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.     

Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments

We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to mangrove forest in the territories of Hong Kong. Both the archaeal and bacterial amoA genes (encoding ammonia monooxygenase subunit A) from all samples supported distinct phylogenetic groups, indicating the presences of niche-specific AOA and AOB in mangrove sediments. The higher AOB abundances than AOA in mangrove sediments, especially in the vicinity of the mangrove trees, might indicate the more important role of AOB on nitrification. The spatial distribution showed that AOA had higher diversity and abundance in the surface layer sediments near the mangrove trees (0 and 10 m) but lower away from the mangrove trees (1,000 m), and communities of AOA could be clustered into surface and bottom sediment layer groups. In contrast, AOB showed a reverse distributed pattern, and its communities were grouped by the distances between sites and mangrove trees, indicating mangrove trees might have different influences on AOA and AOB community structures. Furthermore, the strong correlations among archaeal and bacterial amoA gene abundances and their ratio with NH₄⁺, salinity, and pH of sediments indicated that these environmental factors have strong influences on AOA and AOB distributions in mangrove sediments. In addition, AOA diversity and abundances were significantly correlated with hzo gene abundances, which encodes the key enzyme for transformation of hydrazine into N₂ in anaerobic ammonium-oxidizing (anammox) bacteria, indicating AOA and anammox bacteria may interact with each other or they are influenced by the same controlling factors, such as NH₄⁺. The results provide a better understanding on using mangrove wetlands as biological treatment systems for removal of nutrients.     

Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean

Ammonia oxidation is the first and rate-limiting step of nitrification, which is carried out by two groups of microorganisms: ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). In this study, diversity and abundance of AOB and AOA were investigated in five rock samples from a deep-sea hydrothermal vent site at the Mid-Atlantic Ridge (MAR) of the South Atlantic Ocean. Both bacterial and archaeal ammonia monooxygenase subunit A (amoA) gene sequences obtained in this study were closely related to the sequences retrieved from deep-sea environments, indicating that AOB and AOA in this hydrothermal vent site showed typical deep ocean features. AOA were more diverse but less abundant than AOB. The ratios of AOA/AOB amoA gene abundance ranged from 1/3893 to 1/242 in all investigate samples, indicating that bacteria may be the major members responding to the aerobic ammonia oxidation in this hydrothermal vent site. Furthermore, diversity and abundance of AOA and AOB were significantly correlated with the contents of total nitrogen and total sulfur in investigated samples, suggesting that these two environmental factors exert strong influences on distribution of ammonia oxidizers in deep-sea hydrothermal vent environment.     

Abundance and Diversity of Ammonia-Oxidizing Microorganisms in the Sediments of Jinshan Lake

Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH₄–N, NO₃–N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment.     

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.     

Community Composition and Abundance of Ammonia-Oxidizing Archaea in Sediments from the Changjiang Estuary and its Adjacent Area in the East China Sea

Community composition and abundance of ammonia-oxidizing archaea (AOA) were investigated using ammonia monooxygenase α subunit (amoA) in sediments from the Changjiang estuary and its adjacent area in the East China Sea (ECS). Real-time quantitative polymerase chain reaction (qPCR), clone libraries and sequencing were performed to characterize the AOA community. Clone libraries analysis showed that the majority of amoA sequences fell within the Nitrosopumilus cluster. Correlation analysis showed that AOA diversity was closely related to the nitrite concentration, which was consistent with the canonical correspondence analysis (CCA) where a significant association between nitrite and AOA community composition was observed. The qPCR results were found to be significantly correlated with the environmental parameters. In the gravity cores, a significant positive correlation was found between ammonium concentrations and amoA gene copy numbers from different sediment depths at station S31. At station S33, however, ammonium concentration had a negative correlation and nitrite concentration had a positive correlation with amoA gene copy numbers. In the surface sediments, chlorophyll a concentration had a negative correlation and nitrate concentration had a positive correlation with amoA gene copy numbers. Compared amoA gene copy numbers from AOA with those from ammonia-oxidizing β-proteobacteria (β-AOB) in the same studied areas, the amoA gene copy ratio of β-AOB to AOA was negatively correlated with the phosphate concentration and dissolved oxygen concentration, but was not significantly correlated with either ammonium concentrations or salinity. Our data provided valuable information to achieve a better understanding of the potential role of ammonia oxidizers at the interface between terrestrial and marine environments.     

