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

Thermophilic microorganisms involved in the nitrogen cycle in thermal environments: Advances and prospects

Thermophilic microorganisms mediated significant element cycles and material conversion in the early Earth as well as mediating current thermal environments. Over the past few years, versatile microbial communities that drive the nitrogen cycle have been identified in thermal environments. Understanding the microbial-mediated nitrogen cycling processes in these thermal environments has important implications for the cultivation and application of thermal environment microorganisms as well as for exploring the global nitrogen cycle. This work provides a comprehensive review of different thermophilic nitrogen-cycling microorganisms and processes, which are described in detail according to several categories, including nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and dissimilatory nitrate reduction to ammonium. In particular, we assess the environmental significance and potential applications of thermophilic nitrogen-cycling microorganisms, and highlight knowledge gaps and future research opportunities.

Effect of inoculation with newly isolated thermotolerant ammonia-oxidizing bacteria on nitrogen conversion and microbial community during cattle manure composting

Nitrogen loss during composting is closely related to NH₄⁺-N conversion, and ammonia-oxidizing bacteria (AOB) are important microorganisms that promote NH₄⁺-N conversion. Since the biological activity of conventional AOB agents used for compost inoculation declines rapidly during the thermophilic phase of composting, new compound inoculants should be developed that are active during that phase. In the current study, the effects of inoculating cattle manure compost with newly isolated AOB (5%, v/w) [thermotolerant AOB X-2 strain (T-AOB-2), mesophilic AOB X-4 strain (M-AOB-4), and AOB X-2 combined with AOB X-4 (MT-AOB-2-4)] on the conversion of nitrogen, compost maturity, and the resident microbial community were studied. During 35 days of composting, compared with the control, AOB inoculation reduced NH₃ emissions by 29.98-46.94%, accelerated the conversion of NH₄⁺-N to NO₂^--N, increased seed germination values by 13.00-25.90%, and increased the abundance of the microbial community at the thermophilic phase (16.38-68.81%). Network analysis revealed that Bacillaceae play a crucial role in the composting process, with the correlation coefficients: 0.83 (p < 0.05) with NH₃, 0.64 (p < 0.05) with NH₄⁺-N, and 0.81 (p < 0.05) with NO₂^--N. In addition, inoculation with MT-AOB-2-4 notably increased the total nitrogen content of compost, prolonged the sanitation stage, and promoted compost maturity. Hence, MT-AOB-2-4 may be used to increase the microbial community abundance and improve the efficiency of cattle manure composting.

Metagenomic Analysis of Bacterial Community Structure and Dynamics of a Digestate and a More Stabilized Digestate-Derived Compost from Agricultural Waste

Recycling of different products and waste materials plays a crucial role in circular economy, where the anaerobic digestion (AD) constitutes an important pillar since it reuses nutrients in the form of organic fertilizers. Knowledge about the digestate and compost microbial community structure and its variations over time is important. The aim of the current study was to investigate the microbiome of a slurry cow digestate produced on a farm (ADG) and of a more stabilized digestate-derived compost (DdC) in order to ascertain their potential uses as organic amendments in agriculture. The results from this study, based on a partial fragment of 16S bacterial rRNA NGS sequencing, showed that there is a greater microbial diversity in the DdC originated from agricultural waste compared to the ADG. Overall, the existence of a higher microbial diversity in the DdC was confirmed by an elevated number (1115) of OTUs identified, compared with the ADG (494 OTUs identified). In the DdC, 74 bacterial orders and 125 families were identified, whereas 27 bacterial orders and 54 families were identified in the ADG. Shannon diversity and Chao1 richness indexes were higher in DdC samples compared to ADG ones (Shannon: 3.014 and 1.573, Chao1: 68 and 24.75; p < 0.001 in both cases). A possible association between the microbiome composition at different stages of composting process and the role that these microorganisms may have on the quality of the compost-like substrate and its future uses is also discussed.

