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.     

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.     

Ammonia-oxidizing archaea are more important than ammonia-oxidizing bacteria in nitrification and NO3 −-N loss in acidic soil of sloped land

As part of a long-term sloped land use experiment established in 1995 at Taoyuan Agro-ecosystem Research Station (111°26′ E, 28°55′ N) in China, soil samples were collected from three land use types, including cropland (CL), natural forest, and tea plantation. Quantitative polymerase chain reaction and terminal restriction fragment length polymorphism were used to determine the abundance and community composition of amoA-containing bacteria (AOB) and archaea (AOA). The results indicate that land use type induced significant changes in soil potential nitrification rate and community composition, diversity, and abundance of AOB and AOA. Both AOB and AOA community compositions were generally similar between upper and lower slope positions (UP and LP), except within CL. The LP soils had significantly (p?<?0.05) higher diversity and abundance of both AOB and AOA than in the UP. Potential nitrification rate was significantly correlated (p?<?0.05) with diversity and abundance of AOA, but not with AOB. Among land use types, the NO₃ ^? and amoA-containing AOA runoff loss was greatest in CL. Nitrate-N runoff loss was significantly correlated (p?<?0.05) with the loss of AOA amoA copies in the runoff water. Furthermore, relationships between NO₃ ^?-N runoff loss and abundance of AOA but not of AOB at both slope positions were significantly correlated (p?<?0.05). These findings suggest that AOA are more important than AOB in nitrification and NO₃ ^?-N runoff loss in acidic soils across sloped land use types.     

Co-tolerance to zinc and copper of the soil nitrifying community and its relationship with the community structure

Soil microbial communities can develop trace metal tolerance upon soil contamination with corresponding metals. A few studies have reported co-tolerance in such cases, i.e. tolerance to other metals than those to which the microbial community had been exposed to. This study was set-up to test for co-tolerance of nitrifying communities to zinc (Zn) and copper (Cu) and to relate tolerances to shifts in community structure using amoA AOB (ammonia oxidizing bacteria) DGGE. Seven sets of soils, each representing a Cu or Zn contamination gradient were sampled from four locations. At two locations, both Cu and Zn had been added as single contaminants. Increased Zn and Cu tolerance of the nitrifying communities was consistently observed in response to corresponding soil contamination. Co-tolerance to Zn was obtained in two of the three Cu gradients and that to Cu in one of the four Zn gradients. DGGE analysis and sequencing showed that contamination with either Zn or Cu selected for identical AOB phylotypes in soils at one location but not at the other location. The nitrifying community structures in soils from different locations did not become more similar upon Zn exposure than those in corresponding uncontaminated soils. Hence, trace metal tolerance development was not due to the emergence of specific AOB phylotypes, but due to the emergence of different AOB phylotypes bearing tolerance mechanisms for Zn, Cu or both metals.     

Influence of bacterial-feeding nematodes on nitrification and the ammonia-oxidizing bacteria (AOB) community composition

The effects of bacterial-feeding nematodes on nitrification and the ammonia-oxidizing bacteria (AOB) community composition were studied in soil microcosms. Sterilized soils were inoculated with mixed soil bacteria (obtained by filtering) or with bacteria and bacterial-feeding nematodes, after which the dynamic inorganic nitrogen concentration was measured weekly. After 28 days of incubation, denaturing gradient gel electrophoresis (DGGE) based on PCR amplification of the amoA gene was used to analyze the AOB community composition. In addition, a clone library from the amoA gene fragments was established using clones randomly selected and sequenced from the two treatments. The results showed that the presence of bacterial-feeding nematodes led to significantly greater NH₄⁺ and NO₃⁻ contents over the entire incubation period, indicating that bacterial-feeding nematodes promoted both N mineralization and nitrification. The results of DGGE showed that the AOB community composition was significantly changed in the presence of bacterial-feeding nematodes. Furthermore, the sequencing results suggested that Nitrosospira sp. was the dominant species in the treatment without nematodes, while Nitrosomonas sp. and Nitrosospira sp. were the dominant species in the treatment with nematodes. Such changes in the AOB community may be one of explanation of the important role that nematodes play in promoting nitrification.     

