Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification-Anammox Bioreactor for Treating Ammonium at Low Loadings

Role of comammox bacteria in granular bioreactor for nitrogen removal via partial nitritation/anammox

In this study, two bioprocess models were first constructed with the newly-discovered comammox process described as one-step and two-step nitrification and evaluated against relevant experimental data. The validated models were then applied to reveal the potential effect of comammox bacteria on the granular bioreactor particularly suitable for undertaking partial nitritation/anammox (PN/A) under different operating conditions of bulk dissolved oxygen (DO) and influent NH4+. The results showed although comammox bacteria-based PN/A could achieve > 80.0 % total nitrogen (TN) removal over a relatively wider range of bulk DO and influent NH4+ (i.e., 0.25-0.40 g-O2/m3 and 470-870 g-N/m3, respectively) without significant nitrous oxide (N2O) production (< 0.1 %), the bulk DO should be finely controlled based on the influent NH4+ to avoid the undesired full nitrification by comammox bacteria. Comparatively, conventional ammonium-oxidizing bacteria (AOB)-based PN/A not only required higher bulk DO to achieve > 80.0 % TN removal but also suffered from 1.7 %∼2.8 % N2O production.

A critical review of comammox and synergistic nitrogen removal coupling anammox: Mechanisms and regulatory strategies

Nitrification is highly crucial for both anammox systems and the global nitrogen cycle. The discovery of complete ammonia oxidation (comammox) challenges the inherent concept of nitrification as a two-step process. Its wide distribution, adaptability to low substrate environments, low sludge production, and low greenhouse gas emissions may make it a promising new nitrogen removal treatment process. Meanwhile, anammox technology is considered the most suitable process for future wastewater treatment. The diverse metabolic capabilities and similar ecological niches of comammox bacteria and anammox bacteria are expected to achieve synergistic nitrogen removal within a single system. However, previous studies have overlooked the existence of comammox, and it is necessary to re-evaluate the conclusions drawn. This paper outlined the ecophysiological characteristics of comammox bacteria and summarized the environmental factors affecting their growth. Furthermore, it focused on the enrichment, regulatory strategies, and nitrogen removal mechanisms of comammox and anammox, with a comparative analysis of hydroxylamine, a particular intermediate product. Overall, this is the first critical overview of the conclusions drawn from the last few years of research on comammox-anammox, highlighting possible next steps for research.

Future directions in microbial nitrogen cycling in wastewater treatment

Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.

Comammox Nitrospira cooperate with anammox bacteria in a partial nitritation-anammox membrane bioreactor treating low-strength ammonium wastewater at high loadings

Research has revealed that comammox Nitrospira and anammox bacteria engage in dynamic interactions in partial nitritation-anammox reactors, where they compete for ammonium and nitrite or comammox Nitrospria supply nitrite to anammox bacteria. However, two gaps in the literature are present: the know-how to manipulate the interactions to foster a stable and symbiotic relationship and the assessment of how effective this partnership is for treating low-strength ammonium wastewater at high hydraulic loads. In this study, we employed a membrane bioreactor designed to treat synthetic ammonium wastewater at a concentration of 60 mg N/L, reaching a peak loading of 0.36 g N/L/day by gradually reducing the hydraulic retention time to 4 hr. Throughout the experiment, the reactor achieved an approximately 80 % nitrogen removal rate through strategically adjusting intermittent aeration at every stage. Notably, the genera Ca. Kuenena, Nitrosomonas, and Nitrospira collectively constituted approximately 40 % of the microbial community. Under superior intermittent aeration conditions, the expression of comammox amoA was consistently higher than that of Nitrospira nxrB and AOB amoA in the biofilm, despite the higher abundance of Nitrosomonas than comammox Nitrospira, implying that the biofilm environment is favorable for fostering cooperation between comammox and anammox bacteria. We then assessed the in situ activity of comammox Nitrospira in the reactor by selectively suppressing Nitrosomonas using 1-octyne, thereby confirming that comammox Nitrospira played the primary role in facilitating the nitritation (33.1 % of input ammonium) rather than complete nitrification (7.3 % of input ammonium). Kinetic analysis revealed a specific ammonia-oxidizing rate 5.3 times higher than the nitrite-oxidizing rate in the genus Nitrospira, underscoring their critical role in supplying nitrite. These findings provide novel insights into the cooperative interplay between comammox Nitrospira and anammox bacteria, potentially reshaping the management of nitrogen cycling in engineered environments, and aiding the development of microbial ecology-driven wastewater treatment technologies.

Complete ammonia oxidation (comammox) at pH 3-4 supports stable production of ammonium nitrate from urine

This study developed a new process that stably produced ammonium nitrate (NH4NO3), an important and commonly used fertilizer, from the source-separated urine by comammox Nitrospira. In the first stage, the complete conversion of ammonium to nitrate was achieved by comammox Nitrospira. In this scenario, the pH was maintained at 6 by adding external alkali, which also provided sufficient alkalinity for full nitrification. In the second stage, the NH4NO3 was produced directly by comammox Nitropsira by converting half of the ammonium in urine into nitrate. In this case, no alkali was added and pH automatically dropped and self-maintained at an extremely acidic level (pH 3-4). In both scenarios, negligible nitrite accumulation was observed, while the final product of the second stage contained ammonium and nitrate at the molar ratio of 1:1. The dominance of comammox Nitrospira over canonical ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was systematically proved by the combination of 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction, and metagenomics. Notably, metagenomic sequencing suggested that the relative abundance of comammox Nitrospira was over 20 % under the acidic condition at pH 3-4, while canonical AOB and NOB were undetectable. Batch experiments showed that the optimal pH for the enriched comammox Nitrospira was ∼7, which could sustain their activity in a wider pH range from 4 to 8 surprisingly but lost activity at pH 3 and 9. The findings not only present an application potential of comammox Nitrospira in nitrogen recovery from urine wastewater but also report the survivability of comammox bacteria in acidic environments.

Comammox and unknown ammonia oxidizers contribute to nitrite accumulation in an integrated A-B stage process that incorporates side-stream EBPR (S2EBPR)

A novel integrated pilot-scale A-stage high rate activated sludge, B-stage short-cut biological nitrogen removal and side-stream enhanced biological phosphorus removal (A/B-shortcut N-S2EBPR) process for treating municipal wastewater was demonstrated with the aim to achieve simultaneous and carbon- and energy-efficient N and P removal. In this studied period, an average of 7.62 ± 2.17 mg-N/L nitrite accumulation was achieved through atypical partial nitrification without canonical known NOB out-selection. Network analysis confirms the central hub of microbial community as Nitrospira, which was one to two orders of magnitude higher than canonical aerobic oxidizing bacteria (AOB) in a B-stage nitrification tank. The contribution of comammox Nitrospira as AOB was evidenced by the increased amoB/nxr ratio and higher ammonia oxidation activity. Furthermore, oligotyping analysis of Nitrospira revealed two dominant sub-clusters (microdiveristy) within the Nitrospira. The relative abundance of oligotype II, which is phylogenetically close to Nitrospira_midas_s_31566, exhibited a positive correlation with nitrite accumulation in the same operational period, suggesting its role as comammox Nitrospira. Additionally, the phylogenetic investigation suggested that heterotrophic organisms from the family Comamonadacea and the order Rhodocyclaceae embedding ammonia monooxygenase and hydroxylamine oxidase may function as heterotrophic nitrifiers. This is the first study that elucidated the impact of integrating the S2EBPR on nitrifying populations with implications on short-cut N removal. The unique conditions in the side-stream reactor, such as low ORP, favorable VFA concentrations and composition, seemed to exert different selective forces on nitrifying populations from those in conventional biological nutrient removal processes. The results provide new insights for integrating EBPR with short-cut N removal process for mainstream wastewater treatment.

