Ammonia-oxidizing Prokaryotes Research Articles

Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments.

Ammonia oxidation is a crucial process in global nitrogen cycling, which is catalyzed by the ammonia oxidizers. Emergent plants play important roles in the freshwater ecosystem. Therefore, it is meaningful to investigate the effects of emergent macrophytes on the abundance and community composition of ammonia oxidizers. In the present study, two commonly found emergent macrophytes (Zizania caduciflora and Phragmitas communis) were obtained from freshwater lakes and the abundance and community composition of the ammonia-oxidizing prokaryotes in the rhizosphere sediments of these emergent macrophytes were investigated. The abundance of the bacterial amoA gene was higher in the rhizosphere sediments of the emergent macrophytes than those of bulk sediments. Significant positive correlation was found between the potential nitrification rates (PNRs) and the abundance of bacterial amoA gene, suggesting that ammonia-oxidizing bacteria (AOB) might play an important role in the nitrification process of the rhizosphere sediments of emergent macrophytes. The Nitrosotalea cluster is the dominant ammonia-oxidizing archaea (AOA) group in all the sediment samples. Analysis of AOB group showed that the N. europaeal cluster dominated the rhizosphere sediments of Z. caduciflora and the bulk sediments, whereas the Nitrosospira cluster was the dominant AOB group in the rhizosphere sediments of P. communis.

Effects of macrobenthic bioturbation on the abundance and community composition of ammonia-oxidizing prokaryotes under different temperatures

ABSTRACTIn order to investigate the effects of macrobenthos on the abundance and community composition of ammonia-oxidizing prokaryotes under different temperature conditions, laboratory microcosms containing two kinds of macrobenthos (Corbicula fluminea and Tubificid worms) were constructed. Real-time polymerase chain reaction (PCR) and clone libraries were applied to analyze the ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities in the surface sediments. The lowest abundances of the archaeal and bacterial amoA gene were found in the samples cultured under 28 °C (archaeal amoA gene abundance, 2.71 × 106 copies/g dry sediment; bacterial amoA gene abundance, 1.17 × 107 copies/g dry sediment) of the C. fluminea group. However, there was no significant difference in terms of the abundance of archaeal amoA gene in all Tubificid worms treatment groups. Compared to the community composition of AOB, greater variations in the community composition of AOA were observed among the three different temperature groups.

The Abundance and Community Composition of Ammonia-Oxidizing Prokaryotes in Small-Reservoir Sediments in China’s Huashan Watershed

The Abundance and Community Composition of Ammonia-Oxidizing Prokaryotes in Small-Reservoir Sediments in China’s Huashan Watershed

Soil texture modulates the response of ammonia-oxidizing prokaryotes to biochemical quality of organic inputs in tropical agricultural soils

Soil texture modulates the response of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to biochemical quality of organic inputs in tropical agricultural soils. To verify this assumption, we used the soil organic matter long-term field experiments in Kenya established on contrasting soils (i.e., clayey Humic Nitisol, sandy Ferric Alisol) in 2002. Since the start of the experiments, soils were continuously treated (4 Mg C ha−1 year−1) with biochemically different organic inputs including Tithonia diversifolia (TD; C/N ratio: 13, Lignin: 8.9%; Polyphenols: 1.7%), Calliandra calothyrsus (CC; 13; 13; 9.4) and Zea mays stover (ZM; 59; 5.4; 1.2). In 2013, soils (0–15 cm) were sampled at young growth (EC30) and flowering (EC60) stages of maize and subjected to DNA-based community analysis of AOB, AOA and 16S rRNA genes. Soil texture exerted stronger effects on the dynamics of the assayed genes than organic input quality with AOB being more responsive than AOA. Clayey soil with its predominant soil organic matter background and large surface area of clay minerals revealed generally higher AOB and AOA abundance than the sandy soil. In the sandy soil, N-rich TD and cellulose-rich ZM promoted AOB abundance, while it was decreased under CC due to N limitation induced by high contents of polyphenols and lignin. N limitation under ZM revealed a clear community differentiation of AOB between ZM versus TD and CC in the clayey soil. For the sandy soil, AOA community composition was distinct between CC versus TD and ZM. To provide a more detailed mechanistic understanding of active AOB and AOA in response to organic input quality, we recommend for prospective research RNA-based along with enzymatic analyses as complement to those shown in this study. This should be approached using controlled experiments to eliminate interfering environmental effects including rainfall and soil moisture, respectively.

