Discovery of a new genus of anaerobic ammonium oxidizing bacteria with a mechanism for oxygen tolerance

Potential Growth of Anammox Bacteria under Aerobic Conditions

Anammox bacteria are obligate anaerobic bacteria that exist widely in nature with sufficient amounts of dissolved oxygen. However, whether anammox bacteria can grow under aerobic conditions remains unclear. In this study, we found that the production of nitrate in the anammox system under aerobic conditions was significantly higher than that under anaerobic conditions without total nitrogen loss. Anammox bacteria can grow by oxidizing nitrite and dehydrogenating hydrazine to produce electrons for carbon fixation. The hydrazine dehydrogenase in anammox bacteria was inhibited under aerobic conditions, and the nitrite oxidoreductase transcription expression of anammox bacteria increased by 2.7 times compared to that under anaerobic conditions, which was the main way for anammox bacteria perform carbon fixation. DNA-stable isotope probing with 13C bicarbonate found the existence of anammox bacteria with 13C isotopes in aerobic cultivation, further proving that anammox bacteria can grow under aerobic condition. More than half of the pathways in glycolysis, the Wood-Ljungdahl pathway, and the tricarboxylic acid cycle were upregulated in anammox bacteria in aerobic condition. Large amounts of bacterioferritins are the important antioxidative enzymes in anammox bacteria in the aerobic environment, which contributes to their stronger oxygen adaptation than other anaerobes. This study expands our understanding of the growth mechanism of anammox bacteria as well as the oxygen adaptation strategies of obligate anaerobic bacteria.

Monitoring the Biochemical Activity of Single Anammox Granules with Microbarometers

Granule-based anaerobic ammonium oxidation (Anammox) is a promising biotechnology for wastewater treatments with extraordinary performance in nitrogen removal. However, traditional analytical methods often delivered an average activity of a bulk sample consisting of millions and even billions of Anammox granules with distinct sizes and components. Here, we developed a novel technique to monitor the biochemical activity of individual Anammox granules in real-time by recording the production rate of nitrogen gas with a microbarometer in a sealed chamber containing only one granule. It was found that the specific activity of a single Anammox granule not only varied by tens of folds among different individuals with similar sizes (activity heterogeneity) but also revealed significant breath-like dynamics over time (temporal fluctuation). Statistical analysis on tens of individuals further revealed two subpopulations with distinct color and specific activity, which were subsequently attributed to the different expression levels of heme c content and hydrazine dehydrogenase activity. This study not only provides a general methodology for various kinds of gas-producing microbial processes but also establishes a bottom-up strategy for exploring the structural-activity relationship at a single sludge granule level, with implications for developing a better Anammox process.

Metatranscriptomics provides an in-depth perspective on the resistance and detoxification of anammox bacteria to dissolved oxygen in a pilot CANON process

In the completely autotrophic nitrogen removal over nitrite (CANON) process, the conflicting oxygen requirements of anammox and ammonium-oxidizing bacteria often lead to retardation in anammox activity. However, our study achieved stable nitrogen removal with a maximum capacity of 1096 g-N/m3/d in a 20 m3 CANON reactor under long-term intensive aeration. The anammox bacteria unusually distributed in the outer layer of the biofilm and demonstrated remarkable oxygen tolerance. Their activity only declined by 18.5 % under 2.0 mg/L of dissolved oxygen. When anammox bacteria encountered oxygen exposure, they adopted some strategies. Metatranscriptomics revealed that Candidatus Kuenenia, the dominant anammox species in our system, downregulated its gene expressions involved in carbon metabolism and oxidative phosphorylation. This may reduce electron leakage that combines with O2, thereby minimizing the generation of reactive oxygen species (ROS). By contrast, the secretion of extracellular proteins and conversion of O2·- were upregulated to eliminate ROS promptly. This behavior endowed Ca. Kuenenia with a unique oxygen detoxification pathway: O2·- were initially converted to H2O2 by superoxide dismutase SOD2 and superoxide reductase dfx (major role), followed by reduction to H2O via non-heme chloroperoxidase cpo (a newly recognized mechanism in the oxygen detoxification of anammox) and catalase katE. These results expanded the current knowledge of anammox alleviating oxidative stress.

