Important Role In Nitrification Research Articles

Changes in the activity and abundance of canonical nitrifiers and Comammox bacteria during stream switching: Shifting from a mainstream hybrid reactor for C, N, and P removal to a sidestream biofilm nitrification reactor

This study investigated how mainstream-sidestream switching affected the activity and abundance of canonical nitrifiers and Comammox bacteria. The experiment started in a mainstream hybrid reactor for C, N, and P removal with biomass in the form of activated sludge and biofilm. A highly effective nitrification sidestream reactor with pure moving bed technology was then obtained through gradual reduction of the reactor's organic loading rate (OLR), increase in the temperature (20–30 °C), and increase in the reactor's nitrogen loading rate (NLR). qPCR and kinetic batch test results suggest that Comammox bacteria could play an important role in nitrification in both the mainstream hybrid reactor and sidestream biofilm reactor, dominating even the canonical AOB. Biofilm provided a better environment for Comammox bacteria development, except when the system was transformed into a hybrid nitrifying reactor. In that case, the occurrence of Comammox bacteria in activated sludge was greater. Simultaneously with reduction of OLR an increase in ammonia oxidation rate was reported in both activated sludge and biofilm. An increase in NLR had a greater effect on the activity of NOB.

Community assembly of comammox Nitrospira in coastal wetlands across southeastern China.

Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture.

Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO2) concentrations aiming to understand the interplay between ammonia oxidation and CO2 fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (μ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO2 gassing μ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of μmax) the biomass to ammonium yield (Y(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D crit. Due to changes in Y(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards μmax. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.

Stochastic factors drive dynamics of ammonia-oxidizing archaeal and bacterial communities in aquaculture pond sediment.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in nitrification, which is essential in the global nitrogen cycle. However, their dynamics and the underlying community processes in agricultural ecosystems under disturbance remain largely unknown. In this study we examined the spatiotemporal dynamics of AOA and AOB communities and analyzed their community processes in the sediment of aquaculture ponds across three different areas in China. We found some significant temporal changes in AOA and AOB community diversity and abundances, but no temporal changes in community composition, despite the significant variations in sediment properties between different sampling times. Nevertheless, significant differences were found for AOA and AOB communities between different areas. Distinct area-specific taxa were detected, and they were found to be important in determining the response of AOA and AOB communities to environmental factors. In addition, geographic distance was found to be significantly correlated with AOA and AOB community composition, which demonstrates that dispersal limitation could significantly contribute to the variations in AOA and AOB communities, and stochastic processes were found to be important in structuring AOA/AOB communities in aquaculture ponds. Taken together, our study indicates that the dynamics of AOA and AOB are based on their community characteristics in aquaculture pond sediment. Our results, for the first time, provide evidence for the dynamics of AOA and AOB communities being driven by stochastic factors in a disturbed environment, and might also be of use in the management of the aquaculture environment.

Ammonia-oxidizing bacteria play an important role in nitrification of acidic soils: A meta-analysis

Our knowledge of the abundance and distribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) has substantially expanded over the past decade, but their relative contributions to soil nitrification remain debated, particularly at a global scale. Nitrification inhibitor 1-octyne is the only available selective inhibitor that can exclusively inhibit AOB but not AOA activity, making it a powerful tool to differentiate the functional importance of AOB vs AOA in nitrification. Here, we conducted a meta-analysis of laboratory incubation studies with 1-octyne as the nitrification inhibitor to display a panoramic view of the relative contribution of AOB in soil nitrification across various terrestrial ecosystems. The most pronounced reduction of nitrification rates by 1-octyne was found in cropland (71.4%), followed by grassland (59.6%), forestland (53.2%) and wetland (44.0%), indicating a more dominant role of AOB over AOA in upland soils than in wetland soils. The response ratio of soil nitrification rates with 1-octyne addition to that without 1-octyne addition was negatively correlated to soil pH in upland soils, suggesting that a greater proportion of nitrification was inhibited by 1-octyne with higher soil pH. However, the reduction of nitrification rate by 1-octyne was estimated to be 59.5% in acidic soils (pH ≤ 6.5), indicating a major role of AOB in acidic soil nitrification. The proportion of nitrification rate reduced by 1-octyne was greater in soils incubated in slurry and with nitrogen additions than in microcosm and without nitrogen additions, and this should be taken into consideration during the incubation experiments. Altogether, this meta-analysis provides evidence for an equally or more important role of AOB in nitrification from global acidic soils, advancing our understanding of the microbial nitrification process, which is fundamental to the sustainable management of nitrogen in soils.

Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils.

Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.

SummaryObligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.

Irrigation frequency alters the abundance and community structure of ammonia-oxidizing archaea and bacteria in a northern Chinese upland soil

Ammonia oxidation, the first and rate-limiting step in nitrification, is a key process in biogeochemical nitrogen cycling. However, little is known about how irrigation affects ammonia oxidizing microorganisms in agroecosystems. In this study, effects of irrigation frequency on soil potential nitrification activity (PNA), the abundance and composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated using real-time PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP), and clone libraries for characterizing the ammonium monooxygenase genes (amoA) in a northern Chinese soil. Results showed that irrigation significantly increased soil PNA and archaeal amoA gene abundance but decreased bacterial amoA gene abundance. Soil PNA was positively correlated with archaeal amoA gene abundance and negatively correlated with bacterial. T-RFLP and PCA results showed that irrigation greatly changed the AOA and AOB community structures by altering the relative abundances of four T-RFs of AOA and four other T-RFs of AOB, respectively. Phylogenetic analysis revealed that all archaeal sequences fell into Group 1.1b, and the bacterial clones were dominated by Nitrosospira-like sequences within Cluster 3a.2. Irrigation induced the appearance of two archaeal and two bacterial OTUs and increased the relative abundance of another two archaeal and four bacterial OTUs, respectively. Additionally, soil moisture, soil pH, NH4+-N, and NO3−-N correlated significantly with the AOA community, and soil pH, total nitrogen (TN), and NO3−-N were significantly correlated with the AOB community. Our results demonstrate that irrigation greatly affected the abundance and community structure of AOA and AOB and that AOA appeared to play a more important role in nitrification in the study soil.

Microbiology: A fight for scraps of ammonia.

Bacteria that can oxidize both ammonia to nitrite and nitrite to nitrate seem to be better adapted to ammonia-limited environments than most cultured microbes that oxidize ammonia to nitrite only, contrary to expectations. See Letter p.269 Nitrospira inopinata was the first bacterium identified that is capable of catalysing complete ammonia oxidization (referred to as comammox). Holger Daims and colleagues now report a pure culture of this organism, which enabled a characterization of its physiology. The authors find that N. inopinata has a high affinity for ammonia, a low maximum rate of ammonia oxidation, a high growth yield compared to canonical nitrifiers, and the genomic potential for alternative metabolisms. The team compare the nitrification kinetics of N. inopinata to that of four ammonia-oxidizing archaea. The results suggest that N. inopinata is likely to have an important role in nitrification, especially in oligotrophic environments.

A nitrogen removal system to limit water exchange for recirculating freshwater aquarium using DHS–USB reactor

ABSTRACTThis study proposes a biological nitrogen removal system for freshwater aquaria consisting of a down-flow hanging sponge (DHS) and an up-flow sludge blanket (USB). DHS–USB systems can perform nitrification and denitrification simultaneously, reducing ammonia (NH3) and nitrate (NO3−) toxicity in the water. The performance of the system was evaluated using on-site fresh water aquaria at ambient temperature (23–34°C) over 192 days. NH3 and nitrite (NO2−) were maintained at a detection limit of 0.01 mg N L−1 and NO3− was maintained below 10 mg N L−1, despite limited water exchange. The 16S rRNA gene of microorganisms from the sludge retained in the bioreactors was sequenced to identify the microbial communities present. Microbial community analysis revealed that ammonia oxidizing archaea (AOA), Ca. Nitrososphaera and Nitrosopumilus, played an important role in nitrification in the DHS reactor, while denitrifying bacteria Thauera played an important role in denitrification in the USB reactor. The proposed DHS–USB system is a promising technological advancement in the development of lower maintenance aquaria.

