Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA- and AOB-supported nitrification determined both in soil-water slurries and in unsaturated whole soil at field moisture. Soils were collected from stands of red alder (Alnus rubra Bong.) and Douglas-fir (Pseudotsuga menziesii Mirb. Franco) at three sites (Cascade Head, the H.J. Andrews, and McDonald Forest) on acidic soils (pH 3.9–5.7) in Oregon, USA. The abundances of AOA and AOB were measured using quantitative PCR by targeting the amoA gene, which encodes subunit A of ammonia monooxygenase. Total and AOA-specific (octyne-resistant) nitrification activities in soil slurries were significantly higher at Cascade Head (the most acidic soils, pH < 5) than at either the H.J. Andrews or McDonald Forest, and greater in red alder compared with Douglas-fir soils. The fraction of octyne-resistant nitrification varied among sites (21–74%) and was highest at Cascade Head than at the other two locations. Net nitrification rates of whole soil without NH₄⁺ amendment ranged from 0.4 to 3.3 mg N kg⁻¹ soil d⁻¹. Overall, net nitrification rates of whole soil were stimulated 2- to 8-fold by addition of 140 mg NH₄⁺-N kg⁻¹ soil; this was significant for red alder at Cascade Head and the H.J. Andrews. Red alder at Cascade Head was unique in that the majority of NH₄⁺-stimulated nitrifying activity was octyne-resistant (73%). At all other sites, NH₄⁺-stimulated nitrification was octyne-sensitive (68–90%). The octyne-sensitive activity—presumably AOB—was affected more by soil pH whereas the octyne-resistant (AOA) activity was more strongly related to N availability.     

High contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation related to a potential active AOA species in various arable land soils

Purpose

Ammonia oxidation is the limiting step in soil nitrification and critical in the global nitrogen cycle. The discovery of ammonia-oxidizing archaea (AOA) has improved our knowledge of microbial mechanisms for ammonia oxidation in complex soil environments. However, the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation remain unclear.

Materials and methods

In this study, through large geographical scale sampling in China, totally nine samples representing various types of arable land soils were selected for analyzing the ammonia oxidation activity. The AOA and AOB activities were separately determined by using the dicyandiamide and 1-octyne inhibition method. High-throughput pyrosequencing and DNA stable-isotope probing (DNA-SIP) analysis were applied to investigate the distribution and activity of Candidatus Nitrosocosmicus franklandus in the arable land soils.

Results and discussion

In this study, AOA abundance (3.2?×?10⁷–3.4?×?10⁹ copies g^?1) and activity (0.01–1.33 mg N kg^?1 dry soil day^?1) were evaluated for nine selected arable land soils and accounted for 4–100% of ammonia oxidation. By separately determining AOA and AOB rates, we observed that archaeal ammonia oxidation dominated the ammonia oxidation process in six soils, revealing a considerable contribution of AOA in ammonia oxidation in arable land soils. Based on high-throughput pyrosequencing analysis, the AOA species Ca. N. franklandus with relatively low abundance (0.6–13.5% in AOA) was ubiquitously distributed in all the tested samples. Moreover, according to the DNA-SIP analysis for Urumqi sample, the high activity and efficiency of Ca. N. franklandus in using CO₂ suggests that this species plays an important role in archaeal ammonia oxidation in arable land soils.

Conclusions

Through determining the AOA activity and analyzing the potential predominant functional AOA species, this study greatly improves our understanding of ammonia oxidation in arable land soils.