Biases in community structures of ammonia/ammonium-oxidizing microorganisms caused by insufficient DNA extractions from Baijiang soil revealed by comparative analysis of coastal wetland sediment and rice paddy soil

Repetitive extraction of DNAs from surface sediments of a coastal wetland in Mai Po Nature Reserve (MP) of Hong Kong and surface Baijiang soils from a rice paddy (RP) in Northeast China was conducted to compare the microbial diversity in this study. Community structures of ammonia/ammonium-oxidizing microorganisms in these samples were analyzed by PCR-DGGE technique. The diversity and abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonium-oxidizing (anammox) bacteria were also analyzed based on archaeal and bacterial ammonia monooxygenase subunit A encoding (amoA) and anammox bacterial 16S rRNA genes, respectively. DGGE profiles of archaeal and bacterial amoA and anammox bacterial 16S rRNA genes showed a similar pattern among all five repetitively extracted DNA fractions from both MP and RP, except the anammox bacteria in RP, indicating a more diverse anammox community retrieved in the second to the fifth fractions than the first one. Both soil and marine group AOA were detected while soil and coastal group AOB and Scalindua-anammox bacteria were dominant in MP. Soil group AOA and marine group AOB were dominant in RP, while both Scalindua and Kuenenia species were detected in RP. Pearson correlation analysis showed that the abundance of archaeal and bacterial amoA and anammox bacterial 16S rRNA genes was significantly correlated with the DNA concentrations of the five DNA fractions from MP, but not from RP (except the archaeal amoA gene). Results suggest that anammox bacteria diversity may be biased by insufficient DNA extraction of rice paddy soil samples.     

Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants

In this study, the abundance and sequences of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were determined in seven wastewater treatment plants (WWTPs) whose ammonium concentrations in influent and effluent wastewaters varied considerably (5.6-422.3 mgN l⁻¹ and 0.2-29.2 mgN l⁻¹, respectively). Quantitative real-time PCR showed that the comparative abundance of AOA and AOB amoA genes differed among the WWTPs. In all three industrial WWTPs, where the influent and effluent contained the higher levels of ammonium (36.1-422.3 mgN l⁻¹ and 5.3-29.2 mgN l⁻¹, respectively), more than four orders of magnitude higher numbers of AOB amoA genes than AOA amoA genes arose (with less than the limit of detection of AOA amoA genes). In contrast, significant numbers of AOA amoA genes occurred in all municipal WWTPs (with ammonium levels in the influent and effluent of 5.6-11.0 mgN l⁻¹ and 0.2-3.0 mgN l⁻¹, respectively). Statistical analysis suggested that compared to other plants’ parameters, the ammonium levels in the plants’ effluent showed correlation with the highest p value to the abundance of AOA amoA genes.     

Comparison of the community structures of ammonia-oxidizing bacteria and archaea in rhizoplanes of floating aquatic macrophytes

Some common floating aquatic macrophytes could remove nutrients, such as nitrogen, from eutrophic water. However, the relationship between these macrophytes and the ammonia-oxidizing microorganisms on their rhizoplanes is still unknown. In this study, we examined communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) on the rhizoplanes of common floating aquatic macrophytes (Eichhornia crassipes, Pistia stratiotes and Ipomoea aquatic) in a eutrophic reservoir.The results show that AOB were the predominant ammonia-oxidizer on the three rhizoplanes. The principal AOB were Nitrosomonas europaea and Nitrosomonas ureae clades. The principal group of AOA was most similar to the clone from activated sludge. The ratio of AOB amoA gene copies to AOA varied from 1.36 (on E. crassipes) to 41.90 (on P. stratiotes). Diversity of AOA was much lower than that of AOB in most samples, with the exception of P. stratiotes.     

Seasonal dynamics of ammonia-oxidizing microorganisms in freshwater aquaculture ponds

An annual investigation into the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fresh water aquaculture ponds was performed by quantitative PCR of the amoA gene. The results showed that AOB were the main ammonia-oxidizing microorganisms in water, and significantly higher copy numbers of the AOB amoA gene were observed in the summer (Aug 2012), while no significant differences were detected among the other three seasons. AOA showed low abundances throughout the year. The predominance of AOB in aquaculture water was suggested to be related to photoinhibition. Both the AOB and AOA amoA genes in aquaculture pond sediments showed typical seasonal patterns. The maximum density of AOB was observed in the autumn (Nov 2012) and winter (Jan 2013), while the maximum density of AOA was observed in winter. The minimum densities of both AOA and AOB occurred in the summer. The concentration of the AOA amoA gene was higher than that of the AOB amoA gene in sediments by almost one order of magnitude, which indicates that AOA are the dominant ammonia-oxidizing microorganisms in the aquaculture pond sediments. Dissolved oxygen is suggested to be the key factor determining the predominance of AOA in pond sediments.     

