Soil Ammonia-oxidizing Bacteria Research Articles

Lithology-driven soil properties control of N2O production by ammonia oxidizers in subtropical forest soils

Lithology can strongly influence soil's physical and chemical properties, significantly affecting soil nitrogen (N) transformation rates. Ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete ammonia oxidizers (comammox Nitrospira) constitute the major producers of soil nitrous oxide (N2O), but the importance of different lithology on their relative contributions still poorly understood, especially in terms of newly discovered and widespread comammox. To address this knowledge gap, three nitrification inhibitors, acetylene (ammonia oxidizers inhibitor), 1-octyne (AOB inhibitor) and 3,4-dimethylpyrazole phosphate (DMPP) (both AOB and comammox inhibitor), were used to selectively inhibit the activity of different ammonia oxidation groups in order to discriminate their respective roles in N2O production in forest soils developed on different lithologies (limestone and clastic rock). The results showed that AOB dominated N2O production (63.5 ± 3.3 %) in limestone soils with ammonium amendment, followed by AOA (34.5 ± 7.6 %), while comammox contributed 1 % of total N2O production with N2O yield of 0.03 ± 0.04 %. Higher N2O production by AOB in limestone soils is associated with higher soil pH, exchangeable calcium/magnesium and lower short-range order iron/aluminum minerals. However, the N2O yield by comammox (0.12 ± 0.12 %) in clastic rock soils was comparable to that by AOA (0.15 ± 0.14 %) and AOB (0.20 ± 0.13 %). Based on the results of the correlation analysis, comammox in the clastic rock soils produce greater amounts of N2O is closely related to the higher soil organic carbon and available phosphorus. The present study provided evidence that the lithology-driven soil properties markedly affect the N2O production from different ammonia oxidizers.

The different responses of AOA and AOB communities to irrigation systems in the semi-arid region of Northeast China.

Ammonia oxidation is the rate-limiting step in nitrification and the key step in the nitrogen (N) cycle. Most soil nutrients and biological indicators are extremely sensitive to irrigation systems, from the perspective of improving soil fertility and soil ecological environment, the evaluation of different irrigation systems and suitability of selection, promote crop production and soil quality, study the influence of the soil microenvironment contribute to accurate evaluation of irrigation farmland soil health. Based on the amoA gene, the abundance and community diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their responses to soil physicochemical factors and enzyme activities were studied in semi-arid areas of Northeast China. The study consisted of three irrigation systems: flood irrigation (FP), shallow buried drip irrigation (DI), and mulched drip irrigation (MF). The results showed that DI and MF significantly increased the contents of alkaline hydrolyzed nitrogen (AN), nitrate nitrogen (NO3--N), soil moisture, and the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). Compared with FP, DI significantly increased the abundance of soil AOA and AOB, while MF significantly increased the abundance of soil AOB. Irrigation systems significantly affected the community composition of ammonia-oxidizing microorganisms (AOM). Also, AN and soil moisture had the greatest influence on the community composition of AOA and AOB, respectively. The AOB community had better stability and stress resistance. Moreover, the symbiotic network of AOB in the three irrigation systems was more complex than that of AOA. Compared with FP, the AOA community under treatment DI had higher complexity and stability, maintaining the versatility and sustainability of the ecosystem, while the AOB community under treatment MF had higher transfer efficiency in terms of matter and energy. In conclusion, DI and MF were more conducive to the propagation of soil AOM in the semi-arid area of Northeast China, which can provide a scientific basis for rational irrigation and N regulation from the perspective of microbiology.

Appropriately Reduced Nitrogen and Increased Phosphorus in Ratooning Rice Increased the Yield and Reduced the Greenhouse Gas Emissions in Southeast China