     

pH regulates key players of nitrification in paddy soils

Increasing lines of evidence have suggested the functional importance of ammonia-oxidizing archaea (AOA) rather than bacteria (AOB) for nitrification in upland soils with low pH. However, it remains unclear whether niche specialization of AOA and AOB occurs in rice paddy wetlands constrained by oxygen availability. Using DNA-based stable isotope probing, we conclude that AOA dominated nitrification activity in acidic paddy soils (pH 5.6) while AOB dominated in alkaline soils (pH 8.2). Nitrification activity was stimulated by urea fertilization and accompanied by a significant increase of AOA in acid soils and AOB in alkaline soils. DNA-based stable isotope probing indicated significant assimilation of ¹³CO₂ for AOA only in acidic paddy soil, while AOB was the solely responsible for ammonia oxidation in the alkaline paddy soil. Phylogenetic analysis further indicated that AOA members within the soil group 1.1b lineage dominated nitrification in acid soils. Ammonia oxidation in the alkaline soil was catalyzed by Nitrosospira cluster 3-like AOB, suggesting that the physiological diversity of AOA is more complicated than previously thought, and soil pH plays important roles in shaping the community structures of ammonia oxidizers in paddy field.     

两种农田土壤中的氨氧化细菌和氨氧化古菌对硝化抑制剂DCD和DMPP的响应-盆栽试验

Taking two important agricultural soils with different pH, brown soil （Hap-Udic Luvisol） and cinnamon soil （Hap-Ustic Luvisol）, from Northeast China, a pot culture experiment with spring maize （Zea mays L.） was conducted to study the dynamic changes in the abundance and diversity of soil ammonia-oxidizing bacteria （AOB） and ammonia-oxidizing archaea （AOA） populations during maize growth period in response to the additions of nitrification inhibitors dicyandiamide （DCD） and 3,4-dimethylpyrazole phosphate （DMPP） by the methods of real-time polymerase chain reaction （PCR） assay, PCR-denaturing gradient gel electrophoresis （DGGE）, and construction of clone library targeting the amoA gene. Four treatments were established, i.e., no urea （control）, urea, urea plus DCD, and urea plus DMPP. Both DCD and DMPP inhibited growth of AOB significantly, compared to applying urea alone. Soil bacterial amoA gene copies had a significant positive linear correlation with soil nitrate content, but soil archaeal amoA gene copies did not. In both soils, all AOB sequences fell within Nitrosospira or Nitrosospira-like groups, and all AOA sequences belonged to group 1.1b crenaxchaea. With the application of DCD or DMPP, community composition of AOB and AOA in the two soils had less change except that the AOB community composition in Hap-Udic Luvisol changed at the last two growth stages of maize under the application of DCD. AOB rather than AOA likely dominated soil ammonia oxidation in these two agricultural soils.     

Soil particle surface electrochemical property effects on abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea, NH4 activity, and net nitrification in an acid soil

Soil surface electrochemical properties may have a strong influence on nitrifying microorganisms, H⁺ and NH₄⁺ activities, and therefore on the nitrification process. A gradient of surface electrochemical parameters was obtained by amendment of a subtropical acid pine soil (Oxisol) with 0% (control), 3%, 5%, 8%, 10% and 12% pure Ca-Montmorillonite by weight. The H⁺ and NH₄⁺ activities, the abundance of the ammonia-oxidizing bacterial (AOB) and archaeal (AOA) amoA gene copies, and time-dependent kinetics of net nitrification were investigated. Soil particle surface specific area ranged from 53 to 103 m² g⁻¹ and increased with increasing montmorillonite application rate. Similar to specific area, surface charge quantity, surface charge density, electric field strength and surface potential increased after montmorillonite amendment. The H⁺ and NH₄⁺ activities decreased linearly after montmorillonite addition. AOB amoA gene copy number was 1.82 × 10⁵ copies g⁻¹ for unamended soil, and the highest AOB amoA gene copy numbers were found for the 10% montmorillonite amendment (3.11 × 10⁷ g⁻¹ soil), which was more than 150 times higher than unamended soil. AOA amoA gene copy numbers were 9.19 × 10³ copies g⁻¹ dry unamended soil, and the highest AOA amoA gene copy numbers were found in the 8% montmorillonite amendment (1.22 × 10⁵ g⁻¹ soil). Although pH significantly decreased during the first three weeks of incubation, no significant difference was observed between the unamended control and different rates of montmorillonite addition treatments during the whole incubation. The largest net nitrification (103 mg N kg⁻¹) was observed in the 10% montmorillonite amendment and the lowest in unamended soil (62 mg N kg⁻¹). While montmorillonite did not change the kinetic patterns of net nitrification, the highest nitrification potential (275 mg N kg⁻¹) for the 10% montmorillonite treatment was more than 3 times higher than unamended soil from simulation of time-dependent kinetics. Nitrification was significantly stimulated after montmorillonite amendment in acid soil mainly due to an increase in the quantity and activity of AOB and AOA. We concluded that soil particle surface parameters can significantly influence nitrification, especially in acid soils.     

