Composition Of Ammonia-oxidizing Archaea Research Articles

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments

The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3−-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.

Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities.

Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2–), which can be further oxidized to nitrate (NO3–). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2– and NO3–, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4+) and NO3–—and NO2–—dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.

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.

English

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

Characteristics of Ammonia Removal and Nitrifying Microbial Communities in a Hybrid Biofloc-RAS for Intensive Litopenaeus vannamei Culture: A Pilot-Scale Study

Ammonia is the main pollution factor of the aquatic environment in marine shrimp culture systems. In order to demonstrate the feasibility of the combination of biofloc technology and nitrifying biofilter for the ammonia removal, a 70-day production trial was conducted in a simplified pilot-scale hybrid biofloc-based recirculating aquaculture system (biofloc-RAS) with the intensive culture of Litopenaeus vannamei. Nitrogen dynamics and nitrifying microbial communities were investigated in three replicated systems simultaneously under the conditions of high feed loading and zero water exchange. Along with biofloc development in the culture tank and biofilm formation in the nitrifying biofilter during the trial, nitrification could be fastly and effectively established in the system, which was indicated by the dynamics of total ammonia nitrogen (TAN), NO2–-N, NO3–-N, and total nitrogen (TN) concentrations. Meanwhile, similar nitrifying microorganisms could be found between biofloc and biofilm, despite some differences in abundance, diversity, and composition of ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. High TAN removal rate could be achieved and was significantly and positively correlated with abundances of these nitrifying microbial communities in both biofloc and biofilm, further indicating that both biofloc and biofilm could contribute highly to nitrification performance of the biofloc-RAS. The results of this study indicate a potential application of the biofloc-RAS in coastal intensive aquaculture.

Tillage, not fertilization, dominantly influences ammonia-oxidizing archaea diversity in long-term, continuous maize

Ammonia-oxidizing archaea (AOA) catalyze a rate-limiting step in nitrification - ammonia (NH3) oxidation. There are more AOA than ammonia-oxidizing bacteria (AOB) in many soil systems, including cropland, and AOA dominate in unfavorable environmental conditions, such as soils with low NH4-N. The ecological role of the ubiquitously distributed AOA is unclear, as are the factors regulating AOA community dynamics. This study investigated how long-term N fertilization and tillage management influenced the AOA community in cropland. The study site was a long-term (>40 years) field experiment with either no-tillage (NT) or plow tillage (PT) at three N fertilizer rates (0, 168, and 336 kg ha−1) and continuous maize (Zea mays L.). We used PCR-denaturing gradient gel electrophoresis (DGGE) to assess the archaeal amoA gene as a measure of the changing AOA community. Tillage rather than N fertilizer played the dominant role affecting the AOA community. Fertilizer rate did not significantly influence AOA diversity, but sample season and N fertilization had selection function on AOA composition. In winter, AOA were more diverse in NT than PT. Unique groups were discovered in different treatments, demonstrating selection by tillage, fertilization, season, and/or their interactions. The significant tillage regulation of AOA provides new clues to investigate which environmental factors influence the AOA community and to explore its ecological significance in agricultural land.

Sorgoleone release from sorghum roots shapes the composition of nitrifying populations, total bacteria, and archaea and determines the level of nitrification

