Competition betweenNitrospira spp. andNitrobacter spp. in nitrite-oxidizing bioreactors

Genome-resolved metagenomics reveals the nitrifiers enrichment and species succession in activated sludge under extremely low dissolved oxygen

Nitrification, a process carried out by aerobic microorganisms that oxidizes ammonia to nitrate via nitrite, is an indispensable step in wastewater nitrogen removal. To facilitate energy and carbon savings, applying low dissolved oxygen (DO) is suggested to shortcut the conventional biological nitrogen removal pathway, however, the impact of low DO on nitrifying communities within activated sludge is not fully understood. This study used genome-resolved metagenomics to compare nitrifying communities under extremely low- and high-DO. Two bioreactors were parallelly operated to perform nitrification and DO was respectively provided by limited gas-liquid mass transfer from the atmosphere (AN reactor, DO < 0.1 mg/L) and by sufficient aeration (AE reactor, DO > 5.0 mg/L). Low DO was thought to limit nitrifiers growth; however, we demonstrated that complete nitrification could still be achieved under the extremely low-DO conditions, but with no nitrite accumulation observed. Kinetic analysis showed that after long-term exposure to low DO, nitrifiers had a higher oxygen affinity constant and could maintain a relatively high nitrification rate, particularly at low levels of DO (<0.2 mg/L). Community-level gene analysis indicated that low DO promoted enrichment of nitrifiers (the genera Nitrosomonas and Nitrospira, increased by 2.3- to 4.3-fold), and also harbored with 2.3 to 5.3 times higher of nitrification functional genes. Moreover, 46 high-quality (>90 % completeness and <5 % contamination) with 3 most abundant medium-quality metagenome-assembled genomes (MAGs) were retrieved using binning methods. Genome-level phylogenetic analysis revealed the species succession within nitrifying populations. Surprisingly, compared to DO-rich conditions, low-DO conditions were found to efficiently suppressed the ordinary heterotrophic microorganisms (e.g., the families Anaerolineales, Phycisphaerales, and Chitinophagales), but selected for the specific candidate denitrifiers (within phylum Bacteroidota). This study provides new microbial insights to demonstrate that low-DO favors the enrichment of autotrophic nitrifiers over heterotrophs with species-level successions, which would facilitate the optimization of energy and carbon management in wastewater treatment.

Performances of full-scale biological nitrogen pre-treatment process for drinking water source: Seasonal variations and microbial community

This study investigated the performance of the full-scale unit over a two-year period to enhance nitrification efficiency and provide operational strategies. Results indicated that raw water quality from Donggan River was notably influenced by seasonal variations, particularly during dry and wet seasons, impacting the nitrification efficiency of the biological pretreatment process. Factors such as influent concentrations of ammonia and total Kjeldahl nitrogen were found to have significant effects on nitrification, with temperature and conductivity also showing correlations. The specific rate of ammonia removal was calculated to be approximately 0.1 kg-N/m3/d under the existing operational setup. Moreover, elevating dissolved oxygen levels above 4 mg/L was proposed to potentially boost ammonia oxidation based on findings from experiments conducted in lab-scale bioreactors. In times of increased influent ammonia levels, the elimination of about 1-3 mg-N/L of total nitrogen signified the activation of denitrification processes. This observation was corroborated by results from next-generation sequencing techniques, verifying the existence of denitrifying microorganisms. The real-time PCR analysis results indicated that the abundance of comammox amoA gene was comparable with the abundance of the AOB amoA gene, indicating the presence of comammox Nitrospira and their potential role on nitrification in the system.

The enrichment characterisation of Nitrospira under high DO conditions

Nitrite-oxidizing bacteria (NOB) are crucial to nitrification and nitrogen elimination in wastewater treatment. Mass reports exist on the links between NOB and other microorganisms, for instance, ammonia-oxidizing bacteria (AOB). However, a few studies exist on the enrichment characterisation of NOB under high dissolved oxygen (DO) conditions. In this study, NOB was designed to be enriched individually under high DO conditions in a continuous aeration sequencing batch reactor (SBR), and the kinetic characterisation of NOB was evaluated. The analysis revealed that the average NO2--N removal rate was steady above 98%, with DO and NO2--N being 3-5 mg L-1 and 50-450 mg L-1, respectively. The NO2--N removal efficiency of the system was significantly enhanced and better than in other studies. The high-throughput sequencing suggested that Parcubacteria_ genera_incertae_sedis was the first dominant genus (21.99%), which often appeared in the NOB biological community with Nitrospira. However, the dominant genus NOB was Nitrospira rather than Nitrobacter (8.49%). This result suggested that Nitrospira was capable of higher NO2--N removal. But lower relative abundance indicated that excessive NO2--N had an adverse effect on the enrichment and activity of Nitrospira. In addition, the nitrite half-saturation constant (KNO2) and the oxygen half-saturation constant (KO) were 1.71 ± 0.19 mg L-1 and 0.95 ± 0.10 mg L-1, respectively. These results showed that the enriched Nitrospira bacteria had different characteristics at the strain level, which can be used as a theoretical basis for wastewater treatment plant design and optimisation.

Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments

Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak.

IMPORTANCE

Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.

The coexistence and competition of canonical and comammox nitrite oxidizing bacteria in a nitrifying activated sludge system - Experimental observations and simulation studies

The second step of nitrification can be mediated by nitrite oxidizing bacteria (NOB), i.e. Nitrospira and Nitrobacter, with different characteristics in terms of the r/K theory. In this study, an activated sludge model was developed to account for competition between two groups of canonical NOB and comammox bacteria. Heterotrophic denitrification on soluble microbial products was also incorporated into the model. Four 5-week washout trials were carried out at dissolved oxygen-limited conditions for different temperatures (12 °C vs. 20 °C) and main substrates (NH₄⁺-N vs. NO₂^--N). Due to the aggressive reduction of solids retention time (from 4 to 1 d), the biomass concentrations were continuously decreased and stabilized after two weeks at a level below 400 mg/L. The collected experimental data (N species, biomass concentrations, and microbiological analyses) were used for model calibration and validation. In addition to the standard predictions (N species and biomass), the newly developed model also accurately predicted two microbiological indicators, including the relative abundance of comammox bacteria as well as nitrifiers to heterotrophs ratio. Sankey diagrams revealed that the relative contributions of specific microbial groups to N conversion pathways were significantly shifted during the trial. The contribution of comammox did not exceed 5 % in the experiments with both NH₄⁺-N and NO₂^--N substrates. This study contributes to a better understanding of the novel autotrophic N removal processes (e.g. deammonification) with nitrite as a central intermediate product.