Influence of the nitrification inhibitor DMPP on the community composition of ammonia-oxidizing bacteria at microsites with increasing distance from the fertilizer zone

The effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on N transformations and composition of ammonia-oxidizing bacteria (AOB) communities was investigated at the centimeter scale in a microcosm experiment under laboratory conditions. After 28 days, samples were collected from soil treated with urea or urea and DMPP at increasing distance from the fertilizer zone; this distance ranged from 0 to 5 cm in both horizontal and vertical directions. The results showed that DMPP application significantly increased soil pH and NH ₄ ⁺ -N and mineral N (NH ₄ ⁺ -N, NO ₃ ^? -N, and NO ₂ ^? -N) concentrations but decreased (NO ₃ ^? + NO ₂ ^? )-N concentration, and such effect was decreased by increasing the distance from the fertilizer zone. Fingerprint profiles of denaturing gradient gel electrophoresis showed that the number of bands decreased by increasing the distance from the fertilizer zone due to decreasing NH ₄ ⁺ -N concentrations in the urea treatment. Compared to urea applied alone, DMPP application increased NH ₄ ⁺ -N concentrations and decreased AOB diversity from 0 to 3 cm but promoted diversity from 3 to 5 cm distance from the fertilizer zone. A phylogenetic analysis showed that AOB communities were dominated by Nitrosospira cluster 3. Therefore, the nitrification inhibitor DMPP modified the composition of AOB communities by increasing the distance from the fertilizer zone and this probably was related to the changes in soil pH and inorganic N concentration.     

Effects of 3,4-dimethylpyrazole phosphate (DMPP) on the abundance of ammonia oxidizers and denitrifiers in two different intensive vegetable cultivation soils

Purpose

Nitrification and denitrification in the N cycle are affected by various ammonia oxidizers and denitrifying microbes in intensive vegetable cultivation soils, but our current understanding of the effect these microbes have on N₂O emissions is limited. The nitrification inhibitor, 3,4-dimethylpyrazole phosphate (DMPP), acts by slowing nitrification and is used to improve fertilizer use efficiency and reduce N losses from agricultural systems; however, its effects on nitrifier and denitrifier activities in intensive vegetable cultivation soils are unknown.

Materials and methods

In this study, we measured the impacts of DMPP on N₂O emissions, ammonia oxidizers, and denitrifying microbes in two intensive vegetable cultivation soils: one that had been cultivated for a short term (1 year) and one that had been cultivated over a longer term (29 years). The quantitative PCR technique was used in this study. Three treatments, including control (no fertilizer), urea alone, and urea with DMPP, were included for each soil. The application rates of urea and DMPP were 1800 kg ha^?1 and 0.5% of the urea-N application rate.

Results and discussion

The application of N significantly increased N₂O emissions in both soils. The abundance of ammonia-oxidizing bacteria (AOB) increased significantly with high rate of N fertilizer application in both soils. Conversely, there was no change in the growth rate of ammonia-oxidizing archaea (AOA) in response to the applied urea despite the presence of larger numbers of AOA in these soils. This suggests AOB may play a greater role than AOA in the nitrification process, and N₂O emission in intensive vegetable cultivation soils. The application of DMPP significantly reduced soil NO₃^?-N content and N₂O emission, and delayed ammonia oxidation. It greatly reduced AOB abundance, but not AOA abundance. Moreover, the presence of DMPP was correlated with a significant decrease in the abundance of nitrite reductase (nirS and nirK) genes.

