The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium

Transcriptional and molecular simulation analysis of the response mechanism of anammox bacteria to 3,4-dimethylpyrazole phosphate stress

Anaerobic ammonium oxidation (anammox) and nitrification are two vital biological pathways for ammonium oxidation, pivotal in microbial nitrogen cycling. 3,4-Dimethylpyrazole phosphate (DMPP) is commonly used as inhibitors in agricultural soils to reduce nitrogen losses from farmland, while whether it affect anammox is an open question. Acute inhibition tests revealed that 53.5 mg·L-1 DMPP caused 50 % reduction in anammox bacteria. After 36 days of prolonged exposure to 5 mg·L-1 DMPP, the ammonium(nitrite) removal rate of endnote decreased from 78.39(94.78) to 13.57(15.28) mgN·gVSS-1·d-1. Additionally, the abundance of Ca. Kuenenia decreased from 36.5 % to 6.06 %. Transcriptomic analysis revealed that the mRNA levels of ammonium transport genes (amt_1 and amt_4), and hydrazine synthase (hzs) were significantly downregulated. Molecular docking simulations indicated that DMPP bound with ammonium transport and hydrazine synthesis. This interaction hindered the transcriptional levels of genes encoding ammonium transporters and hzs. The study has guiding value to reduce the nitrogen loss involved in anammox bacteria in agricultural soils under the application of DMPP.

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.

Multidimensional Insights into Organics Stress on Anammox systems: From a "Molecule-Cell-Ecology" Perspective

Anaerobic ammonium oxidation (anammox) is efficient and cost-effective for treating high-strength ammonia wastewater, but the organics in wastewater will affect its stability. To address this challenge, it is crucial to gain a deep understanding of the inhibitory effects and mechanisms of organics stress on anammox bacteria. The review provided a comprehensive classification of organics and evaluated their specific effects on the anammox system according to their respective characteristics. Based on the micro to macro perspective, the "molecule-cell-ecology" inhibitory mechanism of organics on anammox bacteria was proposed. The molecular observation systematically summarized the binding process and action sites of organics with anammox bacteria. At the cellular observation, the mechanisms of organics effects on extracellular polymeric substances, membranes, and anammoxosome of anammox bacteria were also expounded. At the ecological observation, the dynamic changes in coexisting populations and their role in organics transformation were further discussed. Further revelations on response mechanisms and inhibition mitigation strategies were proposed to broaden the applicability of anammox systems for organic wastewater. This review offered a multidimensional understanding of the organics inhibitory mechanism of anammox bacteria and provided a theoretical foundation for anammox systems.

Evidence of nitrogen inputs affecting soil nitrogen purification by mediating root exudates of salt marsh plants

Salt marsh has an important 'purification' role in coastal ecosystems by removing excess nitrogen that could otherwise harm aquatic life and reduce water quality. Recent studies suggest that salt marsh root exudates might be the 'control centre' for nitrogen transformation, but empirical evidence is lacking. Here we sought to estimate the direction and magnitude of nitrogen purification by salt marsh root exudates and gain a mechanistic understanding of the biogeochemical transformation pathway(s). To achieve this, we used a laboratory incubation to quantify both the root exudates and soil nitrogen purification rates, in addition to the enzyme activities and functional genes under Phragmites australis populations with different nitrogen forms addition (NO3-, NH4+ and urea). We found that NO3- and urea addition significantly stimulate P. australis root exudation of total acids, amino acids, total sugars and total organic carbon, while NH4+ addition only significantly increased total acids, amino acids and total phenol exudation. High total sugars, amino acids and total organic carbon concentrations enlarged nitrogen purification potential by stimulating the nitrogen purifying bacterial activities (including enzyme activities and related genes expression). Potential denitrification rates were not significantly elevated under NH4+ addition in comparison to NO3- and urea addition, which should be ascribed to total phenol self-toxicity and selective inhibition. Further, urea addition stimulated urease and protease activities with providing more NH4+ and NO2- substrates for elevated anaerobic ammonium oxidation rates among the nitrogen addition treatments. Overall, this study revealed that exogenous nitrogen could increase the nitrogen purification-associated bacterial activity through accelerating the root exudate release, which could stimulate the activity of nitrogen transformation, and then improve the nitrogen removal capacity in salt marsh.

Nitrogen removal strategy for real swine wastewater by combining partial nitrification-denitrification process with anammox

Anammox process offers reduced operational cost and energy requirement compared to nitrification-denitrification methods due to lower biomass generation and no need for external carbon sources and aeration. High ammonia concetration and low biodegradable anaerobic digester of swaine wastewater provided an advantage for the growth of anammox microorangism. An anoxic/oxic (A/O) SBR and an anammox SBR were implemented parallelly to treat the same swine wastewater with partial nitrification/denitrification and partial nitrification/anammox process, respectively, and to compare their nitrogen removal efficiency. The nitrogen removal rates (NRRs) of the A/O SBR and anammox SBR were 0.054 and 0.26 kg-N/m3/day, respectively. The lower NRR of the A/O SBR could be attributed to insufficient biodegradable organic carbon sources in the denitrification process. The kinetic parameters obtained from the two SBRs were applied to estimate the time required for using the A/O process and partial nitrification/anammox process to treat the same amount of ammonia with the same reaction volume. Results showed that the A/O process required 3.3 times the reaction time of the partial nitrification/anammox process, suggesting that the partial nitrification/anammox process is a more efficient and economic nitrogen removal process for swine wastewater treatment. The next generation sequencing results revealed that Candidatus Brocadia, ranging from 10 to 23%, was the predominant anammox bacteria in the anammox SBR. More than 78.2 % of nitrite in the anammox SBR was removed through the anammox reaction.

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.

Coupling Nitrate-Dependent Anaerobic Ethane Degradation with Anaerobic Ammonium Oxidation

The microbial oxidation of short-chain gaseous alkanes (SCGAs, consisting of ethane, propane, and butane) serves as an efficient sink to mitigate these gases' emission to the atmosphere, thus reducing their negative impacts on air quality and climate. "Candidatus Alkanivorans nitratireducens" are recently found to mediate nitrate-dependent anaerobic ethane oxidation (n-DAEO). In natural ecosystems, anaerobic ammonium-oxidizing (anammox) bacteria may consume nitrite generated from nitrate reduction by "Ca. A. nitratireducens", thereby alleviating the inhibition caused by nitrite accumulation on the metabolism of "Ca. A. nitratireducens". Here, we demonstrate the coupling of n-DAEO with anammox in a laboratory-scale model system to prevent nitrite accumulation. Our results suggest that a high concentration of ethane (6.9-7.9%) has acute inhibition on anammox activities, thus making the coupling process a significant challenge. By maintaining ethane concentrations within the range of 1.7-5.5%, stable ethane and ammonium oxidation, nitrate reduction, and dinitrogen gas generation without nitrite accumulation were finally achieved. After the accomplished coupling of n-DAEO with anammox, nitrate reduction rates increased by 8.1 times compared to the rate observed with n-DAEO alone. Microbial community profiling via 16S rRNA gene amplicon sequencing showed "Ca. A. nitratireducens" (6.6-12.9%) and anammox bacteria "Candidatus Kuenenia" (3.4-5.6%) were both dominant in the system, indicating they potentially form a syntrophic partnership to jointly contribute to nitrogen removal. Our findings offer insights into the cross-feeding interaction between "Ca. A. nitratireducens" and anammox bacteria in anoxic environments.

