Source of nitrous oxide emissions during the cow manure composting process as revealed by isotopomer analysis of and amoA abundance in betaproteobacterial ammonia-oxidizing bacteria

Nitrosomonas stercoris sp. nov., a Chemoautotrophic Ammonia-Oxidizing Bacterium Tolerant of High Ammonium Isolated from Composted Cattle Manure

Among ammonia-oxidizing bacteria, Nitrosomonas eutropha-like microbes are distributed in strongly eutrophic environments such as wastewater treatment plants and animal manure. In the present study, we isolated an ammonia-oxidizing bacterium tolerant of high ammonium levels, designated strain KYUHI-S^T, from composted cattle manure. Unlike the other known Nitrosomonas species, this isolate grew at 1,000 mM ammonium. Phylogenetic analyses based on 16S rRNA and amoA genes indicated that the isolate belonged to the genus Nitrosomonas and formed a unique cluster with the uncultured ammonia oxidizers found in wastewater systems and animal manure composts, suggesting that these ammonia oxidizers contributed to removing higher concentrations of ammonia in strongly eutrophic environments. Based on the physiological and phylogenetic data presented here, we propose and call for the validation of the provisional taxonomic assignment Nitrosomonas stercoris, with strain KYUHI-S as the type strain (type strain KYUHI-S^T = NBRC 110753^T = ATCC BAA-2718^T).

From the ground up: global nitrous oxide sources are constrained by stable isotope values

Rising concentrations of nitrous oxide (N₂O) in the atmosphere are causing widespread concern because this trace gas plays a key role in the destruction of stratospheric ozone and it is a strong greenhouse gas. The successful mitigation of N₂O emissions requires a solid understanding of the relative importance of all N₂O sources and sinks. Stable isotope ratio measurements (δ¹⁵N-N₂O and δ¹⁸O-N₂O), including the intramolecular distribution of ¹⁵N (site preference), are one way to track different sources if they are isotopically distinct. ‘Top-down’ isotope mass-balance studies have had limited success balancing the global N₂O budget thus far because the isotopic signatures of soil, freshwater, and marine sources are poorly constrained and a comprehensive analysis of global N₂O stable isotope measurements has not been done. Here we used a robust analysis of all available in situ measurements to define key global N₂O sources. We showed that the marine source is isotopically distinct from soil and freshwater N₂O (the continental source). Further, the global average source (sum of all natural and anthropogenic sources) is largely controlled by soils and freshwaters. These findings substantiate past modelling studies that relied on several assumptions about the global N₂O cycle. Finally, a two-box-model and a Bayesian isotope mixing model revealed marine and continental N₂O sources have relative contributions of 24–26% and 74–76% to the total, respectively. Further, the Bayesian modeling exercise indicated the N₂O flux from freshwaters may be much larger than currently thought.

Greenhouse gas emissions from dairy manure management: a review of field-based studies

Livestock manure management accounts for almost 10% of greenhouse gas emissions from agriculture globally, and contributes an equal proportion to the US methane emission inventory. Current emissions inventories use emissions factors determined from small-scale laboratory experiments that have not been compared to field-scale measurements. We compiled published data on field-scale measurements of greenhouse gas emissions from working and research dairies and compared these to rates predicted by the IPCC Tier 2 modeling approach. Anaerobic lagoons were the largest source of methane (368 ± 193 kg CH4 hd(-1) yr(-1)), more than three times that from enteric fermentation (~120 kg CH4 hd(-1) yr(-1)). Corrals and solid manure piles were large sources of nitrous oxide (1.5 ± 0.8 and 1.1 ± 0.7 kg N2O hd(-1) yr(-1), respectively). Nitrous oxide emissions from anaerobic lagoons (0.9 ± 0.5 kg N2O hd(-1) yr(-1)) and barns (10 ± 6 kg N2O hd(-1) yr(-1)) were unexpectedly large. Modeled methane emissions underestimated field measurement means for most manure management practices. Modeled nitrous oxide emissions underestimated field measurement means for anaerobic lagoons and manure piles, but overestimated emissions from slurry storage. Revised emissions factors nearly doubled slurry CH4 emissions for Europe and increased N2O emissions from solid piles and lagoons in the United States by an order of magnitude. Our results suggest that current greenhouse gas emission factors generally underestimate emissions from dairy manure and highlight liquid manure systems as promising target areas for greenhouse gas mitigation.