Changes in soil ammonia oxidizers and potential nitrification after clear-cutting of boreal forests in China

The Korean pine and broad-leaved mixed forests are the most typical and complete ecosystem among the global boreal forests, with extremely important ecological functions. However, few studies on the changes of soil ammonia oxidizers and potential nitrification after clear-cutting of forests are reported. In this study, in contrast to primary Korean pine forests, nitrate (NO₃^-) was significantly higher in secondary broad-leaved forests, while ammonium (NH₄⁺) was on the contrary. The abundance of ammonia-oxidizing bacteria (AOB) was greatly higher in secondary broad-leaved forests, while levels of ammonia-oxidizing archaea (AOA) were not significantly different between them. The significant differences of community structure of AOA and AOB were observed in different forest types and soil layers. Compared with AOA, community compositions of AOB was more sensitive to forest type. The dominant groups of AOA were Nitrososphaera and Nitrosotalea, and the dominant group of AOB was Nitrosospira, of which Nitrosospira cluster 2 and 4 were functional groups with highly activity. Soil potential nitrification rate (PNR) was higher in secondary broad-leaved forests. Furthermore, PNR and AOB abundance had a significant positive correlation, but no significant correlation with AOA abundance. These results provide insights into the soil nitrogen balance and effects on forest restoration after clear-cutting.

Insight to nitrification during cattle manure-maize straw and biochar composting in terms of multi-variable interaction

This study investigated nitrification process during cattle manure-maize straw (CM) and biochar (CMB) composting in terms of multi-variable interaction (MVI) among environmental parameters, ammonia-oxidizing archaea (AOA) and bacteria (AOB) community structure, nitrogen-related enzymes as well as substrates using structural equation model (SEM). Results showed that adding biochar significantly reduced potential ammonia oxidation rates. SEM analysis revealed that AOB was affected by temperature and pH, which stimulated the release of urease, increased NH₄⁺-N concentration and finally exerted influence on nitrification in CM. Temperature (0.755) and NO₂^--N (-0.994) were identified as the main factors mediating nitrification in CM and CMB, respectively. Moreover, MVI analysis indicated that nitrification and denitrification occurred simultaneously. Mutual verification of SEM and quantitative analyses (RNA level) confirmed that AOB predominated nitrification. The above results indicated that nitrification could be better explained by MVI using SEM during composting.

Monthly distribution of ammonia-oxidizing microbes in a tropical bay

Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing methods to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17-20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17-20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.

Responses of AOA and AOB activity and DNA/cDNA community structure to allylthiourea exposure in the water level fluctuation zone soil

Ammonia oxidation is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Allylthiourea (ATU) has been found to specifically inhibit ammonia oxidation. However, the effect of ATU on AOA and AOB transcription has been infrequently studied. In the present study, we examined the responses of AOA and AOB activity and DNA/cDNA community structure to ATU exposure. The ammonia oxidation activity in the 100-mg/L ATU group was 4.3% of that in the control group after 7 days. When exposed to ATU, the gene abundance of AOA was favored compared with that of AOB, and there were no statistically significant differences in the abundance of AOB amoA in DNA and cDNA between the two groups. Compared with the control group, the gene abundance of AOA significantly increased by 5.23 times, while the transcription of AOA significantly decreased by 0.70 times. Moreover, the transcriptional ratio of AOA in the ATU group was only 0.05 times as high as that in the control group. ATU selectively affected AOB and completely inhibited Nitrosomonas europaea and Bacterium amoA.22.HaldeII.kultur at the genetic level. Under ATU exposure, all AOA clusters were transcribed, but three AOB clusters were not transcribed. Our results indicated that the ammonia oxidation potential of the soil of water level fluctuation areas, based on ATU inhibition, was associated mainly with AOA amoA gene abundance and AOB community shifts in DNA and cDNA.

Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia-oxidizing archaea communities in a Chinese Mollisols field

In this study, we investigated the physicochemical properties of soil, and the diversity and structure of the soil ammonia-oxidizing archaea (AOA) community, when subjected to fertilizer treatments for over 35 years. We collected soil samples from a black soil fertilization trial in northeast China. Four treatments were tested: no fertilization (CK); manure (M); nitrogen (N), phosphorus (P), and potassium (K) chemical fertilizer (NPK); and N, P, and K plus M (MNPK). We employed 454 high-throughput pyrosequencing to measure the response of the soil AOA community to the long-term fertilization. The fertilization treatments had different impacts on the shifts in the soil properties and AOA community. The utilization of manure alleviated soil acidification and enhanced the soybean yield. The soil AOA abundance was increased greatly by inorganic and organic fertilizers. In addition, the community Chao1 and ACE were highest in the MNPK treatment. In terms of the AOA community composition, Thaumarchaeota and Crenarchaeota were the main AOA phyla in all samples. Compared with CK and M, the abundances of Thaumarchaeota were remarkably lower in the MNPK and NPK treatments. There were distinct shifts in the compositions of the AOA operational taxonomic units (OTUs) under different fertilization management practices. OTU51 was the dominant OTU in all treatments, except for NPK. OTU79 and OTU11 were relatively abundant OTUs in NPK. Only Nitrososphaera AOA were tracked from the black soil. Redundancy analysis indicated that the soil pH and soil available P were the two main factors that affected the AOA community structure. The abundances of AOA were positively correlated with the total N and available P concentrations, and negatively correlated with the soil pH.

Correlation between ammonia-oxidizing microorganisms and environmental factors during cattle manure composting

Cattle manure composting was performed in an aerated vessel. Community structure and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) techniques targeting the ammonia monooxygenase alpha subunit (amoA) gene and the correlation between AOB and AOA communities and environmental factors was explored. Thirteen (13) AOB sequences were obtained, which were closely related to Nitrosomonas spp., Nitrosomonas eutropha, and Nitrosospira spp. and uncultured bacteria, among which Nitrosomonas spp. were predominant. Excessively high temperature and high ammonium concentration were not favorable for AOB growth. Five AOA sequences, belonging to CandidatusNitrososphaera gargensis and to an uncultured archaeon, were obtained. During composting, community diversity of AOB and AOA fluctuated, with AOA showing a higher Shannon-Wiener index. The AOB community changed more dramatically in the mesophilic stage and the early thermophilic stage, whereas the most obvious AOA community succession occurred in the late thermophilic stage, the cooling stage and the maturity stage. Water content, total nitrogen (TN) and ammonium concentration were more relevant to the AOB community structure, while higher correlations were observed between ammonia, nitrate and TN and the AOA community. AOB community diversity was negatively correlated with pH (r = -0.938, p < 0.01) and water content (r = -0.765, p < 0.05), while positively correlated with TN (r = 0.894, p < 0.01). AOA community diversity was negatively correlated with ammonium concentration (r = -0.901, p < 0.01). Ammonium concentration played an important role in the succession of AOB and AOA communities during composting.

Key environmental factors to variation of ammonia-oxidizing archaea community and potential ammonia oxidation rate during agricultural waste composting

In this research, the abundance and structure of AOA amoA gene during agricultural waste composting were determined by quantitative PCR and sequencing techniques, respectively. Pairwise correlations between potential ammonia oxidation (PAO) rate, physicochemical parameters and the AOA abundance were evaluated using Pearson correlation coefficient. Relationships between these parameters, PAO rates and AOA community structure were evaluated by redundancy analysis. Results showed that 22 AOA gene OTUs were divided into the soil/sediment lineage by phylogenetic analyses. Significant positive correlations were obtained between AOA amoA gene abundance and moisture, ammonium, water soluble carbon (WSC) and organic matter (OM), respectively. Redundancy analysis showed OM, pH and nitrate significantly explained the AOA amoA gene structure. Pearson correlation revealed the PAO rate correlated positively to ammonium, AOA amoA gene abundance. These results indicated that AOA communities sense the fluctuations in surrounding environment, and ultimately react and influence the nitrogen transformation during agricultural waste composting.

