Relationship between respirometric activity and community of entrapped nitrifying bacteria: Implications for partial nitrification

Activated sludge obtained from two municipal wastewater treatment facilities (WWTF) was used as seed sludge for enriched nitrifiers, which were later entrapped in polyvinyl alcohol. Seed sludge from one WWTF was acclimated to high ammonia level (1813 mg NH₃-N l^?1) through the return of sludge digester supernatant back to primary clarifier while seed sludge from the other WWTF was un-acclimated. To elucidate on how to control partial nitrification by entrapped cells, which could be different from suspended cells, kinetics of entrapped enriched nitrifiers were studied using a respirometric assay. The community of nitrifiers within the entrapment matrix, which was observed by fluorescence in situ hybridization (FISH) technique, was related to the nitritation and nitratation kinetics based on oxygen uptake rate. Maximum oxygen uptake rate, and substrate and oxygen affinities of both ammonia oxidizing bacteria (AOB) for nitritation and nitrite oxidizing bacteria (NOB) for nitratation in entrapped cells were lower than those of corresponding suspended cells. Under dissolved oxygen (DO) limiting conditions, nitratation was more suppressed than nitritation for suspended cells, while for the entrapped cells, the results were the contrary. A free ammonia (FA) inhibition affected only the un-acclimated sludge. Either FA inhibition or DO limitation might not be a sole effective control parameter to achieve partial nitrification by entrapped cells. FISH results revealed that Nitrosomonas europaea was the dominant AOB while Nitrobacter species was the dominant NOB in all cases. Heterotrophs were also present in the entrapment at 22.8 ± 18.6% and 41.5 ± 4.3% of total bacteria for acclimated and un-acclimated originated sludge. The availability of substrate and oxygen governed the distributions of AOB, NOB and heterotrophs within the entrapment and nitritation kinetics of entrapped nitrifiers.     

Kinetic analysis on the two-step processes of AOB and NOB in aerobic nitrifying granules

Complete granulation of nitrifying sludge was achieved in a sequencing batch reactor. For the granular sludge, batch experiments were conducted to characterize the kinetic features of ammonia oxidizers (AOB) and nitrite oxidizers (NOB) in the granules using the respirometric method. A two-step nitrification model was established to determine the kinetic parameters of both AOB and NOB. In addition to nitrification reactions, the new model also took into account biomass maintenance and mass transfer through the granules. The yield coefficient, maximum specific growth rate, and affinity constant for ammonium for AOB were 0.21 g chemical oxygen demand (COD) g⁻¹ N, 0.09 h⁻¹, and 9.1 mg N L⁻¹, respectively, whereas the corresponding values for NOB were 0.05 g COD g⁻¹ N, 0.11 h⁻¹, and 4.85 mg N L⁻¹, respectively. The model developed in this study performed well in simulating the oxygen uptake rate and nitrogen conversion kinetics and in predicting the oxygen consumption of the AOB and NOB in aerobic granules.     

Estimation of nitrifier abundances in a partial nitrification reactor treating ammonium-rich saline wastewater using DGGE, T-RFLP and mathematical modeling

The bacterial community in a partial nitrification reactor was analyzed on the basis of 16S rRNA gene by cloning–sequencing method, and the percentages of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the activated sludge were quantified by three independent methods, namely, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and Double Monod modeling. The clone library results suggested that there were only a dominant AOB and a dominant NOB species in the reactor, belonging to Nitrosomonas genus and Nitrospira genus, respectively. The percentages of NOB in total bacterial community increased from almost 0% to 30% when dissolved oxygen (DO) levels were changed from 0.15 mg/L to 0.5 mg/L, coinciding with the accumulation and conversion of nitrite, while the percentages of AOB changed little in the two phases. The results confirmed the importance of low DO level for inhibiting NOB to achieve partial nitrification. Furthermore, the percentages of AOB and NOB in the total bacteria community were estimated based on the results of batch experiments using Double Monod model, and the results were comparable with those determined according to profiles of DGGE and T-RFLP.     