Emerging biotechnological applications of anaerobic ammonium oxidation

Anaerobic ammonium oxidation (anammox) is an energy-efficient method for nitrogen removal that opens the possibility for energy-neutral wastewater treatment. Research on anammox over the past decade has primarily focused on its implementation in domestic wastewater treatment. However, emerging studies are now expanding its use to novel biotechnological applications and wastewater treatment processes. This review highlights recent advances in the anammox field that aim to overcome conventional bottlenecks, and explores novel and niche-specific applications of the anammox process. Despite the promising results and potential of these advances, challenges persist for their real-world implementation. This underscores the need for a transition from laboratory achievements to practical, scalable solutions for wastewater treatment which mark the next crucial phase in the evolution of anammox research.

C4-HSL-mediated quorum sensing regulates nitrogen removal in activated sludge process at Low temperatures

The activated sludge process faces challenges in achieving adequate nitrification ability under low-temperature conditions. Therefore, we investigated the effects of different concentrations of exogenous N-butyryl-homoserine lactone (C4-HSL) on nitrogen removal in lab-scale sequencing batch reactors (SBRs) at 10 °C. The results revealed that both 10 and 100 μg/L of C4-HSL could improve NH4+-N removal efficiency by 26% and reduce the effluent TN concentration to below 15 mg/L. Analysis of extracellular polymeric substances (EPS) revealed that adding C4-HSL (especially 100 μg/L) reduced the protein-like substance content while increasing the humic and fulvic acid-like substance content in EPS. Protein-like substances could serve as carbon sources for denitrifiers, thus promoting denitrification. Moreover, exogenous C4-HSL increased the abundance of bacteria and genes associated with nitrification and denitrification. Further analysis of quorum sensing (QS) of microorganisms indicated that exogenous C4-HSL (especially 100 μg/L) promoted regulation, transportation, and decomposition functions in the QS process. Furthermore, CS, sdh, fum, and mdh gene expressions involved in the tricarboxylic acid (TCA) cycle were enhanced by 100 μg/L C4-HSL. Exogenous C4-HSL promoted microbial communication, microbial energy metabolism, and nitrogen metabolism, thereby improving the nitrogen removal efficiency of activated sludge systems at low temperatures. This study provides a feasible strategy for enhancing denitrogenation performance at low temperatures through exogenous C4-HSL.

Competitive enrichment of comammox Nitrospira in floccular sludge

The discovery of complete ammonium oxidation (comammox) has subverted the traditional perception of two-step nitrification, which plays a key role in achieving biological nitrogen removal from wastewater. Floccular sludge-based treatment technologies are being applied at the majority of wastewater treatment plants in service where detection of various abundances and activities of comammox bacteria have been reported. However, limited efforts have been made to enrich and subsequently characterize comammox bacteria in floccular sludge. To this end, a lab-scale sequencing batch reactor (SBR) in the step-feeding mode was applied in this work to enrich comammox bacteria through controlling appropriate operational conditions (dissolved oxygen of 0.5 ± 0.1 g-O2/m3, influent ammonium of 40 g-N/m3 and uncontrolled longer sludge retention time). After 215-d operation, comammox bacteria gradually gained competitive advantages over counterparts in the SBR with a stable nitrification efficiency of 92.2 ± 2.2 %: the relative abundance of Nitrospira reached 42.9 ± 1.3 %, which was 13 times higher than that of Nitrosomonas, and the amoA gene level of comammox bacteria increased to 7.7 ± 2.1 × 106 copies/g-biomass, nearly 50 times higher than that of conventional ammonium-oxidizing bacteria. The enrichment of comammox bacteria, especially Clade A Candidatus Nitrospira nitrosa, in the floccular sludge led to (i) apparent affinity constants for ammonium and oxygen of 3.296 ± 0.989 g-N/m3 and 0.110 ± 0.004 g-O2/m3, respectively, and (ii) significantly low N2O and NO production, with emission factors being 0.136 ± 0.026 % and 0.023 ± 0.013 %, respectively.

Study of bacterial population dynamics in seed culture developed for ammonia reduction from synthetic wastewater

The waterbodies have been polluted by various natural and anthropogenic activities. The aquatic waste includes ammonia as one of the most toxic pollutants. Several biological treatment systems involving anoxic and semi anoxic bacteria have been proposed for reducing nitrogen loads from wastewater and increasing the efficiency and cost effectiveness. These bacteria play a vital role in the processes involved in the nitrogen cycle in nature. However, the enrichment, sustainability and identification of bacterial communities for wastewater treatment is an important aspect. Most of the chemolithotrophs are unculturable hence their identification and measurement of abundance remains a challenging task. In this study the different bacteria involved in total nitrogen removal from the wastewater are enriched for 700 days under anoxic condition. The synthetic wastewater containing 0.382 g/L of ammonium chloride was used. Molecular identification of the bacteria involved in various steps of the nitrogen cycle was carried out based on amplification of functional genes and 16S rRNA gene Polymerase chain reaction followed by DNA sequencing. Change in the abundance of chemolithotrophs was studied using qPCR. The mutual growth of various nitrifiers along with anaerobic bacteria were identified by molecular characterisation of DNA at various time intervals with the different genes involved in the nitrogen cycle. Nitrosomonas species like Nitrosomonas europaea were identified throughout the batch scale studies possessing the genes associated with ammonia oxidizing bacteria and nitrite oxidizing bacteria which act as a complete ammonia oxidizer. The uncultured species of Nitrospira and anammox bacteria were also observed which predicts the coexistence of the anammox and comammox bacteria in a batch scale study. The coexistence of the semi anoxic and anoxic bacteria helped in the growth of these bacteria for a longer duration of time. The nitrite produced by the comammox during nitrification can be utilized by anammox as an electron carrier. The other species of denitrifiers like Pseudomonas denitrificans and Aminobacter aminovorans were also observed. It is concluded that the enrichment of semi anoxic and anoxic bacteria was faster with the increase in growth of the bacteria involved in nitrification, comammox, anammox and partial denitrification process. The bacterial growth is enhanced and the efficiency is increased which can be further used in the development of small pilot scale bioreactor for total nitrogen removal.

Nitrous oxide emissions in novel wastewater treatment processes: A comprehensive review

The proliferation of novel wastewater treatment processes has marked recent years, becoming particularly pertinent in light of the strive for carbon neutrality. One area of growing attention within this context is nitrous oxide (N2O) production and emission. This review provides a comprehensive overview of recent research progress on N2O emissions associated with novel wastewater treatment processes, including Anammox, Partial Nitrification, Partial Denitrification, Comammox, Denitrifying Phosphorus Removal, Sulfur-driven Autotrophic Denitrification and n-DAMO. The advantages and challenges of these processes are thoroughly examined, and various mitigation strategies are proposed. An interesting angle that delve into is the potential of endogenous denitrification to act as an N2O sink. Furthermore, the review discusses the potential applications and rationale for novel Anammox-based processes to reduce N2O emissions. The aim is to inform future technology research in this area. Overall, this review aims to shed light on these emerging technologies while encouraging further research and development.