Seasonal dynamics of ammonia/ammonium-oxidizing prokaryotes in oxic and anoxic wetland sediments of subtropical coastal mangrove

Mangrove wetlands are an important ecosystem in tropical and subtropical regions, and the sediments may contain both oxic and anoxic zones. In this study, ammonia/ammonium-oxidizing prokaryotes (AOPs) in yellow and black sediments with vegetation and non-vegetated sediments in a mangrove wetland of subtropical Hong Kong were investigated in winter and summer. The phylogenetic diversity of anammox bacterial 16S rRNA genes and archaeal and bacterial amoA genes (encoding ammonia monooxygenase alpha-subunit) were analyzed using PCR amplification and denaturing gradient gel electrophoresis to reveal their community structures. Quantitative PCR was also used to detect their gene abundances. The results showed that seasonality had little effect, but sediment type had a noticeable influence on the community structures and abundances of anammox bacteria. For ammonia-oxidizing archaea (AOA), seasonality had a small effect on their community structures, but a significant effect on their abundances: AOA amoA genes were significantly higher in winter than in summer. In winter, the vegetated yellow sediments had lower AOA amoA genes than the other types of sediments, but in summer, the vegetated yellow sediments had higher AOA amoA genes than the other types of sediments. Sediment type had no apparent effect on AOA community structures in winter. In summer, however, the vegetated yellow sediments showed obviously different AOA community structures from the other types of sediments. For ammonia-oxidizing bacteria (AOB), seasonality had a significant effect on their community structures and abundances: AOB amoA genes in winter were apparently higher than in summer, and AOB community structures were different between winter and summer. Sediment type had little effect on AOB community structures, but had a noticeable effect on the abundances: AOB amoA genes of the vegetated yellow sediments were obviously lower than the black ones in both seasons. This study has demonstrated that seasonality and sediment type affected community structures and abundances of AOPs differently in oxic and anoxic sediments of the mangrove wetland.     

RETRACTED ARTICLE: Archaeal <Emphasis Type="Italic">amoA</Emphasis> Genes Outnumber Bacterial <Emphasis Type="Italic">amoA</Emphasis> Genes in Municipal Wastewater Treatment Plants in Bangkok

The contribution of ammonia-oxidizing archaea (AOA) to nitrogen removal in wastewater treatment plants (WWTPs) remains unknown. This study investigated the abundance of archaeal (AOA) and bacterial (ammonia-oxidizing bacteria (AOB)) amoA genes in eight of Bangkok’s municipal WWTPs. AOA amoA genes (3.28 × 10⁷ ± 1.74 × 10⁷–2.23 × 10¹¹ ± 1.92 × 10¹¹ copies l⁻¹ sludge) outnumbered AOB amoA genes in most of the WWTPs even though the plants’ treatment processes, influent and effluent characteristics, removal efficiencies, and operation varied. An estimation of the ammonia-oxidizing activity of AOA and AOB suggests that AOA involved in autotrophic ammonia oxidation in the WWTPs. Statistical analysis shows that the numbers of AOA amoA genes correlated negatively to the ammonium levels in effluent wastewater, while no correlation was found between the AOA amoA gene numbers and the oxygen concentrations in aeration tanks. An analysis of the AOB sequences shows that AOB found in the WWTPs limited to only two AOB clusters which exhibit high or moderate affinity to ammonia. In contrast to AOB, AOA sequences of various clusters were retrieved, and they were previously recovered from a variety of environments, such as thermal and marine environments.     

Higher Abundance of Ammonia Oxidizing Archaea than Ammonia Oxidizing Bacteria and Their Communities in Tibetan Alpine Meadow Soils under Long-term Nitrogen Fertilization

