable soil. All the four NIs obviously inhibited the AOB abundances in both soils. Except for DMPP, the other three NIs effectively suppressed the AOA abundances in both soils. Conclusions: We provided new evidence that growth of comammox Nitrospira clade A can be stimulated by nitrogen fertilisers and inhibited by various nitrification inhibitors, suggesting their potential role in nitrification of agricultural soils. [ABSTRACT FROM AUTHOR]

Purpose: Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, is a pivotal component of the biogeochemical nitrogen cycle. Nitrification was conventionally assumed as a two-step process in which ammonia oxidation was thought to be catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria (NOB). This long-held assumption of labour division between the two functional groups, however, was challenged by the recent unexpected discovery of complete ammonia oxidizers within the Nitrospira genus that are capable of converting ammonia to nitrate in a single organism (comammox). This breakthrough raised fundamental questions on the niche specialization and differentiation of comammox organisms with other canonical nitrifying prokaryotes in terrestrial ecosystems. Materials and methods: This article provides an overview of the recent insights into the genomic analysis, physiological characterization and environmental investigation of the comammox organisms, which have dramatically changed our perspective on the aerobic nitrification process. By using quantitative PCR analysis, we also compared the abundances of comammox Nitrospira clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a wide range of soil pH. Results and discussion: Comammox Nitrospira are environmentally widespread and numerically abundant in natural and engineered habitats. Physiological data, including ammonia oxidation kinetics and metabolic versatility, and comparative genomic analysis revealed that comammox organisms might functionally outcompete other canonical nitrifiers under highly oligotrophic conditions. These findings highlight the necessity in future studies to re-evaluate the niche differentiation between ammonia oxidizers and their relative contribution to nitrification in various terrestrial ecosystems by including comammox Nitrospira in such comparisons. Conclusions: The discovery of comammox and their broad environmental distribution added a new dimension to our knowledge of the biochemistry and physiology of nitrification and has far-reaching implications for refined strategies to manipulate nitrification in terrestrial ecosystems and to maximize agricultural productivity and sustainability. [ABSTRACT FROM AUTHOR]

Purpose: Nitrous oxide (NO) is a trace gas and is mainly produced through the microbial-mediated nitrification and denitrification processes in agricultural soils. Dicyandiamide (DCD) is a powerful nitrification inhibitor (NI) which can mitigate NO production from soil. However, it remains poorly understood how NO emission and associated microbes are affected by DCD application across different agricultural soils. Materials and methods: Here, we carried out a 21-day laboratory microcosm incubation experiment to examine the impact of ammonium sulfate and DCD applications on NO production and the abundance of nitrifiers and denitrifiers in two contrasting agricultural soils. The abundance of the functional genes was quantified by quantitative PCR to investigate the population changes in response to ammonium sulfate and DCD addition. Results and discussion: Higher NO production emitted followed the application of ammonium sulfate (287.9 ng NO-N g soil) in the alluvial soil was obtained compared to that (84.9 ng NO-N g soil) in the red soil. The average NO emission rate in the NH treatment from the alluvial soil was significantly higher than that from the red soil, and DCD addition remarkably reduced NO emission rates in both soils during the 21-day incubation. We also observed that the abundance of ammonia-oxidizing bacteria (AOB) amoA gene and the nirK gene was positively correlated with total NO emissions in the alluvial soil, but only AOB amoA gene abundance was significantly related to the total NO emissions in the red soil. Conclusions: These results suggested that DCD was more effective in inhibiting NO production in the alluvial soil than in the red soil. DCD could effectively reduce NO emission by suppressing the growth of microorganisms containing AOB amoA gene and the nirK gene in the alluvial soil. [ABSTRACT FROM AUTHOR]

Nitrification is believed to be one of the major sources of NO production emitted from soil. Previous studies showed that both ammonia-oxidising bacteria (AOB) and archaea (AOA) can produce NO via nitrification but their relative contributions are still poorly defined. Here, we used acetylene, an inhibitor of AOB and AOA ammonia monooxygenase (AMO), and 1-octyne, a selective inhibitor that specifically inhibits AOB AMO, to investigate how AOB versus AOA contribute to NO emissions in two distinct arable soils. Soil amended with ammonium (NH ) increased NO emissions to a greater extent than nitrate (NO ), and acetylene had a greater impact on NO emissions in NH -treated soils than that in NO -amended soils, which indicated that nitrification was the dominant NO emitting process in these two arable soils. In the alluvial and red soil, the percentage of evolved NO after application of NH by AOB were 70.5 ~ 78.1 % and 18.7 ~ 19.7 % by AOA, respectively. Quantitative PCR revealed that NH addition stimulated AOB growth, and the growth could be significantly inhibited by acetylene or 1-octyne in the two soils. The stimulation of NO emissions by NH and the relative suppression by inhibitors paralleled fluctuations in the AOB growth. In addition, cumulative NO emissions were not correlated with AOA abundance in the two soils. Our results revealed that AOB could contribute more to soil NO production than AOA in the NH -amended arable soils. [ABSTRACT FROM AUTHOR]

