Whole-Community Metagenomics in Two Different Anammox Configurations: Process Performance and Community Structure

Enhance PD/A biofilm formation via a novel biochar/tourmaline modified-biocarriers to treat low-strength contaminated surface water: Initial adhesion and high-substrate microenvironment

In this work, a novel polyurethane carrier modified with biochar and tourmaline/zeolite powder at ratio of 1:1 and 1:2 was developed to promote the formation of biofilms and the synergy of overall bacterial activity for Partial Denitrification/Anammox to treat low-nitrogen contaminated surface water. Based on the batch experiment, the modified biocarrier, BTP2 (biochar: tourmaline = 2: 1), exhibited the highest total nitrogen removal efficiency (83.63%) under influent total nitrogen of 15 mg/L and COD/NO3- of 3. The dense biofilm was formed in inner side of biocarrier owing to the increased surface roughness and various functional groups suggested by scanning electron microscopy and Fourier-transform infrared analysis. The EPS content increased from 200.15 to 220.26 mg/g VSS in BTP2 system. Besides, the rapid NH4+ capture and organics release of the modified carrier fueled the growth of anammox and denitrification bacteria, with the activity of 2.13 ± 0.52 mg N/gVSS/h and 6.70 ± 0.52 mg N/gVSS/h (BTP2). High-throughput sequencing unraveled the increased abundances of Candidatus_Competibacter (0.82%), Thauera (0.60%) and Candidatus_Brocadia (0.55%) which was responsible for the synergy of incomplete reduction of NO3- to NO2- and NH4+ oxidation. Overall, this study provided a valid and simple-control guide for biofilm formation towards rapid enrichment and great collaboration of Anammox and denitrification bacteria.

Enhancement of hydrazine accumulation in anammox bioreactors

The role of hydrazine (N2H4) in anammox metabolism has been widely studied; however, studies on N2H4 biosynthesis by anammox bacteria are limited in the literature. In this context, the current research aims to investigate the enhancement of biological N2H4 production in the anammox process in a long-term manner. The experimental studies started with the optimization of the operating conditions to achieve maximum N2H4 accumulation. Under favorable conditions (pH = 8.97 ± 0.08; T = 35.5 ± 0.5 °C; initial hydroxylamine dose = 1.46 ± 0.01 mM), 17.16 ± 0.64 mg L-1 of N2H4 accumulated in the batch systems. The continuity of N2H4 bioproduction was then evaluated by long-term observations. A continuous flow bioreactor was operated in four consecutive manipulated periods under optimized conditions. In the long-term operated bioreactor, 55.10 ± 0.30 mg L-1 N2H4 was accumulated at optimal conditions, which was 2.5 times higher than reported in the literature. Although manipulation of the bioreactor operating conditions initially resulted in a significant increase in N2H4 bioaccumulation, it subsequently caused a severe deterioration in anammox activity. However, this could be mitigated by increasing the biomass concentration in the anammox systems. In addition, the relative abundance of Candidatus Kuenenia decreased by 1.88% throughout the long-term operation.

Ferric and sulfate coupled ammonium oxidation enhanced nitrogen removal in two-stage partial nitrification - Anammox/denitrification process for food waste liquid digestate treatment

Liquid digestate of food waste is an ammonium-, ferric- and sulfate-laden leachate produced during digestate dewatering, where the carbon source is insufficient for nitrogen removal. A two-stage partial nitrification-anammox/denitrification process was established for nitrogen removal of liquid digestate without pre-treatment (>300 d), through which nitrogen (95 %), biodegradable organics (100 %), sulfate (78 %) and iron (100 %) were efficiently removed. Additional ammonium conversion (20 %N) might be coupled with ferric and sulfate reduction, while produced nitrite could be further converted to di-nitrogen gas through anammox (75 %) and denitrification (25 %). Notably, since increasingly contribution of hydroxylamine producing nitrous oxide, and up-regulated expression of electron transfer and cytochrome c protein, the enhanced ammonium oxidation was probably conducted through extracellular polymeric substances-mediated electron transfer between sulfate/ferric-reducers and aerobic ammonium oxidizers. Thus, the established partial nitrification-anammox/denitrification process might be a cost-efficient nitrogen removal technology for liquid digestate, benefitting to domestic waste recycling and carbon neutralization.

Multi-omics analysis reveals the collaboration and metabolisms of the anammox consortia driven by soluble/non-soluble Fe(III) as the sole iron element

Iron is recognized as a physiological requirement for anammox bacteria (AnAOB), with Fe(II) considered to be the most effective form. However, Fe(III), instead of Fe(II) is the common iron form in natural and artificial ecosystems. In this study, the nitrogen removal performance and metabolic mechanisms in anammox consortia with soluble and non-soluble Fe(III) as the sole iron element were investigated. After the 150-day operation, the soluble (FeCl3) and insoluble (Fe2O3) Fe(III)-fed anammox systems reached nitrogen removal rates of 71.84 ± 0.80% and 50.20 ± 0.98%, respectively. AnAOB could survive with soluble (FeCl3) or insoluble (Fe2O3) Fe(III) as the sole iron element, reaching relative abundances of 18.49% and 13.16%, respectively. The results show that the formation of anammox core consortia can enable AnAOB's survival to adverse external conditions of Fe(II) deficiency. Metagenomic and metatranscriptomic analysis reveal that Ca. Kuenenia can only uptake Fe(II) into the cell for metabolisms either independently through the extracellular electron transfer or with the cross-feeding of symbiotic microbes. This study provides insight into the utilization and metabolic mechanisms of Fe(III) in Ca. Kuenenia-dominated consortia, and deepens the understanding of anammox core consortia in the nitrogen, carbon, and iron cycling, further promoting the practical applications of anammox processes.

Anammox activity improved significantly by the cross-fed NO from ammonia-oxidizing bacteria and denitrifying bacteria to anammox bacteria

Nitric oxide (NO) has been suggested as an obligate intermediate in anaerobic ammonium oxidation (anammox), nitrification and denitrification. At the same time, ammonia-oxidizing bacteria (AOB) and denitrifying bacteria (DNB) are always existed in anammox flora, so what is the role of NO produced from AOB and DNB? Could it accelerate nitrogen removal via the anammox pathway with NO as an electron acceptor? To investigate this hypothesis, nitrogen transforming of an anammox biofilter was analyzed, functional gene expression of anammox bacteria (AnAOB), AOB and DNB were compared, and NO source was verified. For anammox biofilter, anammox contributed to 91.3 % nitrogen removal with only 14.4 % of AnAOB being enriched, while DNB was dominant. Meta-omics analysis and batch test results indicated that AOB could provide NO to AnAOB, and DNB also produced NO via up-regulating nirS/K and down-regulating nor. The activation of the anammox pathway of NH4++NO→N2 caused the downregulation of nirS and nxr in Ca. Kuenenia stuttgartiensis. Additionally, changes in nitrogen transforming pathways affected the electron generation and transport, limiting the carbon metabolism of AnAOB. This study provided new insights into improving nitrogen removal of the anammox system.

Extracellular polymeric substances and microbial community shift during the start-up of a single-stage partial nitritation/anammox process

A sequencing batch reactor (SBR) was operated to investigate variations of extracellular polymeric substances (EPS) and microbial community during the start-up of the single-stage partial nitritation/anammox (SPN/A) process at intermittent aeration mode. The SPN/A system was successfully started on day 34, and the nitrogen removal efficiency and total nitrogen loading rate were 82.29% and 0.31 kg N/(m3 ·day), respectively. Furthermore, the relationship between the protein secondary structures and microbial aggregation was strongly related. The α-helix/ (β-sheet + random coil) ratios increased obviously from 0.20 ± 0.03 to 0.23 ± 0.01, with the sludge aggregation mean size increased from 56 to 107 μm during the start-up of SPN/A. During the start-up of SPN/A, Candidatus Kuenenia was the primary anammox bacteria, whereas Nitrospira was the main functional bacteria of nitrite-oxidizing bacteria. Correlation between the microbial community and EPS components was performed. The EPS and microbial community played important roles in keeping stable nitrogen removal and the formation of sludge granules. PRACTITIONER POINTS: Intermittent aeration strategy promoted SPN/A system start-up. EPS composition and protein secondary structure were related with the sludge disintegration and aggregation. Microbial community shift existed and promoted the stability of sludge and reactor performance during SPN/A start-up.

