Ammonia-oxidizing Communities Research Articles

Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater.

Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.

Enhancing the relative abundance of comammox nitrospira in ammonia oxidizer community decreases N2O emission in nitrification exponentially

Comammox Nitrospira and canonical ammonia-oxidizing bacteria (cAOB) generally coexist in activated sludge. In present study, the effect of comammox Nitrospira on N2O production during nitrification of activated sludge was investigated. Comammox Nitrospira and cAOB were separately enriched in two nitrifying reactors, with respective relative abundance of approximately 98% in ammonia oxidizer community. The N2O emission factor (EF) of nitrification in comammox Nitrospira dominated reactor was 0.35%, consistently lower than that (2.2%) in cAOB dominated reactor. When increasing the relative abundance of comammox Nitrospira in ammonia oxidizer community, the N2O EF of nitrification decreased exponentially, which suggested that comammox Nitrospira not only decreased N2O production directly but also might have reduced N2O yield by cAOB. When cAOB dominated the ammonia oxidizer community of sludge, decreasing pH to 6.3, lowering DO to less than 0.5 mg/L, and increasing nitrite concentration enhanced N2O EF dramatically. When comammox Nitrospira became the dominant ammonia oxidizer, however, the N2O EF correlated to nitrite insignificantly and a low DO of 0.2 mg/L and weakly acidic pH (6.3) decreased N2O EF by approximately 70% and 60%, respectively. These results imply that enhancing the relative abundance of comammox Nitrospira in sludge is an effective way to reducing N2O emissions and can also offset the promoting effects of acidic pH, low DO, and high nitrite concentration on N2O production during nitrification.

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

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

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.

Stability of ammonia oxidizer communities upon nitrogen fertilizer pulse disturbances is dependent on diversity

Diversity of the soil microbial community is an important factor affecting its stability against disturbance. However, the impact of the decline in soil microbial diversity on the stability of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is not known, particularly considering the repeated soil nutrient disturbances occurring in modern agricultural systems. Here, we conducted a microcosm experiment and modified the soil microbial diversity using the dilution-to-extinction approach to determine the stability and population dynamics of AOB and AOA communities with repeated nitrogen (N) fertilizer application. Our results demonstrated that the AOB community became more abundant and stable against repeated disturbances by N in the treatments with the highest microbial diversity. In contrast, the abundance of AOA decreased following repeated N fertilizer application, regardless of the microbial diversity. Notably, during the initial application phase, AOA displayed a potential for increased abundance in treatments with high soil microbial diversity. These findings highlight that the soil microbial diversity controls the stability of ammonia oxidizers during short-interval repeated N disturbances.

Abundance, diversity and physiological preferences of comammox Nitrospira in urban groundwater

Complete ammonia oxidizer (comammox Nitrospira), catalyze complete nitrification process in a single organism, are frequently detected in groundwater ecosystem. However, the ecological niches and environmental driving factors of comammox Nitrospira in urban groundwater are largely unknown. Here we investigated the communities of ammonia oxidizers in urban groundwater located in Shanghai city, China. Quantitative analysis demonstrated the dominance of comammox Nitrospira over classical ammonia oxidizers (ammonia-oxidizing archaea and bacteria, AOA and AOB). Phylogenetic analysis showed clades B and A2 comprise the majority of comammox Nitrospira groups. Temperature was one of the most vital factors affecting comammox Nitrospira community. Furthermore, clade A comammox Nitrospira can be enriched by urea substrate, which was in line with the ability of utilizing urea by the pure clade A comammox culture Nitrospira inopinata. In addition, we observed that relatively low temperature (<20 °C) and high copper levels (>0.04 mg L−1) can stimulate the growth of comammox Nitrospira. Overall, this study revealed the presence, diversity and physiological preferences of comammox Nitrospira in urban groundwater nitrification, shedding insights on the ecological roles of comammox Nitrospira in subsurface environment.

Nine years of low-dose biochar amendment suppresses nitrification rate in low-yield brown soil