Characterization of nitrifying bacteria communities of soils from different ecological regions of China by molecular and conventional methods

Soil nitrification rate is very different among soil types, as a result of differences in physical and chemical properties. Little is known about the composition of the nitrifying bacteria community. In this investigation, three soils (fluvo-aquic soil, permeable paddy soil and red earth) from different geo-ecological regions in China were characterized for their nitrification activities and their nitrifying bacteria communities determined either by molecular approaches or by conventional culture methods. A 28-day long-term soil incubation showed that the maximum nitrification potential was found in the fluvo-aquic soil with almost 100% of inorganic N present as NO₃^–-N, while the minimum nitrification potential was in red earth with only a 4.9% conversion rate from ammonium into nitrate. There was no relationship between nitrification potential and numbers of nitrifiers in the soil. The conventional most probable number (MPN) method could enumerate ammonia oxidizers, but failed in enumerating nitrite oxidizers. Therefore, we used an MPN-PCR procedure which gave a convincing nitrite oxidizer count result, instead of MPN-diphylamine. Soils were characterized by denaturing gradient gel electrophoresis (DGGE) of DNA extracted from soils and amplified using a primer specific for the 16S rRNA gene and/or for the amoA gene. The DGGE columns of the three soils differed from each other. There were two similar bands present in DGGE columns of the fluvo-aquic and permeable paddy soils, but no similar band was found in DGGE columns of the red earth. The sequence of amoA indicated that all ammonia oxidizers in these soils were grouped into Nitrosospira clusters 1 and 3, and each soil had a common band similar to the other soils and a special band which differed from the other soils.     

冬种绿肥对水稻土硝化作用的影响

冬闲田种植绿肥是传统的水稻土培肥增产措施,但绿肥-水稻种植系统中,不同绿肥种类对硝化作用的影响规律及调控机制尚不明确.采用盆栽试验,研究了冬种紫云英、油菜、黑麦草对土壤性状及硝化作用的影响,并通过特异性细菌抑制剂(卡那霉素和大观霉素)研究了氨氧化细菌(AOB)和氨氧化古菌(AOA)对硝化作用的相对贡献.结果表明,冬种三...     

Inhibition of ammonia-oxidizing bacteria promotes the growth of ammonia-oxidizing archaea in ammonium-rich alkaline soils

Disparities in the substrate affinity and tolerance threshold for ammonia have been believed to play a key role in driving niche differentiation between ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, recent surveys argue that direct competition between AOA and AOB is also important in this phenomenon. Accordingly, it is reasonable to predict that diverse AOA lineages would grow in ammonium (NH₄⁺)-rich alkaline arable soils if AOB growth is suppressed. To test this hypothesis, a microcosm study was established using three different types of alkaline arable soils, in which a high NH₄⁺ concentration (200 μg N g^-1 dry soil) was maintained by routinely replenishing urea and the activities of AOB were selectively inhibited by 1-octyne or 3,4-dimethylpyrazole phosphate (DMPP). Compared with amendment with urea alone, 1-octyne partially retarded AOB growth, while DMPP completely inhibited AOB. Both inhibitors accelerated the growth of AOA, with significantly higher ratios of abundance of AOA to AOB observed with DMPP amendment across soils. Nonmetric multidimensional scaling analysis (NMDS) indicated that different treatments significantly altered the community structures of both AOA and AOB and AOA OTUs enriched by high-NH₄⁺ amendment were taxonomically constrained across the soils tested and closely related to Nitrososphaera viennensis EN76 and N. garnensis. Given that these representative strains have been demonstrated to be sensitive to high ammonia concentrations, our results suggest that it is the competitiveness for ammonia, rather than disparities in substrate affinity and tolerance threshold for ammonia, that drives niche differentiation between these phylotypes and AOB in NH₄⁺-rich alkaline soils.     