Conclusions

Long-term intensive vegetable cultivation with heavy N fertilization altered AOB and nirS abundance. In vegetable cultivation soils with high N levels, DMPP can be effective in mitigating N₂O emissions by directly inhibiting both ammonia oxidizing and denitrifying microbes.

     

Nitrification, ammonia-oxidizing communities, and N2O and CH4 fluxes in an imperfectly drained agricultural field fertilized with coated urea with and without dicyandiamide

Agricultural soil is a major source of nitrous oxide (N₂O), and the application of nitrogen and soil drainage are important factors affecting N₂O emissions. This study tested the use of polymer-coated urea (PCU) and polymer-coated urea with the nitrification inhibitor dicyandiamide (PCUD) as potential mitigation options for N₂O emissions in an imperfectly drained, upland converted paddy field. Fluxes of N₂O and methane (CH₄), ammonia oxidation potential, and ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) abundances were monitored after the application of PCU, PCUD, and urea to upland soil. The results showed that urea application increased the ammonia oxidation potential and AOB and AOA abundances; however, the increase rate of AOB (4.6 times) was much greater than that of AOA (1.8 times). These results suggested that both AOB and AOA contributed to ammonia oxidation after fertilizer application, but the response of AOB was greater than AOA. Although PCU and PCUD had lower ammonia oxidation potential compared to urea treatment, they were not effective in reducing N₂O emissions. Large episodic N₂O emissions (up to 1.59 kg N ha^?1 day^?1) were observed following heavy rainfall 2 months after basal fertilizer application. The episodic N₂O emissions accounted for 55–80 % of total N₂O emissions over the entire monitoring period. The episodic N₂O emissions following heavy rainfall would be a major source of N₂O in poorly drained agricultural fields. Cumulative CH₄ emissions ranged from ?0.017 to ?0.07 kg CH₄ ha^?1, and fertilizer and nitrification inhibitor application did not affect CH₄ oxidation.     

Abundance and community structure of ammonia-oxidizing bacteria and archaea in a temperate forest ecosystem under ten-years elevated CO2

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global nitrogen (N) biogeochemical cycling. Responses of the associated microorganisms to global changes remain unclear. This study was to determine if there was a shift in soil AOB and AOA abundances and community structures under free-air carbon dioxide (CO₂) enrichment (FACE) and N fertilization in Duke Forest of North Carolina, by using DNA-based molecular techniques, i.e., quantitative PCR, restriction fragment length polymorphism (RFLP) and clone library. The N fertilization alone increased the abundance of bacterial amoA gene, but this effect was not observed under elevated CO₂ condition. There was no significant effect of the N fertilization on the thaumarchaeal amoA gene abundance in the ambient CO₂ treatments, while such effect increased significantly under elevated CO₂. A total of 690 positive clones for AOA and 607 for AOB were selected for RFLP analysis. Analysis of molecular variance (AMOVA) indicated that effects of CO₂ enrichment and N fertilization on the community structure of AOA and AOB were not significant. Canonical correspondence analysis also showed that soil pH rather than elevated CO₂ or N fertilization shaped the distribution of AOB and AOA genotypes. A negative linear relationship between the δ¹³C and archaeal amoA gene abundance indicated a positive effect of elevated CO₂ on the growth ammonia oxidizing archaea. On the other hand, the community structures of AOB and AOA are determined by the soil niche properties rather than elevated CO₂ and N fertilization.     

Contrasting response of nitrification capacity in three agricultural soils to N addition during short-term incubation

Purpose

Human disturbance is a major culprit driving imbalances in the biological transformation of nitrogen from the nonreactive to the reactive pool and is therefore one of the greatest concerns for nitrogen (N) cycling. The objective of this study was to compare potential nitrification rates and the abundance of ammonia oxidizers responsible for nitrification, with the amendment of external N in different agricultural soils.

Materials and methods

Three typical Chinese agricultural soils, QiYang (QY) acid soil, ShenYang (SY) neutral soil, and FengQiu (FQ) alkaline soil, were amended with 0, 20, 150, and 300 μg NH₄ ⁺-N g^?1 soil and incubated for 40 days. The abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) at the end of incubation in the soil microcosms was determined using the real-time PCR.

