Soil Ammonia-oxidizing Archaea Research Articles

Long‐term inorganic nitrogen application changes the ammonia‐oxidizing archaeal community composition in paddy soils

AbstractThe abundance and taxonomic composition of ammonia‐oxidizing archaea (AOA) were assessed in paddy soils that had received more than 50 years of fertilization with and without inorganic N. The inorganic N fertilized treatments were: NPK and NPK + CO (nitrogen (N), phosphorus (P), potassium (K) and compost (CO)). The treatments without inorganic N were: CO, PK and control (unfertilized soils). Quantitative PCR (qPCR) analysis of the archaeal amoA gene showed no significant changes in AOA abundance following the long‐term application of inorganic N fertilizers. However, subsequent analysis of amoA gene sequencing data showed that inorganic N application significantly changed the AOA community composition and alpha diversity indices. Edge principal components analysis (PCA) showed varying contributions of distinct AOA lineages in separating samples according to the fertilization treatment. Addition of inorganic N favoured an increase in the abundance of AOA lineages belonging to Nitrososphaera, and the treatments without inorganic N additions formed a separate cluster dominated by Nitrosotalea lineage. The distinct response of the two AOA lineages points towards different community organization of soil AOA and strongly supports the concept of habitat partitioning in paddy soil ecosystems.Highlights Lineages of AOA responded differently to different N management practices. Long‐term N fertilization selectively enriched AOA lineages, with C:N ratio a factor associated with such changes Inorganic N favoured Nitrososphaera lineage abundance Regardless of fertilizer status, Nitrosotalea lineage was dominant in the absence of inorganic N fertilization.

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

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

Dominance of comammox Nitrospira in soil nitrification.

The first and limiting step of nitrification is catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recently, complete ammonia oxidizers (comammox Nitrospira) have been discovered to perform complete nitrification in one cell, yet their role in soil nitrification is still unclear. This study investigated the abundance and contribution of aerobic ammonia oxidizers in typical soil habitats, and assessed the role of comammox Nitrospira in ammonia-oxidizing communities. The results showed that comammox Nitrospira were dominant in 70% of the samples and their abundance displayed a significant positive correlation with nitrification potential. The median amoA gene transcription level of comammox Nitrospira exceeded that of AOA and AOB in in-situ soils. The abundance of comammox Nitrospira was negatively correlated with soil pH, dominating in 84% of soil samples with pH<6.17. The results challenge the role of AOA and AOB in soils, highlighting the importance of comammox Nitrospira in soil nitrification, especially in acid soils. This work supports better understanding and regulation of the soil nitrogen cycle.

Investigations of soil autotrophic ammonia oxidizers in farmlands through genetics and big data analysis

Soil ammonia oxidation is a key and rate-limiting process of nitrogen cycle in agriculture. Diverse autotrophic ammonia oxidizers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidation (anammox), complete ammonia oxidation (comammox), and anaerobic ammonium oxidation coupled to iron reduction (feammox), were found to drive the process. However, limited studies have investigated the co-occurrence, abundance and relative contributions of these microbes in agricultural soils. Here, we report the diversity, abundance, environmental factors influencing these microbes and their contributions to soil ammonia oxidation. Results suggest that AOA, AOB, comammox, anammox, and feammox commonly co-existed in soil microbial community regardless of land uses (rice, soybean, orchard, nursery stock, and weed); and had a higher abundance in the topsoil (0–15 cm) than the subsoil (15–30 cm). Both AOA and AOB were important drivers of autotrophic ammonia oxidation in rice soils, with predicted ammonia oxidation rates of 0.48 ± 0.56 and 0.93 ± 1.32 μmol N·g dry soil−1·d−1, respectively. Interestingly, feammox, Acidimicrobiaceae sp. A6, showed an equivalent or even greater predicted ammonia oxidation rate (1.23 ± 0.98 μmol N·g dry soil−1·d−1) than AOA or AOB in rice soils, suggesting the significant contribution of feammox to soil ammonia oxidation. Multiple factors, including nutrients, pH, moisture content, total organic carbon, and reactive heavy metals were confirmed to directly or indirectly affect the autotrophic ammonia oxidizers. Notably, the increase of heavy metal availability enriched the autotrophic ammonia oxidizers, which implied the negative effect of heavy metals on soil nitrogen management. These results suggest that multi-engineering measures, e.g., slow-release fertilizer, soil acidification mitigation, and heavy metal immobilization should be taken together to slow the ammonia oxidation for improving nitrogen-use efficiency in agriculture.

