Efficient nitrification and low N(2)O emission in a weakly acidic bioreactor at low dissolved oxygen levels are due to comammox

Path to zero emission of nitrous oxide in sewage treatment: is nitrification controllable or avoidable?

Amid growing concerns over climate change, the need to reduce nitrous oxide (N2O) emissions from sewage treatment is more urgent than ever. Sewage treatment plants are significant sources of N2O due to its production as an intermediate in nitrification and its release into the air during aeration. Effective management of the nitrification process is therefore vital for controlling or eliminating these emissions. Despite substantial efforts to quantify and understand N2O emissions from sewage treatment, success in reducing them has been limited. This review discusses and proposes promising solutions for reducing N2O emissions in sewage treatment, evaluates the potential of various strategies, and identifies ways to accelerate their development and implementation.

Comammox Nitrospira act as key bacteria in weakly acidic soil via potential cobalamin sharing

The discovery of comammox Nitrospira in low pH environments has reshaped the ammonia oxidation process in acidic settings, providing a plausible explanation for the higher nitrification rates observed in weakly acidic soils. However, the response of comammox Nitrospira to varying pH levels and its ecological role in these environments remains unclear. Here, a survey across soils with varying pH values (ranging from 4.4 to 9.7) was conducted to assess how comammox Nitrospira perform under different pH conditions. Results showed that comammox Nitrospira dominate ammonia oxidation in weakly acidic soils, functioning as a K-strategy species characterized by slow growth and stress tolerance. As a key species in this environment, comammox Nitrospira may promote bacterial cooperation under low pH conditions. Genomic evidence suggested that cobalamin sharing is a potential mechanism, as comammox Nitrospira uniquely encode a metabolic pathway that compensates for cobalamin imbalance in weakly acidic soils, where 86.8% of metagenome-assembled genomes (MAGs) encode cobalamin-dependent genes. Additionally, we used DNA stable-isotope probing (DNA-SIP) to demonstrate its response to pH fluctuations to reflect how it responds to the decrease in pH. Results confirmed that comammox Nitrospira became dominant ammonia oxidizers in the soil after the decrease in pH. We suggested that comammox Nitrospira will become increasingly important in global soils, under the trend of soil acidification. Overall, our work provides insights that how comammox Nitrospira perform in weakly acidic soil and its response to pH changes.

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.

Comammox Nitrospira was the dominant ammonia oxidizer in an acidic biofilm reactor at pH 5.5 and pH 5

Nitrification is a vital process in the biological removal of inorganic nitrogen compounds. In order to ensure the stability and effectiveness of this process, buffer solutions should be added to the system to maintain neutral to slightly alkaline conditions. With a focus on the newly discovered comammox Nitrospira, this research investigates the transition of the nitrifying community within a biofilm reactor under different acidic levels (initiated at pH 6 and gradually decreased to pH 5). During the 305-day continuous operation experiment, it was observed that responsible ammonia oxidizers transitioned from ammonia-oxidizing bacteria (AOB) during the initial stages (setup stage and early stage of pH 6) to comammox Nitrospira under pH 5.5 and pH 5. Further analysis using next-generation sequencing targeting both the 16S rRNA region and amoA region revealed a shift in the dominant cluster of both Nitrospirae and comammox Nitrospira under varying pH conditions. Our study identified a distinct cluster of comammox Nitrospira that is phylogenetically closed to sequences found in acidic environments, but exhibits dissimilarity from known comammox Nitrospira isolates and the majority of environmental sequences. This cluster was found to be prevalent in the acidic biofilm reactor studied and thrived particularly well at pH 5. These findings underscore the potential significance of this distinct, uncultivated group of comammox Nitrospira in performing ammonia oxidation under acidic conditions. KEY POINTS: • Ammonia was effectively removed under pH 5.5 and 5 in the biofilm reactor • The dominant ammonia oxidizer was comammox Nitrospira when pH was 5.5 and 5 • A potential acidophilic cluster of comammox Nitrospira was identified in this acidic biofilm reactor.