Simulation and experimental verification of nitrite-oxidizing bacteria inhibition by alternating aerobic/anoxic strategy

Anaerobic ammonium oxidation (ANAMMOX) is a promising technology for sewage treatment. Alternating aerobic/anoxic conditions have been widely adopted to achieve partial nitrification (PN), so as to provide substrates for ANAMMOX. In this study, the feasibility of PN with the strategy of intermittent aeration was investigated under mainstream conditions. At a low dissolved oxygen (DO) concentration, the nitrogen conversion characteristic under different intermittent aeration modes was evaluated by mathematical simulation and experimental method with (1) ordinary activated sludge, (2) mixed sludge with anaerobic ammonia-oxidizing bacteria (AnAOB), and (3) PN sludge, as seed sludge. The existence of functional microorganisms, such as AnAOB and denitrifying bacteria, which can utilize nitrites, was the prerequisite for NOB activity inhibition in the alternating aerobic/anoxic condition. Therefore, low nitrite may be an important factor in NOB activity inhibition under alternating aerobic/anoxic conditions. This study demonstrated a key controlling factor for NOB activity inhibition with alternating aerobic/anoxic condition.

Mainstream short-cut N removal modelling: current status and perspectives

This work gives an overview of the state-of-the-art in modelling of short-cut processes for nitrogen removal in mainstream wastewater treatment and presents future perspectives for directing research efforts in line with the needs of practice. The modelling status for deammonification (i.e., anammox-based) and nitrite-shunt processes is presented with its challenges and limitations. The importance of mathematical models for considering N₂O emissions in the design and operation of short-cut nitrogen removal processes is considered as well. Modelling goals and potential benefits are presented and the needs for new and more advanced approaches are identified. Overall, this contribution presents how existing and future mathematical models can accelerate successful full-scale mainstream short-cut nitrogen removal applications.

Pharmaceuticals and personal care products' (PPCPs) impact on enriched nitrifying cultures

The impact of pharmaceutical and personal care products (PPCPs) on the performance of biological wastewater treatment plants (WWTPs) has been widely studied using whole-community approaches. These contaminants affect the capacity of microbial communities to transform nutrients; however, most have neither honed their examination on the nitrifying communities directly nor considered the impact on individual populations. In this study, six PPCPs commonly found in WWTPs, including a stimulant (caffeine), an antimicrobial agent (triclosan), an insect repellent ingredient (N,N-diethyl-m-toluamide (DEET)) and antibiotics (ampicillin, colistin and ofloxacin), were selected to assess their short-term toxic effect on enriched nitrifying cultures: Nitrosomonas sp. and Nitrobacter sp. The results showed that triclosan exhibited the greatest inhibition on nitrification with EC₅₀ of 89.1 μg L^-1. From the selected antibiotics, colistin significantly affected the overall nitrification with the lowest EC₅₀ of 1 mg L^-1, and a more pronounced inhibitory effect on ammonia-oxidizing bacteria (AOB) compared to nitrite-oxidizing bacteria (NOB). The EC₅₀ of ampicillin and ofloxacin was 23.7 and 12.7 mg L^-1, respectively. Additionally, experimental data suggested that nitrifying bacteria were insensitive to the presence of caffeine. In the case of DEET, moderate inhibition of nitrification (<40%) was observed at 10 mg L^-1. These findings contribute to the understanding of the response of nitrifying communities in presence of PPCPs, which play an essential role in biological nitrification in WWTPs. Knowing specific community responses helps develop mitigation measures to improve system resilience.

Nitratation in pilot-scale bioreactors fed with effluent from a submerged biological aerated filter used in the treatment of dog wastewater

Nitrification is a biochemical process that allows oxidation of ammonium ion to nitrite, and nitrite to nitrate in a system. Aerobic processes, such as use of submerged biological aerated filter (SBAF), enable nitrification. However, some variables that are entirely unavailable or not available at the required concentration range may hamper the process. In this study, nitratation under high dissolved oxygen (DO) concentrations was evaluated in laboratory-scale bioreactors containing 10% inoculum (0.5 kg kg^-1) fed with affluent from a SBAF that receive the sewage generated from washing the bays of a dog kennel. The following variables were monitored over time: ammoniacal nitrogen (12.44-29.62 mg L^-1), nitrite (0.28-0.54 mg L^-1), nitrate (1.75-3.55 mg L^-1), pH (8.11 ± 0.62), temperature (21.61 ± 1.24°C) and DO (9.69 ± 0.36 mg L^-1). Quantification of nitrifying bacteria by the multiple tube technique showed the value of 1.4 × 10¹² MPN mL^-1for ammonia-oxidizing bacteria (AOB) and 9.2 × 10¹⁴ MPN mL^-1 for nitrite-oxidizing bacteria. These values were higher than those found in a synthetic medium, which can be explained by the greater availability of ammonium and nitrite in the effluent. By the extraction of genomic DNA, and PCR, with specific primers, the presence of the AmoA (Ammonia monooxygenase) gene for AOB and of the Nitrobacter was detected in the bioreactor samples. By PCR-DGGE, the sequenced bands showed high similarity with denitrifying bacteria, such as Pseudomonas, Limnobacter, Thauera, Rhodococcus, and Thiobacillus. Thus, the saturation of dissolved oxygen in the system resulted in improvement in the nitratation step and allowed detection of bacterial genera involved in the process.