Responses of Ammonia-Oxidizing Microorganisms to Intercropping Systems in Different Seasons

Intercropping plays an essential role in agricultural production, impacting the soil’s physical and chemical properties and microbial communities. However, the responses of ammonia-oxidizing microorganisms in the continuous-cropping soil to different intercropping systems in different growing seasons are still insufficiently studied. Here, we investigated the effects of seven intercropping systems (alfalfa (Medicago sativa L.)/cucumber, trifolium (Trifolium repens L.)/cucumber, wheat (Triticum aestivum L.)/cucumber, rye (Secale cereale L.)/cucumber, chrysanthemum (Chrysanthemum coronrium L.)/cucumber, rape (Brassica campestris L.)/cucumber, mustard (Brassica juncea L.)/cucumber) on soil physical and chemical properties, potential nitrification rate (PNR), soil ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) communities in the greenhouse in spring and autumn. The results showed that, compared with cucumber monoculture, intercropping increased the soil NH4+-N and NO3−-N. The chrysanthemum–cucumber, rape–cucumber, and mustard–cucumber treatments increased soil PNR. Intercropping increased the AOA and AOB abundances in two seasons, especially in rape–cucumber, wheat–cucumber, chrysanthemum–cucumber, and trifolium–cucumber treatments. The ratio of AOA and AOB decreased with seasonal variation. The wheat–cucumber and rape–cucumber treatments increased soil AOA community diversity. Seasonal variation had a significant effect on the relative abundance of the AOB community. Nonmetric multidimensional scaling analysis showed that the AOA and AOB community structures were obviously different from spring to autumn. Redundancy analysis showed that the AOA community was significantly regulated by moisture, NO3−–N, and available potassium (AK), while the AOB community was significantly regulated by moisture, available phosphorus (AP), AK, NO3−-N, and pH. Network analysis showed that the co-occurrence relationship and complexity of AOA and AOB communities were different in two growing seasons. The AOB community may play a critical role in ammonia oxidation in autumn. Taken together, intercropping improved soil physicochemical state, increased soil PNR and significantly altered soil AOA and AOB communities. Seasonal variation significantly altered the AOA and AOB communities’ structure and interaction between them. The effect of seasonal variation on AOA and AOB communities was greater than intercropping.

Ammonia-oxidizing archaea are dominant over comammox in soil nitrification under long-term nitrogen fertilization

