Ammonia-oxidizing Bacteria Population Size Research Articles

Calcium-based polymers for suppression of soil acidification by improving acid-buffering capacity and inhibiting nitrification

Soil acidification is a major threat to agricultural sustainability in tropical and subtropical regions. Biodegradable and environmentally friendly materials, such as calcium lignosulfonate (CaLS), calcium poly(aspartic acid) (PASP-Ca), and calcium poly γ-glutamic acid (γ-PGA-Ca), are known to effectively ameliorate soil acidity. However, their effectiveness in inhibiting soil acidification has not been studied. This study aimed to evaluate the effect of CaLS, PASP-Ca, and γ-PGA-Ca on the resistance of soil toward acidification as directly and indirectly (i.e., via nitrification) caused by the application of HNO3 and urea, respectively. For comparison, Ca(OH)2 and lignin were used as the inorganic and organic controls, respectively. Among the materials, γ-PGA-Ca drove the substantial improvements in the pH buffering capacity (pHBC) of the soil and exhibited the greatest potential in inhibiting HNO3-induced soil acidification via protonation of carboxyl, complexing with Al3+, and cation exchange processes. Under acidification induced by urea, CaLS was the optimal one in inhibiting acidification and increasing exchangeable acidity during incubation. Furthermore, the sharp reduction in the population sizes of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) confirmed the inhibition of nitrification via CaLS application. Therefore, compared to improving soil pHBC, CaLS may play a more important role in suppressing indirect acidification. Overall, γ-PGA-Ca was superior to PASP-Ca and CaLS in enhancing the soil pHBC and the its resistance to acidification induced by HNO3 addition, whereas CaLS was the best at suppressing urea-driven soil acidification by inhibiting nitrification. In conclusion, these results provide a reference for inhibiting soil re-acidification in intensive agricultural systems.

Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.

The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management. The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition. The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.

Beneficial dual role of biochars in inhibiting soil acidification resulting from nitrification

The dual role of biochar for inhibiting soil acidification induced by nitrification was determined through two-step incubation experiments in this study. Ca(OH)2 or biochar was added respectively to adjust soil pH to the same values (pH 5.15 and 5.85), and then the amended soils were incubated in the presence of urea for 70 days. The results showed that compared with Ca(OH)2 treatment, both rice straw biochar and peanut straw biochar inhibited the decrease in soil pH and the increase in exchangeable acidity during the incubation. The application of biochars suppressed soil nitrification during the incubation, and thus reduced 7.5 mmol kg−1 and 1.4 mmol kg−1 protons released from nitrification compared to Ca(OH)2 treatments. Compared with Ca(OH)2 treatment, the ammonia-oxidizing bacteria population size was decreased by 8% and 12% in rice straw biochar and peanut straw biochar treatments respectively, which was the main responsibility for the inhibited nitrification after biochar application. In addition, the application of rice straw biochar and peanut straw biochar increased soil pH buffering capacity (pHBC) respectively by 22% and 32%. The increased pHBC played the main role (75%) in inhibiting the acidification of the soil amended with peanut straw biochar, while the rice straw biochar inhibited soil acidification mainly through suppressing nitrification during the incubation. Overall, compared with lime application, biochars can inhibit soil acidification caused by urea application through suppressing the nitrification process and improving the resistance of soils to acidification. The crop residue biochars presented a longer-lasting effect on ameliorating acidic soils than mineral lime.

Spatial and temporal responses of ammonia-oxidizing bacteria and archaea to organic amendments in rice-wheat rotation system

To determine the effects of organic amendment on communities of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in rice-wheat rotation ecosystem, a long-term plot experiment with 5 treatments was conducted, and the temporal dynamics (10 growth stages) and spatial distribution (0–100 cm) of AOB and AOA abundance were determined using qPCR. The five treatments were as follows: no fertilizer control (CK), regular fertilization (RT), straw returning (SR), straw biochar returning (SB) and organic-chemical mixed fertilization (MF). The results showed the following. 1) Organic addition did not affect the temporal dynamics of AOB abundance but altered those of AOA abundance. Relative to RT, SR and MF significantly lowered AOB population sizes across the 10 sampling time points by 34.49% and 16.42%, respectively, whereas no significant differences in total AOA population size were observed among the 4 fertilization regimes. 2) Compared with the other treatments, treatments involving organic addition had higher total AOB abundance in the 0–100 cm soil layer. However, SB was the only treatment with organic addition that had a significantly higher total AOA abundance than RT (by 24.91%). 3) Under organic addition, the potential nitrification rate (PNR) was still highly correlated with AOB abundance (P < 0.01) but not AOA abundance.