How to Provide Nitrite Robustly for Anaerobic Ammonium Oxidation in Mainstream Nitrogen Removal

Innovation in decarbonizing wastewater treatment is urgent in response to global climate change. The practical implementation of anaerobic ammonium oxidation (anammox) treating domestic wastewater is the key to reconciling carbon-neutral management of wastewater treatment with sustainable development. Nitrite availability is the prerequisite of the anammox reaction, but how to achieve robust nitrite supply and accumulation for mainstream systems remains elusive. This work presents a state-of-the-art review on the recent advances in nitrite supply for mainstream anammox, paying special attention to available pathways (forward-going (from ammonium to nitrite) and backward-going (from nitrate to nitrite)), key controlling strategies, and physiological and ecological characteristics of functional microorganisms involved in nitrite supply. First, we comprehensively assessed the mainstream nitrite-oxidizing bacteria control methods, outlining that these technologies are transitioning to technologies possessing multiple selective pressures (such as intermittent aeration and membrane-aerated biological reactor), integrating side stream treatment (such as free ammonia/free nitrous acid suppression in recirculated sludge treatment), and maintaining high activity of ammonia-oxidizing bacteria and anammox bacteria for competing oxygen and nitrite with nitrite-oxidizing bacteria. We then highlight emerging strategies of nitrite supply, including the nitrite production driven by novel ammonia-oxidizing microbes (ammonia-oxidizing archaea and complete ammonia oxidation bacteria) and nitrate reduction pathways (partial denitrification and nitrate-dependent anaerobic methane oxidation). The resources requirement of different mainstream nitrite supply pathways is analyzed, and a hybrid nitrite supply pathway by combining partial nitrification and nitrate reduction is encouraged. Moreover, data-driven modeling of a mainstream nitrite supply process as well as proactive microbiome management is proposed in the hope of achieving mainstream nitrite supply in practical application. Finally, the existing challenges and further perspectives are highlighted, i.e., investigation of nitrite-supplying bacteria, the scaling-up of hybrid nitrite supply technologies from laboratory to practical implementation under real conditions, and the data-driven management for the stable performance of mainstream nitrite supply. The fundamental insights in this review aim to inspire and advance our understanding about how to provide nitrite robustly for mainstream anammox and shed light on important obstacles warranting further settlement.

Model-based development of strategies enabling effective enrichment and application of comammox bacteria in floccular sludge under mainstream conditions

The discovery of complete ammonium oxidation (comammox) has redefined the perception of the nitrification process which plays a vital part in biological nitrogen removal (BNR) from wastewater. Despite the reported detection or cultivation of comammox bacteria in biofilm or granular sludge reactors, limited attempts have been made to enrich or assess comammox bacteria in floccular sludge reactors with suspended growth of microbes, which are most extensively applied at wastewater treatment plants. Therefore, through making use of a comammox-inclusive bioprocess model reliably evaluated using batch experimental data with joint contributions of different nitrifying guilds, this work probed into the proliferation and functioning of comammox bacteria in two commonly-used floccular sludge reactor configurations, i.e., continuous stirred tank reactor (CSTR) and sequencing batch reactor (SBR), under mainstream conditions. The results indicated that compared with the studied SBR, the CSTR was observed to favor the enrichment of comammox bacteria through maintaining a sufficient sludge retention time (40-100 d) while avoiding an extremely low DO level (e.g., 0.05 g-O2/m3), irrespective of the varied influent NH4+-N of 10-100 g-N/m3. Meanwhile, the inoculum sludge was found to greatly influence the start-up process of the studied CSTR. By inoculating the CSTR with a sufficient amount of sludge, finally enriched floccular sludge with a high abundance of comammox bacteria (up to 70.5 %) could be rapidly obtained. These results not only benefitted further investigation and application of comammox-inclusive sustainable BNR technologies but also explained, to some extent, the discrepancy in the reported presence and abundance of comammox bacteria at wastewater treatment plants adopting floccular sludge-based BNR technologies.

Microaerophilic Activated Sludge System for Ammonia Retention toward Recovery from High-Strength Nitrogenous Wastewater: Performance and Microbial Communities

A transition to ammonia recovery from wastewater has started; however, a technology for sustainable nitrogen retention in the form of ammonia and organic carbon removal is still in development. This study validated a microaerophilic activated sludge (MAS) system to efficiently retain ammonia from high-strength nitrogenous wastewater. The MAS is based on conventional activated sludge (CAS) with aerobic and settling compartments. Low dissolved oxygen (DO) concentrations (<0.2 mg/L) and short solids retention times (SRTs) (<5 days) eliminated nitrifying bacteria. The two parallel MASs were successfully operated for 300 days and had ammonia retention of 101.7 ± 24.9% and organic carbon removal of 85.5 ± 8.9%. The MASs mitigated N2O emissions with an emission factor of <0.23%, much lower than the default value of CAS (1.6%). A short-term step-change test demonstrated that N2O indicated the initiation of nitrification and the completion of denitrification in the MAS. The parallel MASs had comparable microbial diversity, promoting organic carbon oxidation while inhibiting ammonia-oxidizing microorganisms (AOMs), as revealed by 16S rRNA gene amplicon sequencing, the quantitative polymerase chain reaction of functional genes, and fluorescence in situ hybridization of β-proteobacteria AOB. The microbial analyses also uncovered that filamentous bacteria were positively correlated with effluent turbidity. Together, controlling DO and SRT achieved organic carbon removal and successful ammonia retention, mainly by suppressing AOM activity. This process represents a new nitrogen management paradigm.

Nitrite Oxidation in Wastewater Treatment: Microbial Adaptation and Suppression Challenges

Microbial nitrite oxidation is the primary pathway that generates nitrate in wastewater treatment systems and can be performed by a variety of microbes: namely, nitrite-oxidizing bacteria (NOB). Since NOB were first isolated 130 years ago, the understanding of the phylogenetical and physiological diversities of NOB has been gradually deepened. In recent endeavors of advanced biological nitrogen removal, NOB have been more considered as a troublesome disruptor, and strategies on NOB suppression often fail in practice after long-term operation due to the growth of specific NOB that are able to adapt to even harsh conditions. In line with a review of the history of currently known NOB genera, a phylogenetic tree is constructed to exhibit a wide range of NOB in different phyla. In addition, the growth behavior and metabolic performance of different NOB strains are summarized. These specific features of various NOB (e.g., high oxygen affinity of Nitrospira, tolerance to chemical inhibitors of Nitrobacter and Candidatus Nitrotoga, and preference to high temperature of Nitrolancea) highlight the differentiation of the NOB ecological niche in biological nitrogen processes and potentially support their adaptation to different suppression strategies (e.g., low dissolved oxygen, chemical treatment, and high temperature). This review implicates the acquired physiological characteristics of NOB to their emergence from a genomic and ecological perspective and emphasizes the importance of understanding physiological characterization and genomic information in future wastewater treatment studies.

Competitive and substrate limited environments drive metabolic heterogeneity for comammox Nitrospira

Nitrospira has been revealed as a high versatile genus. Although previously considered only responsible for the conversion of nitrite to nitrate, now we know that Nitrospira can perform complete ammonia oxidation to nitrate too (comammox). Comammox activity was firstly reported as dominant in extremely limited oxygen environments, where anaerobic ammonia oxidation was also occurring (anammox). To explain the comammox selection, we developed an Individual-based Model able to describe Nitrospira and anammox growth in suspended flocs assembled in a dynamic nitrogen and oxygen-limiting environment. All known and hypothesized nitrogen transformations of Nitrospira were considered: ammonia and nitrite oxidation, comammox, nitrate-reducing ammonia oxidation, and anaerobic nitrite-reducing ammonia oxidation. Through bioenergetics analysis, the growth yield associated to each activity was estimated. The other kinetic parameters necessary to describe growth were calibrated according to the reported literature values. Our modeling results suggest that even extremely low oxygen concentrations (~1.0 µM) allow for a proportional growth of anammox versus Nitrospira similar to the one experimentally observed. The strong oxygen limitation was followed by a limitation of ammonia and nitrite, because anammox, without strong competitors, were able to grow faster than Nitrospira depleting the environment in nitrogen. These substrate limitations created an extremely competitive environment that proved to be decisive in the community assembly of Nitrospira and anammox. Additionally, a diversity of metabolic activities for Nitrospira was observed in all tested conditions, which in turn, explained the transient nitrite accumulation observed in aerobic environments with higher ammonia availability.

