Ammonia-oxidizing Bacteria Species Research Articles

Effects of Vegetable Planting Ages on Community Structure of Ammonia-oxidizing Archaea and Ammonia-oxidizing Bacteria in Greenhouse Vegetable Fields

The ammonia oxidation process driven by microorganisms is a dominant source for nitrous oxide （N2O） emissions. Here, we examined the influence of greenhouse vegetable planting ages on soil ammonia-oxidizing archaea （AOA） and ammonia-oxidizing bacteria （AOB）, which is of great significance for assessing the soil quality status and greenhouse gas transformations. A field study was conducted at different times （1, 5, 10, and 20 a） in greenhouse vegetable soils of Gaoyi, Hebei Province. Chemical analysis and Illumina NovaSeq high-throughput sequencing were used to analyze the soil physicochemical properties and community structures and diversity of AOA and AOB. The variation in AOA and AOB communities and the driving factors in greenhouse soils at different ages were also investigated. The results showed that the contents of total nitrogen, organic matter, alkali-hydrolyzable nitrogen, available phosphorus, and available potassium first increased and then decreased with the prolongation of growth. The contents of nitrate nitrogen, ammonium nitrogen, and electrical conductivity first decreased and then increased with the prolongation of growth. The pH value of soils decreased with the prolongation of growth. The abundance and diversity index of AOA and AOB first decreased and then increased with the prolongation of growth. Nitrososphaeria, unclassified Thaumarchaeota, and Candidatus Nitrosocaldus were the dominant species of AOA, while Betaproteobacteria and Nitrosospira were the dominant species of AOB. The composition of the soil AOA community varied greatly compared to that of AOB with the prolongation of growth. Correlation analysis showed that the changes in soil nutrient factors had a significant correlation with AOA and AOB communities. Redundancy analysis indicated that ammonium nitrogen, alkali-hydrolyzable nitrogen, and nitrate nitrogen were key factors of AOA communities, while electrical conductivity, available potassium, and nitrate nitrogen were key factors for AOB. In summary, long-term planting of greenhouse vegetables significantly affected the abundance and composition of soil AOA and AOB communities. Our results provide a theoretical basis for further studies on the greenhouse gas transformation and microbial mechanisms of the nitrogen cycle in greenhouse soils.

Assessment of oxygen kinetic parameters for closely related ammonia-oxidizing bacteria.

The reaction kinetics of lithotrophic ammonia-oxidizing bacteria (AOB) are strongly dependent on dissolved oxygen (DO) as their metabolism is an aerobic process. In this study, we estimate the kinetic parameters, including the oxygen affinity constant (Km[O2]) and the maximum oxygen consumption rate (Vmax[O2]), of different AOB species, by fitting the data to the Michaelis-Menten equation using nonlinear regression analysis. An example for three different species of Nitrosomonas bacteria (N. europaea, N. eutropha, and N. mobilis) in monoculture is given, finding a Km[O2] of 0.25±0.05mg l-1, 0.47±0.09mg l-1, and 0.28±0.08mg l-1, and a Vmax[O2] of 0.07±0.04 pg h-1cell-1, 0.25±0.06 pg h-1cell-1, and 0.02±0.001 pg h-1cell-1 for N. europaea, N. eutropha, and N. mobilis, respectively. This study shows that of the analyzed AOB, N. europaea has the highest affinity towards oxygen and N. eutropha the lowest affinity towards oxygen, indicating that the former can convert ammonia even under low DO conditions. These results improve the understanding of the ecophysiology of AOB in the environment. The accuracy of mathematically modelled ammonia oxidation can be improved, allowing the implementation of better management practices to restore the nitrogen cycle in natural and engineered water systems.