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4+:NO2-, where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4+:NO2- ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4+:NO2- ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4+:NO2- ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

Anammox-Mediated Hydroxyapatite Granules: Physicochemical Properties, 3D Hierarchy, and Biofilm Thickness

Biomineralization inspired the development of simultaneous biological transformations and chemical precipitation for simultaneous nitrogen removal and phosphorus recovery from wastewater, which could compensate for the incapacity of phosphorus management in the new biological route of anaerobic ammonium oxidation (anammox). In this study, we strengthened anammox-mediated biomineralization by long-term feeding of concentrated N, P, and Ca substrates, and a self-assembled matrix of anammox bacteria and hydroxyapatite (HAP) was fabricated in a granular shape, defined as HAP-anammox granules. HAP was identified as the dominant mineral using elemental analysis, X-ray diffraction, and Raman spectroscopy. The intensive precipitation of HAP resulted in a higher inorganic fraction and substantially improved settleability of anammox biomass, which facilitated HAP precipitation by acting as nucleation and metabolically elevated pH. By using X-ray microcomputed tomography, we visually represented the hybrid texture of interwoven HAP pellets and biomass, the core-shell layered architecture of different-sized HAP-anammox granules, and their homogeneously regulated thickness of the outer biofilm (from 118 to 635 μm). This unique architecture endows HAP-anammox granules with outstanding settleability, active biofilm, and tightly bonded biofilm with the carrier, which may explain the excellent performance of these HAP-anammox granules under various challenging operational conditions in previous studies.

Evaluation of sludge anaerobic fermentation driving partial denitrification capability: In view of kinetics and metagenomic mechanisms

Partial denitrification (PD) provides a promising approach of efficient and stable nitrite (NO₂^--N) generation for annamox. In this study, the feasibility of short-term sludge anaerobic fermentation driving PD was evaluated. It was found that a higher NO₂^--N accumulation in nitrate (NO₃^--N) reduction was obtained with the 5-days fermented sludge compared to 8 and 15-days fermentation. Moreover, compared to acetate as carbon source, sludge fermentation products (SFPs) induced the higher NO₂^--N production with nitrate-to-nitrite transformation ratio (NTR) nearly 100 %. Denitrification activity of fermented sludge were obviously improved with SFPs as electron donor. Metagenomic analysis revealed that Thauera was the dominant bacteria, which was assumed to be the key contributor to PD performance by harboring the highest narGHI and napAB but much lower nirS and nirK. Under the conditions of SFPs and fermented sludge, Thauera was speculated to have higher resistance than other denitrifiers attributed to versatile carbon metabolic capabilities utilizing SFPs with the significantly improved genes for metabolism of complex organic carbon via glycolysis after anaerobic fermentation. A novel integration of sludge fermentation driving PD and anammox for mainstream wastewater treatment and sidestream polishing was proposed to offer a promising application with reduced commercial carbon source consumption and waste sludge reduction.

Microbial dynamics reveal the adaptation strategies of ecological niche in distinct anammox consortia under mainstream conditions

The feasibility of anammox-based processes for nitrogen-contained wastewater treatment has been verified with different anammox bacteria, however, the ecological niche of anammox bacteria under mainstream conditions is still elusive. In this study, six sludge samples collected from different habitats were utilized to culture anammox bacteria under mainstream conditions, and two distinct anammox genera (Ca. Kuenenia and Ca. Brocadia) with a relative abundance of 6.31% (C1) and 3.09% (C3), respectively, were identified. Notably, the microbial dynamics revealed that anammox bacteria (AMX), ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), Chloroflexi bacteria (CFX), and heterotrophic denitrification bacteria (HDB) were the core members in anammox consortia. However, Ca. Kuenenia and Ca. Brocadia occupied different ecological niches in anammox consortia. The dissolved oxygen and microbial structures of the anammox-continuous stirred tank reactor systems were the main factors to affect their niche differentiation. Meanwhile, comammox might exist in the systems and occupy the ecological niche of AOB in nitrogen cycling. The network analysis suggested that Ignavibacterium could be the associated bacteria in Ca. Kuenenia-dominated consortia, while Ca. Nitrotoga was that in the Ca. Brocadia-dominated consortia. Our findings reveal a valuable reference for the observation of distinct anammox genera under mainstream conditions, which provides theoretical guidance for the engineering application of mainstream anammox-based processes.

Nitrogen contribution and microbial community of size-fractionated anammox sludge in continuous stirred-tank reactors

In this study, the microbial diversity of size-fractionated anammox sludge in a well-mixed system and their contribution to nitrogen transformation were investigated. Results showed that small granules (0.2-1.0 mm) contributed to the major part of the nitrogen removal rate (56 %) due to its largest mixed liquor volatile suspended solids (1240 ± 80 mg·L^-1). However, large granules (>1.0 mm) possessed the highest relative abundances of Ca. Kuenenia stuttgartiensis and specific anammox activity, representing 49.34 % and 24.45 ± 0.01 mg-N·g^-1-mixed liquor volatile suspended solids·h^-1, respectively. The microbial diversity decreased as the increase of granular size, resulting in microbial community shifting to a simpler model. Metagenomic analysis showed that fine sludge might be the potential major for NO/N₂O production in the mature well-mixed system under inorganic conditions. This study provides guidance for the evaluation of nitrogen contribution by anammox size-fractionated sludge and the inhibition of the potential NO/N₂O emission in anammox processes.

Microbial electrochemical ammonia recovery from anaerobic digester centrate and subsequent application to fertilize Arabidopsis thaliana

Although ammonia recovery from wastewater can be environmentally friendly and energy efficient compared to the conventional Haber-Bosch process, there is a lack of research on the reuse of the recovered ammonia to exhibit a complete picture of resource recovery. In this study, a microbial electrochemical system (MES) was used to recover ammonia from a mixture of anaerobic digester (AD) centrate and food wastewater at a volume ratio of 3:1. More than 60% of ammonia nitrogen was recovered with energy consumption of 2.7 kWh kg^-1 N. The catholyte of the MES, which contained the recovered ammonia, was used to prepare fertilizers to support the growth of a model plant Arabidopsis thaliana. It was observed that A. thaliana grown on the MES generated fertilizer amended with extra potassium, phosphorus, and trace elements showed comparable sizes and an even lower death rate (0%) than the control group (24%) that was added with a commercial fertilizer. RNA-Seq analyses were used to examine A. thaliana genetic responses to the MES generated fertilizers or the commercial counterpart. The comparative study offered metabolic insights into A. thaliana physiologies subject to the recovered nitrogen fertilizers. The results of this study have demonstrated the potential application of using the recovered ammonia from AD centrate as a nitrogen source in fertilizer and identified the necessity of supplementing other nutrient elements.

Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures

Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic ana­lysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus Brocadia, Ca. Kuenenia, Ca. Jettenia, and Ca. Scalindua), 4 Bacteroidota, and 3 Chloroflexota. Based on the gene sets of metabolic pathways involved in the degradation of polymeric substances found in Chloroflexota and Bacteroidota MAGs, they are expected to be scavengers of extracellular polymeric substances and cell debris.

Efficient nitrogen removal from leachate by coupling Anammox and sulfur-siderite-driven denitrification

High concentrations of nitrate can be generated during anaerobic ammonium oxidation (Anammox) wastewater treatment processes. Addition of sulfur to Anammox reactors stimulates the growth of sulfur-driven denitrifying (SADN) bacteria that can reduce nitrate to nitrogen gas. However, protons released during the SADN process lower the pH of the system and inhibit Anammox activity. The system will keep stable when pH is in the range of 7.5-8.5. This study showed that addition of siderite stabilized the reactor system and significantly improved the nitrogen removal process. In fact, even when concentrations of total nitrogen were 477.15 ± 16.84 mg/L, the sulfur/siderite reactor maintained nitrogen removal efficiencies >90%, while efficiencies in the sulfur reactor were < 80%. Anammox accounted for 31% of the bacterial sequences in the sulfur/siderite reactor compared to only 14% in the sulfur reactor with the majority of sequences clustering with Ca. Brocadia. An abundance of c-type cytochromes in anammox aggregates in the sulfur-siderite reactor also indicated that anammox activity was higher in this system.

