Detection of comammox bacteria in full-scale wastewater treatment bioreactors using tag-454-pyrosequencing

Detection of pathogenic, heteropathogenic and hybrid Escherichia coli strains in psittacines from zoos and breeders in the state of Ceará, Brazil

The current study aimed to detect virulence, hetero-pathogenicity, and hybridization genes in Escherichia coli strains, previously isolated from cloacal swabs in commercial breeding psittacines and zoological collections, via multiplex PCR. A total of 68 strains of E. coli, previously isolated from psittacines in zoos and commercial breeding facilities in Ceará, Brazil, were assessed for the presence of the following genes and/or probes: eae, bfpA (EPEC - Enteropathogenic E. coli), CVD432 (EAEC - Enteroaggregative E. coli); LT gene and ST gene (ETEC - Enterotoxigenic E. coli); ipaH (EIEC - Enteroinvasive E. coli); stx1 and stx2 (STEC - Shiga toxin-producing E. coli); iroN, ompT, hlyF, iss, and iutA (APEC - Avian pathogenic E. coli). Of the 68 E. coli strains analyzed, 61 (98.7 %) were positive for the following genes and/or probes: Stx1 (61/98.7 %), ST gene (54/79.4 %), CVD432 (49/72 %), bfpA (44/64.7 %), eae (42/61.8 %), Stx2 (41/60.3 %), ipaH (34/50 %), LT gene (33/48.5 %), iroN (21/30.9 %), hlyF (11/6.2 %), iss (06/8.8 %) and iutA (06/8.8 %). The following diarrheagenic pathotypes were identified: 66 (97 %) from STEC, 49 (72 %) from EAEC, 35 (52 %) from EIEC, 25 (37 %) from ETEC, and one (1.5 %) from EPEC. Regarding hetero-pathogenicity, 50 (74 %) heterogeneous strains were identified. Positivity for APEC was seen in four (6 %) strains, all characterized as pathogenic hybrids. This study describes significant associations of virulence factors in E. coli strains DEC/DEC and DEC/APEC, which were isolated from psittacines and may be potentially harmful to One Health.

Metatranscriptomic Analysis Reveals Synergistic Activities of Comammox and Anammox Bacteria in Full-Scale Attached Growth Nitrogen Removal System

Leveraging comammox Nitrospira and anammox bacteria for shortcut nitrogen removal can drastically lower the carbon footprint of wastewater treatment facilities by decreasing aeration energy, carbon, alkalinity, and tank volume requirements while also potentially reducing nitrous oxide emissions. However, their co-occurrence as dominant nitrifying bacteria is rarely reported in full-scale wastewater treatment. As a result, there is a poor understanding of how operational parameters, in particular, dissolved oxygen, impact their activity and synergistic behavior. Here, we report the impact of dissolved oxygen concentration (DO = 2, 4, 6 mg/L) on the microbial community's transcriptomic expression in a full-scale integrated fixed film activated sludge (IFAS) municipal wastewater treatment facility where nitrogen removal is predominantly performed by comammox Nitrospira and anammox bacterial populations. 16S rRNA transcript compositions revealed anammox bacteria and Nitrospira were significantly more active in IFAS biofilms compared to suspended sludge biomass. In IFAS biofilms, anammox bacteria significantly increased hzo expression at lower dissolved oxygen concentrations and this increase was highly correlated with the amoA expression levels of comammox bacteria. Interestingly, the genes involved in nitrite oxidation by comammox bacteria were significantly more upregulated, relative to the genes involved in ammonia oxidation with decreasing dissolved oxygen concentrations. Ultimately, our findings suggest that comammox Nitrospira supplies anammox bacteria with nitrite via ammonia oxidation and that this synergistic behavior is dependent on dissolved oxygen concentrations.

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.

Conventional activated sludge vs. photo-sequencing batch reactor for enhanced nitrogen removal in municipal wastewater: Microalgal-bacterial consortium and pathogenic load insights

Municipal wastewater treatment plants are mostly based on traditional activated sludge (AS) processes. These systems are characterised by major drawbacks: high energy consumption, large amount of excess sludge and high greenhouse gases emissions. Treatment through microalgal-bacterial consortia (MBC) is an alternative and promising solution thanks to lower energy consumption and emissions, biomass production and water sanitation. Here, microbial difference between a traditional anaerobic sludge (AS) and a consortium-based system (photo-sequencing batch reactor (PSBR)) with the same wastewater inlet were characterised through shotgun metagenomics. Stable nitrification was achieved in the PSBR ensuring ammonium removal > 95 % and significant total nitrogen removal thanks to larger flocs enhancing denitrification. The new system showed enhanced pathogen removal, a higher abundance of photosynthetic and denitrifying microorganisms with a reduced emissions potential identifying this novel PSBR as an effective alternative to AS.

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.

Wastewater treatment from a science faculty during the COVID-19 pandemic by using ammonium-oxidising and heterotrophic bacteria

During and after the pandemic caused by the SARS-CoV-2 virus, the use of personal care products and disinfectants increased in universities worldwide. Among these, quaternary ammonium-based products stand out; these compounds and their intermediates caused substantial changes in the chemical composition of the wastewater produced by these institutions. For this reason, improvements and environmentally sustainable biological alternatives were introduced in the existing treatment systems so that these institutions could continue their research and teaching activities. For this reason, the objective of this study was to develop an improved culture medium to cultivate ammonium oxidising bacteria (AOB) to increase the biomass and use them in the treatment of wastewater produced in a faculty of sciences in Bogotá, D.C., Colombia. A Plackett Burman Experimental Design (PBED) and growth curves served for oligotrophic culture medium, and production conditions improved for the AOB. Finally, these bacteria were used with total heterotrophic bacteria (THB) for wastewater treatment in a pilot plant. Modification of base ammonium broth and culture conditions (6607 mg L-1 of (NH4)2SO4, 84 mg L-1 CaCO3, 40 mg L-1 MgSO4·7H2O, 40 mg L-1 CaCl2·2H2O and 200 mg L-1 KH2PO4, 10% (w/v) inoculum, no copper addition, pH 7.0 ± 0.2, 200 r.p.m., 30 days) favoured the growth of Nitrosomonas europea, Nitrosococcus oceani, and Nitrosospira multiformis with values of 8.23 ± 1.9, 7.56 ± 0.7 and 4.2 ± 0.4 Log10 CFU mL-1, respectively. NO2- production was 0.396 ± 0.0264, 0.247 ± 0.013 and 0.185 ± 0.003 mg L-1 for Nitrosomonas europea, Nitrosococcus oceani and Nitrosospira multiformis. After the 5-day wastewater treatment (WW) by co-inoculating the three studied bacteria in the wastewater (with their self-microorganisms), the concentrations of AOB and THB were 5.92 and 9.3 Log10 CFU mL-1, respectively. These values were related to the oxidative decrease of Chemical Oxygen Demand (COD), (39.5 mg L-1), Ammonium ion (NH4+), (6.5 mg L-1) Nitrite (NO2-), (2.0 mg L-1) and Nitrate (NO3-), (1.5 mg L-1), respectively in the five days of treatment. It was concluded, with the improvement of a culture medium and production conditions for three AOB through biotechnological strategies at the laboratory scale, being a promising alternative to bio-augment of the biomass of the studied bacteria under controlled conditions that allow the aerobic removal of COD and nitrogen cycle intermediates present in the studied wastewater.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03961-4.

