Linking ultrastructure and function in four genera of anaerobic ammonium-oxidizing bacteria: cell plan, glycogen storage, and localization of cytochrome C proteins

Enhanced-nitrogen removal through Fe(III)-triggered partial dissimilatory nitrate reduction to ammonium coupling with anammox in anammox bioreactor

Anammox is recognized as a prospective alternative for future biological nitrogen removal technologies. However, the nitrate by-products produced by anammox bacteria limit its overall nitrogen removal efficiency below 88 %. This study introduced Fe(III) into the anammox bioreactor to enhance the nitrogen removal efficiency to approximately 95 %, surpassing the biochemical limit of 88 % imposed by anammox stoichiometry. Anammox sludge was demonstrated to utilize extracellular polymeric substances to reduce Fe(III) into Fe(II), and this process promoted the dominance of Ca. Brocadia. The iron addition improved the abundance of narGHI genes and facilitated the partial dissimilatory nitrate reduction to ammonium, with nitrite as the end product. The accumulated nitrite was then eliminated through the anammox pathway, along with the excess ammonium (30 mg/L) in the influent. Overall, this study deepens our understanding of the enhanced nitrogen removal triggered by Fe(III) in anammox sludge and offers an effective approach to boost anammox process.

Evidence of Potential Anammox Activities from Rice Paddy Soils in Microaerobic and Anaerobic Conditions

Anammox, a reaction in which microorganisms oxidize ammonia under anaerobic conditions, is used in the industry to remove ammonium from wastewater in an environmentally friendly manner. This process does not produce intermediate products such as nitrite or nitrate, which can act as secondary pollutants in soil and water environments. For industrial applications, anammox bacteria should be obtained from the environment and cultivated. Anammox bacteria generally exhibit a slow growth rate and may not produce a large number of cells due to their anaerobic metabolism. Additionally, their habitats appear to be limited to specific environments, such as oxidation-reduction transition zones. Consequently, most of the anammox bacteria that are used or studied originate from marine environments. In this study, anammox bacterial evidence was found in rice paddy soil and cultured under various conditions of aerobic, microaerobic, and anaerobic batch incubations to determine whether enrichment was possible. The anammox-specific gene (hzsA) and microbial community analyses were performed on the incubated soils. Although it was not easy to enrich anammox bacteria due to co-occurrence of denitrification and nitrification based on the chemistry data, potential existence of anammox bacteria was assumed in the terrestrial paddy soil environment. For potential industrial uses, anammox bacteria could be searched for in rice paddy soils by applying optimal enrichment conditions.

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.

Potential Role of the Anammoxosome in the Adaptation of Anammox Bacteria to Salinity Stress

The underlying adaptative mechanisms of anammox bacteria to salt stress are still unclear. The potential role of the anammoxosome in modulating material and energy metabolism in response to salinity stress was investigated in this study. The results showed that anammox bacteria increased membrane fluidity and decreased mechanical properties by shortening the ladderane fatty acid chain length of anammoxosome in response to salinity shock, which led to the breakdown of the proton motive force driving ATP synthesis and retarded energy metabolism activity. Afterward, the fatty acid chain length and membrane properties were recovered to enhance the energy metabolic activity. The relative transmission electron microscopy (TEM) area proportion of anammoxosome decreased from 55.9 to 38.9% under salinity stress. The 3D imaging of the anammox bacteria based on Synchrotron soft X-ray tomography showed that the reduction in the relative volume proportion of the anammoxosome and the concave surfaces was induced by salinity stress, which led to the lower energy expenditure of the material transportation and provided more binding sites for enzymes. Therefore, anammox bacteria can modulate nitrogen and energy metabolism by changing the membrane properties and morphology of the anammoxosome in response to salinity stress. This study broadens the response mechanism of anammox bacteria to salinity stress.

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.

Metagenomic insights into the mechanism for the rapid enrichment and high stability of Candidatus Brocadia facilitated by Fe(Ⅲ)

The rapid enrichment of anammox bacteria and its fragile resistance to adverse environment are the critical problems facing of anammox processes. As an abundant component in anammox bacteria, iron has been proved to promote the activity and growth of anammox bacteria in the mature anammox systems, but the functional and metabolic profiles in Fe(III) enhanced emerging anammox systems have not been evaluated. Results indicated that the relative abundance of functional genes involved in oxidative phosphorylation, nitrogen metabolism, cofactors synthesis, and extracellular polymers synthesis pathways was significantly promoted in the system added with 5 mg/L Fe(III) (R5). These enhanced pathways were crucial to energy generation, nitrogen removal, cell activity and proliferation, and microbial self-defense, thereby accelerating the enrichment of anammox bacteria Ca. Brocadia and facilitating their resistance to adverse environments. Microbial community analysis showed that the proportion of Ca. Brocadia in R5 also increased to 64.42 %. Hence, R5 could adapt rapidly to the increased nitrogen loading rate and increase the nitrogen removal rate by 108 % compared to the system without Fe(III) addition. However, the addition of 10 and 20 mg/L Fe(III) showed inhibitory effects on the growth and activity of anammox bacteria, which exhibited the lower relative abundance of Ca. Brocadia and unstable or even collapsed nitrogen removal performance. This study not only clarified the concentration range of Fe(III) that promoted and inhibited the enrichment of anammox bacteria, but also deepened our understanding of the functional and metabolic mechanisms underlying enhanced enrichment of anammox bacteria by Fe(III), providing a potential strategy to hasten the start-up of anammox from conventional activated sludge.