不同施肥方式下土壤氨氧化细菌的群落特征

为了研究长期定位施肥对棕壤中氨氧化细菌（ammonia-oxidizing bacteria,AOB）种群结构多样性和垂直分布特征的影响,本研究采用化学分析、荧光定量PCR（qPCR）和变性梯度凝胶电泳（PCR-DGGE）技术,针对沈阳农业大学试验区不同施肥方式（不施肥、低量无机氮肥、高量无机氮肥、无机氮肥与有机肥配施）下不同土壤深度（0~20 cm、20~40 cm、40~60 cm）的土壤理化性质、AOB丰度及种群多样性进行分析,比较不同施肥方式对土壤AOB种群的影响。结果显示,与不施肥相比,施肥会降低土壤pH,增加土壤铵态氮（70.5%~939.21%）和硝态氮（253.20%~625.48%）含量。随土壤深度增加,土壤pH升高,铵态氮和硝态氮含量除低量无机氮肥处理外,多呈降低趋势。土壤增施氮肥可提高AOB丰度,降低总细菌丰度。其中,0~20 cm土层中AOB丰度较高,且高量无机氮肥处理的AOB数量最高,为9.65×10⁵拷贝数·g^-1（干土）。DGGE图谱分析显示,不同处理下,AOB群落结构多样性指数存在明显差异（P<0.05）,各多样性指数均在表层（0~20 cm）最高,增施氮肥则显著降低AOB的多样性。聚类分析表明,4个施肥处理中,高量无机氮肥处理聚为一类,其他处理则因土壤深度不同而异;3个土壤深度中,除不施肥处理外,所有施肥处理均表现为0~20 cm、20~40 cm土层发生聚类,40~60 cm则明显与其他两层分开。冗余梯度分析（RDA）显示,硝态氮（P=0.027）是造成影响AOB群落结构差异的主要原因。上述研究结果表明,长期定位施肥土壤AOB的数量和群落结构多样性受施肥方式显著影响,并表现出明显的垂直分布特征。与无机氮肥相比,有机无机配施处理有助于改善土壤pH,维持不同土壤深度下AOB群落结构多样性。     

Impacts of continuous excessive fertilization on soil potential nitrification activity and nitrifying microbial community dynamics in greenhouse system

Purpose

Sampling and analysis of greenhouse soils were conducted in Shouguang, China, to study continuous excessive fertilization effect on nitrifying microbial community dynamics in greenhouse environment.

Materials and methods

Potential nitrification activity (PNA), abundance, and structure of nitrifying microbial communities as well as the correlations with soil properties were investigated.

Results and discussion

Short-term excessive fertilization increased soil nutrient contents and the diversity of nitrifying microbial communities under greenhouse cultivation. However, the abundance and diversity of nitrifying communities decreased greatly due to the increase of soil acidity and salinity after 14 years of high fertilization in greenhouse. There was a significant positive correlation between soil PNA and the abundance of ammonia-oxidizing bacteria (AOB) but not that of ammonia-oxidizing archaea (AOA) in topsoil (0–20 cm) when pH ≥7. Soil PNA and AOB were strongly influenced by soil pH. The groups of Nitrososphaeraceae, Nitrosomonadaceae, and Nitrospiraceae were predominant in the AOA, AOB, and nitrite-oxidizing bacteria (NOB) communities, respectively. Nitrifying community structure was significantly correlated with soil electrical salinity (EC), organic carbon (OC), and nitrate nitrogen (NO₃ ^?–N) content by redundancy analysis (RDA).

Conclusions

Nitrification was predominated by AOB in greenhouse topsoil with high fertilizer loads. Soil salinity, OC, NO₃ ^?–N content, and pH affected by continuous excessive fertilization were the major edaphic factors in shaping nitrifying community structure in greenhouse 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.     

Dynamics of the nitrous oxide reducing community during adaptation to Zn stress in soil

Laboratory studies show that the nitrous oxide (N₂O) reduction rate in soil is strongly inhibited by trace metal contamination; however, this effect appears transient. Here we assess if this recovery is due to microbial adaptation associated with shifts in community composition. Soils were spiked with zinc chloride (0-5000 mg Zn kg⁻¹) in a factorial design with 3 application rates of organic matter (OM), i.e. 0, 2 and 4 g milled hay kg⁻¹, to accelerate growth and, potentially, adaptation rate. The soil treatments were incubated outdoors with free drainage during 1 year and periodically sampled. The potential N₂O reduction rate, measured in an anaerobic laboratory assay, was inhibited by Zn during the first 2 months after spiking with 50% inhibition at 500-1000 mg Zn kg⁻¹. After 6 months exposure, the N₂O reduction rate recovered to at least 80% of the rate in the control treatment in the series receiving OM up to the largest Zn dose, but strong inhibition remained in the series which did not receive OM. In this series recovery was only observed after 12 months exposure. Soil pore water Zn concentrations did not explain the recovery of the N₂O reduction rate in the control series suggesting that recovery is due to adaptation and not to reduced Zn bioavailability. The faster recovery in the series receiving OM was partially, but not fully related to the effects of OM on Zn bioavailability. The recovery at all Zn and OM treatments co-varied with a recovery of nosZ gene abundance from about 1 × 10⁷ copies g⁻¹ soil in the soil treatments with decreased activity to 5 × 10⁸ copies g⁻¹ soil in the other soil treatments. The nosZ gene DGGE profile of the soil microbial communities revealed minor changes in the nosZ containing community. This study strongly suggests that the transient effects of trace metal inhibition of N₂O reduction is due to the development of a Zn tolerant denitrifying community.     