In-depth assessment of microbial communities in the full-scale vertical flow treatment wetlands fed with raw domestic wastewater

A multiphase study was proposed to examine microbial communities linked to the nitrogen cycle in the first stage of four full-scale French vertical flow treatment systems. To this end, denaturing gradient gel electrophoresis (DGGE) was performed for structural assessment and quantitative PCR (qPCR) to enumerate the abundance of ammonia-oxidizing (AOB). 16S rRNA sequencing was used to assess the taxonomic profile followed by putative assessment of functional genes. The samples were collected under different conditions, such as operational time (presence/absence of sludge layer on the surface of the filters), season (winter and summer), sampling depth (0, 15 and 30 cm) and operation cycle (rest and feed periods). A structural disparity was noted in the upper layers, whereas higher similarity at 30 cm was observed highlighting the effect of organic matter on bacterial diversity. The 7th rest day was highlighted by an apparent decline in the microbial community abundance. Additionally, qPCR indicated that the largest amount of AOB was found at 30 cm depth and during the feeding period. From the taxonomic profile, Mycobacterium, Acinetobacter, Flavobacterium, and Nitrospira were the most abundant genre found in all systems. The functional prediction results showed predicted genes linked to the denitrification process. The results suggested that operating time and season were responsible for the pattern of the microbial community behavior. This study allowed us to further understand the bacterial dynamics and to advance the idea of design modifications made in the first stage of the classical French system to improve nitrogen removal are promising.

Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate Nitrospira during a Press Disturbance in Nitrifying Activated Sludge

Managing and engineering activated sludge wastewater treatment microbiomes for low-energy nitrogen removal requires process control strategies to stop the oxidation of ammonium at nitrite. Our ability to out-select nitrite-oxidizing bacteria (NOB) from activated sludge is challenged by their metabolic and physiological diversity, warranting measurements of their in situ physiology and activity under selective growth pressures. Here, we examined the stability of nitrite oxidation in activated sludge during a press disturbance induced by treating a portion of return activated sludge with a sidestream flow containing free ammonia (FA) at 200 mg NH₃-N/liter. The nitrite accumulation ratio peaked at 42% by day 40 in the experimental bioreactor with the press disturbance, while it did not increase in the control bioreactor. A subsequent decrease in nitrite accumulation within the experimental bioreactor coincided with shifts in dominant Nitrospira 16S rRNA amplicon sequence variants (ASVs). We applied bioorthogonal noncanonical amino acid tagging (BONCAT) coupled with fluorescence-activated cell sorting (FACS) to investigate changes in the translational activity of NOB populations throughout batch exposure to FA. BONCAT-FACS confirmed that the single Nitrospira ASV washed out of the experimental bioreactor had reduced translational activity following exposure to FA, whereas the two Nitrospira ASVs that emerged after process acclimation were not impacted by FA. Thus, the coexistence of functionally degenerate and physiologically resistant Nitrospira populations provided resilience to the nitrite-oxidizing function during the press disturbance. These results highlight how BONCAT-FACS can resolve ecological niche differentiation within activated sludge and inform strategies to engineer and control microbiome function.

IMPORTANCE Nitrogen removal from activated sludge wastewater treatment systems is an energy-intensive process due to the large aeration requirement for nitrification. This energy footprint could be minimized with engineering control strategies that wash out nitrite-oxidizing bacteria (NOB) to limit oxygen demands. However, NOB populations can have a high degree of physiological diversity, and it is currently difficult to decipher the behavior of individual taxa during applied selective pressures. Here, we utilized a new substrate analog probing approach to measure the activity of NOB at the cellular translational level in the face of a press disturbance applied to the activated sludge process. Substrate analog probing corroborated the time series reactor sampling, showing that coexisting and functionally degenerate Nitrospira populations provided resilience to the nitrite oxidation process. Taken together, these results highlight how substrate analog approaches can illuminate in situ ecophysiologies within shared niches, and can inform strategies to improve microbiome engineering and management.

Insight into functionally active bacteria in nitrification following Na+ and Mg2+ exposure based on 16S rDNA and 16S rRNA sequencing

Despite increasing interests in osmotic membrane bioreactors, the information regarding the bacterial toxicity effects of reversely transported draw solute (RTDS) is limited. In this study, two representative draw solutes (NaCl and MgCl₂) were used at different concentrations (0, 2.5, 5.0, 7.5 and 10.0 g/L) to evaluate their toxicity in a continuous nitrifying bioreactor. Notably, Mg²⁺ selectively inhibited the activity of ammonia-oxidizing bacteria (AOB), which decreased to 11.3% at 7.5 g-Mg²⁺/L. The rRNA-based analysis was more effective than the rDNA-based analysis to elucidate the relationship between active communities of nitrifying bacteria and the actual nitrifying performance. Nitrosomonas europaea, a representative AOB, was vulnerable to Mg²⁺ in comparison to Na⁺. In contrast, the dominant nitrite-oxidizing bacteria (NOB), Nitrobacter winogradskyi and Nitrolancea hollandica, maintained a relevant level of relative abundance for achieving nitrite oxidation after exposure to 10 g/L Na⁺ and Mg²⁺. This fundamental inhibition information of the draw solute can be applied to set the operational regime preventing the critical solute concentration in mixed liquor of nitrifying OMBRs.

Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater

In this study, nitrification before and after abrupt cross-transfer in salinity was investigated in two moving bed biofilm reactors inoculated with nitrifying cultures that had adaptation to freshwater (FR) and seawater salinities (SR). FR and SR MBRRs were exposed to short and long term cross-transfer in salinity, and the functional capacity of nitrifying microbial communities was quantified by the estimation of ammonia and nitrite oxidation rates. Salinity induced successions were evaluated before and after salinity change by deep sequencing of 16S rRNA gene amplicons and statistical analysis. The bacterial community structure was characterized and Venn diagrams were included. The results indicated that after salinity cross-transfer, the FR was not significantly recovered at seawater salinity whereas SR showed high resistance to stress caused by low-salt. Succession and physiological plasticity were the main mechanisms of the long-term adaption of the nitrifying communities exposed to abrupt salinity changes. Independently of salinity, some nitrifiers presented high physiological plasticity towards salinity and were very successful at both zero and full seawater salinity. SR culture is robust and suitable inoculum for ammonium removal from recirculating aquaculture systems and industrial wastewaters with variable and fast salinity changes. Our findings contradict the current perspective of the significance of salinity on the structure of nitrifying communities.