Spatial Abundance, Diversity, and Activity of Ammonia-Oxidizing Bacteria in Coastal Sediments of the Liaohe Estuary

Ammonia-oxidizing bacteria (AOB) play an important role in nitrification in estuaries. The aim of this study was to examine the spatial abundance, diversity, and activity of AOB in coastal sediments of the Liaohe Estuary using quantitative PCR, high-throughput sequencing of the amoA gene coding the ammonia monooxygenase enzyme active subunit, and sediment slurry incubation experiments. AOB abundance ranged from 8.54 × 104 to 5.85 × 106 copies g-1 of wet sediment weight and exhibited an increasing trend from the Liaohe Estuary to the open coastal zone. Potential nitrification rates (PNRs) ranged from 0.1 to 336.8nmol N g-1 day-1 along the estuary to the coastal zone. Log AOB abundance and PNRs were significantly positively correlated. AOB richness decreased from the estuary to the coastal zone. High-throughput sequencing analysis indicated that the majority of amoA gene sequences fell within the Nitrosomonas and Nitrosomonas-like clade, and only a few sequences were clustered within the Nitrosospira clade. This finding indicates that the Nitrosomonas-related lineage may be more adaptable to the specific conditions in this estuary than the Nitrosospira lineage. Sites with high nitrification rates were located in the southern open region and were dominated by the Nitrosomonas-like lineage, whereas the Nitrosospira lineage was found primarily in the northern estuary mouth sites with low nitrification rates. Thus, nitrification potentials in Liaohe estuarine sediments in the southern open region were greater than those in the northern estuary mouth, and the Nitrosomonas-related lineage might play a more important role than the Nitrosospira lineage in nitrification in this estuary.

Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil.

Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.

长期施加氮肥及氧化钙调节对酸性土壤硝化作用及氨氧化微生物的影响

High levels of N fertilization and acid deposition could cause soil acidification directly and indirectly. The nitrogen cycle, especially nitrification, makes a great contribution to the acidification of agricultural soils across China, which further leads to the mobilization of potentially toxic metals such as aluminum (Al) and manganese (Mn) and decerases crop yields. Chemicals (e.g., CaO) are amended as soil conditioners to relieve soil acidification. Ammonia oxidation, the rate-limiting step in the nitrification process, is driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Increasing evidence demonstrates that pH is one of the most important factors determining the niche separation of AOA and AOB, and AOA play the more important role in nitrification of acidic soils. However, abundant AOB have been detected in acidic soils but little is known about their ecological function. In this study, the effects of long-term N fertilization practices and liming on nitrification and ammonia oxidizers in acidic soils were investigated using quantitative PCR and DGGE methods combined with soil physiochemical analysis. Compared with a previous study conducted 6 years ago at the same site, N fertilizer application without liming further decreased soil pH (3.35—3.47) and potential nitrification rate (PNR) (0.02—0.14 µg NO-2 -N g-1 soil h-1), while 2 years liming alleviated soil acidification (pH 4.10—4.46) and increased PNR (0.22—0.34 µg NO-2 -N g-1 soil h-1) significantly. There was a significantly positive correlation between soil pH and PNR, indicating the increase in soil pH via liming had positive effects on nitrification in acidic soils. AOA amoA gene copy numbers (7.40 ×107—4.08 ×108 copies/ g) were significantly higher than their counterpart AOB (1.67 ×106—2.57 ×107 copies/ g) in soils that received different chemical N fertilizers. Ratios of AOA and AOB amoA gene abundance ranged between 10.9 and 44.3. After amending lime for two years in the N fertilizers treatment plots, AOA amoA gene copy numbers (8.23 ×106—4.89 ×107 copies/ g) decreased to a certain degree but AOB amoA gene copy numbers (1.99 ×107—5.42 ×107 copies/ g) increased significantly compared to their corresponding fertilization treatments without liming,resulting in lower ratios of AOA to AOB amoA gene abundance (0.83—1.94). Moreover, liming showed no clear influence on AOA community structure, but significantly increased AOB community diversity. Taken together, these results indicate that although the activity and abundance of AOA was generally greater than those of AOB in acidic soils, both AOA and AOB actively responded to disturbance in acidic soils based on their niche differentiation and had different effects on nitrification of acidic soils.

Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile

Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification.

Distribution and Abundance of Archaeal and Bacterial Ammonia Oxidizers in the Sediments of the Dongjiang River, a Drinking Water Supply for Hong Kong

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b-and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg−1 sediment, NH4+-N >144 mg kg−1 sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg−1 sediment, NH4+-N <93 mg kg−1 sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem.

Spatial distribution of archaeal and bacterial ammonia oxidizers in the littoral buffer zone of a nitrogen-rich lake

The spatial distribution and diversity of archaeal and bacterial ammonia oxidizers (AOA and AOB) were evaluated targeting amoA genes in the gradient of a littoral buffer zone which has been identified as a hot spot for N cycling. Here we found high spatial heterogeneity in the nitrification rate and abundance of ammonia oxidizers in the five sampling sites. The bacterial amoA gene was numerically dominant in most of the surface soil but decreased dramatically in deep layers. Higher nitrification potentials were detected in two sites near the land/water interface at 4.4-6.1 μg NO2−-N/(g dry weight soil-hr), while only 1.0-1.7 μg NO2−-N/(g dry weight soil-hr) was measured at other sites. The potential nitrification rates were proportional to the amoA gene abundance for AOB, but with no significant correlation with AOA. The NH4+ concentration was the most determinative parameter for the abundance of AOB and potential nitrification rates in this study. Higher richness in the surface layer was found in the analysis of biodiversity. Phylogenetic analysis revealed that most of the bacterial amoA sequences in surface soil were affiliated with the genus of Nitrosopira while the archaeal sequences were almost equally affiliated with Candidatus ‘Nitrososphaera gargensis’ and Candidatus ‘Nitrosocaldus yellowstonii’. The spatial distribution of AOA and AOB indicated that bacteria may play a more important role in nitrification in the littoral buffer zone of a N-rich lake.

Effects of urea and (NH4)2SO4 on nitrification and acidification of Ultisols from Southern China

AbstractThe mechanisms for the effects of ammonium-based fertilizers on soil acidification in subtropical regions are not well understood. Two Ultisols collected from cropland and a tea garden in Anhui and Jiangxi Provinces in subtropical southern China, respectively, were used to study the effects of urea and (NH4)2SO4 on the nitrification and acidification of soils with incubation experiments. Nitrification occurred at very low pH with no N fertilizer added and led to lowering of the soil pH by 0.53 and 0.30 units for the soils from Jiangxi and Anhui, respectively. Addition of urea accelerated nitrification and soil acidification in both Ultisols; while nitrification was inhibited by the addition of (NH4)2SO4, and greater input of (NH4)2SO4 led to greater inhibition of nitrification. Ammonia-oxidizing bacteria (AOB) played an important role in nitrification in cropland soil under acidic conditions. Addition of urea increased the soil pH at the early stages of incubation due to hydrolysis and stimulated the increase in the AOB population, and thus accelerated nitrification and soil acidification. At the end of incubation, the pH of Ultisol from Jiangxi had decreased by 1.25, 1.54 and 1.84 units compared to maximum values for the treatments with 150, 300 and 400 mg/kg of urea-N added, respectively; the corresponding figures were 0.95, 1.25 and 1.69 for the Ultisol from Anhui. However, addition of (NH4)2SO4 inhibited the increase in the AOB population and thus inhibited nitrification and soil acidification. Soil pH for the treatments with 300 and 400 mg/kg of (NH4)2SO4-N remained almost constant during the incubation. AOB played an important role in nitrification of the cropland soil under acidic conditions. Addition of urea stimulated the increase in the AOB population and thus accelerated nitrification and soil acidification; while addition of (NH4)2SO4 inhibited the increase in the AOB population and thus inhibited nitrification.