Reducing greenhouse gas emissions while improving productivity is the core of sustainable agriculture development. In recent years, rice ratooning has developed rapidly in China and other Asian countries, becoming an effective measure to increase rice production and reduce greenhouse gas emissions in these regions. However, the lower yield of ratooning rice caused by the application of a single nitrogen fertilizer in the ratooning season has become one of the main reasons limiting the further development of rice ratooning. The combined application of nitrogen and phosphorus plays a crucial role in increasing crop yield and reducing greenhouse gas emissions. The effects of combined nitrogen and phosphorus application on ratooning rice remain unclear. Therefore, this paper aimed to investigate the effect of combined nitrogen and phosphorus application on ratooning rice. Two hybrid rice varieties, ‘Luyou 1831’ and ‘Yongyou 1540’, were used as experimental materials. A control treatment of nitrogen-only fertilization (187.50 kg·ha−1 N) was set, and six treatments were established by reducing nitrogen fertilizer by 10% (N1) and 20% (N2), and applying three levels of phosphorus fertilizer: N1P1 (168.75 kg·ha−1 N; 13.50 kg·ha−1 P), N1P2 (168.75 kg·ha−1 N; 27.00 kg·ha−1 P), N1P3 (168.75 kg·ha−1 N; 40.50 kg·ha−1 P), N2P1 (150.00 kg·ha−1 N; 13.50 kg·ha−1 P), N2P2 (150.00 kg·ha−1 N; 27.00 kg·ha−1 P), and N2P3 (150.00 kg·ha−1 N; 40.50 kg·ha−1 P). The effects of reduced nitrogen and increased phosphorus treatments in ratooning rice on the yield, the greenhouse gas emissions, and the community structure of rhizosphere soil microbes were examined. The results showed that the yield of ratooning rice in different treatments followed the sequence N1P2 > N1P1 > N1P3 > N2P3 > N2P2 > N2P1 > N. Specifically, under the N1P2 treatment, the average two-year yields of ‘Luyou 1831’ and ‘Yongyou 1540’ reached 8520.55 kg·ha−1 and 9184.90 kg·ha−1, respectively, representing increases of 74.30% and 25.79% compared to the N treatment. Different nitrogen and phosphorus application combinations also reduced methane emissions during the ratooning season. Appropriately combined nitrogen and phosphorus application reduced the relative contribution of stochastic processes in microbial community assembly, broadened the niche breadth of microbial communities, enhanced the abundance of functional genes related to methane-oxidizing bacteria and soil ammonia-oxidizing bacteria in the rhizosphere, and decreased the abundance of functional genes related to methanogenic and denitrifying bacteria, thereby reducing greenhouse gas emissions in the ratooning season. The carbon footprint of ratooning rice for ‘Luyou 1831’ and ‘Yongyou 1540’ decreased by 25.82% and 38.99%, respectively, under the N1P2 treatment compared to the N treatment. This study offered a new fertilization pattern for the green sustainable development of rice ratooning.

Shifts in soil ammonia-oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions.

Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.

Ammonia-oxidizing bacteria are the primary N2O producers in long-time tillage and fertilization of dryland calcareous soil

Human intervention in agriculture, such as tillage and fertilization, could result in major changes of N2O emissions that understanding the N2O emission mechanism is of great significance in reducing the N2O emissions of the agricultural system. In this work, we focused on the conventional tillage practice and straw return practice used in the spring maize production system of this region and compared them by the addition of 3,4-dimethylpyrazole phosphate (DMPP) to explore the N2O emission mechanism of the farmland. Compared with conventional farming, straw return significantly increased the N2O emissions from the soil. Soil pH had important effects on soil N2O emissions through its influence on the ammonia oxidizer community. In addition, DMPP was used to distinguish N2O emissions driven by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and the results showed that AOB were the dominant factor regulating N2O emissions after receiving nitrogen from an external source in dryland farming calcareous soil. Through the analyses of soil AOB community composition and the aggregated boosted tree (ABT) model for N2O emissions, Nitrosospira Cluster 3a.2 was found to be the main driving force of soil N2O emissions in AOB communities. These findings will help better understand the physiochemical and biological mechanisms underlying the N2O emissions of agricultural soils and provide insight for reducing the negative impact of agricultural production systems on the ecological environment.

Dichlorodiphenyltrichloroethane inhibits soil ammonia oxidation by altering ammonia-oxidizing archaeal and bacterial communities

Dichlorodiphenyltrichloroethane (DDT), a persistent organic pollutant, has known effects on natural microbes. However, its effects on soil ammonia-oxidizing microbes, significant contributors to soil ammoxidation, remain unexplored. To address this, we conducted a 30-day microcosm experiment to systematically study the effects of DDT contamination on soil ammonia oxidation and the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings revealed that DDT inhibited soil ammonia oxidation in the early stage (0–6 days), but it gradually recovered after 16 days. The copy numbers of amoA gene of AOA decreased in all DDT-treated groups from 2 to 10 days, while that of AOB decreased from 2 to 6 days but increased from 6 to 10 days. DDT influenced the diversity and community composition of AOA but had no significant effect on AOB. Further, the dominant AOA communities comprised uncultured_ammonia-oxidizing_crenarchaeote and Nitrososphaera sp. JG1: while the abundance of the latter significantly and negatively correlated with NH 4+-N (P ≤ 0.001), DDT (0.001 < P ≤ 0.01), and DDD (0.01 < P ≤ 0.05) and positively correlated with NO3−-N (P ≤ 0.001), that of the former significantly and positively correlated with DDT (P ≤ 0.001), DDD (P ≤ 0.001), and NH 4+-N (0.01 < P ≤ 0.05) and negatively correlated with NO3−-N (P ≤ 0.001). Among AOB, the dominant group was the unclassified Nitrosomonadales in Proteobacteria, which showed significant negative correlation with NH 4+-N (0.01 < P ≤ 0.05) and significant positive correlation with NO3−-N (0.001 < P ≤ 0.01). Notably, among AOB, only Nitrosospira sp. III7 exhibited significant negative correlations with DDE (0.001 < P ≤ 0.01), DDT (0.01 < P ≤ 0.05), and DDD (0.01 < P ≤ 0.05). These results indicate that DDT and its metabolites affect soil AOA and AOB, consequently affecting soil ammonia oxidation.