Sealing solid agar in serum bottles for rapid isolation and long-term preservation of chemoautotrophic ammonia-oxidizing bacteria

Ammonia-oxidizing bacteria (AOB) are ubiquitous on the earth and have broad applications in bioremediation. However, the number of their species with standing in nomenclature and deposited in Microbial Culture Collections still remains low. Moreover, only a few novel species have been reported over the last decades. In this study, we sealed agar in serum bottles to develop a kind of solid agar plate with the oxygen concentration in the headspace maintained at low levels. By using these plates, eight AOB isolates including two novel species were obtained. When AOB cells were grown on the sealed solid agar plates, the time to form visible colonies was largely reduced and the maximum diameter of colonies reached 2 mm, which makes the process of AOB isolation rapid and efficient. Based on five AOB isolates, the headspace oxygen concentration had a significant influence on AOB growth either on solid plate or in liquid culture. Especially, when grown under 21 % O2, the number of colonies formed on solid agar plates was very low and sometimes no visible colony formed. Besides the application on AOB isolation, the sealed solid agar plate was also effective for the enumeration and preservation of AOB cells. When preserved under room temperature for more than ten months, the AOB colonies on the plate could still be recovered. This method provides a feasible way to isolate more novel AOB species from the environment and deposit more species in Microbial Culture Collections.

Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process

Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.

Metabolic inhibitor-free assessment of the heterotrophic ammonia-oxidizing activity in activated sludge

When the contributions of three ammonia-oxidizing pathways (heterotrophic or autotrophic aerobic ammonia oxidization, and anammox) to wastewater biological nitrogen removal systems was compared by determining their ammonia-oxidizing activities, the key question is how to accurately determine the potential heterotrophic aerobic ammonia-oxidizing (PHAe) activity when the potential autotrophic aerobic ammonia-oxidizing (PAAe) activity (by ammonia-oxidizing bacteria (AOB) or archaea, or complete ammonia oxidization bacteria) also contributes to ammonia oxidization in PHAe activity assay medium. Using a AOB species and three heterotrophic AOB species as inocula, we demonstrated the feasibility of PHAe activity evaluation in the absence of a metabolic inhibitor, i.e., by subtracting the PAAe activity determined in PAAe activity assay medium from a combination of PAAe and PHAe activity determined in PHAe activity assay medium. Binary organic carbon sources (i.e., glucose and acetate) were included in the PHAe activity assay medium to fulfill the carbon requirements of most heterotrophic AOB genera. Higher ammonia-oxidizing activity in AOB biomass than heterotrophic AOB biomass (35.6 vs. 2.6–10.0 mg NH4+–N g−1 MLSS h−1) provides the remarkable advantages of autotrophic aerobic ammonia oxidization in biological nitrogen removal systems. Ammonia removal in three full-scale biological nitrogen removal systems for sewage treatment was predominantly mediated by PAAe activity (1.9–3.3 vs. 0.0–0.3 mg NH4+–N g1 MLSS h−1).

Abundance, community and driving factor of nitrifiers in western China plateau

Complete ammonia oxidation (comammox) is one of the most important biogeochemical processes, with recent studies showing that comammox process dominates nitrification in many ecosystems. However, the abundance, community and driving factor of comammox bacteria and other nitrifying microorganisms in plateau wetland is still unclear. Here, the abundances and community features of comammox bacteria, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the wetland sediments of western China plateaus were examined using qPCR and high-throughput sequencing. The results indicate that comammox bacteria were more abundant than AOA and AOB, and dominated the nitrification process. Compared with low-elevation samples (below 3000 m: samples 6–10, 12, 13, 15, 16), the abundance of comammox bacteria was much higher at high-elevation samples (above 3000 m: samples 1–5, 11, 14, 17, 18). The key species of AOA, AOB, and comammox bacteria were Nitrososphaera viennensis, Nitrosomonas europaea, and Nitrospira nitrificans, respectively. The key factor affecting comammox bacteria community was elevation. Elevation could increase the interaction links of key species Nitrospira nitrificans, resulting in high comammox bacterial abundance. The results of this study advance our knowledge of comammox bacteria in natural ecosystems.