Sorgoleone is a secondary sorghum metabolite released from roots. It has allelopathic properties and is considered to inhibit ammonia-oxidizing archaea (AOA) and bacteria (AOB) responsible for the rate-limiting step (ammonia oxidation) in nitrification. Low activity of these microorganisms in soil may contribute to slow down nitrification and reduce nitrogen loss via denitrification and NO3− leaching. The potential nitrification rate (PNR) and the composition of microbial communities were monitored in rhizosphere soil to investigate the growth effect sorghum on biological nitrification inhibition (BNI). A greenhouse pipe experiment was conducted using sorghum lines IS20205 (high-sorgoleone release ability), IS32234 (medium-sorgoleone release ability), 296B (low-sorgoleone release ability), and a control (no plants) combined with fertilization application of 0 or 120 kg N ha−1. We applied nitrogen as ammonium sulfate at 16 days (20 N), 37 days (40 N), and 54 days (60 N). We collected soil solutions at 7.5 cm depths every 3 days and measured the pH and nitrate levels. At 1 and 2.3 months, we sampled the bulk and rhizosphere soils and roots in the 0–10 cm, 10–30 cm, and 30–80 cm depths to determine NO2, mineral N, total N, total C, sorgoleone, the composition of AOA, AOB, and total bacteria and archaea. Sorgoleone was continuously released throughout the 2.3 months’ growth and was significantly higher in IS20205, followed by IS32234 then 296B, which showed shallow levels. The IS2020 5rhizosphere showed lower NO2 and nitrate levels and significant inhibition of AOA populations. However, we did not find significant differences in the abundance of AOB between plant treatments. Multivariate analysis and Spearman’s correlations revealed that sorgoleone as well as environmental factors such as soil pH, soil moisture, NO3−-N, and NH4+-N shape the composition of microbial communities. This study demonstrated that the release of higher amounts of sorgoleone has great potential to inhibit the abundance of AOA and soil nitrification. The breeding of sorghum lines with the ability to release higher amounts of sorgoleone could be a strategic way to improve the biological nitrification inhibition during cultivation.

Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests.

Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.

Population and community structure shifts of ammonia oxidizers after four-year successive biochar application to agricultural acidic and alkaline soils

Long-term studies that advance our mechanistic understanding of biochar (BC)‑nitrogen (N) interactions in agricultural soils are lacking. In this study, soil potential nitrification rates (PNR), the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities following 4-year of BC application were investigated using the shaken-slurry procedure and molecular sequencing techniques for an acidic Oxisol (QU) and an alkaline Cambisol (YU). Soils were obtained from an outdoor soil column experiment with straw-BC application rates of 0 (BC0), 2.25 (BC2.25) and 11.3 (BC11.3) Mgha−1 per cropping season for eight consecutive wheat/millet seasons. Quantitative polymerase chain reaction (qPCR) and 454 high-throughput pyrosequencing techniques were performed to quantify and sequence amoA gene copies and composition of AOA and AOB. Results showed that QU had lower PNR and a higher ratio of amoA gene copies of AOA to AOB than YU, PNR of QU with BC application was significantly associated with the amoA gene of AOB. Similar to previous short-term findings, BC application enhanced QU soil nitrification, which may be explained by the significant increase in AOB abundance and a shift in AOB community structure from Nitrosospira cluster 2 toward cluster 3, along with the disappearance of some obligate acidophile AOA groups, leading to the appearance of ammonia-oxidizers from neutral-alkaline soils in BC-amended acid soils. Canonical correspondence analysis (CCA) showed that soil pH was the most important factor driving shifts in ammonia-oxidizers composition. Although BC application did not have significant effects on PNR in YU, BC11.3 decreased AOA and AOB gene copies and influenced the relative abundance of community structure. Our findings represent the first investigation of long-term BC effects on AOA and AOB communities in agricultural soils using 454 high-throughput pyrosequencing, showing that BC application can alter soil characteristics and influence ammonia oxidizer community composition, abundance, especially in acid soils.

Irrigation frequency alters the abundance and community structure of ammonia-oxidizing archaea and bacteria in a northern Chinese upland soil