Increasing usage of nitrogen fertilizer for food production has resulted in severely environmental problems of nutrients enrichment. This study aimed to examine the response of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) to a long-term nitrogen fertilization in Tibetan alpine meadow. The abundance and composition of both AOB and AOA were assessed using quantitative real-time PCR, cloning and sequencing techniques based on amoA gene under different fertilization gradient (0, 30, 60, 90, and 120 g m^?2 year^?1). Our results showed that, abundances of AOA amoA genes (ranging from 1.48 × 10⁹ to 2.00 × 10⁹ copies per gram of dry soil) were significantly higher than those of AOB amoA genes (1.25 × 10⁷ to 2.62 × 10⁸ copies per gram of dry soil) under fertilization scenario. The abundance of AOB amoA genes increased with increasing nitrogen fertilization, whereas fertilization had little effect on AOA abundance. Sequences of clone libraries of the different treatments revealed that AOB communities were dominated by representatives of Cluster 4, constituting 48.94–64.44% in each clone library. Sequences of Clusters 9, 1 and 2 were prevalent in soils under higher fertilization. All archaeal amoA sequences recovered were affiliated with the soil/sediment clade and marine sediment clade, and no significant difference was observed on the community structure among different fertilization treatments. Variations in the AOB community structure and abundance were linked to ammonium-N and soil pH induced by different fertilization treatments. These results showed that the abundance and structure of the AOB community respond to the fertilization gradient, not AOA.     

Aggregate Size Distribution of Ammonia-Oxidizing Bacteria and Archaea at Different Landscape Positions

To quantify the spatial distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and to determine nitrification activity in soil aggregates along a landscape, soil samples were collected from three landscape positions (shoulder, backslope, and toeslope) at two pasture sites with contrasting climatic conditions. The abundance of AOB and AOA was estimated by quantifying their respective bacterial and archaeal amoA gene copies using real-time polymerase chain reaction. Soil organic C (SOC), total N (TN), and the potential nitrification rate (PNR) were measured in aggregate size ranges (4–1, 1–0.25, and 0.25–0.05 mm). At site 1, a decreasing trend in PNR was observed as the size of aggregates decreased. Both bacterial and archaeal amoA genes were higher in the macroaggregates (4–1 and 1–0.25 mm) than in the microaggregates (0.25–0.05 mm) along the landscape. At site 2, PNR was higher in the smallest size of aggregates. In the 0.25–0.05-mm fraction, the abundance of bacterial and archaeal amoA genes was equal to, or greater than, those found in larger aggregate sizes. The relative abundance of archaeal amoA gene and the PNR correlated with relative SOC and TN contents along the landscapes. The positive relationship between relative archaeal amoA gene abundance and PNR suggests that nitrification in the studied pastures is probably driven by ammonia-oxidizing Thaumarchaeota.     

Abundance and diversity of ammonia-oxidizing archaea in a biological aerated filter process

Ammonia-oxidizing archaea (AOA) represent an important group of ammonia-oxidizing microorganisms that are able to convert ammonia to nitrite, a function which is crucial for the removal of nitrogen from wastewater. In this study, we investigated the abundance and diversity of AOA in a full-scale wastewater treatment plant (WWTP) which used a biological aerated filter (BAF) as the main processing mode. According to the quantitative PCR results, AOA clearly outnumbered ammonia-oxidizing bacteria (AOB) during the whole process. The abundance of AOA amoA genes in the filter layer of BAF was highest with the value varied from 6.32 × 10³ to 3.8 × 10⁴ copies/ng DNA. The highest abundance of AOB amoA genes was 1.32 × 10² copies/ng DNA, recorded in the effluent of the ACTIFLO® settling tank. The ratios of AOA/AOB in the WWTP were maintained at two or three orders of magnitude. Most AOA obtained from the WWTP fell within the Nitrosopumilus cluster. The abundance of AOA and AOB was significantly correlated with ammonium nitrogen concentrations and pH value. The community structure of AOA was significantly influenced by dissolved oxygen concentrations, pH value and chemical oxygen demand.     

Community structure and abundance of ammonia-oxidizing archaea and bacteria after conversion from soybean to rice paddy in albic soils of Northeast China

Community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the albic soil grown with soybean and rice for different years was investigated by construction of clone libraries, denaturing gradient gel electrophoresis (DGGE), and quantitative polymerase chain reaction (q-PCR) by PCR amplification of the ammonia monooxygenase subunit A (amoA) gene. Soil samples were collected at two layers (0–5 and 20–25 cm) from a soybean field and four rice paddy fields with 1, 5, 9, and 17 years of continuous rice cultivation. Both the community structures and abundances of AOA and AOB showed detectable changes after conversion from soybean to rice paddy judged by clone library, DGGE, and q-PCR analyses. In general, the archaeal amoA gene abundance increased after conversion to rice cultivation, while bacterial amoA gene abundance decreased. The abundances of both AOA and AOB were higher in the surface layer than the bottom one in the soybean field, but a reverse trend was observed for AOB in all paddy samples regardless of the duration of paddy cultivation. Phylogenetic analysis identified nine subclusters of AOA and seven subclusters of AOB. Community composition of both AOA and AOB was correlated with available ammonium and increased pH value caused by flooding in multiple variance analysis. Community shift of AOB was also observed in different paddy fields, but the two layers did not show any detectable changes in DGGE analysis. Conversion from soybean to rice cultivation changed the community structure and abundance of AOA and AOB in albic agricultural soil, which requires that necessary cultivation practice be followed to manage the N utilization more effectively.     