Successful operation of nitrifying granules at low pH in a continuous-flow reactor: Nitrification performance, granule stability, and microbial community

Acidic nitrification, as a novel process for treating wastewater without sufficient alkalinity, has received increasing attention over the years. In this study, a continuous-flow reactor with aerobic granular sludge was successful operated at low pH (<6.5) performing high-rate acidic nitrification. Volumetric ammonium oxidation rate of 0.4-1.2 kg/(m3·d) were achieved with the specific biomass activities of 5.8-13.9 mg N/(gVSS·h). Stable partial nitritation with nitrite accumulation efficiency over 85% could be maintained at pH above 6 with the aid of residual ammonium, whereas the nitrite accumulation disappeared when pH was below 6. Interestingly, the granule morphology significantly improved during the acidic operation. The increased secretion of extracellular polymeric substances (especially polysaccharides) suggested a self-protective behavior of microbes in the aerobic granules against acidic stress. 16S rRNA gene sequencing analyses indicated that Candidatus Nitrospira defluvii was always the dominant nitrite-oxidizing bacteria, while the dominant ammonia-oxidizing bacteria shifted from Nitrosomonas europaea to Nitrosomonas mobilis. This study, for the first time, demonstrated the improved stability of aerobic granules under acidic conditions, and also highlighted aerobic granules as a useful solution to achieve high-rate acidic nitrification.

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.

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.

Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding

COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4+ to NO3- alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.

Greenhouse gases emissions from aquaculture ponds: Different emission patterns and key microbial processes affected by increased nitrogen loading

Global aquaculture production is expected to rise to meet the growing demand for food worldwide, potentially leading to increased anthropogenic greenhouse gases (GHG) emissions. As the demand for fish protein increases, so will stocking density, feeding amounts, and nitrogen loading in aquaculture ponds. However, the impact of GHG emissions and the underlying microbial processes remain poorly understood. This study investigated the GHG emission characteristics, key microbial processes, and environmental drivers underlying GHG emissions in low and high nitrogen loading aquaculture ponds (LNP and HNP). The N2O flux in HNP (43.1 ± 11.3 μmol m-2 d-1) was significantly higher than in LNP (-11.3 ± 25.1 μmol m-2 d-1), while the dissolved N2O concentration in HNP (52.8 ± 7.1 nmol L-1) was 150 % higher than in LNP (p < 0.01). However, the methane (CH4) and carbon dioxide (CO2) fluxes and concentrations showed no significant differences (p > 0.05). N2O replaced CH4 as the main source of Global Warming Potential in HNP. Pond sediments acted as a sink for N2O but a source for CH4 and CO2. The △N2O/(△N2O + △N2) in HNP (0.015 ± 0.007 %) was 7.7-fold higher than in LNP (0.002 ± 0.001 %) (p < 0.05). The chemical oxygen demand to NO2-N ratio was the most important environmental factor explaining the variability of N2O fluxes. Ammonia-oxidizing bacteria driven nitrification in water was the predominant N2O source, while comammox-driven nitrification and nosZII-driven N2O reduction in water were key processes for reducing N2O emission in LNP but decreased in HNP. The strong CH4 oxidization by Methylocystis and CO2 assimilation by algae resulted in low CH4 emissions and CO2 sink in the aquaculture pond. The Mantel test indicated that HNP increased N2O fluxes mainly through altering functional genes composition in water and sediment. Our findings suggest that there is a significant underestimation of N2O emissions without considering the significantly increased △N2O/(△N2O + △N2) caused by increased nitrogen loading.

Effects of carbon to nitrogen ratio on nitrogen removal in a single-stage microaerobic system: A model-based evaluation

Single-stage microaerobic systems have been proven to be effective for concurrent removal of ammonium and organic carbon from sewage. While mechanistic models derived from activated sludge models (ASMs) have simulated nutrients removal under microaerobic conditions, classic ASMs exhibit limitations in capturing the intricate effects of carbon to nitrogen (C/N) ratio on nitrogen removal performance. To address this issue, a mechanistic model modified from the classic ASMs was proposed to capture the combined inhibitory effects of carbon and ammonium on microaerobic systems. This modified model was established based on experimental data from a single-stage microaerobic reactor encompassing simultaneous nitrification-denitrification and anammox processes. The inhibition coefficient of C/N ratio was integrated into the process rate equations, and its effectiveness was validated through model performance evaluation. Compared to the classic models, the modified one achieved superior predictions for nitrite and nitrate nitrogen concentrations. Simulations revealed that under optimized conditions with a C/N of 4.57 and a dissolved oxygen (DO) of 0.41 mg/L, the system could achieve up to 95.5% of total nitrogen (TN) removal efficiency. Based on the simulation of substrate uptake/production rate, increasing the nitrogen loading rate (NLR) rather than organic loading rate (OLR) was crucial for efficient nitrogen removal. The proposed modified model served as a valuable tool for designing and optimizing similar biological wastewater treatment systems.