亚热带松林中强酸性土壤自养和异养硝化作用的研究

The occurrence of nitrification in some acidic forest soils is still a subject of debate. Identification of main nitrification pathways in acidic forest soils is still largely unknown. Acidic yellow soil (Oxisol) samples were selected to test whether nitrification can occur or not in acidic subtropical pine forest ecosystems. Relative contributions of autotrophs and heterotrophs to nitrification were studied by adding selective nitrification inhibitor nitrapyrin. Soil NH₄⁺-N concentrations decreased, but NO₃^--N concentrations increased significantly for the no-nitrapyrin control during the first week of incubation, indicating that nitrification did occur in the acidic subtropical soil. The calculated net nitrification rate was 0.49 mg N kg^-1 d^-1 for the no-nitrapyrin control during the first week of incubation. Nitrapyrin amendment resulted in a significant reduction of NO₃^--N concentration. Autotrophic nitrification rate averaged 0.28 mg N kg^-1 d^-1 and the heterotrophic nitrification rate was 0.21 mg N kg^-1 d^-1 in the first week. Ammonia-oxidizing bacteria (AOB) abundance increased slightly during incubation, but nitrapyrin amendment significantly decreased AOB amoA gene copy numbers by about 80%. However, the ammonia-oxidizing archaea (AOA) abundance showed significant increases only in the last 2 weeks of incubation and it was also decreased by nitrapyrin amendment. Our results indicated that nitrification did occur in the present acidic subtropical pine forest soil, and autotrophic nitrification was the main nitrification pathway. Both AOA and AOB were the active biotic agents responsible for autotrophic nitrification in the acidic subtropical pine forest soil.     

Overland flow systems for treatment of landfill leachates—Potential nitrification and structure of the ammonia-oxidising bacterial community during a growing season

Overland flow systems are useful for treating landfill leachates, because they provide favourable conditions for nitrification and they are easy to maintain. However, little is known about the microbial communities in such systems or the nitrification capacity of those microorganisms. In this study, seasonal variations in potential nitrification and in community composition of nitrifying bacteria were investigated in two overland flow areas receiving leachate from landfills at Korslöt and Hagby, Sweden. Samples were collected in the settling ponds sediment and at two depths in the overland flow areas (the macrophyte litter layer and the rhizosphere) in May, August and November 2003. A short-term incubation method was used to measure potential oxidation of ammonia and nitrite (designated PAO and PNO). The ammonia-oxidising bacterial (AOB) community was investigated using a 16S rRNA gene approach that included PCR amplification and analysis of PCR products by denaturing gradient gel electrophoresis (DGGE), followed by nucleotide sequencing and phylogenetic analysis.PAO was determined in the range 5-2700 (NO₂⁻+NO₃⁻)-N g⁻¹ dw d⁻¹ and PNO in the range 60-2000 μg NO₂⁻-N g⁻¹ dw d⁻¹. At Korslöt, PAO and PNO showed similar temporal variation in the different ecosystems, whereas no such relationship was noticed at Hagby. Considering both sites, there was no obvious change in the composition of the AOB community over the growing season. However, the composition did differ between the ecosystems: Nitrosomonas-like sequences were more common in the ponds, and in the litter layers they were found as often as Nitrosospira-like sequences, whereas Nitrosospira-like sequences were more common in the rhizospheres. Altogether, we found nine different AOB sequences, five Nitrosomonas-like and four Nitrosospira-like, which belonged to clusters 0, 2, 3b, 6a, 6b and 7. There was no apparent relationship between the number of AOB populations and the PAO in different soil layers and sediments.     