Case study: Bioaugmenting the comammox dominated biomass from B-stage to enhance nitrification in A-stage at Blue Plains AWWTP

A comprehensive case study was undertaken at the Blue Plains wastewater treatment plant (WWTP) to explore the bioaugmentation technique of introducing nitrifying sludge into the non-nitrifying stage over the course of two operational years. This innovative approach involved the return of waste activated sludge (WAS) from the biological nutrient removal (BNR) system to enhance the nitrification in the high carbon removal rate system. The complete ammonia oxidizer (comammox) Nitrospira Nitrosa was identified as the main nitrifier in the system. Bioaugmentation was shown to be successful as nitrifiers returned from BNR were able to increase the nitrifying activity of the high carbon removal rate system. There was a positive correlation between returned sludge from the BNR stage and the specific total kjeldahl nitrogen (TKN) removal rate in A stage. The bioaugmentation process resulted in a remarkable threefold increase in the specific TKN removal rate within the A stage. Result suggested that recycling of WAS is a simple technique to bio-augment a low SRT system with nitrifiers and add ammonia oxidation to a previously non-nitrifying stage. The results from this case study hold the potential for applicable implications for other WWTPs that have a similar operational scheme to Blue Plains, allowing them to reuse WAS from the B stage, previously considered waste, to enhance nitrification and thus improving overall nitrogen removal performance. PRACTITIONER POINTS: Comammox identifying as main nitrifier in the B stage. Comammox enriched sludge from B stage successfully bio-augmented the East side of A stage up to threefold. Bioaugmentation of comammox in the West side of A stage was potentially inhibited by the gravity thickened overflow. Sludge returned from B stage to A stage can improve nitrification with a very minor retrofits and short startup times.

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.

Nitrospira dominant pin-point flocs with granule-like settleability in stirred tank reactors with oxic/hypoxic/oxic zones

The characteristics of biomass and microbial community dynamics, in relation to autotrophic nitrification, were studied in two 20 L stirred tank reactors (STR) with oxic/hypoxic/oxic zones. The bioreactors were fed with synthetic wastewater with stepwise increasing ammonia concentrations (50-200 N mg/L) without organic substrate in the first phase (autotrophic phase) for 35 days (R1) and 15 days (R2), followed by a heterotrophic phase (with supplementation of organic substrate). The settling properties of the biomass, represented by pin-point flocs, gradually improved in both reactors during the autotrophic phase. The pin-point flocs of R1 exhibited granule-like settling properties. The SVI30 in RI gradually improved to 29 mL/g MLSS, and the corresponding SVI30/ SVI10 gradually improved to 0.88 during the autotrophic phase. The settling properties of the biomass deteriorated in both bioreactors during the heterotrophic phase. The protein to polysaccharide ratio (PN:PS ratio) gradually increased in the extracted EPS (in both, loosely bound (LB) and tightly bound (TB) EPS) during the autotrophic phase, in both bioreactors. The TB:LB EPS ratio was higher when the pin-point flocs of R1 showed granule-like settling properties, followed by a decline in TB:LB EPS ratio during the heterotrophic phase. A combination of molecular approaches (droplet digital-PCR (dd-PCR) and 16S rRNA gene sequencing) revealed that Nitrospira were the predominant nitrifying bacteria in the pin-point flocs that show granular sludge-like settling properties during autotrophic phase in R1. Comammox Nitrospira was the dominant ammonia oxidizer in seed biomass and at low ammonia concentrations in both bioreactors. The relative abundance of canonical ammonia-oxidizing bacteria increased with an increase in influent-ammonia concentrations.

Ammonium oxidizing bacterial populations in South African activated sludge wastewater treatment plants

This is the first study that describes ammonium oxidizing bacterial populations and correlations of these populations with a range of criteria in activated sludge wastewater treatment plants in South Africa. In this study, not only the influent but also the activated sludge chemistry was comprehensively characterized. Multivariate statistical analyses were used to determine the relative significances of the geographical location (factor: site), wastewater treatment plant process (factor: configuration), seasonality (factor: season), and environmental parameters on the ammonium oxidizing bacterial genera in six municipal activated sludge wastewater treatments plants from two sites (the cities of Cape Town and Ekurhuleni). The geographical location (site) was significant for selection of the ammonium oxidizing genera (Global ANOSIM R value = 0.538, p = 0.001). It was established that the inter-site differences were not climatic in origin, nor related to the composition of the influent, but were rather driven by the activated sludge chemistry. It was found using BEST analysis that the activated sludge ammonia, activated sludge total phosphate, and activated sludge total chemical oxygen demand were the most significant (p < 0.001) drivers for ammonium oxidizing bacterial selection (ANOSIM Global R value 0.419) and were significantly higher in the activated sludge from the City of Cape Town wastewater treatment plants. Nitrosospira was the most abundant ammonium oxidizing bacterial genus, with notably higher relative and estimated actual abundances in the City of Cape Town wastewater treatment plants than the City of Ekurhuleni wastewater treatment plants. The strong selection of Nitrosospira in the City of Cape Town wastewater treatment plants with higher nutrient concentrations strongly suggests that high concentrations of activated sludge ammonia, activated sludge total phosphate, and activated sludge total chemical oxygen demand are key selective drivers for this genus. PRACTITIONER POINTS: First comprehensive study describing ammonium oxidizing bacterial populations in Southern African domestic activated sludge wastewater treatment plants. The geographical location (site) was significant for selection of different ammonium oxidizing genera (Global ANOSIM R value = 0.538, p = 0.001). Inter-site differences driven by the activated sludge chemistry, not climate or influent wastewater composition. Selection of Nitrosospira driven by high concentrations of activated sludge ammonia, total phosphate and total chemical oxygen demand.