A microbial community snapshot of windrows from a commercial composting facility

The effect of depth on compost microbial communities is unclear but could be relevant to the management of windrows at commercial facilities. DNA extracted from 64 compost samples from seven windrows at a commercial facility were analyzed via deep 16S rRNA gene sequencing. The relative abundance of eight to nine genera was affected by depth during the transition from cooling to maturation phases between 4 and 6 months, whereas very few genera (0-1) showed a depth dependence in young, actively managed windrows or in mature windrows older than 10 months. Seven novel bacterial operational taxonomic units (OTUs) were detected in compost DNA and also in publicly available compost metagenomes. A compost metagenome was used to construct a metagenome-assembled genome for most of the abundant uncharacterized OTU in our samples and suggests its involvement in carbon cycling.

Distribution and genetic diversity of microbial populations in the pilot-scale biofilter for simultaneous removal of ammonia, iron and manganese from real groundwater

A pilot-scale biofilter treating real groundwater was developed in this study, which showed that ammonia, iron and manganese were mainly removed at 0.4, 0.4 and 0.8 m of the filter bed, respectively, and the corresponding removal efficiencies were 90.82%, 95.48% and 95.90% in steady phase, respectively. The variation of microbial populations in the biofilter during start-up process was also investigated using high-throughput pyrosequencing (HTP). Results indicated that the main functional microbes for ammonia, iron and manganese removal were Nitrosomonas, Crenothrix and Crenothrix, respectively, which was mainly distributed at 0.8, 0, and 0.8 m of the filter bed with a corresponding abundance of 8.7%, 28.12% and 11.33% in steady phase, respectively. Kinds of other bacteria which may be related to methane, hydrogen sulfide and organic matter removal, were also found. In addition, small part of archaea was also detected, such as Candidatus Nitrososphaera, which plays a role in nitritation.

Nitrifying Kinetics and the Persistence of Nitrite in the Seine River, France

Although a higher oxidation rate for nitrite than for ammonia generally prevents nitrite accumulation in oxic waters, nitrite concentrations in the Seine River (1-31 μM) exceed European norms. We investigated the kinetics of in situ ammonia- and nitrite-oxidizing communities in river water and wastewater treatment plant (WWTP) effluents to determine the role of pelagic nitrification in the origin and persistence of nitrite downstream of Paris. The main source of nitrite is the major Parisian WWTP, and its persistence, up to tens of kilometers downstream of the plant, is explained by low ammonia and nitrite oxidation rates and high river flow. Furthermore, similar nitrite and ammonia oxidation rates preclude a rapid consumption of both preexisting nitrite and nitrite produced by ammonia oxidation. Maximum ammonia oxidation rates are two to three times higher downstream than upstream of the WWTP, indicating the input of ammonia oxidizers and ammonia from the WWTP. In both river water and WWTP effluents, nitrite oxidizers were unable to oxidize all available nitrite. In the human-impacted Seine River, this phenomenon might be due to mixotrophy. This study highlights the low resilience of the river to nitrite contamination as well as the importance of managing nitrite, nitrifiers, and organic matter concentrations in WWTP effluents to avoid nitrite persistence in rivers.

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to 'Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of (13)C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198±10 and 894±81 mg N g(-1) VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology.

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).

Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost

Biofiltration technology based on microbial degradation and assimilation is used for the removal of malodorous compounds, such as ammonia. Microbes that degrade malodorous and/or organic substances are involved in composting and are retained after composting; therefore, mature composts can serve as an ideal candidate for a biofilter medium. In this study, we focused on different types of raw compost materials, as these are important factors determining the bacterial community profile and the chemical component of the compost. Therefore, bacterial community profiles, the abundance of the bacterial ammonia monooxygenase gene (amoA), and the quantities of chemical components were analyzed in composts produced from either food waste or cattle manure. The community profiles with the lowest beta diversity were obtained from single type of cattle manure compost. However, cattle manure composts showed greater alpha diversity, contained higher amounts of various rRNA gene fragments than those of food waste composts and contained the amoA gene by relative quantification, and Proteobacteria were abundantly found and nitrifying bacteria were detected in it. Nitrifying bacteria are responsible for ammonia oxidation and mainly belong to the Proteobacteria or Nitrospira phyla. The quantities of chemical components, such as salt, phosphorus, and nitrogen, differed between the cattle manure and food waste composts, indicating that the raw materials provided different fermentation environments that were crucial for the formation of different community profiles. The results also suggest that cattle manure might be a more suitable raw material for the production of composts to be used in the biofiltration of ammonia.