Nitrapyrin affects the abundance of ammonia oxidizers rather than community structure in a yellow clay paddy soil

PURPOSE: Yellow clay paddy soil (Oxisols) is a low-yield soil with low nitrogen use efficiency (NUE) in southern China. The nitrification inhibitor nitrapyrin (2-chloro-6- (tricholoromethyl)-pyridine, CP) has been applied to improve NUE and reduce environmental pollution in paddy soil. However, the effects of nitrapyrin combined with nitrogen fertilizers on ammonia oxidizers in yellow clay paddy soil have not been examined. MATERIALS AND METHODS: A randomized complete block design was set with three treatments: (1) without nitrogen fertilizer (CK), (2) common prilled urea (PU), and (3) prilled urea with nitrapyrin (NPU). Soil samples were collected from three treatments where CK, PU, and NPU had been repeatedly applied over 5 years. Soil samples were analyzed by quantitative PCR and 454 high-throughput pyrosequencing of the amoA gene to investigate the influence of nitrapyrin combined with nitrogen on the abundance and community structure of ammonia oxidizers in yellow clay paddy soil. RESULTS AND DISCUSSION: The potential nitrification rate (PNR) of the soil was significantly correlated with the abundances of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Application of urea significantly stimulated AOA and AOB growth, whereas nitrapyrin exhibited inhibitory effects on AOA. Phylogenetic analysis showed that the most dominant operational taxonomic units (OTUs) of AOA and AOB were affiliated with the Nitrosotalea cluster and Nitrosospira cluster 12, respectively. AOA and AOB community structures were not altered by urea and nitrapyrin application. CONCLUSIONS: Nitrogen fertilization stimulated nitrification and increased the population sizes of AOA and AOB. Nitrapyrin affected the abundance, but not community structure of ammonia oxidizers in yellow clay soil. Our results suggested that nitrapyrin improving NUE and inhibiting PNR was attributable to the inhibition of AOA growth.

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N2O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N2O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N2O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N2O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N2O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N2O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.

Characteristics of ammonia oxidation potentials and ammonia oxidizers in mineral soil under Salix polaris–moss vegetation in Ny-Ålesund, Svalbard

Although nitrification is a unique and important process in the nitrogen cycle with respect to ammonium consumption and nitrate production, limited information on this process is available for high-Arctic soils. We elucidated the ammonia oxidation potentials (AOPs) and characteristics of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in mineral soils under climax vegetation, i.e., Salix polaris (polar willow)–moss vegetation, on a coastal hill in Ny-Alesund, Svalbard. AOPs at 10 °C were determined by incubation with sufficient substrate (2 mM ammonium). The ammonia monooxygenase subunit A (amoA) genes of AOB and AOA were analyzed by using quantitative polymerase chain reaction and pyrosequencing. AOPs ranged from 1.1 to 14.1 ng N g−1 dry soil h−1—relatively low but of a similar order to the gross nitrification rates reported in another Svalbard study. AOP was positively correlated with thickness of the moss layer (P < 0.01), soil water content, and ammonium nitrogen content (P < 0.05). The population sizes of both AOB and AOA were not significantly related to AOP or edaphic factors. For AOB-amoA, six major operational taxonomic units (OTUs) were identified, all of which were classified into the Nitrosospira Mount Everest cluster. For AOA-amoA, six major OTUs were also identified, five of which were grouped with sequences from cold environments within clade A of the Nitrososphaera cluster, i.e., species known to have low, or no, AOP. It is, therefore, possible that the AOPs measured at the study site were driven mainly by psychrotolerant AOB.

Smooth brome changes gross soil nitrogen cycling processes during invasion of a rough fescue grassland

Invasive plants have variable effects on net nitrogen cycling, but how invasion alters gross N cycling is poorly understood. We examine how Bromus inermis (smooth brome) invasion affects gross N cycling rates and investigate potential mechanisms for the changes including relationships between smooth brome and ammonia-oxidizing bacteria (AOB) and archaea (AOA), plant community productivity, and litter quality. Gross nitrogen cycling rates, AOA and AOB population sizes, and plant community productivity were examined in native and invaded plots in smooth brome-invaded rough fescue grassland in central Saskatchewan, Canada. Despite no changes in inorganic nitrogen between invaded and native grassland soils, gross nitrogen mineralization rates and total soil nitrogen were higher in invaded soils. Invaded areas had greater plant productivity and litter production, which likely stimulated microbial activity and higher gross mineralization rates. Nitrification rates did not differ between invaded and native soils. Smooth brome had a weak positive effect on AOA in the B horizon but not in the A horizon, and AOB responded positively in both horizons. These results demonstrate that the full effects of plant invasion on soil N cycling may be masked in net N cycling rate measures.