Responses of bacterial and archaeal ammonia oxidisers of an acidic luvisols soil to different nitrogen fertilization rates after 9 years

It is still not clear which group of ammonia-oxidizing microorganisms plays the most important roles in nitrification in soils. Change in abundances and community compositions of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) under long-term different nitrogen (N) fertilization rates were investigated in an acidic luvisols soil using real-time polymerase chain reaction and denaturing gradient gel electrophoresis, respectively, based on the ammonia monooxygenase a-subunit gene. The experimental plan included the following treatments: control without N fertilization (NCK), low N fertilization rate, middle N fertilization rate, and high N fertilization rate as 0, 100, 150, and 250 kg urea-N ha−1, respectively. Long-term different N fertilization rates did not significantly alter the total C and N contents of soil while it significantly decreased soil pH, which ranged from 5.60 to 5.20. The AOB abundance was more abundant in the N fertilization treatments than the NCK treatment; the AOA abundance decreased by the increasing N fertilization rates, as did the ratios of AOA/AOB. The large differences in the potential nitrification rates among four treatments depended on the changes in AOA abundance but not to changes in AOB abundance. Phylogenetic analysis showed that the AOB communities were dominated by Nitrosospira clusters 1, 3, and 9 while all AOA sequences were grouped into soil/sediment cluster except for one sequence. Taken together, these results indicated that AOB and AOA preferred different soil N conditions and AOA were functionally more important in the nitrification than AOB in the acidic luvisols soil.

Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat

Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA) gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 8000 amoA sequences from the literature and public databases in an effort to understand the ecological factors influencing the distribution and diversity of ammonia-oxidizing archaea (AOA), with a particular focus on sequences from aquatic habitats. This broad survey provides strong statistical support for the hypothesis that different environments contain distinct clusters of AOA amoA sequences, as surprisingly few sequences are found in more than one habitat type. Within aquatic environments, salinity, depth in the water column, and temperature were significantly correlated with the distribution of sequence types. These findings support the existence of multiple distinct aquatic AOA populations in the environment and suggest some possible selective pressures driving the partitioning of AOA amoA diversity.

Community Structure and In Situ Activity of Nitrifying Bacteria in &lt;i&gt;Phragmites&lt;/i&gt; Root-Associated Biofilms

The amount of oxygen released by Phragmites roots and the community structure and in situ activity of nitrifying bacteria in the root biofilms were analyzed by the combined use of 16S rRNA gene-cloning analysis, quantitative PCR (qPCR) assay and microelectrodes. Axial and radial O2 microprofiles were obtained for individual roots of Phragmites in a horizontal flow reactor fed with artificial medium continuously. Axial O2 profiles revealed that O2 was released at a rate of 0.21 μmol O2 cm−2 (root surface area) h−1 only in the apical region (up to ca. 40 mm from the root apex), where there was a high abundance (107 to 108 copies g−1 biomass) of Nitrosomonas-like AOB and Nitrospira-like NOB. This abundance, however, sharply declined to the detection limit at positions more basal than 80 mm. Phylogenetic analysis based on 16S rRNA gene identified strains related to Nitrosomonas oligotropha and Nitrosomonas cryotolerans as the predominant AOB and strains related to Nitrospira marina and Nitrospira moscoviensis as the predominant NOB in the root biofilms. Based on radial O2 microprofiles, the oxic region only extended about 0.5 mm into the surrounding sediment due to a high rate of O2 consumption in the rhizosphere. The net NH4+ and O2 consumption rates in the apical region were higher than those determined at the oxic sediment surface in which the abundance of AOB and NOB was one order of magnitude lower than in the rhizosphere. These results clearly indicated that Phragmites root biofilms played an important role in nitrification in the waterlogged anoxic sediment.