Partial nitrification to nitrite using low dissolved oxygen concentration as the main selection factor

Partial nitrification to nitrite (nitritation) can be achieved in a continuous process without sludge retention by wash out of nitrite oxidising bacteria (NOB) while retaining ammonia oxidising bacteria (AOB), at elevated temperatures (the SHARON process) and, as demonstrated in this paper, also at low dissolved oxygen (DO) concentrations. Enriched AOB was attained at a low DO concentration (0.4 mg l⁻¹) and a dilution rate of 0.42 day⁻¹ in a continuous process. A higher oxygen affinity of AOB compared to NOB seemed critical to achieving this. This was verified by determining the oxygen half saturation constant, K _o, with similar oxygen mass transfer resistances for enriched AOB and NOB as 0.033 ± 0.003 mg l⁻¹ and 0.43 ± 0.08 mg l⁻¹, respectively. However, the extent of nitritation attained was found to be highly sensitive to process upsets.     

短程硝化启动运行中功能菌群变化研究

【目的】短程硝化-厌氧氨氧化是可实现的最短生物脱氮工艺,短程硝化是实现该工艺的重要环节和必要条件。【方法】采用序批式反应器(SBR)来实现短程硝化过程的启动和稳定运行,并对该过程中的相关功能菌群变化进行检测分析。【结果】通过控制低DO浓度(<1 mg/L)和逐步提高氨氮进水负荷,可抑制氨氧化细菌(NOB)菌群增殖并促进亚硝酸氧化菌(AOB)菌群规模显著扩大,实现短程硝化过程的启动和稳定运行。在氨氮进水负荷为0.055 kg/(m3.d)时,平均氨氮去除容积负荷和污泥负荷可达到0.043kg/(m3.d)和0.16 kg/(kg.d),平均亚硝酸盐积累率可达到83.4%。在短程硝化启动和稳定运行过程中,NOB菌群密度从2.0×105CFU/mL降至1.5×104CFU/mL,相对丰度从5.51%降至2.14%;AOB菌群密度从4.5×104CFU/mL增加至1.5×107CFU/mL,相对丰度从0.18%增加至7.25%。【结论】AOB菌群规模的扩大是实现短程硝化和氨氮去除能力提高的主要原因,同时较高的进水氨氮浓度和负荷也会造成亚硝化活性的抑制。     

Operation of partial nitrification to nitrite of landfill leachate and its performance with respect to different oxygen conditions

The coupled system of partial nitrification and anaerobic ammonium oxidation (Anammox) is efficient in nitrogen removal from wastewater. In this study, the effect of different oxygen concentrations on partial nitrification performance with a sequencing batch reactor (SBR) was investigated. Results indicate that, partial nitrification of landfill leachate could be successfully achieved under the 1.0–2.0 mg L⁻¹ dissolved oxygen (DO) condition after 118 d long-term operation, and that the effluent is suitable for an Anammox reactor. Further decreasing or increasing the DO concentration, however, would lead to a decay of nitrification performance. Additionally, the MLSS concentration in the reactor increased with increasing DO concentration. Respirometric assays suggest that low DO conditions (<2 mg L⁻¹) favor the ammonia-oxidizing bacteria (AOB) and significantly inhibit nitrite oxidizing bacteria (NOB) and aerobic heterotrophic bacteria (AHB); whereas high DO conditions (>3 mg L⁻¹) allow AHB to dominate and significantly inhibit AOB. Therefore, the optimal condition for partial nitrification of landfill leachate is 1.0–2.0 mg L⁻¹ DO concentration.     

Impact of protozoan grazing on nitrification and the ammonia- and nitrite-oxidizing bacterial communities in activated sludge

In activated sludge, protozoa feed on free-swimming bacteria and suspended particles, inducing flocculation and increasing the turnover rate of nutrients. In this study, the effect of protozoan grazing on nitrification rates under various conditions in municipal activated sludge batch reactors was examined, as was the spatial distribution of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) within the activated sludge. The reactors were monitored for ammonia, nitrite, nitrate, and total nitrogen concentrations, and bacterial numbers in the presence and absence of cycloheximide (a protozoan inhibitor), allylthiourea (an inhibitor of ammonia oxidation), and EDTA (a deflocculating agent). The accumulations of nitrate, nitrite, and ammonia were lower in batches without than with protozoa grazing. Inhibition of ammonia oxidation also decreased the amount of nitrite and nitrate accumulation. Inhibiting protozoan grazing along with ammonia oxidation further decreased the amounts of nitrite and nitrate accumulated. Induction of deflocculation led to high nitrate accumulation, indicating high levels of nitrification; this effect was lessened in the absence of protozoan grazing. Using fluorescent in situ hybridization and confocal laser scanning microscopy, AOB and NOB were found clustered within the floc, and inhibiting the protozoa, inhibiting ammonia oxidation, or inducing flocculation did not appear to lower the number of AOB and NOB present or affect their position within the floc. These results suggest that the AOB and NOB are present but less active in the absence of protozoa.     