Currently, rice straw return in place of burning is becoming more intensive in China than observed previously. However, little is known on the effect of returned rice straw on mercury (Hg) methylation and microbial activity in contaminated paddy fields. Here, we conduct a microcosm experiment to evaluate the effect of rice straw amendment on the Hg methylation and potential nitrification in two paddy soils with distinct Hg levels. Our results show that amended rice straw enhanced Hg methylation for relatively high Hg content soil, but not for low Hg soil, spiking the same additional fresh Hg. methylmercury (MeHg) concentration was significantly correlated to the dissolved organic carbon (DOC) content and relative abundance of dominant microbes associated with Hg methylation. Similarly, amended rice straw was found to only enhance the potential nitrification rate in soil with relatively high Hg content. These findings provide evidence that amended rice straw differentially modulates Hg methylation and nitrification in Hg contaminated soils possibly resulting from different characteristics in the soil microbial community. This highlights that caution should be taken when returning rice straw to contaminated paddy fields, as this practice may increase the risk of more MeHg production. Main finding Rice straw amendment enhanced both Hg methylation and nitrification potential in the relatively high, but not low, Hg soil. [ABSTRACT FROM AUTHOR]

Terrestrial arid and semi-arid ecosystems (drylands) constitute about 41% of the Earth's land surface and are predicted to experience increasing fluctuations in water and nitrogen availability. Mounting evidence has confirmed the significant importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in nitrification, plant nitrogen availability and atmospheric N2O emissions, but their responses to environmental perturbations in drylands remain largely unknown. Here we evaluate how the factorial combinations of irrigation and fertilization in forests and land-use change from grassland to forest affects the dynamics of AOA and AOB following a 6-year dryland field study. Potential nitrification rates and AOA and AOB abundances were significantly higher in the irrigated plots, accompanied by considerable changes in community compositions, but their responses to fertilization alone were not significant. DNA-stable isotope probing results showed increased 13CO2 incorporation into the amoA gene of AOA, but not of AOB, in plots receiving water addition, coupled with significantly higher net mineralization and nitrification rates. High-throughput microarray analysis revealed that active AOA assemblages belonging to Nitrosopumilus and Nitrosotalea were increasingly labelled by 13CO2 following irrigation. However, no obvious effects of land-use changes on nitrification rates or metabolic activity of AOA and AOB could be observed under dry conditions. We provide evidence that water addition had more important roles than nitrogen fertilization in influencing the autotrophic nitrification in dryland ecosystems, and AOA are increasingly involved in ammonia oxidation when dry soils become wetted. [ABSTRACT FROM AUTHOR]

Purpose: Human disturbance is a major culprit driving imbalances in the biological transformation of nitrogen from the nonreactive to the reactive pool and is therefore one of the greatest concerns for nitrogen (N) cycling. The objective of this study was to compare potential nitrification rates and the abundance of ammonia oxidizers responsible for nitrification, with the amendment of external N in different agricultural soils. Materials and methods: Three typical Chinese agricultural soils, QiYang (QY) acid soil, ShenYang (SY) neutral soil, and FengQiu (FQ) alkaline soil, were amended with 0, 20, 150, and 300 μg NH-N g soil and incubated for 40 days. The abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) at the end of incubation in the soil microcosms was determined using the real-time PCR. Results and discussion: There was a significant decrease in ammonium concentration in the QY soil from the highest to the lowest N-loading treatments, while no significant difference in ammonium concentrations was detected among the different N-loading treatments for the SY and FQ soils. A significantly higher potential nitrification rate (PNR) was observed in the FQ soil while lowest PNR was found in the QY soil. Quantitative PCR analysis of AOB amoA genes demonstrated that AOB abundance was significantly higher in the high N-loading treatments than in the control for the QY soil only, while no significant difference among treatments in the SY and FQ soils. A significant positive correlation between PNR and AOB amoA abundance, however, was found for the SY and FQ soils, but not for the QY soil. Little difference in AOA amoA abundance between different N-loading treatments was observed for all the soils. Conclusions: This study suggested that ammonia oxidation capacity in the FQ and SY soils was higher than those in the QY soil with the addition of ammonium fertilizer for a short-term. These findings indicated that understanding the differential responses of biological nitrification to varying input levels of ammonium fertilizer is important for maximizing N use efficiency and thereby improving agricultural fertilization management. [ABSTRACT FROM AUTHOR]