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.

Salinity Tolerance and Osmoadaptation Strategies in Four Genera of Anammox Bacteria: Brocadia, Jettenia, Kuenenia, and Scalindua

The salinity tolerance and osmoadaptation strategies in four phylogenetically distant anammox species, Brocadia, Jettenia, Kuenenia, and Scalindua, were investigated by using highly enriched cell cultures. The first-emerged "Ca. Scalindua sp." showed optimum growth at 1.5-3% salinity and was tolerant to ∼10% salinity (a slight halophile). The second-emerged "Ca. Kuenenia stuttgartiensis" was tolerant to ∼6% salinity with optimum growth at 0.25-1.5% (a halotolerant). These early-emerged "Ca. Scalindua sp." and ″Ca. K. stuttgartiensis" rapidly accumulated K+ ions and simultaneously synthesized glutamate as a counterion. Subsequently, part of the glutamate was replaced by trehalose. In contrast, the late-emerged "Ca. B. sinica" and "Ca. J. caeni" were unable to accumulate sufficient amounts of K+─glutamate and trehalose, resulting in a significant decrease in activity even at 1-2% salinity (nonhalophiles). In addition, the external addition of glutamate may increase anammox activity at high salinity. The species-dependent salinity tolerance and osmoadaptation strategies were consistent with the genetic potential required for the biosynthesis and transport of these osmolytes and the evolutionary history of anammox bacteria: Scalindua first emerged in marine environments and then Kuenenia and other two species gradually expanded their habitat to estuaries, freshwater, and terrestrial environments, while Brocadia and Jettenia likely lost their ability to accumulate K+─glutamate.

Nitrite-oxidizing bacteria adapted to low-oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones

Nitrite is a central molecule in the nitrogen cycle because nitrite oxidation to nitrate (an aerobic process) retains fixed nitrogen in a system and its reduction to dinitrogen gas (anaerobic) reduces the fixed nitrogen inventory. Despite its acknowledged requirement for oxygen, nitrite oxidation is observed in oxygen-depleted layers of the ocean's oxygen minimum zones (OMZs), challenging the current understanding of OMZ nitrogen cycling. Previous attempts to determine whether nitrite-oxidizing bacteria in the anoxic layer differ from known nitrite oxidizers in the open ocean were limited by cultivation difficulties and sequencing depth. Here, we construct 31 draft genomes of nitrite-oxidizing bacteria from global OMZs. The distribution of nitrite oxidation rates, abundance and expression of nitrite oxidoreductase genes, and relative abundance of nitrite-oxidizing bacterial draft genomes from the same samples all show peaks in the core of the oxygen-depleted zone (ODZ) and are all highly correlated in depth profiles within the major ocean oxygen minimum zones. The ODZ nitrite oxidizers are not found in the Tara Oceans global dataset (the most complete oxic ocean dataset), and the major nitrite oxidizers found in the oxygenated ocean do not occur in ODZ waters. A pangenomic analysis shows the ODZ nitrite oxidizers have distinct gene clusters compared to oxic nitrite oxidizers and are microaerophilic. These findings all indicate the existence of nitrite oxidizers whose niche is oxygen-deficient seawater. Thus, specialist nitrite-oxidizing bacteria are responsible for fixed nitrogen retention in marine oxygen minimum zones, with implications for control of the ocean's fixed nitrogen inventory.

Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture

Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2-. Remineralization of organic nitrogen compounds including urea and cyanate (OCN-) into NH4+ has been believed as an NH4+ source of the anammox process in oxygen minimum zones. However, urea- or OCN-- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN- degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN- degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN- was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32-42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).

Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles

The two evolutionarily unrelated nitric oxide-producing nitrite reductases, NirK and NirS, are best known for their redundant role in denitrification. They are also often found in organisms that do not perform denitrification. To assess the functional roles of the two enzymes and to address the sequence and structural variation within each, we reconstructed robust phylogenies of both proteins with sequences recovered from 6973 isolate and metagenome-assembled genomes and identified 32 well-supported clades of structurally distinct protein lineages. We then inferred the potential niche of each clade by considering other functional genes of the organisms carrying them as well as the relative abundances of each nir gene in 4082 environmental metagenomes across diverse aquatic, terrestrial, host-associated, and engineered biomes. We demonstrate that Nir phylogenies recapitulate ecology distinctly from the corresponding organismal phylogeny. While some clades of the nitrite reductase were equally prevalent across biomes, others had more restricted ranges. Nitrifiers make up a sizeable proportion of the nitrite-reducing community, especially for NirK in marine waters and dry soils. Furthermore, the two reductases showed distinct associations with genes involved in oxidizing and reducing other compounds, indicating that the NirS and NirK activities may be linked to different elemental cycles. Accordingly, the relative abundance and diversity of NirS versus NirK vary between biomes. Our results show the divergent ecological roles NirK and NirS-encoding organisms may play in the environment and provide a phylogenetic framework to distinguish the traits associated with organisms encoding the different lineages of nitrite reductases.

Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones

Anammox bacteria inhabiting oxygen-deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss in the global ocean. However, many basic questions regarding the diversity, broad metabolisms, origin, and adaptive mechanisms of ODZ anammox bacteria remain unaddressed. Here we report two novel metagenome-assembled genomes of anammox bacteria affiliated with the Scalindua genus, which represent most, if not all, of the anammox bacteria in the global ODZs. Metagenomic read-recruiting and comparison with historical data show that they are ubiquitously present in all three major ODZs. Beyond the core anammox metabolism, both organisms contain cyanase, and the more dominant one encodes a urease, indicating most ODZ anammox bacteria can utilize cyanate and urea in addition to ammonium. Molecular clock analysis suggests that the evolutionary radiation of these bacteria into ODZs occurred no earlier than 310 million years ago, ~1 billion years after the emergence of the earliest modern-type ODZs. Different strains of the ODZ Scalindua species are also found in benthic sediments, and the first ODZ Scalindua is likely derived from the benthos. Compared to benthic strains of the same clade, ODZ Scalindua uniquely encodes genes for urea utilization but has lost genes related to growth arrest, flagellum synthesis, and chemotaxis, presumably for adaptation to thrive in the global ODZ waters. Our findings expand the known metabolisms and evolutionary history of the bacteria controlling the global nitrogen budget.