Nitrate removal by anammox bacteria utilizing photoexcited electrons via inward extracellular electron transfer channel

Dissimilatory nitrate reduction to ammonium (DNRA) has been found to occur in some anammox bacteria species, and the DNRA metabolites (nitrite and ammonium) can further be removed to nitrogen from water. However, the activation of DNRA pathway of anammox bacteria is usually limited by the access to electron donors. Herein, we constructed a photosensitized hybrid system combining anammox bacteria (Candidatus Kuenenia stuttgartiensis and Candidatus Brocadia anammoxidans) with CdS nanoparticles semiconductor for energy-efficient NO3- removal. Such photosensitized anammox-CdS hybrid systems achieved NO3- removal with an average efficiency of 88% (the maximum of 91%) and a N2 selectivity of 72%, only with photoexcited electrons as donors. The DNRA-anammox metabolism of anammox bacteria was proved to responsible for NO3- removal via inward extracellular electron transfer channel. The greatly up-regulated genes encoding c-type cytochrome proteins (5 or 11 hemes) in the outer membrane, c-type cytochrome protein (4 hemes) and electron transport protein RnfA-E in the inner membrane, ferredoxin (2Fe-2S) in the cytoplasm and c-type cytochrome bc1 in anammoxosome membrane were supposed to play key roles in the inward extracellular electron transfer pathway. This work provides a novel insight into the design of the biotic-abiotic hybrid photosynthetic systems, and opens a new strategy for light-driven NO3- removal from the perspective of light energy input.

Anammox with alternative electron acceptors: perspectives for nitrogen removal from wastewaters

In the context of the anaerobic ammonium oxidation process (anammox), great scientific advances have been made over the past two decades, making anammox a consolidated technology widely used worldwide for nitrogen removal from wastewaters. This review provides a detailed and comprehensive description of the anammox process, the microorganisms involved and their metabolism. In addition, recent research on the application of the anammox process with alternative electron acceptors is described, highlighting the biochemical reactions involved, its advantages and potential applications for specific wastewaters. An updated description is also given of studies reporting the ability of microorganisms to couple the anammox process to extracellular electron transfer to insoluble electron acceptors; particularly iron, carbon-based materials and electrodes in bioelectrochemical systems (BES). The latter, also referred to as anodic anammox, is a promising strategy to combine the ammonium removal from wastewater with bioelectricity production, which is discussed here in terms of its efficiency, economic feasibility, and energetic aspects. Therefore, the information provided in this review is relevant for future applications.

Microbially driven Fe-N cycle: Intrinsic mechanisms, enhancement, and perspectives

The iron‑nitrogen (FeN) cycle driven by microbes has great potential for treating wastewater. Fe is a metal that is frequently present in the environment and one of the crucial trace elements needed by microbes. Due to its synergistic role in the microbial N removal process, Fe goes much beyond the essential nutritional needs of microorganisms. Investigating the mechanisms behind the linked Fe-N cycle driven by microbes is crucial. The Fe-N cycle is frequently connected with anaerobic ammonia oxidation (anammox), nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), Feammox, and simultaneous nitrification denitrification (SND), etc. Although the main mechanisms of Fe-mediated biological N removal may vary depending on the valence state of the Fe, their similar transformation pathways may provide information on the study of certain element-microbial interactions. This review offers a thorough analysis of the facilitation effect and influence of Fe on the removal of nitrogenous pollutants in various biological N removal processes and summarizes the ideal Fe dosing. Additionally, the synergistic mechanisms of Fe and microbial synergistic N removal process are elaborated, covering four aspects: enzyme activity, electron transfer, microbial extracellular polymeric substances (EPS) secretion, and microbial community interactions. The methods to improve biological N removal based on the intrinsic mechanism were also discussed, with the aim of thoroughly understanding the biological mechanisms of Fe in the microbial N removal process and providing a reference and thinking for employing Fe to promote microbial N removal in practical applications.

Electron transfer mechanism of intracellular carbon-dependent DNRA inside anammox bacteria

Generally, anaerobic ammonium oxidation (anammox) converts nitrite (NO2-) and ammonium (NH4+) to nitrogen gas (N2) but generates some nitrate (NO3-) (equivalent to 11% of inlet total nitrogen (TN)). Although it reported that anammox bacteria could degrade NO3- via dissimilatory nitrate reduction to ammonium (DNRA) pathway using the intracellular carbon as the electron donor, it is still unclear the specific electron transfer mechanism in this intracellular carbon-dependent DNRA inside anammox bacteria, and whether the sole anammox bacteria could achieve higher TN removal efficiency more than the theoretical maximum of 89%. In this study, transcriptome analysis and metabolic inhibitor experiments demonstrated that NADH generated from the decomposition of the intracellular carbon (glycogen) supplied electrons for the NO3-conversion; the electrons were transferred from NADH to nitrate reductase (Nar) and nitrite reductase forming ammonium (NrfA) from ubiquinone (UQ) and complex III, respectively. Combining the intracellular carbon-dependent DNRA with normal anammox process, an average TN removal efficiency of 95% was achieved by the sole anammox bacteria in a sequencing batch reactor. Fluorescent in situ hybridization (FISH) images and real-time fluorescence quantitative PCR (qPCR) results illustrated anammox bacteria could survive and proliferate in the SBR. Our work improved the understanding of the electron transfer mechanism inside anammox bacteria, and further exploit its potential in nitrogen pollutants removal.

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

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

Insights into heavy metals shock on anammox systems: Cell structure-based mechanisms and new challenges

Anaerobic ammonium oxidation (anammox) as a low-carbon and energy-saving technology, has shown unique advantages in the treatment of high ammonia wastewater. However, wastewater usually contains complex heavy metals (HMs), which pose a potential risk to the stable operation of the anammox system. This review systematically re-evaluates the HMs toxicity level from the inhibition effects and the inhibition recovery process, which can provide a new reference for engineering. From the perspective of anammox cell structure (extracellular, anammoxosome membrane, anammoxosome), the mechanism of HMs effects on cellular substances and metabolism is expounded. Furthermore, the challenges and research gaps for HMs inhibition in anammox research are also discussed. The clarification of material flow, energy flow and community succession under HMs shock will help further reveal the inhibition mechanism. The development of new recovery strategies such as bio-accelerators and bio-augmentation is conductive to breaking through the engineered limitations of HMs on anammox. This review provides a new perspective on the recognition of toxicity and mechanism of HMs in the anammox process, as well as the promotion of engineering applicability.

