Diversity Of Ammonia-oxidizing Bacteria Research Articles

Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum

River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.

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.

The addition of discrimination inhibitors stimulations discrimination potential and N2O emissions were linked to predation among microorganisms in long term nitrogen application and straw returning systems.

Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) have been proven to be key microorganisms driving the ammonia oxidation process. However, under different fertilization practices, there is a lack of research on the impact of interaction between predators and AOA or AOB on nitrogen cycling at the multi-trophic level. In this study, a network-oriented microscopic culture experiment was established based on four different long-term fertilization practices soils. We used the nitrification inhibitors 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxide-3-oxyl (PTIO) and 3, 4-Dimethylpyrazole phosphate (DMPP) inhibited AOA and AOB, respectively, to explore the impact of interaction between protists and AOA or AOB on nitrogen transformation. The results showed that long-term nitrogen application promoted the potential nitrification rate (PNR) and nitrous oxide (N2O) emission, and significantly increased the gene abundance of AOB, but had no obvious effect on AOA gene abundance. DMPP significantly reduced N2O emission and PNR, while PTIO had no obvious effect on them. Accordingly, in the multi-trophic microbial network, Cercozoa and Proteobacteria were identified as keystone taxa of protists and AOB, respectively, and were significantly positively correlated with N2O, PNR and nitrate nitrogen. However, Nitrososphaerota archaeon as the keystone species of AOA, had an obvious negative linkage to these indicators. The structural equation model (SEM) showed that AOA and AOB may be competitors to each other. Protists may promote AOB diversity through direct trophic interaction with AOA. The interaction pattern between protists and ammonia-oxidizing microorganisms significantly affects potential nitrification rate and N2O emission, which has important implications for soil nitrogen cycle.

Spatial distribution of ammonia oxidizers in marine sediments of the Bohai, Yellow and East China Seas

Ammonia oxidation, an essential process within the global nitrogen cycle, is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). To date, the current knowledge on the biogeography of AOA and AOB in the ocean across a large geographic distance remains poorly known. In this study, the abundance, microbial composition, and diversity of AOA and AOB in marine sediments collected from the Bohai Sea, Yellow Sea, and East China Sea were characterized by employing quantitative PCR and Illumina Miseq sequencing of both archaeal and bacterial amoA genes. qPCR analysis demonstrated significantly higher abundances of archaeal amoA genes than those of bacterial amoA genes with AOA/AOB ratios varying from 1.59 to 292.88, suggesting a greater contribution of AOA to nitrification in the seas. Nitrosopumilus and Nitrosospira were the predominant clusters of AOA and AOB respectively in all sediment samples. The distribution pattern of both AOA and AOB communities revealed by PCoA (principal coordinate analysis) showed distinct geographic separation of sediment samples from the three seas. Correlation analysis indicated that ammonia (NH4+-N) and nitrate (NO3−-N) content were the main selective forces leading to the distinct biogeography of the two ammonia oxidizers in the ocean. The results are of great significance in improving our understanding of the contribution of AOA and AOB in the nitrogen transformation in the marine ecosystem and providing insights into the environmental factors that shape the assembly of aerobic ammonium oxidizers.

Characteristics of soil nitrogen and nitrogen cycling microbial communities in different alfalfa planting years

ABSTRACT Nitrogen cycling in soil and its microbial community characteristics are closely related. Characteristics of soil nitrogen, community diversity of nitrogen-fixing bacteria (NFB) and ammonia oxidizers were study with a traditional farmland as control and five treatment alfalfa fields of 1-, 2-, 3-, 4- and 5-year (a) cultivation. The results showed that total nitrogen (TN) significantly increased in 3, 4 and 5 a, alkali-hydrolysable nitrogen (AHN), NH4 +-N (AN), NO3 −-N (NN) and SOC was the highest in 3, 5, 3, 4 a, respectively. The dominant phylum of NFB and ammonia-oxidizing bacteria (AOB) belonged to Proteobacteria with a higher diversity and abundance in 3 and 4 a. Crenarchaeota was found the dominant phylum of ammonia-oxidizing archaea (AOA) with the highest abundance in the alfalfa field planted for 2 a. The dominant genus of NFB and AOB were Azohydromonas and Nitrosospira, respectively, which showed the highest abundance in the alfalfa fields planted for 2 and 3 a, respectively. The diversity of NFB and AOB showed a significantly positive correlation with TN and AHN (p < 0.05). AOA showed a significantly negative correlation with AN (p < 0.05). Many microbial species cannot be annotated in this study, which deserves future investigation.