Effects of different aeration strategies and ammonia-nitrogen loads on nitrification performance and microbial community succession of mangrove constructed wetlands for saline wastewater treatment

In highly salinized environments, nitrification is the process that limits the rate of nitrogen transformation and removal. Therefore, this study concentrated on the impacts of different aeration strategies and NH4+-N loads on the nitrification performance of mangrove constructed wetlands (CWs), as well as investigating the succession mechanism of ammonia-oxidizing microorganisms (AOMs). The results showed that both the CW with continuous aeration (CA-CW) and intermittent aeration (IA-CW) achieved a nitrification efficiency of more than 98% under an NH4+-N loading of 1.25-4.7 g/(m2·d). However, the total nitrogen removal rates of IA-CW under low and high ammonia-nitrogen loads (LAL, 20.09 ± 4.4% and HAL, 8.77 ± 1.35%, respectively) were higher than those of CA-CW (16.11 ± 4.7% and 3.32 ± 2.3%, respectively), especially under HAL (p < 0.05). Pearson correlation analysis showed that under different operating conditions, the differential secretion of Kandelia candel rhizosphere organic matter had a certain regulatory effect on nitrification and denitrification groups such as Candidatus Nitrocosmicus, Nitrancea, Truepera, Pontibacter, Halomonas, and Sulfurovum in the wetland root layer. The quantitative polymerase chain reaction revealed that the NH4+-N load rate was the primary factor driving the succession of the AOMs, with different aeration strategies exacerbating this process. Overall, this study revealed that the dominant AOMs in mangrove CWs could be significantly altered by regulating the aeration modes and pollution loads to adjust the rhizosphere organic matter in situ, thereby resulting in more efficient nitrification.

Seasonal prevalence of bacteria in the outflow of two full-scale municipal wastewater treatment plants

Despite many modern wastewater treatment solutions, the most common is still the use of activated sludge (AS). Studies indicate that the microbial composition of AS is most often influenced by the raw sewage composition (especially influent ammonia), biological oxygen demand, the level of dissolved oxygen, technological solutions, as well as the temperature of wastewater related to seasonality. The available literature mainly refers to the relationship between AS parameters or the technology used and the composition of microorganisms in AS. However, there is a lack of data on the groups of microorganisms leaching into water bodies whose presence is a signal for possible changes in treatment technology. Moreover, sludge flocs in the outflow contain less extracellular substance (EPS) which interferes microbial identification. The novelty of this article concerns the identification and quantification of microorganisms in the AS and in the outflow by fluorescence in situ hybridization (FISH) method from two full-scale wastewater treatment plants (WWTPs) in terms of 4 key groups of microorganisms involved in the wastewater treatment process in the context of their potential technological usefulness. The results of the study showed that Nitrospirae, Chloroflexi and Ca. Accumulibacter phosphatis in treated wastewater reflect the trend in abundance of these bacteria in activated sludge. Increased abundance of betaproteobacterial ammonia-oxidizing bacteria and Nitrospirae in the outflow were observed in winter. Principal component analysis (PCA) showed that loadings obtained from abundance of bacteria in the outflow made larger contributions to the variance in the PC1 factorial axis, than loadings obtained from abundance of bacteria from activated sludge. PCA confirmed the reasonableness of conducting studies not only in the activated sludge, but also in the outflow to find correlations between technological problems and qualitative and quantitative changes in the outflow microorganisms.

Ubiquitous occurrence and functional dominance of comammox Nitrospira in full-scale wastewater treatment plants

The recent discovery of complete ammonia oxidation (comammox) bacteria has fundamentally upended the traditional two-step nitrification conception, but their functional importance in wastewater treatment plants (WWTPs) is still poorly understood. This study investigated distributions of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in activated sludge samples collected from 25 full-scale WWTPs. Using quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing, our results revealed that comammox Nitrospira ubiquitously occurred in all of 25 WWTPs and even outnumbered AOB and AOA with an average abundance of 1∼183 orders of magnitude higher in 19 WWTPs. Moreover, DNA-based stable isotope probing (DNA-SIP) assays validated that comammox Nitrospira actively participated in ammonia oxidation in the three microcosms seeding with activated sludge from three typical WWTPs, in which the ratios of comammox amoA to AOB amoA were at the range of 1∼10, 10∼100 and >100, respectively. Phylogenetic analysis in heavy fractions further indicated that Nitrospira nitrosa (N. nitrosa) was the dominant and active species. We quantified the contribution of ammonia oxidizers based on the currently available kinetic parameters of the representative species and found that comammox made major contributions to ammonia oxidation than other nitrifiers (5 ∼ 106 times that of AOB). The findings not only demonstrate the ubiquitous occurrence of comammox, but also highlight their functional dominance in ammonia oxidation in WWTPs.

Multi-scale Investigation of Ammonia-Oxidizing Microorganisms in Biofilters Used for Drinking Water Treatment

Ammonia-oxidizing microorganisms (AOMs) include ammonia-oxidizing bacteria (AOB), archaea (AOA), and Nitrospira spp. sublineage II capable of complete ammonia oxidation (comammox). These organisms can affect water quality not only by oxidizing ammonia to nitrite (or nitrate) but also by cometabolically degrading trace organic contaminants. In this study, the abundance and composition of AOM communities were investigated in full-scale biofilters at 14 facilities across North America and in pilot-scale biofilters operated for 18 months at a full-scale water treatment plant. In general, the relative abundance of AOM in most full-scale biofilters and in the pilot-scale biofilters was as follows: AOB > comammox Nitrospira > AOA. The abundance of AOB in the pilot-scale biofilters increased with increasing influent ammonia concentration and decreasing temperature, whereas AOA and comammox Nitrospira exhibited no correlations with these parameters. The biofilters affected AOM abundance in the water passing through the filters via collecting and shedding but exhibited a minor influence on the composition of AOB and Nitrospira sublineage II communities in the filtrate. Overall, this study highlights the relative importance of AOB and comammox Nitrospira compared to AOA in biofilters and the influence of filter influent water quality on AOM in biofilters and their release into the filtrate.

Ammonia-Oxidizing Bacteria Maintain Abundance but Lower amoA-Gene Expression during Cold Temperature Nitrification Failure in a Full-Scale Municipal Wastewater Treatment Plant

In this study, we explore the relationship between community structure and transcriptional activity of ammonia-oxidizing bacteria during cold temperature nitrification failure in three parallel full-scale sequencing batch reactors (SBRs) treating municipal wastewater. In the three reactors, ammonia concentrations increased with declines in wastewater temperature below 15°C. We quantified and sequenced 16S rRNA and ammonia monooxygenase (amoA) gene fragments in DNA and RNA extracts from activated sludge samples collected from the SBRs during the warmer seasons (summer and fall) and when water temperatures were below 15°C (winter and spring). Taxonomic community composition of amoA genes and transcripts did not vary much between the warmer and colder seasons. However, we observed significant differences in amoA transcript copy numbers between fall (highest) and spring (lowest). Ammonia-oxidizing bacteria of the genus Nitrosomonas sp. could maintain their population abundance despite lowering their amoA gene expression during winter and spring. In spite of relatively low population abundance, an amoA amplicon sequence variant (ASV) cluster identified as most similar to the amoA gene of Nitrosospira briensis showed the highest amoA transcript-to-gene ratio throughout all four seasons, indicating that some nitrifiers remain active at wastewater temperatures below 15°C. Our results show that 16S rRNA and amoA gene copy numbers are limited predictors of cell activity. To optimize function and performance of mixed community bioprocesses, we need to collect high-resolution quantitative transcriptomic and potentially proteomic data to resolve the response of individual species to changes in environmental parameters in engineered systems. IMPORTANCE The diverse microbial community of activated sludge used in biological treatment systems exhibits dynamic seasonal shifts in community composition and activity. Many wastewater treatment plants in temperate/continental climates experience seasonal cold temperature nitrification failure. "Seasonal nitrification failure" is the discharge of elevated concentrations of ammonia (greater than 4 mg/liter) with treated wastewater during the winter (influent wastewater temperatures below 13°C). This study aims at expanding our understanding of how ammonia-oxidizing bacteria in activated sludge change in activity and growth across seasons. We quantified the ammonia monooxygenase (amoA) gene and transcript copy numbers using real-time PCR and sequenced the amoA amplicons to reveal community structure and activity changes of nitrifying microbial populations during seasonal nitrification failure in three full-scale sequencing batch reactors (SRBs) treating municipal wastewater. Relevant findings presented in this study contribute to explain seasonal nitrification performance variability in SRBs.

Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China

The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0-20 cm, topsoil; 20-40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH₄ ⁺-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH₄ ⁺-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems.

Photoinhibition of comammox reaction in Nitrospira inopinata in a dose- and wavelength-dependent manner

Apparent contribution of complete ammonia-oxidizing organisms (comammox) to the global nitrogen cycle highlights the necessity for understanding niche differentiation of comammox bacteria among other ammonia oxidizers. While the high affinity for ammonia of the comammox species Nitrospira inopinata suggests their niche partitioning is expected to be centered in oligotrophic environments, their absence in nutrient-depleted environments (such as the oceans) suggests that other (abiotic) factors might control their distribution and spatial localization within microbial communities. Many ammonia- and nitrite-oxidizing organisms are sensitive to light; however, the photosensitivity of comammox has not been explored. Since comammox bacteria encode enzymatic machinery homologous to canonical ammonia-and nitrite-oxidizers, we hypothesized that comammox N. inopinata, the only available pure culture of this group of microorganisms, may be inhibited by illumination in a similar manner. We evaluated the impact of light intensity, wavelength, and duration on the degree of photoinhibition for cultures of the comammox species N. inopinata and the soil ammonia-oxidizing archaea Nitrososphaera viennensis. Both species were highly sensitive to light. Interestingly, mimicking diurnal light exposure caused an uncoupling of ammonia and nitrite oxidation in N. inopinata, indicating nitrite oxidation might be more sensitive to light exposure than ammonia oxidation. It is likely that light influences comammox spatial distribution in natural environments such as surface fresh waters according to diurnal cycles, light attenuation coefficients, and the light penetration depths. Our findings therefore provide ecophysiological insights for further studies on comammox both in field and laboratory settings.

Integrating conventional nitrogen removal with anammox in wastewater treatment systems: Microbial metabolism, sustainability and challenges

The various forms of nitrogen (N), including ammonium (NH₄⁺), nitrite (NO₂^-), and nitrate (NO₃^-), present in wastewaters can create critical biotic stress and can lead to hazardous phenomena that cause imbalances in biological diversity. Thus, biological nitrogen removal (BNR) from wastewaters is considered to be imperatively urgent. Therefore, anammox-based systems, i.e. partial nitrification and anaerobic ammonium oxidation (PN/anammox) and partial denitrification and anammox (PD/anammox) have been universally acknowledged to consider as alternatives, promising and cost-effective technologies for sustainable N removal from wastewaters compared to nitrification-denitrification processes. This review comprehensively presents and discusses the latest advances in BNR technologies, including traditional nitrification-denitrification and anammox-based systems. To a deep understanding of a better-controlled combining anammox with traditional processes, the microbial community diversity and metabolism, as well as, biomass morphological characteristics were clearly reviewed in the anammox-based systems. Explaining simultaneous microbial competition and control of crucial operation parameters in single-stage anammox-based processes in terms of optimization and economic benefits makes this contribution a different vision from available review papers. The most important sustainability indicators, including global warming potential (GWP), carbon footprint (CF) and energy behaviours were explored to evaluate the sustainability of BNR processes in wastewater treatment. Additionally, the challenges and solutions for BNR processes are extensively discussed. In summary, this review helps facilitate a critical understanding of N removal technologies. It is confirmed that sustainability and saving energy would be achieved by anammox-based systems, thereby could be encouraged future outcomes for a sustainable N removal economy.

Comparative analysis of floc characteristics and microbial communities in anoxic and aerobic suspended growth processes

A fully anoxic suspended growth process is an appealing alternative to conventional activated sludge (AS) due to considerable aeration reduction and improved carbon processing efficiency for biological nutrient removal (BNR). With development of the hybrid membrane aerated biofilm reactor (MABR) technology, implementation of a fully anoxic suspended growth community in BNR facilities became practical. To better understand potential limitations with the elimination of aeration, we carried out microscopic examination and 16S rRNA gene-based microbial community profiling to determine how an anoxic suspended growth would differ from the conventional aerobic process in floc characteristics, microbial diversity, microbial temporal dynamics, and community assembly pattern. Fewer filamentous populations were found in the anoxic mixed liquor, suggesting easily sheared flocs. The anoxic microbial community had distinct composition and structure, but its diversity and temporal dynamics were similar to the conventional aerobic community. A variety of well-studied functional guilds were also identified in the anoxic community. The anoxic microbial community assembly was more stochastic than the conventional aerobic community, but deterministic assembly was still significant with a large core microbiome adapted to the anoxic condition. PRACTITIONER POINTS: Flocs developed under the anoxic conditions had less filamentous backbones, implying reduced flocculation capacity and easily sheared flocs. Knowledge about the ecophysiology of Thauera, Thiothrix, and Trichococcus can help achieve good properties of the anoxic flocs. A diverse microbial community sustainably adapted to the fully anoxic condition, containing a variety of filaments, denitrifiers, and PAOs. The anoxic microbial community displayed a similar degree of diversity and temporal dynamics compared to the aerobic counterpart. The anoxic community's assembly was more stochastic, so it may be less subject to changes in environmental variables.