Inactivation kinetics of nitrite-oxidizing bacteria by free nitrous acid

Recent studies have shown that free nitrous acid (FNA, i.e., HNO₂) is biocidal to many microorganisms, promoting the development of FNA-based technology in biological wastewater treatment. Suppression of nitrite-oxidizing bacteria (NOB) is a critical step for autotrophic nitrogen removal via anammox. In this study, the biocidal effect of FNA on NOB was determined by developing a model methodology combined with NOB incubation. Sixteen groups of FNA exposure tests were conducted at five different FNA concentrations from 0 to 4 mg HNO₂-N/L, obtained from three pH values (5.0, 5.5 and 6.0) with nitrite ranged from 21 to 1680 mg NO₂^--N/L, with one as a control. Nitrate production curves were tracked during incubations of the FNA-exposed sludge, and then used to estimate active NOB concentrations by the kinetic model-based fitting. The results showed that with 24-hour exposure to FNA at a level of over 1 mg HNO₂-N/L, the active NOB decreased around two orders of magnitude compared with that in the primordial sludge. The Weibull model can well describe the biocidal effect, which would be useful for the optimization of FNA conditions. The maximum NOB growth rate was increased after FNA exposure. This result suggests that long-term implementation of FNA-based technology can select fast-growing NOB in activated sludge, causing a 'NOB adaptation' issue.

Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from  Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

The occurrence and role of Nitrospira in nitrogen removal systems

Application of the modern microbial techniques changed the paradigm about the microorganisms performing nitrification. Numerous investigations recognized representatives of the genus Nitrospira as a key and predominant nitrite-oxidizing bacteria in biological nutrient removal systems, especially under low dissolved oxygen and substrate conditions. The recent discovery of Nitrospira capable of performing complete ammonia oxidation (comammox) raised a fundamental question about the actual role of Nitrospira in both nitrification steps. This review summarizes the current knowledge about morphological, physiological and genetic characteristics of the canonical and comammox Nitrospira. Potential implications of comammox for the functional aspects of nitrogen removal have been highlighted. The complex meta-analysis of literature data was applied to identify specific individual variables and their combined interactions on the Nitrospira abundance. In addition to dissolved oxygen and influent nitrogen concentrations, temperature and pH may play an important role in enhancing or suppressing the Nitrospira activity.

Separating and Characterizing Functional Nitrogen Degraders via Magnetic Nanoparticle-Mediated Isolation

Magnetic nanoparticle-mediated isolation (MMI) is a new method for isolating active functional microbes from complex microorganisms without substrate labeling. In this study, the composition and properties of magnetic nanoparticles (MNPs) were characterized by a number of techniques, indicating that MNPs have characteristics such as microinterfaces and can be efficiently fixed on the surface of microbial cells. It also introduced the MMI technology in activated sludge after stable long-term treatment. With further addition of promotor carbon sources, the enrichment of the functional nitrogen degraders in MMI was significantly higher than in samples without MNPs, showing the advantages of MMI in identifying the active degraders. Redundancy analysis (RDA) also showed that the functional nitrogen degraders such as Comamonadaceae_unclassified and Thiobacillus absolutely dominated in situ ammonia degradation, and the change in dominant genera had the same trend as the degradation rate of ammonia nitrogen. In the magnetically functionalized system, the separated functional nitrogen degraders significantly improved ammonia nitrogen degradation efficiency, making it basically stable at more than 80%, up to 91.6%. These results prove that the complex flora created after the addition of MNPs is more adaptable to newly introduced pollutants, and MMI is a powerful tool for studying pollutant-degrading microorganisms under in situ conditions.

Simultaneous biological nitrification and desulfurization treatment of ammonium and sulfide-rich wastewater: Effectiveness of a sequential batch operation

Sulfide inhibition to nitrifying bacteria has prevented the integration of digestate nitrification and biogas desulfurization to simplify anaerobic digestion systems. In this study, liquid digestate with NaHS solution was treated using nitrifying sludge in a sequential-batch reactor with a long fill period, with an ammonium loading rate of 293 mg-N L^-1 d^-1 and a stepwise increase in the sulfide loading rate from 0 to 32, 64, 128, and 256 mg-S L^-1 d^-1. Batch bioassays and microbial community analysis were also conducted with reactor sludge under each sulfide loading rate to quantify the microbial acclimatization to sulfide. In the reactor, sulfide was completely removed. Complete nitrification was maintained up to a sulfide load of 128 mg-S L^-1 d^-1, which is higher than that in previous reports and sufficient for biogas treatment. In the batch bioassays, the sulfide tolerance of NH₄⁺ oxidizing activity (the 50% inhibitory sulfide concentration) increased fourfold over time with the compositional shift of nitrifying bacteria to Nitrosomonas nitrosa and Nitrobacter spp. However, the sulfur removal rate of the sludge slightly decreased, although the abundance of the sulfur-oxidizing bacteria Hyphomicrobium increased by 30%. Therefore, nitrifying sludge was probably acclimatized to sulfide not by the increasing sulfide removal rate but rather by the increasing nitrifying bacteria, which have high sulfide tolerance. Successful simultaneous nitrification and desulfurization were achieved using a sequential-batch reactor with a long fill period, which was effective in facilitating the present acclimatization.

Ecological niche differentiation among anammox bacteria

Anaerobic ammonium oxidizing (anammox) bacteria can directly convert ammonium and nitrite to nitrogen gas anaerobically and were responsible for a substantial part of the fixed nitrogen loss and re-oxidation of nitrite to nitrate in freshwater and marine ecosystems. Although a wide variety of studies have been undertaken to investigate the abundance and biodiversity of anammox bacteria so far, ecological niche differentiation of anammox bacteria is still not fully understood. To assess their growth behavior and consequent population dynamics at a given environment, the Monod model is often used. Here, we summarize the Monod kinetic parameters such as the maximum specific growth rate (μ_max) and the half-saturation constant for nitrite (K_NO2-) and ammonium (K_NH4+) of five known candidatus genera of anammox bacteria. We also discuss potential pivotal environmental factors and metabolic flexibility that influence the community compositions of anammox bacteria. Particularly biodiversity of the genus "Scalindua" might have been largely underestimated. Several anammox bacteria have been successfully enriched from various source of biomass. We reevaluate their enrichment methods and culture medium compositions to gain a clue of niche differentiation of anammox bacteria. Furthermore, we formulate the current issues that must be addressed. Overall this review re-emphasizes the importance of enrichment cultures (preferably pure cultures), physiological characterization and direct microbial competition studies using enrichment cultures in laboratories.