Carbon-Restricted Anoxic Zone as an Overlooked Anammox Hotspot in Municipal Wastewater Treatment Plants

The anoxic zone serves as the core functional unit in municipal wastewater treatment plants (MWWTPs). Unfortunately, in most cases, the downstream range of the anoxic zone is severely lacking in available organic carbon and thus contributes little to the removal of nutrients. This undesirable range is termed the "carbon-restricted anoxic zone", representing an insurmountable drawback for traditional MWWTPs. This study uncovers a previously overlooked role for the carbon-restricted anoxic zone: a hotspot for anaerobic ammonium oxidation (anammox). In a continuous-flow pilot-scale plant treating municipal wastewater (55 m3/d), virgin biocarriers were introduced into the carbon-restricted anoxic zone (downstream 25% of the anoxic zone with BOD5 of 5.9 ± 2.3 mg/L). During the 517-day monitoring, anammox bacteria highly self-enriched within the biofilms, with absolute and relative abundance reaching up to (9.4 ± 0.1) × 109 copies/g-VSS and 6.17% (Candidatus Brocadia), respectively. 15N isotopic tracing confirmed that anammox overwhelmingly dominated nitrogen metabolism, responsible for 92.5% of nitrogen removal. Following this upgrade, the contribution ratio of the carbon-restricted anoxic zone to total nitrogen removal increased from 9.2 ± 4.1% to 19.2 ± 4.2% (P < 0.001), while its N2O emission flux decreased by 84.5% (P < 0.001). These findings challenge stereotypes about the carbon-restricted anoxic zone and highlight the multiple environmental implications of this newfound anammox hotspot.

A review of microbial nitrogen transformations and microbiome engineering for biological nitrogen removal under salinity stress

The osmotic stress caused by salinity exerts severe inhibition on the process of biological nitrogen removal (BNR), leading to the deterioration of biosystems and the discharge of nitrogen with saline wastewater. Feasible strategies to solve the bottleneck in saline wastewater treatment have attracted great attention, but relevant studies to improve nitrogen transformations and enhance the salt-tolerance of biosystems in terms of microbiome engineering have not been systematically reviewed and discussed. This work attempted to provide a more comprehensive explanation of both BNR and microbiome engineering approaches for saline wastewater treatment. The effect of salinity on conventional BNR pathways, nitrification-denitrification and anammox, was summarized at cellular and metabolic levels, including the nitrogen metabolic pathways, the functional microorganisms, and the inhibition threshold of salinity. Promising nitrogen transformations, such as heterotrophic nitrification-aerobic denitrification, ammonium assimilation and the coupling of conventional pathways, were introduced and compared based on advantages and challenges in detail. Strategies to improve the salt tolerance of biosystems were proposed and evaluated from the perspective of microbiome engineering. Finally, prospects of future investigation and applications on halophilic microbiomes in saline wastewater treatment were discussed.

Nitrite accumulation and anammox bacterial niche partitioning in Arctic Mid-Ocean Ridge sediments

By consuming ammonium and nitrite, anammox bacteria form an important functional guild in nitrogen cycling in many environments, including marine sediments. However, their distribution and impact on the important substrate nitrite has not been well characterized. Here we combined biogeochemical, microbiological, and genomic approaches to study anammox bacteria and other nitrogen cycling groups in two sediment cores retrieved from the Arctic Mid-Ocean Ridge (AMOR). We observed nitrite accumulation in these cores, a phenomenon also recorded at 28 other marine sediment sites and in analogous aquatic environments. The nitrite maximum coincides with reduced abundance of anammox bacteria. Anammox bacterial abundances were at least one order of magnitude higher than those of nitrite reducers and the anammox abundance maxima were detected in the layers above and below the nitrite maximum. Nitrite accumulation in the two AMOR cores co-occurs with a niche partitioning between two anammox bacterial families (Candidatus Bathyanammoxibiaceae and Candidatus Scalinduaceae), likely dependent on ammonium availability. Through reconstructing and comparing the dominant anammox genomes (Ca. Bathyanammoxibius amoris and Ca. Scalindua sediminis), we revealed that Ca. B. amoris has fewer high-affinity ammonium transporters than Ca. S. sediminis and lacks the capacity to access alternative substrates and/or energy sources such as urea and cyanate. These features may restrict Ca. Bathyanammoxibiaceae to conditions of higher ammonium concentrations. These findings improve our understanding about nitrogen cycling in marine sediments by revealing coincident nitrite accumulation and niche partitioning of anammox bacteria.

A critical review on microbial ecology in the novel biological nitrogen removal process: Dynamic balance of complex functional microbes for nitrogen removal

The novel biological nitrogen removal process has been extensively studied for its high nitrogen removal efficiency, energy efficiency, and greenness. A successful novel biological nitrogen removal process has a stable microecological equilibrium and benign interactions between the various functional bacteria. However, changes in the external environment can easily disrupt the dynamic balance of the microecology and affect the activity of functional bacteria in the novel biological nitrogen removal process. Therefore, this review focuses on the microecology in existing the novel biological nitrogen removal process, including the growth characteristics of functional microorganisms and their interactions, together with the effects of different influencing factors on the evolution of microbial communities. This provides ideas for achieving a stable dynamic balance of the microecology in a novel biological nitrogen removal process. Furthermore, to investigate deeply the mechanisms of microbial interactions in novel biological nitrogen removal process, this review also focuses on the influence of quorum sensing (QS) systems on nitrogen removal microbes, regulated by which bacteria secrete acyl homoserine lactones (AHLs) as signaling molecules to regulate microbial ecology in the novel biological nitrogen removal process. However, the mechanisms of action of AHLs on the regulation of functional bacteria have not been fully determined and the composition of QS system circuits requires further investigation. Meanwhile, it is necessary to further apply molecular analysis techniques and the theory of systems ecology in the future to enhance the exploration of microbial species and ecological niches, providing a deeper scientific basis for the development of a novel biological nitrogen removal process.

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.

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

In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems.