Evaluation on factors influencing the heterotrophic growth on the soluble microbial products of autotrophs

In this work, the heterotrophic growth on the microbial products of autotrophs and the effecting factors were evaluated with both experimental and modeling approaches. Fluorescence in situ hybridization (FISH) analysis illustrated that ammonia oxidizers (AOB), nitrite oxidizers (NOB), and heterotrophs accounted for about 65%, 20%, and 15% of the total bacteria, respectively. The mathematical evaluation of experimental data reported in literature indicated that heterotrophic growth in nitrifying biofilm (30–50%) and granules (30%) was significantly higher than that of nitrifying sludge (15%). It was found that low influent ammonium resulted in a lower availability of soluble microbial products (SMP) and a slower heterotrophic growth, but high ammonium (>150 mg N L⁻¹) feeding would lead to purely AOB dominated sludge with high biomass‐associated products contained effluent, although the absolute heterotrophic growth increased. Meanwhile, the total active biomass concentration increased gradually with the increasing solids retention time, whereas the factions of active AOB, NOB, and heterotrophs varied a lot at different solids retention times. This work could be useful for better understanding of the autotrophic wastewater treatment systems. Biotechnol. Bioeng. 2011; 108:804–812. © 2010 Wiley Periodicals, Inc.     

Distinctive microbial ecology and biokinetics of autotrophic ammonia and nitrite oxidation in a partial nitrification bioreactor

Biological nitrogen removal (BNR) based on partial nitrification and denitrification via nitrite is a cost-effective alternate to conventional nitrification and denitrification (via nitrate). The goal of this study was to investigate the microbial ecology, biokinetics, and stability of partial nitrification. Stable long-term partial nitrification resulting in 82.1 +/- 17.2% ammonia oxidation, primarily to nitrite (77.3 +/- 19.5% of the ammonia oxidized) was achieved in a lab-scale bioreactor by operation at a pH, dissolved oxygen and solids retention time of 7.5 +/- 0.1, 1.54 +/- 0.87 mg O(2)/L, and 3.0 days, respectively. Bioreactor ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) populations were most closely related to Nitrosomonas europaea and Nitrobacter spp., respectively. The AOB population fraction varied in the range 61 +/- 45% and was much higher than the NOB fraction, 0.71 +/- 1.1%. Using direct measures of bacterial concentrations in conjunction with independent activity measures and mass balances, the maximum specific growth rate (micro(max)), specific decay (b) and observed biomass yield coefficients (Y(obs)) for AOB were 1.08 +/- 1.03 day(-1), 0.32 +/- 0.34 day(-1), and 0.15 +/- 0.06 mg biomass COD/mg N oxidized, respectively. Corresponding micro(max), b, and Y(obs) values for NOB were 2.6 +/- 2.05 day(-1), 1.7 +/- 1.9 day(-1), and 0.04 +/- 0.02 mg biomass COD/mg N oxidized, respectively. The results of this study demonstrate that the highly selective partial nitrification operating conditions enriched for a narrow diversity of rapidly growing AOB and NOB populations unlike conventional BNR reactors, which host a broader diversity of nitrifying bacteria. Further, direct measures of microbial abundance enabled not only elucidation of mixed community microbial ecology but also estimation of key engineering parameters describing bioreactor systems supporting these communities.     