Unraveling the structure and function of bacterioferritin in Candidatus Kuenenia stuttgartiensis: Iron storage sites maintain cellular iron homeostasis

Anammox bacteria rely heavily on iron and have many iron storage sites. However, the biological significance of these iron storage sites has not been clearly defined. In this study, we explored the properties and location of iron storage sites to better understand their cellular function. To do this, the Candidatus Kuenenia stuttgartiensis iron storage protein, bacterioferritin (K.S Bfr), was successfully expressed and purified. In vitro, correctly assembled globulins were observed by transmission electron microscopy. The self-assembled K.S Bfr has active redox and can bind Fe²⁺ and mineralize it in the protein cavity. In vivo, engineered bacteria with K.S Bfr showed good adaptability to Fe²⁺, with a survival rate of 78.9% when exposed to 5 mM Fe²⁺, compared with only 66.0% for wild-type bacteria lacking K.S Bfr. A potential iron regulatory strategy similar to that of Anammox was identified in transcriptomic analysis of engineered bacteria. This system may be controlled by the iron uptake regulator Furto transport Fe²⁺ via FeoB and store excess Fe²⁺ in K.S Bfr to maintain cellular homeostasis. K.S Bfr has superior iron storage capacity both intracellularly and in vitro. The discovery of K.S Bfr reveals the storage location of iron-rich nanoparticles, increases our understanding of the adaptability of iron-dependent bacteria to Fe²⁺, and suggests possible iron regulation strategies in Anammox bacteria.

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.

Enhancement and mechanisms of iron-assisted anammox process

Anaerobic ammonium oxidation (anammox) is a sustainable biological nitrogen removal technology that has limited large-scale applications owing to the low cell yield and high sensitivity of anammox bacteria (AnAOB). Fortunately, iron-assisted anammox, being a highly practical method could be an effective solution. This review focused on the iron-assisted anammox process, especially on its performance and mechanisms. In this review, the effects of iron in three different forms (ionic iron, zero-valent iron and iron-containing minerals) on the performance of the anammox process were systematically reviewed and summarized, and the strengthening effects of Fe (II) seem to be more prominent. Moreover, the detailed mechanisms of iron-assisted anammox in previous researches were discussed from macro to micro perspectives. Additionally, applicable iron-assisted methods and unified strengthening mechanisms for improving the stability of nitrogen removal and shortening the start-up time of the system in anammox processes were suggested to explore in future studies. This review was intended to provide helpful information for scientific research and engineering applications of iron-assisted anammox.

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

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

Key enzymes involved in anammox-based processes for wastewater treatment: An applied overview

The anaerobic ammonium oxidation (anammox) process has attracted significant attention as an economic, robustness, and sustainable method for the treatment of nitrogen (N)-rich wastewater. Anammox bacteria (AnAOB) coexist with other microorganisms, and particularly with ammonia-oxidizing bacteria (AOB) and/or heterotrophic bacteria (HB), in symbiosis in favor of the substrate requirement (ammonium and nitrite) of the AnAOB being supplied by these other organisms. The dynamics of these microbial communities have a significant effect on the N-removal performance, but the corresponding metabolic pathways are still not fully understood. These processes involve many common metabolites that may act as key factors to control the symbiotic interactions between these organisms, to maximize N-removal efficiency from wastewater. Therefore, this work overviews the current state of knowledge about the metabolism of these microorganisms including key enzymes and intermediate metabolites and summarizes already reported experiences based on the employment of certain metabolites for the improvement of N-removal using anammox-based processes. PRACTITIONER POINTS: Approaches knowledge about the biochemistry and metabolic pathways involved in anammox-based processes. Some molecular tools can be used to determine enzymatic activity, serving as an optimization in nitrogen removal processes. Enzymatic evaluation allied to the physical-chemical and biomolecular analysis of the nitrogen removal processes expands the application in different effluents.

Metagenomics: A Tool for Exploring Key Microbiome With the Potentials for Improving Sustainable Agriculture

Microorganisms are immense in nature and exist in every imaginable ecological niche, performing a wide range of metabolic processes. Unfortunately, using traditional microbiological methods, most microorganisms remain unculturable. The emergence of metagenomics has resolved the challenge of capturing the entire microbial community in an environmental sample by enabling the analysis of whole genomes without requiring culturing. Metagenomics as a non-culture approach encompasses a greater amount of genetic information than traditional approaches. The plant root-associated microbial community is essential for plant growth and development, hence the interactions between microorganisms, soil, and plants is essential to understand and improve crop yields in rural and urban agriculture. Although some of these microorganisms are currently unculturable in the laboratory, metagenomic techniques may nevertheless be used to identify the microorganisms and their functional traits. A detailed understanding of these organisms and their interactions should facilitate an improvement of plant growth and sustainable crop production in soil and soilless agriculture. Therefore, the objective of this review is to provide insights into metagenomic techniques to study plant root-associated microbiota and microbial ecology. In addition, the different DNA-based techniques and their role in elaborating plant microbiomes are discussed. As an understanding of these microorganisms and their biotechnological potentials are unlocked through metagenomics, they can be used to develop new, useful and unique bio-fertilizers and bio-pesticides that are not harmful to the environment.

Biofilm carriers for anaerobic ammonium oxidation: Mechanisms, applications, and roles in mainstream systems

The anaerobic ammonium oxidation (ANAMMOX) process was proposed as the most promising nitrogen removal process. Biofilm carriers were demonstrated to effectively enhance the anaerobic ammonium oxidating bacteria (AnAOB) retention. This paper reviews the effect of carrier properties on the AnAOB biofilm development according to the biofilm development process and the application state-of-art of three major kinds of conventional carriers, organic-based, inorganic-based carriers, and gel carriers, from the view of system performance and functional microorganisms. The carrier modification methods and purpose are thoroughly summarized and classified into three categories corresponding to various carrier defects. Four important aspects of the desirable carrier for the mainstream ANAMMOX process were proposed, including providing spatial configuration, enhancing the biomass retention, reinforcing the activity, and improving the growth environment, which needs to combine the advantages of organic and inorganic materials. Eventually, the future application directions of novel carriers for the ANAMMOX-based process were also highlighted.