The responses of marine anammox bacteria-based microbiome to multi-antibiotic stress in mariculture wastewater treatment

Saline mariculture wastewater containing multi-antibiotics poses a challenge to anaerobic ammonia oxidation (anammox) process. Herein, the halophilic marine anammox bacteria (MAB)-based microbiome was used for treating mariculture wastewater (35‰ salinity) under multi-antibiotics (enrofloxacin + oxytetracycline + sulfamethoxazole, EOS) stress. And the main focus of this study lies in the response of MAB-based microbiome against multi-antibiotics stress. It is found that MAB-based microbiome shows stable community structure and contributes high nitrogen removal efficiency (>90%) even under high stress of EOS (up to 4 mg·L^-1). The relative abundance of main functional genus Candidatus Scalindua, responsible for anammox, had little change while controlling the influent EOS concentration within 4 mg·L^-1, whereas, significantly decreased to 2.23% at EOS concentration of as high as 24 mg·L^-1. As an alternative, antibiotic resistance bacteria (ARB) species Rheinheimera dominated the microbial community of MAB-based biological reactor under extremely high EOS stress (e.g. 24 mg·L^-1 in influent). The response mechanism of MAB-based microbiome consists of extracellular and intracellular defenses with dependence of EOS concentration. For example, while EOS within 4 mg·L^-1 in this study, most of the antibiotics were retained by extracellular polymeric substances (EPS) via adsorption; If increasing the EOS concentration to 8 and even 24 mg·L^-1, part of antibiotics could intrude into the cells and cause the intracellular accumulation of antibiotic resistance genes (ARGs) (total abundance up to 2.44 × 10^-1 copies/16S rRNA) for EOS response. These new understandings will facilitate the practical implementation of MAB-based bioprocess for saline nitrogen- and antibiotics-laden wastewater treatment.

Deciphering the Inhibition of Ethane on Anaerobic Ammonium Oxidation

Anaerobic ammonium oxidation (anammox) and nitrification, two common biological ammonium oxidation pathways, are critical for the microbial nitrogen cycle. Short chain alkanes (C₂-C₈) have been well-known as inhibitors for nitrification through interaction with the ammonia monooxygenase, while whether these alkanes affect anammox is an open question. Here, this work demonstrated significant inhibition of ethane on anammox and revealed the inhibitory mechanism. The acute inhibition of ethane on anammox was concentration-dependent and reversible; 0.86 mM dissolved ethane caused 50% inhibition (IC₅₀), and 1.72 mM ethane almost completely inhibited anammox. After long-term exposure to 0.09 mM ethane for 30 days, the ammonium (nitrite) removal rate dropped from 202 (267) mg N L^-1 d^-1 to 1 (1) mg N L^-1 d^-1, and the abundance of anammox bacteria decreased from 61.9% to 9.5%. The intercellular ammonium concentration of anammox bacteria decreased after ethane exposure, while metatranscriptome analysis showed significant upregulation of genes for ammonium transport of anammox bacteria. Thus, ethane could suppress ammonium uptake resulting in the inhibition of anammox activities. As ethane is the second most prevalent alkane after methane in various anoxic environments, ethane may have an important effect on the nitrogen cycle driven by anammox that should be investigated in future research.

Glutamate Enhances Osmoadaptation of Anammox Bacteria under High Salinity: Genomic Analysis and Experimental Evidence

An osmoprotectant that alleviates the bacterial osmotic stress can improve the bioreactor treatment of saline wastewater. However, proposed candidates are expensive, and osmoprotectants of anammox bacteria and their ecophysiological roles are not fully understood. In this study, a comparative analysis of 34 high-quality public metagenome-assembled genomes from anammox bacteria revealed two distinct groups of osmoadaptation. Candidatus Scalindua and Kuenenia share a close phylogenomic relation and osmoadaptation gene profile and have pathways for glutamate transport and metabolisms for enhanced osmoadaptation. The batch assay results demonstrated that the reduced Ca. Kuenenia activity in saline conditions was substantially alleviated with the addition and subsequent synergistic effects of potassium and glutamate. The operational test of two reactors demonstrated that the reduced anammox performance under brine conditions rapidly recovered by 35.7-43.1% as a result of glutamate treatment. The Ca. Kuenenia 16S rRNA and hydrazine gene expressions were upregulated significantly (p < 0.05), and the abundance increased by approximately 19.9%, with a decrease in dominant heterotrophs. These data demonstrated the effectiveness of glutamate in alleviating the osmotic stress of Ca. Kuenenia. This study provides genomic insight into group-specific osmoadaptation of anammox bacteria and can facilitate the precision management of anammox reactors under high salinity.

Introducing Candidatus Bathyanammoxibiaceae, a family of bacteria with the anammox potential present in both marine and terrestrial environments

Anaerobic ammonium oxidation (Anammox) bacteria are a group of extraordinary bacteria exerting a major impact on the global nitrogen cycle. Their phylogenetic breadth and diversity, however, are not well constrained. Here we describe a new, deep-branching family in the order of Candidatus Brocadiales, Candidatus Bathyanammoxibiaceae, members of which have genes encoding the key enzymes of the anammox metabolism. In marine sediment cores from the Arctic Mid-Ocean Ridge (AMOR), the presence of Ca. Bathyanammoxibiaceae was confined within the nitrate-ammonium transition zones with the counter gradients of nitrate and ammonium, coinciding with the predicted occurrence of the anammox process. Ca. Bathyanammoxibiaceae genomes encode the core genetic machinery for the anammox metabolism, including hydrazine synthase for converting nitric oxide and ammonium to hydrazine, and hydrazine dehydrogenase for hydrazine oxidation to dinitrogen gas, and hydroxylamine oxidoreductase for nitrite reduction to nitric oxide. Their occurrences assessed by genomes and 16S rRNA gene sequencings surveys indicate that they are present in both marine and terrestrial environments. By introducing the anammox potential of Ca. Bathyanammoxibiaceae and charactering their ideal niche in marine sediments, our findings suggest that the diversity and abundance of anammox bacteria may be higher than previously thought, and provide important insights on cultivating them in the future to not only assess their biogeochemical impacts but also constrain the emergence and evolutionary history of this functional guild on Earth.

Metagenomic evidence of a novel family of anammox bacteria in a subsea environment

Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.

Physiology of anammox adaptation to low temperatures and promising biomarkers: A review

The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies, crucially including metaproteomics and metabolomics. Anammox bacteria adapt to low temperatures by synthesizing both chaperones of RNA and proteins and chemical chaperones. Furthermore, they preserve energy for the core metabolism by reducing biosynthesis in general. Thus, in this study, a number of biomarkers are proposed to help practitioners assess the extent of anammox bacteria adaptation and predict the decomposition of biofilms/granules or slower growth. The promising biomarkers also include unique ladderane lipids. Further proteomic and metabolomic studies are necessary for a more detailed understanding of anammox low-temperature adaptation, thus easing the transition to more cost-effective and sustainable wastewater treatment.

Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers

Anaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon-poor environments. However, the diversity and prevalence of anammox bacteria in the terrestrial subsurface-a typically oligotrophic environment-are little understood. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analyzed 16S rRNA genes and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells and metagenomes and metatranscriptomes from an oxic-to-dysoxic subset. Data indicate that anammox and anammox-associated bacteria (class "Candidatus Brocadiae") are prevalent in the aquifers studied, and that anammox community composition is strongly differentiated by dissolved oxygen (DO), but not ammonia/nitrite. While "Candidatus Brocadiae" diversity decreased with increasing DO, "Candidatus Brocadiae" 16S rRNA genes and hydrazine synthase (hzsB) genes and transcripts were detected across a wide range of bulk groundwater DO concentrations (0 to 10 mg/L). Anammox genes and transcripts correlated significantly with those involved in aerobic ammonia oxidation (amoA), potentially representing a major source of nitrite for anammox. Eight "Candidatus Brocadiae" genomes (63 to 95% complete), representing 2 uncharacterized families and 6 novel species, were reconstructed. Six genomes have genes characteristic of anammox, all for chemolithoautotrophy. Anammox and aerotolerance genes of up to four "Candidatus Brocadiae" genomes were transcriptionally active under oxic and dysoxic conditions, although activity was highest in dysoxic groundwater. The coexpression of nrfAH nitrite reductase genes by "Candidatus Brocadiae" suggests active regeneration of ammonia for anammox. Our findings indicate that anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, which is likely supported by nitrite from aerobic ammonia oxidation. IMPORTANCE Anammox is increasingly shown to play a major role in the aquatic nitrogen cycle and can outcompete heterotrophic denitrification in environments low in organic carbon. Given that aquifers are characteristically oligotrophic, anammox may represent a major route for the removal of fixed nitrogen in these environments, including agricultural nitrogen, a common groundwater contaminant. Our research confirms that anammox bacteria and the anammox process are prevalent in aquifers and occur across diverse lithologies (e.g., sandy gravel, sand-silt, and volcanic) and groundwater physicochemistries (e.g., various oxygen, carbon, nitrate, and ammonium concentrations). Results reveal niche differentiation among anammox bacteria largely driven by groundwater oxygen contents and provide evidence that anammox is supported by proximity to oxic niches and handoffs from aerobic ammonia oxidizers. We further show that this process, while anaerobic, is active in groundwater characterized as oxic, likely due to the availability of anoxic niches.

Function of Fe(III)-minerals in the enhancement of anammox performance exploiting integrated network and metagenomics analyses

Iron is a recognized physiological requirement for microorganisms but, for anaerobic ammonium oxidation (anammox) bacteria, its role extends well beyond that of a nutritional necessity. In this study, the function of two typical Fe(III)-minerals (ferrihydrite and magnetite) in anammox processes was evaluated in the absence/presence of Fe(II) by integrated network and metagenomics analyses. Results showed that Fe-(III) minerals addition increased the activity of cellular processes and pathways associated with granule formation, enabling the peak values of particle size to increase by 144% and 115%, respectively. Notably, ferrihydrite (5 mM) enhanced nitrogen removal by 4.8% and 4.1%, respectively, in the short-term and long-term absence of Fe(II). Ferrihydrite also promoted the retention of anammox bacteria affiliated with phylum Planctomycetes in the reactor, contributing to an 11% higher abundance with ferrihydrite amendment when compared with the control (without iron additions) in the short-term absence of Fe(II). Network-based analyses revealed that ferrihydrite facilitated the microbial community to form densely clustered and complex topologies to improve resistance to environmental disturbance (i.e., Fe(II) deficiency), and effectively increased the underlying cooperation and facilitation in the community. Metagenomic analysis revealed that there was limited promotion of anammox central metabolism by the extra addition of Fe(III)-minerals in the presence of Fe(II), highlighting the poor utilization of Fe(III)-minerals by anammox bacteria under Fe(II) sufficiency. This study deepens our understanding of the function of Fe(III)-minerals in anammox systems at the community and functional level, and provides a fundamental basis for developing Fe-based anammox enhancement technologies.

Response and resilience of anammox consortia to nutrient starvation

BACKGROUND

It is of critical importance to understand how anammox consortia respond to disturbance events and fluctuations in the wastewater treatment reactors. Although the responses of anammox consortia to operational parameters (e.g., temperature, dissolved oxygen, nutrient concentrations) have frequently been reported in previous studies, less is known about their responses and resilience when they suffer from nutrient interruption.

RESULTS

Here, we investigated the anammox community states and transcriptional patterns before and after a short-term nutrient starvation (3 days) to determine how anammox consortia respond to and recover from such stress. The results demonstrated that the remarkable changes in transcriptional patterns, rather than the community compositions were associated with the nutritional stress. The divergent expression of genes involved in anammox reactions, especially the hydrazine synthase complex (HZS), and nutrient transportation might function as part of a starvation response mechanism in anammox bacteria. In addition, effective energy conservation and substrate supply strategies (ATP accumulation, upregulated amino acid biosynthesis, and enhanced protein degradation) and synergistic interactions between anammox bacteria and heterotrophs might benefit their survival during starvation and the ensuing recovery of the anammox process. Compared with abundant heterotrophs in the anammox system, the overall transcription pattern of the core autotrophic producers (i.e., anammox bacteria) was highly resilient and quickly returned to its pre-starvation state, further contributing to the prompt recovery when the feeding was resumed.

CONCLUSIONS

These findings provide important insights into nutritional stress-induced changes in transcriptional activities in the anammox consortia and would be beneficial for the understanding of the capacity of anammox consortia in response to stress and process stability in the engineered ecosystems. Video Abstract.

Insight into the structure and metabolic function of iron-rich nanoparticles in anammox bacteria

Anaerobic ammonium-oxidizing (anammox) bacteria are iron abundant and depend heavily on iron-binding proteins. The iron demand of anammox bacteria is relatively large. However, it still remains some doubts where these large quantities of available iron come from and how they are regulated in anammox bacteria. Herein, iron-rich nanoparticles in anammoxosomes were detected by synchrotron soft X-ray tomography coupled with scanning transmission X-ray microscopy (STXM). The iron-rich nanoparticles were identified as ferric oxide (α-Fe₂O₃) mineral cores, and the local atomic structure of iron-rich nanoparticles was obtained by X-ray absorption fine-structure (XAFS) spectra. The bacterioferritin of Q1Q315 and Q1Q5F8 were detected by proteomics analysis. On this basis, the metabolic pathway centered on iron-rich nanoparticles was proposed.