Enhanced nitrite accumulation under mainstream conditions by a combination of free ammonia-based sludge treatment and low dissolved oxygen: reactor performance and microbiome analysis

Partial nitritation under mainstream conditions is one of the major bottlenecks for the application of deammonification processes to municipal wastewater treatment plants. This study aimed at evaluating the combination effect of a side-stream free ammonia (FA) treatment and low dissolved oxygen (0.2 ± 0.1 mg L⁻¹) on inhibiting nitrite oxidizing bacteria (NOB) from enhancing nitrite accumulation in long-term lab-scale experiments. Two continuous floccular sludge reactors treating low-strength synthetic wastewater (60 mg N–NH₄⁺ L⁻¹ without COD) with a fixed nitrogen loading rate of 0.22 ± 0.03 g N per L per day were operated in a varied temperature range of 7–31 °C, with one acting as the experimental reactor and the other as the control. Side-stream sludge treatment with a stepwise elevation of FA concentration (65.2–261.1 mg NH₃ L⁻¹) was carried out every day in the experimental reactor; the nitrite accumulation ratio (NAR, (NO₂–N/(NO₂⁻–N + NO₃⁻–N) × 100%)) in the experimental reactor was always about twice that in the control one. Quantitative PCR (q-PCR) and high-throughput sequencing analyses showed the dominant NOB was mostly Nitrobacter, while there was an alternating trend between Nitrobacter and Nitrospira. Even though the whole microbial communities of each experimental stage between the two reactors were relatively clustered due to an incomplete NOB washout, three abundant metabolisms (amino acid metabolism, pyruvate metabolism and nitrogen metabolism) and key functional genes of nitrification predicted by PICRUSt in the experimental reactor were enriched, providing a better understanding of nitrite accumulation. These results have demonstrated that the positive hybrid effects of FA side-stream sludge treatment and a low DO could enhance nitrite accumulation. It is expected that a complete washout of NOB would be achieved after further process optimization.

An introduction of the combination of side-stream sludge treatment using FA and low DO could more effectively enhance nitrite accumulation than single low DO.

Potential bacterial bioindicators of urban pollution in mangroves

Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.

Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media

Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.

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.

Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing

Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.

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.

A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA

Low biomass and productivity of arid-land caves with limited availability of nitrogen (N) raises the question of how microbes acquire and cycle this essential element. Caves are ideal environments for investigating microbial functional capabilities, as they lack phototrophic activity and have near constant temperatures and high relative humidity. From the walls of Fort Stanton Cave (FSC), multicolored secondary mineral deposits of soil-like material low in fixed N, known as ferromanganese deposits (FMD), were collected. We hypothesized that within FMD samples we would find the presence of microbial N cycling genes and taxonomy related to N cycling microorganisms. Community DNA were sequenced using Illumina shotgun metagenomics and 16S rRNA gene sequencing. Results suggest a diverse N cycle encompassing several energetic pathways including nitrification, dissimilatory nitrate reduction and denitrification. N cycling genes associated with assimilatory nitrate reduction were also identified. Functional gene sequences and taxonomic findings suggest several bacterial and archaeal phyla potentially play a role in nitrification pathways in FSC and FMD. Thaumarchaeota, a deep-branching archaeal division, likely play an essential and possibly dominant role in the oxidation of ammonia. Our results provide genomic evidence for understanding how microbes are potentially able to acquire and cycle N in a low-nutrient subterranean environment.

The threshold of influent ammonium concentration for nitrate over-accumulation in a one-stage deammonification system with granular sludge without aeration

Low-strength ammonium is still a challenge for the mainstream deammonification because of nitrate over-accumulation. In this study, the threshold of influent ammonium concentration of one-stage deammonification system with granular sludge was investigated, by stepwise decreasing influent ammonium from high concentrations (280mg/L to 140mg/L) to the low concentration (70mg/L) in 108d at 32°C without aeration. Results showed that, under 70mg/L NH₄⁺-N, ΔNO₃^--N/ΔNH₄⁺-N ratio increased to 0.2, deviated from the theoretical value of 0.11, with ammonium and TN removal efficiencies of 91% and 71%, respectively. However, under both high ammonium concentrations (280mg/L and 140mg/L), nitrate production stabilized at only 13%. Chloroflexi, Planctomycetes and Proteobacteria contributed >70% of the communities under all three ammonium concentrations. As influent ammonium decreasing, the relative abundances of bacteria for anammox, aerobic oxidizing and denitrifying decreased, while NOB (nitrite oxidizing bacteria) abundance increased greatly. So 70mg/L was the threshold of influent ammonium concentration for stable deammonification without organic influent. It was the decrease of functional bacteria and overgrowth of NOB that worsen the deammonification performance under low-strength ammonium.

Characterization of nutrient-removing microbial communities in two full-scale WWTP systems using a new qPCR approach

Biological wastewater treatment processes involve very complex microbial communities. Culture-independent molecular methods are feasible tools used to analyze and control the structure of different microbial communities, such as bacterial communities that remove nutrients. Here, we used the gBlocks gene fragments method, a new real-time PCR approach for the development of DNA standards, to quantify total bacterial cells, AOB, NOB, and Archaeal genes at two different WWTPs. PAOs were also quantified using the FISH technique. Our findings highlight a significant improvement in real-time PCR detection for the microorganisms studied. The qPCR and FISH technique applied allowed characterization of the microbial composition of two WWTPs operated as a conventional WWTP and a biological nutrient-removal WWTP. The results revealed a significant difference in the microbial profiles of the WWTPs, with a higher abundance of nitrifying bacterial communities and PAOs in the nutrient removal plant, which were in accordance with operational performance.

The transformation from anammox granules to deammonification granules in micro-aerobic system by facilitating indigenous ammonia oxidizing bacteria

Granular deammonification process is a good way to retain aerobic and anaerobic ammonia oxidizing bacteria (AOB and anammox bacteria) and exhaust flocculent nitrite oxidizing bacteria (NOB). In this study, to facilitate indigenous AOB growth on anammox granules, by stepwise reducing influent nitrite, anammox granules were effectively transformed into deammonification granules in a micro-aerobic EGSB in 100 days. Total nitrogen removal efficiency of 90% and nitrogen removal rate of 2.3 g N/L/d were reached at stable deammonification stage. High influent FA and limited oxygen supply contributed suppression for Nitrospira-like NOB. In transition stages, Proteobacteria and Chloroflexi were always dominated. Anammox abundance decreased, while AOB abundance grew fast. Anammox bacteria and AOB were dominated by Brocadia fulgida and Nitrosomonas europaea, respectively. Denitrification activity and bacteria existed although without influent organic. The final AOB abundance was about 4.55-13.8 times more than anammox bacteria abundance, with almost equal potential activities.