Sulfur cycle-mediated biological nitrogen removal and greenhouse gas abatement processes: Micro-oxygen regulation tells the story

Sulfur-mediated autotrophic biological nitrogen removal (BNR) processes favor the reduction of greenhouse gas (GHG) emissions compared to heterotrophic BNR processes. Micro-oxygen environments are widely prevalent in practical BNR systems, and the mechanisms of GHG emissions mediated by multi-elements, including nitrogen (N), sulfur (S), and oxygen (O), remain to be systematically summarized. This review reveals the functional microorganisms involved in sulfur-mediated BNR processes under micro-oxygen regulation, elucidating their metabolic mechanisms and interactions. The GHG abatement potential of sulfur-mediated BNR processes under micro-oxygen regulation is highlighted, along with recent advances in multi-scenario applications. The fate of GHG in wastewater treatment systems is explored and insights into future multi-scale GHG regulatory strategies are provided. Overall, the application of sulfur-mediated BNR processes under micro-oxygen regulation exhibits great potential. This review can act as a guide for the effective implementation of strategies to mitigate the environmental impacts of GHG emissions from wastewater treatment processes.

Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures

In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m3/(m2⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.

Enrichment and characterization of thermophilic anaerobic ammonium oxidizing bacteria from hot spring

Anaerobic ammonium oxidization (Anammox) process plays a crucial role in the global nitrogen cycle and sustainable biological nitrogen removal from wastewater. Although Anammox bacteria have been detected across mesophilic and thermophilic conditions, the direct cultivation of Anammox bacteria from thermal environments has remained elusive. This impedes limiting our understanding of their physiology and ecology in high-temperature habitats. Here, we successfully enriched Anammox bacteria from hot spring sediments at 45 °C, achieving an ammonium oxidation rate of 158.0 mg NH4+-N l-1d-1, with the genus 'Candidatus Brocadia' presenting 22.9 % of the total microbial community after about 500 days of operation. Metagenomic analysis recovered two high-quality genomes of novel Anammox bacteria, which we designed as 'Candidatus Brocadia thermophilus' and 'Candidatus Brocadia thermoanammoxidans'. Both of them encoded and actively expressed key metabolic genes involved in Anammox process and several genes associated with thermotolerance, demonstrating their remarkable ability to perform Anammox reaction in thermophilic environments. Notably, phylotypes related to 'Candidatus Brocadia thermoanammoxidans' have frequently been retrieved from geographically distinct natural habitats. These findings expand our understanding of thermophilic Anammox bacteria and underscore their potential in the nitrogen cycle of thermal natural and engineering ecosystems.

Oxygen-induced evolution of anammox granular sludge explains its unique responses during preservation

Anammox granular sludge (AnGS) preservation is indispensable for the application of anammox technology. Oxygen is a common and crucial factor for anammox, yet its long-term effects on AnGS during preservation remain incomplete clarification. This study investigated the effect of oxygen on AnGS in two simulated preservation systems with open and sealed conditions, and the mechanism was discussed. The results showed that the open system was in an oxidized state with an average dissolved oxygen (DO) concentration and oxidation-reduction potential (ORP) of (3.10 ± 1.36) mg·L-1 and (112.58 ± 46.78) mV, while a reduced state for the sealed system with no detected DO and a lower average ORP of (-153.96 ± 64.32) mV. Both systems showed declines in AnGS activity, while with different responses of AnGS demonstrated by the evolution in terms of granular morphology and structure, bacterial communities, bacteria survival, and bacteria antioxidation. In the open system, reactive oxygen species were generated and destroyed the unsaturated fatty acids in the cell membrane, further leading to the destructed cell structure and declined activity. However, in the sealed system, AnAOB tended to enter a dormant state after long-term preservation, contributing to better conditions in granular morphology and structure, higher AnAOB abundance, and higher live cell ratio. The findings of this study are expected to offer vital information and guidelines for the preservation technologies of AnGS.

Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation

Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.