Results and discussion

There was a significant decrease in ammonium concentration in the QY soil from the highest to the lowest N-loading treatments, while no significant difference in ammonium concentrations was detected among the different N-loading treatments for the SY and FQ soils. A significantly higher potential nitrification rate (PNR) was observed in the FQ soil while lowest PNR was found in the QY soil. Quantitative PCR analysis of AOB amoA genes demonstrated that AOB abundance was significantly higher in the high N-loading treatments than in the control for the QY soil only, while no significant difference among treatments in the SY and FQ soils. A significant positive correlation between PNR and AOB amoA abundance, however, was found for the SY and FQ soils, but not for the QY soil. Little difference in AOA amoA abundance between different N-loading treatments was observed for all the soils.

Conclusions

This study suggested that ammonia oxidation capacity in the FQ and SY soils was higher than those in the QY soil with the addition of ammonium fertilizer for a short-term. These findings indicated that understanding the differential responses of biological nitrification to varying input levels of ammonium fertilizer is important for maximizing N use efficiency and thereby improving agricultural fertilization management.     

Growth of comammox Nitrospira is inhibited by nitrification inhibitors in agricultural soils

Purpose

The discovery of comammox Nitrospira being capable of complete oxidising ammonia to nitrate radically challenged the conventional concept of two-step nitrification. However, the response of comammox Nitrospira to nitrification inhibitors (NIs) and their role in soil nitrification remain largely unknown, which has hindered our ability to predict the efficiency of NIs in agroecosystems.

Materials and methods

We evaluated the effect of four NIs, 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin), 3,4-dimethylpyrazole phosphate (DMPP), allylthiourea (ATU) and dicyandiamide (DCD) on the growth of comammox Nitrospira, ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in two pasture and arable soils.

Results and discussion

The amendment of nitrogen fertiliser significantly increased soil nitrate concentrations over time, indicating a sustaining nitrification activity in both soils. The addition of all the four NIs effectively reduced the production of nitrate in both soils, but to varying degrees during incubation. The abundances of comammox Nitrospira clade A were significantly increased by addition of nitrogen fertilisers and significantly impeded by the four NIs in the pasture soil, but their abundances were only remarkably hindered by nitrapyrin in the arable soil. All the four NIs obviously inhibited the AOB abundances in both soils. Except for DMPP, the other three NIs effectively suppressed the AOA abundances in both soils.

Conclusions

We provided new evidence that growth of comammox Nitrospira clade A can be stimulated by nitrogen fertilisers and inhibited by various nitrification inhibitors, suggesting their potential role in nitrification of agricultural soils.

     

Stimulated activity of the soil nitrifying community accelerates community adaptation to Zn stress

Field data have shown that soil nitrifying communities gradually adapt to zinc (Zn) after a single contamination event with reported adaptation times exceeding 1 year. It was hypothesized that this relatively slow adaptation relates to the restricted microbial diversity and low growth rate of the soil nitrifying community. This hypothesis was tested experimentally by recording adaptation rates under varying nitrification activities (assumed to affect growth rates) and by monitoring shifts in community composition. Soils were spiked at various Zn concentrations (0-4000 mg Zn kg⁻¹) and two NH₄⁺-N doses (N1, N2) were applied to stimulate growth. A control series receiving no extra NH₄⁺-N was also included. Soils were incubated in pots under field conditions with free drainage. The pore water Zn concentration at which nitrification was halved (EC50, mg Zn l⁻¹) did not change significantly during 12 months in the control series (without NH₄⁺-N applications), although nitrification recovered after 12 months at the highest Zn dose only. The EC50 after 12 months incubation increased by more than a factor 10 with increasing NH₄⁺-N dose (p < 0.05) illustrating that increased activity accelerates adaptation to Zn. Zinc tolerance tests confirmed the role of Zn exposure, time and NH₄⁺-N dose on adaptation. Zinc tolerance development was ascribed to the AOB community since the AOB/AOA ratio (AOB = ammonia oxidizing bacteria; AOA = ammonia oxidizing archaea) increased from 0.4 in the control to 1.4 in the most tolerant community. Moreover, the AOB amoA DGGE profile changed during Zn adaptation whereas the AOA amoA DGGE profile remained unaffected. These data confirm the slow but pronounced adaptation of nitrifiers to Zn contamination. We showed that adaptation to Zn was accelerated at higher activity and was associated with a shift in soil AOB community that gradually dominated the nitrifying community.     