Nitrification is the crucial process of nitrogen (N) transformation and ammonia oxidation is the first and the speed-limited step of nitrification. The one-time amendment of large quantities of biochar has been reported to alter soil fertility. However, it remains unclear how continuous low-dose biochar application affects the abundance and community composition of ammonia oxidizers and the subsequent nitrification and crop production. In this article, we calculate the soil net nitrification rate and the abundance and communities of ammonia-oxidizers across different growth stages of peanuts at 0–20 cm soil layer under four fertilization regimes, namely control with zero fertilization (CK), biochar application (BC), chemical fertilizer application (NPK) and biochar-based fertilizer application (BBF). Results showed that continuous application of low-dose biochar can significantly increase crop yield by 7.8 % compared to unfertilized soil indirectly through regulating the microbial mechanism in the nitrification process. The highest bacterial amoA gene copy numbers were found in the NPK treatment, 2.35-fold higher than the CK treatment. Compared to the single input of NPK chemical fertilizer, biochar-based fertilizer reduced the nitrification rate by reducing the relative abundance of bacteria, especially Nitrosomonas and Nitrosospira. In summary, our findings provide evidence that: (1) sustained low-dose biochar input could also increase the ammonia-oxidizing bacterial abundance, changing soil properties and increasing the crop yield; (2) biochar-based fertilizer could significantly reduce the nitrification rate compared to NPK application by reducing the AOB-amoA gene abundance and the relative abundance of Nitrosomonas and Nitrosospira; (3) soil C/N ratio was also important for the ammonia-oxidizing community.

Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China

Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg−1 N ha−1) was 23.35 % higher than that at the intermediate rate (100–150 kg−1 N ha−1) and 20.77 % higher than that at the low rate (< 100 kg−1 N ha−1). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4+ content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.

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.

Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling

The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N2O), to the atmosphere. Most of that N2O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N2O production and their kinetics, however, are not completely understood. Here, we use 15N and 18O isotopes to determine the kinetics of N2O production and trace the source of nitrogen (N) and oxygen (O) atoms in N2O produced by a model marine AOA species, Nitrosopumilus maritimus. We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N2O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N2O are derived from ammonia, nitrite, O2, and H2O via multiple pathways. Ammonia is the primary source of N atoms in N2O, but its contribution varies with ammonia to nitrite ratio. The ratio of 45N2O to 46N2O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N2O pool. O2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N2O. Our study highlights the power of dual 15N-18O isotope labeling to disentangle N2O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N2O sources.

Genome-centered metagenomics illuminates adaptations of core members to a partial Nitritation-Anammox bioreactor under periodic microaeration.

The partial nitritation-anaerobic ammonium oxidation (anammox; PN-A) process has been considered a sustainable method for wastewater ammonium removal, with recent attempts to treat low-strength wastewater. However, how microbes adapt to the alternate microaerobic-anoxic operation of the process when treating low ammonium concentrations remains poorly understood. In this study, we applied a metagenomic approach to determine the genomic contents of core members in a PN-A reactor treating inorganic ammonium wastewater at loading as low as 0.0192 kg-N/m3/day. The metabolic traits of metagenome-assembled genomes from 18 core species were analyzed. Taxonomically diverse ammonia oxidizers, including two Nitrosomonas species, a comammox Nitrospira species, a novel Chloroflexota-related species, and two anammox bacteria, Ca. Brocadia and Ca. Jettenia, accounted for the PN-A reactions. The characteristics of a series of genes encoding class II ribonucleotide reductase, high-affinity bd-type terminal oxidase, and diverse antioxidant enzymes revealed that comammox Nitrospira has a superior adaptation ability over the competitors, which may confer the privileged partnership with anammox bacteria in the PN-A reactor. This finding is supported by the long-term monitoring experiment, showing the predominance of the comammox Nitrospira in the ammonia-oxidizing community. Metagenomic analysis of seven heterotrophs suggested that nitrate reduction is a common capability in potentially using endogenous carbohydrates and peptides to enhance nitrogen removals. The prevalence of class II ribonucleotide reductase and antioxidant enzymes genes may grant the adaptation to cyclically microaerobic/anoxic environments. The predominant heterotroph is affiliated with Chloroflexota; its genome encodes complete pathways for synthesizing vitamin B6 and methionine. By contrast, other than the two growth factors, Nitrospira and anammox bacteria are complementary to produce various vitamins and amino acids. Besides, the novel Chloroflexota-related ammonia oxidizer lacks corresponding genes for detoxifying the reactive oxygen species and thus requires the aid of co-existing members to alleviate oxidative stress. The analysis results forecast the exchanges of substrates and nutrients as well as the collective alleviation of oxidative stress among the core populations. The new findings of the genomic features and predicted microbial interplay shed light on microbial adaptation to intermittent microaeration specific to the PN-A reactor, which may aid in improving its application to low-strength ammonium wastewater.