Effects of ferrous iron on the performance and microbial community in aerobic granular sludge in relation to nutrient removal

Lab‐scale experiments were conducted to investigate the effects of ferrous iron on nutrient removal performance and variations in the microbial community inside aerobic granular sludge for 408 days. Two reactors were simultaneously operated, one without added ferrous iron (SBR1), and one with 10 mg Fe²⁺ L^?1 of added ferrous iron (SBR2). A total of 1 mg Fe²⁺ L^?1 of added ferrous iron was applied to SBR1 starting from the 191st day to observe the resulting variations in the nutrient removal performance and the microbial community. The results show that ammonia‐oxidizing bacteria (AOB) could not oxidize ammonia due to a lack of iron compounds, but they could survive in the aerobic granular sludge. Limited ferrous iron addition encouraged nitrification. Enhanced biological phosphorus removal (EBPR) from both reactors could not be maintained regardless of the amount of ferrous iron that was applied. EBPR was established in both reactors when the concentration of mixed liquor suspended solid (MLSS) and the percentage of Accumulibacteria increased. A total of 10 mg Fe²⁺ L^?1 of added ferrous iron had a relatively adverse effect on the growth of AOB species compared to 1 mg Fe²⁺ L^?1 of added ferrous iron, but it encouraged the growth of Nitrospira sp. and Accumulibacteria, which requires further study. It could be said that the compact and stable structure of aerobic granular sludge preserved AOB and NOB from Fe‐deficient conditions, and wash‐out during the disintegration period. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:716–725, 2017     

Characterization of the Microbial Community in a Partial Nitrifying Sequencing Batch Biofilm Reactor

A lab-scale partial nitrifying sequencing batch biofilm reactor was a successful start-up. Denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial community dynamics in three periods together with inocula sludge at ambient temperature. The DGGE profiles of bacteria and Shannon–Wiener index (H′) results showed that high free ammonia (FA) concentration referred to lower diversity in the bioreactor system. Cluster analysis indicated that microorganism in period III was similar with inocula sludge and was different from that in periods I and II. Similar results also appeared in ammonia-oxidizing bacteria (AOB) community structure and nitrite-oxidizing bacteria (NOB) community structure, and at least four AOB species and two NOB species were present in period III, respectively. Phylogenetic analysis of amoA gene sequences showed that Nitrosomonas eutropha cluster was predominant in all the three periods. With lower ammonium loads, three new operational taxonomic units formed and consisted Nitrosomonas sp. Cluster. This article demonstrated that microbial community, AOB, and NOB diversity were related with FA concentration closely at ambient temperature.     

Long-term starvation and subsequent reactivation of a high-rate partial nitrification activated sludge pilot plant

The starvation process of a high-rate partial nitrification system during 30 days and its controlled recovery were studied in an activated sludge pilot plant. Four ammonium-starved reactors under anoxic, aerobic and two different alternating aerobic/anoxic conditions were evaluated. The highest and the lowest decay rates of ammonia oxidizing bacteria (AOB) were obtained under full aerobic (0.24 d⁻¹) and full anoxic (0.11 d⁻¹) conditions, respectively. The evolution of biomass activity correlated well with the AOB quantification using FISH technique. AOB fractions lower than 1% were measured in the four reactors after 23 days of starvation. The recovery of the system was achieved in only 5 days using a nitrogen loading rate (NLR) control loop, obtaining the same conditions than before the long-term starvation period with a NLR of 1.2 g N L⁻¹ d⁻¹ and 98% of nitrite accumulation in the effluent.     

Long-term continuous partial nitritation-anammox reactor aeration optimization at different nitrogen loading rates for the treatment of ammonium rich digestate lagoon supernatant

Dissolved oxygen (DO) is an important parameter for partial nitritation-anammox process but previously not evaluated for the treatment of digested biosolid thickening lagoon supernatant. Using intermittent aeration we investigated nitrogen removal from such supernatant in an integrated fixed film activated sludge (IFAS) process operated under a variety of hydraulic retention times (1.2–2.5 days). The overall nitrogen removal rate (NRR) was significantly increased (P < 0.01) from 0.26 ± 0.01 kg N m⁻³ d^-1 at HRT of 2.5 days to 0.50 ± 0.01 kg N m^-3 d^-1 at HRT of 1.2 day. Higher nitrogen loading rates needed higher DO concentrations in order to cope with the increased oxygen demand by ammonium-oxidizing bacteria (AOB). Enhancing the DO concentration from 0.18 mg L^-1 to 0.35 mg L^-1 improved AOB activity. However, when the bulk liquid DO was in the range of 0.28−0.35 mg L^-1, anammox activity inhibition was observed associated with a significant free nitrous acid (FNA) accumulation (21.70 ± 4.10 μg L^-1). Batch studies confirmed the inhibition of anammox activity under high DO conditions (0.28−0.35 mg L^-1). Aeration strategies, other than increasing the DO set points, should be investigated in order to be able to work at high nitrogen loading rates without compromising anammox activity.     