Purpose: The nitrification inhibitor dicyandiamide (DCD) has been shown to be highly effective in reducing nitrate (NO) leaching and nitrous oxide (NO) emissions when used to treat grazed pasture soils. However, there have been few studies on the possible effects of long-term DCD use on other soil enzyme activities or the abundance of the general soil microbial communities. The objective of this study was to determine possible effects of long-term DCD use on key soil enzyme activities involved in the nitrogen (N) cycle and the abundance of bacteria and archaea in grazed pasture soils. Materials and methods: Three field sites used for this study had been treated with DCD for 7 years in field plot experiments. The three pasture soils from three different regions across New Zealand were Pukemutu silt loam in Southland in the southern South Island, Horotiu silt loam in the Waikato in the central North Island and Templeton silt loam in Canterbury in the central South Island. Control and DCD-treated plots were sampled to analyse soil pH, microbial biomass C and N, protease and deaminase activity, and the abundance of bacteria and archaea. Results and discussion: The three soils varied significantly in the microbial biomass C (858 to 542 μg C g soil) and biomass N (63 to 28 μg N g), protease (361 to 694 μg tyrosine g soil h) and deaminase (4.3 to 5.6 μg NH g soil h) activity, and bacteria (bacterial 16S rRNA gene copy number: 1.64 × 10 to 2.77 × 10 g soil) and archaea (archaeal 16S rRNA gene copy number: 2.67 × 10 to 3.01 × 10 g soil) abundance. However, 7 years of DCD use did not significantly affect these microbial population abundance and enzymatic activities. Soil pH values were also not significantly affected by the long-term DCD use. Conclusions: These results support the hypothesis that DCD is a specific enzyme inhibitor for ammonia oxidation and does not affect other non-target microbial and enzyme activities. The DCD nitrification inhibitor technology, therefore, appears to be an effective mitigation technology for nitrate leaching and nitrous oxide emissions in grazed pasture soils with no adverse impacts on the abundance of bacteria and archaea and key enzyme activities. [ABSTRACT FROM AUTHOR]

Abstract: Recent studies of ammonia-oxidizing archaea (AOA) suggested their significant contributions to global nitrogen cycling, and phylogenetic analysis categorized AOA into a novel archaeal phylum, the Thaumarchaeota. AOA are ubiquitous in terrestrial ecosystems, have unique mechanisms for nitrification, better adaptation to low-pH pressures, and strikingly lower ammonia requirements compared with ammonia-oxidizing bacteria (AOB). Previous perceptions that microbial ammonia oxidation in acidic soils was minimal, and entirely meditated by autotrophic bacteria and occasionally by heterotrophic nitrifiers have been dramatically challenged, and the dominant nitrifying groups urgently called for re-assessment. Controversially, the relative contributions of AOA and AOB to autotrophic ammonia oxidation have been reported to vary in different soils, but ammonia substrate availability, which was largely restricted under acidic conditions, seemed to be the key driver. Theoretically predicted ammonia concentrations in acidic soils below the substrate threshold of AOB and remarkably high ammonia affinity of AOA raised the supposition that thaumarchaea could represent the dominant ammonia-oxidizing group in ammonia-limited acidic environments. Recently, the functional dominance of thaumarchaea over its bacterial counterpart and autotrophic thaumarchaeal ammonia oxidation in acidic soils has been compellingly confirmed by DNA-stable isotope probing (SIP) experiments and the cultivation of an obligate acidophilic thaumarchaeon, Nitrosotalea devanaterra. Here, we review the currently available knowledge concerning the history and progress in our understanding of the ammonia-oxidizing microorganisms (AOB and AOA) and the mechanisms of nitrification in nutrient-depleted acidic soils, present the possible mechanisms shaping the distinct niches of AOA and AOB, and thus strengthen the assumption that AOA dominate over AOB in ammonia oxidation of acidic soils. [Copyright &y& Elsevier]

Summary Ammonia-oxidizers play a key role in nitrification, which is important for nitrogen cycling and soil function. However, little is known about how vegetation successions and agricultural practices caused by human activities impact the ammonia-oxidizers and nitrification process. Putative ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities under different land utilization patterns of restoration (forest), degradation (pasture), cropland and pine plantation were analysed in an acidic red soil based on bacterial and archaeal amoA genes together with archaeal 16S rRNA gene. Real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries were conducted to study their abundance and community structure. Land utilization pattern showed significant effects on the copy numbers of all these genes, but only the bacterial amoA gene correlated significantly with potential nitrification rates (PNR). The cropland plot possessed the highest bacterial amoA gene copies and PNR, while the degradation plot was opposite to that. There were no significant variations in the bacterial amoA gene structure, which was dominated by Clusters 10 and 11 in Nitrosospira. However, archaeal amoA gene structure varied among different land utilization patterns especially for the cropland. The degradation plot was dominated by Crenarchaea 1.1c-related groups from which the amoA gene could not been amplified in this study, while other plots were dominated by Crenarchaea 1.1a/b group based on archaeal 16S rRNA gene analysis. These results indicated significant effects of land utilization patterns on putative ammonia oxidizers, which were especially obvious in the degradation and cropland plots where frequent human disturbance occurred. [ABSTRACT FROM AUTHOR]