Effect of ammonium nitrogen concentration on the ammonia-oxidizing bacteria community in a membrane bioreactor for the treatment of anaerobically digested swine wastewater

A membrane bioreactor (MBR) was developed for the treatment of anaerobically digested swine wastewater and to investigate the effect of ammonium nitrogen concentration on biological nitrogen removal and ammonia-oxidizing bacteria (AOB) community structures. The MBR achieved a high NH4(+)-N removal efficiency of 0.08 kgNMLSS(-1)d(-1) and removed 95% of the influent NH4(+)-N. The TN removal rate was highest of 82.62% at COD/TN and BOD5/TN ratios of 8.76 ± 0.30 and 3.02 ± 0.09, respectively. With the decrease in ammonium nitrogen concentrations, the diversity of the AOB community declined and showed a simple pattern of DGGE. However, the AOB population size remained high, with abundance of 10(7)-10(9) copies mL(-1). With the decrease of ammonium nitrogen concentrations, Nitrosomonas eutropha gradually disappeared, whereas Nitrosomonas sp. OZK11 showed constant adaptability to survive during each treatment stage. The selective effect of ammonium concentration on AOB species could be due to the affinity for NH4(+)-N. In this study, the changes of ammonium nitrogen concentrations in digested swine wastewater were found to have selective effects on the composition of AOB community, and biological nitrogen removal was improved by optimising the influencing parameters.

Effects of chlorimuron-ethyl application with or without urea fertilization on soil ammonia-oxidizing bacteria and archaea

Chlorimuron-ethyl (CE) has been widely used in modern agriculture, but little is known regarding the influence of CE on ammonia-oxidizing bacteria (AOB) and archaea (AOA) populations in soils. In this study, microcosm incubation of aquic brown soil was conducted for 60 d. Associated changes in the population sizes of AOB and AOA in response to CE application with or without urea fertilization were examined via quantitative real-time PCR (qPCR) assays of the ammonia monooxygenase gene (amoA). The half-life of CE ranged from 11.80 d to 14.54 d in the tested soil. Compared to the untreated control, the application of CE alone had no strong effects on soil pH, and urea fertilization temporarily increased soil pH in the first 7 days. The abundance of the AOA amoA gene was greater than the abundance of the AOB amoA gene in all treatments, but both were significantly suppressed by CE application in a dose-dependent manner. Urea fertilization generally increased AOB and AOA amoA gene abundances, except that the AOA amoA gene level was slightly reduced at the early stage of the incubation period. AOB and AOA preferred different N levels for growth, with AOB only growing significantly at high NH4+ levels and AOA growing substantially at low NH4+ levels. The stimulation effects of urea fertilization on AOA and AOB amoA gene abundances were strongly suppressed by the CE application. This study indicated that the CE application substantially suppressed soil nitrification via inhibiting the AOB and AOA population regardless of urea fertilization, which resulted in significant changes in the soil NH4+-N and NO3−-N levels. Furthermore, AOB and AOA inhabiting separate ecological niches with different NH4+ levels played various roles in N cycling.

Impact of coastal wetland cultivation on microbial biomass, ammonia-oxidizing bacteria, gross N transformation and N2O and NO potential production

A 15N dilution experiment was carried out to investigate effects of cultivation on the gross N transformation rate in coastal wetland zone. Microbial community composition was estimated by phospholipid fatty acid (PLFA) analysis and abundance of soil ammonia-oxidizing bacteria (AOB) was quantified by real-time polymerase chain reaction (PCR). Soil salinity decreased significantly, while total N increased after coastal wetland was cultivated. Microbial biomass (total PLFA), bacterial biomass, fungal biomass, and actinomycete biomass of the native coastal wetland soils were significantly (p < 0.05) lower than those of the cultivated soils whereas AOB population size also significantly increased after coastal wetland cultivation. Multiple regression analysis showed that total PLFA biomass and soil total N (TN) explained 97% of the variation of gross N mineralization rate in the studied soils (gross mineralization rate = 0.179 total PLFA biomass + 5.828TN − 2.505, n = 16, p < 0.01). Gross nitrification rate increased by increasing the soil AOB population size and gross mineralization rate (M) (gross nitrification rate = 3.39AOB + 0.18 M − 0.075, R2 = 0.98, n = 16, p < 0.01). Management of salt discharge and mineral N fertilization during the cultivation of wetland soils might have changed composition of soil microflora and AOB population size, thus influencing mineralization and nitrification. Probably, the cultivation of coastal wetland soils increased the risk of N losses from soil through nitrate leaching and gas emission (e.g., N2O and NO).