Proper organic substitution attenuated both N2O and NO emissions derived from AOB in vegetable soils by enhancing the proportion of Nitrosomonas

The ammonia oxidation process driven by microorganisms is an essential source of nitrous oxide (N2O) and nitric oxide (NO) emissions. However, few evaluations have been performed on the changes in the community structure and abundance of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) under substituting portion of chemical fertilizers with organic manure (organic substitution) and their relative contribution to the ammonia oxidation process. Here, five long-term fertilization strategies were applied in field (SN: synthetic fertilizer application; OM: organic manure; M1N1: substituting 50 % of chemical N fertilizer with organic manure; M1N4: substituting 20 % of chemical N fertilizer with organic manure; and CK: no fertilizer). We investigated the response characteristics of AOB and AOA community structures by selective inhibitor shaking assays and high-throughput sequencing and further explained their relative contribution to the ammonia oxidation process during three consecutive years of vegetable production. Compared to SN and M1N4, the potential of ammonia oxidation (PAO) was significantly reduced by 26.4 % and 22.3 % in OM and 9.5 % and 4.4 % in M1N1, resulting in N2O reductions of 38.9 % and 30.8 % (OM) and 31.2 % and 21.1 % (M1N1), respectively, and NO reductions of 45.0 % and 34.1 % (OM) and 40.1 % and 28.3 % (M1N1). RDA and correlation analyses showed that the soil organic carbon and ammonium nitrogen content increased while AOB gene abundance and diversity significantly decreased with increasing organic replacement ratio; however, the relative abundance of Nitrosomonas in AOB increased in OM and M1N1, which further demonstrates that AOB are the main driver in vegetable soils. Therefore, the appropriate proportion of organic substitution (OM and M1N1) could decrease the N2O and NO emissions contributed by AOB by affecting the soil physicochemical properties and AOB community structure.

Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions.

BackgroundNitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification.Materials and MethodsA simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively.Results and discussionsSoil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4+ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA.ConclusionsPNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4+, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.

Snow Exclusion Does Not Affect Soil Ammonia-Oxidizing Bacteria and Archaea Communities

Soil ammonia-oxidizing microorganisms play important roles in nitrogen (N) cycling in cold ecosystems, but how changes in snow cover will affect their distribution and associated functional characteristics remains unclear. A snow manipulation experiment was conducted to explore the effects of snow exclusion on soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities and functional characteristics in a spruce forest in the eastern Tibet Plateau. Results showed that the amoA gene abundance and community composition of AOA and AOB did not differ between snow regimes but varied among winter periods. AOA and AOB gene abundances showed a decreasing trend during the snow cover melting period. During the deep snow cover period, Thaumarchaeota and Crenarchaeota in the AOA community decreased significantly, while Proteobacteria and Nitrosospira in the AOB community increased significantly. The main factors affecting the changes in AOA and AOB community diversity and composition were soil MBN, nitrate nitrogen, and temperature, while AOA and AOB community diversity and composition were also significantly correlated with soil enzyme activities related to N cycling. These results recommend that the season-driven variations strongly affected soil ammonia-oxidizing community and functional characteristics more than momentary snow cover change. Such findings offer new insights into how soil N-cycling processes would respond to reduced snowfall in high-altitude regions.

Effects of Nitrification Inhibitors on Nitrogen Dynamics and Ammonia Oxidizers in Three Black Agricultural Soils