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.

Reassembly of active ammonia oxidizing bacteria following invasion of exogenous microbiome in an acidic soil

Ammonia oxidation is the rate-limiting step of the global nitrogen cycle, and it is mainly catalyzed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). AOA can carry out nitrification even in acidic soils, whereas AOB activity was not consistently observed in acidic soils. In this study, we manipulated two environmental variables, i.e., the microbial composition and ammonium source (urea and ammonium sulphate), in an acidic forest soil and tested their impacts on AOB abundance, diversity and activity. Soil microcosms were established either using the native forest soil (FS) or after amending the forest soil with 5% (w/w) agricultural soil (AFS) to inoculate new, exogenous microbes. Under the same microcosm incubation condition for 28 days, AOB did not grow in FS but they grew in AFS, suggesting that exogenous microbial invasion could stimulate AOB activity in the acidic soil. Urea amendment led to higher growth of AOB than ammonium sulphate amended in AFS microcosms. DNA-based stable isotope probing revealed that the active AOB lineages were dominated by Nitrosospira cluster 3a.2 and Nitrosospira cluster 10 in the ammonium sulphate supplied soil, but shifted to co-dominance of Nitrosospira cluster 3a.2 and Nitrosospira cluster 1 after urea amendment, demonstrating differential preferences of ammonia sources of phylogenetically distinct AOB lineages. Additionally, AOB abundance showed lower stability than AOA in soils subjected to these two environmental changes, suggesting AOB are more important in determining the fate of soil nitrification following short-term environmental disturbances.

The activity of ammonia-oxidizing bacteria on the residual effect of biochar-compost amended soils in two cropping seasons

Ammonia-oxidizing bacteria (AOB) are vital in regulating nitrification in agricultural soils. Nevertheless, the knowledge of the AOB community's response to fortified and composted biochar application in the maize/soybean agroecosystem is scarce. This study examined the residual effects of a control soil (CNZ), biochar (BIZ), compost (CPZ), composted biochar (CBZ), and fortified biochar (FBZ) on the AOB community composition, soil chemical properties, and enzyme activities in 2018 and 2019 of a maize/soybean agroecosystem. The AOB community was unravelled using Illumina Miseq sequencing, and multivariate approaches were used to explain the data collected. In 2018, FBZ increased the content of NO3--N, while CPZ, CBZ, and FBZ improved total nitrogen (TN) in the soil. In 2019, CBZ and FBZ increased NO3--N content, while CPZ improved TN and NO2--N in the soil. Likewise, CPZ significantly differed from FBZ, CBZ, and BIZ in AOB richness, while CBZ significantly differed from BIZ in AOB diversity in 2019. Furthermore, distance-based redundancy analysis (db-RDA) and Spearman correlation showed a significant correlation with NH4+-N and NO2--N in 2018 and TN and NO3--N in 2019, while Nitrosomonas eutropha and Nitrosomonas nitrosa had the highest weighted degree in the co-occurrence network in both years. This research demonstrates that co-application of biochar with compost in the maize/soybean agroecosystem could result in changes in the AOB community structure.

Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea

Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.

Manure combined with biochar reduces rhizosphere nitrification potential and amoA gene abundance of ammonia-oxidizing microorganisms in acid purple soil