Abstract Long-term field fertilization trials have suggested that reduced chemical nitrogen (N) plus organic fertilization can effectively reduce N loss without sacrificing crop yield, while the knowledge of how organic fertilizers regulate soil microorganisms and their function in N transformation are limited. In this study, the response of net nitrification rate and the ammonia-oxidizer community within soil aggregates to long-term combined organic N and reduced chemical N fertilization was evaluated to understand the underlying mechanism of the practice in mitigating soil N loss. The fertilization experiment included an unfertilized control; chemical N fertilizer (N), superphosphate (P) and potassium sulfate (K) fertilizer (NPK); NPK plus straw (NPKS); and NPK plus manure (NPKM). The results showed that the large macro-aggregates mass (>2 mm) in soil significantly increased from 34.1% in NPK to 47.2% in NPKS (P < 0.05). NPKS and NPKM both had positive effects on soil moisture retention, total N (TN), soil organic carbon (SOC), ammonium (NH 4 +-N) and nitrate (NO 3 −-N) accumulation, particularly within micro- (<0.25 mm) and small macro-aggregates. Compared with the NPK treatment, soil net nitrification rate (NNR) and ammonia-oxidizing bacterial (AOB) abundance decreased by 67.1% and 40.7% respectively under NPKS (P < 0.05), and the decrease mainly appeared in large macro-aggregate and micro-aggregates. The net nitrification rate was significantly correlated with ammonia-oxidizing archaea (AOA) abundance only in small macro-aggregates (r = 0.642, n = 12, P < 0.05). In contrast, NRR was positively correlated with AOB abundance within small macro- and micro-aggregate size classes (r values ranged from 0.654 to 0.813, P < 0.05). The community structure of AOB varied among different fertilization treatments, while AOA community differentiation was mainly dependent on aggregate size. The shift of the AOA and AOB communities corresponded with high moisture and lower ammonia content in the large macro-aggregates and were potentially responsible for the suppressed nitrification activity in the NPKS treatment. These results indicated that reduced chemical N plus organic fertilization is beneficial for increasing N concentration in large macro-aggregates. Highlights • Long-term combined organic and reduced chemical fertilization (NPKS and NPKM) significantly improved soil aggregation. • Nitrification and AOB abundance were significantly suppressed in NPKS, particularly in its large macro-aggregates. • The shift of nitrifiers communities among three soil aggregates contributed to the suppressed nitrification activity. [ABSTRACT FROM AUTHOR]

Abstract: Acid soils, extensively used for nitrogen-fertilized agriculture and agroforestry, have important roles in maintaining global biogeochemical cycling and ecosystem functions. Huge inputs of nitrogen-based fertilizers into terrestrial ecosystems accelerate soil acidification, concomitantly altering the nitrogen transformation processes. Nitrification, as a critical component of the nitrogen cycle, is a microbially mediated process from ammonia to nitrate via nitrite, contributing to enormous losses of fertilizers through atmospheric emissions of greenhouse gas N2O and nitrate leaching to groundwater. However, the functionally dominant nitrifiers and underlying mechanisms for the acid soil nitrification are a long-standing mystery, which have confused scientists for more than 100 years. This century-long paradox originated from the early observations of active nitrification activity in acid soils, intensified by the failure of ammonia-oxidizing bacteria (AOB) cultures to sustain the nitrification in liquid batch under acid conditions, might be resolved by the recent progress in metagenomic, isotopic probing studies, and isolation of acidophilic ammonia-oxidizing archaea (AOA). Emerging evidence led to the supposition of the predominant role of AOA in controlling the autotrophic ammonia oxidation of acid soils, which has radically revised the previous perception that this oxidative reaction was exclusively regulated by autotrophic AOB and occasionally by heterotrophic nitrifiers. In this chapter, we review the recent progress in our understanding of the pH-impacted distribution of ammonia oxidizers, the niche differentiation of AOA and AOB shaped by acid stress, and the possible mechanisms of autotrophic nitrification in acid soils. The unveiling of this key process in widely distributed acid soils would help to identify effective biological strategies for better management of terrestrial nitrogen turnover and balance. [Copyright &y& Elsevier]