The application of nitrification inhibitors (NIs) based on ammonium (NH4+) is considered to be an efficient way to reduce nitrogen (N) loss by delaying the nitrification process through influencing ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, the inhibition mechanisms of NIs on AOA and AOB in different soils remain unclear. Hence, we explored the two commonly used NIs (3, 4-dimethylepyrazole phosphate (DMPP) and dicyandiamide (DCD) and their combination (DMPP + DCD) on the soil nitrification and abundance of ammonia oxidizers (AOA and AOB) in three black soils (HLJ, NA, and DA) with different physicochemical properties using a 120-day incubation experiment. The results demonstrated that NIs significantly increased NH4+-N concentrations and decreased NO3−-N concentrations in all three tested soils. There was no significant difference in inhibiting nitrification in HLJ among all NI treatments, while DCD was more efficient in NA, DMPP + DCD had better efficiency in DA. The potential nitrification rate (PNR) was greatly decreased by NIs addition, and PNR was significantly positively correlated with AOB (p &lt; 0.05). AOA was dominant in the acid soil. All NI treatments significantly inhibited soil nitrification through inhibiting the growth of AOB in the two soils with higher pH. The abundance of AOA and AOB was significantly correlated with different soil types (positively correlated with soil pH, and negatively correlated with organic matter). Moreover, soil pH and soil organic matter were considered to be the most important factors influencing the inhibition efficiency of NIs and the abundance of AOA and AOB. The application of the NIs combination (DMPP + DCD) was considered to be the most cost-effective way to inhibit soil nitrification in soil with higher pH and lower SOM, which provides a theoretical basis for a field experiment.

Di(2-ethylhexyl) phthalate and dibutyl phthalate have a negative competitive effect on the nitrification of black soil

Di (2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) are the most widely used plasticizers for agricultural mulching films and one of the most common organic pollutants in black soil. However, little is known about the effect of these two contaminants on nitrification in black soil. This study investigated the changes of 20 mg/kg DEHP and DBP on the diversity of nitrification microbial communities, the abundance of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) related genes, and the activities of key enzymes involved in nitrification. During ammonia oxidation, DEHP and DBP had uncompetitive inhibition of urease, reducing the copy number of amoA gene, and microorganisms (Azoarcus, Streptomyces and Caulobacter) would use inorganic nitrogen as a nitrogen source for physiological growth. During nitrite oxidation, the copy number of nxrA gene also reduced, and the relative abundance of chemoautotrophic nitrifying bacteria (Nitrosomonas and Nitrobacter) decreased. Moreover, the path analysis results showed that DEHP and DBP mainly directly or indirectly affect AOB and NOB through three ways. These results help better understand the ecotoxicological effects of DEHP and DBP on AOB and NOB in black soil.

Earthworm regulation of nitrogen pools and dynamics and marker genes of nitrogen cycling: A meta-analysis

Earthworms, as the ecosystem engineers, both directly and indirectly affect the nitrogen (N) cycle. We aimed to provide a quantitative assessment of the contribution of earthworms to the terrestrial ecosystem N cycle using meta-analysis of 130 publications selected. The natural logarithm of the response ratio (lnRR) was used to indicate the effect size of earthworms on N dynamic variables. The results showed that earthworms significantly affected soil N-cycling microorganisms, including the amoA gene abundance of soil ammonia-oxidizing bacteria (AOB), and significantly promoted soil N cycle processes, including denitrification, mineralization, and plant assimilation. The effects of earthworms on the N cycle were experimental design dependent and affected by factors such as the functional group of earthworm and residue input. The presence of the anecic earthworms decreased the rates of mineralization and nitrification, and increased nitrification and denitrification responses were more pronounced in the presence of the endogeic earthworms than that of the other two functional groups of earthworms. In addition, residue input enhanced the effects of earthworms on the N cycle. The effects of earthworms on nitrous oxide (N 2 O) emission increased when residues were added. These findings indicate that residue input and introducing suitable functional groups of earthworms into the field can lead to N sustainability without increasing N 2 O emission. This meta-analysis also provides systematic evidence for the positive effects of earthworms on the plant N pool, N availability (soil ammonium (NH 4 + ) content), and soil microbial biomass N content, showing the potential to alter ecosystem functions and services in relation to N cycling.

Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil

Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha−1 for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.

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

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

Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.

The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management. The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition. The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.

3, 4-Dimethylpyrazole phosphate is an effective and specific inhibitor of soil ammonia-oxidizing bacteria

A microcosm study was established using three arable soils differing in both physicochemical properties and AOB or AOA dominance of ammonia oxidization. Nitrification and N2O emissions were quantified under 10 Pa C2H2, 1-octyne, or 3,4-dimethylpyrazole phosphate (DMPP), and the community composition and abundance of AOA and AOB were assessed. Amendment of soil with DMPP had a comparable effect to 1-octyne on AOB activities, composition, and N2O emissions across soils. By blocking AOB activity, both DMPP and 1-octyne supported higher rates of AOA growth in both the acid and alkaline soils. Approximately, 50% of ammonia-oxidizing activity in the acid soil was attributed to AOB activity by phylotypes affiliated with Nitrosomonas communis. When AOB were blocked by DMPP or 1-octyne across all soils, recovery of AOA communities was associated with the increased abundance of Nitrososphaera viennesis.

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.

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.