Comparing abundance, composition and environmental influences on prokaryotic ammonia oxidizers in two subtropical constructed wetlands

Microbial communities in wastewater treatment can be critical indicators for proper design and functional management of constructed wetlands (CWs). The aim of this study was to examine changes in abundance and composition of ammonia-oxidizing prokaryotes (ammonium-oxidizing archaea and bacteria, AOA and AOB, respectively) and how these relate functionally to nutrient depletion, by comparing a series of treatment cells in two CWs in subtropical Taiwan. Abundance and composition of AOA and AOB were measured by amoA-gene targeted denaturing gradient gel electrophoresis (DGGE) and quantitative PCR, respectively. Prokaryotic composition (including archaea and bacteria) was also determined by 16S rRNA-gene targeted DGGE, while concurrently measuring environmental characteristics. Dominant AOA and AOB were related to uncultured Nitrososphaera and Nitrosomonas groups, respectively. Treatment cells of the two CWs had special clusters with regards to composition of bacteria and AOA, whereas composition of archaea and AOB were evenly distributed in the wetland enclosing a small treatment area. Composition of AOA reflected distinct environmental requirements compared to archaeal composition. Based on abundance analysis, there were more AOB in middle treatment cells, with abundance highly correlated to concentrations of ammonium and phosphate. However, AOA was distributed throughout most of the treatment cells, and was poorly correlated to measured environmental characteristics. With regards to distribution, community complexity, environmental affiliation and environmental demands, we inferred that AOA may be more critical than AOB for depleting nutrients in the CWs.

Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas.

The eastern China marginal seas (ECMS) are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in mud deposits of the South Yellow Sea (SYS) and the East China Sea (ECS) by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia, and silicate (SiO), was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ15NTN and SiO, and nitrate and δ13C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits.

Temperature responses of ammonia-oxidizing prokaryotes in freshwater sediment microcosms.

In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups.

Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments.

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.

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.

Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu)

Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic ecosystems. Recent findings have expanded the known ammonia-oxidizing prokaryotes from Bacteria to Archaea. However, the relative importance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in nitrification is still debated. Here we showed that, in two large eutrophic lakes in China (Lake Taihu and Lake Chaohu), the abundance of AOA and AOB varied in opposite patterns according to the trophic state, although both AOA and AOB were abundant. In detail, from mesotrophic to eutrophic sites, the AOA abundance decreased, while the AOB increased in abundance and outnumbered the AOA at hypertrophic sites. In parallel, the nitrification rate increased along these trophic gradients and was significantly correlated with both the AOB abundance and the numerical ratio of AOB to AOA. Phylogenetic analysis of bacterial amoA sequences showed that Nitrosomonas oligotropha- and Nitrosospira-affiliated AOB dominated in both lakes, while Nitrosomonas communis-related AOB were only detected at the eutrophic sites. The diversity of AOB increased from mesotrophic to eutrophic sites and was positively correlated with the nitrification rate. Overall, this study enhances our understanding of the ecology of ammonia-oxidizing prokaryotes by elucidating conditions that AOB may numerically predominated over AOA, and indicated that AOA may play a less important role than AOB in the nitrification process of eutrophic lakes.

Ammonia-oxidizer communities in an agricultural soil treated with contrasting nitrogen sources

The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for six seasons with contrasting nitrogen (N) sources. Molecular tools based on the genes encoding ammonia monooxygenase were used to characterize the ammonia oxidizer (AO) communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control), dairy waste compost, liquid dairy waste (LW), and ammonium sulfate (AS) treatments at approximately 100 and 200 kg available N ha-1 over 6 years. The N treatment affected the quantity of AO based on estimates of amoA by real-time PCR. Ammonia oxidizing bacteria (AOB) were higher in soils from the AS200, AS100, and LW200 treatments (2.5 × 107, 2.5 × 107, and 2.1 × 107copies g-1 soil, respectively) than in the control (8.1 × 106 copies g-1 soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 107 copies g-1 soil, average). The ratio of AOA/AOB was higher in the control and compost treated soils, both treatments have the majority of their ammonium supplied through mineralization of organic nitrogen. Clone libraries of partial amoA sequences indicated AOB related to Nitrosospira multiformis and AOA related to uncultured Nitrososphaera similar to those described by soil fosmid 54d9 were prevalent. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira- and Nitrosomonas-type AOB were present in all soils examined. In contrast to the intergenic amoC-amoA profile results, Nitrosomonas-like clones were recovered only in the LW200 treated soil-DNA. The impact of 6 years of contrasting nitrogen sources applications caused changes in AO abundance while the community composition remained relatively stable for both AOB and AOA.

Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments

Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit (amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11 × 10(4)-6.47 × 10(5) copies g(-1) sediment) was always greater than that of AOA amoA gene (7.98 × 10(3)-3.51 × 10(5) copies g(-1) sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03-5.39pmol N copy(-1) day(-1)) compared with winter (0.16-0.38pmol N copy(-1) day(-1)), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons.