Effect of initial ammonium concentration on a one-stage partial nitrification/anammox biofilm system: Nitrogen removal performance and the microbial community

One-stage partial nitrification coupled with anammox (PN/A) technology effectively reduces the energy consumption of a biological nitrogen removal system. Inhibiting nitrite-oxidizing bacteria (NOB) is essential for this technology to maintain efficient nitrogen removal performance. Initial ammonium concentration (IAC) affects the degree of inhibited NOB. In this study, the effect of the IAC on a PN/A biofilm was investigated in a moving bed biofilm reactor. The results showed that nitrogen removal efficiency decreased from 82.49% ± 1.90% to 64.57% ± 3.96% after the IAC was reduced from 60 to 20 mg N/L, while the nitrate production ratio increased from 13.87% ± 0.90% to 26.50% ± 3.76%. NOB activity increased to 1,133.86 mg N/m2/day after the IAC decreased, approximately 4-fold, indicating that the IAC plays an important inhibitory role in NOB. The rate-limiting step in the mature biofilm of the PN/A system is the nitritation process and is not shifted by the IAC. The analysis of the microbial community structure in the biofilm indicates that the IAC was the dominant factor in changes in community structure. Ca. Brocadia and Ca. Jettenia were the main anammox bacteria, and Nitrosomonas and Nitrospira were the main AOB and NOB, respectively. IAC did not affect the difference in growth between Ca. Brocadia and Ca. Jettenia. Thus, modulating the IAC promoted the PN/A process with efficient nitrogen removal performance at medium to low ammonium concentrations.

External redox couple enhanced anammox sludge activity at low temperature: Insight into intracellular resource synthesis

Anaerobic ammonium oxidation (anammox), an energy-efficient deamination biotechnology, faces operational challenges in low-temperature environments. Enhancing the metabolic activity of anammox bacteria (AnAOB) is pivotal for advancing its application in mainstream municipal wastewater treatment. Inspired by the metabolic adaptability of AnAOB and based on our previous findings, this work investigated the enhancement of intracellular ATP and NADH synthesis through the exogenous supply of reduced humic acid (HAred) and H2O2 redox couple, aiming to augment AnAOB activity under low-temperature conditions. Our experimental setup involved continuous dosing of 0.0067 μmol g-1 volatile suspended solid of H2O2 and 10 mg g-1 volatile suspended solid of HAred into a mainstream anammox reactor operated at 15 °C with an influent TN content of 60 mg/L. The results showed that HAred / H2O2 couple succeeded in maintaining the effluent TN at 10.72 ± 0.91 mg l-1. The specific anammox activity, ATP and NADH synthesis levels of sludge increased by 1.34, 2.33 and 6.50 folds, respectively, over the control setup devoid of the redox couple. High-throughput sequencing analysis revealed that the relative abundance of Candidatus Kuenenia after adding HAred / H2O2 couple reached 3.65 % at the end of operation, which was 5.14 folds higher than that of the control group. Further metabolomics analysis underscored an activation in the metabolism of amino acids, nucleotides, and phospholipids, which collectively enhanced the availability of ATP and NADH for the respiratory processes. These findings may provide guidance on strategy development for improving the electron transfer efficiency of AnAOB and underscore the potential of using redox couples to promote the mainstream application of anammox technology.

Metagenomic evidence of a novel anammox community in a cold aquifer with high nitrogen pollution

The process of anaerobic ammonium oxidation by nitrite (anammox) is a globally essential part of N cycle. To date, 8 Candidatus genera and more than 22 species of anammox bacteria have been discovered in various anthropogenic and natural habitats, including nitrogen-polluted aquifers. In this work, anammox bacteria were detected for the first time in the groundwater ecosystem with high anthropogenic nitrogen pollution (up to 1760 mg NO3--N/L and 280 mg NH4+-N/L) and low year-round temperature (7-8 °C) in the zone of a uranium sludge repository. Further metagenomic analysis resulted in retrieval of metagenome-assembled genomes of 4 distinct anammox bacteria: a new genus named Ca. Frigussubterria, new species in Ca. Kuenenia, and two strains of a new species in Ca. Scalindua. Analysis of the genomes revealed essential genes involved in anammox metabolism. Both strains of Ca. Scalindua chemeplantae had a high copy number of genes encoding the cold shock proteins CspA/B, which can also function as an antifreeze protein (CspB). Ca. Kuenenia glazoviensis and Ca. Frigussubterria udmurtiae were abundant in less N-polluted site, while Ca. Scalindua chemeplantae inhabited both sites. Genes for urea utilization, reduction of insoluble Fe2O3 or MnO2, assimilatory sulfate reduction, reactive oxygen detoxification, nitrate reduction to ammonium, and putatively arsenate respiration were found. These findings enrich knowledge of the functional and phylogenetic diversity of anammox bacteria and improve understanding of the nitrogen cycle in polluted aquifers.