Influence of nitrogen fertilization on soil ammonia oxidizer and denitrifier abundance,microbial biomass,and enzyme activities in an alpine meadow

Terrestrial ecosystems are predicted to experience an increasing level of atmospheric nitrogen (N) deposition, which may cause significant shifts in plant community composition and concomitantly stimulate soil acidification. However, little is known concerning the effects of N deposition on belowground microbial communities in alpine grassland ecosystems such as on the Tibetan Plateau. This study examined the responses of soil N-transforming microbes (measured after DNA extraction and quantitative PCR), soil microbial biomass C (SMBC) and N (SMBN), and soil enzyme activities to different forms (NH₄ ⁺-N, NO₃ ^?-N, and NH₄NO₃-N) and rates (1.5 and 7.5 g N m^?2 year^?1, denoted as low and high N, respectively) of N fertilization (addition) in two successive plant growing seasons. The N rate, not N form, influenced the abundance of ammonia-oxidizing archaea (AOA). High N addition significantly increased ammonia-oxidizing bacteria (AOB) abundance which differed across different N form treatments. Nitrogen addition had no significant impact on the abundance of soil denitrifiers. The SMBC and SMBN were significantly decreased by high N additions, but no difference was found among different N forms. Despite higher urease activities being detected in the late plant growing season, the activities of invertase and alkaline phosphomonoesterase stayed unchanged irrespective of the different N amendments and plant growing season. Significant positive correlations were found between potential nitrification rates and AOB abundances. These results highlight that AOB seemed to respond more sensitively to different N fertilization and might have prominent roles in soil N cycling processes in this Tibetan Plateau alpine meadow than AOA.     

Variation in NH4 mineralization and microbial communities with stand age in lodgepole pine (Pinus contorta) forests, Yellowstone National Park (USA)

Soils and vegetation were analyzed in 20 lodgepole pine (Pinus contorta) forest stands, varying in age from 50 to 350 years, that had initiated following stand-replacing fire. Our goal was to determine how nitrogen availability (NH₄⁺-N) and microbial community composition varied with stand age-class and to determine whether differences could be explained by canopy, soil, or understory characteristics. Gross NH₄⁺ mineralization was measured using laboratory isotopic pool dilution, and microbial community composition was evaluated using microbial membrane lipids. The microbial community composition of stands in the 300-350 age class was distinct from stands in younger age classes. Microbial community composition among sites varied with pH, % organic matter, and phosphorus. Gross NH₄⁺ mineralization rates averaged 1.45±0.07 mg NH₄⁺ kg soil⁻¹ d⁻¹ while consumption averaged 1.37±0.20 mg NH₄⁺ kg soil⁻¹ d⁻¹, resulting in low net NH₄⁺ mineralization rates (0.08±0.18 mg NH₄⁺ kg soil⁻¹ d⁻¹), but rates were not significantly different with stand age-class at p<0.05. At p<0.10, net NH₄⁺ mineralization was significantly higher in the 300-350 age class compared to the 125-175 age class. None of the measured variables significantly explained NH₄⁺ consumption and net mineralization patterns. However, gross NH₄⁺ mineralization rates were best explained by information on microbial community structure (i.e. lipids). Variation among stands within a given age-classes was high, indicating that patterns of N cycling across landscapes reflect substantial heterogeneity among mature stands.     

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.     

Chronic Nitrogen Fertilization Modulates Competitive Interactions Among Microbial Ammonia Oxidizers in a Loess Soil

Nitrogen(N) application may lead to niche segregation of soil ammonia-oxidizing archaea(AOA) and bacteria(AOB), thereby reducing the competitive interactions between AOA and AOB due to higher ammonium substrate availability. However, the adaptive mechanisms of AOA and AOB under N enrichment remain poorly understood. Stable isotope probing(SIP) microcosm incubation was employed to reveal community changes of active AOA and AOB in a loess soil from a field experiment growing potatoes that received no N(control, CK), low N(LN, 75 kg N ha~(-1)), and high N(HN, 375 kg N ha~(-1)). The results showed that the soil potential nitrification rate(PNR) was measured by culturing of the soil samples from the field experiment. Soil PNR was significantly increased in HN by87.5% and 67.5% compared with CK and LN, respectively. Compared with CK, the~(13)C-amoA genes of soil AOA and AOB in HN had 2.58 × 10~4 and 1.55 × 10~6 copies, representing 1.6-and 16.2-fold increase respectively. It was indicated that AOB dominated soil ammonia oxidation. A phylogenetic analysis of the~(13)C-amoA gene showed that N application significantly increased the proportion of54 d9-like AOA up to 90% in HN, while the Nitrososphaera gargensis-like and Nitrososphaera viennensis-like AOA were inhibited and completely disappeared. Nitrogen application also resulted in the community shift of active AOB-dominant group from Nitrosospira briensis-like to Nitrosospira sp. TCH711-like. Our study provides compelling evidence for the emergence and maintenance of active nitrifying communities under the intensified N input to an agricultural ecosystem.     