Abundance and Diversity of Ammonia-Oxidizing Prokaryotes in the Root–Rhizosphere Complex of Miscanthus × giganteus Grown in Heavy Metal-Contaminated Soils

Mine wastes have been considered as a source of heavy metal (HM) contamination in the environment and negatively impact many important ecosystem services provided by soils. Plants like Miscanthus, which tolerate high HM concentrations in soil, are often used for phytoremediation and provide the possibility to use these soils at least for the production of energy crops. However, it is not clear if plant growth at these sites is limited by the availability of nutrients, mainly nitrogen, as microbes in soil might be affected by the contaminant. Therefore, in this study, we investigated in a greenhouse experiment the response of ammonia-oxidizing microbes in the root-rhizosphere complex of Miscanthus × giganteus grown in soils with different levels of long-term arsenic (As) and lead (Pb) contamination. Quantitative PCR of the ammonia monooxigenease gene (amoA) was performed to assess the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) at two different points of plant growth. Furthermore, bulk soil samples before planting were analyzed. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to investigate the diversity of archaeal amoA amplicons. Whereas high concentrations of As and Pb in soil (83 and 15 g/kg, respectively) resulted independent from plant growth in a clear reduction of AOA and AOB compared to the control soils with lower HM contents, in soils with contamination levels of 10 g/kg As and 0.2 g/kg Pb, only AOB were negatively affected in bulk soil samples. Diversity analysis of archaeal amoA genes revealed clear differences in T-RFLP patterns in response to the degree of HM contamination. Therefore, our results could clearly prove the different response patterns of AOA and AOB in HM-contaminated soils and the development of archaeal amoA phylotypes which are more tolerant towards HMs in soil samples from the areas that were impacted the most by mining waste, which could contribute to functional redundancy of ammonia-oxidizing microbes in soils and stability of nitrification pattern.

The influence of salinity and ammonium levels on amoA mRNA expression of ammonia-oxidizing prokaryotes

This study investigated the influence of salinity and ammonium levels on ammonia-oxidizing bacteria (AOB) and archaea (AOA) by monitoring their amo subunit A (amoA) messenger RNA (mRNA) expression. The aerobic mini-continuous stirred-tank reactors (mini-CSTRs) were operated for 48 h under different salinity or ammonium levels. Quantification of archaeal and bacterial amoA mRNA levels using real-time reverse transcription polymerase chain reaction, combined with terminal restriction fragment length polymorphism (T-RFLP) analysis, was applied to investigate the differential transcriptional responses among AOA species. High salinity levels repressed both archaeal and bacterial amoA mRNA expressions. On the other hand, high ammonium levels repressed only archaeal mRNA expression, suggesting that ammonium is a significant environmental factor shaping abundance of AOA and AOB. T-RFLP results indicated that the impacts of salinity and ammonium levels were different among AOA species. Although further study is necessary to add significance to our findings, the combination of the short-term mini-CSTR operations and amoA mRNA-based analyses allow a preliminary study on the influences of environmental factors on competition between the AOA and AOB communities.

Lower Abundance of Ammonia-Oxidizing Archaea Than Ammonia-Oxidizing Bacteria Detected in the Subsurface Sediments of the Northern South China Sea

Diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in samples of the northern South China Sea subsurface sediment were assessed by analyzing the amoA gene sequences retrieved from the samples. The microbial diversity was assessed using rarefaction and phylogenetic analyses. The deep-sea subsurface sediments harbored diverse and distinct AOA and AOB communities, but the abundance of AOA was lower than that of AOB, consistent with many other studies about bacteria and archaea in subsurface sediments. Diversity of AOA shown in the OTUs and Shannon index was correlated with the concentration of nitrite in the Pearson analysis, but no obvious relationships between the diversity or abundance of AOB and the physicochemical parameters could be identified in the present study, indicating the concentration of ammonium may not be an important factor to determine the diversity and abundance of ammonia-oxidizing prokaryotes in the subsurface sediments. Additionally, Nitrosomonas-like AOB was found to be dominant in subsurface sediments of the northern South China Sea showing a different adaption strategy comparing with some Nitrosospira-like AOB lineages. Concentration of nitrite was correlated with diversity of AOA, but no correlations between diversity and abundance of AOB and the physicochemical parameters were established in the study. Supplementary materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files.

Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea

In the present study the diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) were investigated, along with the physicochemical parameters potentially affecting them, in a transect of surface sediments from the coastal margin adjacent to the Pearl River estuary to the slope in the deep South China Sea. Nitrifying microbial diversity was determined by detecting the amoA (ammonia monooxygenase subunit A) gene. An obvious community structure shift for both AOA and beta-AOB from the coastal marginal areas to the slope in the deep-sea was detected, while the OTU numbers of AOA amoA were more stable than those of the beta-AOB. The OTUs of beta-AOB increased with the distance from the coastal margin areas to the slope in the deep-sea. Beta-AOB showed lower diversity with dominant strains in a polluted area but higher diversity without dominant strains in a clean area. Moreover, the diversity of beta-AOB was correlated with pH values, while no noticeable relationships were established between AOA and physicochemical parameters. Beta-AOB was more sensitive to transect environmental variability and might be a potential indicator for environmental changes. Additionally, the surface sediments surveyed in the South China Sea harboured diverse and distinct AOA and beta-AOB phylotypes different from other environments, suggesting the endemicity of some nitrifying prokaryotes in the South China Sea.Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-011-9610-1) contains supplementary material, which is available to authorized users.