Short-term population dynamics of ammonia oxidizing bacteria in an agricultural soil

Ammonia oxidizing bacteria (AOB) control the rate limiting step of nitrification, the conversion of ammonia (NH₄⁺) to nitrite (NO₂⁻). The AOB therefore have an important role to play in regulating soil nitrogen cycling. Tillage aerates the soil, stimulating rapid changes in soil N cycling and microbial communities. Here we report results of a study of the short term responses of AOB and net nitrification to simulated tillage and NH₄⁺ addition to soil. The intensively farmed vegetable soils of the Salinas Valley, California, provide the context for this study. These soils are cultivated frequently, receive large N fertilizer inputs and there are regional concerns about groundwater N concentrations. An understanding of N dynamics in these systems is therefore important. AOB population sizes were quantified using a real-time PCR approach. In a 15 day experiment AOB populations, increased rapidly following tillage and NH₄⁺ addition and persisted after the depletion of soil NH₄⁺. AOB population sizes increased to a similar degree, over a 1.5-day period, irrespective of the amount of NH₄⁺ supplied. These data suggest selection of an AOB community in this intensively farmed and C-limited soil, that rapidly uses NH₄⁺ that becomes available. These data also suggest that mineralization may play an especially important role in regulating AOB populations where NH₄⁺ pool sizes are very low. Methodological considerations in the study of soil AOB communities are also discussed.     

Effects of biochar and 3,4-dimethylpyrazole phosphate (DMPP) on soil ammonia-oxidizing bacteria and nosZ-N2O reducers in the mitigation of N2O emissions from paddy soils

Purpose

Paddy fields are an important source of nitrous oxide (N₂O) emission. The application of biochar or the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) to paddy soils have been proposed as technologies to mitigate N₂O emissions, but their mechanisms remain poorly understood.

Methods

An experiment was undertaken to study the combined and individual effects of biochar and DMPP on N₂O emission from a paddy field. Changes in soil microbial community composition were investigated. Four fertilized treatments were established as follows: fertilizer only, biochar, DMPP, and biochar combined with DMPP; along with an unfertilized control.

Results

The application of biochar and/or DMPP decreased N₂O emission by 18.9–39.6% compared with fertilizer only. The combination of biochar and DMPP exhibited higher efficiency at suppressing N₂O emission than biochar alone but not as effective as DMPP alone. Biochar promoted the growth of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), while DMPP suppressed AOB and increased AOA. Applying biochar with DMPP reduced the impact of DMPP on AOB. The nirS-/nirK- denitrifiers were decreased and nosZ-N₂O reducers were increased by DMPP and the combination of DMPP and biochar. The abundance of the nirK gene was increased by biochar at the elongation and heading stages of rice development. Compared with fertilizer only, the application of biochar and/or DMPP promoted the abundance of nosZ genes.

Conclusion

These results suggest that applying biochar and/or DMPP to rice paddy fields is a promising strategy to reduce N₂O emissions by regulating the dynamics of ammonia oxidizers and N₂O reducers.

     

Shift in abundance and structure of soil ammonia-oxidizing bacteria and archaea communities associated with four typical forest vegetations in subtropical region

Purpose

Nitrogen (N) is one of the most important elements that can limit plant growth in forest ecosystems. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global N biogeochemical cycling. Soil ammonia-oxidizing microbial communities associated with subtropical vegetation remain poorly characterized. The aim of this study was to determine how AOA and AOB abundance and community structure shift in response to four typical forest vegetations in subtropical region.

