Nitrification in a biofilm at low pH values: role of in situ microenvironments and acid tolerance

Mathematical modelling and comparative analysis of treatment technologies for upgrading wastewater treatment plants: A case study of biofilm reactors in El-Gouna, Egypt

In recent years, Moving Bed Biofilm Reactors (MBBRs) have been preferred to conventional processes with suspended biomass. The main reason for this preference is that it can achieve better removal efficiencies than conventional systems with smaller footprints. However, unlocking the full potential of MBBRs in large-scale WWTPs remains challenging in real life. In this study, the performance of three different treatment technologies, Extended Aeration Activated Sludge (EAAS), Hybrid Fixed Bed Biofilm Reactor (HFBBR), and Hybrid Moving Bed Biofilm Reactor (HMBBR), was investigated over a year in a WWTP located in El-Gouna, Egypt. The COD removal efficiencies of the three systems were comparable, with the EAAS achieving 93.5%, HFBBR 94%, and HMBRR 95%. Nevertheless, the NH4 removal efficiency of the EAAS was slightly lower (97.5%) than that of the HFBBR and the HMBBR, that achieved a removal efficiency of 98%. BioWin Software was able to mimic the real case of the WWTP of El-Gouna and critically defined all plant limitations and operational data. Different simulations were modeled to test the hydraulic and organic loading capacities of the three systems under different scenarios and operating conditions. The HMBBR system failed to withstand the increase in organic load because of the biomass sloughing effect and subsequently high TSS loads in the settlers. Biomass sloughing overloaded the settlers and lead to biomass loss in the effluent. As the settleability of the HMBBR sludge was significantly lower than for the HFBBR the TSS loss in the effluent happened that much earlier that the moving carrier application had an adverse effect contradicting with the primary purpose of adding media carriers. Model simulations and data analysis findings were used to recommend the most suitable configuration for upgrading an existing system using the attached growth technique with all kinetic parameters and operational conditions. The recommended configuration focuses mainly on the separation of plastic media in a compartment with a very low hydraulic retention time to absorb the incoming shock load.

Adaptation of anammox process for nitrogen removal from acidic nitritation effluent in a low pH moving bed biofilm reactor

Acidic partial nitritation (PN) has emerged to be a promisingly stable process in wastewater treatment, which can simultaneously achieve nitrite accumulation and about half of ammonium reduction. However, directly applying anaerobic ammonium oxidation (anammox) process to treat the acidic PN effluent (pH 4-5) is susceptible to the inhibition of anammox bacteria. Here, this study demonstrated the adaptation of anammox process to acidic pH in a moving bed biofilm reactor (MBBR). By feeding the laboratory-scale MBBR with acidic PN effluent (pH = 4.6 ± 0.2), the pH of an anammox reactor was self-sustained in the range of pH 5 - 6. Yet, a high total nitrogen removal efficiency of over 80% at a practical loading rate of up to 149.7 ± 3.9 mg N/L/d was achieved. Comprehensive microbial assessment, including amplicon sequencing, metagenomics, cryosection-FISH, and qPCR, identified that Candidatus Brocadia, close to known neutrophilic members, was the dominant anammox bacteria. Anammox bacteria were found present in the inner layer of thick biofilms but barely present in the surface layer of thick biofilms and in thin biofilms. Results from batch tests also showed that the activity of anammox biofilms could be maintained when subjected to pH 5 at a nitrite concentration of 10 mg N/L, whereas the activity was completely inhibited after disturbing the biofilm structure. These results collectively indicate that the anammox bacteria enriched in the present acidic MBBR could not be inherently acid-tolerant. Instead, the achieved stable anammox performance under the acidic condition is likely due to biofilm stratification and protection. This result highlights the biofilm configuration as a useful solution to address nitrogen removal from acidic PN effluent, and also suggests that biofilm may play a critical role in protecting anammox bacteria found in many acidic nature environments.

Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations

Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.

Reactive and microbial inhibitory mechanisms depicting the panoramic view of pH stress effect on common biological nitrification

pH is a crucial factor of microbial nitrification, which often combines with high-strength ammonium to influence nitrogen removal pathway in wastewater treatment. However, the detailed inhibitory mechanisms of pH stress are not sufficiently disclosed yet. In this study, the pH stress effect on nitrification was comprehensively studied by a set of experiments which identified the reactivity of nitrification processes and activity of nitrifiers, the time dependence of inhibition effect and the hybrid pH stress effect with ammonium. The results revealed two distinct inhibitory mechanisms dominating in alkaline and acid ranges. In alkaline range (pH > 8), pH stress causes physiological damages on microorganisms which is named as microbial inhibition. It has the features of less recoverability of nitrifiers, time-dependent inhibition effect and low pH-tolerance of nitrite oxidation bacteria. Free ammonia enhanced microbial inhibition and greatly promoted nitrite accumulation. A novel reactive inhibition mechanism dominated in acid range (pH < 7) was disclosed. It only impedes ammonia oxidation process (AOP) but not impair microbial activity obviously and the effect is time-independent. The mechanism was clarified from H⁺ transport because AOP involved H⁺ production. The H⁺ transport was impeded under acid stress owing to the decrease of pH gradient across cell membrane. The two mechanisms formed a panoramic view of pH stress effect on nitrification advancing the understanding of nitrifier adaptability and nitritation regulation in wastewater treatment processes.

Suitability of lectin binding studies for the characterization of redox-active microbial environmental biofilms

Aquatic environmental microbial biofilms grow in a broad range of redox environments from oxic to methanogenic, and they often also establish internal redox gradients. In technical applications, biofilms are also subjected to controlled redox conditions. Studies on biofilms often make use of fluorescence microscopic imaging techniques together with lectin binding analysis to gain insights into structure, composition, and functions of the biofilms. Here we studied the direct influence of redox potentials on fluorescence lectin binding analyses (FLBA) for two commonly used lectin-fluorophore conjugates. An effect of the electrical potential on signal intensity was observed and found to be statistically significant. The signal intensity changes however, remained within the range of a few percent total. A significant drop in intensity was only observed for extremely oxidizing potentials, typically not found under environmental conditions. Our results showed that the fluorophore itself and not the lectin binding to the respective glycoconjugate causes fluorescence changes. The two tested lectin-fluorophores are shown to be suitable for studying the distribution and composition of EPS in environmental biofilms or technical applications and under varying redox conditions.

Determining Factors for Nitrite Accumulation in an Acidic Nitrifying System: Influent Ammonium Concentration, Operational pH, and Ammonia-Oxidizing Community

Acidic nitrification is attracting wide attention because it can enable robust suppression of nitrite-oxidizing bacteria (NOB) in wastewater treatment. This study reports a comprehensive assessment of the novel acidic nitrification process to identify the key factors that govern stable nitrite accumulation. A laboratory-scale moving-bed biofilm reactor receiving low-alkalinity wastewater was continuously operated under acidic conditions (pH < 6) for around two years, including nine stages varying influent and operational conditions. The results revealed that nitrite accumulation was related to three factors, i.e., influent ammonium concentration, operating pH, and ammonia-oxidizing microbial community. These three factors impact nitrite accumulation by altering the in situ concentration of free nitrous acid (FNA), which is a potent inhibitor of NOB. The critical FNA concentration is approximately one part per million (ppm, ∼1 mg HNO₂-N/L), above which nitrite accumulation is stably maintained in an acidic nitrifying system. The findings of this study suggest that stable nitrite accumulation via acidic ammonia oxidation can be maintained under a range of influent and operational conditions, as long as a ppm-level of FNA is established. Taking low-strength mainstream wastewater (40-50 mg NH₄⁺-N/L) with limited alkalinity as an example, stable nitrite accumulation was experimentally demonstrated at a pH of 4.35, under which an in situ FNA of 2.3 ± 0.6 mg HNO₂-N/L was attained. Under these conditions, Candidatus Nitrosoglobus became the only ammonia oxidizer detectable by 16S rRNA gene sequencing. The results of this study deepen our understanding of acidic nitrifying systems, informing further development of novel wastewater treatment technologies.