Population Size and Nitrification Activity of Soil Ammonia-Oxidizing Bacteria in Long-Term Intensive Managed Phyllostachys praecox Stands

High rate of fertilization and heavy winter mulch have been a common practice to gain a good yield in Phyllostachys praecox stands, but the long-term impact of this intensive management on soil ammonia-oxidizing bacteria (AOB) is largely unknown. Population size of soil AOB was quantified by real-time PCR in Phyllostachys praecox stands with different intensive management history. AOB population sizes and nitrification activities in intensive managed bamboo stands were significantly higher than that of the control. However, both soil AOB abundance and activity significantly decreased after long-term intensive management, and they correlated positively with soil mineral N and available potassium but negatively with soil pH. The results indicated that, although AOB activity and growth responded strongly to high rate of mineral fertilization during the first few years of intensive management, soil pH should be a dominant factor regulating the communities on a long-term basis.

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.

Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil

Nitrification is essential to the nitrogen cycle in paddy soils. However, it is still not clear which group of ammonia-oxidizing microorganisms plays more important roles in nitrification in the paddy soils. The changes in the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated by real-time PCR, terminal restriction fragment length polymorphism, and clone library approaches in an acid red paddy soil subjected to long-term fertilization treatments, including treatment without fertilizers (CT); chemical fertilizer nitrogen (N); N and potassium (NK); N and phosphorus (NP); N, P, and K (NPK); and NPK plus recycled crop residues (NPK+C). The AOA population size in NPK+C was higher than those in CT, while minor changes in AOB population sizes were detected among the treatments. There were also some changes in AOA community composition responding to different fertilization treatments. Still few differences were detected in AOB community composition among the treatments. Phylogenetic analysis showed that the AOA sequences fell into two main clusters: cluster A and cluster soil/sediment. The AOB composition in this paddy soil was dominated by Nitrosospira cluster 12. These results suggested that the AOA were more sensitive than AOB to different fertilization treatments in the acid red paddy soil.

A quantitative method for detecting ammonia-oxidizing bacteria in coastal aquaculture systems

There is a need to quantify autotrophic nitrifiers in coastal aquaculture systems for evolving a bioremediation strategy. Autotrophic nitrifiers are extremely slow-growing organisms, which cannot be detected by traditional methods as they are notoriously difficult to culture. Molecular techniques based on functional genes could be deployed for the detection of nitrifiers. Ammonia monooxygenase (amoA), that catalyses the oxidation of ammonia to hydroxylamine in the rate-determining step of nitrification is largely unique to ammonia-oxidizing bacteria (AOB). In the present study, a quantitative real-time polymerase chain reaction assay targeting amoA was developed to estimate AOB population size in coastal soil, ammonia-removing bioaugmentors and the solid matrix. To achieve this objective, different set of primers and a dual labelled probe have been designed for SYBR Green and TaqMan real-time assays. The abundance of AOB ranged from 104 to 106 order of magnitude in the samples. In the present study, biofilm formation of the consortium of nitrifying bacteria onto bagasse has also been quantified. The results demonstrate that the developed method is a rapid and sensitive tool for the quantitative detection of nitrifying bacteria in aquatic and related environment. This helps in making the bioremediation approach for ammonia removal by immobilization of nitrifying bacteria onto the natural substrate.

Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils

Ammonia oxidation plays an important role in global nitrogen cycle. However, little information is available on ammonia oxidizers in paddy soils. This study aimed to understand the controlling factors of ammonia oxidizers in the paddy soils. Three types of paddy soils were collected from southwest [Chongqing City (CQ)], central [Honghu City (HH)], and northeast [Panjin City (PJ)] of China, respectively. The soils were cultured with unplanted and rice-planted pot experiments for 10 weeks. The abundance and composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) of the paddy soil samples were investigated by real-time polymerase chain reaction and denaturing gradient gel electrophoresis approaches based on amoA genes. In this study, minor changes in the abundance and community structure of both AOB and AOA were observed among the treatments of unplanted and rhizosphere and bulk of rice-planted soil samples in the same type of paddy soil. The AOB population sizes in CQ were lower than those in HH and PJ, while the AOA in CQ and HH were lower than those in PJ. The amoA gene copy numbers of AOA were more abundant than those of AOB in all treatments of the three paddy soils. The community structure of both AOB and AOA in all paddy soils was different from each other. The population size and community structure of AOB and AOA in the flooded paddy soils were mainly determined by the soil types, irrespective of rice-planted or unplanted.