Assessment of nitrification in groundwater filters for drinking water production by qPCR and activity measurement

In groundwater treatment for drinking water production, the causes of nitrification problems and the effectiveness of process optimization in rapid sand filters are often not clear. To assess both issues, the performance of a full-scale groundwater filter with nitrification problems and another filter with complete nitrification and pretreatment by subsurface aeration was monitored over nine months. Quantitative real-time polymerase chain reaction (qPCR) targeting the amoA gene of bacteria and archaea and activity measurements of ammonia oxidation were used to regularly evaluate water and filter sand samples. Results demonstrated that subsurface aeration stimulated the growth of ammonia-oxidizing prokaryotes (AOP) in the aquifer. Cell balances, using qPCR counts of AOP for each filter, showed that the inoculated AOP numbers from the aquifer were marginal compared with AOP numbers detected in the filter. Excessive washout of AOP was not observed and did not cause the nitrification problems. Ammonia-oxidizing archaea grew in both filters, but only in low numbers compared to bacteria. The cell-specific nitrification rate in the sand and backwash water samples was high for the subsurface aerated filter, but systematically much lower for the filter with nitrification problems. From this, we conclude that incomplete nitrification was caused by nutrient limitation.

Quantitative analyses of ammonia-oxidizing Archaea and bacteria in the sediments of four nitrogen-rich wetlands in China

With the rapid development of ammonia-synthesizing industry, the ammonia-nitrogen pollution in wetlands acting as the sink of point and diffuse pollution has been increased dramatically. Most of ammonia-nitrogen is oxidized at least once by ammonia-oxidizing prokaryotes to complete the nitrogen cycle. Current research findings have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex wetlands environment, it remains unclear whether ammonia oxidation is exclusively or predominantly linked to Archaea or Bacteria as implied by specific high abundance. In this research, the abundance and composition of Archaea and Bacteria in sediments of four kinds of wetlands with different nitrogen concentration were investigated by using quantitative real-time polymerase chain reaction, cloning, and sequencing approaches based on amoA genes. The results indicated that AOA distributed widely in wetland sediments, and the phylogenetic tree revealed that archaeal amoA functional gene sequences from wetlands sediments cluster as two major evolutionary branches: soil/sediment and sediment/water. The bacteria functionally dominated microbial ammonia oxidation in different wetlands sediments on the basis of molecule analysis, potential nitrification rate, and soil chemistry. Moreover, the factors influencing AOA and AOB abundances with environmental indicator were also analyzed, and the results addressed the copy numbers of archaeal and bacterial amoA functional gene having the higher correlation with pH and ammonia concentration. The pH had relatively great negative impact on the abundance of AOA and AOB, while ammonia concentration showed positive impact on AOB abundance only. These findings could be fundamental to improve understanding of the importance of AOB and AOA in nitrogen and other nutrients cycle in wetland ecosystems.

Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter

Ammonia oxidation, the first step in nitrification, is performed by certain Beta- and Gammaproteobacteria and Crenarchaea to generate metabolic energy. Ammonia monooxygenase (amoA) genes from both Bacteria and Crenarchaea have been found in a variety of marine ecosystems, but the relative importance of Bacteria versus Crenarchaea in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal amoA genes in the coastal Arctic Ocean during summer and winter over 2 years. Summer and winter betaproteobacterial amoA clone libraries were significantly different, although the gene sequences were similar to those found in temperate and polar environments. Betaproteobacterial and crenarchaeal amoA genes were 30- to 115-fold more abundant during the winter than during the summer in both years of the study. Archaeal amoA genes were more abundant than betaproteobacterial amoA genes in the first year, but betaproteobacterial amoA was more abundant than archaeal amoA the following year. The ratio of archaeal amoA gene copies to marine group I crenarchaeal 16S rRNA genes averaged 2.9 over both seasons and years, suggesting that ammonia oxidation was common in Crenarchaea at this location. Potential nitrification rates, as well as the total amoA gene abundance, were highest in the winter when competition with phytoplankton was minimal and ammonium concentrations were the highest. These results suggest that ammonium concentrations were important in determining the rates of ammonia oxidation and the abundance of ammonia-oxidizing Betaproteobacteria and Crenarchaea.