Effects of salinity on the denitrification efficiency and community structure of a combined partial nitritation- anaerobic ammonium oxidation process

The effects of salinity changes on nitrogen transformation efficiency and recoverability were studied by using a partial nitration (PN)- anaerobic ammonium oxidation (Anammox) integrated reactor. The changes of microbial community structure and population abundance during the increase and decrease of salinity were also analyzed by 16S rRNA gene high-throughput sequencing. The results showed that when the salinity was increased to 1.35%, the combined PN-Anammox process achieved the maximum stimulated and total nitrogen removal rate (TNRR) arrived at 1.1kg/(m³·d). When the salinity was higher than 1.35%, the activities of AOB and Anammox bacteria began to be inhibited. When the salinity reached 2.4%, the TNRR decreased to 60%. TNRR was fast restored, when salinity was reduced to 0.11%. The genes of AOB and Anammox bacteria indicated that the TNRR of the reactor was restored after salinity inhibition, but the functional microbial community structure and abundance had relatively large, irreversible changes.

Microbial competition among anammox bacteria in nitrite-limited bioreactors

Phylogenetically diverse anammox bacteria have been detected in most of anoxic natural and engineered ecosystems and thus regarded as key players in the global nitrogen cycle. However, ecological niche differentiation of anammox bacteria remains unresolved despite its ecological and practical importance. In this study, the microbial competitions for a common substrate (nitrite) among three anammox species (i.e. "Candidatus Brocadia sinica", "Candidatus Jettenia caeni" and "Candidatus Kuenenia stuttgartiensis") were systematically investigated in nitrite-limited gel-immobilized column reactors (GICR) and membrane bioreactors (MBRs) under different nitrogen loading rates (NLRs). 16 S rRNA gene-based population dynamics revealed that "Ca. J. caeni" could proliferate only at low NLRs, whereas "Ca. B. sinica" outcompeted other two species at higher NLRs in both types of reactors. Furthermore, FISH analysis revealed that "Ca. J. caeni" was mainly present as spherical microclusters at the inner part (low NO₂^- environment), whereas "Ca. B. sinica" was present throughout the gel beads and granules. This spatial distribution supports the outcomes of the competition experiments. However, the successful competition of "Ca. J. caeni" at low NLR could not be explained with the Monod model probably due to inaccuracy of kinetic parameters such as half saturation constant (K_s) for nitrite and a difference in the maintenance rate (m). In addition, the growth of "Ca. K. stuttgartiensis" could not be observed in any experimental conditions, suggesting possible unknown factor(s) is missing. Taken together, NLR was one of factors determining ecological niche differentiation of "Ca. B. sinica" and "Ca. J. caeni".

Effect of the dilution rate on microbial competition: r-strategist can win over k-strategist at low substrate concentration

The conditions present in both in vitro and in vivo ecosystems determine the microbial population harbouring it. One commonly accepted theory is that a species with a high substrate affinity and low growth rate (k-strategist) will win the competition against a second species with a lower substrate affinity and higher growth rate (r-strategist) if both species are subjected to low substrate concentrations. In this study two nitrite oxidizing bacteria (NOB), Nitrospira defluvii (k-strategist) and Nitrobacter vulgaris (r-strategist), were cultivated in a continuous reactor systems. The minimal hydraulic retention time (HRT) required for maintaining the slower growing Nitrospira was first determined. A reactor containing Nitrobacter was set to the same HRT and Nitrospira was injected to evaluate the effect of the dilution rate on the competition between both species. By following the microbial population dynamics with qPCR analysis, it was shown that not only the substrate affinity drives the competition between k- and r-strategists but also the dilution rate. Experimental data and numerical simulations both revealed that the washout of Nitrobacter was significantly delayed at dilution rates close to the μmax of Nitrospira. The competition could be even reverted towards Nitrobacter (r-strategist) despite of low nitrite concentrations and dilution rates lower than the μmax of Nitrospira.

Molecular and Kinetic Characterization of Planktonic Nitrospira spp. Selectively Enriched from Activated Sludge

Nitrospira spp. are chemolithoautotrophic nitrite-oxidizing bacteria (NOB), which are ubiquitous in natural and engineered environments. However, there exist few independent biokinetic studies on Nitrospira spp., likely because their isolation and selective enrichment from environmental consortia such as activated sludge can be challenging. Herein, planktonic Nitrospira spp. cultures closely related to Candidatus Nitrospira defluvii (Nitrospira lineage I) were successfully enriched from activated sludge in a sequencing batch reactor by maintaining sustained limiting extant nitrite and dissolved oxygen concentrations. Morphologically, the enrichment consisted largely of planktonic cells with an average characteristic diameter of 1.3 ± 0.6 μm. On the basis of respirometric assays, estimated maximum specific growth rate (μ_max), nitrite half saturation coefficient (K_S), oxygen half saturation coefficient (K_O), and biomass yield coefficient (Y) of the enriched cultures were 0.69 ± 0.10 d^-1, 0.52 ± 0.14 mg-N/L, 0.33 ± 0.14 mg-O₂/L, and 0.14 ± 0.02 mg-COD/mg-N, respectively. These parameters collectively reflect not just higher affinities of this enrichment for nitrite and oxygen, respectively, but also a higher biomass yield and energy transfer efficiency relative to Nitrobacter spp. Used in combination, these kinetic and thermodynamic parameters can help toward the development and application of energy-efficient biological nutrient removal processes through effective Nitrospira out-selection.