Effective leachate treatment by a pilot-scale submerged electro-membrane bioreactor

Most landfill leachates contain organic compounds that cannot be easily separated by conventional biological processes. Recently, integration of membrane bioreactors and electro-oxidation has been proposed as a suitable option for the treatment and separation of organic and inorganic contaminants in leachate. Therefore, in the present study, the performance of submerged electro-membrane bioreactor (SEMBR) along with a conventional membrane bioreactor (MBR) on a pilot scale was evaluated for the treatment of leachate. Both bioreactors were used to compare treatment efficiency under the same conditions. The removal rates of chemical oxygen demand (COD), ammonia nitrogen (NH₄⁺-N), phosphate (PO₄^3--P), color, UV₂₅₄, and metals were investigated. The results showed that applying electric current to the MBR could approximately increase the COD removal efficiency from 94 to 98.5%; PO₄^3--P removal from 70 to 99%; NH₃⁺-N removal from 91 to 99%; UV₂₅₄ removal from 80 to 96%; and heavy metals removal from 40 to 95%. Humic acid removal efficiency as another indicator of humic substances was increased from 75% in the MBR to 96% in the SEMBR process. The results also showed that the effluent can be introduced into the wastewater treatment plant for further treatment. The SEMBR process achieved a minimization of fouling of membranes compared to conventional MBR. The consumption of the energy and electrode was in accordance with the previous results, and the required energy of 1.57 kWh/m³ of wastewater was calculated. The sludge volume index (SVI) in SEMBR (105 ml/g) was better than MBR (135 ml/g) due to the electrokinetic effect on the production of denser flocs. Based on the results, it can be concluded that the application of electric current can improve the performance of MBR in removing PO₄^3-, NH₄⁺, and membrane fouling.

Phosphorus solubility and dynamics in a tropical soil under sources derived from wastewater and sewage sludge

Conventional phosphate fertilizers are usually highly water-soluble and rapidly solubilize when moistened by the soil solution. However, if this solubilization is not in alignment with plants demand, P can react with the soil colloidal phase, becoming less available over time. This is more pronounced in acidic, oxidic tropical soils, with high P adsorption capacity, reducing the efficiency of P fertilization. Furthermore, these fertilizers are derived from phosphate rock, a non-renewable resource, generating an environmental impact. To assess these concerns, waste-recycled P sources (struvite, hazenite and AshDec®) were studied for their potential of reducing P fixation by the soil and improving the agronomic efficiency of the P fertilization. In our work, we compared the solubilization dynamics of struvite, hazenite, AshDec® to triple superphosphate (TSP) in a sandy clay loam Ferralsol, as well as their effect on solution pH and on soil P pools (labile, moderately-labile and non-labile) via an incubation experiment. Leaching columns containing 50 g of soil with surface application of 100 mg per column (mg col^-1) of P from each selected fertilizer and one control (nil-P) were evaluated for 60 days. Daily leachate samples from the column were analyzed for P content and pH. Soil was stratified in the end and submitted to P fractionation. All results were analyzed considering p < 0.05. Our findings showed that TSP and struvite promoted an acid P release reaction (reaching pHs of 4.3 and 5.5 respectively), while AshDec® and hazenite reaction was alkaline (reaching pHs of 8.4 and 8.5 respectively). Furthermore, TSP promoted the highest P release among all sources in 60 days (52.8 mg col^-1) and showed rapid release dynamic in the beginning, while struvite and hazenite showed late release dynamics and lower total leached P (29.7 and 15.5 mg col^-1 P respectively). In contrast, no P-release was detected in the leachate of the AshDec® over the whole trial period. Struvite promoted the highest soil labile P concentration (7938 mg kg^-1), followed by hazenite (5877 mg kg^-1) and AshDec® (4468 mg kg^-1), all higher than TSP (3821 mg kg^-1), while AshDec® showed high moderately-labile P (9214 mg kg^-1), reaffirming its delayed release potential.

How does temperature trigger biofilm adhesion and growth in Candida albicans and two non-Candida albicans Candida species?

BACKGROUND

Biofilm formation on biotic and abiotic surfaces is finely regulated by genetic factors but also by oxygen concentration, pH, temperature and other environmental factors, already extensively explored for bacterial biofilms. Much less is known about fungal biofilm, that is considered a virulence factor for Candida pathogenic species among the few fungal species able to grow and survive at high temperatures such as 37°C as well as those induced by fever. The resistance to high temperatures coupled with the ability to form biofilm are threatening factors of these fungal species that could severely impact at an epidemiological level.

OBJECTIVES

In this framework, we decided to study the thermal tolerance of biofilms formed by three medical relevant species such as Candida albicans and two non-Candida albicans Candida species.

METHODS

Thirty nosocomial strains were investigated for their ability to adhere and grow in proximity and over body temperature (from 31 to 43°C), mimicking different environmental conditions or severe febrile-like reactions.

RESULTS

Candida sessile cells reacted to different temperatures showing a strain-specific response. It was observed that the attachment and growth respond differently to the temperature and that mechanism of adhesion has different outputs at high temperature than the growth.

CONCLUSIONS

This strain-dependent response is probably instrumental to guarantee the best success to cells for the infection, attachment and growth to occur. These observations reinforce the concept of temperature as a major trigger in the evolution of these species especially in this period of increasing environmental temperatures and excessive domestic heating.

Efficient Nitrification and Low-Level N2O Emission in a Weakly Acidic Bioreactor at Low Dissolved-Oxygen Levels Are Due to Comammox

Nitrification is an essential process for nutrient removal from wastewater and an important emission source of nitrous oxide (N2O), which is a powerful greenhouse gas and a dominant ozone-depleting substance. In this study, nitrification and N2O emissions were tested in two weakly acidic (pH 6.3 to 6.8) reactors: one with dissolved oxygen (DO) at over 2.0 mg/liter and the other with DO at approximately 0.5 mg/liter. Efficient nitrification was achieved in both reactors. Compared to that in the high-DO reactor, N2O emission in the low-DO reactor decreased slightly, by 20%, and had insignificant correlation with the fluctuations of DO (P = 0.935) and nitrite (P = 0.713), indicating that N2O might not be produced mainly via nitrifier denitrification. Based on quantitative PCR (qPCR), quantitative fluorescent in situ hybridization (qFISH), and functional gene amplicon and metagenome sequencing, it was found that complete ammonia oxidizers (comammox), i.e., Nitrospira organisms, significantly outnumbered canonical ammonia-oxidizing bacteria (AOB) in both weakly acidic reactors, especially in the low-DO reactor with the comammox/AOB amoA gene ratio increasing from 6.6 to 17.1. Therefore, it was speculated that the enriched comammox was the primary cause for the slightly decreased N2O emission under long-term low DO in the weakly acidic reactor. This study demonstrated that the comammox Nitrospira can survive well under the weakly acidic and low-DO conditions, implying that achieving efficient nitrification with low N2O emission as well as low energy and alkalinity consumption is feasible for wastewater treatment.IMPORTANCE Nitrification in wastewater treatment is an important process for eutrophication control and an emission source for the greenhouse gas N2O. The nitrifying process is usually operated at a slightly alkaline pH and high DO (>2 mg/liter) to ensure efficient nitrification. However, it consumes a large amount of energy and chemicals, especially for wastewater without sufficient alkalinity. This paper demonstrates that comammox can adapt well to the weakly acidic and low-DO bioreactors, with a result of efficient nitrification and low N2O emission. These findings indicate that comammox organisms are significant for sustainable wastewater treatment, which provides an opportunity to achieve efficient nitrification with low N2O production as well as low energy and chemical consumption simultaneously.