Materials and methods

Broad-leaved forest (BF), Chinese fir forest (CF), Pinus massoniana forest (PF), and moso bamboo forest (MB) were widely distributed in the subtropical area of southern China and represented typical vegetation types. Four types of forest stands of more than 30 years grew adjacent to each other on the same soil type, slope, and elevation, were chosen for this experiment. The abundance and community structure of AOA and AOB were characterized by using real-time PCR and denaturing gradient gel electrophoresis (DGGE). The impact of soil properties on communities of AOA and AOB was tested by canonical correspondence analysis (CCA).

Results and discussion

The results indicated that AOB dominated in numbers over AOA in both BF and MB soils, while the AOA/AOB ratio shifted with different forest stands. The highest archaeal and bacterial amoA gene copy numbers were detected in CF and BF soils, respectively. The AOA abundance showed a negative correlation with soil pH and organic C but a positive correlation with NO₃ ^??N concentration. The structures of AOA communities changed with vegetation types, but vegetation types alone would not suffice for shaping AOB community structure among four forest soils. CCA results revealed that NO₃ ^??N concentration and soil pH were the most important environmental gradients on the distribution of AOA community except vegetation type, while NO₃ ^??N concentration, soil pH, and organic C significantly affected the distribution of the AOB communities.

Conclusions

These results revealed the differences in the abundance and structure of AOA and AOB community associated with different tree species, and AOA was more sensitive to vegetation and soil chemical properties than AOB. N bioavailability could be directly linked to AOA and AOB community, and these results are useful for management activities, including forest tree species selection in areas managed to minimize N export to aquatic systems.     

Relationship between ammonia oxidizing bacteria and bioavailable nitrogen in harvested forest soils of central Alberta

Forest soils are commonly limited in nitrogen (N), and the removal of aboveground biomass in harvesting operations can exacerbate the problem. Thus, the soil organisms that facilitate the rate-limiting step in the N cycle, the oxidation of ammonium (NH₄⁺), are of special interest in harvested environments. The objective of this study was to investigate the changes in ammonia oxidizing bacteria (AOB) communities that occurred in the years following clear cutting, and link those community shifts to availability of inorganic N forms NH₄⁺ and nitrate (NO₃^?). Genetic fingerprinting targeting the amoA gene coupled with denaturing gel gradient electrophoresis was carried out over two summers on forest floor (LFH) and mineral (Ae) soils of three similar cutblocks harvested during different years. In-situ NH₄⁺ and NO₃^? availability was measured over the growing seasons of 2009 and 2010, as well as a suite of physical soil characteristics. Results indicated that the AOB community composition differed in younger vs. older cutblocks, but not by soil horizon. The changes seen in the AOB paralleled the change in N bioavailability across sites, soil horizons, and sampling years, thus indicating that N bioavailability may be directly linked to AOB community composition. This link may provide the basis for the use of AOB as indicators of nutrient availability in the future.     

Nitrification activity and putative ammonia-oxidizing archaea in acidic red soils

Purpose  

Acidic red soils account for 21% of land area in China and contain low ammonia concentration due to ionization to ammonium. The unusual high affinity for ammonia of marine Nitrosopumilus maritimus and acidophilic soil Nitrosotalea devanaterra has suggested that ammonia-oxidizing archaea (AOA) may have greater selective advantage over ammonia-oxidizing bacteria (AOB) in ammonia-limited environment because ammonia rather than ammonium is thought to be the actual substrate for oxidation. The aim of this study was to assess whether nitrification activity can be attributed to AOA and/or AOB by relating community structures of AOA and AOB to nitrification activity in acidic red soils in southern China.     