Biodegradability of fluoxetine, mefenamic acid, and metoprolol using different microbial consortiums

The biodegradation of fluoxetine, mefenamic acid, and metoprolol using ammonium-nitrite-oxidizing consortium, nitrite-oxidizing consortium, and heterotrophic biomass was evaluated in batch tests applying different retention times. The ammonium-nitrite-oxidizing consortium presented the highest biodegradation percentages for mefenamic acid and metoprolol, of 85 and 64% respectively. This consortium was also capable to biodegrade 79% of fluoxetine. The heterotrophic consortium showed the highest ability to biodegrade fluoxetine reaching 85%, and it also had a high potential for biodegrading mefenamic acid and metoprolol, of 66 and 58% respectively. The nitrite-oxidizing consortium presented the lowest biodegradation of the three pharmaceuticals, of less than 48%. The determination of the selected pharmaceuticals in the dissolved phase and in the biomass indicated that biodegradation was the major removal mechanism of the three compounds. Based on the obtained results, the biodegradation kinetics was adjusted to pseudo-first-order for the three pharmaceuticals. The values of k _biol for fluoxetine, mefenamic acid, and metoprolol determined with the three consortiums indicated that ammonium-nitrite-oxidizing and heterotrophic biomass allow a partial biodegradation of the compounds, while no substantial biodegradation can be expected using nitrite-oxidizing consortium. Metoprolol was the less biodegradable compound. The sorption of fluoxetine and mefenamic acid onto biomass had a significant contribution for their removal (6-14%). The lowest sorption coefficients were obtained for metoprolol indicating that the sorption onto biomass is poor (3-4%), and the contribution of this process to the global removal can be neglected.

Mainstream partial nitritation-anammox in municipal wastewater treatment: status, bottlenecks, and further studies

Driven by energy neutral/positive of wastewater treatment plants, significant efforts have been made on the research and development of mainstream partial nitritation and anaerobic ammonium oxidation (anammox) (PN/A) (deammonification) process since the early 2010s. To date, feasibility of mainstream PN/A process has been demonstrated and proven by experimental results at various scales although with the low loading rates and elevated nitrogen concentration in the effluent at low temperatures (15-10 °C). This review paper provides an overview of the current state of research and development of mainstream PN/A process and critically analyzes the bottlenecks for its full-scale application. The paper discusses the following: (i) the current status of research and development of mainstream PN/A process; (ii) the interactions among aerobic ammonium-oxidizing bacteria, aerobic nitrite-oxidizing bacteria, anammox bacteria, and heterotrophic bacteria; (iii) the suppression of aerobic nitrite-oxidizing bacteria; (iv) process and bioreactors; and (v) suggested further studies including efficient and robust carbon concentrating pretreatment, deepening of understanding competition between autotrophic nitrogen-converting organisms, intensification of biofilm anammox activity, reactor design, and final polishing.

Artificial Intelligence for the Evaluation of Operational Parameters Influencing Nitrification and Nitrifiers in an Activated Sludge Process

Nitrification at a full-scale activated sludge plant treating municipal wastewater was monitored over a period of 237 days. A combination of fluorescent in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qPCR) were used for identifying and quantifying the dominant nitrifiers in the plant. Adaptive neuro-fuzzy inference system (ANFIS), Pearson's correlation coefficient, and quadratic models were employed in evaluating the plant operational conditions that influence the nitrification performance. The ammonia-oxidizing bacteria (AOB) abundance was within the range of 1.55 × 10(8)-1.65 × 10(10) copies L(-1), while Nitrobacter spp. and Nitrospira spp. were 9.32 × 10(9)-1.40 × 10(11) copies L(-1) and 2.39 × 10(9)-3.76 × 10(10) copies L(-1), respectively. Specific nitrification rate (qN) was significantly affected by temperature (r 0.726, p 0.002), hydraulic retention time (HRT) (r -0.651, p 0.009), and ammonia loading rate (ALR) (r 0.571, p 0.026). Additionally, AOB was considerably influenced by HRT (r -0.741, p 0.002) and temperature (r 0.517, p 0.048), while HRT negatively impacted Nitrospira spp. (r -0.627, p 0.012). A quadratic combination of HRT and food-to-microorganism (F/M) ratio also impacted qN (r (2) 0.50), AOB (r (2) 0.61), and Nitrospira spp. (r (2) 0.72), while Nitrobacter spp. was considerably influenced by a polynomial function of F/M ratio and temperature (r (2) 0.49). The study demonstrated that ANFIS could be used as a tool to describe the factors influencing nitrification process at full-scale wastewater treatment plants.

The effects of different seeding ratios on nitrification performance and biofilm formation in marine recirculating aquaculture system biofilter

Rapid start-up of biofilter is essential for intensive marine recirculating aquaculture system (RAS) production. This study evaluated the nitrifying biofilm formation using mature biofilm as an inoculum to accelerate the process in RAS practice. The effects of inoculation ratios (0-15 %) on the reactor performance and biofilm structure were investigated. Complete nitrification was achieved rapidly in reactors with inoculated mature biofilm (even in 32 days when 15 % seeding ratio was applied). However, the growth of target biofilm on blank carrier was affected by the mature biofilm inoculated through substrate competition. The analysis of extracellular polymeric substance (EPS) and nitrification rates confirmed the divergence of biofilm cultivation among reactors. Besides, three N-acyl-homoserine lactones (AHLs) were found in the process, which might regulate the activities of biofilm. Multivariate analysis based on non-metric multidimensional scaling (nMDS) also indicated the great roles of AHLs and substrate supply which might fundamentally determine varied cultivation performance on target biofilm.

A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is in contrast to new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate) and this finding will have far-reaching implications for nitrification research. We review recent work that has changed our perspective on NOB and provides a new basis for future studies on these enigmatic organisms.

Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach

Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO₂ concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the ‘High CO₂+Nitrogen+Precipitation’ treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.

Nitrification at different salinities: Biofilm community composition and physiological plasticity

This paper describes an experimental study of microbial communities of three moving bed biofilm reactors (MBBR) inoculated with nitrifying cultures originated from environments with different salinity; freshwater, brackish (20‰) and seawater. All reactors were run until they operated at a conversion efficiency of >96%. The microbial communities were profiled using 454-pyrosequencing of 16S rRNA gene amplicons. Statistical analysis was used to investigate the differences in microbial community structure and distribution of the nitrifying populations with different salinity environments. Nonmetric multidimensional scaling analysis (NMDS) and the PERMANOVA test based on Bray-Curtis similarities revealed significantly different community structure in the three reactors. The brackish reactor showed lower diversity index than fresh and seawater reactors. Venn diagram showed that 60 and 78% of the total operational taxonomic units (OTUs) in the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) guild, respectively, were unique OTUs for a given reactor. Similarity Percentages (SIMPER) analysis showed that two-thirds of the total difference in community structure between the reactors was explained by 10 OTUs, indicating that only a small number of OTUs play a numerically dominant role in the nitrification process. Acute toxicity of salt stress on ammonium and nitrite oxidizing activities showed distinctly different patterns, reaching 97% inhibition of the freshwater reactor for ammonium oxidation rate. In the brackish culture, inhibition was only observed at maximal level of salinity, 32‰. In the fully adapted seawater culture, higher activities were observed at 32‰ than at any of the lower salinities.