Effect of steel slag on ammonia removal and ammonia-oxidizing microorganisms in zeolite-based tidal flow constructed wetlands

The ammonia removal performance of tidal flow constructed wetlands (TFCWs) requires to be improved under high hydraulic loading rates (HLRs). The pH decrease caused by nitrification may adversely affect the NH₄⁺-N removal and ammonia-oxidizing microorganisms (AOMs) of TFCWs. Herein, TFCWs with zeolite (TFCW_Z) and a mixture of zeolite and steel slag (TFCW_S) were built to investigate the influence of steel slag on NH₄⁺-N removal and AOMs. Both TFCWs were operated under short flooding/drying (F/D) cycles and high HLRs (3.13 and 4.69 m³/(m² d)). The results revealed that a neutral effluent pH (6.98-7.82) was achieved in TFCW_S owing to the CaO dissolution of steel slag. The NH₄⁺-N removal efficiencies in TFCW_S (91.2 ± 5.1%) were much higher than those in TFCW_Z (73.2 ± 7.1%). Total nitrogen (TN) removal was poor in both TFCWs mainly due to the low influent COD/TN. Phosphorus removal in TFCW_S was unsatisfactory because of the short hydraulic retention time. The addition of steel slag stimulated the flourishing AOMs, including Nitrosomonas (ammonia-oxidizing bacteria, AOB), Candidatus_Nitrocosmicus (ammonia-oxidizing archaea, AOA), and comammox Nitrospira, which may be responsible for the better ammonia removal performance in TFCW_S. PICRUSt2 showed that steel slag also enriched the relative abundance of functional genes involved in nitrification (amoCAB, hao, and nxrAB) but inhibited genes related to denitrification (nirK, norB, and nosZ). Quantitative polymerase chain reaction (qPCR) revealed that complete AOB (CAOB) and AOB contributed more to the amoA genes in TFCW_S and TFCW_Z, respectively. Therefore, this study revealed that the dominant AOMs could be significantly changed in zeolite-based TFCW by adding steel slag to regulate the pH in situ, resulting in a more efficient NH₄⁺-N removal performance.

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.

Rearrangements of the nitrifiers population in an activated sludge system under decreasing solids retention times

Due to the key role of nitrite in novel nitrogen removal systems, nitrite oxidizing bacteria (NOB) have been receiving increasing attention. In this study, the coexistence and interactions of nitrifying bacteria were explored at decreasing solids retention times (SRTs). Four 5-week washout experiments were carried out in laboratory-scale (V = 10 L) sequencing batch reactors (SBRs) with mixed liquor from two full-scale activated sludge systems (continuous flow vs SBR). During the experiments, the SRT was gradually reduced from the initial value of 4.0 d to approximately 1.0 d. The reactors were operated under limited dissolved oxygen conditions (set point of 0.6 mg O₂/L) and two process temperatures: 12 °C (winter) and 20 °C (summer). At both temperatures, the progressive SRT reduction was inefficient for the out-selection of both canonical NOB and comammox Nitrospira. However, the dominant NOB switched from Nitrospira to Ca. Nitrotoga, whereas the dominant AOB was always Nitrosomonas. The results of this study are important for optimizing NOB suppression strategies in the novel N removal processes, which are based on nitrite accumulation.

Diversity distribution and characteristics of comammox in different ecosystems

The discovery of complete ammonia oxidizers (comammox), which can oxidize ammonia into nitrate, has recently changed the concept of traditional nitrification. However, comparative studies on the analysis of comammox microbial community in different ecosystems are still scarce. In this study, the distribution and diversity of the comammox microbial community in farmlands, riparian zones, and river sediments in summer and winter were investigated by high-throughput sequencing. And the relative abundance of ammonia-oxidizing microorganisms was measured via their amoA genes of real-time quantitative polymerase chain reaction (qPCR). The relationships between ammonia oxidation microorganisms and the environmental factors were further analyzed. The abundance of comammox clade A was one order of magnitude lower than that of ammonia-oxidizing archaea (AOA) but higher than that of ammonia-oxidizing bacteria (AOB). The abundance of comammox was higher in summer than in winter and higher in farmland soils (1.81 ± 0.95 × 10⁷ copies g^-1) than in riparian zones and river sediments. Meanwhile, Candidatus Nitrospira nitrosa were the most widespread comammox in most samples (up to 86.31%), followed by Candidatus Nitrospira nitrificans, with a low abundance of Candidatus Nitrospira inopinata (lower than 0.61%). Furthermore, the abundance of comammox clade A had a significantly negative correlation with pH and NH₄⁺ concentration (P < 0.05). The study revealed the potential advantages of comammox in farmlands and may be conducive to further research on comammox in microbial nitrogen cycling.

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.

Comammox bacteria predominate among ammonia-oxidizing microorganisms in municipal but not in refinery wastewater treatment plants

Comammox bacteria have proved to be one dominant and significant ammonia-oxidizing microorganisms (AOMs) in municipal wastewater treatment plants (WWTPs), however, it still remains unknown about their abundance and diversity in industrial WWTPs. In this study, activated sludge samples from 8 municipal WWTPs and 6 industrial WWTPs treating refinery wastewater were taken and analyzed using qPCR and amoA gene sequencing. Intriguingly, quantitative real-time PCR (qPCR) results suggested that comammox bacteria had a higher numerical abundance compared with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in municipal WWTPs but did not in refinery WWTPs. Moreover, comammox amoA sequences obtained from high-throughput sequencing were retrieved from all the 8 municipal samples but only 1 industrial sample. Further phylogenetic analysis revealed that N. nitrosa cluster accounted for as high as 79.56% of the total comammox affiliated sequences, which was the most numerically abundant comammox species in municipal WWTPs. This study provided new insights into the abundance and diversity of comammox bacteria in the biological nitrification process in municipal and refinery wastewater treatment systems.

Changes in the Species and Functional Composition of Activated Sludge Communities Revealed Mechanisms of Partial Nitrification Established by Ultrasonication

To achieve energy-efficient shortcut nitrogen removal of wastewater in the future, selective elimination of nitrite-oxidizing bacteria (NOB) while enriching ammonia-oxidizing microorganisms is a crucial step. However, the underlying mechanisms of partial nitrification are still not well understood, especially the newly discovered ultrasound-based partial nitrification. To elucidate this issue, in this study two bioreactors were set up, with one established partial nitrification by ultrasonication while the other didn't. During the operation of both reactors, the taxonomic and functional composition of the microbial community were investigated through metagenomics analysis. The result showed that during ultrasonic partial nitrification, ammonia-oxidizing archaea (AOA), Nitrososphaerales, was enriched more than ammonia-oxidizing bacteria (AOB), Nitrosomonas. The enrichment of microorganisms in the community increased the abundance of genes involved in microbial energy generation from lipid and carbohydrates. On the other hand, the abundance of NOB, Nitrospira and Nitrolancea, and Comammox Nitrospira decreased. Selective inhibition of NOB was highly correlated with genes involved in signal transduction enzymes, such as encoding histidine kinase and serine/threonine kinase. These findings provided deep insight into partial nitrification and contributed to the development of shortcut nitrification in wastewater treatment plants.

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.