The complete ammonia oxidizers (comammox) capable of catalyzing nitrification, oxidizing ammonia to nitrate, via activity of only one type of microbes were recently discovered which has updated our knowledge of traditional two-step nitrification. The extent of contribution of comammox and canonical ammonia oxidizers including ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to soil nitrification, especially in soils with long-term input of nitrogen (N) fertilizers, remains unknown. The transcriptional abundance of amoA gene from comammox, AOA, and AOB in soils fertilized for 29 years was investigated in different seasons and soil layers via quantitative PCR. The results showed that comammox were detected in all soil samples; however, AOA and AOB had significantly higher transcriptional abundance of amoA gene than comammox. Nitrification activity was most significantly correlated with the transcriptional abundance of AOA amoA gene (Pearson correlation, r = 0.217, P < 0.05) suggesting AOA were the dominant contributors to soil potential nitrification. Lower abundances of amoA gene transcripts were observed in July than in April and November. The application of high level of mineral N fertilizer decreased the abundance of both AOA and AOB; however, long-term input of organic manure combined with mineral N fertilizer stabilized the abundances of ammonium-oxidizing microbes in soils. Seasonal variation and fertilization regimes substantially affected the abundance of both AOA and AOB, but AOB were not as sensitive in responding to the seasonal variation and fertilization as AOA. The analysis of RDA and VPA demonstrated that sampling month, soil depth, and fertilization regime explained 30.20%, 11.46%, and 5.40% of the variation in nitrification microorganism amoA gene composition, respectively. Seasonal variation exerted the most influences on the nitrifiers’ composition, and soil depth and fertilization regime were also important factors in shaping the nitrifier communities. According to the correlation analysis, NO3−–N content was the most important soil property in impacting the transcriptional abundance of amoA gene, and the amoA gene transcript abundance decreased with increasing NO3−–N content. The results suggest that the activity of comammox may be more inhibited by the long-term nitrogen fertilization than canonical ammonia oxidizers in agricultural soils. This study provides insights into the different responses of comammox and canonical ammonia oxidizers to fertilization, seasonal variation, and soil depth and their relative contributions to nitrification in agricultural soil.

English

Ammonia-oxidizing archaea (AOA) are one of the main regulators of ammoxidation, which is the primary rate-limiting step of nitrification. However, the biofertilizers’ effects on soil AOA are not presently well-understood. Therefore, soil samples treated with three biofertilizers viz., nitrogen-fixing bacterium, phosphate-solubilizing bacterium and Piriformospora indica, both individually and mixed (MI) were collected, in order to explore the variation in the AOA composition and diversity using high-throughput sequencing. The results revealed that the available nitrogen content in soil treated with nitrogen-fixing bacterium and MI were significantly higher than that in soil treated with sterile water. In addition, the MI treatment significantly increased the diversity of AOA in soil. The composition of AOA was not different among the treatments at phylum, class, order, or family level. However, this was somewhat different at the genus and species level. Nitrososphaera was dominant at the genus level among the different soil samples. The structural similarity of AOA communities was higher in the three soil samples treated with Piriformospora indica, phosphate-solubilizing bacterium and sterile water, while the communities in soil treated with nitrogen-fixing bacterium and the mixture of nitrogen-fixing bacterium (MI) were different from that in sterile water. The partial least squares discriminant analysis revealed that the classification models for P. indica, sterile water and phosphate-solubilizing bacterium performed well. The correlation network analysis demonstrated that there was a positive correlation between Candidatus, Nitrosotalea and Nitrosopumilus. The phylogenetic analysis of the AOA community revealed that ammonia-oxidizing archaea mostly belonged to Thaumarchaeota, followed by Crenarchaeota. In addition, there were some unknown archaea. © 2021 Friends Science Publishers