Efficient nitrification and low N2O emission in a weakly acidic bioreactor at low dissolved oxygen levels are due to comammox

Nitrification is an essential process for nutrient removal from wastewater and an important emission source of nitrous-oxide (N₂O), which is a powerful greenhouse gas and a dominant ozone-depleting substance. In this study, nitrification and N₂O emissions were tested in two weakly acidic (pH = 6.3-6.8) reactors: one with dissolved oxygen (DO) over 2.0 mg/L and the other with DO approximately 0.5 mg/L. Efficient nitrification was achieved in both reactors. Compared to the high-DO reactor, N₂O emission in the low-DO reactor decreased slightly by 20% and had insignificant correlation with the fluctuations of DO (P = 0.935) and nitrite (P = 0.713), indicating that N₂O might not be mainly produced via nitrifier denitrification. Based on qPCR, qFISH, functional gene amplicon and metagenome sequencing, it was found that complete ammonia oxidizer (comammox) Nitrospira significantly outnumbered canonical ammonia-oxidizing bacteria (AOB) in both weakly acidic reactors, especially in the low DO reactor with the comammox/AOB amoA gene ratio increasing from 6.6 to 17.1. Therefore, it was speculated that the enriched comammox was the primary cause for the slightly decreased N₂O emission under long-term low DO in weakly acidic reactor. This study demonstrated that comammox Nitrospira can survive well under the weakly acidic and low-DO conditions, implying that achieving efficient nitrification with low N₂O emission as well as low energy and alkalinity consumption is feasible for wastewater treatment.ImportanceNitrification in wastewater treatment is an important process for eutrophication control and an emission source for greenhouse gas of N₂O. The nitrifying process is usually operated at a slightly alkaline pH and high DO (>2 mg/L) to ensure efficient nitrification. However, it consumes a large amount of energy and chemicals especially for wastewater without sufficient alkalinity. This manuscript demonstrated that comammox can adapt well to the weakly acidic and low-DO bioreactors, with a result of efficient nitrification and low N₂O emission. These findings indicate that comammox are significant for sustainable wastewater treatment, which provides an opportunity to achieve efficient nitrification with low N₂O production as well as low energy and chemical consumption simultaneously.

Hydroxylamine and the nitrogen cycle: A review

Aerobic ammonium oxidizing bacteria were first isolated more than 100 years ago and hydroxylamine is known to be an intermediate. The enzymatic steps involving hydroxylamine conversion to nitrite are still under discussion. For a long time it was assumed that hydroxylamine was directly converted to nitrite by a hydroxylamine oxidoreductase. Recent enzymatic evidences suggest that the actual product of hydroxylamine conversion is NO and a third, yet unknown, enzyme further converts NO to nitrite. More recently, ammonium oxidizing archaea and complete ammonium oxidizing bacteria were isolated and identified. Still the central nitrogen metabolism of these microorganisms presents to researchers the same puzzle: how hydroxylamine is transformed to nitrite. Nitrogen losses in the form of NO and N₂O have been identified in all three types of aerobic ammonium oxidizing microorganisms and hydroxylamine is known to play a significant role in the formation. Yet, the pathways and the factors promoting the greenhouse gas emissions are to be fully characterized. Hydroxylamine also plays a yet poorly understood role on anaerobic ammonium oxidizing bacteria and is known to inhibit nitrite oxidizing bacteria. In this review, the role of this elusive intermediate in the metabolism of different key players of the nitrogen cycle is discussed, as well as the putative importance of hydroxylamine as a key nitrogen metabolite for microbial interactions within microbial communities and engineered systems. Overall, for the first time putting together the acquired knowledge about hydroxylamine and the nitrogen cycle over the years in a review, setting potential hypothesis and highlighting possible next steps for research.

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient

In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 μM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 μM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 μM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%– 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O₂, NO₃^-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane–a potent greenhouse gas.

Achieving Stable Partial Nitritation in an Acidic Nitrifying Bioreactor

Partial nitritation providing a suitable effluent for subsequent anammox is a critical step in a two-stage autotrophic nitrogen removal system. This study demonstrates an innovative approach for attaining partial nitritation in an acidic bioreactor operating at a slightly low pH (i.e., 5-6). This approach is based on our hypothesis in this study that acid-tolerant ammonia-oxidizing bacteria (AOB) can produce nitrite and protons to self-sustain free nitrous acid (FNA, NO₂^- + H⁺ ↔ HNO₂) at a parts per million level, as an inhibitor of nitrite-oxidizing bacteria (NOB). With influent nitrogen of about 200 mg/L and operating conditions of high dissolved oxygen, long sludge retention time, and moderate temperature, a lab-scale acidic bioreactor with FNA up to 2 mg of HNO₂-N/L successfully established stable nitrite accumulation in the effluent for 200 days, with an average ratio [NO₂^-/(NO₂^- + NO₃^-)] exceeding 95%. A 16S rRNA amplicon sequencing analysis showed that Nitrosospira was the dominant AOB in the biomass of the bioreactor, while Nitrosomonas and Nitrospira, two typical nitrifying genera in neutral wastewater treatment, both disappeared after the startup of partial nitritation. Kinetic characterization revealed that Nitrosospira had a substrate affinity of 11.4-16.5 mg of total ammonia (NH₄⁺ + NH₃)/L. It also revealed that less than 3.5 mg of HNO₂-N/L FNA did not inhibit AOB activity significantly. Acidic operation is economically attractive because it can be achieved via acidophilic ammonia oxidation without adding chemical acid. However, hazardous gas, nitric oxide (NO), should be removed from gas produced by acidic nitrifying bioreactors.

Removal characteristics of a composite active medium for remediation of nitrogen-contaminated groundwater and metagenomic analysis of degrading bacteria

To investigate the removal characteristics of ammonium-nitrogen (NH₄⁺-N), nitrite-nitrogen (NO₂^--N), nitrate-nitrogen (NO₃^--N), and total nitrogen from groundwater by a degradable composite active medium, kinetics, thermodynamics, and equilibrium adsorption, experiments were performed using scoria and degrading bacteria immobilized on scoria. Removal of NH₄⁺-N, NO₂^--N, and NO₃^--N was conducted in adsorption experiments using different times, initial concentrations, pH values, and groundwater chemical compositions (Ca²⁺, Mg²⁺, HCO₃^-, CO₃^2-, Fe²⁺, Mn²⁺, and SO₄^2-). The results showed that the removal of nitrogen by the composite active medium was obviously better than that of scoria alone. The removal rates of NH₄⁺-N (C₀ = 5 mg/L), NO₂^--N (C₀ = 5 mg/L), and NO₃^--N (C₀ = 100 mg/L) by the composite active medium within 1 h were 96.05%, 82.40%, and 83.16%, respectively. The adsorption kinetics were well fitted to a pseudo-second order model, whereas the equilibrium adsorption agreed with the Freundlich model. With changes in the pH, variation in the removal could be attributed to the combined effect of hydrolysis and competitive ion adsorption, and the optimum pH was 7. Different concentration conditions, hardness, alkalinity, anions, and cations showed different promoting and inhibiting effects on the removal of nitrogen. A careful examination of ionic concentrations in adsorption batch experiments suggested that the sorption behavior of nitrogen onto the immobilized medium was mainly controlled by ion exchange. The degrading bacteria on the scoria surface were eluted and analyzed by metagenomic sequencing. There were significant differences in the number of operational taxons, relative abundances, and community diversity among degrading bacteria after adsorption of the three forms of nitrogen. The relative abundance of degrading bacteria was highest after NO₃^--N removal, and the diversity was highest after NO₂^--N removal. Pseudomonas and Serratia were the dominant genera that could efficiently remove NH₄⁺-N and NO₂^--N.