Performance and recovery of nitrifying biofilm after exposure to prolonged starvation

Achieving consistent ammonia removal in post-lagoon processes faces two major challenges impacting nitrifiers due to the unique seasonal variation of lagoon-based systems: summer to winter temperature drop and summer to fall ammonia starvation period while lagoon is removing ammonia. The objective of this study was to follow microbial diversity and define conditions that could overcome these challenges in a post-lagoon moving bed biofilm reactor (MBBR) operated at an initial surface area loading rate (SALR) of 0.3 g-NH4-N m^-2d^-1 from mesophilic (20 °C) to psychrophilic (4 °C). Initially the temperature was maintained at 20 °C and decreased to 10 °C until steady state was achieved. During starvation conditions (i.e., continuous, intermittent and no aeration without inflow; decanted media; and intermittent and continuous ammonia supplement) the temperature was decreased by 2 °C per week until 4 °C. The results indicated that operational procedures, such as intermittent ammonia supplement with SALR of 0.15 g-NH₄-N m^-2d^-1 could improve performance with 80% ammonia removal achieved immediately after starvation period. Intermittent ammonia supplement had produced the greatest biofilm preservation comparable to the initial load with the highest specific and surface area removal rates. In the recovery phase (initial load restoration) 10 days were required to reestablish performance above 95% ammonia removal. When temperature was decreased from mesophilic to psychrophilic, the microbial diversity was found higher when starving biofilm compared to the control operated at the initial load while it converged to a similar population over recovery. The main actors associated to nitrification enriched at psychrophilic conditions were Proteobacteria and Bacteriodotes at phyla level. Ammonia oxidation to nitrite was mainly driven by the order Burkholderiales and nitrite oxidation to nitrate by Pseudomonadales. This procedure should be considered in the implementation of full-scale post-lagoon MBBR technologies to ensure reliable, robust, and consistent performance despite the inherent seasonal variability of lagoon-based processes.

Incorporation of the complete ammonia oxidation (comammox) process for modeling nitrification in suspended growth wastewater treatment systems

The newly discovered process complete ammonia oxidation (comammox) has changed the traditional understanding of nitrification. In this study, three possible concepts of comammox were developed and incorporated as part of an extended two-step nitrification model. For model calibration and validation, two series of long-term biomass washout experiments were carried out at 12 °C and 20 °C in a laboratory sequencing batch reactor. The inoculum biomass was withdrawn from a large biological nutrient removal wastewater treatment plant. The efficiency of the examined models was compared based on the behaviors of ammonia, nitrite, and nitrate in the studied reactor. Predictions of the conventional approach to comammox, assuming the direct oxidation of ammonia to nitrate, were slightly better than the two other approaches. Simulation results revealed that comammox could be responsible for the conversion of >20% of the influent ammonia load. Therefore, the role of commamox in the nitrogen mass balance in activated sludge systems should not be neglected and requires further investigation. Furthermore, sensitivity and correlation analysis revealed that the maximum growth rates (μ), oxygen half-saturation (K_O), and decay rates (b) of the canonical nitrifiers and comammox were the most sensitive factors, and the highest correlation was found between μ and b among all considered kinetic parameters. The estimated μ values by the best model were 0.57, 0.11, and 0.15 d^-1 for AOB, NOB, and comammox bacteria, respectively.

Temperature Influenced the Comammox Community Composition in Drinking Water and Wastewater Treatment Plants

Nitrification is a pivotal step applied in water engineered systems for nitrogen removal. Temperature variation due to seasonal changes is a great challenge for maintaining nitrogen removal efficiency in water engineered ecosystems by affecting nitrifier activities. Research on the abundance, activity, and metabolic characteristics of nitrifiers can provide information for selecting suitable design parameters to ensure efficient nitrogen removal in different seasons. To date, the temperature-related niche separation of comammox, a newly discovered nitrifier with potential high-growth yield, has been rarely investigated. This study addressed the distribution of comammox and canonical nitrifying guilds in drinking water treatment plants (DWTPs) and wastewater treatment plants (WWTPs) in different seasons. qPCR-based surveys showed that comammox ubiquitously distributed and greatly outnumbered other ammonia-oxidizing prokaryotes in both DWTPs and WWTPs, except in Aug samples from DWTPs, suggesting the potential competitive advantage of AOA in summer. The nitrificans-like comammox and nitrosa-like comammox comprised the majority of the comammox community in DWTPs and WWTPs, respectively, and COD and NH₄⁺ concentrations significantly contributed to the distinct comammox phylotype distribution between DWTPs and WWTPs. The temperature-related distribution pattern of the comammox community was observed at each site. Moreover, the network complex of comammox communities was highest in Dec at all the sites, possibly contributing to the survival of comammox community in low temperature conditions.

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.

Realizing the role of N-acyl-homoserine lactone-mediated quorum sensing in nitrification and denitrification: A review

Nitrification and denitrification are crucial processes in the nitrogen cycle, a vital microbially driven biogeochemical cycle. N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) is widespread in bacteria and plays a key role in their physiological status. Recently, there has been an increase in research into how the AHL-mediated QS system is involved in nitrification and denitrification. Consequentially, the AHL-mediated QS system has been considered a promising regulatory approach in nitrogen metabolism processes, with high potential for real-world applications. In this review, the universal presence of QS in nitrifiers and denitrifiers is summarized. Many microorganisms taking part in nitrification and denitrification harbor QS genes, and they may produce AHLs with different chain lengths. The phenotypes and processes affected by QS in real-world applications are also reviewed. In wastewater bioreactors, QS could affect nitrogen metabolism efficiency, granule aggregation, and biofilm formation. Furthermore, methods commonly used to identify the existence and functions of QS, including physiological tests, genetic manipulation and omics analyses are discussed.

Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox

Few studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.

Role of Ammonia Oxidation in Organic Micropollutant Transformation during Wastewater Treatment: Insights from Molecular, Cellular, and Community Level Observations

Organic micropollutants (OMPs) are a threat to aquatic environments, and wastewater treatment plants may act as a source or a barrier of OMPs entering the environment. Understanding the fate of OMPs in wastewater treatment processes is needed to establish efficient OMP removal strategies. Enhanced OMP biotransformation has been documented during biological nitrogen removal and has been attributed to the cometabolic activity of ammonia-oxidizing bacteria (AOB) and, specifically, to the ammonia monooxygenase (AMO) enzyme. Yet, the exact mechanisms of OMP biotransformation are often unknown. This critical review aims to fundamentally and quantitatively evaluate the role of ammonia oxidation in OMP biotransformation during wastewater treatment processes. OMPs can be transformed by AOB via direct and indirect enzymatic reactions: AMO directly transforms OMPs primarily via hydroxylation, while biologically produced reactive nitrogen species (hydroxylamine (NH₂OH), nitrite (NO₂^-), and nitric oxide (NO)) can chemically transform OMPs through nitration, hydroxylation, and deamination and can contribute significantly to the observed OMP transformations. OMPs containing alkyl, aliphatic hydroxyl, ether, and sulfide functional groups as well as substituted aromatic rings and aromatic primary amines can be biotransformed by AMO, while OMPs containing alkyl groups, phenols, secondary amines, and aromatic primary amines can undergo abiotic transformations mediated by reactive nitrogen species. Higher OMP biotransformation efficiencies and rates are obtained in AOB-dominant microbial communities, especially in autotrophic reactors performing nitrification or nitritation, than in non-AOB-dominant microbial communities. The biotransformations of OMPs in wastewater treatment systems can often be linked to ammonium (NH₄⁺) removal following two central lines of evidence: (i) Similar transformation products (i.e., hydroxylated, nitrated, and desaminated TPs) are detected in wastewater treatment systems as in AOB pure cultures. (ii) Consistency in OMP biotransformation (r_bio, μmol/g VSS/d) to NH₄⁺ removal (r_NH4+, mol/g VSS/d) rate ratios (r_bio/r_NH4+) is observed for individual OMPs across different systems with similar r_NH4+ and AOB abundances. In this review, we conclude that AOB are the main drivers of OMP biotransformation during wastewater treatment processes. The importance of biologically driven abiotic OMP transformation is quantitatively assessed, and functional groups susceptible to transformations by AMO and reactive nitrogen species are systematically classified. This critical review will improve the prediction of OMP transformation and facilitate the design of efficient OMP removal strategies during wastewater treatment.