Mainstream nitrogen removal from low temperature and low ammonium strength municipal wastewater using hydrogel-encapsulated comammox and anammox

Application of partial nitritation (PN)-anammox to mainstream wastewater treatment faces challenges in low water temperature and low ammonium strength. In this study, a continuous flow PN-anammox reactor with hydrogel-encapsulated comammox and anammox was designed and operated for nitrogen removal from mainstream wastewater with low temperature. Long-term operation with synthetic and real wastewater as the feed demonstrated nearly complete ammonium and total inorganic nitrogen (TIN) removal by the reactor at temperatures as low as 10 °C. A significantly decreased nitrogen removal performance and biomass activity was observed in the reactor at 4 °C before a selective heating strategy was employed. A novel heating technology using radiation to heat carbon black co-encapsulated in the hydrogel matrix with biomass was used to selectively heat biomass but not water in the treatment system. This selective heating technology enabled nearly complete ammonium removal and 89.4 ± 4.3 % TIN removal at influent temperature of 4 °C and reactor temperature 5 °C. Activity tests suggested selective heating brought the biomass activity at influent temperatures of 4 °C and reactor temperature 5 °C to a level comparable to that at 10 °C. Comammox and anammox were consistently present in the system and spatially organized in the hydrogel beads as revealed by qPCR and fluorescence in-situ hybridization (FISH). The abundance of comammox largely decreased by 3 orders of magnitude during the operation at 4 °C, and rapidly recovered after the application of selective heating. The anammox-comammox technology tested in this study essentially enabled mainstream shortcut nitrogen removal, and the selective heating ensured good performance of the technology at temperature as low as 5 °C.

Insights into the mechanism of the deterioration of mainstream partial nitritation/anammox under low residual ammonium

Residual ammonium is a critical parameter affecting the stability of mainstream partial nitritation/anammox (PN/A), but the underlying mechanism remains unclear. In this study, mainstream PN/A was established and operated with progressively decreasing residual ammonium. PN/A deteriorated as the residual ammonium decreased to below 5 mg/L, and this was paralleled by a significant loss in anammox activity in situ and an increasing nitrite oxidation rate. Further analysis revealed that the low-ammonium condition directly decreased anammox activity in situ via two distinct mechanisms. First, anammox bacteria were located in the inner layer of the granular sludge, and thus were disadvantageous when competing for ammonium with ammonium-oxidizing bacteria (AOB) in the outer layer. Second, the complete ammonia oxidizer (comammox) was enriched at low residual ammonium concentrations because of its high ammonium affinity. Both AOB and comammox presented kinetic advantages over anammox bacteria. At high residual ammonium concentrations, nitrite-oxidizing bacteria (NOB) were effectively suppressed, even when their maximum activity was high due to competition for nitrite with anammox bacteria. At low residual ammonium concentrations, the decrease in anammox activity in situ led to an increase in nitrite availability for nitrite oxidation, facilitating the activation of NOB despite the dissolved oxygen limitation (0.15-0.35 mg/L) for NOB persisting throughout the operation. Therefore, the deterioration of mainstream PN/A at low residual ammonium was primarily triggered by a decline in anammox activity in situ. This study provides novel insights into the optimized design of mainstream PN/As in engineering applications.

Co-Occurrence and Cooperation between Comammox and Anammox Bacteria in a Full-Scale Attached Growth Municipal Wastewater Treatment Process

Cooperation between comammox and anammox bacteria for nitrogen removal has been recently reported in laboratory-scale systems, including synthetic community constructs; however, there are no reports of full-scale municipal wastewater treatment systems with such cooperation. Here, we report intrinsic and extant kinetics as well as genome-resolved community characterization of a full-scale integrated fixed film activated sludge (IFAS) system where comammox and anammox bacteria co-occur and appear to drive nitrogen loss. Intrinsic batch kinetic assays indicated that majority of the aerobic ammonia oxidation was driven by comammox bacteria (1.75 ± 0.08 mg-N/g TS-h) in the attached growth phase, with minimal contribution by ammonia-oxidizing bacteria. Interestingly, a portion of total inorganic nitrogen (∼8%) was consistently lost during these aerobic assays. Aerobic nitrite oxidation assays eliminated the possibility of denitrification as a cause of nitrogen loss, while anaerobic ammonia oxidation assays resulted in rates consistent with anammox stoichiometry. Full-scale experiments at different dissolved oxygen (DO = 2 - 6 mg/L) setpoints indicated persistent nitrogen loss that was partly sensitive to DO concentrations. Genome-resolved metagenomics confirmed the high abundance (relative abundance 6.53 ± 0.34%) of two Brocadia-like anammox populations, while comammox bacteria within the Ca. Nitrospira nitrosa cluster were lower in abundance (0.37 ± 0.03%) and Nitrosomonas-like ammonia oxidizers were even lower (0.12 ± 0.02%). Collectively, our study reports for the first time the co-occurrence and cooperation of comammox and anammox bacteria in a full-scale municipal wastewater treatment system.

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.

Nitrogen-metabolising microorganism analysis in rapid sand filters from drinking water treatment plant

Sand filters (SFs) are common treatment processes for nitrogen pollutant removal in drinking water treatment plants (DWTPs). However, the mechanisms on the nitrogen-cycling role of SFs are still unclear. In this study, 16S rRNA gene amplicon sequencing was used to characterise the diversity and composition of the bacterial community in SFs from DWTPs. Additionally, metagenomics approach was used to determine the functional microorganisms involved in nitrogen cycle in SFs. Our results showed that Pseudomonadota, Acidobacteria, Nitrospirae and Chloroflexi dominated in SFs. Subsequently, 85 high-quality metagenome-assembled genomes (MAGs) were retrieved from metagenome datasets of selected SFs involving nitrification, assimilatory nitrogen reduction, denitrification and anaerobic ammonia oxidation (anammox) processes. Read mapping to reference genomes of Nitrospira and the phylogenetic tree of the ammonia monooxygenase subunit A gene, amoA, suggested that Nitrospira is abundantly found in SFs. Furthermore, according to their genetic content, a nitrogen metabolic model in SFs was proposed using representative MAGs and pure culture isolate. Quantitative real-time polymerase chain reaction (qPCR) showed that ammonia-oxidising bacteria (AOB) and archaea (AOA), and complete ammonia oxidisers (comammox) were ubiquitous in the SFs, with the abundance of comammox being higher than that of AOA and AOB. Moreover, we identified a bacterial strain with a high NO₃-N removal rate as Pseudomonas sp. DW-5, which could be applied in the bioremediation of micro-polluted drinking water sources. Our study provides insights into functional nitrogen-metabolising microbes in SFs of DWTPs.