Sulfonamide antibiotic removal and nitrogen recovery from synthetic urine by the combination of rotating advanced oxidation contactor and methylene urea synthesis process

The combination of nitrogen recovery and pharmaceutical removal processes for livestock urine treatment were investigated to suppress the discharge of pollutants and recover nitrogen as resources. We combined methylene urea synthesis from urea and adsorption and photocatalytic decomposition of sulfonamide antibiotic using rotating advanced oxidation contactor (RAOC) contained for obtaining both safe fertilizer and reclaimed water. The methylene urea synthesis could recover urea in synthetic urine, however, almost all sulfonamide antibiotic was also incorporated, which is unfavorable from a safety aspect if the methylene urea is to be used as fertilizer. Conversely, RAOC could remove sulfonamide antibiotic without consuming urea. It was also confirmed that the methylene urea could be synthesized from synthetic urine treated by RAOC. Thus, we concluded that RAOC should be inserted prior to the nitrogen recovery process for effective treatment of urine and safe use of methylene urea as fertilizer.

Impact of the addition of a nitrifying activated sludge on ammonia oxidation during composting of residual household wastes

AIMS

To investigate the nitrogen-microbial community dynamics during composting of a mixture of nitrifying waste activated sludge (WAS) and fine organic fraction of residual household waste (RHW). To examine whether the addition of nitrifying sludge could promote ammonia oxidation and reduce ammonia emissions.

METHODS AND RESULTS

The fine organic fraction of RHW was mixed with the WAS and homogenized. The mixture and each waste alone were loaded in aerobic cells under controlled conditions, respectively. Both nitrogen and microbial community dynamics were monitored during 50 days of composting. The ammonia oxidizers were quantified and identified in the sludge and compost. The changes in ammonia-oxidizing bacteria (AOB) concentrations corresponded to the ammonia oxidation rates calculated from nitrogen balance. The addition of WAS did not efficiently reduce ammonia emissions because the Nitrosomonas oligotropha-like AOB introduced declined during the active stage of composting. Ammonia oxidation was probably limited by the intense heterotrophic activities at the active stage. Nitrosomonas europaea/eutropha and Nitrosomonas nitrosa-like AOB were established only during the maturation stage. They were the main contributors to ammonia oxidation during composting.

CONCLUSIONS

The mixing of nitrifying WAS with the RHW during the early stages of composting does not promote ammonia oxidation nor reduce ammonia emissions because of limiting biologic factors during the active stage of composting.

SIGNIFICANCE AND IMPACT OF THE STUDY

The mixing of activated sludge with RHW before composting is a common practice on composting plants. This study proved the limitation of this practice to reduce ammonia emissions during composting via bioaugmentation of ammonia-oxidizing organisms. It correlated successfully the ammonia oxidation rate with different groups of ammonia oxidizers and explains the fail of promoting ammonia oxidation during the early stages of composting. It suggests Nit. europaea/eutropha and Nit. nitrosa-like AOB were the main contributors to ammonia oxidation during composting.

Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules

The identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real-time gas-monitoring analysis, (15)N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20-30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations.

Tracking organic matter and microbiota dynamics during the stages of lignocellulosic waste composting

The dynamics of biologically meaningful soluble and polymeric carbon fractions and the combined relationships between physical, chemical and biological parameters during composting of lignocellulosic waste were evaluated. The first thermophilic stage is crucial in determining the further evolution of soluble and polymeric carbon fractions but the dynamics of carbon is still important at the maturation stage. Multivariate data analysis showed that not only are all parameters interrelated but also influence one another's variability. To discern completion of bio-oxidative stage other parameters in addition to temperature should be measured. Evaluation of soluble organic carbon, microbial biomass carbon, pH and inorganic nitrogen can be of great use in detecting the composting stage. This study offers new insights into the mechanisms involved in the biodegradation of organic matter and help to prioritize the parameters that contribute at critical stages of the process.