Fertilization and soil environmental factors determine the niche differentiation of ammonia-oxidizing microorganisms, thereby affecting the ammonia-oxidation process. However, the characteristics of rhizosphere potential nitrification rate (PNR), ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) population under manure combined biochar are unclear. In this study, a pot experiment growing lemon was conducted, setting up six treatments, namely no fertilization (CK), chemical fertilizer (CF), manure (M), chemical fertilizer combined with biochar (CFBC), manure combined with biochar (MBC), fresh manure combined with biochar (FMBC). We investigated the effects of manure, chemical fertilizer and manure combined with biochar on soil physical-chemical properties, PNR, and the amoA gene abundance, diversity and structure of AOA and AOB in the rhizosphere. Our results showed that compared with CK treatment, CF and CFBC increases PNR by 19.3–34.7 % in the rhizosphere, M, MBC and FMBC decrease PNR about 60.0 %; CF and CFBC increased AOA amoA gene copies by 40.2–101.7 %, while M, MBC and FMBC treatments decreased it by 66.5–81.9 %, five fertilization treatments decreased the AOB amoA gene copy by 33.1–81.9 %. The redundancy analysis showed that chemical fertilizer and manure combined with biochar affects the population structure of AOA and AOB by pH, available phosphorus (AP), ratio of carbon to nitrogen (C/N), soil moisture content (SMC), nitrate nitrogen (NO3−-N) and ammonium nitrogen (NH4+-N) in the rhizosphere. The results of partial least squares indicated that pH, total nitrogen (TN), AOA amoA gene copy and AOA Shannon index were main factors affecting nitrification potential in the rhizosphere. Therefore, AOA dominates the ammonia oxidation process in the acid purple soil under the condition of chemical fertilizer and pig manure combined with rice husk biochar. Meanwhile, fertilization affected ammonia oxidation process by regulating soil pH and TN in lemon rhizosphere soil.

Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers.

The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4+-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4+, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.

Effects of aquatic nitrogen pollution on particle-attached ammonia-oxidizing bacteria in urban freshwater mesocosms.

Ammonia-oxidizing bacteria (AOB) attached to aquatic particles are important participants in ammonia oxidation within hypereutrophic urban river systems. To explore the effects of aquatic nitrogen pollution on particle-attached AOB in urban river, we utilized laboratory mesocosms to investigate the responses of abundances and community structure of particle-attached AOB to ammonium (NH4+) and glycine (C2H5NO2) amendments. The abundance and community structure of particle-attached AOB were determined with quantitative real-time polymerase chain reaction (qRT-PCR) analysis and high-throughput sequencing based on the AOB amoA gene, respectively. Most of the bacterial amoA sequences from different treatments were affiliated with uncultured Nitrosomonadaceae bacterium, uncultured Nitrosomonadales bacterium, and uncultured Nitrosomonas sp., which are closely associated with organic pollution. The species richness and diversity of particle-attached AOB communities increased with increasing NH4+ and glycine concentrations. Treatment effects contributed significantly to the variance in particle-attached AOB communities. Although, glycine was completely transformed to ammonium within a few days and ammonium amendments would change the community structure of particle-attached AOB, the effect of glycine on the particle-attached AOB community was regulated by both the resulting ammonium concentration, as well as organic matter availability to the heterotrophic bacteria. Results suggested that high anthropogenic nitrogen loadings appeared to promote higher particle-attached AOB richness and diversity in the hypereutrophic urban river, but the effect of organic nitrogen on the particle-attached AOB community was different from the effect of inorganic nitrogen. This study informs ammonia oxidization mechanisms in the hypereutrophic urban rivers, which contributes to remediation/restoration strategies.

Biochar Addition Inhibits Nitrification by Shifting Community Structure of Ammonia-Oxidizing Microorganisms in Salt-Affected Irrigation-Silting Soil.

Biochar has been widely recognized as an effective and eco-friendly ameliorant for saline soils, but information about the mechanism of how biochar influences nitrification in salt-affected agroecosystem remains fragmented. An incubation experiment was performed on the salt-affected soil collected from a three-consecutive-year experiment at biochar application gradients of 7.5 t⋅ha−1, 15 t⋅ha−1 and 30⋅t ha−1 and under nitrogen (N) fertilization. Responses of the nitrification rate (NR), numbers of ammonia monooxygenase (amoA) gene copies, and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to biochar application were investigated. The results indicated that, under N fertilization, the NR and numbers of amoA-AOB and amoA-AOA gene copies negatively responded to biochar addition. Biochar application increased the community diversity of AOB but decreased that of AOA. Biochar addition and N fertilization shifted the AOB community from Nitrosospira-dominated to Nitrosospira and Nitrosomonas-dominated, and altered the AOA community from Nitrososphaera-dominated to Nitrososphaera and Nitrosopumilus-dominated. The relative abundance of Nitrosospira, Nitrosomonas and Nitrosopumilus decreased, and that of Nitrosovibrio and Nitrososphaera increased with biochar application rate. Soil SOC, pH and NO3−-N explained 87.1% of the variation in the AOB community, and 78.1% of the variation in the AOA community was explanatory by soil pH and SOC. The SOC and NO3−-N influenced NR through Nitrosovibrio, Nitrosomonas, Norank_c_environmental_samples_p_Crenarchaeota and amoA-AOB and amoA-AOA gene abundance. Therefore, biochar addition inhibited nitrification in salt-affected irrigation-silting soil by shifting the community structures of AOB and AOA and reducing the relative abundance of dominant functional ammonia-oxidizers, such as Nitrosospira, Nitrosomonas and Nitrosopumilus.