攀枝花不同海拔高度烤烟农田红壤中氨氧化细菌与氨氧化古菌的群落结构分析

为探究攀枝花干热河谷区农田土壤氨氧化古菌（Ammonia oxidizing archaea，AOA）与氨氧化细菌（Ammonia oxidizing bacteria，AOB）群落对海拔高度的响应特征，深入认识该区域的氮素循环过程。以攀枝花米易县不同海拔（1600 m、1800 m和2000 m）农田红壤为研究对象，运用化学分析和末端限制性片段长度多态性（Terminal restriction fragment length polymorphism，T-RFLP）分别测定土壤理化性质、AOA和AOB群落组成及多样性，研究不同海拔农田土壤中AOA和AOB群落变异及其驱动因子。研究结果显示，不同海拔农田土壤pH均小于7，土壤有机碳（SOC）、全氮（TN）、速效钾（AK）和铵态氮（NH₄⁺-N）含量随海拔升高而降低，碱解氮（AN）、有效磷（AP）和硝态氮（NO₃^--N）含量随海拔升高先增加后降低；随海拔升高，AOA群落多样性指数增加，而AOB群落多样性指数先增加后降低；AOA以亚硝基球菌属（Nitrososphaera）为优势菌群，AOB以亚硝化螺菌属（Nitrosospira）为优势菌群；土壤有机碳（SOC）、速效钾（AK）和硝态氮（NO₃^--N）是影响该区域农田土壤AOA和AOB群落发育的主要因子。总体而言，攀枝花干热河谷区不同海拔农田土壤AOA和AOB群落结构变化明显，土壤硝态氮、速效钾和有机碳是影响AOA和AOB群落结构变异的主要因子；研究结果可为揭示干热河谷区农田红壤氮循环相关微生物的海拔分布格局提供理论依据。;This papers aims to explore the response of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) communities to elevation changes in the dry-hot valleys of Panzhihua City, China, and further reveal the nitrogen biogeochemical cycling of this area. Soil samples were collected from the tobacco cultivation field of different altitudes (e.g. 1600 m, 1800 m, and 2000 m) in the dry-hot valleys of Miyi county, Panzhihua City, China. Chemical analysis and terminal restriction fragment length polymorphism (T-RFLP) were used to analyze the soil physicochemical properties and community structures and diversity of AOB and AOA, respectively. The variation of AOA and AOB communities and the driving factors in farmland soils at different altitudes were also investigated. The results showed that the pH value of soils from the three different elevations were below seven which suggests that the soils being studied were acidic soils. The contents of soil organic carbon (SOC), total nitrogen (TN), available potassium (AK) and ammonium nitrogen (NH₄⁺-N) decreased along the increase of elevation. The contents of alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), and nitrate nitrogen (NO₃^--N) first increased and then decreased along the increase of elevation. The highest contents of the AN, AP, and NO₃^--N were detected in the 1800 m elevation while the lowest were detected in the 2000 m. The diversity index of AOA community increased along the increase of altitude while the diversity index of AOB peaked in 1800m, and both the lowest diversity index of AOA and AOB were detected in 1600 m elevation. Nitrososphaera and Nitrosospira were the dominant species of AOA and AOB in the dry-hot valleys of Panzhihua City. Redundancy analysis (RDA) showed that the SOC, AK, and NO₃^--N were key factors in shaping the AOA and AOB communities. In total, both of the composition and diversity of soil AOA and AOB community varied significantly along the increase of altitude in the dry-hot valleys in Panzhihua City, and closely related with SOC, AK, and NO₃^--N. The results provide a theoretical basis for revealing the altitude distribution pattern of nitrogen cycling related microorganisms in red soil in dry- hot valley.

Contingent Effects of Liming on N2O-Emissions Driven by Autotrophic Nitrification

Liming acidic soils is often found to reduce their N2O emission due to lowered N2O/(N2O + N2) product ratio of denitrification. Some field experiments have shown the opposite effect, however, and the reason for this could be that liming stimulates nitrification-driven N2O production by enhancing nitrification rates, and by favoring ammonia oxidizing bacteria (AOB) over ammonia oxidizing archaea (AOA). AOB produce more N2O than AOA, and high nitrification rates induce transient/local hypoxia, thereby stimulating heterotrophic denitrification. To study these phenomena, we investigated nitrification and denitrification kinetics and the abundance of AOB and AOA in soils sampled from a field experiment 2–3 years after liming. The field trial compared traditional liming (carbonates) with powdered siliceous rocks. As expected, the N2O/(N2O + N2) product ratio of heterotrophic denitrification declined with increasing pH, and the potential nitrification rate and its N2O yield (YN2O: N2O-N/NO3–-N), as measured in fully oxic soil slurries, increased with pH, and both correlated strongly with the AOB/AOA gene abundance ratio. Soil microcosm experiments were monitored for nitrification, its O2-consumption and N2O emissions, as induced by ammonium fertilization. Here we observed a conspicuous dependency on water filled pore space (WFPS): at 60 and 70% WFPS, YN2O was 0.03-0.06% and 0.06–0.15%, respectively, increasing with increasing pH, as in the aerobic soil slurries. At 85% WFPS, however, YN2O was more than two orders of magnitude higher, and decreased with increasing pH. A plausible interpretation is that O2 consumption by fertilizer-induced nitrification cause hypoxia in wet soils, hence induce heterotrophic nitrification, whose YN2O decline with increasing pH. We conclude that while low emissions from nitrification in well-drained soils may be enhanced by liming, the spikes of high N2O emission induced by ammonium fertilization at high soil moisture may be reduced by liming, because the heterotrophic N2O reduction is enhanced by high pH.