Nitrogen Removal from Mature Landfill Leachate via Anammox Based Processes: A Review

Mature landfill leachate is a complex and highly polluted effluent with a large amount of ammonia nitrogen, toxic components and low biodegradability. Its COD/N and BOD5/COD ratios are low, which is not suitable for traditional nitrification and denitrification processes. Anaerobic ammonia oxidation (anammox) is an innovative biological denitrification process, relying on anammox bacteria to form stable biofilms or granules. It has been extensively used in nitrogen removal of mature landfill leachate due to its high efficiency, low cost and sludge yield. This paper reviewed recent advances of anammox based processes for mature landfill leachate treatment. The state of the art anammox process for mature landfill leachate is systematically described, mainly including partial nitrification–anammox, partial nitrification–anammox coupled denitrification. At the same time, the microbiological analysis of the process operation was given. Anaerobic ammonium oxidation (anammox) has the merit of saving the carbon source and aeration energy, while its practical application is mainly limited by an unstable influent condition, operational control and seasonal temperature variation. To improve process efficiency, it is suggested to develop some novel denitrification processes coupled with anammox to reduce the inhibition of anammox bacteria by mature landfill leachate, and to find cheap new carbon sources (methane, waste fruits) to improve the biological denitrification efficiency of the anammox system.

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 ana-lysis 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.

Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua

The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.

Metagenomic prediction analysis of microbial aggregation in anammox-dominated community

Aggregation of anammox bacteria is essential to maintain high biomass concentrations and prevent the loss of biomass in anammox processes. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used in this study to predict the metagenomic potentials and characterize the microbial community structure and functional features in anammox aggregates (e.g., sludge flocs, biofilms, and granules). The results showed that Candidatus Brocadia was the most dominant anammox genera in all aggregates (38.0% in flocs, 69.4% in biofilm, and 52.0% in granules) and the functional gene involved in the anammox process was detected in the highest amount in biofilms, followed by granules and flocs. Furthermore, the anammox microbial aggregation pathway was explored that anammox bacteria have strong motility and high capability for early attachment. Anammox bacteria could produce large amounts of EPS (extracellular polymeric substances) regulated by quinolone and transport to extracellular environment through type II secretion system. The strong ability of c-di-GMP (bis-(3'-5')-cyclic dimeric guanosine monophosphate) synthesis enabled a stable architectural structure of aggregation. This study elucidated the aggregation mechanism of anammox microorganisms at the genetic level to enhance the stability of anammox processes. PRACTITIONER POINTS: Candidatus Brocadia was the most dominant anammox genera in aggregates. Anammox bacteria have strong motility and high attachment capability. Anammox bacteria possess strong EPS synthesis regulated by quinolone. c-di-GMP synthesis enables a stable structure of aggregation.

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.

Nitratation in pilot-scale bioreactors fed with effluent from a submerged biological aerated filter used in the treatment of dog wastewater

Nitrification is a biochemical process that allows oxidation of ammonium ion to nitrite, and nitrite to nitrate in a system. Aerobic processes, such as use of submerged biological aerated filter (SBAF), enable nitrification. However, some variables that are entirely unavailable or not available at the required concentration range may hamper the process. In this study, nitratation under high dissolved oxygen (DO) concentrations was evaluated in laboratory-scale bioreactors containing 10% inoculum (0.5 kg kg^-1) fed with affluent from a SBAF that receive the sewage generated from washing the bays of a dog kennel. The following variables were monitored over time: ammoniacal nitrogen (12.44-29.62 mg L^-1), nitrite (0.28-0.54 mg L^-1), nitrate (1.75-3.55 mg L^-1), pH (8.11 ± 0.62), temperature (21.61 ± 1.24°C) and DO (9.69 ± 0.36 mg L^-1). Quantification of nitrifying bacteria by the multiple tube technique showed the value of 1.4 × 10¹² MPN mL^-1for ammonia-oxidizing bacteria (AOB) and 9.2 × 10¹⁴ MPN mL^-1 for nitrite-oxidizing bacteria. These values were higher than those found in a synthetic medium, which can be explained by the greater availability of ammonium and nitrite in the effluent. By the extraction of genomic DNA, and PCR, with specific primers, the presence of the AmoA (Ammonia monooxygenase) gene for AOB and of the Nitrobacter was detected in the bioreactor samples. By PCR-DGGE, the sequenced bands showed high similarity with denitrifying bacteria, such as Pseudomonas, Limnobacter, Thauera, Rhodococcus, and Thiobacillus. Thus, the saturation of dissolved oxygen in the system resulted in improvement in the nitratation step and allowed detection of bacterial genera involved in the process.

Nitrate removal by anammox biomass with intracellular carbon source as electron donors via DNRA pathway

In this work, a novel nitrate (NO₃^-) reduction pathway by anaerobic ammonium oxidation (anammox) biomass was firstly discovered with the intracellular carbon sources as the only electron donors. And the possible reaction mechanism was deduced to be intracellular dissimilatory nitrate reduction to ammonium (DNRA) pathway according to the experimental results. In batch experiments, without any external electron donors, NO₃^--N (about 50 mg/L) was reduced to N₂ within 48 h, and a small amount of NO₂^--N was detected (the maximum of 2 mg/L) with the anammox biomass concentration of 4400 mg/L. Acetylene (4.46 mmol/L) addition resulted in obvious NH₄⁺ accumulation during NO₃^- degradation by anammox biomass, since acetylene mainly interfered in hydrazine (N₂H₄) generation from NH₄⁺ and NO. Without HCO₃^- addition, the NO₃^--N degradation rate was slower than that with HCO₃^- addition. Simultaneously, glycogen contents inside anammox biomass decreased to 133.22 ± 1.21 mg/g VSS and 129.79 ± 1.21 mg/g VSS with and without HCO₃^-, respectively, from 142.20 ± 0.61 mg/g VSS. In the long-term experiment, anammox biomass stably degraded NO₃^--N without external electron donors addition, and the maximum removal efficiency of NO₃^--N reached 55.4%. The above results indicated the anammox bacteria utilized the DNRA pathway to reduce NO₃^- to NO₂^- and further NH₄⁺, then normal anammox metabolism would continue to convert the produced NO₂^- and NH₄⁺ to N₂. The intracellular stored carbon sources (e.g., glycogen) were supposed to be electron donors for NO₃^- degradation. This capability would enhance the viability and living space of anammox bacteria in different natural ecosystems, and make it plausible that complete nitrogen removal could be implemented only by the anammox process.