The effects of different irrigation regimes on nitrous oxide emissions and influencing factors in greenhouse tomato fields

Purpose

Intensive agricultural practices have enhanced problems associated with the competing use of limited water resources. Nitrous oxide (N₂O) is a major contributor to global warming. It is important for researchers to ascertain the relationship between irrigation and soil N₂O emissions in order to identify mitigation strategies to reduce nitrous oxide emissions. Different irrigation amounts affect soil water dynamics and nitrogen turnover. The effect of three lower limits of irrigation on soil N₂O emissions, influencing factors, and abundance of genes involved in nitrification and denitrification were investigated in tomato irrigated in a greenhouse.

Materials and methods

Observations were performed between April and August 2015 in a long-term irrigated field subjected to different lower limits of irrigation: 20 kPa (D₂₀), 30 kPa (D₃₀), and 40 kPa (D₄₀) from greenhouse soil during the tomato crop season. Soil N₂O fluxes were monitored using the static chamber-gas chromatograph method. Copy numbers of genes were determined using the real-time quantitative polymerase chain reaction (real-time PCR) technique. Characteristics of soil N₂O emissions were analyzed, and differences between irrigation regimes were determined. The effects of influencing factors on soil N₂O emissions were analyzed, including soil temperature, soil moisture, soil pH, and soil mineral nitrogen, as well as changes in the abundance of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) based on amoA genes and denitrifier genes (nosZ, nirK, and cnorB).

Results and discussion

Our results showed that peaks in N₂O emissions occurred 1–5 days after each irrigation. During the whole tomato growth period, soil N₂O fluxes were lowest under D₃₀ treatment compared with those under D₂₀ and D₄₀ treatments. Soil NO₃ ^?-N concentrations were significantly higher than NH₄ ⁺-N concentrations. Soil N₂O fluxes were significantly related to soil moisture, NH₄ ⁺-N concentrations (P < 0.01), soil pH, and AOA copy numbers (P < 0.05). There was no consistent correlation between soil N₂O emissions, soil temperature, and soil NO₃ ^?-N concentrations. Different irrigation regimes significantly affected AOA copy numbers but did not affect the expression of other genes. AOA copy numbers were higher than those of AOB. Soil N₂O fluxes significantly affected the AOA copy numbers and potential nitrification rates (P < 0.05).

Conclusions

Soil moisture, pH, and NH₄ ⁺-N concentration were important factors affecting soil N₂O emissions. Compared with other genes associated with nitrification and denitrification, AOA plays an important role in N₂O emissions from greenhouse soils. Selecting a lower limit of irrigation of 30 kPa could effectively reduce N₂O emissions from vegetable soils.

     

Effect of green manure Sesbania sesban and nitrification inhibitor encapsulated calcium carbide (ECC) on soil mineral-N,enzyme activity and nitrifying organisms in a rice–wheat cropping system

Green manure Sesbania sesban (S. sesban) and the nitrification inhibitor encapsulated calcium carbide (ECC) have been used to improve N supply and management in rice–wheat production systems in India. However, the ecological impact of combined use of these materials is largely unknown. We conducted a net-house pot culture experiment for 2 years, to investigate the effects of S. sesban and ECC on mineral N availability (NH₄⁺ and NO₃^–), soil enzyme activities (dehydrogenase and nitrate reductase) and populations (MPN) of nitrifying organisms under a rice–wheat cropping system. Green manure S. sesban and ECC (+ECC or –ECC) were applied along with urea in various combinations to hybrid rice under flooded conditions. For wheat, it was urea alone or urea + ECC. Soil samples were studied at 10 days after top dressing, i.e. 40 days after rice transplanting and 35 days after wheat sowing, for above characteristics. The mineral-N in soil revealed the significant effect of combined use of S. sesban and ECC to enhance NH₄⁺ and total mineral-N (NH₄⁺ + NO₃^–) contents. Dehydrogenase and nitrate reductase activities and population (MPN) of ammonia oxidizing bacteria (AOB) revealed a significant reduction in soils, whereas nitrite oxidizing bacteria (NOB) remained almost unaffected (P > 0.05) in response to application of ECC with S. sesban and urea. Our results suggest that slow release of acetylene (C₂H₂) from ECC has reduced ammonia mono-oxygenase with reducing population of AOB, and has the potential to retard the enzyme activities in favor of C and N conservations in a semi-arid agro-ecosystem.