Ammonia oxidation, the first and rate-limiting step in nitrification, is a key process in biogeochemical nitrogen cycling. However, little is known about how irrigation affects ammonia oxidizing microorganisms in agroecosystems. In this study, effects of irrigation frequency on soil potential nitrification activity (PNA), the abundance and composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated using real-time PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP), and clone libraries for characterizing the ammonium monooxygenase genes (amoA) in a northern Chinese soil. Results showed that irrigation significantly increased soil PNA and archaeal amoA gene abundance but decreased bacterial amoA gene abundance. Soil PNA was positively correlated with archaeal amoA gene abundance and negatively correlated with bacterial. T-RFLP and PCA results showed that irrigation greatly changed the AOA and AOB community structures by altering the relative abundances of four T-RFs of AOA and four other T-RFs of AOB, respectively. Phylogenetic analysis revealed that all archaeal sequences fell into Group 1.1b, and the bacterial clones were dominated by Nitrosospira-like sequences within Cluster 3a.2. Irrigation induced the appearance of two archaeal and two bacterial OTUs and increased the relative abundance of another two archaeal and four bacterial OTUs, respectively. Additionally, soil moisture, soil pH, NH4+-N, and NO3−-N correlated significantly with the AOA community, and soil pH, total nitrogen (TN), and NO3−-N were significantly correlated with the AOB community. Our results demonstrate that irrigation greatly affected the abundance and community structure of AOA and AOB and that AOA appeared to play a more important role in nitrification in the study soil.

Distinct drivers of activity, abundance, diversity and composition of ammonia-oxidizers: evidence from a long-term field experiment

Ammonia oxidation, the primary and rate-limiting step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the dominant environmental driver of the activity, abundance, diversity and composition of ammonia-oxidizers has not been well understood enough, and the relative contribution of AOA and AOB to nitrification is still under debate. Soils treated with different fertilization regimes in an over 35-year field experiment were collected to explore the variation in function and structure of ammonia-oxidizer communities and corresponding driver. The highest nitrification activity (44.49 mg N kg−1 soil d−1) was found in only organic fertilizer (O) treated soil, whereas the lowest activity (2.81 mg N kg−1 soil d−1) was observed in only mineral fertilizer (NPK) treated soil. Moreover, as 1-octyne was employed to discriminate AOA- and AOB-supported nitrification, AOA dominated (93.53%) the nitrification in the Control soil, while AOB contributed dominantly (84.73–89.10%) in all of the organic amended soils, and NPK-treated soil showed an almost equal contribution to AOA (45.79%) and AOB (54.21%). Compared with the Control soil, AOA abundance increased in soils with organic and low chemical fertilizer but decreased in only chemically treated soil, whereas the AOB abundance in all fertilized soils was greatly enhanced. The AOA activity was linearly dependent on AOA abundance, whereas the AOB activity was exponentially correlated with AOB abundance. The sequences of AOA and AOB in the Control soil were mostly affiliated with group I.1b thaumarchaeota and genus Nitrosospira clusters 3a.1. Soil treated with NPK increased the abundance of AOA that belonged to group I.1a-associated lineage, whereas more abundant AOB was related to Nitrosospira clusters 3a.2 and 8b. In contrast, the O-treated soil showed more abundant AOB that belonged to Nitrosospira clusters 3b and 8b. As revealed by aggregated boosted tree analysis, the soil ammonium (NH4+) content was identified as the dominant driver of activity and diversity of AOA, and soil pH was considered to be the major influencing factor in abundance and composition of AOA; the AOB composition was mainly affected by soil NH4+ content, the relative activity and diversity by soil pH, and the relative abundance by soil electrical conductivity (EC). Collectively, different fertilization regimes will result in variations in activity, abundance, diversity and composition of ammonia-oxidizers with distinct drivers. Our research could be helpful to identify better strategies for the mitigation of nitrate production in agricultural soils.

Ammonia-oxidizing archaea and bacteria responding differently to fertilizer type and irrigation frequency as revealed by Illumina Miseq sequencing