Effects of submerged macrophytes on the abundance and community composition of ammonia-oxidizing prokaryotes in a eutrophic lake

Abundances and community compositions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in unvegetated sediment and the rhizosphere sediments of three submerged macrophytes (Ceratophyllum demersum, Vallisneria spinulosa, and Potamogeton crispus) were investigated in a large, eutrophic freshwater lake, Lake Taihu. Abundances of archaeal ammonia monooxygenase alpha-subunit (amoA) gene (from 6.56 × 10(6) copies to 1.06 × 10(7) copies per gram of dry sediment) were higher than those of bacterial amoA (from 6.13 × 10(5) to 3.21 × 10(6) copies per gram of dry sediment) in all samples. Submerged macrophytes exhibited no significant effect on the abundance and diversity of archaeal amoA gene. C. demersum and V. spinulosa increased the abundance and diversity of bacterial amoA gene in their rhizosphere sediment. However, the diversity of bacterial amoA gene in the rhizosphere sediments of P. crispus was decreased. The data obtained in this study would be helpful to elucidate the roles of submerged macrophytes involved in the nitrogen cycling of eutrophic lake ecosystems.

Enhancing methane production during the anaerobic digestion of crude glycerol using Japanese cedar charcoal

The use of Japanese cedar charcoal as a support material for microbial attachment could enhance methane production during anaerobic digestion of crude glycerol and wastewater sludge. Methane yield from a charcoal-containing reactor was approximately 1.6 times higher than that from a reactor without charcoal, and methane production was stable over 50 days when the loading rate was 2.17 g chemical oxygen demand (COD) L(-1) d(-1). Examination of microbial communities on the charcoal revealed the presence of Uncultured Desulfovibrio sp. clone V29 and Pelobacter seleniigenes, known as 1,3-propandiol degraders. Hydrogenotrophic methanogens were also detected in the archaeal community on the charcoal. Methanosaeta, Methanoregula, and Methanocellus were present in the charcoal-containing reactor. The concentration of propionate in the charcoal-containing reactor was also lower than that in the control reactor. These results suggest that propionate degradation was enhanced by the consumption of hydrogen by hydrogenotrophic methanogens on the charcoal.

Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada

The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3- or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities.

Gaseous nitrogen and bacterial responses to raw and digested dairy manure applications in incubated soil

A study was conducted under laboratory conditions to compare rates of nitrous oxide (N(2)O) and ammonia (NH(3)) emissions when soil was amended with anaerobically digested dairy manure slurry containing <30% food byproducts, raw dairy manure slurry, or urea. Slurries were applied via surface and subsurface methods. A second objective was to correlate genes regulating nitrification and denitrification with rates of N(2)O production, slurry treatment, and application method. Ammonia volatilization from incubated soil ranged from 140 g kg(-1) of total N applied in digested slurry to 230 g kg(-1) in urea. Subsurface application of raw dairy manure slurry decreased ammonia volatilization compared with surface application. Anaerobic digestion increased N(2)O production. Cumulative N(2)O loss averaged 27 g kg(-1) of total N applied for digested slurry, compared with 5 g kg(-1) for raw dairy slurry. Genes of interest included a 16S rRNA gene selective for β-subgroup proteobacterial ammonia-oxidizers, amoA, narG, and nosZ quantified with quantitative polymerase chain reaction (qPCR) and real-time polymerase chain reaction (RT-PCR). Application of anaerobically digested slurry increased nitrifier and denitrifier gene copies that correlated with N(2)O production. Expression of all genes measured via mRNA levels was affected by N applications to soil. This study provides new information linking genetic markers in denitrifier and nitrifier populations to N(2)O production.

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.

Drivers of archaeal ammonia-oxidizing communities in soil

Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.