Biochar-mediated DNRA pathway of anammox bacteria under varying COD/N ratios

Coupling dissimilatory nitrate reduction to ammonium (DNRA) pathway with anammox process has a prominent advantage in enhancement of nitrogen removal. However, the anammox bacteria driven-DNRA is difficult to proceed at normal autotrophic circumstance. Herein, for the first time, biochar (prepared by bamboo) was used as a mediator to stimulate the DNRA pathway of anammox bacteria under varying chemical oxygen demand (COD) to nitrogen (COD/N) ratios (0.1-0.7), and the underlying stimulation mechanism was elucidated by metagenomics sequencing analysis. Results showed that biochar addition (10 g/L) stimulated DNRA pathway of anammox bacteria at low COD/N ratios (0.1-0.5), thus enhancing the nitrogen removal efficiency (NRE) of the anammox system by 7.2%-16.4% and 0.9%-3.0%, respectively, compared to that of tests without sodium acetate and biochar (p<0.05). This enhancement was attributed to the improved extracellular electron accepting capacity of anammox biomass by biochar. The easily obtained electrons (from sodium acetate) further increased the relative abundances of anammox-related (hzs) and complete DNRA-related (napAB and nrfAH) genes (p<0.05), which catalyze electron-consuming reactions. The stimulated anammox pathway and DNRA pathway further increased the specific anammox activity and the relative abundance of anammox bacteria (especially Ca. Jettenia) by 15.5%-23.0% and 11.3%-82.6% compared with that without biochar, respectively. Metagenomics sequencing also revealed that anammox bacteria, Ca. Jettenia caeni, was the main bacteria for DNRA metabolism in this system. Our findings reveal that biochar could selectively stimulate DNRA pathway of anammox bacteria affiliated by a low amount of carbon, which provides a novel strategy to improve the nitrogen removal of anammox-based processes.

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.

Adaptation and evolution of freshwater Anammox communities treating saline/brackish wastewater

The most common way to apply Anammox for saline wastewater treatment is via salt adaptation of freshwater Anammox bacteria (FAB). To better apply this process in practice, it's essential to understand the salt adaptation process of FBA, as well as the underlying mechanisms. This study investigated the long-term salt adaptation process of a fixed-film FAB culture in three reactors (namely R1-R3), under salinities of 2, 8, and 12 NaCl g/L, correspondingly. All three reactors were under stable operation and achieved 80-90% total inorganic nitrogen removal efficiency throughout the 425-day operation period. R1 servers as a blank control, based on the clear microbial community shifts in R2 and R3, the operation period was divided into 2 phases. During Phase 1, all FAB in the three reactors belonged to Ca. Brocadia sp.. The Anammox activity (AA) and the ratio of nitrite/ammonium (NO₂^--N/NH₄⁺-N) consumption in R2 and R3 decreased with the increase of salinity and did not recover to the initial levels. During Phase 2, the relative abundance of Ca. Kuenenia sp. in R2 and R3 increased from nearly 0 to about 60 and 77%, respectively. With the growth of Ca. Kuenenia sp., the AA and stoichiometry of R2 and R3 gradually recovered. AA of R2 and R3 both reached 1.0 g NH₄⁺-N/L/day at the end of this phase, which was about 80% of that in R1. These results indicated that the salt adaptation of FAB culture was achieved by species shift from a low salt-tolerance one to a high salt-tolerance one.

Architecture of HAP-anammox granules contributed to high capacity and robustness of nitrogen removal under 7°C

The anaerobic ammonium oxidation (anammox) process is an autotrophic nitrogen removal process with great potential as a cost-effective and highly efficient technology in the wastewater treatment field. The main challenges yet to be overcome in this new frontier technology are operating at lower temperatures and achieving a high and stable nitrogen removal efficiency. In this study, an up-flow expanded bed reactor with hydroxyapatite (HAP)-anammox granules was operated for more than 200 days at 7°C. The nitrogen loading rate (NLR) was improved from 1.0 g-N/L/d to 3.6 g-N/L/d, together with a high-level nitrogen removal efficiency of 84-92%, which is the highest to date at extremely low temperatures in a continuous experiment. Candidatus Kuenenia was revealed to be the only dominant anammox genus, with a relative abundance of 35.3-37.5%. The optimal operational temperature was around 35°C and the apparent activation energy (E_a) was calculated as 78.37 kJ/mol. The three-layers architecture and architectural evolution of HAP-anammox granules into HAP-cores and peeling biofilms with outstanding settling performance were characterized. Under 7°C, the high capacity of nitrogen removal with robust removal efficiency using HAP-anammox granules was achieved.

Denitrifying anaerobic methane oxidation (DAMO) cultures: Factors affecting their enrichment, performance and integration with anammox bacteria

The recently discovered process, denitrifying anaerobic methane oxidation (DAMO), links the carbon and nitrogen biogeochemical cycles via coupling the anaerobic oxidation of methane to denitrification. The DAMO process, in this respect, has the potential to mitigate the greenhouse effect through the assimilation of dissolved methane. Denitrification via methane oxidation rather than organic matter, provides a new perspective to performing this once thought to be well established process. The two main species responsible for this process are "Candidatus Methylomirabilis oxyfera (M. oxyfera), and "Candidatus Methanoperedens nitroreducens" (M. nitroreducens). M. oxyfera is responsible of reducing nitrite while M. nitroreducens reduces nitrate to nitrite. These two microorganisms, despite their different pathways, were found to exist together in nature through a syntrophic relationship. Their co-existence with anaerobic ammonium oxidation (Anammox) bacteria was also revealed in the last decade. Anammox bacteria are chemolithoautotrophs, converting ammonium and nitrite to N₂ and nitrate. They are responsible for the release of more than 50% of oceanic N₂, hence play an important role in the global nitrogen cycle. Factors leading to the enrichment of DAMO cultures and their cultivation with Anammox cultures are of significance for improved nitrogen removal systems with decreased greenhouse effect, and even for further full-scale applications. This study, therefore, aims to present an updated review of the DAMO process, by focusing on the factors that might have a significant role in enrichment of DAMO microorganisms and their co-existence with Anammox bacteria. Factors such as temperature, pH, inoculum and feed type, trace metals and reactor configuration are among the ones discussed in detail. Factors, which have not been investigated, are also elucidated to provide a better understanding of the process and set research goals that will aid in the development of DAMO-centered wastewater treatment alternatives.