• Succession of soil ammonia oxidizing microorganisms during glacier degradation. • Nitrification related gene abundance tended to increase with glacier retreat. • Comammox were the most abundant group of ammonia oxidizers in glacier forelands. This study investigated the abundance of comammox bacteria and canonical ammonia-oxidizing bacteria (AOB) and archaea (AOA), and their relative contribution to nitrification along a chronosequence of deglaciated forelands. The results showed that nitrification related gene abundance tended to increase with glacier retreat, with comammox bacteria and AOA appearing to be the most critical drivers for soil nitrification rates. These findings provide new evidence for the presence of comammox bacteria in glacier forelands and enhance our understanding of the niche differentiation of canonical nitrifier and comammox bacteria. [ABSTRACT FROM AUTHOR]

Abstract The new discovery of complete ammonia oxidizers (comammox), single organisms capable of oxidizing ammonia into nitrate, redefined the traditional view of nitrification. However, little is known about the relative contributions of comammox and other nitrifiers to nitrification, particularly in agricultural soils with long-term intensive input of nutrients. Herein, we investigated the communities of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and comammox Nitrospira in agricultural soils under nutrients input gradient of nitrogen (0–675 kg N ha−1 year−1), phosphorus (0–405 kg P 2 O 5 ha−1 year−1), and potassium (0–675 kg K 2 O ha−1 year−1) fertilizers for 19 years. The results showed that N and K fertilizers input significantly (P < 0.05) increased the AOB- amoA gene abundance, while AOA were not as sensitive as AOB. The comammox- amoA gene copies were increased in all fertilizer treatments and was significantly correlated (P < 0.05) with the amount of N fertilizer added. Terminal restriction fragment length polymorphism (T-RFLP) combined with clone-library assays of comammox- amoA gene showed that increasing gradient of nutrients input increased the relative abundance of 73 bp T-RF (assigned to Clade A) but decreased the relative abundance of 198 bp T-RF (representing Clade B). Correlation analyses and stepwise linear regression analyses demonstrated that AOB were the dominate contributors to soil potential nitrification, while comammox Nitrospira did not play a significant role (P > 0.05). This study provided insights into the adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations and their relative contributions to potential nitrification in arable soils. Graphical abstract Unlabelled Image Highlights • Long-term fertilizers inputs increased the abundance of comammox. • Specific comammox clades responded distinctly to fertilizers inputs. • Comammox played a less important role in soil nitrification than AOB. • The abundance of AOB increased with the gradients of fertilizers inputs. [ABSTRACT FROM AUTHOR]

The recent discovery of comammox Nitrospira capable of converting ammonia to nitrate in a single organism radically challenged our century-long perception of the classic two-step nitrification performed by ammonia oxidizers and nitrite oxidizers. However, our understanding of the niche separation of comammox Nitrospira and canonical nitrifiers in forest ecosystems remains limited, especially under a global scenario of elevated nitrogen (N) deposition. Here we evaluated the impacts of six-year N deposition on the dynamics of comammox Nitrospira , ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a subtropical forest soil. Soil inorganic N concentrations significantly increased under the six-year simulation of N deposition, while soil pH, available phosphorus, total carbon (C), C/N ratio and microbial biomass significantly decreased. Quantitative PCR showed that the amoA gene abundances of comammox Nitrospira clade B and AOA substantially increased under the increasing rates of N deposition. By contrast, the AOB amoA gene abundance significantly decreased with the higher levels of N deposition (100 and 150 kg N ha−1 yr−1). Increased 13CO 2 incorporation into the AOA communities, rather than comammox Nitrospira or AOB, was demonstrated in a DNA-stable isotope probing microcosm, indicative of the capacity of AOA to assimilate 13CO 2 through autotrophic nitrification in the investigated subtropical forest soil under long-term N deposition. Phylogenetic analysis revealed that the autotrophic AOA assemblages belonged to the Nitrosotalea cluster, and their capacity for assimilating CO 2 through autotrophic nitrification was not affected by the long-term N deposition. Taken together, we provided new evidence for the niche separation of comammox Nitrospira and canonical ammonia oxidizers in soil nitrification under the long-term N deposition in the acidic subtropical forest soil. Highlights • The abundances of comammox Nitrospira clade B and AOA increased with N input. • The abundance of AOB decreased with N input rates higher than 100 kg N ha−1 yr−1. • Increased 13CO 2 was only incorporated into soil AOA through autotrophic pathway. • N input showed no effect on autotrophic AOA within the Nitrosotalea cluster. [ABSTRACT FROM AUTHOR]