Distinct microbial nitrogen cycling processes in the deepest part of the ocean

The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, via their CO2 fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome c oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing Ketobacter species can fix inert N2 released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.

IMPORTANCE

The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.

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.

Potential electron acceptors for ammonium oxidation in wastewater treatment system under anoxic condition: A review

Anaerobic ammonium oxidation has been considered as an environmental-friendly and energy-efficient biological nitrogen removal (BNR) technology. Recently, new reaction pathway for ammonium oxidation under anaerobic condition had been discovered. In addition to nitrite, iron trivalent, sulfate, manganese and electrons from electrode might be potential electron acceptors for ammonium oxidation, which can be coupled to traditional BNR process for wastewater treatment. In this paper, the pathway and mechanism for ammonium oxidation with various electron acceptors under anaerobic condition is studied comprehensively, and the research progress of potentially functional microbes is summarized. The potential application of various electron acceptors for ammonium oxidation in wastewater is addressed, and the N2O emission during nitrogen removal is also discussed, which was important greenhouse gas for global climate change. The problems remained unclear for ammonium oxidation by multi-electron acceptors and potential interactions are also discussed in this review.

Chemomixoautotrophy and stress adaptation of anammox bacteria: A review

Anaerobic ammonium oxidizing (anammox) bacteria, which were first discovered nearly three decades ago, are crucial for treating ammonium-containing wastewater. Studies have reported on the biochemical nitrogen conversion process and the physiological, phylogenic, and ecological features of anammox bacteria. For a long time, anammox bacteria were assumed to have a lithoautotrophic lifestyle. However, recent studies have suggested the functional versatility of anammox bacteria. Genome-based analysis and experiments with enrichment cultures have demonstrated the association of the metabolic activities of anammox bacteria with different stress conditions, revealing the importance of utilizing specific organic substances, including organoautotrophy, for growth and adaptation to stress conditions. Our understanding regarding the utilization and metabolism of organic substances and their associations with anammox reactions in anammox bacteria is growing but still incomplete. In this review, we summarize the effect of the utilization of organic substances by anammox bacteria under environmental stress conditions, emphasizing their potential organoautotrophic activity and metabolic flexibility. Although most anammox bacteria may utilize specific organic substances, Ca. Brocadia exhibited the highest level of mixoautotrophic activity. The environmental factors that substantially affect the organoautotrophic activities of anammox bacteria were also examined. This review provides a new perspective on the organoautotrophic capacity of anammox bacteria.

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

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

Novel and innovative approaches to partial denitrification coupled with anammox: A critical review

The partial denitrification (PD) coupled with anaerobic ammonium oxidation (Anammox) (PD/A) process is a unique biological denitrification method for sewage that concurrently removes nitrate (NO3--N) and ammonium (NH4+-N) in sewage. Comparing PD/A to conventional nitrification and denitrification technologies, noticeable improvements are shown in energy consumption, carbon source demand, sludge generation and emissions of greenhouse gasses. The PD is vital to obtaining nitrites (NO2--N) in the Anammox process. This paper provided valuable insight by introduced the basic principles and characteristics of the process and then summarized the strengthening strategies. The functional microorganisms and microbial competition have been discussed in details, the S-dependent denitrification-anammox has been analyzed in this review paper. Important factors affecting the PD/A process were examined from different aspects, and finally, the paper pointed out the shortcomings of the coupling process in experimental research and engineering applications. Thus, this research provided insightful information for the PD/A process's optimization technique in later treating many types of real and nitrate-based wastewater. The review paper also provided the prospective economic and environmental position for the actual design implementation of the PD/A process in the years to come.

Diversity and ecology of NrfA-dependent ammonifying microorganisms

Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.