Differences in nitrite-oxidizing communities and kinetics in a brackish environment after enrichment at low and high nitrite concentrations

Nitrite accumulation in shrimp ponds can pose serious adverse effects to shrimp production and the environment. This study aims to develop an effective process for the enrichment of ready-to-use nitrite-oxidizing bacteria (NOB) inocula that would be appropriate for nitrite removal in brackish shrimp ponds. To achieve this objective, the effects of nitrite concentrations on NOB communities and nitrite oxidation kinetics in a brackish environment were investigated. Moving-bed biofilm sequencing batch reactors and continuous moving-bed biofilm reactors were used for the enrichment of NOB at various nitrite concentrations, using sediment from brackish shrimp ponds as seed inoculum. The results from NOB population analysis with quantitative polymerase chain reaction (qPCR) show that only Nitrospira were detected in the sediment from the shrimp ponds. After the enrichment, both Nitrospira and Nitrobacter coexisted in the reactors controlling effluent nitrite at 0.1 and 0.5 mg-NO2(-)-N/L. On the other hand, in the reactors controlling effluent nitrite at 3, 20, and 100 mg-NO2(-)-N/L, Nitrobacter outcompeted Nitrospira in many orders of magnitude. The half saturation coefficients (Ks) for nitrite oxidation of the enrichments at low nitrite concentrations (0.1 and 0.5 mg-NO2(-)-N/L) were in the range of 0.71-0.98 mg-NO2(-)-N/L. In contrast, the K(s) values of NOB enriched at high nitrite concentrations (3, 20, and 100 mg-NO2(-)-N/L) were much higher (8.36-12.20 mg-NO2(-)-N/L). The results suggest that the selection of nitrite concentrations for the enrichment of NOB inocula can significantly influence NOB populations and kinetics, which could affect the effectiveness of their applications in brackish shrimp ponds.

High-resolution phylogenetic microbial community profiling

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.

Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination

Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles.

Detection of nitrifiers and evaluation of partial nitrification for wastewater treatment: A review

Partial nitrification has gained broad interests in the biological nitrogen removal (BNR) from wastewater, since it alleviates carbon limitation issues and acts as a shortcut nitrogen removal system combined with anaerobic ammonium oxidation (Anammox) process. The occurrence and maintenance of partial nitrification relies on various conditions, which favor ammonium oxidizing bacteria (AOB) but inhibit or limit nitrite oxidizing bacteria (NOB). The studies of the AOB and NOB activities have been conducted by state-of-the-art molecular techniques, such as Polymerase Chain Reaction (PCR), Quantitative PCR, denaturing gradient gel electrophoresis (DGGE), Fluorescence in situ hybridization (FISH) technique, Terminal Restriction Fragment Length Polymorphism (T-RFLP), Live/Dead BacLight, and quinone profile. Furthermore, control strategies for obtaining partial nitrification are mainly focused on the pH, temperature, dissolved oxygen concentration, real-time aeration control, sludge retention time, substrate concentration, alternating anoxic and aerobic operation, inhibitor and ultrasonic treatment. Existing problems and further perspectives for the scale-up of partial nitrification are also proposed and suggested.

Impact of Water Chemistry, Pipe Material and Stagnation on the Building Plumbing Microbiome

A unique microbiome establishes in the portion of the potable water distribution system within homes and other buildings (i.e., building plumbing). To examine its composition and the factors that shape it, standardized cold water plumbing rigs were deployed at the treatment plant and in the distribution system of five water utilities across the U.S. Three pipe materials (copper with lead solder, CPVC with brass fittings or copper/lead combined pipe) were compared, with 8 hour flush cycles of 10 minutes to simulate typical daily use patterns. High throughput Illumina sequencing of 16S rRNA gene amplicons was employed to profile and compare the resident bulk water bacteria and archaea. The utility, location of the pipe rig, pipe material and stagnation all had a significant influence on the plumbing microbiome composition, but the utility source water and treatment practices were dominant factors. Examination of 21 water chemistry parameters suggested that the total chlorine concentration, pH, P, SO₄^2- and Mg were associated with the most of the variation in bulk water microbiome composition. Disinfectant type exerted a notably low-magnitude impact on microbiome composition. At two utilities using the same source water, slight differences in treatment approaches were associated with differences in rare taxa in samples. For genera containing opportunistic pathogens, Utility C samples (highest pH of 9–10) had the highest frequency of detection for Legionella spp. and lowest relative abundance of Mycobacterium spp. Data were examined across utilities to identify a true universal core, special core, and peripheral organisms to deepen insight into the physical and chemical factors that shape the building plumbing microbiome.

Influence of Partial Denitrification and Mixotrophic Growth of NOB on Microbial Distribution in Aerobic Granular Sludge

In aerobic granular sludge (AGS), the growth of nitrite oxidizing bacteria (NOB) can be uncoupled from the nitrite supply of ammonia oxidizing bacteria (AOB). Besides, unlike for conventional activated sludge, Nitrobacter was found to be the dominant NOB and not Nitrospira. To explain these experimental observations, two possible pathways have been put forward in literature. The first one involves the availability of additional nitrite from partial denitrification (nitrite-loop) and the second one consists of mixotrophic growth of Nitrobacter in the presence of acetate (ping-pong). In this contribution, mathematical models were set up to assess the possibility of these pathways to explain the reported observations. Simulation results revealed that both pathways influenced the nitrifier distribution in the granules. The nitrite-loop pathway led to an elevated NOB/AOB ratio, while mixotrophic growth of Nitrobacter guaranteed their predominance among the NOB population. Besides, mixotrophic growth of Nitrobacter could lead to NO emission from AGS. An increasing temperature and/or a decreasing oxygen concentration led to an elevated NOB/AOB ratio and increased NO emissions.