Niche Differentiation of Bacterial Versus Archaeal Soil Nitrifiers Induced by Ammonium Inhibition Along a Management Gradient.

Soil nitrification, mediated mainly by ammonia oxidizing archaea (AOA) and bacteria (AOB), converts ammonium (NH4+) to nitrite (NO2−) and thence nitrate (NO3−). To better understand ecological differences between AOA and AOB, we investigated the nitrification kinetics of AOA and AOB under eight replicated cropped and unmanaged ecosystems (including two fertilized natural systems) along a long-term management intensity gradient in the upper U.S. Midwest. For five of eight ecosystems, AOB but not AOA exhibited Haldane kinetics (inhibited by high NH4+ additions), especially in perennial and successional systems. In contrast, AOA predominantly exhibited Michaelis-Menten kinetics, suggesting greater resistance to high nitrogen inputs than AOB. These responses suggest the potential for NH4+-induced niche differentiation between AOA and AOB. Additionally, long-term fertilization significantly enhanced maximum nitrification rates (Vmax) in the early successional systems for both AOA and AOB, but not in the deciduous forest systems. This was likely due to pH suppression of nitrification in the acidic forest soils, corroborated by a positive correlation of Vmax with soil pH but not with amoA gene abundance. Results also demonstrated that soil nitrification potentials were relatively stable, as there were no seasonal differences. Overall, results suggest that (1) NH4+ inhibition of AOB but not AOA could be another factor contributing to niche differentiation between AOA and AOB in soil, and (2) nitrification by both AOA and AOB can be significantly promoted by long-term nitrogen inputs.

Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments.

Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.

Diversity and community structure of ammonia-oxidizing archaea in rhizosphere soil of four plant groups in Ebinur Lake wetland.

The aim of this study was to reveal the differences in the community structure of ammonia-oxidizing archaea (AOA) between rhizosphere and non-rhizosphere soil, to provide a theoretical basis for further study on the relationship between halophyte rhizosphere soil microorganisms and salt tolerance. The results of diversity and community structure showed that the diversity of the AOA community in rhizosphere soil of Reeds was higher than that in non-rhizosphere soil in spring and lower than that in non-rhizosphere soil in summer and autumn. In summer, the diversity of rhizosphere soil of Karelinia caspica was higher than that of non-rhizosphere soil and lower than that of non-rhizosphere soil in spring and autumn. The diversity of rhizosphere soil of Halocnemum strobilaceum in 3 seasons was lower than that in non-rhizosphere soil. The diversity of rhizosphere soil of Salicornia was higher than that in non-rhizosphere soil in 3 seasons. In addition, the relative abundance of AOA in rhizosphere soil of 4 plants was higher than that in non-rhizosphere soil. The AOA community in all soil samples was mainly concentrated in Crenarchaeota and Thaumarchaeota. Redundancy analysis results showed salinity, soil water moisture, pH, and soil organic matter were important factors affecting the differentiation of AOA communities.

Influences of different manure N input on soil ammonia-oxidizing archaea and bacterial activity and community structure in a double-cropping rice field.