Ammonia oxidation, the first and rate-limiting step of nitrification, can be strongly influenced by agricultural practices, but little is known about the effects of fertilization and irrigation combination on ammonia oxidizers in agricultural soils. This study was designed to reveal how fertilizer type and irrigation frequency affect the ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities in a northern Chinese wheat-maize rotation soil. Soil samples were collected from a long-term field experiment under different fertilization and irrigation regimes located in Wuqiao Experimental Station of China Agricultural University in June 2016. The abundance, diversity, and composition of AOA and AOB in the soils were investigated by using real-time PCR and Illumina Miseq sequencing approaches. The abundance of AOA was higher in the irrigated treatments, but lower in the treatments without irrigation, than that of AOB. The AOA abundance was positively correlated with soil moisture, pH, and NO3 −-N, while the AOB abundance was positively correlated with TN and NO3 −-N. Soil potential nitrification activity (PNA) was significantly positively correlated with the AOB abundance. Both fertilizer type and irrigation frequency significantly affected Shannon, ACE, and Chao1 indices of the AOB community, while only irrigation frequency had a significant impact on Shannon index of the AOA community. PCoA analysis results indicated that irrigation frequency greatly affected the AOA community structure, while fertilizer type played a more important role in affecting the AOB community structure. Mantel test and correlation heatmap analysis results indicated that soil moisture, pH, and NH4 +-N were significantly correlated to the AOA community structure, and TN and SOC were significantly correlated to the AOB community structure. This study demonstrated that irrigation frequency greatly influenced the AOA community, while fertilizer type had a stronger effect on the AOB community. It was AOB but not AOA played a more important role in soil nitrification. Moreover, soil moisture, pH, and TN were the main determinants in driving the AOA community and TN and SOC were the main factors in influencing the AOB community.

Ammonia-oxidizing bacteria rather than archaea respond to short-term urea amendment in an alpine grassland

Chemical fertilizers, especially nitrogen (N) and phosphorus (P), are used in grasslands to maximize plant biomass production for livestock. Despite a substantial body of work on how fertilization affects aboveground plant and belowground microbial communities, the short-term response of soil ammonia-oxidizing microbial communities, which play the central role in nitrification, to fertilization is not well understood. The responses of ammonia-oxidizing microbial communities to short-term (3 years) N and/or P additions were investigated in an alpine grassland of the Qinghai-Tibetan Plateau. Quantitative polymerase chain reaction (qPCR) analysis of the amoA genes showed that ammonia-oxidizing archaea (AOA) dominated over ammonia-oxidizing bacteria (AOB) in non-amended soil. Short-term urea addition significantly increased the abundance of AOB, whereas AOA abundance remained unchanged, resulting in a shift from AOA to AOB dominance, which suggests that AOB are likely to be more important in the first step of the nitrification following urea amendment. Pyrosequencing demonstrated a significant shift in AOB but not AOA community composition within short-term N fertilizer plots, indicating that AOB community composition was more sensitive than AOA in response to urea amendment. This study demonstrated that the abundance and composition of AOA and AOB communities responded differently to 3 years of urea addition, suggesting that N fertilizer may be an important controller of ammonia-oxidizing microbial communities in managed alpine grasslands, such as those of the Qinghai-Tibet Plateau.

Determinants of the biodiversity patterns of ammonia-oxidizing archaea community in two contrasting forest stands

The variation in soil microbial community patterns is primarily influenced by ecological processes associated with spatial distance and environmental heterogeneities. However, the relative importance of these processes in determining the patterns of soil microbial biodiversity in different successional forests remains unclear. Based on the species data from denaturing gradient gel electrophoresis (DGGE) analysis, we described the composition and beta diversity of ammonia-oxidizing archaea (AOA) community, an important functional microbial group in regulating nitrogen cycle, in a middle-succeed stand (60 years of secondary succession) and an undisturbed native stand in a subtropical forest in southern China. The composition pattern was examined using a multi-response permutation procedure (MRPP), and the beta diversity was described using the Sorensen index. The relative influence of edaphic, vegetational, spatial, and topographical factors on AOA composition and beta diversity was assessed by variation partitioning and multiple regression on distance matrices (MRM), respectively. We did not find any stand-specific patterns in AOA community composition in the two stands; however, the influential variables were different between the two stands; 7.3 and 4.5 % of the total variation in AOA community composition could be explained by edaphic (i.e., available potassium and total phosphorus) and spatial variables, respectively, in the middle-succeed stand, while 3.7 and 2.8 % of the variation were explained by spatial variable and available phosphorus, respectively, in the native stand. Soil total phosphorus influenced the beta diversity of AOA community most in the middle-succeed stand, while genetic distance of tree species was found to be the most important factor in driving the beta diversity pattern in the native stand. Soil nutrients influenced the beta diversity of AOA community in the middle-succeed stand more than that in the native stand, while vegetation is more important in the native stand. The substantial unexplained variations were possibly due to the effects of other unmeasured variables. Nevertheless, dispersal process is more important in controlling AOA community composition in the native stand, while processes associated with environmental heterogeneities are more important in the middle-succeed stand in this subtropical forest.