Ammonia-oxidizing bacteria and fungal denitrifier diversity are associated with N2O production in tropical soils

Nitrous oxide (N2O) production in tropical soils cultivated with sugarcane is associated with ammonia-oxidizing bacteria (AOB) and fungal denitrifiers. However, the taxonomic identities and the community diversities, compositions, and structures of AOB and fungal denitrifiers in these soils are not known. Here, we examined the effects of applying different concentrations of an organic recycled residue (vinasse: regular non-concentrated or 5.8-fold concentrated) on the dynamics of AOB and fungal denitrifier community diversity and composition and greenhouse gas emissions during the sugarcane cycle in two different seasons, rainy and dry. DNA was extracted from soil samples collected at six timepoints to determine the dynamics of amoA-AOB and nirK-fungal community diversity and composition by amplicon sequencing with gene-specific primers. Bacterial and archaeal amoA, fungal and bacterial nirK, bacterial nirS and nosZ, total bacteria (16S rRNA) and total fungi (18S rRNA) were quantified by real-time PCR, and N2O and CO2 emissions were measured. The genes amoA-AOB and bacterial nirK clade II correlated with N2O emissions, followed by fungal nirK. The application of inorganic nitrogen fertilizer combined with organic residue, regardless of concentration, did not affect the diversity and structure of the AOB and fungal denitrifier communities but increased their abundances and N2O emissions. Nitrosospira sp. was the dominant AOB, while unclassified fungi were the dominant fungal denitrifiers. Furthermore, the community structures of AOB and fungal denitrifiers were affected by season, with dominance of uncultured Nitrosospira and unclassified fungi in the rainy season and the genera Nitrosospira and Chaetomium in the dry season. Nitrosospira, Chaetomium, Talaromyces purpureogenus, and Fusarium seemed to be the main genera governing N2O production in the studied tropical soils. These results highlight the importance of deciphering the main players in N2O production and demonstrate the impact of fertilization on soil microbial N functions.

Global meta-analysis of terrestrial nitrous oxide emissions and associated functional genes under nitrogen addition

Functional genes involved in nitrogen (N) cycling regulate soil nitrification, denitrification and N2O emissions. However, the general patterns and variability of N functional genes in response to N addition, and their association with N2O emission have not been synthesized for terrestrial ecosystems. We synthesized 2068 observations from 144 papers to explore the impact of N addition on the abundance and diversity of N functional genes, and their relationship to N2O emissions in croplands, grasslands and forests on a global scale. In croplands, N addition increased N2O emissions (109%), the abundance of ammonia-oxidizing archaea (AOA) (19%), ammonia-oxidizing bacteria (AOB) (95%), nirK (52%), nirS (40%) and nosZ (41%), and the diversity of AOB (15%), nirS (12%) and nosZ (11%). In grassland, N addition increased AOB abundance (130%) and decreased the abundance of nirS (−99%) and nosZ (−58%) genes, but in forests, significant effects were only found for the abundance of AOA (35%) and AOB (121%). N2O emission was negatively correlated with the abundance of nosZ, but positively correlated with the abundance of AOA and AOB. Apart from the abundance of functional AOA, AOB and nosZ genes, climate variables (precipitation and temperature), and available N concentrations were the main factors explaining the variation in N2O emission with N addition, as shown by random forest analysis. These findings indicate that impacts on N functional genes that encode enzymes involved in nitrification (AOA, AOB) and in the transformation of N2O to N2 (nosZ) are the main mechanisms behind the effect on N fertilizer-induced N2O emissions.

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.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (PN) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and PN values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH3 and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

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.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes.

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages.

Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages. We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and β-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase. AOA and AOB play the different ecological roles in SCP sediments at different culture stages. Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.