The potential contributions to organic carbon utilization in a stable acetate-fed Anammox process under low nitrogen-loading rates

The unique ability of Anammox bacteria to metabolize short-chain fatty acids have been demonstrated. However, the potential contributions of active Anammox species to carbon utilization in a mixotrophic Anammox-denitrification process are less well understood. In this study, we combined genome-resolved metagenomics and DNA stable isotope probing (DNA-SIP) to characterize an Anammox process fed with acetate under COD/TN ratios of around 0.30-0.40 and low nitrogen-loading rates. A draft genome of "Candidatus Jettenia caeni" and a novel species that was phylogenetically close to "Candidatus Brocadia sinica" were recovered. Essential genes encoding the key enzymes for acetate metabolism and dissimilatory nitrate reduction to ammonium were identified in the two Anammox draft genomes. The DNA-SIP revealed that Ignavibacterium, "Candidatus Jettenia caeni," Thauera, Denitratisoma, and Calorithrix predominantly contributed to organic carbon utilization in the acetate-fed Anammox process. In particular, the "Candidatus Jettenia caeni" accounted for a higher proportion of ¹³C-DNA communities than "Candidatus Brocadia sinica." This result well confirmed the theory of maintenance energy between the interspecies competition of the two Anammox species under low nitrogen-loading rates. Our study revealed its potential important role of the Anammox genus "Candidatus Jettenia" in the treatment of wastewater containing low organic matter and ammonia.

Simultaneous nitrogen and phosphorus removal from simulated digested piggery wastewater in a single-stage biofilm process coupling anammox and intracellular carbon metabolism

A Single-stage biofilm process coupling Anammox and Intracellular Carbon metabolism (SAIC) was constructed for treating simulated digested piggery wastewater with low carbon/nitrogen ratio (C/N) in this study. TN removal in SAIC system increased by more than 12.77% compared to the reference, and the maximum total phosphorus (TP) removal efficiency reached to 83.70% (C/N = 1.5). Denitrification driven by intracellular carbon, mainly poly-β-hydroxybutyrate (PHB, 78.57%), contributed 32.60% of TN elimination at most, and at least 67.40% should be attributed to anammox. Phosphorus was thought to be mainly removed through biological route, while chemical precipitation also explained around 10% of removed TP. Furthermore, commensalism of glycogen accumulating organisms (GAOs), phosphate accumulating organisms (PAOs), nitrifiers and anammox bacteria was revealed by combining 16S rRNA amplicon sequencing and metagenomics. As a result, multiple metabolic pathways including anammox, (partial) nitrification, endogenous (partial) denitrification and biological P-removal played synergistic effect in SAIC system.

Rethinking microbial infallibility in the metagenomics era

The 'principle of microbial infallibility' was a mainstay of microbial physiology and environmental microbiology in earlier decades. This principle asserts that wherever there is an energetic gain to be made from environmental resources, microorganisms will find a way to take advantage of the situation. Although previously disputed, this claim was revived with the discovery of anammox bacteria and other major contributors to biogeochemistry. Here, we discuss the historical background to microbial infallibility, and focus on its contemporary relevance to metagenomics. Our analysis distinguishes exploration-driven metagenomics from hypothesis-driven metagenomics. In particular, we show how hypothesis-driven metagenomics can use background assumptions of microbial infallibility to enable the formulation of hypotheses to be tested by enrichment cultures. Discoveries of comammox and the anaerobic oxidation of methane are major instances of such strategies, and we supplement them with outlines of additional examples. This overview highlights one way in which metagenomics is making the transition from an exploratory data-analysis programme of research to a hypothesis-testing one. We conclude with a discussion of how microbial infallibility is a heuristic with far-reaching implications for the investigation of life.

The physiological potential of anammox bacteria as revealed by their core genome structure

We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2− reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. Kuenenia stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologues. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least five paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH₂OH by self-production for anammox metabolism.

A review of quorum sensing improving partial nitritation-anammox process: Functions, mechanisms and prospects

Partial nitritation-anammox (PNA) is a promising and energy-efficient process for the sustainable nitrogen removal. However, its wide applications are still limited by the long start-up period and instability of long-term operation. Quorum sensing (QS), as a way of cell-to-cell communication generally regulating various microbial behaviors, has been increasingly investigated in PNA process, because QS may substantially manipulate the metabolism of microorganisms and overcome the limitations of PNA process. This critical review provides a comprehensive analysis of QS in PNA systems, and identifies the challenges and opportunities for the optimization of PNA process based on QS. The analysis is grouped based on the configurations of PNA process, including partial nitritation, anammox and single-stage PNA systems. QS is confirmed to regulate various properties of PNA systems, including microbial activity, microbial growth rate, microbial aggregation, microbial interactions and the robustness under adverse conditions. Major challenges in the mechanisms of QS, such as QS circuits, target genes and the response to environmental inputs, are identified. Potential applications of QS, such as short-term addition of certain acyl-homoserine lactones (AHLs) or substances containing AHLs, transient unfavorable conditions to stimulate the secretion of AHLs, are also proposed. This review focuses on the theoretical and practical cognation for QS in PNA systems, and serves as a stepping stone for further QS-based strategies to enhance nitrogen removal through PNA process.

Impacts of organics on the microbial ecology of wastewater anammox processes: Recent advances and meta-analysis

Anaerobic ammonium oxidation (anammox) represents a promising technology for wastewater nitrogen removal. Organics management is critical to achieving efficient and stable performance of anammox or integrated processes, e.g., denitratation-anammox. The aim of this systematic review is to synthesize the state-of-the-art knowledge on the multifaceted impacts of organics on wastewater anammox community structure and function. Both exogenous and endogenous organics are discussed with respect to their effects on the biofilm/granule structure and function, as well as the interactions between anammox bacteria (AnAOB) and a broad range of coexisting functional groups. A global core community consisting of 19 taxa is identified and a co-occurrence network is constructed by meta-analysis on the 16S rDNA sequences of 149 wastewater anammox samples. Correlations between core taxa, keystone taxa, and environmental factors, including COD, nitrogen loading rate (NLR) and C/N ratio are obtained. This review provides a holistic understanding of the microbial responses to different origins and types of organics in wastewater anammox reactors, which will facilitate the design and operation of more efficient anammox-based wastewater nitrogen removal process.

Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope

The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.

Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex

Nitrate is an abundant nutrient and electron acceptor throughout Earth's biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein's electron transport chain, and elucidate the electron transfer pathways within the complex.