Halophilic Martelella sp. AD-3 enhanced phenanthrene degradation in a bioaugmented activated sludge system through syntrophic interaction

Polycyclic aromatic hydrocarbons (PAHs) are a group of common recalcitrant pollutant in industrial saline wastewater that raised significant concerns, whereas traditional activated sludge (AS) has limited tolerance to high salinity and PAHs toxicity, restricting its capacity to degrade PAHs. It is therefore urgent to develop a bioaugmented sludge (BS) system to aid in the effective degradation of these types of compounds under saline condition. In this study, a novel bioaugmentation strategy was developed by using halophilic Martelella sp. AD-3 for effectively augmented phenanthrene (PHE) degradation under 3% salinity. It was found that a 0.5∼1.5% (w/w) ratio of strain AD-3 to activated sludge was optimal for achieving high PHE degradation activity of the BS system with degradation rates reaching 2.2 mg⋅gVSS^-1⋅h^-1, nearly 25 times that of the AS system. Although 1-hydroxy-2-naphthoic acid (1H2N) was accumulated obviously, the mineralization of PHE was more complete in the BS system. Reads-based metagenomic coupled metatranscriptomic analysis revealed that the expression values of ndoB, encoding a dioxygenase associated with PHE ring-cleavage, was 5600-fold higher in the BS system than in the AS system. Metagenome assembly showed the members of the Corynebacterium and Alcaligenes genera were abundant in the strain AD-3 bioaugmented BS system with expression of 10.3±1.8% and 1.9±0.26%, respectively. Moreover, phdI and nahG accused for metabolism of 1H2N have been annotated in both above two genera. Degradation assays of intermediates of PHE confirmed that the activated sludge actually possessed considerable degradation capacity for downstream intermediates of PHE including 1H2N. The degradation capacity ratio of 1H2N to PHE was 87% in BS system, while it was 26% in strain AD-3. These results indicated that strain AD-3 contributed mainly in transforming PHE to 1H2N in BS system, while species in activated sludge utilized 1H2N as substrate to grow, thus establishing a syntrophic interaction with strain AD-3 and achieving the complete mineralization of PHE. Long-term continuous experiment confirmed a stable PHE removal efficiency of 93% and few 1H2N accumulation in BS SBR system. This study demonstrated an effective bioaugmented strategy for the bioremediation of saline wastewater containing PAHs.

Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms

The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.

Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations

Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.

Treating the filtrate of mainstream anaerobic membrane bioreactor with the pilot-scale sludge-type one-stage partial nitritation/anammox process operated from 25 to 15 °C

At ambient temperature condition, the one-stage partial nitritation/anammox (PNA) process has been successfully adopted to treat the filtrate from the mainstream anaerobic membrane bioreactor (AnMBR). However, there is no investigation of the performance of this process at low-temperature condition. In this study, the nitrogen removal performance of a pilot-scale PNA reactor at the temperature of 15 °C for treating the filtrate of a mainstream AnMBR was investigated. The nitrogen removal rate of 0.09 kg/m³/d and the nitrogen removal efficiency of 37.6% were achieved. The anammox reaction was the rate-limiting step of the nitrogen removal. Nitrogen removal was attributed in part to denitrification activity. The microbial community analysis confirmed that the main functional bacteria comprised of genus Nitrosomonas and genus Kuenenia. In sum, this research demonstrated the applicability of PNA process for mainstream AnMBR filtrate treatment to some extent and enriched the related knowledge.

Comparison of Different Carriers to Maintain a Stable Partial Nitrification Process for Low-Strength Wastewater Treatment

Practical application of the partial nitritation–anaerobic ammonium oxidation (anammox) process has attracted increasing attention because of its low operational costs. However, the nitritation process, as a promising way to supply nitrite for anammox, is sensitive to the variations in substrate concentration and dissolved oxygen (DO) concentration. Therefore, a stable supply of nitrite becomes a real bottleneck in partial nitritation–anammox process, limiting their potential for application in mainstream wastewater treatment. In this study, five 18-L sequencing batch reactors were operated in parallel at room temperature (22°C ± 4°C) to explore the nitritation performance with different carrier materials, including sepiolite-nonwoven carrier (R1), zeolite-nonwoven carrier (R2), brucite-nonwoven carrier (R3), polyurethane carrier (R4), and nonwoven carrier (R5). The ammonia oxidation rate (AOR) in R1 reached the highest level of 0.174 g-N L−1 d−1 in phase II, which was 1.4-fold higher than the control reactor (R4). To guarantee a stable supply of nitrite for anammox process, the nitrite accumulation efficiency (NAE) was always higher than 77%, even though the free ammonia (FA) decreases to 0.08 mg-N/L, and the pH decreases to 6.8 ± 0.3. In phase V, the AOR in R1 reached 0.206 g-N L−1 d−1 after the DO content increase from 0.7 ± 0.3 mg/L to 1.7 ± 0.3 mg/L. The NAE in R1 was consistently higher than 68.6%, which was much higher than the other reactor systems (R2: 43.8%, R3: 46.6%, R4: 23.7%, R5: 22.7%). Analysis of 16S rRNA gene sequencing revealed that the relative abundance of Nitrobacter and Nitrospira in R1 was significantly lower than other reactors, indicating that the sepiolite carrier plays an important role in the inhibition of nitrite-oxidizing bacteria. These results indicate that the sepiolite nonwoven composite carrier can effectively improve the nitritation process, which is highly beneficial for the application of partial nitritation–anammox for mainstream wastewater treatment.

The startup of the partial nitritation/anammox-hydroxyapatite process based on reconciling biomass and mineral to form the novel granule sludge

The synchronous nitrogen elimination and phosphorus (P) recovery can be realized by the novel one-stage partial nitritation/anammox (PN/A)-hydroxyapatite (HAP) crystallization (PN/A-HAP) process, which seems promising in actual application. This research firstly conducted the startup of the PN/A-HAP process based on reconciling biomass and mineral to cultivate the novel sludge with the strategy of alternating enhancement of biomass accumulation and mineral formation. Within three months, the nitrogen removal rate of 1.1 kg/m³/d and the P removal efficiency of 54.2% were achieved. The biomass reached to 3.7 g/L and the average particle size of sludge granules was about 260 μm. The microbial analysis indicated that in sludge the ammonium-oxidizing bacteria (AOB) mainly belonged to the genus Nitrosomonas, and the anammox bacteria mainly the genus Kuenenia. The main mineral in sludge was identified as HAP. This startup strategy is guidable for the application of one-stage PN/A-HAP process in actual wastewater treatment.