Nitrous oxide emissions from China's croplands based on regional and crop-specific emission factors deviate from IPCC 2006 estimates

Calculated N₂O emission factors (EFs) of applied nitrogen (N) fertilizer are currently based upon a single, universal value advocated by the IPCC (Inter-governmental Panel on Climate Change) even though EFs are thought to vary with climate and soil types. Here, we compiled and analyzed 151 N₂O EF values from agricultural fields across China. The EF of synthetic N applied to these croplands was 0.60%, on average, but differed significantly among six climatic zones across the country, with the highest EF found in the north subtropical zone for upland fields (0.93%) and the lowest in the middle subtropical zone for paddy fields (0.20%). Precipitation and soil pH, which showed non-linear relationships with EF, are among the factors governing it, explaining 7.0% and 8.0% of the regional variation in EFs, respectively. Annual precipitation was the key factor regulating N₂O emissions from synthetic N fertilizers. Among crop types, legume crops had the highest EFs, which were significantly (P < 0.05) higher than those of cereals. Total soil N₂O emissions from fertilized croplands with maize, rice, wheat, and vegetables in China, calculated using the climatic zone (regional) EFs, were estimated to be 239 Gg N yr^-1 with an uncertainty of 21%. Importantly, this value was substantially (33%) lower than that (357 Gg N yr^-1) derived from the IPCC default EF but close to the 253 Gg N yr^-1 estimated using crop-specific EFs. N₂O emissions from applied synthetic N fertilizer accounted for 66.5% of the total annual N₂O emissions from China's maize, rice, wheat and vegetable fields. Taken together, our study's results strongly suggest that regional EFs should be included for accurate N₂O inventories from croplands across China.

Low Temperature and Neutral pH Define "Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii

Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and nitrite. Besides Nitrospira, "Candidatus Nitrotoga" has been identified as a key nitrite-oxidizing bacterium (NOB) performing the second step of nitrification, nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species.IMPORTANCE "Ca. Nitrotoga" is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.

Self-Sustained Nitrite Accumulation at Low pH Greatly Enhances Volatile Solids Destruction and Nitrogen Removal in Aerobic Sludge Digestion

Aerobic sludge digestion of waste activated sludge (WAS) is widely used as a stabilization option in small- and midsized wastewater treatment plants. However, the digestion process is often limited by low volatile solids (VS) destruction and poor pathogen removal efficiency. This study presents a novel operational strategy that achieves enhanced VS destruction and nitrogen removal by inducing sustained nitrite accumulation via a single spike of nitrite to aerobic digester operated at a natively low pH (<5.5). The strategy was demonstrated through the use of three laboratory aerobic sludge digesters, each continuously operated for over 300 days. Compared to control reactors, the strategy enhanced volatile solids destruction by 35.0-38.4%, nitrogen removal by 58.5-70.8%, and pathogen reduction by approximately 1 log. The standard oxygen uptake rate (SOUR) was reduced to 0.49 ± 0.03 mgO₂/gVS/h, compared to 0.85 ± 0.01-1.68 ± 0.02 mgO₂/gVS/h in the control, indicating enhanced stabilization. Free nitrous acid formed from nitrite at low pH, rather than nitrite itself, was identified to be the cause of improved digestion performance. Since the nitrite production is self-supporting, no additional ongoing costs are incurred.

Aquaponic Systems for Sustainable Resource Recovery: Linking Nitrogen Transformations to Microbial Communities

Aquaponics is a technology for food production (fish and vegetables/fruits) with concomitant remediation of nitrogen-rich aquaculture effluent. There is, however, a critical need to improve the nitrogen use efficiency (NUE) in aquaponics. Here, we employed quantitative polymerase chain reactions and next-generation sequencing to evaluate the bacterial communities and their links to nitrogen transformations for improving NUEs in four bench-scale plant-based floating-raft aquaponics (pak choi, lettuce, chive, and tomato) and three pH levels (7.0, 6.0, and 5.2). Low relative abundance of nitrifiers in plant roots and biofilters suggested nitrogen loss, which decreased NUE in aquaponics. Low pH level was a major factor that shifted the microbial communities and reduced the relative abundance of nitrifiers in aquaponic systems, leading to total ammonia nitrogen accumulation in recirculating water. In plant roots, the abundance of nitrite-oxidizing bacteria (e.g., Nitrospira spp.) did not decrease at low pH levels, suggesting the benefit of growing plants in aquaponics for efficient nitrification and improving NUE. These findings on microbial communities and nitrogen transformations provided complementary strategies to improve the performance of the aquaponics regarding water quality and extent of nutrient recovery from aquaculture effluent.

Alkalinity and external carbon requirements for denitrification-nitrification of coke wastewater

The Industrial Emissions Directive requires that coke wastewater is treated to reach an effluent with < 50 mg/L total nitrogen (TN). A shortage of alkalinity (3.6 mg as CaCO₃/mg [Formula: see text]) in the wastewater limited nitrification to 45%. Various compounds were tested as a source of additional alkalinity, with optimal results being found for sodium carbonate, which enabled 95% nitrification at 300 mg/L (as CaCO₃). Sodium bicarbonate led to incomplete ammonia oxidation (76%) whilst soda ash prevented nitrite oxidation. Addition of sodium hydroxide enabled 98% nitrification but was associated with [Formula: see text] accumulation. Ammonia and nitrite oxidation had optimal pH ranges of 7.0-8.3 and 5.5-6.8, respectively. As organic carbon concentrations in coke wastewater are at times insufficient for effective denitrification external organic carbon was also considered to enhance denitrification. A laboratory-scale anoxic-aerobic activated sludge process was used to investigate glycerol and acetic acid as carbon sources. Glycerol was associated with a low biomass production (0.18 mg of biomass produced per 1 mg of glycerol) and mixed liquor suspended solids (MLSS) declined from 2235 to 750 mg/L leading to incomplete nitrification (< 30%) and an effluent TN of 59 mg/L. Acetic acid had a higher biomass production (0.31 mg of biomass produced per 1 mg of acetic acid) maintaining stable MLSS concentrations (3137 mg/L). Overall, a denitrification-nitrification process with alkalinity (Na₂CO₃ at 300 mg/L) and acetic acid dosing enabled an effluent TN of 24 mg/L.