Strengthened attachment of anammox bacteria on iron-based modified carrier and its effects on anammox performance in integrated floating-film activated sludge (IFFAS) process

Moving-bed biofilm reactor (MBBR) or integrated floating-film activated sludge (IFFAS) process has been proved to be one of the ideal candidates for anammox application. However, the slow development of anammox bacteria (AnAOB) biofilm and unstable bioactivity always limit their wide application. This study developed a type of novel zero-valent iron (ZVI)-based modified carrier for strengthening AnAOB attachment and enhancing anammox performance. Surface properties analysis indicated the iron-based modified carrier revealed electropositive, less hydrophobic, and higher surface free energy compared with conventional high density polyethylene (HDPE) carrier. These surface parameters were positively correlated with total biomass attachment, anammox biofilm development, EPS secretion and heme-c production. IFFAS process filled with iron-based modified carriers could keep relatively stable and high anammox activity at different influent TN loadings (varied from 0.6 to 1.4 kg/(m³∙d)) and showed potential to keep and recover AnAOB bioactivity after six-months-freeze. Microbial analysis confirmed that anammox genus, Candidatus Kuenenia, had a significant niche preference on iron-based modified carrier than conventional HDPE carrier. As a result, the population of Candidatus Kuenenia in IFFAS process filled with modified carriers that contained 2 wt% or 3 wt% ZVI was 1.34 × 10⁶-1.55 × 10⁶ copies/ mg DNA, increased by 20.7-39.6% comparing with that in the control reactor (1.11 × 10⁶ copies/ mg DNA). This study demonstrated AnAOB could be enriched and maintained in situ with high abundance and bioactivity on the iron-based modified carriers, which would be significant for anammox process wide application in full-scale.

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.

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline

Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean's interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine-seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.

Glycogen metabolism of the anammox bacterium "Candidatus Brocadia sinica"

Presence of glycogen granules in anaerobic ammonium-oxidizing (anammox) bacteria has been reported so far. However, very little is known about their glycogen metabolism and the exact roles. Here, we studied the glycogen metabolism in "Ca. Brocadia sinica" growing in continuous retentostat cultures with bicarbonate as a carbon source. The effect of the culture growth phase was investigated. During the growing phase, intracellular glycogen content increased up to 32.6 mg-glucose (g-biomass dry wt)-1 while the specific growth rate and ATP/ADP ratio decreased. The accumulated glycogen begun to decrease at the onset of entering the near-zero growth phase and was consumed rapidly when substrates were depleted. This clearly indicates that glycogen was synthesized and utilized as an energy storage. The proteomic analysis revealed that "Ca. B. sinica" synthesized glycogen via three known glycogen biosynthesis pathways and simultaneously degraded during the progress of active anammox, implying that glycogen is being continuously recycled. When cells were starved, a part of stored glycogen was converted to trehalose, a potential stress protectant. This suggests that glycogen serves at least as a primary carbon source of trehalose synthesis for survival. This study provides the first physiological evidence of glycogen metabolism in anammox bacteria and its significance in survival under natural substrate-limited habitat.

Deciphering correlation between permeability and size of anammox granule: "pores as medium"

Anammox granular sludge bed technology has been widely applied for its attractive advantages. Efficient mass transfer is an important factor for the anammox granules to play their role. In this study, steady-state anammox granules were used to investigate the correlation between the permeability and granule size with the granule pore as pivot. The results of size distribution showed that the anammox granules could be divided into 6 groups: 200-500 µm (I), 500-1000 µm (II), 1000-1500 µm (III), 1500-2000 µm (IV), 2000-3000 µm (V) and ≥3000 µm (VI). The results of settling experiment demonstrated that the permeability of anammox granules was negatively correlated with the granule size. The fluid collection efficiency declined from 39.4% to 9.3% for granule group I to III, and further to 0 for granule group IV to VI (granule size was larger than 1.5 mm). The observation of micro-CT revealed that the pore structure of anammox granules varied significantly with the increase of granule size, forming a denser surface layer and sparser interior. The chemical analysis and microscopic observation indicated that the pore plugging of surface layer by cell proliferation and EPS secretion was the main cause for the permeability deterioration. The findings of this study will help to understand the mass transfer of anammox granules and promote the development of anammox processes.

Hydroxyapatite crystallization-based phosphorus recovery coupling with the nitrogen removal through partial nitritation/anammox in a single reactor

For digestion effluent treatment, while the anammox-based process has been successfully applied for nitrogen removal, in most cases, phosphorus (P) represents another major concern. In this study, a novel process, integrating the partial nitritation/anammox and hydroxyapatite crystallization (PNA-HAP) in a single airlift reactor, was developed for the simultaneous nitrogen removal and P recovery from synthetic digestion effluent. With a stable influent P concentration of 20.0 mg/L, an HRT of 6 h, and alternating increases of influent calcium and ammonium, the final achieved nitrogen removal rate was 1.2 kg/m³/d and the P removal efficiency was 83.0%. The settleability of sludge was desirably enhanced with the calcium addition and a high biomass concentration was achieved in reactor. Quantitative and qualitative analyses confirmed that HAP was the main inorganic content in sludge, which could be harvested for P recovery. According to the Scanning Electron Microscope observation and the Energy Dispersive X-ray spectrometry analysis, the microbes were mainly distributed on the outer layer of the sludge aggregate, while the HAP mainly in the interior. The relevant theoretical calculation also revealed that the sludge discharge manipulation has direct effect on the sludge composition and aggregate structure. In sum, the results are evidence of the feasibility of simultaneous nitrogen removal and P recovery through one-stage PNA-HAP process for digestion effluent.

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.

In situ elimination of nitrite inhibition on AnAOB by acetate dosing in an up-flow granular anammox reactor

The inhibition of over-accumulated nitrite on anaerobic ammonium oxidation (anammox) activity has been widely reported and intensively studied. Surprisingly, there are limited researches on the strategy to deal with nitrite inhibition. In this work, to eliminate nitrite inhibition in an up-flow granular anammox reactor, acetate dosing (600 mg COD L^-1) and simultaneous acetate and denitrifying sludge dosing (600 mg COD L^-1 and 1.4 g dry weight L^-1) were implemented to temporarily activate microbial denitrification to reduce nitrite, respectively. In two strategies, reactor nitrogen removal and extracellular ATP were resumed to initial levels, while the recovery ratios of intracellular ATP and nitrite removal rate (67.1% and 15.6 mg N h^-1) of the former were higher than those (52.5% and 11.2 mg N h^-1) of the latter, indicating acetate dosing was more qualified to nitrite removal. Meanwhile, although a decrease of the dominated Ca. Brocadia from 30.7 to 25.8% was not reversed through high-throughput sequencing, acetate dosing did not cause denitrifiers proliferation. As easily implemented acetate dosing was as effective as direct discharge of inhibitory nitrite as the control strategy, it was recommended when nitrite inhibition happened. Additionally, an irregular behavior of nitrate overproduction via nitrite oxidation and the drastic increase of extracellular ATP were detected and proposed as the response of AnAOB to nitrite inhibition.

Characterization of membrane-bound metalloproteins in the anaerobic ammonium-oxidizing bacterium "Candidatus Kuenenia stuttgartiensis" strain CSTR1

Membrane-bound metalloproteins are the basis of biological energy conservation via respiratory processes, however, their biochemical characterization is difficult. Here, we followed a gel-based proteomics and metallomics approach to identify membrane-associated metalloproteins in the anaerobic ammonium-oxidizing "Candidatus Kuenenia stuttgartiensis" strain CSTR1. Membrane-associated protein complexes were separated by two dimensional Blue Native/SDS gel electrophoresis and subunits were identified by mass spectrometry; protein-bound metal ions were quantified from the gel by connecting either a desolvating nebulizer system or laser ablation to inductively coupled plasma triple quadrupole mass spectrometry (ICP-QqQ-MS). We identified most protein complexes predicted to be involved in anaerobic ammonium oxidation and carbon fixation. The ICP-QqQ-MS data showed the presence of Fe and Zn in a wide range of high molecular weight protein complexes (230-800 kDa). Mo was prominently found in gel slices with proteins of a size of 500-650 kDa, whereas Ni was only found using the desolvating nebulizer system in the protein range of 350-500 kDa. The detected protein complexes and their metal content were consistent with genome annotations. Gel-based metalloproteomics is a sensitive and reliable approach for the characterization of metalloproteins and could be used to characterize many multimeric metalloprotein complexes in biological systems.

Gel immobilization: A strategy to improve the performance of anaerobic ammonium oxidation (anammox) bacteria for nitrogen-rich wastewater treatment

Anaerobic ammonium oxidation (anammox) process appears a suitable substitute to nitrification-denitrification at a lower C/N ratios. Anammox is a chemolithoautotrophic process, belong to phylum Planctomycetes, and they are slow growing bacteria. Different strategies, e.g., biofilm formation, granulation and gel immobilization, have been applied to maintain a critical mass of bacterial cells in the system by avoiding washout from the bioreactor. Gel immobilization of anammox appears the best alternative to the natural process of biofilm formation and granulation. Polyvinyl alcohol-sodium alginate, polyethylene glycol, and waterborne polyurethane are the most reported materials used for the entrapment of anammox bacteria. However, dissolution of the gel beads refrains its application for long term bioprocess. Magnetic powder could coat on the surface of the beads which may increase the mechanical strength and durability of pellets. Application and problem of immobilization technology for the commercialization of this technology also addressed.

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.

Formation and function of bacterial organelles

Advances in imaging technologies have revealed that many bacteria possess organelles with a proteomically defined lumen and a macromolecular boundary. Some are bound by a lipid bilayer (such as thylakoids, magnetosomes and anammoxosomes), whereas others are defined by a lipid monolayer (such as lipid bodies), a proteinaceous coat (such as carboxysomes) or have a phase-defined boundary (such as nucleolus-like compartments). These diverse organelles have various metabolic and physiological functions, facilitating adaptation to different environments and driving the evolution of cellular complexity. This Review highlights that, despite the diversity of reported organelles, some unifying concepts underlie their formation, structure and function. Bacteria have fundamental mechanisms of organelle formation, through which conserved processes can form distinct organelles in different species depending on the proteins recruited to the luminal space and the boundary of the organelle. These complex subcellular compartments provide evolutionary advantages as well as enabling metabolic specialization, biogeochemical processes and biotechnological advances. Growing evidence suggests that the presence of organelles is the rule, rather than the exception, in bacterial cells.

Quantitative three-dimensional nondestructive imaging of whole anaerobic ammonium-oxidizing bacteria

Anaerobic ammonium-oxidizing (anammox) bacteria play a key role in the global nitrogen cycle and in nitrogenous wastewater treatment. The anammox bacteria ultrastructure is unique and distinctly different from that of other prokaryotic cells. The morphological structure of an organism is related to its function; however, research on the ultrastructure of intact anammox bacteria is lacking. In this study, in situ three-dimensional nondestructive ultrastructure imaging of a whole anammox cell was performed using synchrotron soft X-ray tomography (SXT) and the total variation-based simultaneous algebraic reconstruction technique (TV-SART). Statistical and quantitative analyses of the intact anammox bacteria were performed. High soft X-ray absorption composition inside anammoxosome was detected and verified to be relevant to iron-binding protein. On this basis, the shape adaptation of the anammox bacteria response to iron was explored.

Non-essentiality of canonical cell division genes in the planctomycete Planctopirus limnophila

Most bacteria divide by binary fission using an FtsZ-based mechanism that relies on a multi-protein complex, the divisome. In the majority of non-spherical bacteria another multi-protein complex, the elongasome, is also required for the maintenance of cell shape. Components of these multi-protein assemblies are conserved and essential in most bacteria. Here, we provide evidence that at least three proteins of these two complexes are not essential in the FtsZ-less ovoid planctomycete bacterium Planctopirus limnophila which divides by budding. We attempted to construct P. limnophila knock-out mutants of the genes coding for the divisome proteins FtsI, FtsK, FtsW and the elongasome protein MreB. Surprisingly, ftsI, ftsW and mreB could be deleted without affecting the growth rate. On the other hand, the conserved ftsK appeared to be essential in this bacterium. In conclusion, the canonical bacterial cell division machinery is not essential in P. limnophila and this bacterium divides via budding using an unknown mechanism.

A novel anammox granules-circulating expanded granular sludge bed reactor for the efficient circulation and retention of floating anammox granules

In application of anammox process, the operation of the conventional expanded granular sludge bed reactor (EGSB_conv.) is severely limited by the blocking and decay of floating anammox granules.To address this emerging issue, a novel three-phase separator configuration was designed and an anammox granules circulating EGSB (EGSB_GC) was proposed in this study. In the EGSB_GC, an influent scour on floating granules, whose effect was confirmed by simulation with a three-dimensional flow model, was obtained by integrating the external three-phase separator with the influent and the external cycle. After 166-d operation, the nitrogen removal efficiency of the EGSB_GC reached 75.6%, being 1.28-times that of the EGSB_conv. (58.9%). The sludge concentration in the main body of the EGSB_GC reached 3112 ± 65 mg/L, compared with 2613 ± 42 mg/L in the EGSB_conv. (p < 0.05). Moreover, the severe granules blockage and decay problem that is frequently encountered in the EGSB_conv. no longer occurred in the EGSB_GC. The relative abundance of anammox bacteria in granules from the three-phase separator of the EGSB_GC was 29.7%, significantly higher than that from the EGSB_conv. (16.1%, p < 0.05). The blockage and decay of granules in the three-phase separator of the EGSB_conv. led to an obvious proliferation of heterotrophic bacteria, with their relative abundance increased by 9.4% compared with the seed sludge (38.6% vs. 29.2%). This study proposed a practical three-phase separator configuration to sustain efficient and stable operation of anammox processes toward the promotion of granules circulation, retention and reaction.

A nitric oxide-binding heterodimeric cytochrome c complex from the anammox bacterium Kuenenia stuttgartiensis binds to hydrazine synthase

Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochromes called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme-binding motifs upon complex formation, a finding that may be of functional relevance, because NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex.

Successful operation performance and syntrophic micro-granule in partial nitritation and anammox reactor treating low-strength ammonia wastewater

The stable operation of the partial nitritation and anammox (PN/A) process is a challenge in the treatment of low-strength ammonia wastewater like sewage mainstream. This study demonstrated the feasibility of achieving stable operation in the treatment of 50 mg/L ammonia wastewater with a micro granule-based PN/A reactor. The long-term operation results showed nitrogen removal efficiencies of 71.8 ± 9.9% were stably obtained under a relatively short hydraulic retention time (HRT) of 2 h. The analysis on the physicochemical properties of the granules indicated most of the granules were in a size in a range of 265-536 μm, and the elementary composition of the granules was determined to be CH_1.61O_0.61N_0.17S_0.01P_0.03. The microbial analysis revealed Candidatus Kuenenia stuttgartiensis anammox bacteria and Nitrosomonas-like AOB were the two most dominant bacteria with 27.6% and 10.5% abundance, respectively, both of which formed spatially syntrophic co-immobilization within the micro-granules. The ex-situ activity tests showed the activity of NOB was well limited through DO regulation in the reactor. These results provide an alternative PN/A process configuration for low-strength wastewater treatment by sustaining microstate granules. Optimization of the nitrogen sludge loading rate and DO regulation are important for the successful performance.

A secret of high-rate mass transfer in anammox granular sludge: "Lung-like breathing"

The granulation of anaerobic ammonium oxidation (Anammox) biomass can play a key role in developing stable and high-rate working of anammox process. It is important to know the working mechanism of anammox granular sludge (AnGS) for the optimization of reactor performance. In this study, a "lung-like breathing" determinator was invented to investigate the working behavior of AnGS in the bioreactor. The results showed that the AnGS had a regular expansion and contraction phenomenon, which was called "lung-like breathing". With the biological loading rate (BLR) at 0.114 kg-N/(kg-VSS·d), the expansion and contraction amplitude (ExCA) was 1.29 ± 0.05%, and the expansion and contraction frequency (ExCF) was 39.3 ± 1.6 times/h. The AnGS cultivated in a bioreactor with higher nitrogen removal rate (NRR) was found to have the higher ExCA and ExCF when determinated at the same BLR, and the "lung-like breathing" behavior of one type of AnGS was revealed to bear a significantly (p < 0.05) positive correlation with the specific anammox activity (SAA). The mass transfer flux from "lung-like breathing" was far greater than that from molecular diffusion, which was regarded as a vital mechanism for the AnGS to demonstrate its high activity. These findings provided theoretical basis and technical parameters for the optimization of anammox nitrogen removal process.

Effect of external hydrazine addition on anammox reactor start-up time

Hydrazine is an intermediate product of the anaerobic ammonium oxidation (Anammox) process where both ammonium and nitrite in wastewater are converted to nitrogen gas by bacteria. In this study the effect of external hydrazine addition (5, 10, 15, and 20 mg/L) on the start-up period of the Anammox process was studied using sequencing batch reactors (SBRs). The SBR with an addition of 10 mg/L hydrazine took only 7 weeks to stabilize and achieve the maximum removal of ammonium and nitrite, whereas the SBR without the addition of hydrazine took 12 weeks. The amount of Heme C extracted from the biomass indicated that externally added hydrazine accelerated the growth of Anammox bacteria and reduced the release of nitrous oxide gas from the reactors.

Anammox bacteria exhibit capacity to withstand long-term starvation stress: A proteomic-based investigation of survival mechanisms

Although anammox bacteria are commonly exposed to long-term starvation during transportation and preservation process, physiological changes in these organisms during long-term starvation are not well understood, nor are the molecular bases of their starvation survival strategies. To reveal survival mechanisms during long-term anaerobic and anoxic starvation (60 days at 20 ± 1 °C), metaproteomic technology was utilized to identify differentially expressed proteins in Candidatus Kuenenia stuttgartiensis. Our results showed that Candidatus Kuenenia stuttgartiensis exhibits a capacity to withstand long-term starvation stress. Although activity decay rates of 0.0129 d^-1 and 0.0049 d^-1 were observed for anammox sludge in anoxic and anaerobic starvation, the relative abundance of Candidatus Kuenenia stuttgartiensis, the shape of anammox granules, and the fraction of viable cells remained constant under both anaerobic and anoxic starvation conditions. Metaproteomics results illustrated that Candidatus Kuenenia stuttgartiensis maintained stable levels of most intracellular proteins, especially enzymes involved in principal metabolic pathways after 60-d of anaerobic or anoxic starvation, thereby allowing cells to regain metabolic activities once substrates became available. Induction of starvation proteins could be a survival strategy employed by Candidatus Kuenenia stuttgartiensis to resist long-term starvation stresses. During anaerobic starvation, 34 proteins were upregulated, five of which were associated with carbohydrate catabolism and oxidation of organic compounds, thereby increasing potential for utilization of endogenous carbon sources to produce energy. During anoxic starvation, only two proteins were upregulated, which may be attributed to insufficient energy for the synthesis of starvation-induced proteins.

Enhancement of the adaptability of anammox granules to zinc shock by appropriate organic carbon treatment

Heavy metals, which are commonly present in high ammonia-containing wastewater, can cause inhibitory effects to anammox reaction. This study proposes a novel approach to enhance the adaptability of anammox granules to heavy metal [Zn(II)] shock by organic carbon (sodium acetate, NaAc) treatment, paying special attention to optimization of the treatment dosage and duration. For granules treated with 200 mg chemical oxygen demand (COD)/L NaAc for 2 d, the activity recovery (six cycles) efficiency after Zn(II) (40 mg/L) shock reached 127.4%. The extracellular polymeric substance (EPS) production increased by 168% and heterotrophic bacteria mildly proliferated (increased by 14%) in such granules compared with the control. The dramatic recovery capacity was likely due to the entrapment and barrier function of EPS and the outer-layer proliferated heterotrophic bacteria. This finding offers a useful process to enable maximum adaptability of anammox granules from heavy metals shocks, allowing anammox technology to be more widely applied.

A metabolomic view of how low nitrogen strength favors anammox biomass yield and nitrogen removal capability

The low yield of anaerobic ammonium oxidation (anammox) biomass has attracted great attention because of its difficulty to be abundantly enriched. Patterns of substrate supply greatly influence microbial metabolism and behavior. The present study proposed that low nitrogen strength was beneficial to anammox biomass yield and nitrogen removal when comparing a membrane bioreactor (MBR) operated at low nitrogen strength with short hydraulic retention time (HRT) (R-low; influent: fixed at 100 mg-N L^-1) and one operated at high nitrogen strength with long HRT (R-stepwise; influent: 100-700 mg-N L^-1). Different nitrite concentrations in the two MBRs would indicate discrepant environments, and inevitably resulted in the discrepant microbial responses for anammox community. In particular, we found that at low nitrogen strength, increased activities of purine and pyrimidine metabolism pathways provided more abundant nucleic acids for bacterial proliferation. More active reaction of lipid and protein synthesis favored the synthesis of cellular structure. Importantly, the metabolism of cheaper amino acids was more active under low nitrogen strength, which was coupled with higher metabolic flux and potentially more active exchange of costly amino acids as public goods. In this way, more energy could be saved and applied to biomass yield. Higher active bacterial diversity and more positive interactions among bacterial species in R-low further favored biomass yield and nitrogen removal. The present study highlighted the significant effect of substrate supply patterns on anammox, which is meaningful to overcome the current bottleneck of deficient anammox biomass for application in wastewater treatment.

Organelle Formation in Bacteria and Archaea

Uncovering the mechanisms that underlie the biogenesis and maintenance of eukaryotic organelles is a vibrant and essential area of biological research. In comparison, little attention has been paid to the process of compartmentalization in bacteria and archaea. This lack of attention is in part due to the common misconception that organelles are a unique evolutionary invention of the "complex" eukaryotic cell and are absent from the "primitive" bacterial and archaeal cells. Comparisons across the tree of life are further complicated by the nebulous criteria used to designate subcellular structures as organelles. Here, with the aid of a unified definition of a membrane-bounded organelle, we present some of the recent findings in the study of lipid-bounded organelles in bacteria and archaea.

Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy

Phylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multicelled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches, including correlative fluorescence in situ hybridization-electron microscopy (FISH-EM), transmission electron microscopy (TEM), and serial block face scanning electron microscopy (SBEM) three-dimensional (3D) reconstructions. FISH-EM of methane seep-derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortium types revealed cellular volumes of ANME and their symbiotic partners that were larger than previous estimates based on light microscopy. Polyphosphate-like granule-containing ANME (tentatively termed ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell, and the volume of the cell was larger in proportion to the number of granules inside it, but the percentage of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their ability to perform anaerobic methane oxidation.IMPORTANCE Methane oxidation in anaerobic environments can be accomplished by a number of archaeal groups, some of which live in syntrophic relationships with bacteria in structured consortia. Little is known of the distinguishing characteristics of these groups. Here, we applied imaging approaches to better understand the properties of these cells. We found unexpected morphological, structural, and volume variability of these uncultured groups by correlating fluorescence labeling of cells with electron microscopy observables.