Anaerobic Storage Completely Removes Suspected Fungal Pathogens but Increases Antibiotic Resistance Gene Levels in Swine Wastewater High in Sulfonamides

Wastewater storage before reuse is regulated in some countries. Investigations of pathogens and antibiotic resistance genes (ARGs) during wastewater storage are necessary for lowering the risks for wastewater reuse but are still mostly lacking. This study aimed to investigate pathogens, including harmful plant pathogens, and ARGs during 180 d of swine wastewater (SWW) storage in an anaerobic storage experiment. The contents of total organic carbon and total nitrogen in SWW were found to consistently decrease with the extension of storage time. Bacterial abundance and fungal abundance significantly decreased with storage time, which may be mainly attributed to nutrient loss during storage and the long period of exposure to a high level (4653.2 μg/L) of sulfonamides in the SWW, which have an inhibitory effect. It was found that suspected bacterial pathogens (e.g., Escherichia-Shigella spp., Vibrio spp., Arcobacter spp., Clostridium_sensu_stricto_1 spp., and Pseudomonas spp.) and sulfonamide-resistant genes Sul1, Sul2, Sul3, and SulA tended to persist and even become enriched during SWW storage. Interestingly, some suspected plant fungal species (e.g., Fusarium spp., Ustilago spp. and Blumeria spp.) were detected in SWW. Fungi in the SWW, including threatening fungal pathogens, were completely removed after 60 d of anaerobic storage, indicating that storage could lower the risk of using SWW in crop production. The results clearly indicate that storage time is crucial for SWW properties, and long periods of anaerobic storage could lead to substantial nutrient loss and enrichment of bacterial pathogens and ARGs in SWW.

Genome-centered metagenomics illuminates adaptations of core members to a partial Nitritation-Anammox bioreactor under periodic microaeration

The partial nitritation-anaerobic ammonium oxidation (anammox; PN-A) process has been considered a sustainable method for wastewater ammonium removal, with recent attempts to treat low-strength wastewater. However, how microbes adapt to the alternate microaerobic-anoxic operation of the process when treating low ammonium concentrations remains poorly understood. In this study, we applied a metagenomic approach to determine the genomic contents of core members in a PN-A reactor treating inorganic ammonium wastewater at loading as low as 0.0192 kg-N/m³/day. The metabolic traits of metagenome-assembled genomes from 18 core species were analyzed. Taxonomically diverse ammonia oxidizers, including two Nitrosomonas species, a comammox Nitrospira species, a novel Chloroflexota-related species, and two anammox bacteria, Ca. Brocadia and Ca. Jettenia, accounted for the PN-A reactions. The characteristics of a series of genes encoding class II ribonucleotide reductase, high-affinity bd-type terminal oxidase, and diverse antioxidant enzymes revealed that comammox Nitrospira has a superior adaptation ability over the competitors, which may confer the privileged partnership with anammox bacteria in the PN-A reactor. This finding is supported by the long-term monitoring experiment, showing the predominance of the comammox Nitrospira in the ammonia-oxidizing community. Metagenomic analysis of seven heterotrophs suggested that nitrate reduction is a common capability in potentially using endogenous carbohydrates and peptides to enhance nitrogen removals. The prevalence of class II ribonucleotide reductase and antioxidant enzymes genes may grant the adaptation to cyclically microaerobic/anoxic environments. The predominant heterotroph is affiliated with Chloroflexota; its genome encodes complete pathways for synthesizing vitamin B6 and methionine. By contrast, other than the two growth factors, Nitrospira and anammox bacteria are complementary to produce various vitamins and amino acids. Besides, the novel Chloroflexota-related ammonia oxidizer lacks corresponding genes for detoxifying the reactive oxygen species and thus requires the aid of co-existing members to alleviate oxidative stress. The analysis results forecast the exchanges of substrates and nutrients as well as the collective alleviation of oxidative stress among the core populations. The new findings of the genomic features and predicted microbial interplay shed light on microbial adaptation to intermittent microaeration specific to the PN-A reactor, which may aid in improving its application to low-strength ammonium wastewater.

Novel insights into aerobic duration control-based partial nitritation in source-separated blackwater treatment: Growth type, inoculation source, and comammox threat

Aerobic duration control (ADC), whereby aeration is terminated before nitrite is extremely oxidized during the nitrification process, is an effective strategy to achieve partial nitritation (PN) for blackwater. This study evaluated the effects of microbial growth type, influent ammonia-oxidizing organisms (AOO), and comammox bacteria from seeding sludge to ADC-based PN. The long-term operation of lab-scale reactors and model simulations were implemented to select the best growth type. The biofilm formed on the inner wall of the activated sludge reactor decreased the nitrite accumulation ratio (NAR) from 99.2% to 77.2%. Meanwhile, the NAR of the pure-biofilm reactor decreased from 95.9% to 47.8%. The deteriorated PN of the biofilm-related reactors was due to the extended solid retention time and increased substrate saturation constants of AOOs compared with those of nitrite-oxidizing organisms (NOO). Periodic biofilm carrier regeneration and biofilm thickness control can recover PN performance but are difficult to implement. In contrast, the optimized activated sludge reactor exhibited high (NAR >94%) and stable (>3 months) PN performance when treating real blackwater. Nitrifiers were found in blackwater, and chemically enhanced high-rate activated sludge pretreatment removed more NOOs than AOOs (41.8% vs. 24.3%) and increased the influent AOO/NOO ratio. Interestingly, the influent AOOs supported fast PN start-up in the moving-bed biofilm reactor without the initial inoculation of activated sludge. Moreover, model simulations verified that high and stable PN could also be realized in an activated sludge reactor by the continuous inoculation of influent AOOs, which is a novel PN start-up strategy. Metagenomic analyses showed that the comammox bacteria from the seeding sludge eventually disappeared owing to their intrinsic specific growth rates and free ammonia inhibition. The findings of this study will provide insightful guidelines for PN application in decentralized and semi-centralized wastewater treatment systems.

Predominance of comammox bacteria among ammonia oxidizers under low dissolved oxygen condition

Although low-oxygen nitrification can significantly cut down the aeration demand in wastewater treatment plants, little is known about the community dynamics of relevant microorganisms under different oxygen concentrations. Here, by conducting a series of bioreactors with oxygen concentrations of 0%, 2%, 5%, 10%, 20%, 40%, and 70%, we provided a comprehensive investigation on the behaviors and performances of comammox bacteria (CMX), ammonia-oxidizing bacteria (AOB) and archaea (AOA) during the nitrification process. Quantitative PCR analysis demonstrated that CMX was the dominant ammonia-oxidizer under low oxygen condition (10%) after the four-month operation with the abundance increased by 8.65 times higher than the initial operation, whereas the growth of AOA and AOB was inhibited. Moreover, Nitrospira nitrosa dominated the CMX species (relative abundance >96%) in low dissolved oxygen concentrations, while Nitrospira nitrificans (3.39%) seemed to prefer high oxygen conditions. Our study indicates the long-term effects of oxygen concentrations on the niche differentiation of ammonia oxidizers, and highlights the significance of CMX in low-oxygen nitrification for reducing global carbon emission and energy consumption.

Double anammox process in the AOAO process of treating real low C/N sewage: Validation, enhancement, and quantification of the contribution of anammox in the oxic zone

Enhancement of anaerobic ammonium oxidation (anammox) process and enrichment of anammox bacteria in the oxic zone of mainstream sewage treatments are complex. Also, quantification of the anammox contribution for nitrogen removal in the oxic zone is hindered owing to the simultaneous occurrence of anammox and nitrification. An alternating anaerobic/oxic/anoxic/oxic bioreactor whose oxic zone boosted partial nitrification coupling anammox (PN/A) and anoxic zone boosted partial denitrification coupling anammox (PD/A), respectively, was operated to treat real sewage for >380 days. Desirable nitrogen removal (effluent total inorganic nitrogen (TIN) of 4.7 ± 1.9 mg N/L) was obtained from low carbon/nitrogen (3.6 ± 0.5) sewage with ammonium concentration of 52.5 ± 2.2 mg N/L in the influent. Under the condition of dissolved oxygen (DO) of 1.5-3 mg/L, anammox bacteria was still enriched within the aerobic biofilms, with the relative abundance increasing to 8.2 % (day 345) from 0 % (no biomass on day 1), which was higher than the value in the flocculent sludge (0.03 %) (P < 0.001). PN driven by flocculent sludge with high activity of ammonium oxidized bacteria (AOB) ensured sufficient nitrite supply for the anammox process with the existence of continuous DO. During the steady operation period, the maximum anammox contribution in the oxic zone was quantified to be 10.6 % by withdrawing aerobic biofilms from the system.