Achieving nitrite accumulation in a continuous system treating low-strength domestic wastewater: switchover from batch start-up to continuous operation with process control

Although biological nitrogen removal via nitrite is recognized as one of the cost-effective and sustainable biological nitrogen removal processes, nitrite accumulation has proven difficult to achieve in continuous processes treating low-strength nitrogenous wastewater. Partial nitrification to nitrite was achieved and maintained in a lab-scale completely stirred tank reactor (CSTR) treating real domestic wastewater. During the start-up period, sludge with ammonia-oxidizing bacteria (AOB) but no nitrite-oxidizing bacteria (NOB) was obtained by batch operation with aeration time control. The nitrifying sludge with the dominance of AOB was then directly switched into continuous operation. It was demonstrated that partial nitrification to nitrite in the continuous system could be repeatedly and reliably achieved using this start-up strategy. The ratio of dissolved oxygen to ammonium loading rate (DO/ALR) was critical to maintain high ammonium removal efficiency and nitrite accumulation ratio. Over 85% of nitrite accumulation ratio and more than 95% of ammonium removal efficiency were achieved at DO/ALR ratios in an optimal range of 4.0–6.0 mg O₂/g N d, even under the disturbances of ammonium loading rate. Microbial population shift was investigated, and fluorescence in situ hybridization analysis indicated that AOB were the dominant nitrifying bacteria over NOB when stable partial nitrification was established.     

Differential distribution of ammonia- and nitrite-oxidising bacteria in flocs and granules from a nitrifying/denitrifying sequencing batch reactor

A lab-scale sequencing batch reactor was operated with alternating anoxic/aerobic conditions for nitrogen removal. Flocs and granules co-existed in the same reactor, with distinct aggregate structure and size, for over 180 days of reactor operation. Process data showed complete nitrogen removal, with temporary nitrite accumulation before full depletion of ammonia in the aerobic phase. Microbial quantification of the biomass by fluorescence in situ hybridisation showed that granules contained most of the nitrite-oxidising bacteria (NOB) whereas the ammonium-oxidising bacteria (AOB) seemed to be more abundant in the flocs. This was supported by microsensor measurements, which showed a higher potential of NO₂⁻ uptake than NH₄ uptake in the granules. The segregation is possibly linked to the different growth rates of the two types of nitrifiers and the reactor operational conditions, which produced different sludge retention time for flocs and granules. The apparent physical separation of AOB and NOB in two growth forms could potentially affect mass transfer of NO₂⁻ from AOB to NOB, but the data presented here shows that it did not impact negatively on the overall nitrogen removal.     

Aerobic granulation and nitrogen removal with the effluent of internal circulation reactor in start-up of a pilot-scale sequencing batch reactor

Aerobic granular sludge was successfully cultivated with the effluent of internal circulation (IC) reactor in a pilot-scale sequencing batch reactor (SBR) using activated sludge as seeding sludge. N removal was investigated in the start-up of aerobic granulation process. Initially, the phenomenon of partial nitrification was observed and nitrite accumulation rates (NO₂ ^?-N/NO _x ^? -N) were between 84.6 and 99.1?%. It was potentially caused by ammonium oxidizing bacteria (AOB) in the seeding activated sludge, high external environmental temperature (~32?°C) and free ammonia (FA) concentration. After 50?days’ running, the aerobic granules-based bioreactor demonstrated perfect performance in simultaneous removal of organic matter and ammonia nitrogen, and average removal efficiencies were maintained above 93 and 96?%, respectively. The maximum nitrogen removal efficiency of 83.1?% was achieved after the formation of aerobic granules. The average diameter of mature aerobic granular sludge mostly ranged from 0.5 to 1.0?mm. Furthermore, one typical cyclic test indicated that pH and DO profiles could be used as effective parameters for biological reactions occurring in the aerobic/anoxic process. The obtained results could provide further information on the cultivation of aerobic granular sludge with practical wastewater, especially with regard to nitrogen-rich industrial wastewater.     