Long-term fertilization effects on active ammonia oxidizers in an acidic upland soil in China

The effects of long-term fertilization of acidic soils on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities and its ecological implications remain poorly understood. We chose an acidic upland soil site under long-term (27-year) fertilization to investigate ammonia oxidizer communities under four different regimes: mineral N fertilizer (N), mineral NPK fertilizer (NPK), organic manure (OM) and an unfertilized control (CK). Soil net nitrification rates were significantly higher in OM soils than in CK, N or NPK soils. Quantitative analysis of the distribution of amoA genes by DNA-based stable isotope probing revealed that AOA dominate in CK, N and NPK soils, while AOB dominate in OM soils. Denaturing gradient gel electrophoresis and clone library analyses of amoA genes revealed that Group 1.1a-associated AOA (also referred to as Nitrosotalea) were the most dominant active AOA population (>92%), while Nitrosospira Cluster 3 and Cluster 9 were predominant among active AOB communities. The functional diversity of active ammonia oxidizers in acidic soils is affected by long-term fertilization practices, and the responses of active ammonia oxidizers to mineral fertilizer and organic manure are clearly different. Our results provide strong evidence that AOA are more highly adapted to growth at low pH and low substrate availability than AOB, and they suggest that the niche differentiation and metabolic diversity of ammonia oxidizers in acidic soils are more complex than previously thought.     

Biochar addition affected the dynamics of ammonia oxidizers and nitrification in microcosms of a coastal alkaline soil

Biochar amendments have frequently been reported to alter microbial communities and biogeochemical processes in soils. However, the impact of biochar application on bacterial (AOB) and archaeal ammonia oxidizers (AOA) remains poorly understood. In this study, we investigated the responses of AOB and AOA to the application of biochar derived from cotton stalk at rates of 5, 10, and 20 % by weight to a coastal alkaline soil during a 12-week incubation. The results showed that the amoA gene of AOB consistently outnumbered that of AOA, whereas only the AOA amoA gene copy number was significantly correlated with the potential ammonia oxidation (PAO) rate (P?<?0.01). The significant decrease of PAO rates in biochar treatments occurred after incubation for 4–6 weeks, which were distinctly longer than that in the control (2 weeks). The PAO rates were significantly different among treatments during the first 4 weeks of incubation (P?<?0.05), with the highest usually in the 10 % treatment. Biochar application significantly increased the abundance of both nitrifiers in the 4 weeks of incubation (P?<?0.05). Biochar amendment also decreased AOA diversity, but increased AOB diversity, which resulted in different community structures of both nitrifiers (P?<?0.01), as shown by the differences between the 5 % biochar and the control treatments. We conclude that biochar application generally enhanced the abundance and altered the composition of ammonia oxidizers; the rate of biochar application also affected the rate and dynamics of nitrification, and the risk for increasing the alkalinity and N leaching of the studied soil was lower with a lower application rate.     

Potato cultivar type affects the structure of ammonia oxidizer communities in field soil under potato beyond the rhizosphere

The effects of plants on the microbiota involved in the oxidation of ammonia in soils have been controversial. Here, we investigated the dynamics in the abundances and community structures of the bacterial and archaeal ammonia oxidizers (AOB and AOA, respectively) in two fields that were cropped with potato. Six different potato cultivars were used, including a genetically-modified one, in a fourfold replicated experimental set-up. On the basis of bulk and rhizosphere soil extracted microbial community DNA, AOB and AOA quantitative PCR as well as PCR-DGGE were performed. In addition, samples were used for the production and analysis of amoA gene fragment based clone libraries. Regardless of sample type (bulk versus rhizosphere soil) and across soils, the population sizes of AOA (of the order 10⁴–10⁸ amoA gene copies g⁻¹ dry soil), were generally higher than those of AOB in the same samples (about 10⁴–10⁵ g⁻¹ dry soil), resulting in ratio's of log-transformed values > 1.0. Whereas the AOB numbers were generally raised in the rhizosphere versus bulk soils in both soils, the opposite was true for the AOA numbers. Moreover, significant effects of cultivar type on both the AOB and AOA community structures were found in both soils, and these extended to beyond the rhizospheres. The effects were found across the whole growth season. Soil type did not significantly affect the community structures of AOA, but had a small effect on the community structure of AOB. Analysis of the structures of the AOB communities revealed a prevalence of AOB subgroups 2, 3a, 3b and 4 in one field soil and of 2 and 4 in the other one. With respect to the AOA, soil/sediment clusters (SS) I, II, III and IV were found to prevail.