Effect of temperature on N2O emissions from a highly enriched nitrifying granular sludge performing partial nitritation of a low-strength wastewater

In the race to achieve a sustainable urban wastewater treatment plant, not only the energy requirements have to be considered but also the environmental impact of the facility. Thus, nitrous oxide (N₂O) emissions are a key-factor to pay attention to, since they can dominate the total greenhouse gases emissions from biological wastewater treatment. In this study, N₂O production factors were calculated during the operation of a granular sludge airlift reactor performing partial nitritation treating a low-strength synthetic influent, and furthermore, the effect of temperature on N₂O production was assessed. Average gas emission relative to conversion of ammonium was 1.5 ± 0.3% and 3.7 ± 0.5% while the effluent contained 0.5 ± 0.1% and 0.7 ± 0.1% (% N-oxidized) at 10 and 20 °C, respectively. Hence, temperature increase resulted in higher N₂O production. The reasons why high temperature favoured N₂O production remained unclear, but different theoretical hypotheses were suggested.

Growth of Nitrosococcus-Related Ammonia Oxidizing Bacteria Coincides with Extremely Low pH Values in Wastewater with High Ammonia Content

Ammonia oxidation decreases the pH in wastewaters where alkalinity is limited relative to total ammonia. The activity of ammonia oxidizing bacteria (AOB), however, typically decreases with pH and often ceases completely in slightly acidic wastewaters. Nevertheless, nitrification at low pH has been reported in reactors treating human urine, but it has been unclear which organisms are involved. In this study, we followed the population dynamics of ammonia oxidizing organisms and reactor performance in synthetic fully hydrolyzed urine as the pH decreased over time in response to a decrease in the loading rate. Populations of the β-proteobacterial Nitrosomonas europaea lineage were abundant at the initial pH close to 6, but the growth of a possibly novel Nitrosococcus-related AOB genus decreased the pH to the new level of 2.2, challenging the perception that nitrification is inhibited entirely at low pH values, or governed exclusively by β-proteobacterial AOB or archaea. With the pH shift, nitrite oxidizing bacteria were not further detected, but nitrous acid (HNO₂) was still removed through chemical decomposition to nitric oxide (NO) and nitrate. The growth of acid-tolerant γ-proteobacterial AOB should be prevented, by keeping the pH above 5.4, which is a typical pH limit for the N. europaea lineage. Otherwise, the microbial community responsible for high-rate nitrification can be lost, and strong emissions of hazardous volatile nitrogen compounds such as NO are likely.

Enrichment and characterization of acid-tolerant nitrifying sludge

Nitrification is an acidifying process that requires the addition of external alkalinity because of the alkaliphilic nature of the most ammonia-oxidizing bacteria. In this study, aerobic activated sludge was used as inoculum in an internal loop air-lift reactor, which resulted in successful enrichment of acid-tolerant nitrifying (ACIN) sludge at pH 6.0 by sequential addition of tea orchard soil suspension. The results showed that ACIN sludge had a remarkable acid tolerant capability with a volumetric ammonia conversion rate of 1.13 kg N m^-3 day^-1. ACIN sludge showed a higher maximum specific ammonia conversion rate (0.29 g N g^-1 VSS day^-1) than neutrophilic nitrifying sludge (0.14 g N g^-1 VSS day^-1) at pH 6.0 and had good resistance against pH fluctuations, with a maximum specific ammonia conversion rate (0.584 g N g^-1 VSS day^-1) at pH 7.5. Microbial community analysis indicated that the higher abundance of acid tolerant Nitrosospira and ammonia-oxidizing archaea laid a solid foundation for the remarkable acid-tolerant capability of ACIN sludge.

Effects of the residual ammonium concentration on NOB repression during partial nitritation with granular sludge

Partial nitritation was stably achieved in a bench-scale airlift reactor (1.5L) containing granular sludge. Continuous operation at 20 °C treating low-strength synthetic wastewater (50 mg N-NH₄⁺/L and no COD) achieved nitrogen loading rates of 0.8 g N-NH₄⁺/(L·d) during partial nitritation. The switch between nitrite-oxidizing bacteria (NOB) repression and NOB proliferation was observed when ammonium concentrations in the reactor were below 2-5 mg N-NH₄⁺/L for DO concentrations lower than 4 mg O₂/L at 20 °C. Nitrospira spp. were detected to be the dominant NOB population during the entire reactor operation, whereas Nitrobacter spp. were found to be increasing in numbers over time. Stratification of the granule structure, with ammonia-oxidizing bacteria (AOB) occupying the outer shell, was found to be highly important in the repression of NOB in the long term. The pH gradient in the granule, containing a pH difference of ca. 0.4 between the granule surface and the granule centre, creates a decreasing gradient of ammonia towards the centre of the granule. Higher residual ammonium concentration enhances the ammonium oxidation rate of those cells located further away from the granule surface, where the competition for oxygen between AOB and NOB is more important, and it contributes to the stratification of both populations in the biofilm.

Association of running manner with bacterial community dynamics in a partial short-term nitrifying bioreactor for treatment of piggery wastewater with high ammonia content

Optimization of running parameters in a bioreactor requires detailed understanding of microbial community dynamics during the startup and running periods. Using a novel piggery wastewater treatment system termed “UASB + SHARON + ANAMMOX” constructed in our laboratory, we investigated microbial community dynamics using the Illumina MiSeq method, taking activated sludge samples at ~2-week intervals during a ~300-day period. Ammonia-oxidizing bacteria (AOB) were further investigated by quantification of AOB amoA genes and construction of gene clone libraries. Major changes in bacterial community composition and dynamics occurred when running manner was changed from continuous flow manner (CFM) to sequencing batch manner (SBM), and when effluent from an upflow anaerobic sludge blanket (UASB) reactor for practical treatment of real piggery wastewater was used as influent; differences among these three experimental groups were significant (R² = 0.94, p < 0.01). When running manner was changed from CFM to SBM, relative abundance of the genus Nitrospira decreased sharply from 18.1 % on day 116 to 1.5 % on day 130, and to undetectable level thereafter. Relative abundance of the genus Nitrosomonas increased from ~0.67 % during the CFM period to 8.0 % by day 220, and thereafter decreased to a near-constant ~1.6 %. Environmental factors such as load ammonia, effluent ammonia, effluent nitrite, UASB effluent, pH, and DO levels collectively drove bacterial community dynamics and contributed to maintenance of effluent NH₄⁺-N/NO₂⁻-N ratio ~1. Theses results might provide useful clues for the control of the startup processes and maintaining high efficiency of such bioreactors.

Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH

The functioning of recirculation aquaculture systems (RAS) is essential to maintain water quality for fish health, and one crucial process here is nitrification. The investigated RAS was connected to a rainbow trout production system and operated at an average temperature of 13°C and pH 6.8. Community analyses of the nitrifying biofilm revealed a coexistence of Nitrospira and Nitrotoga, and it is hypothesized that a slightly acidic pH in combination with lower temperatures favors the growth of the latter. Modification of the standard cultivation approach toward lower pH values of 5.7 to 6.0 resulted in the successful enrichment (99% purity) of Nitrotoga sp. strain HW29, which had a 16S rRNA sequence similarity of 99.0% to Nitrotoga arctica. Reference cultures of Nitrospira defluvii and the novel Nitrotoga sp. HW29 were used to confirm differentiation of these nitrite oxidizers in distinct ecological niches. Nitrotoga sp. HW29 revealed pH and temperature optima of 6.8 and 22°C, respectively, whereas Nitrospira defluvii displayed the highest nitrite oxidation rate at pH 7.3 and 32°C. We report here the occurrence of Nitrotoga as one of the main nitrite-oxidizing bacteria in freshwater aquaculture systems and indicate that a slightly acidic pH, in addition to temperatures below 20°C, can be applied as a selective isolation criterion for this microorganism.