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China.

Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira.

Comparison of straw-biochar-mediated changes in nitrification and ammonia oxidizers in agricultural oxisols and cambosols

The responses of nitrification on intensively managed agricultural soils following long-term biochar (BC) amendment are poorly understood. The nitrification potential, abundance, and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in acidic oxisols and alkaline cambosols following a 3-year BC treatment were investigated using 42-day aerobic incubation, quantitative polymerase chain reaction (qPCR), and clone library approach, respectively. Fresh soils were collected from a wheat/millet rotated pot trial in which 0 (control), 2.25, and 22.5 Mg ha−1 rice straw BCs were added for six consecutive crop seasons. The 22.5 Mg ha−1 BC (BC22.5) treatment enhanced nitrification in oxisols and even altered nitrification pattern from zero-order to first-order reaction model. AOA and AOB gene copies in the BC22.5 treatment were 9.55 and 22.0 times, respectively, compared with those in the BC0 treatment. The relative abundance of operational taxonomic units (OTUs) in AOA group 1.1a changed due to BC application, and that of OTU-20 was high in group 1.1b-related under the BC22.5 treatment. AOB community composition shifted toward Nitrosospira cluster 3 and 3-related group under the BC22.5 treatment. Basal nitrification was already high in cambosols, and BC had minimal effect on nitrification or AOA/AOB abundance. However, the BC22.5 treatment increased the relative abundance of OTU-9 in Nitrosospira cluster 3 group and that of OTU-13 and OTU-16 in Nitrosospira cluster 3-related groups both being AOB. The BC amendment had minimal effect on ammonia oxidizer composition in cambosols but influenced ammonia oxidizer composition and stimulated nitrification activity in oxisols.

Long-term application of organic manure changes abundance and composition of ammonia-oxidizing archaea in an acidic red soil

Ammonia-oxidizing archaea (AOA) have more importance in ammonia oxidation than ammonia-oxidizing bacteria (AOB) in acidic red soils. The aim of this study was to investigate if the abundance and composition of AOA could be altered by long-term application of organic manure in an acidic red soil. The abundance and composition of AOA were evaluated by polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) targeting archaeal amoA genes after long-term (24-year) application of mineral fertilizer and/or organic manure. The treatments were: non-fertilized control, mineral nitrogen (N) fertilizer only, mineral N, phosphorus (P) and potassium (K) fertilizer only, organic manure only, and organic manure plus mineral NPK fertilizer. The abundance of archaeal amoA genes was significantly increased after the long-term application of organic manures, either with or without mineral NPK fertilizer. So were the Shannon and Richness diversity indices of AOA deduced from the DGGE patterns. Phylogenetic analyses showed that most of the AOA sequences from various fertilization treatments were affiliated with group 1.1b thaumarchaea and only one with the group 1.1a-associated thaumarchaea. Nitrification potential was significantly increased after the long-term application of organic manures in comparison with the non-fertilized control. Our results strengthened the importance of organic manure in promoting the growth of AOA and thus nitrification potential in the acidic red soils.