The elevation of salinity above 1% deteriorated nitrification performance and reshaped nitrifier community of an MBR: An often overlooked factor in the treatment of high-strength ammonium wastewater

The effects of synchronous variations of influent salinity with the elevation of NH4+-N concentration on nitrification performance and microbial community structure of bioreactor are often ignored. In this study, we investigated the dynamic response of nitrifying activated sludge to synchronously increased salinity and ammonia loading rate (ALR) in a nitrification membrane bioreactor (MBR). We found that the increase in influent salinity above 1% (from 0.91 to 1.32%) led to the deterioration of the nitrification performance of the MBR. The combined inhibition effect of salinity (1.32%), free ammonia (FA, an average of 1.37 mg/L), and free nitrous acid (FNA, an average of 0.155 mg/L) on nitrite-oxidizing bacteria (NOB) resulted in long-term (35 days) nitrite accumulation. The further increase of salinity and ALR exhibited little influence on the nitrification performance of MBR after the activated sludge had adapted to high salinity (>1%), effective nitrification performance was achieved at high ALR up to 1.71 kg NH4+-N/m3·d and high salinity (2.13%). The microbial analysis showed that the elevated salinity and accumulation of FNA reshaped the microbial community structure of ammonia-oxidizing bacteria (AOB) and NOB. The dominant species of AOB and NOB shifted from the salinity-resistant species Nitrosomonas aestuarii to the species Nitrosomonas mobilis with dual resistant to salinity and FNA, and from non-salinity-resistant species Candidatus Nitrospira defluvii to salinity-resistant species Nitrobacter winogradskyi and Nitrospira marina, respectively. Therefore, the salinity of 1% may be a critical level for the nitrification performance and the shift in the nitrifier community of activated sludge without salinity acclimation.

Biodegradation of quinoline by Nitrosomonas mobilis Ms1 through nitrification: A mechanistic study

Effluents from pharmaceutical and coal gasification industries contain recalcitrant aromatic pollutants such as quinoline. Ammonia oxidizing bacteria (AOB) has been known to simultaneously oxidize ammonia and aromatic compounds. This study investigated the impact of quinoline, a nitrogen-containing heterocyclic aromatic compound, on nitrification by pure culture of AOB- Nitrosomonas mobilis Ms1. Quinoline has been found to inhibit nitrification to suspension culture by IC 50 value 40.01 μM. However, biofilm culture could withstand its inhibitory effect upto 50 μM. Morphological analysis of biofilm culture showed destruction in extracellularpolymeric substances (EPS) in the presence of quinoline at concentration of 1.5 mM and above. X-ray photoelectron spectroscopy (XPS) analysis of the biofilm surface showed loss of NH4+ peak in quinoline treated biofilm which indicated lower protein in EPS. Biodegradation analysis showed pyridine derivatives – 2,3-Pyridinedicarbonitrile, 2,4-Dicyanopyridine, and Pyridine, 2-[(3-methoxyphenyl) methyl] and hydroxylated aromatic such as 3-Hydroxy-4-methylbenzaldehyde and phenol, 4-[2-(methylamino) ethyl] as metabolic intermediates of quinoline degradation. These metabolic intermediates have been found to inhibit nitrification by blocking enzyme active site. Quinoline caused change in fatty acid methyl ester (FAME) profile which resulted in higher fraction of unsaturated FAME. This is one of the pioneer studies on quinoline biodegradation by a pure culture of AOB species, which could in turn aid to improve the efficacy of biological treatment of nitrogen-containing (heterocyclic compounds such as quinoline) wastewater.

Removal of Mg2+ inhibition benefited the growth and isolation of ammonia-oxidizing bacteria: An inspiration from bacterial interaction.