Characterization of the internal ion environment of biofilms based on charge density and shape of ion

Biofilm polymers contain both electrically positively and negatively charged sites. These charged sites enable the biofilm to trap and retain ions leading to an important role of biofilm such as nutrient recycling and pollutant purification. Much work has focused on the ion-exchange capacity of biofilms, and they are known to adsorb ions through an exchange mechanism between the ions in solution and the ions adsorbed to the charged sites on the biofilm polymer. However, recent studies suggest that the adsorption/desorption behavior of ions in a biofilm cannot be explained solely by this ion exchange mechanism. To examine the possibility that a substantial amount of ions are held in the interstitial region of the biofilm polymer by an electrostatic interaction, intact biofilms formed in a natural environment were immersed in distilled water and ion desorption was investigated. All of the detected ion species were released from the biofilms over a short period of time, and very few ions were subsequently released over more time, indicating that the interstitial region of biofilm polymers is another ion reserve. The extent of ion retention in the interstitial region of biofilms for each ion can be determined largely by charge density, |Z|/r, where |Z| is the ion valence as absolute value and r is the ion radius. The higher |Z|/r value an ion has, the stronger it is retained in the interstitial region of biofilms. Ion shape is also a key determinant of ion retention. Spherical and non-spherical ions have different correlations between the condensation ratio and |Z|/r. The generality of these findings were assured by various biofilm samples. Thus, the internal regions of biofilms exchange ions dynamically with the outside environment.

Assessing the Effects of Acidification on N Dynamics in Jiyun River System of Tianjin, China

Alterations in pH have significant effects on nitrification and denitrification processes in aquatic systems. The Jiyun River in northern China experiences significant acid precipitation, and as such was selected to investigate the effects of decreasing pH (river pH at 8.2, pH at 6 and 5) on N dynamics via incubation experiments (35 and 10°C). Statistical results indicated that the NO3 (-) concentrations of the control (pH at 8.2) were either significantly lower (at 35°C) or significantly higher (at 10°C) than the treatments of pH at 6 and 5 at the alpha level of 0.05 in the incubation. However, the NO3 (-) concentrations of the two pH treatments showed significant difference during part of the reaction stage at 35°C and no difference at 10°C. Analysis indicated that nitrification and coupled nitrification-aerobic denitrification occurred for all treatments, which resulted in NO3 (-) being either accumulated or removed at the end of the incubation.

Modeling the low pH limit of Nitrosomonas eutropha in high-strength nitrogen wastewaters

In wastewater treatment, the rate of ammonia oxidation decreases with pH and stops very often slightly below a pH of 6. Free ammonia (NH3) limitation, inhibition by nitrous acid (HNO2), limitation by inorganic carbon or direct effect of high proton concentrations have been proposed to cause the rate decrease with pH as well as the cessation of ammonia oxidation. In this study, we compare an exponential pH term common for food microbiology with conventionally applied rate laws based on Monod-type kinetics for NH3 limitation and non-competitive HNO2 inhibition as well as sigmoidal pH functions to model the low pH limit of ammonia oxidizing bacteria (AOB). For this purpose we conducted well controlled batch experiments which were then simulated with a computer model. The results showed that kinetics based on NH3 limitation and HNO2 inhibition can explain the rate decrease of ammonia oxidation between pH 7 and 6, but fail in predicting the pH limit of Nitrosomonas eutropha at pH 5.4 and rates close to that limit. This is where the exponential pH term becomes important: this term decreases the rate of ammonia oxidation to zero, as the pH limit approaches. Previously proposed sigmoidal pH functions that affect large pH regions, however, led to an overestimation of the pH effect and could therefore not be applied successfully. We show that the proposed exponential pH term can be explained quantitatively with thermodynamic principles: at low pH values, the energy available from the proton motive force is too small for the NADH production in Nitrosomonas eutropha and related AOB causing an energy limited state of the bacterial cell. Hence, energy limitation and not inhibition or limitation of enzymes is responsible for the cessation of the AOB activity at low pH values.

The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB.

Ammonia oxidizers in a pilot-scale multilayer rapid infiltration system for domestic wastewater treatment

A pilot-scale multilayer rapid infiltration system (MRIS) for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD) was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material) was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacteria dominated in the MRIS. Relative abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) showed contrary tendency. In the flowing phase (water effluent), AOA diversity was significantly correlated with the concentration of dissolve oxygen (DO), NO₃-N and NH₃-N. AOB abundance was significantly correlated with the concentration of DO and chemical oxygen demand (COD). NH₃-N and COD were identified as the key factors to shape AOB community structure, while no variable significantly correlated with that of AOA. AOA might play an important role in the MRIS. This study could reveal key environmental factors affecting the community composition and abundance of ammonia oxidizers in the MRIS.

Assessment of soil nitrogen and related enzymes as influenced by the incorporation time of field pea cultivated as a catch crop in Alfisol

The effect of the time of catch crop (field pea) incorporation [catch crop incorporated in the autumn (A) or in the spring (B) versus plots without a catch crop (C)] on the soil enzymes related to N transformation (urease - UR, protease - PRO, nitrate reductase - NR, arginine ammonification rate - AAR), the total N and mineral N as well as microbial biomass N (MBN) contents were investigated in a 3-year experiment. The catch crop was sown at the beginning of August and plowed in the autumn in 2008, 2009 and 2010 or left as mulch during the winter. Soil samples for microbial activity were taken from spring barley plots that were grown in 2009, 2010 and 2011 before sowing (March), during the tillering phase (May), shooting (June) and after the harvesting of spring barley (August). The use of catch crop significantly increased the soil mineral and MBN contents as well as the activities of PRO and NR as compared to the control soil. The spring incorporation of the field pea significantly increased the MBN content in contrast to the autumn application, while the activity of N-cycle enzymes were clearly unaffected (UR and AAR) regardless of the time of the incorporation of field pea or else the results were inconsistent (PRO and NR). When the catch crop was incorporated in the spring, a significantly higher content of mineral N as compared to autumn incorporation was noted on only two of the four sampling dates. The enzymatic activity (PRO and AAR) was about 1.3-2.8 times higher in May and June as compared with March and August. Both spring or autumn incorporation of catch crop can be a useful management practice to increase the soil mineral N content and enhance the soil biological activity.

Bacteria of the candidate phylum TM7 are prevalent in acidophilic nitrifying sequencing-batch reactors

Laboratory-scale acidophilic nitrifying sequencing-batch reactors (ANSBRs) were constructed by seeding with sewage-activated sludge and cultivating with ammonium-containing acidic mineral medium (pH 4.0) with or without a trace amount of yeast extract. In every batch cycle, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate. Attempts to detect nitrifying functional genes in the fully acclimated ANSBRs by PCR with previously designed primers mostly gave negative results. 16S rRNA gene-targeted PCR and a subsequent denaturating gradient gel electrophoresis analysis revealed that a marked change occurred in the bacterial community during the overall period of operation, in which members of the candidate phylum TM7 and the class Gammaproteobacteria became predominant at the fully acclimated stage. This result was fully supported by a 16S rRNA gene clone library analysis, as the major phylogenetic groups of clones detected (>5% of the total) were TM7 (33%), Gammaproteobacteria (37%), Actinobacteria (10%), and Alphaproteobacteria (8%). Fluorescence in situ hybridization with specific probes also demonstrated the prevalence of TM7 bacteria and Gammaproteobacteria. These results suggest that previously unknown nitrifying microorganisms may play a major role in ANSBRs; however, the ecophysiological significance of the TM7 bacteria predominating in this process remains unclear.