The long-term effects of using nitrite and urea on the enrichment of comammox bacteria

The discovery of complete ammonia oxidizer (comammox) was a breakthrough in the study of nitrification. However, slow growth of comammox bacteria makes it challenging to distinguish them from traditional ammonia oxidizing microorganisms. Genomic data indicated that comammox bacteria encoded genes that can metabolize urea and had higher nitrite tolerance, which could only be found in several ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This implies that using nitrite and urea as nitrogen sources may accelerate comammox bacteria's enrichment efficiency. In this study, two reactors using nitrite and urea as substrates, respectively, were operated for 390 days. At the end of cultivation, the reactor fed with urea exhibited higher nitrification potential than the reactor fed with nitrite. Comammox bacteria outcompeted AOA and AOB, regardless of whether they were cultured with nitrite or urea. Using nitrite can improve the proportion of comammox amoA to total amoA of 92%, while using urea may increase the proportion of comammox bacteria among total bacteria to 14.2%. Metagenomic results implied that nitrite was converted to ammonia by nitrate reduction and absorbed by comammox bacteria. On the other hand, urea may be directly utilized as substrate. These results demonstrated that using different nitrogen sources caused niche differentiation of comammox bacteria, AOA, and AOB. Using nitrite can increase the relative abundance of comammox amoA to total amoA, while using urea can increase the quantity of comammox amoA. Comammox bacteria were dominant among ammonia oxidizing microorganisms for both nitrite and urea cultures.

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.

Quantification and Phylogenetic Analysis of Ammonia Oxidizers on Biofilm Carriers in a Full-Scale Wastewater Treatment Plant

Biofilm carriers have been used to remove ammonia in several wastewater treatment plants (WWTPs) in Japan. However, the abundance and species of ammonia oxidizers in the biofilms formed on the surface of carriers in full-scale operational WWTP tanks remain unclear. In the present study, we conducted quantitative PCR and PCR cloning of the amoA genes of ammonia-oxidizing bacteria and archaea (AOB and AOA) and a complete ammonia oxidizer (comammox) in the biofilm formed on the carriers in a full-scale WWTP. The quantification of amoA genes showed that the abundance of AOB and comammox was markedly greater in the biofilm than in the activated sludge suspended in a tank solution of the WWTP, while AOA was not detected in the biofilm or the activated sludge. A phylogenetic analysis of amoA genes revealed that as-yet-uncultivated comammox Nitrospira and uncultured AOB Nitrosomonas were predominant in the biofilm. The present results suggest that the biofilm formed on the surface of carriers enable comammox Nitrospira and AOB Nitrosomonas to co-exist and remain in the full-scale WWTP tank surveyed in this study.

Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems

The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.

Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems

The discovery of the complete ammonia oxidizing (comammox) bacteria overturns the traditional two-organism nitrification paradigm which largely underpins the design and operation of nitrogen removal during wastewater treatment. Quantifying the abundance, diversity, and activity of comammox bacteria in wastewater treatment systems is important for ensuring a clear understanding of the nitrogen biotransformations responsible for ammonia removal. To this end, we conducted a yearlong survey of 14 full-scale nitrogen removal systems including mainstream conventional and simultaneous nitrification-denitrification and side-stream partial nitrification-anammox systems with varying process configurations. Metagenomics and genome-resolved metagenomics identified comammox bacteria in mainstream conventional and simultaneous nitrification-denitrification systems, with no evidence for their presence in side-stream partial nitrification-anammox systems. Further, comammox bacterial diversity was restricted to clade A and these clade A comammox bacteria were detected in systems with long solids retention times (>10 days) and/or in the attached growth phase. Using a newly designed qPCR assay targeting the amoB gene of clade A comammox bacteria in combination with quantitation of other canonical nitrifiers, we show that long solids retention time is the key process parameter associated with the prevalence and abundance of comammox bacteria. The increase in comammox bacterial abundance was not associated with concomitant decrease in the abundance of canonical nitrifiers; however, systems with comammox bacteria showed significantly better and temporally stable ammonia removal compared to systems where they were not detected. Finally, in contrast to recent studies, we do not find any significant association of comammox bacterial prevalence and abundance with dissolved oxygen concentrations in this study.

Comammox Nitrospira are the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor

Recent findings show that a subset of bacteria affiliated with Nitrospira, a genus known for its importance in nitrite oxidation for biological nutrient removal applications, are capable of complete ammonia oxidation (comammox) to nitrate. Early reports suggested that they were absent or present in low abundance in most activated sludge processes, and thus likely functionally irrelevant. Here we show the accumulation of comammox Nitrospira in a nitrifying sequencing batch reactor operated at low dissolved oxygen (DO) concentrations. Actual mainstream wastewater was used as influent after primary settling and an upstream pre-treatment process for carbon and phosphorus removal. The ammonia removal rate was stable and exceeded that of the treatment plant's parallel full-scale high DO nitrifying activated sludge reactor. 16S rRNA gene sequencing showed a steady accumulation of Nitrospira to 53% total abundance and a decline in conventional ammonia oxidizing bacteria to <1% total abundance over 400 + days of operation. After ruling out other known ammonia oxidizers, qPCR confirmed the accumulation of comammox Nitrospira beginning around day 200, to eventually comprise 94% of all detected amoA and 4% of total bacteria by day 407. Quantitative fluorescence in-situ hybridization confirmed the increasing trend and high relative abundance of Nitrospira. These results demonstrate that comammox can be metabolically relevant to nitrogen transformation in wastewater treatment, and can even dominate the ammonia oxidizing community. Our results suggest that comammox may be an important functional group in energy efficient nitrification systems designed to operate at low DO levels.