Ammonia-oxidizing bacteria (AOB) play an important role in the global nitrogen cycle and have broad applications in the nitrogen removal from wastewater. However, the AOB species are sensitive to environmental factors and usually form tight relationships with other microbes, making the AOB isolation and maintenance are difficult and time-consuming. In this study, the relationship that occurred between AOB and their bacterial partners was found to be able to improve the ammonia oxidation; during the co-cultivation, the magnesium ions (Mg2+) with removal rate as high as 36.7% was removed from culture medium by the concomitant bacterial species, which was regarded as the main reason for improving ammonia oxidation. During the pure cultivation of AOB isolate, when the concentration of Mg2+ reduced to low levels, the ammonia-oxidizing activity was more than 5 times and the amoA gene expression was more than 12 times higher than that grown in the initial culture medium. Based on a newly designed culture medium, the ammonia oxidation of AOB isolate grown in liquid culture was significantly promoted and the visible AOB colonies with much more number and larger diameter were observed to form on agar plates. With the addition of high concentration of calcium carbonate (CaCO3), AOB colonies could be easily and specifically identified by following the hydrolytic zones that formed around AOB colonies. Another AOB isolates were successively obtained from different samples and within a short time, suggesting the feasibility and effectivity of this culture medium and strategy on the AOB isolation from environments.

Improved insights into the adaptation and selection of Nitrosomonas spp. for partial nitritation under saline conditions based on specific oxygen uptake rates and next generation sequencing

Partial nitritation (PN) is a bioprocess that is essential for developing cost-effective biological nitrogen removal processes. Understanding the abundant bacterial communities responsible for nitrification under salt stress conditions is important to achieve a stable PN system for treating saline wastewater. Therefore, in this study, we identified the core nitrifying communities and investigated their correlations with the process parameters in a nitrifying bioreactor that was used for treating saline high-strength ammonia wastewater. A PN system worked efficiently under saline conditions with varying operational factors, such as temperature, dissolved oxygen (DO), and alkalinity. Interestingly, the specific oxygen uptake rate (SOUR) became similar under salt-free and saline media after the salt adaption. Next generation sequencing results suggested that the inactivation of Nitrobacter winogradskyi was a key factor for the PN reaction under salt stress conditions. We also found that Nitrosomonas europaea, a freshwater type ammonia-oxidizing bacteria (AOB), was predominantly found under both salt-free and saline conditions, whereas other halotolerant or halophilic AOB species, including Nitrosomonas nitrosa and Nitrosomonas mobilis, became selectively abundant under saline conditions. This implies that adaptation (training of N. europaea) and selection (presence of N. nitrosa and N. mobilis) were simultaneously attributed to selective ammonia conversion for the PN reaction. The redundancy analysis showed that the salinity and ammonia loading rates were statistically significant process parameters that determined the nitrifying bacterial community, suggesting that these parameters drive the adaptation and selection of the core AOB species during the PN reaction. Furthermore, the correlation analysis revealed that the abundance of N. nitrosa and N. mobilis was critically correlated with the specific oxygen uptake rates in saline media containing ammonia.

Ammonia Nitrogen Removal Performance with Parallel Operation of Conventional and Inverted A2/O Sewage Treatment Processes in Winter