Organic fertilizers are frequently applied to soils to improve soil multifunctionality and maintain crop productivity in agricultural practices. However, how organic fertilizations influence soil nitrous oxide (N 2 O) emissions remains ambiguous, especially considering their linkage with the abundance of nitrogen (N)-cycling microorganisms. Here, we conducted an incubation experiment to examine the effect of partial replacement of mineral fertilizers with organic fertilizers on the abundance of N-cycling functional genes and N 2 O emissions at 60 % and 100 % water-filled pore space (WFPS) in an acidic Ultisol. Soil samples were collected from 32-year fertilization trials, including four treatments of control (no fertilizer), mineral NPK fertilizer (NPK), NPK + Peanut Straw (NPKS), and NPK + Pig Manure (NPKM). The N 2 O emissions from soils incubated at 100 % WFPS were significantly higher than those at 60 % WFPS in all treatments. Compared with NPK, NPKS and NPKM reduced N 2 O emissions, with a more pronounced effect in NPKM. The N 2 O flux was positively associated with the abundance of AOA and AOB amoA genes, and the abundance ratio of amoA / nosZ (i.e., the ratio of AOA amoA plus AOB amoA and nosZ І plus nosZ ІІ) when the peak N 2 O flux appeared. Random forest analysis showed that the abundance ratio of amoA / nosZ was the best predictor for N 2 O emissions. Compared with NPK, NPKM increased soil pH but reduced the abundance ratio of amoA / nosZ , which might be the key factor in reducing N 2 O emissions. Together, our findings suggested that long-term manure application reduced N 2 O emissions by decreasing the abundance ratio of amoA / nosZ and provided novel insights into the impact of organic fertilizers on N 2 O emissions in acidic agricultural soils. • N 2 O emissions are higher in soils incubated at 100 % WFPS than at 60 % WFPS. • Partial replacement of mineral fertilizers with pig manure reduces soil N 2 O emissions. • N 2 O emissions are positively associated with the abundance ratio of amoA / nosZ. • Manure application increases soil pH and reduces the abundance ratio of amoA / nosZ. [ABSTRACT FROM AUTHOR]

Long-term lime and manure amendment can alleviate soil acidification, but their impacts on nitrous oxide (N 2 O) emissions and their production pathways remain largely unclear. Here, a 15N tracing study was conducted to explore the effect of lime and manure amendment on N 2 O production pathways and gross nitrogen (N) transformation rates of an acidic Ultisol. Soils were sampled from a 33-year field fertilization experiment, including three treatments of mineral NPK fertilizer (NPK), NPK plus lime (NPKL), and NPK plus manure (NPKM). Compared to NPK, N 2 O emissions increased by 25.2% for NPKL but decreased by 22.1% for NPKM, indicating that different pH-raising substances may have different effects on N 2 O emissions. The 15N tracing analysis indicated that heterotrophic nitrification-derived N 2 O played a dominant role in N 2 O emissions while NPKL significantly increased autotrophic nitrification-derived N 2 O production. The increased relative contribution of autotrophic nitrification to N 2 O emissions by NPKL resulted in an increase of N 2 O emissions in the acidic Ultisol. In contrast, NPKM decreased heterotrophic nitrification and autotrophic nitrification-derived N 2 O production, leading to a decrease of N 2 O emissions. Our results show that lime and manure amendment can have different impacts on N 2 O emissions due to their differential effects on autotrophic and heterotrophic nitrification, providing important insights for the sustainable management of acidic arable soils. • Liming increased N 2 O emissions while manure amendment decreased N 2 O emissions. • Heterotrophic nitrification played a dominant role in N 2 O emissions from acidic Ultisols. • Liming increased N 2 O emissions through increasing autotrophic nitrification. • Manure amendment reduced N 2 O emissions by suppressing heterotrophic nitrification. [ABSTRACT FROM AUTHOR]

The newly discovered comammox Nitrospira has fundamentally overturned the perception of labor division in nitrification and attracted growing interests in the niche preferences of comammox Nitrospira in soils. Here, we investigated the abundance and community structure of comammox Nitrospira in an acidic Ultisol which received the fertilizers continuously for 32 years. Fertilization treatments included chemical nitrogen (N), phosphorus (P), and potassium (K) fertilizers (NPK), NP, NK, PK, and NPK plus peanut straw, rice straw, radish residue or pig manure. Our results revealed that comammox Nitrospira were undetectable in the NK, which was excluded from further analysis. Compared with NPK, NPK plus pig manure significantly increased the abundance of comammox Nitrospira clade A, while the other treatments did not. Available P was the most important factor positively associated with the abundance of clade A. In contrast, soil pH was the best predictor for the variation of comammox Nitrospira community structure, which was distinctly separated by three groups: PK, NPK plus pig manure and the other treatments. Four comammox Nitrospira clusters were identified: clades A.2.1, A.2.2, B.1, and B.2. Of these clusters, clade A.2.1 accounted for 100% of the comammox Nitrospira sequences in NPK, whereas PK and NPK plus pig manure increased the relative abundance of clades A.2.2, B.1, and B.2. The relative abundance of clade A.2.1 was negatively correlated to soil pH, while that of clade A.2.2 showed an opposite trend, indicating the potential niche differentiation of clade A in the soils. Moreover, clade B.1 were more abundant in NPK plus pig manure soils while clade B.2 favored growth in PK, suggesting their different niche preferences. Together, we provide novel evidence for the niche differentiation of individual clusters of comammox Nitrospira clades A and B in an acidic agricultural soil, which was fundamental to the sustainable management of microbial N cycle. • Pig manure rather than crop residues increases comammox Nitrospira clade A abundance. • Available P was the strongest factor positively associated with the abundance of clade A. • Soil pH was the key driver for the community structure of comammox Nitrospira. • Clade A.2.1 was the dominant comammox Nitrospira cluster in tested soils. • Niche differentiation of the individual clusters of clades A and B was found in the soils. [ABSTRACT FROM AUTHOR]