An indispensable role of overlying water in nitrogen removal in shallow lakes

The nitrogen (N) removal characteristics in water columns and sediments of shallow lakes, influenced by various factors, may exhibit spatial variations in lakes with algal-macrophyte dominance. The N removal rates in water columns and sediments of Lake Taihu were investigated. Our findings indicated that the total N removal rates in Lake Taihu followed the order of algae-dominance > macrophyte-dominance > pelagic lake (without the presence of algae and macrophytes). Correlation analysis revealed that the key environmental factors affecting denitrification and anammox in sediments of algae/macrophyte-type lakes were nitrate nitrogen (NO3--N), nitrite nitrogen (NO2--N), ammonia nitrogen (NH4+-N), and chlorophyll a (Chl-a). The linear regression demonstrated that a significant correlation between the denitrification and the anammox in sediments, with a correlation coefficient of 0.81 (p < 0.01). The contributions to N removal from the water columns and sediments in Lake Taihu were 53 % and 47 %, respectively. Denitrification predominantly drove N removal from sediments, whereas anammox dominated the N removal in water columns. Thus, N removal from the water columns is nonnegligible in shallow eutrophic lakes. This study enhances our understanding of N biogeochemical cycling dynamics in sediment-water and algae/macrophyte ecosystems across various shallow eutrophic lake regions.

Deciphering behaviors of 6:2 chlorinated polyfluorinated ether sulfonate (alternative-PFOS) on anammox processes: Nitrogen removal efficiency and microbial adaptability

This study investigates the behaviors and effects of F-53B, an alternative to perfluorooctane sulfonate on anaerobic ammonium oxidation (anammox) processes. Results showed that the nitrogen removal efficiency (NRE) reached 83.8 % at a F-53B concentration of 0.5 mg·L-1, while NRE decreased to 66.9 % with 5 mg·L-1 of F-53B. The defluorination rates of 17.8 % (0.5 mg·L-1) and 9.3 % (5 mg·L-1) were observed, respectively, suggesting the occurrence of F-53B degradation. The relative abundance of Ca. Kuenenia decreased from 26.1 % to 16.2 % with the F-53B concentration increasing from 0.5 mg·L-1 to 5 mg·L-1. Meanwhile, Denitratisoma was selectively enriched with a relative abundance of 40.7 % at an F-53B concentration of 0.5 mg·L-1. Ca. Kuenenia could reduce reactive oxygen species induced by F-53B to maintain the balance of oxidative stress. This study gains insight into the behaviors and metabolic mechanisms of F-53B in anammox consortia, suggesting the feasibility of anammox processes for industrial wastewater.

Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure

Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.

Anammox Coupled with Photocatalyst for Enhanced Nitrogen Removal and the Activated Aerobic Respiration of Anammox Bacteria Based on cbb3-Type Cytochrome c Oxidase

This study introduced photogenerated electrons into the anammox system by coupling them to a g-C3N4 nanoparticle photocatalyst. A high nitrogen removal efficiency (94.25%) was achieved, exceeding the biochemical limit of 89% imposed by anammox stoichiometry. Photogenerated electrons boosted anammox metabolic activity by empowering key enzymes (NIR, HZS, and WLP-related proteins) and triggered rapid algal enrichment by enhancing the algal Calvin cycle, thus developing multiple anammox-algae synergistic nitrogen removal processes. Remarkably, the homologous expression of cbb3-type cytochrome c oxidase (CcO) in anammox bacteria was discovered and reported in this study for the first time. This conferred aerobic respiration capability to anammox bacteria and rendered them the principal oxygen consumer under 7.9-19.8 mg/L dissolved oxygen, originating from algal photosynthesis. Additionally, photogenerated electrons selectively targeted the cb1 complex and cbb3-type CcO as activation sites while mobilizing the RegA/B regulatory system to activate the expression of cbb3-type CcO. Furthermore, cbb3-type CcO blocked oxidative stress in anammox by depleting intracellular oxygen, a substrate for reactive oxygen species synthesis. This optimized the environmental sensitivity of anammox bacteria and maintained their high metabolic activity. This study expands our understanding of the physiological aptitudes of anammox bacteria and provides valuable insights into applying solar energy for enhanced wastewater treatment.

A critical review of improving mainstream anammox systems: Based on macroscopic process regulation and microscopic enhancement mechanisms

Full-scale anaerobic ammonium oxidation (anammox) engineering applications are vastly limited by the sensitivity of anammox bacteria to the complex mainstream ambience factors. Therefore, it is of great necessity to comprehensively summarize and overcome performance-related challenges in mainstream anammox process at the macro/micro level, including the macroscopic process variable regulation and microscopic biological metabolic enhancement. This article systematically reviewed the recent important advances in the enrichment and retention of anammox bacteria and main factors affecting metabolic regulation under mainstream conditions, and proposed key strategies for the related performance optimization. The characteristics and behavior mechanism of anammox consortia in response to mainstream environment were then discussed in details, and we revealed that the synergistic nitrogen metabolism of multi-functional bacterial genera based on anammox microbiome was conducive to mainstream anammox nitrogen removal processes. Finally, the critical outcomes of anammox extracellular electron transfer (EET) at the micro level were well presented, carbon-based conductive materials or exogenous electron shuttles can stimulate and mediate anammox EET in mainstream environments to optimize system performance from a micro perspective. Overall, this review advances the extensive implementation of mainstream anammox practice in future as well as shedding new light on the related EET and microbial mechanisms.

Effects of ammonia nitrogen and organic carbon availability on microbial community structure and ecological interactions in a full-scale partial nitritation and anammox (PN/A) system

Nutrient availability significantly impacts microbial biosynthesis, cell growth, and cell cycle progression. In this study, a full-scale plug-flow partial nitritation/anammox (PN/A) system was used to investigate variations in the microbial community structure in both immobilized carriers and flocs, as well as a gradual decrease in nutrient availability from upstream to downstream. We found that reduced ammonia nitrogen (from 150.4 to 30.6 mg/L) and organic carbon (from 415.7 to 342.8 mg/L) availability significantly lowered microbial diversity and altered microbial communities in biofilms other than flocs from upstream to downstream. The abundance of all anammox bacteria increased by 1.97 times, from 3.25 × 1010 to 6.40 × 1010 copies per gram of wet sludge, in the biofilm core microbiome. Furthermore, from upstream to downstream, taxa with lower ribosomal RNA operon copy numbers were consistently enriched in both biofilm and floc communities, indicating that slow-growing microorganisms are more likely to be enriched in low-nutrient environments. Rare taxa with a relative abundance of less than 0.1% exhibited unique metabolic functions, including amino acid, carbohydrate, cofactor, and vitamin metabolisms, which was inferred by PICRUST2 and persisted across the nutrient gradient in both the biofilm and floc communities. Despite their low abundance, they may play important roles in mediating the stability and function of the PN/A system. Overall, the results demonstrate the impact of a naturally formed ammonia nitrogen and organic carbon gradient in a full-scale plug-flow PN/A installation on nutrient availability and its effects on microbial diversity, community composition, and microbial interactions, which expands our fundamental understanding of this energy-efficient and promising biotechnology for treating high-strength ammonium wastewater.

"Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces

Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.

Sustainable nitrogen removal in anammox-mediated systems: Microbial metabolic pathways, operational conditions and mathematical modelling

Anammox-mediated systems have attracted considerable attention as alternative cost-effective technologies for sustainable nitrogen (N) removal from wastewater. This review comprehensively highlights the importance of understanding microbial metabolism in anammox-mediated systems under crucial operation parameters, indicating the potentially wide applications for the sustainable treatment of N-containing wastewater. The partial nitrification-anammox (PN-A), simultaneous PN-A and denitrification (SNAD) processes have demonstrated sustainable N removal from sidestream wastewater. The partial denitrification-anammox (PD-A) and denitrifying anaerobic methane oxidation-anammox (DAMO-A) processes have advanced sustainable N removal efficiency in mainstream wastewater treatment. Moreover, N2O production/emission hotspots are extensively discussed in anammox-based processes and are related to the dominant ammonia-oxidizing bacteria (AOB) and denitrifying heterotrophs. In contrast, N2O is not produced in the metabolism pathways of AnAOB and DAMO-archaea; Moreover, the actual contribution of N2O production by dissimilatory nitrate reduction to ammonium (DNRA) and DAMO-bacteria in their species remains uncertain. Thus, PD-A and DAMO-A processes would achieve reduction in greenhouse gas production, as well as energy consumption for the reliability of N removal efficiencies. In addition to reaction mechanisms, this review covers the mathematical models for simultaneous anammox, partial nitrification and/or denitrification (i.e., PN-A, PD-A, and SNAD). Promising NO3- reduction technologies by endogenous PD, sulfur-driven autotrophic denitrification, and DNRA by anammox are also discussed. In summary, this review provides a better understanding of sustainable N removal in anammox-mediated systems, thereby encouraging future investigation and exploration of the sustainable N bio-treatment from wastewater.

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

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

Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel

The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.