Abundance and diversity based on amoA genes of ammonia-oxidizing archaea and bacteria in ten wastewater treatment systems

The abundance and diversity of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in ten wastewater treatment systems (WTSs) by polymerase chain reaction (PCR), cloning, sequencing, and quantitative real-time PCR (qPCR). The ten WTSs included four full-scale municipal WTSs, three full-scale industrial WTSs, and three lab-scale WTSs. AOB were present in all the WTSs, whereas AOA were detected in nine WTSs. QPCR data showed that AOB amoA genes (4.625?×?10⁴–9.99?×?10⁹ copies g^?1 sludge) outnumbered AOA amoA genes (<limit of detection–1.90?×?10⁷ copies g^?1 sludge) in each WTS, indicating that AOB may play an important role than AOA in ammonia oxidization in WTSs. Interestingly, it was found that AOA and AOB coexisted with anaerobic ammonia oxidation (anammox) bacteria in three anammox WTSs with relatively higher abundance. In a full-scale industrial WTS where effluent ammonia was higher than influent ammonia, both AOA and AOB showed higher abundance. The phylogenetic analysis of AOB amoA genes showed that genera Nitrosomonas was the most dominant species in the ten WTSs; Nitrosomonas europaea cluster was the dominant major cluster, followed by Nitrosomonas-like cluster and Nitrosomonas oligotropha cluster; and AOB species showed higher diversity than AOA species. AOA were found to be affiliated with two major clusters: Nitrososphaera cluster and Nitrosopumilus cluster. Nitrososphaera cluster was the most dominant species in different samples and distributed worldwide.     

Spatial Distribution and Factors Shaping the Niche Segregation of Ammonia-Oxidizing Microorganisms in the Qiantang River,China

Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, the current knowledge of the distribution, diversity, and relative abundance of these two microbial groups in freshwater sediments is insufficient. We examined the spatial distribution and analyzed the possible factors leading to the niche segregation of AOA and AOB in the sediments of the Qiantang River, using clone library construction and quantitative PCR for both archaeal and bacterial amoA genes. pH and NH₄⁺-N content had a significant effect on AOA abundance and AOA operational taxonomy unit (OTU) numbers. pH and organic carbon content influenced the ratio of AOA/AOB OTU numbers significantly. The influence of these factors showed an obvious spatial trend along the Qiantang River. This result suggested that AOA may contribute more than AOB to the upstream reaches of the Qiantang River, where the pH is lower and the organic carbon and NH₄⁺-N contents are higher, but AOB were the principal driver of nitrification downstream, where the opposite environmental conditions were present.     

Ammonia-Oxidizing Archaea Dominate Ammonia-Oxidizing Communities within Alkaline Cave Sediments

Nitrification represents one of the key steps in the global nitrogen cycle. While originally considered an exclusive metabolic capability of bacteria, the identification of the Thaumarchaeota revealed that ammonia-oxidizing archaea (AOA) are also important contributors to this process, particularly in acidic environments. Nonetheless, the relative contribution of AOA to global nitrification remains difficult to ascertain, particularly in underexplored neutrophilic and alkalinophilic terrestrial systems. In this study we examined the contribution of AOA to nitrification within alkaline (pH 8.3–8.7) cave environments using quantitative PCR, crenarchaeol lipid identification and measurement of potential nitrification rates. Our results showed that AOA outnumber ammonia-oxidizing bacteria (AOB) by up to four orders of magnitude in cave sediments. The dominance of Thaumarchaeota in the archaeal communities was confirmed by both archaeal 16S rRNA gene clone library and membrane lipid analyses, while potential nitrification rates suggest that Thaumarchaeota may contribute up to 100% of ammonia oxidation in these sediments. Phylogenetic analysis of Thaumarchaeota amoA gene sequences demonstrated similarity to amoA clones across a range of terrestrial habitats, including acidic ecosystems. These data suggest that despite the alkaline conditions within the cave, the low NH₃ concentrations measured continue to favor growth of AOA over AOB populations. In addition to providing important information regarding niche differentiation within Thaumarchaeota, these data may provide important clues as to the factors that have historically led to nitrate accumulation within cave sediments.     

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.