Spatiotemporal evolution and assembly processes of ammonia-oxidizing prokaryotic communities in 1000 years of coastal reclaimed soils

Coastal marshes are transitional areas between terrestrial and aquatic ecosystems and are sensitive to climate change and anthropogenic activities. In recent decades, the reclamation of coastal marshes has greatly increased, and its effects on microbial communities in coastal marshes have been studied with great interest. However, most of these studies have explained short-term spatiotemporal variation in soil microbial community dynamics. Besides, the impact of reclamation on functional microbial community composition and assembly processes is often ignored. Therefore, community structure and assembly processes of ammonia-oxidizing prokaryotes in long-term reclaimed coastal marshes have not been studied. In the current study, using qPCR and IonS5™XL sequencing platform, we investigated the spatiotemporal dynamics, assembly processes, and diversity patterns of ammonia-oxidizing prokaryotes in 1000-year-old reclaimed coastal salt marshes. The taxonomic and phylogenetic diversity and composition of ammonia oxidizers showed apparent spatiotemporal variations along with the reclamation of the soil. The phylogenetic null modelling-based analysis showed across all sites, the archaeal ammonia-oxidizing community was assembled by a deterministic process (84.71%), while stochastic processes dominated in the ammonia-oxidizing bacterial assemblage at stage 60 years (|βNTI| < 2), despite the relatively dominant deterministic process (55.2%). The assembly process and nitrification activity in reclaimed soils were positively correlated. An abundance of the amoA gene and changes in ammonia-oxidizing archaea (AOA) and bacteria (AOB) diversity significantly affect nitrification activity in reclaimed soils. These findings suggest that long-term coastal salt marsh reclamation affects nitrification by modulating the activities of ammonia-oxidizing microorganisms and regulating their community structures and assembly processes. These results provide a better understanding of the effects of long-term land reclamation on soil nitrogen-cycling microbial communities.

Meta-analysis of the effect of nitrification inhibitors on the abundance and community structure of N2O-related functional genes in agricultural soils

Application of nitrification inhibitors (NIs) in agricultural systems is an important strategy to enhance fertilizer nitrogen use efficiency and mitigate soil nitrous oxide (N2O) emissions. Here, we conducted a global meta-analysis of 88 published studies to assess the response of N2O-related functional gene and transcript abundances, and community structure to NIs application. Application of NIs significantly reduced the abundance of ammonia-oxidizing bacteria ammonia monooxygenase (AOB amoA) genes, AOB amoA transcript and nitrite reductase (nirS and nirK) genes. The effectiveness of NIs on reducing the AOB amoA abundance was influenced by N form, soil texture, soil pH and the experimental type (field vs. laboratory). Specifically, NIs were more effective when a mixed inorganic and organic N source was applied to a medium-textured soils. The NIs effectiveness increased with increasing soil pH. The response of AOB amoA abundance to NIs application was not affected by NI type, N rate, soil moisture, soil temperature and soil organic carbon (SOC). The inhibitory effect of NIs on nirS abundance increased with increasing soil temperature. NIs decreased soil nitrifying enzyme activity (NEA) and denitrifying enzyme activity (DEA) by 34.5 % and 27.0 %, respectively, leading to an overall 63.6 % reduction of N2O emissions. Soil NEA correlated positively with the abundance and community structure of AOB amoA but not with AOA amoA. Decrease in DEA with NIs application coincided with the decreasing nirS and nirK abundances. This global-scale assessment demonstrates that the effectiveness of NIs in reducing N2O emissions was attributed to the inhibiting effects on AOB amoA, nirS and nirK genes. Our findings highlight that NIs' inhibition effects on bacterial ammonia-oxidizing community and the encode enzymes in transformation of nitrite to nitric oxide are the main mechanisms for mitigation of N fertilizer-induced N2O emissions.

Effects of straw returning combined with earthworm addition on nitrification and ammonia oxidizers in paddy soil.

Soil ammonia oxidation, which acts as the first and rate-limiting step of nitrification, is driven by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox, amoA gene of clade-A and clade-B). Straw returning, widely used ecological technology in China, is an effective measure for promoting straw decomposition and soil nutrient cycling when combined with earthworm addition. However, the effects of straw returning combined with earthworm addition on soil ammonia oxidizers remain poorly understood. A 2-year plot experiment was conducted with 5 treatments: no fertilizer (CK); regular fertilization (RT); straw returning (SR); earthworm addition (W); straw returning + earthworm addition (SRW). The AOA, AOB, comammox clade-A and clade-B community microbial diversities and structures were investigated by high-throughput sequencing. The results showed that (1) compared to RT treatment, W, SR, and SRW treatments all significantly increased the richness of AOA and comammox clade-A and clade-B (p < 0.05), and the richness of AOB was only significantly promoted by SRW treatment (p < 0.05). However, only SRW had a higher comammox clade-B diversity index than RT. (2) The ammonia oxidizer community structures were altered by both straw returning and earthworm addition. Soil NH4 +-N was the critical environmental driver for altering the ammonia oxidizer community structure. (3) Compared with RT treatment, the soil potential nitrification rate (PNR) of W and SRW treatments increased by 1.19 and 1.20 times, respectively. The PNR was significantly positively correlated with AOB abundance (path coefficient = 0.712, p < 0.05) and negatively correlated with clade-B abundance (path coefficient = -0.106, p < 0.05). This study provides scientific support for the application of straw returning combined with earthworm addition to improve soil nitrification with respect to soil ammonia-oxidizing microorganisms.