Microbial immigration in wastewater treatment systems: analytical considerations and process implications

Microbial immigration from sewers to wastewater treatment systems is attracting increasing attention for understanding community assembly mechanisms, and improving process modeling and operation. While there is no consensus on approaches to analyze immigration, we suggest to classify them as relevant to either rare (non-observable) diffusive immigration or to time-continuous high-rate mass flow immigration (i.e. mass effects). When analyzed by a mass flow approach, heterotrophs appear to be strongly influenced by deterministic selection, suggesting that the heterotrophs should be subdivided into several functional guilds when assessing their assembly mechanisms. Conversely, nitrifiers appear to transfer neutrally from sewer to activated sludge, and this immigration can restore full nitrification in otherwise non-nitrifying reactors. With further refinement, these findings could be included in predictive process models with various objectives.

Transcriptional activity and diversity of comammox bacteria as a previously overlooked ammonia oxidizing prokaryote in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) has fundamentally overturned the traditional recognition of nitrification. However, little was known about the transcriptional activity and diversity of the newly recognized ammonia oxidizing prokaryote in engineered ecosystems. To fill this gap, transcriptional investigations of CAOB amoA genes were carried out comparatively with the canonical ammonia oxidizing bacteria (AOB) and archaea (AOA) in eight full-scale wastewater treatment plants (WWTPs). Remarkably, qPCR results revealed the transcriptional levels of CAOB amoA gene were unexpectedly high in most of samples with the highest 24-fold that of AOB amoA, suggesting CAOB were actively participating in ammonia oxidation while they were previously overlooked. This result also well explained the confusing high abundances of genus Nitrospira which were frequently detected in WWTPs. Furthermore, phylogenetic analysis based on high throughput sequencing indicated the CAOB amoA gene sequences formed three well-supported clusters and Nitrospira nitrosa cluster accounted for 97% of all the retrieved sequences, which was supposed to be the dominant taxon of CAOB in the ammonia-intensive environment due to niche partitioning. This study highlighted the significance of including the newly discovered ammonia oxidizing bacterial member when assessing the nitrification process and ecological function in the future.

Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure

Wastewater treatment plants in temperate climate zones frequently undergo seasonal nitrification failure in the winter month yet maintain removal efficiency for other contaminants. We tested the hypothesis that nitrification failure can be correlated to shifts in the nitrifying microbial community. We monitored three parallel, full-scale sequencing batch reactors over the course of a year with respect to reactor performance, microbial community composition via 16S rRNA gene amplicon sequencing, and functional gene abundance using qPCR. All reactors demonstrated similar changes to their core microbiome, and only subtle variations among seasonal and transient taxa. We observed a decrease in species richness during the winter, with a slow recovery of the activated sludge community during spring. Despite the change in nitrification performance, ammonia monooxygenase gene abundances remained constant throughout the year, as did the relative sequence abundance of Nitrosomonadacae. This suggests that nitrification failure at colder temperatures might result from different reaction kinetics of nitrifying taxa, or that other organisms with strong seasonal shifts in population abundance, e.g. an uncultured lineage of Saprospiraceae, affect plant performance in the winter. This research is a comprehensive analysis of the seasonal microbial community dynamics in triplicate full-scale sequencing batch reactors and ultimately strengthens our basic understanding of the microbial ecology of activated sludge communities by revealing seasonal succession patterns of individual taxa that correlate with nutrient removal efficiency.

Design and Assessment of Species-Level qPCR Primers Targeting Comammox

Published PCR primers targeting the ammonia monooxygenase gene (amoA) were applied to samples from activated sludge systems operated with low dissolved oxygen (DO) to quantify total and clade-level Nitrospira that perform complete ammonium oxidation (comammox); however, we found these existing primers resulted in significant artifact-associated non-target amplification. This not only overestimated comammox amoA copies but also resulted in numerous false positive detections in the environmental samples tested, as confirmed by gel electrophoresis. Therefore, instead of attempting to quantify comammox diversity, we focused on accurately quantifying the candidate comammox species. We designed specific and sensitive primers targeting 3 candidate species: Candidatus (Ca.) Nitrospira nitrosa, Ca. N. inopinata, and Ca. N. nitrificans. The primers were tested with amoA templates of these candidate species and used to quantify comammox at the species level in low DO activated sludge systems. We found that comammox related to Ca. N. nitrosa were present and abundant in the majority of samples from low DO bioreactors and were not detected in samples from a high DO system. In addition, the greatest abundance of Ca. N. nitrosa was found in bioreactors operated with a long solids retention time. Ca. N. inopinata and Ca. N. nitrificans were only detected sporadically in these samples, indicating a minor role of these comammox in nitrification under low DO conditions.

Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox)

The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.

Newly designed primer pair revealed dominant and diverse comammox amoA gene in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) capable of performing the two-step nitrification process on their own has fundamentally upended our traditional perception. However, their environmental distribution and ecological significance in driving ammonia oxidation are still urgently awaited to be assessed. In this study, the diversity and abundance of CAOB amoA gene in wastewater treatment plants (WWTPs) were presented taking advantage of a newly designed primer pair specifically targeting CAOB amoA gene. Phylogenetic results demonstrated the novel amoA gene formed a clearly distinct cluster from the canonical amoA and pmoA genes. Among the five well-supported sub-clusters, Nitrospira nitrosa cluster accounted for 94.34% of all the currently retrieved sequences from WWTPs. More importantly, qPCR results demonstrated a remarkably high abundance of CAOB amoA gene, which were up to 182.7-fold more abundant than AOB amoA gene. This study provided new dimension and fundamental basis for future researches towards biogeochemical nitrogen cycle.

The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships

Nitrification failure of wastewater treatment plants (WWTPs) in cold season calls into investigations of the functional ammonia-oxidizing microorganisms (AOMs). In this study, we report the abundance of ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia-oxidizing (comammox) Nitrospira in 23 municipal WWTPs in cold season, and explore the correlations between AOMs abundance and their relative contribution to nitrification. The copy numbers of AOA and AOB amoA gene ranged from 2.42 × 10⁷ to 2.47 × 10⁹ and 5.54 × 10⁶ to 3.31 × 10⁹ copies/g sludge, respectively. The abundance of amoA gene of Candidatus Nitrospira inopinata, an important strain of comammox Nitrospira, was stable with averaged abundance of 8.47 × 10⁶ copies/g sludge. DNA-based stable isotope probing (DNA-SIP) assays were conducted with three typical WWTPs in which the abundance of AOA was lower than, similar to and higher than that of AOB, respectively. The results showed that considerable ¹³C-assimilation by AOA was detected during active nitrification in all WWTPs, whereas just a much lesser extent of ¹³C-incorporation by AOB and comammox Nitrospira was found in one WWTP. High-throughput sequencing with ¹³C-labeled DNA also showed the higher reads abundance of AOA than AOB and comammox Nitrospira. Nitrososphaera viennensis was the dominant active AOA, while Nitrosomonas oligotropha and Nitrosomonas europaea were identified as active AOB. The results obtained suggest that AOA, rather than AOB and comammox Nitrospira, dominate ammonia oxidation in WWTPs in cold season despite the numerical relationships of AOMs.

The hunt for the most-wanted chemolithoautotrophic spookmicrobes

Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.