New insights into modeling two-step nitrification in activated sludge systems - The effects of initial biomass concentrations, comammox and heterotrophic activities

In this study, the conventional two-step nitrification model was extended with complete ammonia oxidation (comammox) and heterotrophic denitrification on soluble microbial products. The data for model calibration/validation were collected at four long-term washout experiments when the solid retention time (SRT) and hydraulic retention time (HRT) were progressively reduced from 4 d to 1 d, with mixed liquor suspended solids (MLSS) of approximately 2000 mg/L at the start of each trial. A new calibration protocol was proposed by including a systematic calculation of the initial biomass concentrations and microbial relationships as the calibration targets. Moreover, the impact assessment of initial biomass concentrations (X) and maximum growth rates (μ) for ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), comammox Nitrospira, and heterotrophs on the calibration accuracy were investigated using the response surface methodology (RSM). The RSM results revealed the strongest interaction of X_AOB and μ_AOB on the model calibration accuracy. All the examined model efficiency measures confirmed that the extended model was accurately calibrated and validated. The estimated μ values were as follows: μ_AOB = 0.38 ± 0.005 d^-1, μ_NOB = 0.20 ± 0.01 d^-1, μ_CMX = 0.20 ± 0.01 d^-1, μ_HET = 1.0 ± 0.03 d^-1. For comparison, when using the conventional model, μ_AOB and μ_NOB increased respectively by 26 and 15 % (μ_AOB = 0.48 ± 0.02 d^-1 and μ_NOB = 0.23 ± 0.005 d^-1). This study provides better understanding of the effects of the initial biomass composition and the accompanying processes (comammox and heterotrophic denitrification) on modeling two-step nitrification.

Evaluation of a liquid-phase plasma discharge process for ammonia oxidation in wastewater: Process optimization and kinetic modeling

Removing ammonia-nitrogen (NH₃N) from wastewater is of paramount importance for wastewater treatment. In this study, a novel continuous liquid plasma process (CLPD) was evaluated to remove NH₃N from synthetic wastewater. The Box-Behnken experimental design was used to optimize the main process parameters, including the initial NH₃N concentration (50-200 mg/L), power input (150-300 W), and gas-flow rate (1.5-2.5 L/min), for efficient NH₃N removal from wastewater. The gas-flow rate and power input were found to be significant factors affecting the removal efficiency of NH₃N, whereas the initial concentration of NH₃N played a vital role in determining the energy efficiency of the process. Under the optimal conditions of an initial NH₃N concentration of 200 mg/L, applied power of 223 W, and gas-flow rate of 2.4 L/min, 98.91% of NH₃N could be removed with a N₂ selectivity of 92.91%, and the corresponding energy efficiency was 0.527 g/kWh after 2 hrs of treatment. A small fraction of undesirable NO₃^--N (7.05 mg/L) and NO₂^--N (2.83 mg/L) were also produced. Kinetic modeling revealed that NH₃N degradation by the CLPD followed a pseudo-first-order reaction model, with a rate constant (k) of 0.03522 min^-1. Optical emission spectroscopy (OES) was used to gather information about the active chemical species produced during the plasma discharge. The obtained spectra revealed the presence of several highly oxidative radicals, including ‧OH, ‧O, and ‧O₂⁺. These results demonstrate the potential of liquid phase plasma discharge as a highly efficient technology for removing ammonia from aqueous solutions.

Establishment and optimization of partial nitrification/anammox/partial nitrification/anammox (PN/A/PN/A) process based on multi-stage ammonia oxidation: Using response surface method as a tool

The presence of nitrite-oxidizing bacteria (NOB) when treating low-strength ammonia wastewater was a challenge in the application of the PN/A process. The partial nitrification/ANAMMOX/partial nitrification/ANAMMOX (PN/A/PN/A) process based on multiple oxidations of ammonia was proposed to solve this problem. The influence of independent variables such as nitrite concentration was analyzed based on the response surface method (RSM). The model showed that nitrite concentration has an adverse impact on ammonia removal efficiency and nitrite accumulation rate. The model provided optimal parameters for the PN/A/PN/A process: the dissolved oxygen concentration was 0.60 mg/L, and the cycle duration was 90 min. Advanced nitrogen removal was achieved by maintaining the nitrite concentration below 10.0 mg/L. The nitrogen removal efficiency was 81.44 ± 4.15 %, and the nitrogen removal rate was 0.18 ± 0.02 kg N/(m³⋅d). Potential functions of microorganisms were analyzed by functional annotation of prokaryotic taxa (FAPROTAX) and the correlation network analysis was performed.

Deciphering the concurrence of comammox, partial denitrification and anammox in a single low-oxygen mainstream nitrogen removal reactor

One-stage anammox-based autotrophic nitrogen removal technology has attracted increasing interest to sustainable biological nitrogen removal for future wastewater treatment. However, its application in mainstream municipal wastewater treatment is still challenging due to low nitrogen and high organics of raw wastewater. Herein, a novel Simultaneous Carbon Oxidation, partial Comammox, Denitratation and Anammox (SCOCDA) was firstly developed in a single sequencing batch biofilm reactor operated at a dissolved oxygen concentration of ∼0.5 mg/L for treating synthetic municipal wastewater (50 mg/L NH₄⁺-N and 100-250 mg/L COD). The long-term operation showed that almost complete COD and nitrogen removal performance could be achieved at a carbon/nitrogen ratio (COD/NH₄⁺-N) of 3-5 with the corresponding effluent total nitrogen (TN)＜5 mg/L. Microbial community and amoA-targeting amplicon sequencing analysis further verified that comammox Nitrospira spp., denitrifier Thauera and other aerobic/facultative heterotrophs could work synergistically with anammox bacteria, Candidatus Kuenenia. Moreover, nitrogen metabolic and inorganic carbon fixation pathways through the interaction between comammox and anammox were also revealed with the aid of Kyoto Encyclopedia of Genes and Genomes (KEGG). Lastly, potential application of proposed SCOCDA process was illustrated. This research sheds new light on advanced nitrogen removal towards limit of technology via the synergy of comammox and anammox.

Selective Enrichment of Comammox Nitrospira in a Moving Bed Biofilm Reactor with Sufficient Oxygen Supply

The recent discovery of comammox (complete ammonia oxidation) Nitrospira has upended the long-held nitrification paradigm. Although comammox Nitrospira have been identified in wastewater treatment systems, the conditions for their dominance over canonical ammonia oxidizers remain unclear. Here, we report the dominance of comammox Nitrospira in a moving bed biofilm reactor (MBBR) fed with synthetic mainstream wastewater. Integrated 16S rRNA gene amplicon sequencing, fluorescence in situ hybridization (FISH), and metagenomic sequencing methods demonstrated the selective enrichment of comammox bacteria when the MBBR was operated at a dissolved oxygen (DO) concentration above 6 mg O₂/L. The dominance of comammox Nitrospira over canonical ammonia oxidizers (i.e., Nitrosomonas) was attributed to the low residual ammonium concentration (0.02-0.52 mg N/L) formed in the high-DO MBBR. Two clade A comammox Nitrospira were identified, which are phylogenetically close to Candidatus Nitrospira nitrosa. Interestingly, cryosectioning-FISH showed these two comammox species spatially distributed on the surface of the biofilm. Moreover, the ammonia-oxidizing activity of comammox Nitrospira-dominated biofilms was susceptible to the oxygen supply, which dropped by half with the DO concentration decrease from 6 to 2 mg O₂/L. These features collectively suggest a low apparent oxygen affinity for the comammox Nitrospira-dominated biofilms in the high-DO nitrifying MBBR.