The anammox coupled partial-denitrification process in an integrated granular sludge and fixed-biofilm reactor developed for mainstream wastewater treatment: Performance and community structure

This study describes an integrated granular sludge and fixed-biofilm (iGB) reactor innovatively designed to carry out the anammox/partial-denitrification (A/PD) process for nitrogen removal with mainstream municipal wastewater. The iGB-A/PD reactor consists of anammox granules inoculated in the lower region of reactor and an acclimated fixed-biofilm positioned in the upper region. Compared to the other reported A/PD systems for mainstream wastewater treatment, this iGB-A/PD reactor is notable due to its higher quality effluent with a total inorganic nitrogen (TIN) of ∼3 mg•L^-1 and operation at a high nitrogen removal rate (NRR) of 0.8 ± 0.1 kg-N•m^-3•d^-1. Reads-based metatranscriptomic analysis found that the expression values of hzsA and hdh, key genes associated with anammox, were much higher than other functional genes on nitrogen conversion, confirming the major roles of the anammox bacteria in nitrogen bio-removal. In both regions of the reactor, the nitrate reduction genes (napA/narG) had expression values of 56-99 RPM, which were similar to that of the nitrite reduction genes (nirS/nirK). The expression reads from genes for dissimilatory nitrate reduction to ammonium (DNRA), nrfA and nirB, were unexpectedly high, and were over the half of the levels of reads from genes required for nitrate reduction. Kinetic assays confirmed that the granules had an anammox activity of 16.2 g-NH₄⁺-N•kg^-1-VSS•d^-1 and a nitrate reduction activity of 4.1 g-N•kg^-1-VSS•d^-1. While these values were changed to be 4.9 g- NH₄⁺-N•kg^-1-VSS•d^-1and 4.3 g-N•kg^-1-VSS•d^-1 respectively in the fixed-biofilm. Mass flux determination found that PD and DNRA was responsible for ∼50% and ∼25% of nitrate reduction, respectively, in the whole reactor, consistent with high effluent quality and treatment efficiency via a nitrite loop. Metagenomic binning analysis revealed that new and unidentified anammox species, affiliated with Candidatus Brocadia, were the dominant anammox organisms. Myxococcota and Planctomycetota were the principal organisms associated with the PD and DNRA processes, respectively.

Biological Nitrogen Removal Database: A Manually Curated Data Resource

Biological nitrogen removal (BNR) technologies are the most effective approaches for the remediation of environmental nitrogen pollutants from wastewater treatment plants (WWTPs). Presently, research is going on to elucidate the structure and function of BNR microbial communities and optimizing BNR treatment systems to enhance nitrogen removal efficiency. The literature on BNR microbial communities and experimental datasets is not unified across various repositories, while a uniform resource for the collection, annotation, and structuring of these BNR datasets is still unavailable. Herein, we present the Biological Nitrogen Removal Database (BNRdb), an integrated resource containing various manually curated BNR-related data. At present, BNRdb contains 23,308 microbial strains, 46 gene families, 24 enzymes, 18 reactions, 301 BNR treatment datasets, 860 BNR-associated next-generation sequencing datasets, and 6 common BNR bioreactor systems. BNRdb provides a user-friendly interface enabling interactive data browsing. To our knowledge, BNRdb is the first BNR data resource that systematically integrates BNR data from archaeal, bacterial, and fungal communities. We believe that BNRdb will contribute to a better understanding of BNR process and nitrogen bioremediation research.

A novel anammox aggregate nourished sustainably internal heterotrophic nitrate removal pathway with endogenous carbon source

Anaerobic ammonium oxidation (anammox) is a cost-effective nitrogen removal pathway but instinctively generated nitrate limits its application. A novel anammox aggregate reduced the production of nitrate significantly with efficient removal of ammonia and nitrite in this work. The results demonstrated that the internal heterotrophic nitrate removal (IHNAR) pathway exists stably at inner of anammox aggregates, which eliminated 42.31 ± 3.85 % nitrate generated in anammox at without consuming external carbon source. The observed volatile fatty acids (VFAs) and adequate protein, polysaccharide and humic acids in the aggregates verified that the in-situ fermentation supplied sustainably endogenous carbon sources for the IHNAR. The efficient interspecies cooperation between anammox bacteria, heterotrophic denitrifiers and fermentative bacteria was identified, as the intrinsic justification for the obtained sustainability of IHNAR pathway. The findings were expected to provide theoretical guidance for promotions and applications of the anammox process with high-efficiency total nitrogen removal capabilities.

Achieving stable mainstream nitrogen and phosphorus removal assisted by hydroxylamine addition in a continuous partial nitritation/anammox process from real sewage

Hydroxylamine (NH₂OH) as the putative intermediate for anammox ensures the robustness of partial nitritation/anammox (PN/A) process; however, the feasible for NH₂OH addition to improve the stability of PN/A process under low-strength ammonia (NH₄⁺-N) condition need to be further investigated. In this study, the restoration and steady operation of mainstream PN/A process were investigated to treat real sewage with in situ NH₂OH added in a continuous alternating anoxic/aerobic with integrated fixed-film activated sludge (A³-IFAS) reactor. Results showed that the deteriorated PN/A process caused by nitrate (NO₃^--N) built-up was rapidly restored with a distinct decrease of the NO₃^--N_produced/NH₄⁺-N_consumed ratio from 28.7% to <10.0% within 20 days, after 5 mg N/L of NH₂OH was added daily into the aerobic zone of A³-IFAS reactor. After 230 days of operation, the average total nitrogen (TN) and phosphate (PO₄^3--P) removal efficiencies of 80.8% and 91.5%, respectively were stably achieved, with average effluent sCOD, NH₄⁺-N, TN and PO₄^3--P concentrations reaching 23.1, 2.3, 7.7 and 0.4 mg/L, respectively. Microbial community characterization revealed Candidatus Brocadia (3.60% and 2.92%) and Ignavibacteriae (1.56% and 2.66%) as the dominant anammox bacteria and denitrifying bacteria, respectively, jointly attached in the biofilm_1 and biofilm_2, while Candidatus Microthrix (5.17%) dominant in floc sludge was main responsible for phosphorus removal. This study confirmed that NH₂OH addition is an effective strategy for nitrite-oxidizing bacteria suppression, contributing to the in situ restoration of PN/A process and high stable mainstream nitrogen and phosphorus removal in a continuous PN/A process from real sewage.

Activities and metabolic versatility of distinct anammox bacteria in a full-scale wastewater treatment system

Anaerobic ammonium oxidation (anammox) is a key N₂-producing process in the global nitrogen cycle. Major progress in understanding the core mechanism of anammox bacteria has been made, but our knowledge of the survival strategies of anammox bacteria in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Here, by combining metagenomics with in situ metatranscriptomics, complex anammox-driven nitrogen cycles in an anoxic tank and a granular activated carbon (GAC) biofilm module of a full-scale WWTP treating landfill leachate were constructed. Four distinct anammox metagenome-assembled genomes (MAGs), representing a new genus named Ca. Loosdrechtii, a new species in Ca. Kuenenia, a new species in Ca. Brocadia, and a new strain in "Ca. Kuenenia stuttgartiensis", were simultaneously retrieved from the GAC biofilm. Metabolic reconstruction revealed that all anammox organisms highly expressed the core metabolic enzymes and showed a high metabolic versatility. Pathways for dissimilatory nitrate reduction to ammonium (DNRA) coupled to volatile fatty acids (VFAs) oxidation likely assist anammox bacteria to survive unfavorable conditions and facilitate switches between lifestyles in oxygen fluctuating environments. The new Ca. Kuenenia species dominated the anammox community of the GAC biofilm, specifically may be enhanced by the uniquely encoded flexible ammonium and iron acquisition strategies. The new Ca. Brocadia species likely has an extensive niche distribution that is simultaneously established in the anoxic tank and the GAC biofilm, the two distinct niches. The highly diverse and impressive metabolic versatility of anammox bacteria revealed in this study advance our understanding of the survival and application of anammox bacteria in the full-scale wastewater treatment system.

Distinct growth stages controlled by the interplay of deterministic and stochastic processes in functional anammox biofilms

Mainstream anaerobic ammonium oxidation (anammox) represents one of the most promising energy-efficient mechanisms of fixed nitrogen elimination from wastewaters. However, little is known about the exact processes and drivers of microbial community assembly within the complex microbial biofilms that support anammox in engineered ecosystems. Here, we followed anammox biofilm development on fresh carriers in an established 8m³ mainstream anammox reactor that is exposed to seasonal temperature changes (~25-12°C) and varying NH₄⁺ concentrations (5-25 mg/L). We use fluorescence in situ hybridization and 16S rRNA gene sequencing to show that three distinct stages of biofilm development emerge naturally from microbial community composition and biofilm structure. Neutral modelling and network analysis are employed to elucidate the relative importance of stochastic versus deterministic processes and synergistic and antagonistic interactions in the biofilms during their development. We find that the different phases are characterized by a dynamic succession and an interplay of both stochastic and deterministic processes. The observed growth stages (Colonization, Succession and Maturation) appear to be the prerequisite for the anticipated growth of anammox bacteria and for reaching a biofilm community structure that supports the desired metabolic and functional capacities observed for biofilm carriers already present in the system (~100g_NH4-N m³ d^-1). We discuss the relevance of this improved understanding of anammox-community ecology and biofilm development in the context of its practical application in the start-up, configuration, and optimization of anammox biofilm reactors.