Abstract: Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles. [Copyright &y& Elsevier]

Abstract: Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) are important drivers of a key step of the nitrogen cycle — nitrification, which affects the production of the potent greenhouse gas, nitrous oxide (N2O). A field experiment was conducted to determine the effect of nitrogen application rates and the nitrification inhibitor dicyandiamide (DCD) on the abundance of AOB and AOA and on N2O emissions in a grazed pasture soil. Nitrogen (N) was applied at four different rates, with urea applied at 50 and 100kgNha−1 and animal urine at 300 and 600kgNha−1. DCD was applied to some of the N treatments at 10kgha−1. The results showed that the AOB amoA gene copy numbers were greater than those of AOA. The highest ratio of the AOB to AOA amoA gene copy numbers was 106.6 which occurred in the urine-N 600 treatment. The AOB amoA gene copy numbers increased with increasing nitrogen application rates. DCD had a significant impact in reducing the AOB amoA gene copy numbers especially in the high nitrogen application rates. N2O emissions increased with the N application rates. DCD had the most significant effect in reducing the daily and total N2O emissions in the highest nitrogen application rate. The greatest reduction of total N2O emissions by DCD was 69% in the urine-N 600 treatment. The reduction in the N2O emission factor by DCD ranged from 58% to 83%. The N2O flux and NO3 −-N concentrations were significantly correlated to the growth of AOB, rather than AOA. This study confirms the importance of AOB in nitrification and the effect of DCD in inhibiting AOB growth and in decreasing N2O emissions in grazed pasture soils under field conditions. [Copyright &y& Elsevier]

• AOB play a more important role in nitrification in upland soils than in wetland soils. • The contribution of AOB to nitrification is higher in cropland than in other upland soils. • The contribution of AOB to nitrification increases with increasing pH in upland soils. • AOB play an equally or more important role than AOA in nitrification in acidic soils. Our knowledge of the abundance and distribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) has substantially expanded over the past decade, but their relative contributions to soil nitrification remain debated, particularly at a global scale. Nitrification inhibitor 1-octyne is the only available selective inhibitor that can exclusively inhibit AOB but not AOA activity, making it a powerful tool to differentiate the functional importance of AOB vs AOA in nitrification. Here, we conducted a meta-analysis of laboratory incubation studies with 1-octyne as the nitrification inhibitor to display a panoramic view of the relative contribution of AOB in soil nitrification across various terrestrial ecosystems. The most pronounced reduction of nitrification rates by 1-octyne was found in cropland (71.4%), followed by grassland (59.6%), forestland (53.2%) and wetland (44.0%), indicating a more dominant role of AOB over AOA in upland soils than in wetland soils. The response ratio of soil nitrification rates with 1-octyne addition to that without 1-octyne addition was negatively correlated to soil pH in upland soils, suggesting that a greater proportion of nitrification was inhibited by 1-octyne with higher soil pH. However, the reduction of nitrification rate by 1-octyne was estimated to be 59.5% in acidic soils (pH ≤ 6.5), indicating a major role of AOB in acidic soil nitrification. The proportion of nitrification rate reduced by 1-octyne was greater in soils incubated in slurry and with nitrogen additions than in microcosm and without nitrogen additions, and this should be taken into consideration during the incubation experiments. Altogether, this meta-analysis provides evidence for an equally or more important role of AOB in nitrification from global acidic soils, advancing our understanding of the microbial nitrification process, which is fundamental to the sustainable management of nitrogen in soils. [ABSTRACT FROM AUTHOR]