Ammonia nitrogen (NH4+-N) removal capacities of the A2/O and inverted A2/O processes were analyzed with the same inlet and parallel operation during winter. When the operating water temperature was 14℃, the inverted A2/O process exhibited lower NH4+-N removal from the volumetric load[0.13 kg ·(m3 ·d)-1vs. 0.29 kg ·(m3 ·d)-1] and a lower ammonia oxidation rate (AOR)[0.07 kg ·(kg ·d)-1 vs. 0.11 kg ·(kg ·d)-1] than the A2/O process, whereas the two processes exhibited similar performance at 26℃.The quantitative results for the ammonia oxidizing bacteria (AOB) population were almost the same in the two parallel processes (3.2%±0.24% for the inverted A2/O process and 3.4%±0.31% for the A2/O process). Clone library analysis showed that at low temperatures, the inverted A2/O process had a lower capacity for ammonia nitrogen removal than A2/O process. This is because the particular AOB species[spirillum (Nitrosospira)] facilitated the slower AOR type (K-growth strategy) of nitrosation in the inverted A2/O process, whereas in the A2/O process, the faster AOR type (r-growth strategy) of nitrosation was facilitated by bacterium (Nitrosomonas). At 26℃, the dominant species in the two processes were Nitrosomonas. Through comprehensive analysis of the pollutants during the removal process, we found that although temperature is the leading cause of AOB advantage in species succession, the changes in the inverted A2/O process structure, caused by the aerobic unit, resulted in high COD load and high NH4+-N concentration, which were unfavorable for the growth of AOB. This shows that under conventional sewage conditions, the K-growth strategy is advantageous for the AOB species. Therefore, the structure of the inverted A2/O process for heterotrophic bacteria (phosphorus accumulating bacteria and denitrifying bacteria) indirectly affects the population distribution and succession of autotrophic ammonia-oxidizing bacteria, through COD load and other factors, thereby leading to weakened nitrification capacity at low temperatures.

攀枝花不同海拔高度烤烟农田红壤中氨氧化细菌与氨氧化古菌的群落结构分析

为探究攀枝花干热河谷区农田土壤氨氧化古菌（Ammonia oxidizing archaea，AOA）与氨氧化细菌（Ammonia oxidizing bacteria，AOB）群落对海拔高度的响应特征，深入认识该区域的氮素循环过程。以攀枝花米易县不同海拔（1600 m、1800 m和2000 m）农田红壤为研究对象，运用化学分析和末端限制性片段长度多态性（Terminal restriction fragment length polymorphism，T-RFLP）分别测定土壤理化性质、AOA和AOB群落组成及多样性，研究不同海拔农田土壤中AOA和AOB群落变异及其驱动因子。研究结果显示，不同海拔农田土壤pH均小于7，土壤有机碳（SOC）、全氮（TN）、速效钾（AK）和铵态氮（NH₄⁺-N）含量随海拔升高而降低，碱解氮（AN）、有效磷（AP）和硝态氮（NO₃^--N）含量随海拔升高先增加后降低；随海拔升高，AOA群落多样性指数增加，而AOB群落多样性指数先增加后降低；AOA以亚硝基球菌属（Nitrososphaera）为优势菌群，AOB以亚硝化螺菌属（Nitrosospira）为优势菌群；土壤有机碳（SOC）、速效钾（AK）和硝态氮（NO₃^--N）是影响该区域农田土壤AOA和AOB群落发育的主要因子。总体而言，攀枝花干热河谷区不同海拔农田土壤AOA和AOB群落结构变化明显，土壤硝态氮、速效钾和有机碳是影响AOA和AOB群落结构变异的主要因子；研究结果可为揭示干热河谷区农田红壤氮循环相关微生物的海拔分布格局提供理论依据。;This papers aims to explore the response of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) communities to elevation changes in the dry-hot valleys of Panzhihua City, China, and further reveal the nitrogen biogeochemical cycling of this area. Soil samples were collected from the tobacco cultivation field of different altitudes (e.g. 1600 m, 1800 m, and 2000 m) in the dry-hot valleys of Miyi county, Panzhihua City, China. Chemical analysis and terminal restriction fragment length polymorphism (T-RFLP) were used to analyze the soil physicochemical properties and community structures and diversity of AOB and AOA, respectively. The variation of AOA and AOB communities and the driving factors in farmland soils at different altitudes were also investigated. The results showed that the pH value of soils from the three different elevations were below seven which suggests that the soils being studied were acidic soils. The contents of soil organic carbon (SOC), total nitrogen (TN), available potassium (AK) and ammonium nitrogen (NH₄⁺-N) decreased along the increase of elevation. The contents of alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), and nitrate nitrogen (NO₃^--N) first increased and then decreased along the increase of elevation. The highest contents of the AN, AP, and NO₃^--N were detected in the 1800 m elevation while the lowest were detected in the 2000 m. The diversity index of AOA community increased along the increase of altitude while the diversity index of AOB peaked in 1800m, and both the lowest diversity index of AOA and AOB were detected in 1600 m elevation. Nitrososphaera and Nitrosospira were the dominant species of AOA and AOB in the dry-hot valleys of Panzhihua City. Redundancy analysis (RDA) showed that the SOC, AK, and NO₃^--N were key factors in shaping the AOA and AOB communities. In total, both of the composition and diversity of soil AOA and AOB community varied significantly along the increase of altitude in the dry-hot valleys in Panzhihua City, and closely related with SOC, AK, and NO₃^--N. The results provide a theoretical basis for revealing the altitude distribution pattern of nitrogen cycling related microorganisms in red soil in dry- hot valley.

Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 108 copies g−1 dry sludge) were higher than those of AOA (averaged: 3.4 × 107 copies g−1 dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.

Microbial abundance and community composition in biofilms on in-pipe sensors in a drinking water distribution system

Collecting biofilm samples from drinking water distribution systems (DWDSs) is challenging due to limited access to the pipes during regular operations. We report here the analysis of microbial communities in biofilm and water samples collected from sensors installed in a DWDS where monochloramine is used as a residual disinfectant. A total of 52 biofilm samples and 14 bulk water samples were collected from 17 pipe sections representing different water ages. Prokaryotic genome copies (bacterial and archaeal 16S rRNA genes, Mycobacterium spp., ammonia-oxidizing bacteria (AOB), and cyanobacteria) were quantified with droplet digital PCR, which revealed the abundance of these genes in both biofilm and water samples. Prokaryotic 16S rRNA gene sequencing analysis was carried out for a subset of the samples (12 samples from four sites). Mycobacterium and AOB species were dominant in the DWDS sections with low water age and sufficient residual monochloramine, whereas Nitrospira species (nitrite-oxidizing bacteria) dominated in the sections with higher water age and depleted monochloramine level, suggesting the occurrence of nitrification in the studied DWDS. The present study provides novel information on the abundance and identity of prokaryotes in biofilms and water in a full-scale operational DWDS.

Impact of dissolved oxygen and loading rate on NH3 oxidation and N2 production mechanisms in activated sludge treatment of sewage

SummaryMicroaerobic activated sludge (MAS) is a one‐stage process operated at 0.5–1.0 mg l−1 dissolved oxygen (DO) aiming at simultaneous nitrification and denitrification. We used molecular techniques and a comprehensive nitrogen (N)‐transformation activity test to investigate the dominant NH3‐oxidizing and N2‐producing mechanism as well as the dominant ammonia‐oxidizing bacteria (AOB) species in sludge samples individually collected from an MAS system and a conventional anoxic/oxic (A/O) system; both systems were operated at a normal loading rate (i.e. 1.0 kg chemical oxygen demand (COD) m−3 day−1 and 0.1 kg NH4 +‐N m−3 day−1) in our previous studies. The DO levels in both systems (aerobic: conventional A/O system; microaerobic: MAS system) did not affect the dominant NH3‐oxidizing mechanism or the dominant AOB species. This study further demonstrated the feasibility of a higher loading rate (i.e. 2.30 kg COD m−3 day−1 and 0.34 kg NH4 +‐N m−3 day−1) with the MAS process during sewage treatment, which achieved a 40% reduction in aeration energy consumption than that obtained in the conventional A/O system. The increase in loading rates in the MAS system did not affect the dominant NH3‐oxidizing mechanism but did impact the dominant AOB species. Besides, N2 was predominantly produced by microaerobic denitrification in the MAS system at the two loading rates.

Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary

PurposeThe abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.ResultThe results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.ConclusionsThe results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.