Achieving superior nitrogen removal performance in low-strength ammonium wastewater treatment by cultivating concentrated, highly dispersive, and easily settleable granule sludge in a one-stage partial nitritation/anammox-HAP reactor

In low-strength ammonium wastewater (LSAWW) treatment, the application of anammox-based process is still limited due to extreme instability and the poor nitrogen removal rate (NRR). In this work, granule sludge, comprised of functional microbes and hydroxyapatite (HAP), was inoculated and cultivated in a one-stage partial nitritation/anammox (PNA) reactor for LSAWW treatment. The results showed that at the hydraulic retention time (HRT) of about 1.0 h and the influent ammonium concentration of 63.0 mg/L, an average NRR of 1.28 kg/m³/d was achieved, which far exceeds that reported in similar studies. The main inorganic matter in sludge was identified as HAP through the X-ray diffractometer and Raman spectrum analysis. The tomographic images of wet granule created through computed tomography revealed that the interior density of the granules was uneven and many hollow structures existed in the granule interior. Combined with the Scanning Electron Microscope images of dry granules, it was found that the granules were comprised of hollow sub-granules. Since the biomass in the reactor increased with no obvious increase in the granule size, it was inferred that the hollow sub-granules had fragile connections with each other and that granules division occurred easily, resulting in the high dispersity of sludge. Florescence in situ hybridization results also showed that the ammonium-oxidizing bacteria and anammox bacteria were mainly distributed in the two sides of the sub-granule shells and the HAP in the middle. This kind of structure raised the density of granules and improved the settleability of sludge, which made it possible to achieve a high biomass in the reactor at a short HRT. Therefore, the sludge formed in the reactor was concentrated, highly dispersive and easily settleable. These factors appear to be crucial for achieving the desired nitrogen removal performance. This study marks a big leap in LSAWW treatment through the one-stage PNA process and has great potential in actual applications.

Research progress on enhancing the performance of autotrophic nitrogen removal systems using microbial immobilization technology

The autotrophic nitrogen removal process has great potential to be applied to the biological removal of nitrogen from wastewater, but its application is hindered by its unstable operation under adverse environmental conditions, such as those presented by low temperatures, high organic matter concentrations, or the presence of toxic substances. Granules and microbial entrapment technology can effectively retain and enrich microbial assemblages in reactors to improve operating efficiency and reactor stability. The carriers can also protect the reactor's internal microorganisms from interference from the external environment. This article critically reviews the existing literature on autotrophic nitrogen removal systems using immobilization technology. We focus our discussion on the natural aggregation process (granulation) and entrapment technology. The selection of carrier materials and entrapment methods are identified and described in detail and the mechanisms through which entrapment technology protects microorganisms are analyzed. This review will provide a better understanding of the mechanisms through which immobilization operates and the prospects for immobilization technology to be applied in autotrophic nitrogen removal systems.

Highly enriched anammox within anoxic biofilms by reducing suspended sludge biomass in a real-sewage A2/O process

This study proposes a novel strategy of stably enriching anammox in mainstream, based on the competitive difference to NO₂^- between anoxic biofilms and suspended sludge. A modified anaerobic-anoxic-oxic (A²/O) process run for 500 days with actual municipal wastewater. Microbial analysis revealed that anoxic-carrier biofilms had a significantly higher abundance of anammox (qPCR: 0.74% - 4.34%) than suspended sludge (P< 0.001). Batch tests showed that anammox within anoxic-carrier biofilms contributed to significant nitrogen removal, coupled with partial-denitrification (NO₃^- → NO₂^-). The anammox genus, Ca. Brocadia, was highly enriched when suspended sludge was accidentally lost. Further batch tests found that reducing suspended biomass helped anammox enrichment in anoxic-carrier biofilms, because the suspended sludge had strong NO₂^- competition (NO₂^- → N₂) with anammox (increased nirK). Metagenomic sequencing revealed that Ca. Brocadia dominates in the anoxic-carrier biofilms, and is the most important narG contributor to NO₃^- → NO₂^-, which could have promoted the competition of NO₂^- with heterotrophic bacteria. For this A²/O process, the low effluent total nitrogen (8.9 mg ± 1.0 mg N/L) was attributed to partial-denitrification coupling with anammox, demonstrating that this process is applicable to the general influent N-concentration range (30 mg - 50 mg NH₄⁺-N/L) of municipal wastewater treatment plants (WWTPs). Based on the special competitive preference of anammox for NO₂^-, this study provides a promising and practical alternative for enriching anammox bacteria in municipal WWTPs.

Critical Analysis of Biomass Retention Strategies in Mainstream and Sidestream ANAMMOX-Mediated Nitrogen Removal Systems

ANAMMOX (anaerobic ammonium oxidation) represents an energy-efficient process for biological nitrogen removal, particularly from wastewater streams with low chemical oxygen demand (COD) to nitrogen (C/N) ratios. Its widespread application, however, is still hampered by a lack of access to biomass-enriched with ANAMMOX bacteria (AMX), slow growth rates of AMX, and their sensitivity to inhibition. Although the coupling of ANAMMOX processes with partial nitrification is already widespread, especially for sidestream treatment, maintaining a functional population density of AMX remains a challenge in these systems. Therefore, strategies that maximize retention of AMX-rich biomass are essential to promote process stability. This paper reviews existing methods of biomass retention in ANAMMOX-mediated systems, focusing on (i) granulation; (ii) biofilm formation on carrier materials; (iii) gel entrapment; and (iv) membrane technology in mainstream and sidestream systems. In addition, the microbial ecology of different ANAMMOX-mediated systems is reviewed.

Temperature modulates stress response in mainstream anammox reactors

Autotrophic nitrogen removal by anaerobic ammonium oxidizing (anammox) bacteria is an energy-efficient nitrogen removal process in wastewater treatment. However, full-scale deployment under mainstream conditions remains challenging for practitioners due to the high stress susceptibility of anammox bacteria towards fluctuations in dissolved oxygen (DO) and temperature. Here, we investigated the response of microbial biofilms with verified anammox activity to DO shocks under 20 °C and 14 °C. While pulse disturbances of 0.3 mg L-1 DO prompted only moderate declines in the NH4+ removal rates, 1.0 mg L-1 DO led to complete but reversible inhibition of the NH4+ removal activity in all reactors. Genome-centric metagenomics and metatranscriptomics were used to investigate the stress response on various biological levels. We show that temperature regime and strength of DO perturbations induced divergent responses from the process level down to the transcriptional profile of individual taxa. Community-wide gene expression differed significantly depending on the temperature regime in all reactors, and we found a noticeable impact of DO disturbances on genes involved in transcription, translation, replication and posttranslational modification at 20 °C but not 14 °C. Genome-centric analysis revealed that different anammox species and other key biofilm taxa differed in their transcriptional responses to distinct temperature regimes and DO disturbances.

Anammox process dosed with biochars for enhanced nitrogen removal: Role of surface functional groups

Biochar is an inexpensive redox-active carbon material that has been demonstrated to enhance microbial nitrogen-transforming processes. However, how redox-active biochar affects anammox remains unclear. Here, the effects of three functionally distinct biochars produced from corn stover biomass at varied pyrolysis temperatures (CS300, CS500, CS800) were evaluated as additives on the anammox performance in three reactors (R300, R550, R800) over the long term, during which nitrogen loading rate was either increased drastically (pulse strategy) or gradually (gradual strategy). Nitrogen removal was achieved at 86.5% (R300), 77.1% (Control), 59.3% (R550) and 57.7% (R800) under pulse strategy, and at 95.4% (R300), 92.3% (R550), 86.2% (Control) and 82.0% (R800) under gradual strategy, respectively. Compared with Control, addition of CS300 increased abundance of Candidatus Kuenenia with superior anammox activity. CS300 enriched with reduced functional groups (phenolic/hydroquinone) could donate electrons to support bioenergetics of anammox metabolism, whereas electron-accepting CS800 functioned inversely. Overall, this study highlights the importance of surface functional groups and redox property of biochar such that determines whether its addition impose stimulatory or suppressive effect on anammox process.