Enhancing the relative abundance of comammox nitrospira in ammonia oxidizer community decreases N2O emission in nitrification exponentially

Comammox Nitrospira and canonical ammonia-oxidizing bacteria (cAOB) generally coexist in activated sludge. In present study, the effect of comammox Nitrospira on N2O production during nitrification of activated sludge was investigated. Comammox Nitrospira and cAOB were separately enriched in two nitrifying reactors, with respective relative abundance of approximately 98% in ammonia oxidizer community. The N2O emission factor (EF) of nitrification in comammox Nitrospira dominated reactor was 0.35%, consistently lower than that (2.2%) in cAOB dominated reactor. When increasing the relative abundance of comammox Nitrospira in ammonia oxidizer community, the N2O EF of nitrification decreased exponentially, which suggested that comammox Nitrospira not only decreased N2O production directly but also might have reduced N2O yield by cAOB. When cAOB dominated the ammonia oxidizer community of sludge, decreasing pH to 6.3, lowering DO to less than 0.5 mg/L, and increasing nitrite concentration enhanced N2O EF dramatically. When comammox Nitrospira became the dominant ammonia oxidizer, however, the N2O EF correlated to nitrite insignificantly and a low DO of 0.2 mg/L and weakly acidic pH (6.3) decreased N2O EF by approximately 70% and 60%, respectively. These results imply that enhancing the relative abundance of comammox Nitrospira in sludge is an effective way to reducing N2O emissions and can also offset the promoting effects of acidic pH, low DO, and high nitrite concentration on N2O production during nitrification.

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.

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.

Efficient nitrogen removal from municipal wastewater by an autotrophic-heterotrophic coupled anammox system: The up-regulation of key functional genes

The metabolic pathways based on key functional genes were innovatively revealed in the autotrophic-heterotrophic coupled anammox system for real municipal wastewater treatment. The nitrogen removal performance of the system was stabilized at 88.40 ± 3.39 % during the treatment of real municipal wastewater. The relative abundances of the nitrification functional genes ammonia oxidase (amoA/B/C), hydroxylamine oxidoreductase (hao), and nitrite oxidoreductases (nxrA/B) were increased by 1.2-2.4 times, and these three nitrification functional genes were mostly contributed by Nitrospira that dominated the efficient nitrification of the system. The relative abundance of anammox bacteria Candidatus Brocadia augmented from 0.35 % to 0.75 %, accompanied with the increased expression of hydrazine synthase (hzs) and hydrazine dehydrogenase (hdh), resulting in the major role of anammox (81.24 %) for nitrogen removal. The expression enhancement of the functional genes nitrite reductase (narG/H, napA/B) that promoted partial denitrification (PD) of the system weakened the adverse effects of the sharp decline in the population of PD microbe Thauera (from 5.7 % to 2.2 %). The metabolic module analysis indicated that the carbon metabolism pathways of the system mainly included CO2 fixation and organic carbon metabolism, and the stable enrichment of autotrophic bacteria ensured stable CO2 fixation. Furthermore, the enhanced expression of the glucokinases (glk, GCK, HK, ppgk) and the abundant pyruvate kinase (PK) achieved stable hydrolysis ability of organic carbon metabolism function of the system. This study offers research basics to practical application of the mainstream anammox process.

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.

Metagenomic insights into the effects of benzyl dodecyl dimethyl ammonium bromide (BDAB) shock on bacteria-driven nitrogen removal in a moving-bed biofilm reactor (MBBR)

The use of disinfectants made from quaternary ammonium compounds (QACs) has greatly increased since the outbreak of SARS-CoV-2. However, the effect of QACs on wastewater treatment performance is still unclear. In this study, a commonly used QAC, i.e., benzyl dodecyl dimethyl ammonium bromide (BDAB), was added to a moving-bed biofilm reactor (MBBR) to investigate BDAB's effect on nutrient removal. When the BDAB concentration was increased to 50 mg L^-1, the ammonia removal efficiency (ARE) greatly decreased, as did the nitrate production rate constants (NPR). This inhibition was partly recovered by decreasing the BDAB concentration to 30 mg L^-1. Metagenomic sequencing revealed the functional genera present during different stages of the control (Rc) and BDAB-added reactors (Re). The enriched genera (Rudaea, Nitrosospira, Sphingomonas, and Rhodanobacter) in Rc mainly related to the nitrogen metabolism, while the enriched genera in Re was BDAB-concentration dependent. Functional genes analysis suggested that a lack of ammonia oxidase-encoding genes (amoABC) may have caused a decrease in ARE in Re, while the efflux pump-encoding genes emrE, mdfA, and oprM and a gene encoding BAC oxygenase (oxyBAC) were responsible for BDAB resistance. The increase in the total abundance of antibiotic resistance genes (ARGs) in Re revealed a potential risk arising from BDAB. Overall, this study revealed the potential effect and ecological risks of BDAB introduction in WWTPs.