Diversity, abundance, and spatial distribution of ammonia-oxidizing β-proteobacteria in sediments from Changjiang Estuary and its adjacent area in East China Sea

Changjiang Estuary, the largest estuary in China, encompasses a wide range of nutrient loading and trophic levels from the rivers to the sea, providing an ideal natural environment to explore relationships between functional diversity, physical/chemical complexity, and ecosystem function. In this study, molecular biological techniques were used to analyze the community structure and diversity of ammonia-oxidizing bacteria (AOB) in the sediments of Changjiang Estuary and its adjacent waters in East China Sea. The amoA gene (encoding ammonia monooxygenase subunit A) libraries analysis revealed extensive diversity within the β-Proteobacteria group of AOB, which were grouped into Nitrosospira-like and Nitrosomonas-like lineages. The majority of amoA gene sequences fell within Nitrosospira-like clade, and only a few sequences were clustered with the Nitrosomonas-like clade, indicating that Nitrosospira-like lineage may be more adaptable than Nitrosomonas-like lineage in this area. Multivariate statistical analysis indicated that the spatial distribution of the sedimentary β-Proteobacterial amoA genotype assemblages correlated significantly with nitrate, nitrite, and salinity. The vertical profile of amoA gene copies in gravity cores showed that intense sediment resuspension led to a deeper mixing layer. The horizontal distribution pattern of amoA gene copies was nearly correlated with the clayey mud belt in Changjiang Estuary and its adjacent area in East China Sea, where higher β-Proteobacteria phylogenetic diversity was observed. Meanwhile, those areas with high amoA copies in the surface sediments nearly matched those with low concentrations of dissolved oxygen and ammonium in the bottom water.

Investigation of microbial biofilm structure by laser scanning microscopy

Microbial bioaggregates and biofilms are hydrated three-dimensional structures of cells and extracellular polymeric substances (EPS). Microbial communities associated with interfaces and the samples thereof may come from natural, technical, and medical habitats. For imaging such complex microbial communities confocal laser scanning microscopy (CLSM) is the method of choice. CLSM allows flexible mounting and noninvasive three-dimensional sectioning of hydrated, living, as well as fixed samples. For this purpose a broad range of objective lenses is available having different working distance and resolution. By means of CLSM the signals detected may originate from reflection, autofluorescence, reporter genes/fluorescence proteins, fluorochromes binding to specific targets, or other probes conjugated with fluorochromes. Recorded datasets can be used not only for visualization but also for semiquantitative analysis. As a result CLSM represents a very useful tool for imaging of microbiological samples in combination with other analytical techniques.

No nitrification in lakes below pH 3

Lakes affected by acid mine drainage (AMD) or acid rain often contain elevated concentrations of ammonium, which threatens water quality. It is commonly assumed that this is due to the inhibition of microbial nitrification in acidic water, but nitrification was never directly measured in mine pit lakes. For the first time, we measured nitrification by (15)NH4Cl isotope tracer addition in acidic as well as neutral mine pit lakes in Spain and Germany. Nitrification activity was only detected in neutral lakes. In acidic lakes no conversion of (15)NH4(+) to (15)NO3(-) was observed. This was true both for the water column as well as for biofilms on the surface of macrophytes or dead wood and the oxic surface layer of the sediment. Stable isotope analysis of nitrate showed (18)O values typical for nitrification only in neutral lakes. In a comparison of NH4(+) concentrations in 297 surface waters with different pH, ammonium concentrations higher 10 mg NH4-N L(-1) were only observed in lakes below pH 3. On the basis of the results from stable isotope investigations and the examination of a metadata set we conclude that the lower limit for nitrification in lakes is around pH 3.

Effect of long-term compost and inorganic fertilizer application on background N2O and fertilizer-induced N2O emissions from an intensively cultivated soil

The influence of inorganic fertilizer and compost on background nitrous oxide (N2O) and fertilizer-induced N2O emissions were examined over a maize-wheat rotation year from June 2008 to May 2009 in a fluvo-aquic soil in Henan Province of China where a field experiment had been established in 1989 to evaluate the long-term effects of manure and fertilizer on soil organic status. The study involved five treatments: compost (OM), fertilizer NPK (nitrogen-phosphorus-potassium, NPK), half compost N plus half fertilizer N (HOM), fertilizer NK (NK), and control without any fertilizer (CK). The natural logarithms of the background N2O fluxes were significantly (P<0.05) correlated with soil temperature, but not with soil moisture, during the maize or wheat growing season. The 18-year application of compost alone and inorganic fertilizer not only significantly (P<0.05) increased soil organic carbon (SOC) by 152% and 10-43% (respectively), but also increased background N2O emissions by 106% and 48-76% (respectively) compared with the control. Total N in soils was a better indicator for predicting annual background N2O emission than SOC. The estimated emission factor (EF) of mineralized N, calculated by dividing annual N2O emission by mineralized N was 0.13-0.19%, significantly (P<0.05) lower than the EF of added N (0.30-0.39%). The annual N2O emission in the NPK, HOM and OM soils amended with 300 kg ha(-1) organic or inorganic N was 1427, 1325 and 1178 g N ha(-1), respectively. There was a significant (P<0.05) difference between the NPK and OM. The results of this study indicate that soil indigenous N was less efficiently converted into N2O compared with exogenous N. Increasing SOC by compost application, then partially increasing N supply to crops instead of adding inorganic N fertilizer, may be an effective measure to mitigate N2O emissions from arable soils in the North China plain.

Investigation on characteristics of leachate and concentrated leachate in three landfill leachate treatment plants

Concentrated leachate from membrane treatment processes is a potential pollution source for the surroundings. In this study, with comparison of the landfill leachate, chemical and microbial characteristics of concentrated leachate including biodegradability, amount of nitrogenous compounds and heavy metals, dissolved organic matter composition, and microbial community were investigated in three landfill leachate treatment plants. The results showed that hydrophilic (HyI) fraction was the major dissolved organic carbon in the landfill leachates, accounting for 54.6-60.7%, while humic substances including humic acid (HA) and fulvic acid (FA) were relatively higher in the concentrated leachates, ranging from 61.7% to 69.2%. Conjugated nitrogen existed mainly in FA and HyI in the concentrated leachates. The analysis of excitation emission matrix fluorescence spectroscopy, specific ultraviolet absorbance at 254nm (SUVA254) and GC/MS showed that aromatic compounds, long-chain hydrocarbons and halohydrocarbons were abundant in the concentrated leachates. During landfill leachate treatment processes, Cl(-), SO4(2-) and heavy metals were commonly accumulated in the concentrated leachates. NO3(-)N and/or NH4(+)N were the major nitrogenous compounds in the concentrated leachates. All the leachates from three landfill sites contained toluene in the range of 44.5-728.4μgL(-1). Ethylbenzene, chlorobenzene, and the phthalic acid esters including dibutyl phthalate, dimethyl phthalate and di-n-octyl phthalate were also detected in the concentrated leachates. Higher microbial diversity was observed in the concentrated leachate in comparison with landfill leachate.