Comparative genomics in "Candidatus Kuenenia stuttgartiensis" reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins

Background

Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the databases, little is known about the stability and variability of their genomes and how the genomes evolve in response to changing environments.

Results

Here we report the complete genome of the anammox bacterium “Candidatus Kuenenia stuttgartiensis” strain CSTR1 which was enriched planktonically in a semi-continuous stirred-tank reactor. A comparison of the genome of strain CSTR1 with the genome of “Ca. Kuenenia stuttgartiensis” MBR1 and the draft genome of KUST showed > 99% average nucleotide identity among all. Rearrangements of large genomic regions were observed, most of which were associated with transposase genes. Phylogenetic analysis suggests that strain MBR1 is more distantly related to the other two strains. Proteomic analysis of actively growing cells of strain CSTR1 (growth rate ~ 0.33 d^− 1) failed to detect the annotated cytochrome cd₁-type nitrite reductase (NirS) although in total 1189 proteins were found in the proteome. Yet, this NirS was expressed when strain CSTR1 was under stress or starvation (growth rate < 0.06 d^− 1). We also observed large sequence shifts in the strongly expressed S-layer protein compared to other “Ca. Kuenenia” strains, indicating the formation of hybrids of genes encoding the surface proteins.

Conclusions

“Ca. Kuenenia” strains appear to be relatively stable in their basic physiological traits, but show high variability in overall genome structure and surface proteins.

Insight into the benefits of anammox bacteria living as aggregates

This work tried understanding aggregation preference of anammox bacteria from benefit-driven perspective. Aggregated anammox sludge (AGS) gained benefits in specific anammox activity (SAA) (increased by 40.47 ± 12.64%) and in toxicity resistance (enhanced by 65.41%) than scattered anammox sludge (SCS), which were verified by kinetics. The increased heme c content by 35.67 ± 5.77% and enhanced relative abundance of anammox bacteria by 9.29% supported the benefits in biological activity and improved EPS content by 1097.59 ± 43.06% (622.16 ± 61.73% for protein (PN), 2403.47 ± 162.75% for humic acid (HA) and 1145.34 ± 97.33% for polysaccharide (PS)) justified the benefits in toxicity resistance. The diverse microbial communities and organized spatial structures owned by AGS promoted interactions between species, as the intrinsic justification for obtaining the benefits. We expect our findings to provide theoretical guidance for promotions and applications of the anammox process with excellent nitrogen removal capacity and stability.

Larger Anammox Granules not only Harbor Higher Species Diversity but also Support More Functional Diversity

Granule-based partial nitritation and anammox (PN/A) represents one of the most energy-efficient biotechniques for ammonium removal from wastewater. The PN/A granules appear in a continuum of sizes, yet little is known about the extent to which microbial communities and microbial metabolisms are partitioned between size-fractionated granules. Here, we divided granules harvested from a pilot-scale PN/A reactor into five discrete size fractions (<0.2, 0.2-0.5, 0.5-0.8, 0.8-1.0, and >1.0 mm). The composition and functional attribute of five pools of the size-fractionated granules were characterized by 16S ribosomal RNA (rRNA) gene amplicon and metagenomic and metatranscriptomic sequencing to provide a comprehensive insight into the key microbial group in a PN/A system. Larger granules were shown to not only harbor higher microbial diversity but also support more diverse functions than smaller granules. De novo coassembly and binning of metagenomic reads yielded 22 draft genomes of dominant microorganisms, which allowed us to infer an ecological model of the microbial ecosystem in anammox-based granules. This genome-based ecological model indicates that nitrifying organisms in smaller granules feed nitrite to anammox bacteria in larger granules. The results improve our understanding of the PN/A system, especially for the metabolic interactions between small and large granules.

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

BACKGROUND

Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retrieved in a single study contributed by the cost-effective short-read sequencing and developed assembly/binning pipelines. However, conventional binning methods usually yield highly fragmented draft genomes that limit our ability to comprehensively understand these microbial communities. Thus, to leverage advantage of both the long and short reads to retrieve more complete genomes from environmental samples is a must-do task to move this direction forward.

RESULTS

Here, we used an iterative hybrid assembly (IHA) approach to reconstruct 49 metagenome-assembled genomes (MAGs), including 27 high-quality (HQ) and high-contiguity (HC) genomes with contig number ≤ 5, eight of which were circular finished genomes from a partial-nitritation anammox (PNA) reactor. These 49 recovered MAGs (43 MAGs encoding full-length rRNA, average N50 of 2.2 Mbp), represented the majority (92.3%) of the bacterial community. Moreover, the workflow retrieved HQ and HC MAGs even with an extremely low coverage (relative abundance < 0.1%). Among them, 34 MAGs could not be assigned to the genus level, indicating the novelty of the genomes retrieved using the IHA method proposed in this study. Comparative analysis of HQ MAG pairs reconstructed using two methods, i.e., hybrid and short reads only, revealed that identical genes in the MAG pairs represented 87.5% and 95.5% of the total gene inventory of hybrid and short reads only assembled MAGs, respectively. In addition, the first finished anammox genome of the genus Ca. Brocadia reconstructed revealed that there were two identical hydrazine synthase (hzs) genes, providing the exact gene copy number of this crucial phylomarker of anammox at the genome level.

CONCLUSIONS

Our results showcased the high-quality and high-contiguity genome retrieval performance and demonstrated the feasibility of complete genome reconstruction using the IHA workflow from the enrichment system. These (near-) complete genomes provided a high resolution of the microbial community, which might help to understand the bacterial repertoire of anammox-associated systems. Combined with other validation experiments, the workflow can enable a detailed view of the anammox or other similar enrichment systems. Video Abstract.

Comparing nitrite-limited and ammonium-limited anammox processes treating low-strength wastewater: Functional and population heterogeneity

Biomass segregation between granules/biofilm and flocs is widespread in anammox-based processes. The segregation of biomass allows for easy control of processes stability. The goal of this study is to understand the biomass segregation in two anoxic anammox reactors respectively operated in nitrite-limited (R_NO2) and ammonium-limited (R_NH4) modes treating low-strength wastewater at 20 °C. Results showed that size-based biomass segregation was developed in both reactors. But the functional and population heterogeneity was more significant in the ammonium-limited anammox reactor. The activity and abundance of anammox bacteria in large granules were significantly higher than that in flocs under the ammonium-limited conditions. The large granules played a major role in nitrogen removal in R_NH4. By contrast, both large granules and small flocs contributed significantly to the nitrogen loss in the nitrite-limited anammox reactor, since a large number of anammox bacteria existed in both granules and flocs. Besides, a number of Nitrospira-like NOB were also detected in both anoxic anammox reactors, which primarily inhabited in flocs seemingly droved by the availability of oxygen. But the abundance of Nitrospira in R_NH4 was much higher than that in R_NO2. All these results suggested that selective flocs removal would be necessary for R_NH4 to improve its anammox performance but non-essential for R_NO2. The two anammox reactors shared the predominant anammox species with the closest relative to Ca. Brocadia sp. 40 (98%). Unexpectedly, the anammox species grew faster in R_NH4. But the microbial diversity and evenness was much greater in R_NO2, suggesting its higher functional stability.