Nitrogen removal mechanism of marine anammox bacteria treating nitrogen-laden saline wastewater in response to ultraviolet (UV) irradiation: High UV tolerance and microbial community shift

Salt stress can be naturally overcome by marine anammox bacteria (MAB), while their low growth rate and sensitivity to operational conditions are still challenges for the application of anammox. To enhance the enrichment of MAB and decipher the effects of ultraviolet (UV) irradiation on MAB, UV was introduced in the nitrogen removal of MAB treating nitrogen-laden saline wastewater for the first time. The results indicated that MAB were resistant to a fairly high UV-C dose, 12000 mJ/cm². Their relative abundance was enhanced by 1.2 folds under 12000 mJ/cm² UV-C. However, the relative abundance of Actinobacteria, Acidobacteria, Chloroflexi and Marinicella were greatly dropped with enhanced UV-C dose. The tolerance mechanism was diversified, e.g. excessive extracellular polymeric substances, special structure of MAB and interspecific competition/cooperation. Although further study was still needed, the findings shed a light on MAB enrichment and exploited great potentials of MAB in nitrogen-laden saline wastewater treatment.

Geochemical transition zone powering microbial growth in subsurface sediments

No other environment hosts as many microbial cells as the marine sedimentary biosphere. While the majority of these cells are expected to be alive, they are speculated to be persisting in a state of maintenance without net growth due to extreme starvation. Here, we report evidence for in situ growth of anaerobic ammonium-oxidizing (anammox) bacteria in ∼80,000-y-old subsurface sediments from the Arctic Mid-Ocean Ridge. The growth is confined to the nitrate-ammonium transition zone (NATZ), a widespread geochemical transition zone where most of the upward ammonium flux from deep anoxic sediments is being consumed. In this zone the anammox bacteria abundances, assessed by quantification of marker genes, consistently displayed a four order of magnitude increase relative to adjacent layers in four cores. This subsurface cell increase coincides with a markedly higher power supply driven mainly by intensified anammox reaction rates, thereby providing a quantitative link between microbial proliferation and energy availability. The reconstructed draft genome of the dominant anammox bacterium showed an index of replication (iRep) of 1.32, suggesting that 32% of this population was actively replicating. The genome belongs to a Scalindua species which we name Candidatus Scalindua sediminis, so far exclusively found in marine sediments. It has the capacity to utilize urea and cyanate and a mixotrophic lifestyle. Our results demonstrate that specific microbial groups are not only able to survive unfavorable conditions over geological timescales, but can proliferate in situ when encountering ideal conditions with significant consequences for biogeochemical nitrogen cycling.

Biostimulation of a marine anammox bacteria-dominated bioprocess by Co(II) to treat nitrogen-rich, saline wastewater

The biostimulation of a marine anammox bacteria (MAB)-dominated bioprocess with Co(II) was studied in a sequencing batch reactor (SBR) treating nitrogen-rich saline wastewater at 15 °C. The low Co(II) load of 0.0015 kgCo²⁺_added/(m^3.d) had little effect on the removal of nitrogen. The nitrite removal rate (NRR), ammonia removal rate (ARR), and specific anammox activity (SAA) reached 0.73 kg/(m³·d), 0.59 kg/(m³·d), and 0.23 kg/(kg·d), respectively, under the Co(II) load of 0.009 kgCo²⁺_added/(m^3.d). However, the loadings of Co(II) at 0.024-0.03 kgCo²⁺_added/(m^3.d) negatively affected the activity of MAB. Besides, the values of ΔNO₂^--N/ΔNH₄⁺-N (1.15-1.29) were lower than the theoretical ratio values (around 1.32) likely because of the marine commamox process. The removal of nitrogen from nitrogen-rich saline wastewater was achieved by the synergy between Candidatus Scalindua (27.11%) and Candidatus Kuenenia (9.55%). The nitrogen removal with Co(II) addition could be well described by a modified Logistic model.

Hydroxylamine metabolism of Ca. Kuenenia stuttgartiensis

Hydroxylamine is a key intermediate in several biological reactions of the global nitrogen cycle. However, the role of hydroxylamine in anammox is still not fully understood. In this work, the impact of hydroxylamine (also in combination with other substrates) on the metabolism of a planktonic enrichment culture of the anammox species Ca. Kuenenia stuttgartiensis was studied. Anammox bacteria were observed to produce ammonium both from hydroxylamine and hydrazine, and hydroxylamine was consumed simultaneously with nitrite. Hydrazine accumulation - signature for the presence of anammox bacteria - strongly depended on the available substrates, being higher with ammonium and lower with nitrite. Furthermore, the results presented here indicate that hydrazine accumulation is not the result of the inhibition of hydrazine dehydrogenase, as commonly assumed, but the product of hydroxylamine disproportionation. All kinetic parameters for the identified reactions were estimated by mathematical modelling. Moreover, the simultaneous consumption and growth on ammonium, nitrite and hydroxylamine of anammox bacteria was demonstrated, this was accompanied by a reduction in the nitrate production. Ultimately, this study advances the fundamental understanding of the metabolic versatility of anammox bacteria, and highlights the potential role played by metabolic intermediates (i.e. hydroxylamine, hydrazine) in shaping natural and engineered microbial communities.

Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes

Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N₂). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.

Nutrient Limitation Causes Differential Expression of Transport- and Metabolism Genes in the Compartmentalized Anammox Bacterium Kuenenia stuttgartiensis

Anaerobic ammonium-oxidizing (anammox) bacteria, members of the "Candidatus Brocadiaceae" family, play an important role in the nitrogen cycle and are estimated to be responsible for about half of the oceanic nitrogen loss to the atmosphere. Anammox bacteria combine ammonium with nitrite and produce dinitrogen gas via the intermediates nitric oxide and hydrazine (anammox reaction) while nitrate is formed as a by-product. These reactions take place in a specialized, membrane-enclosed compartment called the anammoxosome. Therefore, the substrates ammonium, nitrite and product nitrate have to cross the outer-, cytoplasmic-, and anammoxosome membranes to enter or exit the anammoxosome. The genomes of all anammox species harbor multiple copies of ammonium-, nitrite-, and nitrate transporter genes. Here we investigated how the distinct genes for ammonium-, nitrite-, and nitrate- transport were expressed during substrate limitation in membrane bioreactors. Transcriptome analysis of Kuenenia stuttgartiensis planktonic cells showed that four of the seven ammonium transporter homologs and two of the nine nitrite transporter homologs were significantly upregulated during ammonium-limited growth, while another ammonium transporter- and four nitrite transporter homologs were upregulated in nitrite limited growth conditions. The two nitrate transporters were expressed to similar levels in both conditions. In addition, genes encoding enzymes involved in the anammox reaction were differentially expressed, with those using nitrite as a substrate being upregulated under nitrite limited growth and those using ammonium as a substrate being upregulated during ammonium limitation. Taken together, these results give a first insight in the potential role of the multiple nutrient transporters in regulating transport of substrates and products in and out of the compartmentalized anammox cell.