Biofilms as living catalysts in continuous chemical syntheses

Biofilms are resilient to a wide variety of environmental stresses. This inherited robustness has been exploited mainly for bioremediation. With a better understanding of their physiology, the application of these living catalysts has been extended to the production of bulk and fine chemicals as well as towards biofuels, biohydrogen, and electricity production in microbial fuel cells. Numerous challenges call for novel solutions and concepts of analytics, biofilm reactor design, product recovery, and scale-up strategies. In this review, we highlight recent advancements in spatiotemporal biofilm characterization and new biofilm reactor developments for the production of value-added fine chemicals as well as current challenges and future scenarios.

Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments

Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

Analysis of ammonia monooxygenase and archaeal 16S rRNA gene fragments in nitrifying acid-sulfate soil microcosms

The present study describes the occurrence of a unique archaeal ammonia monooxygenase alpha subunit (amoA) gene in nitrifying acid-sulfate soil microcosms at pH 3.5. The soil was collected from an abandoned paddy field in Thailand. Microcosms were incubated in the dark at 30°C for 372 days with the following three treatments: addition of ammonium sulfate solution once a month (I) or once a week (II), and addition of only sterilized water (III). A quantitative PCR analysis revealed an increase in abundance of the archaeal amoA gene in microcosm soils in which nitrate concentrations increased after incubation. A phylogenetic analysis indicated a predominance of the novel gene, and a predominance of a betaproteobacterial amoA gene affiliated with the genus Nitrosospira. A 16S rRNA gene-based PCR assay revealed that crenarchaeotic Group I.1d was predominant among the Crenarchaeota in microcosms. These results suggest the presence of ammonia-oxidizing archaea corresponding to the unique amoA lineage in nitrifying acid-sulfate soil microcosms at pH 3.5.

Spatial Architecture of Nitrifying Bacteria Biofilm Immobilized on Polyurethane Foam in an Automatic Biodetector for Water Toxicity

We describe the architecture of nitrifying bacteria biofilms immobilized on a three-dimensional (3D) polyurethane foam that permits efficient water flow through a bioreactor. The 3D spatial organization of immobilized bacterial colonies is characterized on three resolution levels with X-ray tomography, light confocal microscopy, and scanning electron microscopy (SEM). Using these techniques we demonstrate biofilm distribution in the foam and the existence of several modes of binding of bacteria to the foam. Computed X-ray tomography permits observation of the distribution of the biofilm in the whole open cellular polyurethane material volume and estimation of biofilm volume. SEM and confocal laser scanning microscopy techniques permit 3D visualization of biofilm structure. Three distinct immobilization patterns could be observed in the open cellular polyurethane material: (1) large irregular aggregates of bacterial biofilm that exist as irregular biofilm fragments, rope-like structures, or biofilm layers on the foam surface; (2) spherical (pom-pom) aggregates of bacteria localized on the external surface of biofilm; and (3) biofilm threads adherent to the surface of polyurethane foam. Finally, we demonstrate that immobilized bacteria exhibit metabolic activity and growth.

Microbial community distribution and activity dynamics of granular biomass in a CANON reactor

The application of microelectrodes to measure oxygen and nitrite concentrations inside granules operated at 20 degrees C in a CANON (Complete Autotrophic Nitrogen-removal Over Nitrite) reactor and the application of the FISH (Fluorescent In Situ Hybridization) technique to cryosectioned slices of these granules showed the presence of two differentiated zones inside of them: an external nitrification zone and an internal anammox zone. The FISH analysis of these layers allowed the identification of Nitrosomonas spp. and Candidatus Kuenenia Stutgartiensis as the main populations carrying out aerobic and anaerobic ammonia oxidation, respectively. Concentration microprofiles measured at different oxygen concentrations in the bulk liquid (from 1.5 to 35.2 mg O(2) L(-1)) revealed that oxygen was consumed in a surface layer of 100-350 microm width. The obtained consumption rate of the most active layers was of 80 g O(2) (L(granule))(-1) d(-1). Anammox activity was registered between 400 and 1000 microm depth inside the granules. The nitrogen removal capacity of the studied sequencing batch reactor containing the granular biomass was of 0.5 g N L(-1) d(-1). This value is similar to the mean nitrogen removal rate obtained from calculations based on in- and outflow concentrations. Information obtained in the present work allowed the establishment of a simple control strategy based on the measurements of NH(4)(+) and NO(2)(-) in the bulk liquid and acting over the dissolved oxygen concentration in the bulk liquid and the hydraulic retention time of the reactor.

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.

Functional tomographic fluorescence imaging of pH microenvironments in microbial biofilms by use of silica nanoparticle sensors

Attached bacterial communities can generate three-dimensional (3D) physicochemical gradients that create microenvironments where local conditions are substantially different from those in the surrounding solution. Given their ubiquity in nature and their impacts on issues ranging from water quality to human health, better tools for understanding biofilms and the gradients they create are needed. Here we demonstrate the use of functional tomographic imaging via confocal fluorescence microscopy of ratiometric core-shell silica nanoparticle sensors (C dot sensors) to study the morphology and temporal evolution of pH microenvironments in axenic Escherichia coli PHL628 and mixed-culture wastewater biofilms. Testing of 70-, 30-, and 10-nm-diameter sensor particles reveals a critical size for homogeneous biofilm staining, with only the 10-nm-diameter particles capable of successfully generating high-resolution maps of biofilm pH and distinct local heterogeneities. Our measurements revealed pH values that ranged from 5 to >7, confirming the heterogeneity of the pH profiles within these biofilms. pH was also analyzed following glucose addition to both suspended and attached cultures. In both cases, the pH became more acidic, likely due to glucose metabolism causing the release of tricarboxylic acid cycle acids and CO(2). These studies demonstrate that the combination of 3D functional fluorescence imaging with well-designed nanoparticle sensors provides a powerful tool for in situ characterization of chemical microenvironments in complex biofilms.

Cytoplasmic pH measurement and homeostasis in bacteria and archaea

Of all the molecular determinants for growth, the hydronium and hydroxide ions are found naturally in the widest concentration range, from acid mine drainage below pH 0 to soda lakes above pH 13. Most bacteria and archaea have mechanisms that maintain their internal, cytoplasmic pH within a narrower range than the pH outside the cell, termed "pH homeostasis." Some mechanisms of pH homeostasis are specific to particular species or groups of microorganisms while some common principles apply across the pH spectrum. The measurement of internal pH of microbes presents challenges, which are addressed by a range of techniques under varying growth conditions. This review compares and contrasts cytoplasmic pH homeostasis in acidophilic, neutralophilic, and alkaliphilic bacteria and archaea under conditions of growth, non-growth survival, and biofilms. We present diverse mechanisms of pH homeostasis including cell buffering, adaptations of membrane structure, active ion transport, and metabolic consumption of acids and bases.

Analysis of How a Biofilm Forms on the Surface of the Aquatic Macrophyte Phragmites australis

The process by which a biofilm forms on the surface of the aquatic macrophyte Phragmites australis was investigated over a period of about two months (from mid-May to late-July, 2008) in Lake Biwa. The biofilm formed relatively quickly, its wet weight per unit area after seven day being that of a mature biofilm. This speed can be attributed to the many active bacteria in the early stage of its formation and the extracellular polymeric substances (EPS) they produce. The EPS carried electric charges that attracted nutrient ions from surrounding lake water, which, by electrostatic interaction, reached a high concentration as early as day 7 of the formation process. This significantly affected the biofilm community, which differed greatly from that of the lake water even at the beginning of biofilm formation. Brown amorphous compounds (a complex of organic and inorganic substances), covered the biofilm in the second half of its formation process producing a different community structure from that initially. This study revealed a fast and dynamic process of biofilm formation on the reed surface of reed.