The short-term effects of different organic manure nitrogen (N) input on soil ammonia-oxidizing archaea (AOA) and bacterial (AOB) activity and community structure at maturity stages of early rice and late rice were investigated in the present paper, in a double-cropping rice system in southern China. A field experiment was done by applying five different organic and inorganic N input treatments: (i) 100% N of chemical fertilizer (M0), (ii) 30% N of organic manure and 70% N of chemical fertilizer (M30), (iii) 50% N of organic manure and 50% N of chemical fertilizer (M50), (iv) 100% N of organic manure (M100) and (v) without N fertilizer input as control (CK). Microbial community changes were assessed using fatty acid methyl esters, and ammonia oxidizer (AO) changes were followed using quantitative PCR. The results showed that AOA were higher than that of AOB based upon amoA gene copy at maturity stages of early rice and late rice. Also, the abundance of AOB and AOA with M30, M50 and M100 treatments was significantly higher than that of CK treatment. Manure N input treatments had significant effect on AOB and AOA abundance, and a higher correlation between AOB and manure N input was observed. AOB correlated moderately with soil organic carbon content, and AOA correlated moderately with water-filled pore space. This study found that abundance of AOB and AOA was increased under the given organic N conditions, and the soil AOB and AOA community and diversity were changed by different short-term organic manure N input treatments. Soil microbial community and specific N-utilizing microbial groups were affected by organic manure N input practices.

Niche differentiation of clade A comammox Nitrospira and canonical ammonia oxidizers in selected forest soils

Unravelling the ecological niche differentiation between comammox Nitrospira, ammonia-oxidizing archaea (AOA) and bacteria (AOB) is essential to understand forest nitrogen dynamics. Although genomic and physiological studies have suggested that comammox Nitrospira may outcompete AOA and AOB under oligotrophic conditions, empirical evidence is lacking in terrestrial ecosystems. Here we investigated the environmental prevalence and functional importance of comammox Nitrospira and their niche differentiation with AOA and AOB in forest soils from eastern Australia. Clade A comammox Nitrospira was widely detected in these forest soils, and their abundance was positively correlated with ammonium, total nitrogen and pH. The ammonium concentration was the most important driver of clade A comammox Nitrospira abundance, based on random forest regression analysis. Clade B comammox Nitrospira was not detected in these forest soils and thus excluded from the downstream analyses. Urea application stimulated the growth of clade A comammox Nitrospira and AOB, but not AOA, during a microcosm incubation. DNA-stable isotope probing revealed that clade A comammox Nitrospira incorporated 13C–CO2 in the incubations, suggesting that clade A comammox Nitrospira may contribute to autotrophic carbon fixation in these forest soils. Taken together, our findings indicate that clade A comammox Nitrospira is prevalent and probably contributing to nitrification in forest soils of eastern Australia.

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.

Negative effects of rare earth oxide nanoparticles of La2O3, Nd2O3, and Gd2O3 on the ammonia-oxidizing microorganisms

Nanoparticles released into soil environment potentially impact microorganisms, which furtherly disturb terrestrial biogeochemical cycles. However, how rare earth oxide nanoparticles affect the functional microorganisms inhabited in natural soil is still unknown. This study was aimed to investigate the effect of different types of rare earth oxide nanoparticles on the ammonia-oxidizing microorganisms. Soil respectively added with 0, 10, 50, and 100 mg kg−1 of La2O3, Nd2O3, or Gd2O3 nanoparticle were incubated at 25 °C in the dark for 60 days. The potential ammonia oxidation (PAO), abundance and communities of ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) were measured at the 1st, 7th, and 60th day. Our results showed that the PAO in soils with nanoparticles significantly decreased due to nanoparticle toxicity at the 1st day, but it gradually increased to the control level owing to the adaptation of AOA and AOB in soils with nano-Nd2O3 and nano-Gd2O3. Interestingly, the abundance of AOB as reflected by the qPCR analysis was upregulated for the hormesis effect of AOB responding to nano-Nd2O3 or nano-Gd2O3 with 50 mg kg−1 level. Moreover, terminal restriction fragment length polymorphism (T-RFLP) results suggested that the communities for AOA and AOB shifted with nanoparticles type and incubation time. Rare earth oxide nanoparticles could inhibit activities of ammonia-oxidizing microorganisms, and thus they might be used as potential nitrification inhibitors to improve nitrogen use efficiency in the agricultural ecosystems.