Comammox Nitrospira Bacteria Are Dominant Ammonia Oxidizers in Mainstream Nitrification Bioreactors Emended with Sponge Carriers

Complete ammonia oxidation (i.e., comammox) is a newly discovered microbial process performed by a subset of the Nitrospira genus, and this unique microbial process has been ubiquitously detected in various wastewater treatment units. However, the operational conditions favoring comammox prevalence remain unclear. In this study, the dominance of comammox Nitrospira in four sponge biofilm reactors fed with low-strength ammonium (NH₄⁺ = 23 ± 3 mg N/L) wastewater was proved by coupling 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. The results showed that comammox Nitrospira dominated in the nitrifying guild over canonical ammonia-oxidizing bacteria (AOB) constantly, despite the significant variation in the residual ammonium concentration (0.01-15 mg N/L) under different sets of operating conditions. This result indicates that sponge biofilms greatly favor retaining comammox Nitrospira in wastewater treatment and highlights an essential role of biomass retention in the comammox prevalence. Moreover, analyses of the assembled metagenomic sequences revealed that the retrieved amoA gene sequences affiliated with comammox Nitrospira (53.9-66.0% read counts of total amoA gene reads) were always higher than those (28.4-43.4%) related to β-proteobacterial AOB taxa. The comammox Nitrospira bacteria detected in the present biofilm systems were close to clade A Candidatus Nitrospira nitrosa.

Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge

Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.

Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox)

In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N₂O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.

Microbial response on the first full-scale DEMON® biomass transfer for mainstream deammonification

Sidestream partial nitritation and deammonification (pN/A) of high-strength ammonia wastewater is a well-established technology. Its expansion to the mainstream is, however mainly impeded by poor retention of anaerobic ammonia oxidizing bacteria (AnAOB), insufficient repression of nitrite oxidizing bacteria (NOB) and difficult control of soluble chemical oxygen demand and nitrite levels. At the municipal wastewater treatment plant in Strass (Austria) the microbial consortium was exhaustively monitored at full-scale over one and a half year with regular transfer of sidestream DEMON® biomass and further retention and enrichment of granular anammox biomass via hydrocyclone operation. Routine process parameters were surveyed and the response and evolution of the microbiota was followed by molecular tools, ex-situ activity tests and further, AnAOB quantification through particle tracking and heme measurement. After eight months of operation, the first anaerobic, simultaneous depletion of ammonia and nitrite was observed ex-situ, together with a direction to higher nitrite generation (68% of total NO_x-N) as compared to nitrate under aerobic conditions. Our dissolved oxygen (DO) scheme allowed for transient anoxic conditions and had a strong influence on nitrite levels and the NOB community, where Nitrobacter eventually dominated Nitrospira. The establishment of a minor but stable AnAOB biomass was accompanied by the rise of Chloroflexi and distinct emergence of Chlorobi, a trend not seen in the sidestream system. Interestingly, the most pronounced switch in the microbial community and noticeable NOB repression occurred during unfavorable conditions, i.e. the cold winter season and high organic load. Further abatement of NOB was achieved through bioaugmentation of aerobic ammonia oxidizing bacteria (AerAOB) from the sidestream-DEMON® tank. Performance of the sidestream pN/A was not impaired by this operational scheme and the average volumetric nitrogen removal rate of the mainstream even doubled in the second half of the monitoring campaign. We conclude that a combination of both, regular sidestream-DEMON® biomass transfer and granular SRT increase via hydrocyclone operation was crucial for AnAOB establishment within the mainstream.

A 20-Year Journey of Partial Nitritation and Anammox (PN/A): from Sidestream toward Mainstream

Anaerobic ammonium oxidation (anammox) was discovered as a new microbial reaction in the late 1990s, which led to the development of an innovative energy- and carbon-efficient technology─partial nitritation and anammox (PN/A)─for nitrogen removal. PN/A was first applied to remove the nitrogen from high-strength wastewaters, e.g., anaerobic digestion liquor (i.e., sidestream), and further expanded to the main line of wastewater treatment plants (i.e., mainstream). While sidestream PN/A has been well-established with extensive full-scale installations worldwide, practical application of PN/A in mainstream treatment has been proven extremely challenging to date. A key challenge is achieving stable suppression of nitrite-oxidizing bacteria (NOB). This study examines the progress of NOB suppression in both sidestream- and mainstream PN/A over the past two decades. The successful NOB suppression in sidestream PN/A was reviewed, and these successes were evaluated in terms of their transferability into mainstream PN/A. Drawing on the learning over the past decades, we anticipate that a hybrid process, comprised of biofilm and floccular sludge, bears great potential to achieve efficient mainstream PN/A, while a combination of strategies is entailed for stable NOB suppression. Furthermore, the recent discovery of novel nitrifiers would trigger new opportunities and new challenges for mainstream PN/A.

Niche differentiation of comammox Nitrospira in sediments of the Three Gorges Reservoir typical tributaries, China

Complete ammonia oxidizer (Comammox) can complete the whole nitrification process independently, whose niche differentiation is important guarantee for its survival and ecological function. This study investigated the niche differentiation of comammox Nitrospira in the sediments of three typical tributaries of the Three Gorges Reservoir (TGR). Clade A and clade B of comammox Nitrospira coexisted in all sampling sites simultaneously. The amoA gene abundance of clade A and B was gradually increased or decreased along the flow path of the three tributaries with obvious spatial differentiation. The amoA gene abundance of comammox Nitrospira clade A (6.36 × 10³ - 5.06 × 10⁴ copies g^-1 dry sediment) was higher than that of clade B (6.26 × 10² - 6.27 × 10³ copies g^-1 dry sediment), and the clade A amoA gene abundance was one order of magnitude higher than that of AOA (7.24 × 10² - 6.89 × 10³ copies g^-1 dry sediment) and AOB (1.44 × 10² - 1.46 × 10³ copies g^-1 dry sediment). A significant positive correlation was observed between comammox Nitrospira clade A amoA gene abundance and flow distance (P < 0.05). The number of operational taxonomic units (OTUs) in two sub-clades of clade A accounted for the majority in different tributaries, indicating that clade A also had population differentiation among different tributaries. This study revealed that comammox Nitrospira in the sediments of TGR tributaries have niche differentiation and clade A.2 played a more crucial role in comammox Nitrospira community.

Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability in biofiltration systems

Complete ammonia oxidizing bacteria coexist with canonical ammonia and nitrite oxidizing bacteria in a wide range of environments. Whether this is due to competitive or cooperative interactions, or a result of niche separation is not yet clear. Understanding the factors driving coexistence of nitrifiers is critical to manage nitrification processes occurring in engineered and natural ecosystems. In this study, microcosm-based experiments were used to investigate the impact of nitrogen source and loading on the population dynamics of nitrifiers in drinking water biofilter media. Shotgun sequencing of DNA followed by co-assembly and reconstruction of metagenome assembled genomes revealed clade A2 comammox bacteria were likely the primary nitrifiers within microcosms and increased in abundance over Nitrsomonas-like ammonia and Nitrospira-like nitrite oxidizing bacteria irrespective of nitrogen source type or loading. Changes in comammox bacterial abundance did not correlate with either ammonia or nitrite oxidizing bacterial abundance in urea amended systems where metabolic reconstruction indicated potential for cross feeding between ammonia and nitrite oxidizing bacteria. In contrast, comammox bacterial abundance demonstrated a negative correlation with nitrite oxidizers in ammonia amended systems. This suggests potentially weaker synergistic relationships between ammonia and nitrite oxidizers might enable comammox bacteria to displace nitrite oxidizers from complex nitrifying communities.