Abstract: Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global nitrogen (N) biogeochemical cycling. Responses of the associated microorganisms to global changes remain unclear. This study was to determine if there was a shift in soil AOB and AOA abundances and community structures under free-air carbon dioxide (CO2) enrichment (FACE) and N fertilization in Duke Forest of North Carolina, by using DNA-based molecular techniques, i.e., quantitative PCR, restriction fragment length polymorphism (RFLP) and clone library. The N fertilization alone increased the abundance of bacterial amoA gene, but this effect was not observed under elevated CO2 condition. There was no significant effect of the N fertilization on the thaumarchaeal amoA gene abundance in the ambient CO2 treatments, while such effect increased significantly under elevated CO2. A total of 690 positive clones for AOA and 607 for AOB were selected for RFLP analysis. Analysis of molecular variance (AMOVA) indicated that effects of CO2 enrichment and N fertilization on the community structure of AOA and AOB were not significant. Canonical correspondence analysis also showed that soil pH rather than elevated CO2 or N fertilization shaped the distribution of AOB and AOA genotypes. A negative linear relationship between the δ13C and archaeal amoA gene abundance indicated a positive effect of elevated CO2 on the growth ammonia oxidizing archaea. On the other hand, the community structures of AOB and AOA are determined by the soil niche properties rather than elevated CO2 and N fertilization. [Copyright &y& Elsevier]

Comammox Nitrospira are a newly discovered group of nitrifying prokaryotes and might be key contributors to nitrogen cycling in terrestrial ecosystems. Their large-scale distribution patterns and the dominant environmental factors shaping their ecological niches are not yet well documented. Here, we investigated the biogeographic distribution of comammox Nitrospira over 4000 km in eastern Australia and explored the niche specialization of individual comammox Nitrospira phylotypes. Our results revealed that the abundance, richness and community composition of comammox Nitrospira clade A were best predicted by mean annual precipitation (MAP) among all the determined environmental parameters. We identified four phylogenetic clusters of comammox Nitrospira : clade A.1, A.2.1, A.2.2 and A.3. MAP was consistently the strongest factor correlated with the relative abundances of the dominant clades, A.2.1 and A.3. MAP and other variables including soil nitrate, mean annual temperature and total nitrogen showed contrasting effects on the relative abundances of comammox Nitrospira clade A.2.1 and A.3, indicating their potential ecological niche differentiation in the soils. Together, we found a broad distribution of comammox Nitrospira clade A, but not clade B, in various terrestrial ecosystems across eastern Australia, and the abundance and diversity of comammox Nitrospira clade A can be mainly predicted by MAP among all the determined environmental parameters. These findings provide novel evidence for the environmental adaptation and niche specialization of comammox Nitrospira in the terrestrial ecosystems. • A broad distribution of comammox Nitrospira clade A was found in soils collected over 4000 km in eastern Australia. • Mean annual precipitation was a key driver of soil comammox Nitrospira clade A in terrestrial ecosystems. • Two comammox Nitrospira clade A clusters dominated in the terrestrial ecosystems. • These two comammox Nitrospira clade A clusters had contrasting ecological preferences. [ABSTRACT FROM AUTHOR]

The recent discovery of complete ammonia oxidizers (comammox Nitrospira) challenged the paradigm of the two-step nitrification mediated by two distinct groups of nitrifiers, and raised fundamental questions regarding their niche specialization and relative contribution to nitrification in agricultural soils. Previous studies suggest that comammox Nitrospira have an oligotrophic lifestyle and would outcompete canonical ammonia oxidizers (ammonia-oxidizing bacteria and ammonia-oxidizing archaea) under ammonia-limited conditions. Here, we demonstrated that comammox Nitrospira clade A were significantly more abundant than canonical ammonia oxidizers and 13CO 2 -DNA-stable isotope probing revealed that comammox Nitrospira clade A incorporated 13CO 2 into their genomes in fertilized agricultural soils during the microcosm incubation. Phylogenetic analysis of the amoA gene revealed that 13CO 2 -labelled comammox Nitrospira clade A belonged to the Nitrospira inopinata -related cluster and a new cluster that was distinct from the known comammox isolates. These results demonstrated the potential important role of comammox Nitrospira in autotrophic ammonia oxidation in agricultural soils amended with nitrogen fertilizers and their lifestyle may be not strictly restricted to oligotrophic habitats. There is a potential contribution of comammox Nitrospira to soil nitrification, which calls re-evaluation of the microbial nitrogen cycling processes and the subsequent impacts on agriculture and the environment. • Comammox Nitrospira clade A played a potential role in nitrification of fertilized agricultural soils. • The N fertilizer input significantly increased the abundances of comammox Nitrospira clade A, AOA and AOB. • Acetylene significantly impeded comammox clade A, AOA and AOB, but 1-octyne only inhibited AOB abundance. • Comammox Nitrospira clade A incorporated 13CO 2 into their genomes during the incubation. • A new cluster of comammox Nitrospira may play an important role in nitrification of fertilized soils. [ABSTRACT FROM AUTHOR]