Effects of long-term fertilization on soil ammonia-oxidizing microorganisms

Long-term fertilization can change the supply of soil carbon and nitrogen (N), with consequences on the abundance and community structure of soil microorganisms. Based on the long-term fertilization positioning experiment station of brown earth, we analyzed the dynamics of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) under different fertilization treatments, including no fertilization (CK), low level of inorganic N fertilizer (N2), high level of inorganic N fertilizer (N4), and organic manure combined with inorganic N fertilizer (M2N2), aiming to provide a basis for microbiological mechanism of soil N transformation and improvement of soil fertility. The results showed that the ratio of AOA to AOB abundance was 2.28-61.95 under different fertilization treatments. Compared with that in CK, the AOA abundance was reduced by 1.6%-13.6% after long-term fertilization. The abundance of AOB in N4 treatment decreased first and then increased with soil depths, but with contrary results in other treatments. The Shannon diversity index (H), evenness index (J), and Simpson index (S) of AOB were higher than those of AOA. The AOB diversity was increased at 0-20 cm soil layer in M2N2 treatment, while that of AOA was decreased. Soil AOB clustered with soil depths, and neither AOA nor AOB community clustered with fertilization treatments. In summary, long-term fertilization altered the composition of AOA and AOB. AOA was sensitive to environment, whereas AOB was more abundant and stable.

Responses of soil ammonia-oxidizing bacteria and archaea diversity to N, P and NP fertilization: Relationships with soil environmental variables and plant community diversity

Chemical fertilizers are often used in managed grasslands to alleviate nutrient deficiency, especially for nitrogen (N) and phosphorus (P), and to maximize plant production. Soil microbial communities can respond to N/P fertilization-induced changes in soil environmental variables, like increased N availability or soil acidification, and to fertilization-induced changes in plant species richness which can determine the diversity of niches available for microbial taxa. Thus, analyzing the concurrent responses of soil environmental variables and of plant and soil microbial diversity is needed to understand the effect of N/P fertilization on soil microbial communities. Here we investigated the effects of different N, P and NP fertilization treatments (4 N levels without P; 4 P levels without N; and 4 P levels with constant N addition) on the communities of plants and of soil ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively). AOA and AOB community compositions were more sensitive to NP and N fertilization, respectively. Simple regressions and structural equation modeling demonstrate that AOA richness was correlated, though weakly, to plant species richness rather than to soil environmental variables. AOB richness was mostly correlated with plant richness and soil available P. This study demonstrates that plant richness is an important determinant of AOA and AOB richness, and helps understanding the ecology of soil ammonia oxidizers in the context of altered phosphorus and nitrogen availabilities.

Abundance of AOA, AOB, nirS, nirK, and nosZ in red soil of China under different land use

In this study, four land use type soils from Yingtan Jiangxi Province China, i.e., forest (F), bamboo (B), tea plantation (TP) and upland (U), were collected, and gene of ammonia-oxidizing archaea (AOA) and bacteria (AOB), nirS, nirK, and nosZ were determined, to identify the effects of land use on abundance of microorganism in red soil and their role to nitrification and denitrification. The result shows that AOA copy numbers ranged from 6.20 × 106 to 6.58 × 106 copies/g soil and AOB varied from 4.18 × 106 to 7.41 × 106 copies/g soil. The highest AOA and AOB were all measured in U soil that was the highest pH and the lowest C/N ratio. The Abundance of AOB is stimulated by enhancing soil pH due to lime application and more available NH4+ from N fertilization that could be responsible for the high net nitrification rate in U soil. Meanwhile, nirK copy numbers ranged from 6.46 × 106 to 7.05 × 106 copies/g soil, nirS from 5.50 × 106 to 5.85 × 106 copies/g soil, and nosZ from 6.57 × 106 to 7.35 × 106 copies/g soil. The nirS (p<0.05) and nirK (p<0.05) was positively correlated with soil potential denitrification rate.

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N2 O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N2 O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N2 O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N2 O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N2 O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N2 O emissions.