Ammonia-oxidizing archaea and ammonium concentration as drivers of nitrification in a protected freshwater lake

Nitrification rates and ammonia-oxidizer functional gene abundance were measured in the water column of Lake Lacawac, Pennsylvania, USA, a freshwater lake on a nature sanctuary that allowed an investigation with minimal human impacts. Nitrification is a 2-step process consisting of ammonia oxidation followed by nitrite oxidation. Recent studies have shown that these 2 nitrification steps may be uncoupled and respond in different ways to environmental conditions. Additionally, the relative contribution of ammonia-oxidizing archea (AOA) vs ammonia-oxidizing bacteria (AOB) to nitrification rates varies widely across aquatic systems. To determine how nitrification rates are related to environmental parameters and the ammonia-oxidizing community in a nearly pristine environment, rates and gene abundance were measured over multiple seasons where in-situ environmental conditions varied. Rates of ammonia and nitrite oxidation were measured separately and summed to calculate total nitrification rates ranging from 1 to 568 nM/d. Ammonia oxidation rates generally outpaced nitrite oxidation rates, and rates of both ammonia and nitrite oxidation were higher at depth (10 m) compared with near-surface and mid water column. Ammonia oxidation, nitrite oxidation, and total nitrification rates were all strongly, positively correlated with in-situ [NH4+] (Kendall’s τ > 0.35, p < 0.02). AOB ammonia monooxygenase (amoA) gene copy numbers were generally greater than AOA amoA. However, AOB gene copy numbers were not correlated with any ammonia oxidation or total nitrification rates, whereas AOA abundance was positively correlated with both ammonia oxidation and total nitrification rates (Kendall’s τ > 0.41, p < 0.01). A Bayesian generalized additive model, which accounted for sampling month, indicated that total nitrification rates were best explained by AOA and [NH4+]. Thus, substrate concentration and AOA likely play key roles in regulating rates of nitrification in this small, nearly pristine freshwater lake. These reported relationships between rates of ammonia and nitrite oxidation (and, thus, total nitrification), in-situ environmental parameters, and the ammonia-oxidizer community in a protected environment establish a reference for evaluating the impact of a changing environment on mesotrophic lake water quality.

Effect of gradual increase of atmospheric CO2 concentration on nitrification potential and communities of ammonia oxidizers in paddy fields

Currently, the influence of elevated atmospheric CO2 concentration (eCO2) on ammonia oxidation to nitrite, the rate-limiting step of nitrification in paddy soil, is poorly known. Previous studies that simulate the effect of eCO2 on nitrification are primarily based on an abrupt increase of atmospheric CO2 concentration. However, paddy ecosystems are experiencing a gradual increase of CO2 concentration. To better understand how the nitrification potential, abundance and communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) respond to eCO2 in paddy ecosystems, a field experiment was conducted using the following two treatments: a gradual increase of CO2 (EC, increase of 40 ppm per year until 200 ppm above ambient) and ambient CO2 (CK). The results demonstrated that the EC treatment significantly (P < 0.05) stimulated the soil potential nitrification rate (PNR) at the jointing and milky stages, which increased by 127.83% and 27.35%, respectively, compared with CK. Furthermore, the EC treatment significantly (P < 0.05) stimulated the AOA and AOB abundance by 56.60% and 133.84%, respectively, at the jointing stage. Correlation analysis showed that the PNR correlated well with the abundance of AOB (R2 = 0.7389, P < 0.001). In addition, the EC treatment significantly (P < 0.05) altered the community structure of AOB, while it had little effect on that of AOA. A significant difference in the proportion of Nitrosospira was observed between CO2 treatments. In conclusion, the gradual increase of CO2 positively influenced the PNR and abundance of ammonia oxidizers, and AOB could be more important than AOA in nitrification under eCO2.