Fast start-up of PN/A process in a single-stage packed bed and mechanism of nitrogen removal

The single-stage partial nitritation-anammox (PN/A) process is severely limited by a long start-up time and unstable removal efficiency. In this study, PN/A was developed in 67 days in a novel packed bed equipped with porous bio-carriers by gradually increasing the influent nitrogen loading rate (0.15-0.73 kg-N m^-3·d^-1) and controlling the dissolved oxygen (< 1.2 mg L^-1). An average ammonium nitrogen removal efficiency (ARE) and total nitrogen removal efficiency (TNR) of 87.01 and 72.41%, respectively, were obtained. This represents a reliable alternative method of achieving rapid PN/A start-up. The results of 16S rRNA sequencing showed that Proteobacteria and Planctomycetes, with which ammonia-oxidizing bacteria and anammox bacteria were affiliated, accounted for 38.8%, representing the dominant phylum in the system after acclimation. The abundance of Nitrosomonas and Candidatus Brocadia increased by 16 and 1.79%, respectively. The results of metagenomics and metatranscriptomics revealed that the nitrite oxidation process was blocked by the transcriptional suppression of nitrite oxidoreductase and the entire nitrogen metabolism process was dominated by the partial nitritation and anammox process. Moreover, a high abundance of heterotrophic bacteria with potential for nitrogen removal was detected. In the nitrogen cycle, a widespread nitrite-accumulated denitrification helps to form a nitrite loop, which promotes the efficiency of total nitrogen removal. This is crucial for further improving the nitrogen removal mechanism in the PN/A system.

Achieving efficient nitrite accumulation in glycerol-driven partial denitrification system: Insights of influencing factors, shift of microbial community and metabolic function

Partial denitrification (PD), which could provide sufficient nitrite for subsequent anaerobic ammonium oxidation, is a novel strategy for mainstream nitrogen removal. In this study, the performance of using glycerol as electron donor for nitrite accumulation in PD process was evaluated. Results showed that a C/N of 4.5 was effective for nitrite production (average nitrite accumulation rate: 34.32 mg N h^-1 gMLVSS^-1; average nitrate-to-nitrite transformation ratio (NTR): 91.1%) with pH ranging from 6.0 to 9.0. Also, a stable nitrite accumulation was achieved in long-term operation with the average NTR of 80.1%. Mechanism investigation found that the denitrifying bacteria Saccharibacteria (77.9%) was enriched in glycerol-driven reactors. Moreover, the enzymatic activity as well as the encoding genes (i.e. narG, narH and napA) involved in nitrate reduction were much higher than that for nitrite reduction (i.e. nirK), and this disparity was responsible for the efficient nitrite accumulation in glycerol-driven PD system.

Targeted metagenomics reveals extensive diversity of the denitrifying community in partial nitritation anammox and activated sludge systems

The substantial presence of denitrifiers has already been reported in partial nitritation anammox (PNA) systems using the 16S ribosomal RNA (rRNA) gene, but little is known about the phylogenetic diversity based on denitrification pathway functional genes. Therefore, we performed a metagenomic analysis to determine the distribution of denitrification genes and the associated phylogeny in PNA systems and whether a niche separation between PNA and conventional activated sludge (AS) systems exists. The results revealed a distinct abundance pattern of denitrification pathway genes and their association to the microbial species between PNA and AS systems. In contrast, the taxonomic analysis, based on the 16S rRNA gene, did not detect notable variability in denitrifying community composition across samples. In general, narG and nosZa2 genes were dominant in all samples. While the potential for different stages of denitrification was redundant, variation in species composition and lack of the complete denitrification gene pool in each species appears to confer niche separation between PNA and AS systems. This study suggests that targeted metagenomics can help to determine the denitrifying microbial composition at a fine-scale resolution while overcoming current biases in quantitative polymerase chain reaction approaches due to a lack of appropriate primers.

Reducing carbon source consumption through a novel denitratation/anammox biofilter to remove nitrate from synthetic secondary effluent

This study presents a novel denitratation/anammox biofilter (DABF) for nitrate removal from secondary effluent, where denitratation (NO₃^-→NO₂^-) is coupled with anammox (NO₂^- +NH₄⁺→N₂) instead of denitritation (NO₂^-→N₂). Total nitrogen (TN) was removed by 81.90% in this DABF when the average effluent TN concentration was 7.82 mg/L. Meanwhile, organic carbon source consumption and backwash sludge production in the DABF were reduced by 63% and 70%, respectively, compared to conventional denitrifying biofilter (DNBF). Nitrogen banlance analysis indicates that 93% of the nitrogen gas produced in DABF was via anammox. Batch tests confirmed that the DABF biofilm reduced nitrite using ammonium as the electron donor, and accumulated nitrite during denitratation, thus providing nitrite for the anammox bacteria. Moreover, high-throughput sequencing approach also revealed that the anammox bacteria Candidatus Brocadia dominated the community, which could also be responsible for the stable processes in DABF by interacting with the other denitrifying bacteria.

Assessment of Anammox process against acute and long-term exposure of ZnO nanoparticles

The impacts of nanoparticles (NPs) on wastewater treatment have become a great concern because of their widespread applications. Although the acute responses of anammox bacteria to NPs have enhanced the knowledge about the potential risks of them, deep understanding of the cumulative impacts of NPs must be assessed. The purpose of this research was therefore to further extend the current knowledge by evaluating both acute and long-term effects of Zinc oxide (ZnO) NPs on Anammox process based on nitrogen removal performance, self-recovery ability and microbial community structure. The acute exposure tests indicated that, the median inhibition concentration (IC50) of ZnO NPs on Anammox process was 84.7 mg/L (54.82 mg ZnO NPs/g VSS). Acute exposure of 200 mg/L ZnO NPs (117.54 mg Zn/g VSS) caused 80% inhibition in batch assays while the long-term inhibition dosage was 100 mg/L ZnO NPs (187.50 mg ZnO NPs/g VSS) corresponding to 1022 mg/L total Zn (1916.27 mg Zn/g VSS) in the reactor due to the accumulation of NPs. Total, soluble and biomass-associated Zn concentrations were measured throughout the long-term exposure to observe the behavior of ZnO NPs in the reactor. Total Zn in the reactor was cumulatively increased and mostly originated from biomass-associated Zn. Following the long-term inhibition tests, self-recovery of Anammox process within 120 days demonstrated that, the ZnO NPs inhibition is reversible for the applied dose. Furthermore, next generation sequencing results indicated a symbiotic relationship between the microbial groups in the anammox bioreactor while relative abundance of Candidatus (Ca.) Brocadiaceae family showed a decrease parallel to the deterioration in nitrogen removal performance of bioreactor. At the end of the long-term exposure studies, 48.76% decline on anammox quantity was detected.

Bacteriophage-mediated extracellular DNA release is important for the structural stability of aerobic granular sludge

The aim of this study was to investigate the microbial characteristics and the structural role of exDNA in different size AGSs. Metagenomic results showed that exDNA has a significantly lower GC content, ~46.0%, than the ~65.0% GC of intracellular DNA (inDNA). Taxonomic predictions showed most of the reads from the exDNA that could be taxonomically assigned were from members of the phyla Bacteroidetes (55.0-64.2% of the total exDNA reads). Assigned inDNA reads were mainly from Proteobacteria (50.9-57.8%) or Actinobacteria (18.0-28.0%). Reads mapping showed that exDNA read depths were similar across all predicted open reading frames from assembled genomes that were assigned as Bacteroidetes which is consistent with cell lysis as a source of exDNA. Enrichment of CRISPR-CAS proteins in exDNA reads and CRISPR spacers in Bacteroidetes associated draft genomes suggested that bacteriophage infection may be an important cause of lysis of these cells. A critical role for this exDNA was found using DNase I digestion experiments which showed that the exDNA was vital for the structural stability of relatively small sized AGS but not for the larger sized AGS. The characteristics of exDNA in AGSs revealed in this work provide a new perspective on AGS components and structural stability.

Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nitrogen Removal Processes

There is a lack of understanding of the interaction between anammox bacteria and the flanking microbial communities in both freshwater (non-saline) and marine (saline) ecosystems. Here, we present a comparative genome-based exploration of two different anammox bioreactors, through the analysis of 23 metagenome-assembled genomes (MAGs), 12 from freshwater anammox reactor (FWR), and 11 from marine anammox reactor (MWR). To understand the contribution of individual members to community functions, we applied the index of replication (iRep) to determine bacteria that are actively replicating. Using genomic content and iRep information, we provided a potential ecological role for the dominant members of the community based on the reactor operating conditions. In the non-saline system, anammox (Candidatus Brocadia sinica) and auxotrophic neighboring bacteria belonging to the phyla Ignavibacteriae and Chloroflexi might interact to reduce nitrate to nitrite for direct use by anammox bacteria. Whereas, in the saline reactor, anammox bacterium (Ca. Scalindua erythraensis) and flanking community belonging to phyla Planctomycetes (different than anammox bacteria)—which persistently growing in the system—may catabolize detritus and extracellular material and recycle nitrate to nitrite for direct use by anammox bacteria. Despite different microbial communities, there was functional redundancy in both ecosystems. These results signify the potential application of marine anammox bacteria for treating saline N-rich wastewaters.

A novel strategy for anammox consortia preservation: Transformation into anoxic sulfide oxidation consortia

The preservation of anaerobic ammonia oxidation (anammox) consortia is crucial for the rapid start-up and the process stability of the anammox based bioreactor. This work proposed and evaluated the feasibility of an anammox consortia preservation strategy, in which the anammox sludge was transformed into intermediate anoxic sulfide oxidation (ASO) functional microorganisms. Initially, the ASO process was successfully started up by inoculating anammox sludge and the overall sulfide and nitrate removal rates stabilized at 57.5 ± 0.22 and 10.0 ± 0.18 kg m^-3 day^-1, respectively. Then, the bioreactor function was reversely transformed into anammox, whose nitrogen removal rate reached 1.68 kg m^-3 day^-1. Granule characteristics analysis revealed that both biomass and extracellular polymeric substance content returned to their original states after the reverse start-up. Although the population of Candidatus_Kuenenia was greatly declined during ASO process, its richness was successfully recovered after the reverse start-up of the anammox process. The inferred metagenomes analysis demonstrated that the shifts in functional microorganisms were related to variation in the main metabolic pathways. The specific activities of anammox and ASO both are regarded as key indicators for the successful start-up of bioreactor. This work revealed a novel technique for the preservation of anammox consortia and might be a potential strategy for overcoming the drawback of long start-up time.

Enhance the treatment of low strength wastewater at low temperature with the coexistence system of AnAOB and heterotrophic bacteria: Performance and bacterial community

The application of anammox process in mainstream wastewater treatment process is still facing challenges especially at the low temperature. To resolve this problem, the coexistence system of anaerobic ammonia-oxidizing bacteria (AnAOB) and heterotrophic bacteria (HB) was built in this study. The nitrogen removal efficiency mainly maintained at above 90% during the process of temperature reducing from 35 °C to 10 °C. The nitrogen removal rate were 0.30 g N·L^-1·d^-1 at both 25 and 15 °C and 0.10 g N·L^-1·d^-1 at 10 °C, respectively. Analysis of 16S rRNA genus sequencing revealed that as the temperature reduced to 10 °C, the Denutrotisoma genera presented a downward trend but Comamonadaceae genera showed an upward trend. At 10 °C, the contrast of anammox activities between granular and flocculent sludge in the system revealed that although the abundance of anammox genera was much lower in flocculent sludge than that in granular sludge, the anammox activities showed no significant discrepancy. And the abundance of Comamonadaceae and Chloroflexales genera were much higher in flocculent sludge than those in granular sludge, presenting their key roles to anammox activity at low temperature. The Circos diagram and Cluster of orthologous Group of protein functional predication showed that the functional abundance related to interaction among microbial communities were higher in flocculent sludge but those related to self-growth was higher in granular sludge. This result indicated the significance of the interactions based on the microbial diversity in the application of annamox process at low temperature.

Metagenomics reveals microbial community differences lead to differential nitrate production in anammox reactors with differing nitrogen loading rates

Nitrate production during anammox can decrease total nitrogen removal efficiency, which will negatively impact its usefulness for the removal of nitrogen from waste streams. However, neither the performance characteristics nor physiological shifts associated with nitrate accumulation in anammox reactors under different nitrogen loading rates (NLRs) is well understood. Consequently, these parameters were studied in a lower NLR anammox reactor, termed R1, producing higher than expected levels of nitrate and compared with a higher NLR reactor, termed R2, showing no excess nitrate production. While both reactors showed high NH₄⁺-N removal efficiencies (>90%), the total nitrogen removal efficiency (<60%) was much lower in R1 due to higher nitrate production. Metagenomic analysis found that the number of reads derived from anammox bacteria were significantly higher in R2. Another notable trend in reads occurrence was the relatively higher levels of reads from genes predicted to be nitrite oxidoreductases (nxr) in R1. Binning yielded 27 high quality draft genomes from the two reactors. Analysis of bin occurrence found that R1 showing both a decrease in anammox bacteria and an unexpected increase in nxr. In-situ assays confirmed that R1 had higher rates of nitrite oxidation to nitrate and suggested that it was not solely due to obligate NOB, but other nxr-containing bacteria are important contributors as well. Our results demonstrate that nitrate accumulation can be a serious operational concern for the application of anammox technology to low-strength wastewater treatment and provide insight into the community changes leading to this outcome.

Enhanced microbial metabolism in one stage partial nitritation-anammox system treating low strength wastewater by novel composite carrier

One stage partial nitritation-anammox (PN-A) process has attracted more and more attention due to the low investment cost but the instability in treating low strength wastewater. In this study, for producing a novel composite carrier that could provide high ammonia microenvironment in low strength wastewater, the zeolites and floating materials were combined in the spherical shell and distributed evenly by the spherical polyhedron. And a moving bed biofilm reactor (MBBR) with the composite carriers and ordinary carriers without zeolites as control group was operated for nearly 120 days. The PN-A process were realized in 53 days, and the total nitrogen removal efficiency reached around 85% at influent ammonium concentration of 50 mg/L finally. Analysis of 16S rRNA gene sequencing revealed that the composite carriers showed significant promotion on the proliferation of ammonium oxidizing bacteria (AOB) and enrichment of anaerobic ammonium oxidizing bacteria (AnAOB), accounting for 19.14% and 41.65% on the surface, respectively. Moreover, the existence of relative higher abundance of ammonia on the composite carrier surface was validated by the metabolite biomarker of glutamate and especially spermidine. The metabolomics analysis and 16S rRNA function prediction showed that the protein synthesis pathway was obviously upregulated on the composite carriers surface compared with that on the ordinary carriers surface. The higher abundance of glutamate and putrescine indicated that the composite carrier could stimulate the metabolism and growth of bacteria. The present study provided a functional carrier to realize the transformation of activated sludge system into PN-A system treating low strength wastewater, which is significant to the application of the process in mainstream.

Metagenomic insights into functional traits variation and coupling effects on the anammox community during reactor start-up

Anammox technology is an energy-efficient wastewater treatment process and anammox community structure has gained extensive attention. However, the dynamics of community functional traits are still elusive. Here, we combined the long-term reactor operation and metagenomic, multiple bioinformatic and network analyses to reveal the succession of anammox community and function traits during reactor start-up. We found the cooperation of denitrifiers that affiliated to the phylum Proteobacteria could reduce nitrite to dinitrogen gas. These organisms and genes had higher abundance after the inhibition phase, which could contribute to nitrite consuming and reactor performance recovery. Importantly, the Terrimonas and Anaerolinea organisms had ability of extracellular polymers secretion or aggregate formation. They had the highest abundance at the end of the lag phase, which could benefit for promoting the nitrogen removal rate (NRR). Meanwhile, Terrimonas and Anaerolinea bacteria could cooperate with methanogenic and nitrite-denitrifying methanotrophic organisms based on H₂ and CH₄, respectively. Since these organisms also had higher abundance after the inhibition phase, their cooperation could prevent anammox bacteria from nitrite inhibiting when the influent nitrite concentration was higher. The analysis of community and function shift is expected to emphasize the importance of functional bacteria in anammox process and provides a potential control strategy for nitrogen-containing wastewater treatment process.