Review of ammonia-oxidizing bacteria and archaea in freshwater ponds

Aquaculture ponds are simple and unique ecosystems, which are affected intensively by human activities. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in pond water and sediments, as well as the possible ecological mechanisms involved. Moreover, we discuss the possibility of increasing the activity of ammonia-oxidizing organisms in order to improve the water quality in aquaculture ponds. Compared with eutrophic lakes, the significantly higher ammonia concentration in pond water does not lead to significantly higher AOB levels, and the abundance of AOA is too low to quantify accurately. Similar to eutrophic lakes, high abundances of AOA and AOB are present in the surface sediments at the same time, where the oxidation of ammonia is performed mainly by AOB. AOB and AOA exhibit significant seasonal variations in aquaculture ponds, which are affected by the temperature, pH, and dissolved oxygen. The dominant AOB species are Nitrosomonas and the Nitrosospira lineage in pond environments. Nitrososphaera or members of the Nitrososphaera-like cluster dominate the AOA species in surface sediments, whereas the Nitrosopumilus cluster dominates the deeper sediments. AOB and AOA can be enriched on artificial substrates suspended in the pond water, thereby potentially improving the water quality.

Evaluation of Ammonia Oxidizing Bacterial Community Structure of a Municipal Activated Sludge Plant by 454 High-Throughput Pyrosequencing

The ammonia oxidizing bacteria (AOB) community structure in a municipal wastewater treatment plant (WWTP) was monitored over the winter and summer periods. The AOB distribution in the full-scale WWTP was investigated using barcoded 454-pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. Using the quantitative polymerase chain reaction (qPCR) technique, the AOB population was quantified over 237 days. The plant operational parameters and its nitrification performance were also monitored. As revealed by pyrosequencing, majority of the identified AOB during the study were related to uncultured ammonia oxidizing bacteria, and Nitrosomonas oligotropha. Furthermore, it revealed higher AOB abundance during the summer which was 6 times more compared to winter. Substantial percentages of the reads from both seasons could not be assigned to any phylum, which suggests that vast population of novel, ecologically significant AOB species still inhabit the complex activated sludge communities unexploited. A significant seasonal variation in temperature (α = 0.05; P = < 0.0001) was recorded in the reactor with maximum temperature amplitude of 10.2 °C. The average nitrification rate recorded during the summer was 0.09 ± 0.03 g N-NH4+/g MLSS/d, whereas it was 0.04 ± 0.02 g N-NH4+/g MLSS/d during the winter. The nitrification rate of the plant had significant correlation with AOB population abundance (r = 0.70; P = 0.01) and temperature (α = 0.05; P = 0.0018). This study indicates that AOB diversity and population abundance were contributory factors to efficient nitrification in activated sludge system.

Nitrogen, season, and tillage management influence ammonia oxidizing bacterial communities in long-term maize

Nitrification is the biological oxidation of NH3 to NO2− and NO3− for which ammonia-oxidizing bacteria (AOB) are the functionally dominant group in cropland responsible for the rate-limiting step of NH3 oxidation. Different AOB species have functional differentiation and do not equally contribute to nitrification. This investigation explored if long-term N fertilization and tillage influenced AOB community structure. The study site was a long-term (>40 years) continuous maize (Zea mays L.) experiment with three N fertilization rates (0, 168, and 336 kg ha−1) and either no-tillage (NT) or moldboard plow tillage (PT). We used denaturing gradient gel electrophoresis (DGGE) to analyze PCR-amplified bacterial ammonia monooxygenase genes and detect changes among NH3-oxidizing bacteria. Tillage, fertilization, and sample season all significantly influenced the AOB community. The AOB were more diverse in NT than PT. The AOB became more diverse with increasing N input and were more diverse in summer than winter samples. Nitrosomonas-like and Nitrosospira-like groups were identified based on gel migration patterns. Unique bands occurred in different treatments, manifesting environmental selection. The long-term field trial showed soil management consistently influenced AOB communities. Significantly, AOB diversity differed at a small scale within a relatively uniform landscape, even in the presence of long-term management practices.

Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria.

Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.