Distinct comammox Nitrospira catalyze ammonia oxidation in a full-scale groundwater treatment bioreactor under copper limited conditions

Microbial ammonia oxidation is the initial nitrification step used in biological nitrogen-removal during water treatment processes, and the discovery of complete ammonia-oxidizing (comammox) bacteria added a novel member to this functional group. It is important to identify and understand the predominant microorganisms responsible for ammonium removal in biotechnological process design and optimization. In this study, we used a full-scale bioreactor to treat ammonium in groundwater (9.3 ± 0.5 mg NH₄⁺-N/L) and investigated the key ammonia-oxidizing prokaryotes present. The groundwater ammonium was stably and efficiently oxidized throughout ∼700 days of bioreactor operation. 16S rRNA gene amplicon sequencing of the bioreactor community showed a high abundance of Nitrospira (12.5-45.9%), with the dominant sequence variant (3.5-37.8%) most closely related to Candidatus Nitrospira nitrosa. Furthermore, analyses of amoA, the marker gene for ammonia oxidation, indicated the presence of two distinct comammox Nitrospira populations, however, the relative abundance of only one of these populations was strongly correlated to ammonia oxidation rates and was robustly expressed. After 380 days of operation copper wires were immersed into the reactor at 0.04-0.06 m²/m³ tank, which caused a gradual abundance increase of one discrete comammox Nitrospira population. However, further increase of the copper dosing (0.08 m²/m³ tank) inverted the most abundant ammonia-oxidizing population to Nitrosomonas sp. These results indicate that comammox Nitrospira were capable of efficient ammonium removal in groundwater without exogenous nutrients, but copper addition can stimulate comammox Nitrospira or lead to dominance of Nitrosomonas depending on dosage.

A successful start-up of an anaerobic membrane bioreactor (AnMBR) coupled mainstream partial nitritation-anammox (PN/A) system: A pilot-scale study on in-situ NOB elimination, AnAOB growth kinetics, and mainstream treatment performance

In this pilot-scale study, an innovative mainstream treatment process that couples the anaerobic membrane reactor (AnMBR) with a one-stage PN/A system was proposed for advancing the concept of carbon neutrality in the municipal wastewater treatment plant. This work demonstrates the start-up procedure of a pilot-scale one-stage PN/A system for mainstream treatment. The 255-day start-up of the one-stage PN/A system involved the cultivation of ammonium-oxidizing bacteria (AOB) from the activated sludge, suppression of nitrite-oxidizing bacteria (NOB), investigation of in-situ growth kinetics of anammox bacteria (AnAOB), and the 50-day operation of the pilot-scale AnMBR-PN/A process for natural mainstream treatment. It is verified in the pilot-scale system for the first time that the in-situ free ammonia (FA) and free nitrous acid (FNA) exposure could effectively eliminate the Nitrospira (the NOB genus) while retaining the Nitosonomas (the AOB genus) community in the suspended sludge. NOB community rebounding was not detected even at the mainstream conditions with low nitrogen concentrations (Influent ammonium concentration=38±6 mg-NH₄⁺-N/L) by intermittent aeration to control the system dissolved oxygen (DO) below 0.5 mg/L. The results of the mainstream treatment showed that the average effluent total nitrogen (TN) in the coupled process was generally lower than 10 mg-N/L, which meets the discharge limits of most prefectures in Japan. The investigated results of the in-situ anammox bacteria (AnAOB) growth kinetics suggested that the promoted start-up strategy of taking advantage of the warm months with higher mainstream temperature to achieve the rapid in-situ growth of the AnAOB is applicable in the investigated regions. From the perspective of the removal performance of the TN and organic substance, the AnMBR-PN/A process has great potential as the layouts of the carbon-neutral mainstream wastewater treatment plants.

Role of air scouring in anaerobic/anoxic tanks providing nitrogen removal by mainstream anammox conversion in a hybrid biofilm/suspended growth full-scale WWTP in China

A full-scale wastewater treatment plant in China experienced unintentional anammox bacterial enrichment on biofilm carriers placed in the anaerobic and anoxic zones of an anaerobic/anoxic/oxic process under ambient temperatures and without bioaugmentation. Here, we show that microaerophilic conditions resulting from air scouring needed for biofilm carrier suspension in the anaerobic/anoxic zones can support a robust nitritation/anammox process. Results from an in situ on/off air scouring test showed that air scouring strongly induced both ammonia and total inorganic nitrogen removal in the anaerobic/anoxic zones. Ammonium concentration in the anaerobic and anoxic tanks remained constant or even slightly increased when air scouring was off, indicating that air scouring made a noticeable difference in nitrogen profiles in the anaerobic/anoxic zones. Various batch tests further indicated that partial denitrification is not likely to generate nitrite for anammox bacteria. Robust nitritation, and anammox on the carriers, can occur at low dissolved oxygen conditions, as measured in the full-scale facility. The observations show that mainstream deammonification without sidestream bioaugmentation at moderate temperature is feasible and further optimization by a more dedicated design can result in improved nitrogen removal in cases when chemical oxygen demand is limited in mainstream wastewater treatment. PRACTITIONER POINTS: Microaerophilic conditions in a full-scale IFAS reactor caused mainstream anammox in moderate temperate area. Robust nitritation, and anammox on the carriers, can occur at low dissolved oxygen conditions in anaerobic/anoxic tanks with air scouring. Anammox can function well with conventional nitrification and denitrification process at mainstream conditions for stable nitrogen removal.

Insights into Nitrous Oxide Mitigation Strategies in Wastewater Treatment and Challenges for Wider Implementation

Nitrous oxide (N₂O) emissions account for the majority of the carbon footprint of wastewater treatment plants (WWTPs). Many N₂O mitigation strategies have since been developed while a holistic view is still missing. This article reviews the state-of-the-art of N₂O mitigation studies in wastewater treatment. Through analyzing existing studies, this article presents the essential knowledge to guide N₂O mitigations, and the logics behind mitigation strategies. In practice, mitigations are mainly carried out by aeration control, feed scheme optimization, and process optimization. Despite increasingly more studies, real implementation remains rare, which is a combined result of unclear climate change policies/incentives, as well as technical challenges. Five critical technical challenges, as well as opportunities, of N₂O mitigations were identified. It is proposed that (i) quantification methods for overall N₂O emissions and pathway contributions need improvement; (ii) a reliable while straightforward mathematical model is required to quantify benefits and compare mitigation strategies; (iii) tailored risk assessment needs to be conducted for WWTPs, in which more long-term full-scale trials of N₂O mitigation are urgently needed to enable robust assessments of the resulting operational costs and impact on nutrient removal performance; (iv) current mitigation strategies focus on centralized WWTPs, more investigations are warranted for decentralised systems, especially decentralized activated sludge WWTPs; and (v) N₂O may be mitigated by adopting novel strategies promoting N₂O reduction denitrification or microorganisms that emit less N₂O. Overall, we conclude N₂O mitigation research is reaching a maturity while challenges still exist for a wider implementation, especially in relation to the reliability of N₂O mitigation strategies and potential risks to nutrient removal performances of WWTPs.