Altitudinal Distribution of Ammonia-Oxidizing Archaea and Bacteria in Alpine Grassland Soils Along the South-Facing Slope of Nyqentangula Mountains, Central Tibetan Plateau

Nitrogen is a major limiting nutrient for the net primary production of terrestrial ecosystems, especially on sentinel alpine ecosystem. Ammonia oxidation is the first and rate-limiting step on nitrification process and is thus crucial to nitrogen cycle. To decipher climatic influence on ammonia oxidizers, their communities were characterized by qPCR and clone sequencing by targeting amoA genes (encoding the alpha subunit of ammonia mono-oxygenase) in soils from 7 sites over an 800 m elevation transect (4400–5200 m a.s.l.), based on “space-to-time substitution” strategy, on a steppe-meadow ecosystem located on the central Tibetan Plateau (TP). Archaeal amoA abundance outnumbered bacterial amoA abundance at lower altitude (<4800 m a.s.l.), but bacterial amoA abundance was greater in surface soils at higher altitude (≥4800 m a.s.l.). Archaeal amoA abundance decreased with altitude in surface soil, while its abundance stayed relatively stable and was mostly greater than bacterial amoA abundance in subsurface soils. Conversely, bacterial amoA abundance gradually increased with altitude at all three soil depths. Statistical analysis indicated that altitude-dependent factors, in particular pH and precipitation, had a profound effect on the abundance and community of ammonia-oxidizing bacteria, but only on the community composition of ammonia-oxidizing archaea along the altitudinal gradient. These findings imply that the shifts in the relative abundance and/or community structure of ammonia-oxidizing bacteria and archaea may result from the precipitation variation along the altitudinal gradient. Thus, we speculate that altitude-related factors (mainly precipitation variation combing changed pH), would play a vital role in affecting nitrification process on this alpine grassland ecosystem located at semi-arid area on TP.

Abundance of ammonia-oxidizing bacteria and archaea in industrial and domestic wastewater treatment systems

Nitrification plays a significant role in the global nitrogen cycle. Ammonia oxidation, the first step of nitrification, is performed in wastewater treatment by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Most previous studies focused on their distribution in natural environments. In this study we qualified and quantified AOB, AOA, total bacteria, and total archaea in six different wastewater treatment systems (WTSs) using clone library and real-time PCR techniques. The results revealed that wastewater quality was an essential factor for the distribution of AOB and AOA in aerobic reactors. Although both AOB and AOA were present in all samples and contributed to nitrification simultaneously, AOB were the dominant nitrifiers in the three industrial WTSs, whereas AOA were dominant in the three domestic WTSs. This indicates AOA may be more sensitive to some toxic compounds than AOB. In addition, the dominant groups of AOB in the industrial WTSs were Nitrosomonas and Nitrosospira; the composition of AOA in the domestic WTSs was very similar, possibly due to the same source of raw sewage.

Impacts of Spartina alterniflora invasion on abundance and composition of ammonia oxidizers in estuarine sediment

Spartina alterniflora widely invades coastal wetland in China and might change nitrification in sediment. Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are involved in nitrification in this environment. The objective of this study was to examine the effect of S. alterniflora invasion on abundance and composition of AOA and AOB. The abundance and composition of AOA, AOB, and total bacteria in the sediments from S. alterniflora-invaded native mangrove vegetated and unvegetated zones at two depths of 0–5 cm (O) and 5–20 cm (R) were investigated using quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis. Relationships were also determined between sediment properties and the AOB and AOA population sizes. Compared with native mangrove vegetated zone, the archaeal amoA gene abundance was reduced by 11.3-fold (O) and 46.1-fold (R), but the bacterial amoA gene abundance was increased by 9.8-fold (O) and 1.8-fold (R), respectively, in the S. alterniflora-invaded zone. The AOA abundance was always higher than AOB, especially in the native mangrove zone. Both AOA and AOB population sizes in the upper layer (O) were bigger than those in the deeper layer (R). Little difference was found in the AOB community composition among different zones, while diversity of AOA community was increased by the presence of S. alterniflora. This study demonstrated that the S. alterniflora invasion affects the abundance of both AOA and AOB, but only affects the community composition of AOA in the tidal sediments.