Soil Ammonia‐Oxidizing Bacterial Communities in Paddy Rice Fields as Affected by Upland Conversion History

Rotation of paddy rice and upland crop cultivation is a major type of land use in eastern Asia. Temporary upland conversion of paddy field also occurs frequently in this region. Little is known about the affects of these agricultural practices on soil microbial communities. The purpose of this study was to investigate the effect of former upland conversion (upland rice [Oryza sativa L.] cultivation or soybean [Glycine max (L.) Merill]–wheat [Triticum aestivum L.] cultivation) on soil ammonia‐oxidizing bacteria (AOB) in a paddy rice field. The AOB population size and community structures were determined by real‐time polymerase chain reaction (PCR) and PCR‐denaturing gradient gel electrophoresis (DGGE), respectively. Soil AOB communities were more diverse and had larger population size in the plots with upland conversion history than in consecutive paddy rice plots. Former soybean–wheat cultivation had a much larger effect on soil AOB communities than former upland rice cultivation. Phylogenetic analysis showed that DGGE bands derived from former upland conversion belonged to Nitrosospira amoA cluster 1. Nitrosospira amoA Cluster 1 became dominant over Nitrosospira amoA Cluster 3 in the plots with former soybean–wheat cultivation. Our results demonstrate that upland conversion history exhibit a significant effect on soil AOB communities in paddy rice field, and the effect depends strongly on the type of upland crop.

Population dynamics of ammonia-oxidizing bacteria in an aerated submerged biofilm reactor for micropolluted raw water pretreatment

Population dynamics of ammonia-oxidizing bacteria (AOB) in a full-scale aerated submerged biofilm reactor for micropolluted raw water pretreatment was investigated using molecular techniques for a period of 1 year. The ammonia monooxygenase (amoA) gene fragments were amplified from DNA and RNA extracts of biofilm samples. Denaturing gradient gel electrophoresis (DGGE) profile based on the amoA messenger RNA approach exhibited a more variable pattern of temporal dynamics of AOB communities than the DNA-derived approach during the study. Phylogenetic analysis of excised DGGE bands revealed three AOB groups affiliated with the Nitrosomonas oligotropha lineage, Nitrosomonas communis lineage, and an unknown Nitrosomonas group. The population size of betaproteobacterial AOB, quantified with 16S ribosomal RNA gene real-time polymerase chain reaction assay, ranged from 6.63 x 10(5) to 2.67 x 10(9) cells per gram of dry biofilm and corresponded to 0.23-1.8% of the total bacterial fraction. Quantitative results of amoA gene of the three specific AOB groups revealed changes in competitive dominance between AOB of the N. oligotropha lineage and N. communis lineage. Water temperature is shown to have major influence on AOB population size in the reactor by the statistic analysis, and a positive correlation between AOB cell numbers and ammonia removal efficiency is suggested (r = 0.628, P < 0.05).

Population size and specific nitrification potential of soil ammonia-oxidizing bacteria under long-term fertilizer management

Population size of soil ammonia-oxidizing bacteria (AOB) was quantified by real-time PCR in a long-term (16 years) field experiment under different fertilizer managements. AOB population sizes in mineral nitrogen-fertilized soils and organic manure-fertilized soil were 10.3 and 3.1 times, respectively, that of the control, while phosphorus and potassium fertilization had no significant effect. On the other hand, the AOB specific nitrification potential (soil nitrification potential per AOB cell) was significantly higher ( P < 0.05) in organic manure-fertilized soil than in mineral-fertilized soils and the control, indicating that AOB was likely more metabolically active in organic manure-fertilized soils than in mineral nitrogen-fertilized soils after long-term application.

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 (NH 4 +) to nitrite (NO 2 −). 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 NH 4 + 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 NH 4 + addition and persisted after the depletion of soil NH 4 +. AOB population sizes increased to a similar degree, over a 1.5-day period, irrespective of the amount of NH 4 + supplied. These data suggest selection of an AOB community in this intensively farmed and C-limited soil, that rapidly uses NH 4 + that becomes available. These data also suggest that mineralization may play an especially important role in regulating AOB populations where NH 4 + pool sizes are very low. Methodological considerations in the study of soil AOB communities are also discussed.