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

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

Low diversity and microdiversity of comammox bacteria in wastewater systems suggest specific adaptations within the Ca. Nitrospira nitrosa cluster

Studies have found Ca. Nitrospira nitrosa-like bacteria to be the principal or sole comammox bacteria in nitrogen removal systems for wastewater treatment. In contrast, multiple populations of strict ammonia and nitrite oxidizers co-exist in similar systems. This apparent lack of diversity is surprising and could impact the feasibility of leveraging comammox bacteria for nitrogen removal. We used full-length 16S rRNA gene sequencing and genome-resolved metagenomics to compare the species-level diversity of comammox bacteria with that of strict nitrifiers in full-scale wastewater treatment systems and assess whether this comparison is consistent or diverged at the strain-level. Full-length 16S rRNA gene sequencing indicated that Nitrosomonas-like bacteria exhibited higher species-level diversity in comparison with other nitrifying bacteria, while the strain-level diversity (also called microdiversity) of most Nitrospira-like bacteria were higher than Nitrosomonas-like bacteria with few exceptions (one Nitrospira lineage II population). Comammox bacterial metagenome assembled genomes (MAGs) were associated with Ca. Nitrospira nitrosa. The average amino acid identity between principal comammox bacterial MAGs (93% ± 3) across systems was significantly higher than that of the Nitrosomonas-like ammonia oxidizers (73% ± 8), the Nitrospira_A-like nitrite oxidizer (85% ± 4), and the Nitrospira_D-like nitrite oxidizer (83% ± 1). This demonstrated the low species-level diversity of comammox bacteria compared with strict nitrifiers and further suggests that the same comammox population was detected in all systems. Comammox bacteria (Nitrospira lineage II), Nitrosomonas and, Nitrospira_D (Nitrospira lineage II) MAGs were significantly less microdiverse than the Nitrospira_A (lineage I) MAGs. Interestingly, strain-resolved analysis also indicates that different nitrogen removal systems harbor different comammox bacterial strains within the Ca. Nitrospira nitrosa cluster. These results suggest that comammox bacteria associated with Ca. Nitrospira nitrosa have low species- and strain-level diversity in nitrogen removal systems and may thus harbor specific adaptations to the wastewater ecosystem.

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.

Suppressing Methane Production to Boost High-Purity Hydrogen Production in Microbial Electrolysis Cells

Hydrogen gas (H₂) is an attractive fuel carrier due to its high specific enthalpy; moreover, it is a clean source of energy because in the combustion reaction with oxygen (O₂) it produces water as the only byproduct. The microbial electrolysis cell (MEC) is a promising technology for producing H₂ from simple or complex organics present in wastewater and solid wastes. Methanogens and non-archaeal methane (CH₄)-producing microorganisms (NAMPMs) often grow in the MECs and lead to rapid conversion of produced H₂ to CH₄. Moreover, non-archaeal methane production (NAMP) catalyzed by nitrogenase of photosynthetic bacteria was always overlooked. Thus, suppression of CH₄ production is required to enhance H₂ yield and production rate. This review comprehensively addresses the principles and current state-of-the-art technologies for suppressing methanogenesis and NAMP in MECs. Noteworthy, specific strategies aimed at the inhibition of methanogenic enzymes and nitrogenase could be a more direct approach than physical and chemical strategies for repressing the growth of methanogenic archaea. In-depth studies on the multiomics of CH₄ metabolism can possibly provide insights into sustainable and efficient approaches for suppressing metabolic pathways of methanogenesis and NAMP. The main objective of this review is to highlight key concepts, directions, and challenges related to boosting H₂ generation by suppressing CH₄ production in MECs. Finally, perspectives are briefly outlined to guide and advance the future direction of MECs for production of high-purity H₂ based on genetic and metabolic engineering and on the interspecific interactions.

Dissolved oxygen control strategies for water treatment: a review

Dissolved oxygen (DO) is one of the most important water quality factors. Maintaining the DO concentration at a desired level is of great value to both wastewater treatment plants (WWTPs) and aquaculture. This review covers various DO control strategies proposed by researchers around the world in the past 20 years. The review focuses on published research related to determination and control of DO concentrations in WWTPs in order to improve control accuracy, save aeration energy, improve effluent quality, and achieve nitrogen removal. The strategies used for DO control are categorized and discussed through the following classification: classical control such as proportional-integral-derivative (PID) control, advanced control such as model-based predictive control, intelligent control such as fuzzy and neural networks, and hybrid control. The review also includes the prediction and control strategies of DO concentration in aquaculture. Finally, a critical discussion on DO control is provided. Only a few advanced DO control strategies have achieved successful implementation, while PID controllers are still the most widely used and effective controllers in engineering practice. The challenges and limitations for a broader implementation of the advanced control strategies are analyzed and discussed.