Nitrous oxide emission mechanisms during intermittently aerated composting of cattle manure

To investigate the mechanisms of nitrous oxide (N₂O) emission during intermittent aeration in the composting process, a laboratory scale experiment with continuous measurement of N₂O emission was conducted with cattle manure. A low oxygen mode (2.5% oxygen in the inlet for 1 day), anaerobic mode (0.13% oxygen for 0.25 day), and aerated mode (20.5% oxygen for 2 days) were sequentially set up three times after 22 days of continuous aeration to replicate intermittent aeration. The total N₂O emission was 0.26-0.35 mmol, 0.27-0.32 mmol, and 0.14-0.23 mmol during the low oxygen, anaerobic, and aerated modes, respectively. Denitrification was indicated as the main N₂O emission pathway in the anaerobic and low-oxygen modes, while nitrification was indicated as the main pathway in the aerated mode and under continuous aeration. Results from this study suggest that nitrification is an important pathway for N₂O emission as well as denitrification.

Insight into the effects of biochar on manure composting: evidence supporting the relationship between N2O emission and denitrifying community

Although nitrous oxide (N2O) emissions from composting contribute to the accelerated greenhouse effect, it is difficult to implement practical methods to mitigate these emissions. In this study, the effects of biochar amendment during pig manure composting were investigated to evaluate the inter-relationships between N2O emission and the abundance of denitrifying bacteria. Analytical results from two pilot composting treatments with (PWSB, pig manure + wood chips + sawdust + biochar) or without (PWS, pig manure + wood chips + sawdust) biochar (3% w/w) demonstrated that biochar amendment not only lowered NO2(-)-N concentrations but also lowered the total N2O emissions from pig manure composting, especially during the later stages. Quantification of functional genes involved in denitrification and Spearman rank correlations matrix revealed that the N2O emission rates correlated with the abundance of nosZ, nirK, and nirS genes. Biochar-amended pig manure had a higher pH and a lower moisture content. Biochar amendment altered the abundance of denitrifying bacteria significantly; less N2O-producing and more N2O-consuming bacteria were present in the PWSB, and this significantly lowered N2O emissions in the maturation phase. Together, the results demonstrate that biochar amendment could be a novel greenhouse gas mitigation strategy during pig manure composting.

Correlating denitrifying catabolic genes with N2O and N2 emissions from swine slurry composting

This work evaluated N dynamics that occurs over time within swine slurry composting piles. Real-time quantitative PCR (qPCR) analyzes were conducted to estimate concentrations of bacteria community harboring specific catabolic nitrifying-ammonium monooxygenase (amoA), and denitrifying nitrate- (narG), nitrite- (nirS and nirG), nitric oxide- (norB) and nitrous oxide reductases (nosZ) genes. NH3-N, N2O-N, N2-N emissions represented 15.4 ± 1.9%, 5.4 ± 0.9%, and 79.1 ± 2.0% of the total nitrogen losses, respectively. Among the genes tested, temporal distribution of narG, nirS, and nosZ concentration correlated significantly (p<0.05) with the estimated N2 emissions. Denitrifying catabolic gene ratio (cnorB+qnorB)/nosZ ≥ 100 was indicative of N2O emission potential from the compost pile. Considering our current empirical limitations to accurately measure N2 emissions from swine slurry composting at field scale the use of these catabolic genes could represent a promising monitoring tool to aid minimize our uncertainties on biological N mass balances in these systems.

Impact of biodegradation of organic matters on ammonia oxidation in compost

Nitrification plays an important role in nitrogen turnover in composting process. It has been believed that nitrification occurs mainly during the maturation phase due to the elevated temperature during the active phase of composting. In this work, the intense biodegradation of organic matters is demonstrated to be another negative impact on the ammonia oxidation, the first step of nitrification. We investigated the ammonia oxidation in compost following organic matters addition at intermediate temperature. Different indicators of ammonia oxidation were studied, respectively. The accumulation of nitrite and nitrate was 10(2)-10(3) lower in composts with organic matters addition. The nitrous oxide emissions were absent or 40-fold inferior in these composts. The nitrogen mass balance indicated a less amount of oxidized ammonia after the addition. The ammonia-oxidizing bacteria declined following the organic matters addition. In contrast, the ammonia-oxidizing archaea were supported by the organic matters. Possible mechanisms of this impact were also discussed.