NOB suppression and adaptation strategies in the partial nitrification–Anammox process for a poultry manure anaerobic digester

Poultry manure contains high levels of ammonia, which result in a suboptimal bioconversion to methane in anaerobic digesters (AD). A simultaneous process of nitrification, Anammox and denitrification (SNAD) in a continuous granular bubble column reactor to treat the anaerobically digested poultry manure was implemented. Thus, two strategies to achieve high efficiencies were proposed in this study: (1) ammonia overload to suppress nitrite oxidizing bacteria (NOB) and (2) gradual adaptation of the partial nitrification–Anammox (PN–A) biomass to organic matter. During the NOB-suppression stage, microbial and physical biomass characterizations were performed and the NOB abundance decreased from 31.3% to 3.3%. During the adaptation stage, with a nitrogen loading rate of 0.34 g L⁻¹ d⁻¹, a hydraulic retention time of 1.24 d and an influent COD/N ratio of 2.63 ± 0.02, a maximum ammonia and total nitrogen removal of 100% and 91.68% were achieved, respectively. The relative abundances of the aerobic and the anaerobic ammonia-oxidizing bacteria were greater than 35% and 40% respectively, during the study. These strategies provided useful design tools for the efficient removal of nitrogen species in the presence of organic matter.     

污水短程硝化体系氨氧化菌与亚硝酸盐氧化菌的生态学研究进展

短程硝化(partial nitrification, PN)是一种绿色低碳的生物脱氮创新技术,伴随厌氧氨氧化(anaerobic ammonia oxidation, Anammox)污水脱氮技术的进一步推广,短程硝化作为提供其电子受体的重要环节,已成为了污水脱氮领域的研究热点。氨氧化菌(ammonia-oxidizing bacteria,AOB)和亚硝酸盐氧化菌(nitrite-oxidizing bacteria, NOB)是该技术的核心竞争微生物,掌握这两类微生物的生态学特征,借助生态学理论和手段调控AOB淘汰NOB,提高种群的可预测性,对于实现稳定高效的短程硝化具有重要意义。本文基于生态学角度介绍了AOB和NOB基础分类、生理性能及生态位分离,重点综述了短程硝化系统中AOB和NOB的生长动力学、群落构建、环境因素和相互作用,最后对这两类微生物的未来研究重点和研究方法进行了展望,为短程硝化工艺的快速启动和稳定运行提供理论指导。     

Nanosilver inhibits nitrification and reduces ammonia‐oxidising bacterial but not archaeal amoA gene abundance in estuarine sediments

Silver nanoparticles (AgNPs) enter estuaries via wastewater treatment effluents, where they can inhibit microorganisms, because of their antimicrobial properties. Ammonia‐oxidising bacteria (AOB) and archaea (AOA) are involved in the first step of nitrification and are important to ecosystem function, especially where effluent discharge results in high nitrogen inputs. Here, we investigated the effect of a pulse addition of AgNPs on AOB and AOA ammonia monooxygenase (amoA) gene abundances and benthic nitrification potential rates (NPR) in low‐salinity and mesohaline estuarine sediments. Whilst exposure to 0.5 mg L^?1 AgNPs had no significant effect on amoA gene abundances or NPR, 50 mg L^?1 AgNPs significantly decreased AOB amoA gene abundance (up to 76% over 14 days), and significantly decreased NPR by 20‐fold in low‐salinity sediments and by twofold in mesohaline sediments, after one day. AgNP behaviour differed between sites, whereby greater aggregation occurred in mesohaline waters (possibly due to higher salinity), which may have reduced toxicity. In conclusion, AgNPs have the potential to reduce ammonia oxidation in estuarine sediments, particularly where AgNPs accumulate over time and reach high concentrations. This could lead to long‐term risks to nitrification, especially in polyhaline estuaries where ammonia‐oxidation is largely driven by AOB.     

Autotrophic growth of nitrifying community in an agricultural soil

The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by ¹³CO₂ after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the ¹³C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the ¹³C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that ¹³CO₂ assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested.