Potential Ammonia Oxidation Rates Research Articles

Effects of copper contamination on N cycling microbial guilds and plant performance in two contrasting grassland soils

Heavy metal pollution has important effects on ecosystem nitrogen (N) cycling, but factors driving differences between the direction, onset and intensity of responses are poorly understood. We used two contrasting grassland soils to examine the effects of copper (Cu) on the abundance and activity of N cycling microbial guilds and plant responses, including plant δ15N as an integrator of the N cycle. A low pH sandy soil and a high pH sandy loam soil were aged two years in outdoor mesocosms with copper (Cu) treatments of background, 200, 400 or 1000 mg kg−1 Cu. After two years, increased Cu treatments resulted in significantly lower abundances of ammonia oxidizing archaea, Nitrospira nitrite oxidizing bacteria (NOB), potential ammonia oxidation rates and plant biomass in both soils. Plants possessed significantly increased N content and enriched shoot δ15N in with higher Cu in both soils. While abundances of ammonia oxidizing bacteria were unaffected by Cu, the response among Nitrobacter NOB and denitrifiers and plant δ13C differed between the two soils. In contrast to plants, differences in the intensity and direction of microbial guild responses were not explained by increasing soluble Cu but rather shaped by soil type. This indicates that the two soils differed in metal bioavailability to plants, as well as harbored microbial communities with inherent differences in metal sensitivity. Furthermore, effects of increasing Cu on microbial N-cycling guilds became more apparent with longer incubation time, emphasizing the importance of long-term studies to assess important ecosystem effects of Cu contamination. Taken together, we conclude that a combination of plant and microbial responses can give better insights on how Cu is affecting the N cycle in polluted soils.

Shifts of ammonia-oxidation process along salinity gradient in an estuarine wetland

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play an important role in nitrogen (N) cycling of the estuarine sediments. However, the shifts of potential ammonia oxidation rates (PARs) of AOA and AOB along different salinity gradients are not well understood. Here, salinity-treated (0, 5, 15, 25 and 35 ‰) incubation experiments of sediment from the Pearl River Estuary were performed to explore the influence of salinity on ammonia oxidation process, including the PARs and gene abundances of AOA and AOB. Significant shifts of PARs and amoA gene abundances of ammonia oxidation process along salinity gradient were observed during the incubation (0–60 d). After a long-term incubation, both PARtotal (4.61 ± 0.93 μg N g−1 d−1) and PARaob (3.05 ± 1.04 μg N g−1 d−1) reached their maximum values at 25 ‰ salinity, and PARaoa (1.96 ± 0.10 μg N g−1 d−1) reached its maximum values at 35 ‰ salinity, which showed that PARs had higher values under high salinity conditions. AOB amoA gene was more abundant than AOA under moderate and high salinity, and only a significant linear correlation was observed between PARaob and AOB abundances. In addition, the ammonia oxidation activities showed a wide range of salinity tolerance, which is worthy of further study on community structure and transcript richness. Our study illustrates that salinity plays a key role in regulating the ammonia oxidation process in estuarine sediments, and has guiding significance for N fixation and N loss associated with saltwater incursion.

Comammox biogeography subject to anthropogenic interferences along a high-altitude river

The recent discovery of comammox Nitrospira performing complete ammonia oxidation to nitrate has overturned the long-held dogma of two-step nitrification on Earth, yet little is known about the effect of urbanization interference on their distribution. Using gene-centric metagenomics, we provided the first blueprints about comammox community, biogeography, and environmental drivers along a high-elevation (> 2000 m) river flowing through the largest city on the vulnerable Qinghai-Tibetan Plateau. Our study confirmed a wide presence and diversity of yet-uncultured comammox clade B across wet and dry seasons, with average 3.0 and 2.0 times as abundant as clade-A amoA genes in water and sediments, respectively. Species identified from freshwater and drinking water treatment plants dominated the comammox guilds (58∼100%), suggesting this plateau river shared a similar comammox assemblage with the above habitat types. Compared with the urban area harboring more abundant canonical Nitrospira identified in wastewater (average 24%), the upstream suburban reach had a smaller human population but larger proportions of comammox in ammonia-oxidizing prokaryotes (24∼72% of abundances) and Nitrospira sublineages I/II. Higher contents of nitrate and nitrite in water, and antibiotics in water and sediments, may restrain comammox niches in nitrifiers over the urban area. Further random forest analysis revealed that lincosamides and quinolones were the most important antibiotic predictors for the niche differentiations between comammox and canonical nitrifiers in water, while macrolides for those in sediments. Finally, by incubation experiments, we demonstrated higher activity contributions of benthic comammox in the suburban area (36.2∼92.8% of potential ammonia-oxidation rates) than in the urban reach, and that the contribution variation had significant negative relations with macrolides and their major components. Overall, this study highlighted that anthropogenic activities hampered the advantage of riverine complete nitrifiers over the canonical two-step ones.

Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels

Deep oligotrophic lakes sustain large populations of the class Nitrososphaeria (Thaumarchaeota) in their hypolimnion. They are thought to be the key ammonia oxidizers in this habitat, but their impact on N-cycling in lakes has rarely been quantified. We followed this archaeal population in one of Europe’s largest lakes, Lake Constance, for two consecutive years using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8–39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species present in major inland water bodies, for which we propose the name “Candidatus Nitrosopumilus limneticus”. Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations incorporated significantly more ammonium than most other microorganisms in the hypolimnion and were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l‒1 d‒1, corresponding to potential cell-specific rates of 0.21 ± 0.11 fmol cell–1 d–1. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1.76 × 109 g N-ammonia per year or 11% of N-biomass produced annually by phytoplankton. We show that ammonia-oxidizing archaea play an equally important role in the nitrogen cycle of deep oligotrophic lakes as their counterparts in marine ecosystems.

Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil

Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.

Insight into the influence of biochar on nitrification based on multi-level and multi-aspect analyses of ammonia-oxidizing microorganisms during cattle manure composting

In this study, influence of biochar on nitrification was explored using multi-level (DNA, RNA, protein) and multi-aspect (diversity, structure, key community, co-occurrence pattern and functional modules) analyses (M−LAA) of ammonia-oxidizing microorganisms (AOMs) during cattle manure composting. Biochar addition increased the copy numbers and diversity of AOMs, restricted (36.02%) the amoA gene transcripts of archaea but increased (24.53%) those of bacteria, and reduced (75.86%) ammonooxygenase (AMO) activity. Crenarchaeota and Thaumarcheota mediated NH4+-N, Unclassified_k_norank_d_Archaea and Crenarchaeota regulated AMO activity and potential ammonia oxidation (PAO) rates. Nitrosomonas and Nitrosospira were the predominant microbial taxa influencing NH4+-N variation and PAO rates, respectively. Additionally, both Crenarchaeota and Nitrosospira played crucial roles in mediating NO3–-N and NO2–-N. Furthermore, biochar altered the network patterns of AOMs community by changing the keystone species and the interactivity among communities. These findings indicated that influence of biochar on nitrification could be better explained using M−LAA of AOMs.

Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river–estuary–adjacent sea continuum

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river–estuary–sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g−1 d−1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 106 and 2.4 ± 3.54 × 106 copies g−1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4+) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4+ consumption pathways, total aerobic oxidation accounted for 12–26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.

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.

Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia.

Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols.

Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica

Abstract. The colonization by a large number of sea animals, including penguins and seals, plays an important role in the nitrogen cycle of the tundra ecosystem in coastal Antarctica. However, little is known about the effects of sea animal colonization on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities involved in nitrogen transformations. In this study, we chose active seal colony tundra soils (SSs), penguin colony soils (PSs), adjacent penguin-lacking tundra soils (PLs), tundra marsh soils (MSs), and background tundra soils (BSs) to investigate the effects of sea animal colonization on the abundance, activity, and diversity of AOA and AOB in maritime Antarctica. Results indicated that AOB dominated over AOA in PS, SS, and PL, whereas AOB and AOA abundances were similar in MS and BS. Penguin or seal activities increased the abundance of soil AOB amoA genes but reduced the abundance of AOA amoA genes, leading to very large ratios (1.5×102 to 3.2×104) of AOB to AOA amoA copy numbers. Potential ammonia oxidation rates (PAORs) were significantly higher (P=0.02) in SS and PS than in PL, MS, and BS and were significantly positively correlated (P&lt;0.001) with AOB amoA gene abundance. The predominance of AOB over AOA and their correlation with PAOR suggested that AOB play a more important role in the nitrification in animal colony soils. Sequence analysis for gene clones showed that AOA and AOB in tundra soils were from the Nitrososphaera and Nitrosospira lineages, respectively. Penguin or seal activities led to a predominance of AOA phylotypes related to Nitrososphaera cluster I and AOB phylotypes related to Nitrosospira clusters I and II but very low relative abundances in AOA phylotypes related to cluster II, and AOB phylotypes related to clusters III and IV. The differences in AOB and AOA community structures were closely related to soil biogeochemical processes under the disturbance of penguin or seal activities: soil C : N alteration and sufficient input of NH4+–N and phosphorus from animal excrements. The results significantly enhanced the understanding of ammonia-oxidizing microbial communities in the tundra environment of maritime Antarctica.

Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media

Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.

Effects of Silver Nanoparticles and Silver Ions on Soil Nitrification Microorganisms and Ammoxidation

In order to study the effect of nanosilver on soil nitrification microorganisms and nitrogen transformation, soil culture experiments were carried out. Yellow brown soil and paddy soil were first spiked with different doses of nanosilver (10, 50, 100 mg·kg-1) and silver ions (1, 5, 10 mg·kg-1). Then, the number of nitrifying bacteria, activity of soil invertase, amoA gene abundance, NH4+-N content, NO3--N content, and soil potential ammonia oxidation rate were determined. The results showed that the number of nitrite bacteria and nitrate bacteria decreased significantly when the soils were treated with nanosilver and silver ions. Soil invertases were inhibited, and the effect on urease was greater than that on catalase. The amoA gene abundances of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) decreased, and the effect on the gene abundance of AOB was greater than that of AOA. When (NH4)2SO4 was added to the soil, nanosilver and silver ion pollutants caused NH4+-N to accumulate, and the contents of NO3--N were reduced, the rate of ammonia oxidation decreased, and the transformation of ammonium nitrogen to nitrate nitrogen was inhibited. This research suggests that nanosilver and silver ions can have toxic effects on soil nitrification microorganisms and ammonium nitrogen conversion, and the degree of influence was found to be related to the soil physical and chemical properties.

Linkage of plant and abiotic properties to the abundance and activity of N-cycling microbial communities in Tibetan permafrost-affected regions

Ammonia oxidation and denitrification are crucial for nitrogen (N) availability and nitrous oxide production in N-limited permafrost soils. However, it remains unclear about the relative roles of abiotic and biotic properties in controlling the abundance and activity of ammonia-oxidizing and denitrifying microorganisms in permafrost-affected soils. We analysed the potential ammonia oxidation and denitrification rates (PAO and PDR), the abundance of archaeal amoA, bacterial amoA, nirK, nirS and nosZ genes, soil characteristics, climatic and plant properties across two vegetation types in Tibetan permafrost-affected soils. The relative importance of abiotic and biotic properties in driving functional N gene abundance, PAO and PDR were assessed using variation partition analysis (VPA) and random forest (RF) model. The functional N gene abundance and PDR were lower in alpine steppe than in alpine meadow. Variations in the PAO and PDR and functional N gene abundance were mainly explained by abiotic variables such as organic carbon and total N, then by plant properties such as plant N concentration, plant species richness and productivity based on the VPA. The RF model showed that abiotic properties (e.g., precipitation) and plant properties (e.g., plant N concentration or plant productivity) predicted the PDR and the abundance of functional N genes. Both VPA and RF model showed that the PAO and PDR could be determined by the abundance of functional N genes such as archaeal amoA gene and nosZ gene, respectively. Our study highlights that abiotic and plant properties are important predictors of the abundance and activity of ammonia-oxidizing and denitrifying communities in permafrost-affected regions, implying that plant properties, which were previously overlooked, should be incorporated into ecosystem models for improved prediction of belowground N process rates in a changing environment.

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.

Comparative characterization of digestate versus pig slurry and cow manure – Chemical composition and effects on soil microbial activity

The growing number of biogas plants in Europe has resulted in increased production of nutrient-rich digestate with great potential as fertilizer for arable land. The nutrient composition of digestate varies with the substrate treated in the biogas plant and may contain compounds that stimulate or inhibit soil microbial activity. This study compared 20 digestates (D) with 10 pig slurries (PS) and 10 cow manures (CM) regarding their chemical content and their effect on soil microbial activities, i.e. potential ammonia oxidation rate (PAO) and soil respiration. The results showed no significant differences within the D group when divided based on substrate type. i.e. manure dominated vs. other organic waste materials in any of the tests. In general D contained significantly higher concentrations of ammonium while the concentrations of total carbon and volatile fatty acids were higher in PS and CM than in D. The D showed both stimulating and inhibiting effects on PAO, while all CM and all PS except one showed inhibiting effects on PAO. However, PAO activity was negatively correlated with the content of volatile fatty acids in the residues indicating that these compounds may be the cause of the inhibition. The maximum respiration activity (hpeakmax) was lower and the time point for the maximum respiration activity (tpeakmax) occurred earlier for D compared with CM and PS. This earlier peak time could be indicative of a high proportion of easily degradable carbon in D compared with PS and CM. However, the utilization rate of carbon, i.e. the proportion of added organic C converted to CO2-C during 12days, did not differ significantly between D, PS and CM, indicating that overall carbon quality in the different fertilizers was still roughly comparable. In short, our results suggest that digestates were different compared with PS and CM but without posing a higher risk with respect to their impact on soil microbial activity.

Biochar addition affected the dynamics of ammonia oxidizers and nitrification in microcosms of a coastal alkaline soil

Biochar amendments have frequently been reported to alter microbial communities and biogeochemical processes in soils. However, the impact of biochar application on bacterial (AOB) and archaeal ammonia oxidizers (AOA) remains poorly understood. In this study, we investigated the responses of AOB and AOA to the application of biochar derived from cotton stalk at rates of 5, 10, and 20 % by weight to a coastal alkaline soil during a 12-week incubation. The results showed that the amoA gene of AOB consistently outnumbered that of AOA, whereas only the AOA amoA gene copy number was significantly correlated with the potential ammonia oxidation (PAO) rate (P < 0.01). The significant decrease of PAO rates in biochar treatments occurred after incubation for 4-6 weeks, which were distinctly longer than that in the control (2 weeks). The PAO rates were significantly different among treatments during the first 4 weeks of incubation (P < 0.05), with the highest usually in the 10 % treatment. Biochar application significantly increased the abundance of both nitrifiers in the 4 weeks of incubation (P < 0.05). Biochar amendment also decreased AOA diversity, but increased AOB diversity, which resulted in different community structures of both nitrifiers (P < 0.01), as shown by the differences between the 5 % biochar and the control treatments. We conclude that biochar application generally enhanced the abundance and altered the composition of ammonia oxidizers; the rate of biochar application also affected the rate and dynamics of nitrification, and the risk for increasing the alkalinity and N leaching of the studied soil was lower with a lower application rate.

Preliminary study on the distribution of ammonia oxidizers and their contribution to potential ammonia oxidation in the plant-bed/ditch system of a constructed wetland

Ammonia oxidation—as the rate-limiting step of nitrification—has been found to be performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, how ammonium content and oxidation–reduction status regulate the distribution of ammonia oxidizers in constructed wetlands and their contribution to potential ammonia oxidation rate are still in dispute. This study aimed to explore the effects of ammonium content and oxidation–reduction status on the abundances of AOA/AOB and examine the contributions of AOA and AOB populations to ammonia oxidation rates in the plant-bed/ditch system of a constructed wetland. Sampling was carried out in the plant-bed/ditch system of the Shijiuyang Constructed Wetland, China. Three plant-bed soil cores were collected using a soil auger and sampled at depths of 0, 20, and 50 cm in 5-cm increments. Five ditch surface sediments (0–5 cm) were collected along the water flow direction. The abundances of AOA and AOB were investigated by quantitative polymerase chain reaction based on amoA genes. The potential ammonia oxidation rate was determined using the chlorate inhibition method. The results showed that AOA outnumbered AOB in the plant-bed surface soil which had lower ammonium content (4.67–7.63 mg kg−1), but that AOB outnumbered AOA in the ditch surface sediment which had higher ammonium content (14.0–22.9 mg kg−1). Ammonium content was found to be the crucial factor influencing the relative abundances of AOA and AOB in the surface samples of the plant-bed/ditch system. In the deep layers of the plant bed, AOA abundance outnumbered AOB, though much lower oxidation–reduction potential occurred along the water flow direction. Thus, the oxidation–reduction potential may be another factor influencing the distributions of AOA and AOB in the deep layers of the plant bed without significant difference in ammonium content (p < 0.05). Moreover, the potential ammonia oxidation rate was significantly dominated by AOB rather than AOA in the plant-bed/ditch system. The high ammonium content in the ditch sediment likely favored AOB. AOA seemed to persist more readily even under low oxidation–reduction potential in the deep layers of the plant bed. Ammonium content and the oxidation–reduction potential were important parameters influencing the distribution of AOA and AOB in the plant-bed/ditch system of Shijiuyang Constructed Wetland. AOB contributed more to ammonia oxidation than AOA, both in the plant-bed soils (r = 0.592, p = 0.0096) and in the ditch sediments (r = 0.873, p = 0.0002).

English

Biomass burning, a form of disturbance in soil ecosystem, is frequently carried out in farmland after harvest in China, which has potential influence on soil biological properties. To study the short-term effects of biomass burning on soil ammonia-oxidizing bacteria (AOB) and archaea (AOA), a field investigation utilizing poplar branch (PB) and corn stalk (CS) as feedstock for experimental biomass burning was conducted in farmland in Yanqing County, Beijing, China (116&deg;12&#39;E, 40&deg;25&#39;N). The shifts in abundance and community composition of AOB and AOA were investigated utilizing real-time polymerase chain reaction (PCR), cloning and sequencing approaches based on&nbsp;amoA&nbsp;genes. Striking increase in potential ammonia oxidation rate and abundance of soil AOA and AOB after fire were observed, as well as community composition of AOA. For AOB, little changes in diversity but significant shifts in relative abundance of different Clusters were observed after fire. Phylogenetic analyses of the&nbsp;amoA&nbsp;gene fragments showed that all AOB clones from different treatments were affiliated with&nbsp;Nitrosospira&nbsp;species and grouped into 5 clusters (3a, 3b, 3c, A&nbsp;and&nbsp;B). Most of the clones were almost evenly distributed in&nbsp;Cluster 3a, 3b, A and B before burning. However, domination in the clones by Cluster 3a was observed after fire. All AOA clones fell within Soil cluster (soil origin). Although Group 1.1b was found dominant in the obtained AOA clones in all the treatments, the relative abundance of clones belonging to Group 1.1b&nbsp;decreased after fire. These findings could be fundamental to improve our understanding of the effect of biomass burning on soil AOB and AOA in agricultural ecosystems. &nbsp; Key words:&nbsp;Biomass burning, soil ammonia-oxidizing bacteria, soil ammonia-oxidizing archaea, ammonia oxidation.

Pathways and Organisms Involved in Ammonia Oxidation and Nitrous Oxide Emission

Ammonia oxidation is a central step in the global nitrogen cycle that involves several different-conditions and metabolic bioprocesses, including aerobic versus anaerobic ammonia oxidation, and autotrophic versus heterotrophic ammonia oxidation. With the development and application of metagenomics and other modern molecular approaches, some new organisms (particularly ammonia-oxidizing archaea) and novel pathways related to ammonia oxidation have been identified. Consequently, the understanding of nitrogen cycling processes and the microorganisms that mediate them have been greatly improved. Here the authors summarize the biochemistry, microbiology, and ecophysiology of these organisms (including autotrophic ammonia-oxidizing bacteria, heterotrophic nitrifying bacteria, anaerobic ammonia-oxidizing bacteria, and ammonia-oxidizing archaea) and discuss the current knowledge and important concepts associated with their corresponding pathways. Factors influencing their distribution, abundance, community structure and potential ammonia oxidation rates in natural and engineered ecosystems are also addressed. Furthermore, the mechanism of nitrous oxide emission during these processes and the specific control strategies are explained or proposed. The significant roles of these organisms in novel biological wastewater treatment processes are also evaluated. Finally, several urgent issues and significant perspectives related to these novel pathways and players have been addressed to evoke the involvement of researchers in broadening future studies.

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.