Substituting Inorganic Fertilizers with Organic Amendment Reduced Nitrous Oxide Emissions by Affecting Nitrifiers’ Microbial Community

Excessive inorganic fertilizers are one of the main causes of nitrous oxide (N2O) emissions. Organic fertilizers can not only reduce the use of nitrogen (N) fertilizers by increasing soil organic matter but are also safe for the environment. The partial replacement of nitrogen (N) fertilizers with organic fertilizers can potentially reduce N2O emissions. To illuminate the best ratio for the nitrogen replacement of inorganic fertilizer, the present experiment was conducted in dryland areas of central Gansu Province and different portions of inorganic N fertilizers (200 kg ha−1); i.e., 0, 50, 37.5, 25, and 12.5% were replaced with commercial organic fertilizers to test their effects on soil physicochemical properties, the grain yield of maize, N2O emissions, and the diversity of ammonia-oxidizing archaea (AOA) and bacterial (AOB) communities. Results showed that the maximum N2O emission was obtained by 100% inorganic fertilizers and the lowest was obtained at the control (no fertilizer). Substituting inorganic fertilizers with organic manure not only reduced N2O emissions but also improved soil organic carbon content and soil moisture and typically improves grain yield and biomass. The highest reduction in N2O emissions was recorded by 50% substitution. Furthermore, 37.5% and 12.5% substitutions did not reduce the grain yield and biomass compared to 100% inorganic fertilizer, and a 37.5% substitution performed better in improving soil fertility. Organic fertilizer increased the amoA copy number of AOA but decreased that of AOB. Nitrososphaera (AOA) and Nitrosospira (AOB) were the most dominant ammonia-oxidizing communities. Structural equation modeling indicated that AOB contributes more N2O emissions than AOA and is more sensitive to changes in pH, moisture, and NO3−−N, and the input of organic fertilizers may affect AOB by influencing soil physicochemical traits. In summary, replacing a reasonable proportion (37.5%) of inorganic fertilizers with organic manure improves soil fertility, reduces N2O emissions, and stabilizes production.

Distinct Nitrification Rates and Nitrifiers in Needleleaf and Evergreen Broadleaf Forest Soils.

Research on niche specialization in the microbial communities of ammonia oxidizers is important for assessing the consequences of vegetation shift on nitrogen (N) cycling. In this study, soils were sampled from three tree stands (needleleaf, mixed, and evergreen broadleaf) from the Hannam experimental forest in South Korea in spring (May 2019), summer (August 2019), autumn (November 2019), and winter (January 2020). Quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to measure the abundance and community structure of various nitrifiers: ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) as well as complete ammonia oxidizers (comammox). Nitrification rates and total ammonia oxidizer abundance were significantly higher in needleleaf forest soil than those in other forest stands, and they were lowest in evergreen broadleaf forest soil. Comammox clade B was most abundant in needleleaf and evergreen broadleaf forest soils, while AOA were significantly more abundant in mixed forest soil. The abundances of comammox clade B and AOA were negatively correlated with dissolved organic carbon. Phylogenetic analysis showed that NT-alpha and NS-gamma-2.3.2 were the most abundant AOA lineages in all the samples. The seasonal of AOA, AOB, and comammox varied with the sites, suggesting the need to examine the combinations of environmental factors when considering the effects of seasonal changes in the environment. Overall, the results suggest that potential vegetation shifts in forest ecosystems might affect nitrification activities by regulating the abundance and community structure of ammonia oxidizers.

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.

Biochar and lime amendments promote soil nitrification and nitrogen use efficiency by differentially mediating ammonia-oxidizer community in an acidic soil

Lime and biochar have been proposed as effective ameliorants for increasing soil fertility and nitrogen (N) cycling by regulating the ammonia-oxidizer community. However, the biological mechanisms of lime- and biochar-induced changes in the ammonia-oxidizer community, soil nitrification, crop productivity, and N use efficiency (NUE) remain largely unknown. Here, we established a 9-year field experiment to explore the ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and measure potential nitrification activity (PNA), crop productivity, and NUE in response to biochar and lime amendments. We found that soil pH was significantly increased under lime amendment more than under biochar amendment, while soil organic carbon, total nitrogen, and ammonia nitrogen followed the opposite trend. Lime and biochar amendments significantly increased the abundance and diversity of AOA and AOB, and substantially shaped the AOA and AOB community compositions. The co-occurrence networks analysis indicated that potential keystone taxa had negative relationships with connected members in the network, which exhibited significant correlations with the abundance and diversity of AOA and AOB communities, PNA, crop productivity, and NUE. Structural equation modelling indicated that biochar amendment may mediate potential keystone taxa to increase the abundance and diversity of AOB community, and exhibit a stronger impact on PNA, crop productivity, and NUE than lime amendment. Collectively, our results highlight the ecological importance of lime- and biochar-induced effects on the ammonia-oxidizer community and soil N cycling dynamics.