Abundance and Niche Differentiation of Comammox in the Sludges of Wastewater Treatment Plants That Use the Anaerobic-Anoxic-Aerobic Process

Complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate, were recently identified and found to be ubiquitous in artificial systems. Research on the abundance and niche differentiation of comammox in the sludges of wastewater treatment plants (WWTPs) would be useful for improving the nitrogen removal efficiency of WWTPs. Here, we investigated the relative abundance and diversity of comammox in fifteen sludges of five WWTPs that use the anaerobic−anoxic−aerobic process in Jinan, China, via quantitative polymerase chain reaction and high-throughput sequencing of the 16S rRNA gene and ammonia monooxygenase gene. In the activated sludges in the WWTPs, comammox clade A.1 was widely distributed and mostly comprised Candidatus Nitrospira nitrosa-like comammox (>98% of all comammox). The proportion of this clade was negatively correlated (p < 0.01) with the dissolved oxygen (DO) level (1.7−8 mg/L), and slight pH changes (7.20−7.70) affected the structure of the comammox populations. Nitrospira lineage I frequently coexisted with Nitrosomonas, which generally had a significant positive correlation (p < 0.05) with the DO level. Our study provided an insight into the structure of comammox and other nitrifier populations in WWTPs that use the anaerobic−anoxic−aerobic process, broadening the knowledge about the effects of DO on comammox and other nitrifiers.

Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms during wastewater treatment processes

Studies on antibiotic removal during wastewater treatment processes are crucial since their release into the environment could bring potential threats to human health and ecosystem. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms (AOMs) has received special attentions due to the enhanced removal of antibiotics during nitrification processes. However, the interactions between antibiotics and AOMs are less well-elucidated. In this review, the recent research proceedings on cometabolic biodegradation of antibiotics by AOMs were summarized. Ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) played significant roles in both nitrification and cometabolic biodegradation of antibiotics. Antibiotics at varying concentrations might pose inhibiting or stimulating effect on AOMs, influencing the microbial activity, community abundance and ammonia monooxygenase subunit A gene expression level. AOMs-induced cometabolic biodegradation products were analyzed as well as the corresponding pathways for each type of antibiotics. The effects of ammonium availability, initial antibiotic concentration, sludge retention time and temperature were assessed on the cometabolic biodegradation efficiencies of antibiotics. This work might provide further insights into the fate and removal of antibiotics during nitrification processes.

Development of an aquaponics microbial inoculum for efficient nitrification at acidic pH

Maintaining an optimal pH that simultaneously supports plants, fish, and nitrifying microorganisms is a challenge in recirculating aquaponics systems as nitrification is optimal at a slightly alkaline pH and plant growth is optimal at a slightly acidic pH. Freshwater fish tolerate pH > 5.5. Our aim was to adapt a microbial inoculum for a recirculating aquaponics system from an operational pH of 7.6 to 5.6, compare nitrification activity and production of N₂O, and describe changes in the adapted versus unadapted microbial communities. Four adaptation strategies were tested; our results indicated that a gradual reduction from pH 7.6 to 5.6, along with a gradual reduction followed by a gradual return of available ammonium, was the best strategy resulting in retention of 81% nitrification activity at pH 5.6 compared to pH 7.6. 16S rRNA gene amplicon sequencing and qPCR enumeration of nitrification-related genes showed that the composition of pH 5.6 adapted microbial communities from all four adaptation strategies was similar to one another and distinct from those operating at pH 7.6, with enrichment of comammox clade B bacteria over ammonia-oxidizing bacteria and thaumarchaeota. N₂O production of the pH 5.6 adapted microbial communities was below detection in all adaptation experiments, likely due to the increased proportion of comammox bacteria. Aquaponics biofilters enriched with comammox bacteria and adapted to function at pH 5.6 can be a desirable inoculum for freshwater recirculating aquaponics systems to retain nitrification activity and improve crop yields.Key points• Microbial communities adapted from pH 7.6 to pH 5.6 retained 81% nitrification activity.• Microbial communities adapted from pH 7.6 to pH 5.6 were enriched in comammox bacteria.• Comammox-enriched microbial communities did not produce N₂ O.

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.