Denitrifiers in the surface zone are primarily responsible for the nitrous oxide emission of dairy manure compost

During the dairy manure composting process, significant nitrous oxide (N2O) emissions occur just after the pile turnings. To understand the characteristics of this N2O emission, samples were taken from the compost surface and core independently, and the N2O production was monitored in laboratory incubation experiments. Equal amounts of surface and core samples were mixed to simulate the turning, and the (15)N isotope ratios within the molecules of produced N2O were analyzed by isotopomer analysis. The results showed that the surface samples emitted significant levels of N2O, and these emissions were correlated with NOx(-)-N accumulation. Moreover, the surface samples and surface-core mixed samples incubated at 30°C produced N2O with a low site preference (SP) value (-0.9 to 7.0‰) that was close to bacteria denitrification (0‰), indicating that denitrifiers in the surface samples are responsible for this N2O production. On the other hand, N2O produced by NO2(-)-amended core samples and surface samples incubated at 60°C showed unrecognized isotopic signatures (SP=11.4-20.3‰). From these results, it was revealed that the N2O production occurring just after the turnings was mainly derived from bacterial denitrification (including nitrifier denitrification) of NOx(-)-N under mesophilic conditions, and surface denitrifying bacteria appeared to be the main contributor to this process.

Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea were widely distributed in animal manure composts from field-scale facilities

The distribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in cattle, swine, and chicken manure compost was analyzed. PCR-denaturing gradient gel electrophoresis (DGGE) showed that a Candidatus Nitrososphaera gargensis-like sequence dominated in cattle manure compost, while few AOA were detected in other composts. In the case of AOB, Nitrosomonas-like sequences were detected with higher diversity in cattle and swine manure composts. The relative abundance of ammonia oxidizers by real-time PCR revealed that more AOB was present in compost except in one swine manure compost. Our results indicated that AOB rather than AOA are widely distributed in animal manure compost.

Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems.

Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations

A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46°C and 10 mM NH (4) (+) -N. Incubation with allylthiourea indicated that the AOB and AOA grew by oxidizing ammonia. Denaturing gradient gel electrophoresis and subsequent sequencing analyses revealed that a bacterium related to Nitrosomonas halophila and an archaeon related to Candidatus Nitrososphaera gargensis were the predominant AOB and AOA, respectively, in the seed compost and in cultures after incubation. This is the first report to demonstrate that the predominant AOA in cattle manure compost can grow and can probably oxidize ammonia under moderately thermophilic conditions.

Nitrification and microbiological evolution during aerobic treatment of municipal solid wastes

Nitrification is a key step in the nitrogen cycle in various ecosystems. In this study, the nitrogen dynamic and the evolution of groups of microorganisms were studied during aerobic treatment of fine organic fraction of municipal solid wastes. Mineralization of organic nitrogen exhibited two phases and resulted in two ammonia emissions peaks. The nitrogen balance indicated the onset of nitrification only during the maturation stage, which was confirmed by the accumulations of both nitrite and nitrate and the nitrous oxide emissions in this period. A significant development of ammonia-oxidizing bacteria correlated to the onset of nitrification. On the contrary, ammonia-oxidizing archaea were less abundant and declined through treatment. Identification of these ammonia oxidizers indicates that the Nitrosomonas europaea/eutropha-like ammonia oxidizing bacteria were responsible for ammonia oxidation instead of other groups of ammonia oxidizers during aerobic treatment of fine organic fraction of municipal solid wastes.

Microbiology of nitrogen cycle in animal manure compost

Composting is the major technology in the treatment of animal manure and is a source of nitrous oxide, a greenhouse gas. Although the microbiological processes of both nitrification and denitrification are involved in composting, the key players in these pathways have not been well identified. Recent molecular microbiological methodologies have revealed the presence of dominant Bacillus species in the degradation of organic material or betaproteobacterial ammonia-oxidizing bacteria on nitrification on the surface, and have also revealed the mechanism of nitrous oxide emission in this complicated process to some extent. Some bacteria, archaea or fungi still would be considered potential key players, and the contribution of some pathways, such as nitrifier denitrification or heterotrophic nitrification, might be involved in composting. This review article discusses these potential microbial players in nitrification-denitrification within the composting pile and highlights the relevant unknowns through recent activities that focus on the nitrogen cycle within the animal manure composting process.

Nitrogen cycling in rice paddy environments: past achievements and future challenges

Nitrogen is generally the most limiting nutrient for rice production. In rice paddy soils, various biochemical processes can occur regarding N cycling, including nitrification, denitrification, and nitrogen fixation. Since its discovery in the 1930s, the nitrification-denitrification process has been extensively studied in Japan. It may cause N loss from rice paddy soils, while it can also reduce environmental pollutions such as nitrate leaching and emission of nitrous oxide (N(2)O). In this review article, we first summarize the early and important findings regarding nitrification-denitrification in rice paddy soils, and then update recent findings regarding key players in denitrification and N(2)O reduction. In addition, we also discuss the potential occurrence of other newly found reactions in the N cycle, such as archaeal ammonia oxidization, fungal denitrification, anaerobic methane oxidation coupled with denitrification, and anaerobic ammonium oxidation.

Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting

The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R²=0.554; P<0.001), indicating that archaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R²=0.503; P=0.03) especially during the mesophilic and maturation stages.

Effects of physico-chemical parameters on the bacterial and fungal communities during agricultural waste composting

The goal of this study was to identify and prioritize some of the physico-chemical parameters that contributed to bacterial and fungal community compositions during agricultural waste composting. Relationships between those parameters and microbial community compositions determined by PCR-DGGE were simultaneously evaluated by redundancy analysis (RDA). The results showed that the temporal variation of bacterial community composition was significantly related to water soluble carbon (WSC), ammonium and nitrate (P<0.05), while the most variation in distribution of fungal community composition was statistically explained by pile temperature, WSC, and moisture content (P<0.05). Significant amounts of the variation (54.9% and 56.0% for bacterial and fungal species data, respectively) were explained by those parameters, suggesting that those parameters were the most likely ones to influence, or be influenced by the bacterial and fungal species. Variation partitioning analyses indicated that WSC and pile temperature showed predominant effect on the bacterial and fungal community composition, respectively.

Pile mixing increases greenhouse gas emissions during composting of dairy manure

The effect of pile mixing on greenhouse gas (GHG) emissions during dairy manure composting was determined using large flux chambers designed to completely cover replicate pilot-scale compost piles. GHG emissions from compost piles that were mixed four times during the 80 day trial were approximately 20% higher than emissions from unmixed (static) piles. For both treatments, carbon dioxide (CO(2)), methane (CH(4)), and nitrous oxide (N(2)O) accounted for 75-80%, 18-21%, and 2-4% of GHG emissions, respectively. Seventy percent of CO(2) emissions and 95% of CH(4) emissions from all piles occurred within first 23 days. By contrast, 80-95% of N(2)O emissions occurred after this period. Mixed and static piles released 2 and 1.6 kg GHG (CO(2)-Eq.) for each kg of degraded volatile solids (VS), respectively. Our results suggest that to minimize GHG emissions, farmers should store manure in undisturbed piles or delay the first mixing of compost piles for approximately 4 weeks.

Effects of struvite formation and nitratation promotion on nitrogenous emissions such as NH3, N2O and NO during swine manure composting

To reduce nitrogenous emissions from composting, two different countermeasures were applied simultaneously in swine manure composting. One was forming struvite by adding Mg and P at the start of composting, and the other was to promote nitratation (nitrite being oxidized nitrate) by adding nitrite-oxidizing bacteria after the thermophilic phase of composting. In the laboratory- and mid-scale composting experiments, 25-43% of NH3, 52-80% of N2O and 96-99% of NO emissions were reduced. From the nitrogen balance, it was revealed that the struvite formation reduced not only NH3, but also other nitrogenous emissions except N2O. The amount of total nitrogen losses was reduced by 60% by the two combined countermeasures, against 51% by the struvite formation alone. However, the nitratation promotion dissolved struvite crystals due to the pH decline, diminishing the effect of struvite as a slow-release fertilizer.

Diversity and abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during cattle manure composting

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play important roles in nitrification in various environments. They may also be key communities for ammonia oxidation in composting systems, although few studies have discussed their presence. We investigated the relative diversity and abundance of AOB and AOA using cloning procedures, denaturing gradient gel electrophoresis analysis, and real-time PCR during several stages in the process of cattle manure composting. Our results revealed that the AOB community structure changed during the process. At the high-temperature stage (>60°C), a member of the Nitrosomonas europaea/eutropha cluster dominated while the uncultured Nitrosomonas spp. cluster appeared after the temperature decreased. Additionally, our analysis indicated that AOA sequences, which were classified into a soil/sediment cluster, were present after the temperature decreased during the composting process. At these stages, the number of the archaeal amoA gene copies (3.2 or 3.9 × 10(7) copies per gram freeze-dried compost) was significantly higher than that of bacterial amoA gene copies (2.2-7.2 × 10(6) copies per gram freeze-dried compost). Our results suggest that both AOB and AOA are actively involved in nitrification of composting systems.