A 192-heme electron transfer network in the hydrazine dehydrogenase complex

The core anammox redox reaction system of 12 anammox bacterial genera and their evolution and application implications

Anaerobic ammonium-oxidation (anammox) is a typical redox reaction driven by membrane electron transformation. However, the electron transfer mechanism of the core redox reaction and its evolutionary origins are still not thoroughly identified. In this study, a preliminary analysis was conducted for such interaction based on the 64 anammox bacterial genomes representing 12 genera available currently. The results suggested that enzymes involved in anammox reaction share the similar catalytic and electron transfer modes in different lineages, while the electron-carrying proteins shuttled between membrane and soluble enzymes are very different. A comparatively simple electronic shuttle protein system was encoded in the early-branching groundwater lineages Candidatus (Ca.) Avalokitesvara and Ca. Tripitaka, which was replaced by a sophisticated electron carrier scheme in the late-branching marine and terrestrial groups within family Ca. Brocadiaceae. Remarkably, the increasing availability of nitrite after Great Oxidation Event (GOE) potentially drove the adaptive evolution of the core redox systems by successively recruiting the nitrite reductase (NIR) for nitrite balance, a stable complex of two small cytochrome c proteins (NaxL and NaxS homologues) for electron transfer to HZS, as well as optimizing the structure of nitrite oxidoreductase gamma (NxrC) for electron conservation. In particular, a tubule-inducing nitrite oxidoreductase subunit (NxrT homologue) was further formed for electron transformation after the Neoproterozoic Oxygenation Event (NOE). Finally, based on two full-scale anammox-based wastewater treatment systems (WWTPs), we identified core gene transcriptional activities affecting the abundance of the family Ca. Brocadiaceae and their association with environmental factors. Overall, our study not only provides key information for understanding the dynamic patterns and evolutionary mechanisms of the anammox reactions and the associated electron transfers in conjunction with major geological events, but also provides new insights for future enrichment and effective applications.

Cytochrome "nanowires" are physically limited to sub-picoamp currents that suffice for cellular respiration

Mineral-respiring microorganisms from hydrothermal vents to terrestrial soils express filaments that electrically connect intracellular respiration to extracellular geochemistry. Filaments dubbed "cytochrome nanowires" (CNs) have been resolved by CryoEM, but whether they are the two-decades-long sought-after physiological "nanowires" remains unproven. To assess their functional competence, we analyzed biological redox conduction in all CNs by computing driving forces in the presence of redox anti-cooperativities, reorganization energies with electronic polarizability, and Marcus rates for diffusive and protein-limited flux models. The chain of heme cofactors in any CN must be densely packed to realize weak (≤0.01 eV) electronic coupling for electron transfer, as evidenced by a single Soret band produced from coincidental absorptions on multiple hemes. Dense packing, in turn, has three consequences: (1) limited driving forces (≤|0.3| eV) due to shared electrostatic microenvironments, (2) strong (≤0.12 eV) redox anti-cooperativities that would accentuate the free energy landscape if the linear heme arrangement did not dictate a contra-thermodynamic oxidation order, and (3) an entropic penalty that is offset by thioether 'tethers' of the hemes to the protein backbone. These linkages physically necessitate the rate-throttling T-stacked motif (10-fold slower than the other highly conserved slip-stacked motif). If the sequence of slip- and T-stacked hemes in the CNs had the fastest known nanosecond rates at every step, a micron-long filament would carry a diffusive 0.02 pA current at a physiological 0.1 V, or a protein-limited current of 0.2 pA. Actual CNs have sub-optimal (≤102-fold lower), but sufficient conductivities for cellular respiration, with at most thousands of filaments needed for total cellular metabolic flux. Reported conductivities once used to argue for metallic-like pili against the cytochrome hypothesis and now attributed to CNs remain inconsistent by 102-105-fold with the physical constraints on biological redox conduction through multiheme architectures.

Fractionating proteins with nitrite-reducing activity in "Candidatus Kuenenia stuttgartiensis" strain CSTR1

The anammox bacteria "Candidatus Kuenenia stuttgartiensis" (Ca. Kuenenia) are able to gain energy by combining ammonium and nitrite to produce nitrogen gas, which is an ecologically and technically significant activity process. In this reaction, nitric oxide serves as a recognized intermediate in the reduction of nitrite, which is subsequently combined with ammonium to produce hydrazine. However, the enzyme that converts nitrite to nitric oxide remains elusive. In this study, we investigated the nitrite-reducing activity in "Ca. Kuenenia stuttgartiensis" strain CSTR1 to identify candidates for such an enzyme. An optimized in vitro assay was established to measure nitrite-reducing activities, with which we followed the activity in protein fractions obtained from various fractionation methods. Separation of the cell extract of strain CSTR1 with size exclusion chromatography yielded active fractions corresponding to a molecular size range of 150-200 kDa. Several proteins coeluted with the nitrite-reducing activity, including the hydroxylamine dehydrogenase HOX, an NADP-dependent isopropanol dehydrogenase (Adh), an electron-transfer 4Fe-4S subunit protein (Fcp), and a nitric oxide detoxifying flavorubredoxin (NorVW). However, further separation of the cell extract with anion exchange chromatography, resulted in much lower activity yields, and activities were distributed among several fractions. In addition, fractionation of cell extracts using ultracentrifugation and ultrafiltration linked the activity to HOX, but could not exclude the involvement of other proteins in the activity. Overall, our results suggest that the molecular mechanism for nitrite reduction in "Ca. Kuenenia" strains is more complex than that currently described in the literature. Nitrite reduction appears to be strongly associated with HOX but may additionally require the participation of other proteins.

A powerful but frequently overlooked role of thermodynamics in environmental microbiology: inspirations from anammox

Thermodynamics has long been applied in predicting undiscovered microorganisms or analyzing energy flows in microbial metabolism, as well as evaluating microbial impacts on global element distributions. However, further development and refinement in this interdisciplinary field are still needed. This work endeavors to develop a whole-cycle framework integrating thermodynamics with microbiological studies, focusing on representative nitrogen-transforming microorganisms. Three crucial concepts (reaction favorability, energy balance, and reaction directionality) are discussed in relation to nitrogen-transforming reactions. Specifically, reaction favorability, which sheds lights on understanding the diversity of nitrogen-transforming microorganisms, has also provided guidance for novel bioprocess development. Energy balance, enabling the quantitative comparison of microbial energy efficiency, unravels the competitiveness of nitrogen-transforming microorganisms under substrate-limiting conditions. Reaction directionality, revealing the niche-differentiating patterns of nitrogen-transforming microorganisms, provides a foundation for predicting biogeochemical reactions under various environmental conditions. This review highlights the need for a more comprehensive integration of thermodynamics in environmental microbiology, aiming to comprehensively understand microbial impacts on the global environment from micro to macro scales.

Recent advances in isolation and physiological characterization of planktonic anaerobic ammonia-oxidizing bacteria

Anaerobic ammonia oxidation (anammox) is widely regarded as an efficient biological nitrogen removal technology and is increasingly applied in wastewater treatment processes. However, the long doubling time and sensitivity to environmental pressures of anaerobic ammonia-oxidizing bacteria (AnAOB) often lead to unstable nitrogen removal performance. Various combined processes are being explored to overcome these limitations, providing insights into the ecological, physiological, and biochemical characteristics of AnAOB. Nevertheless, due to the lack of AnAOB pure cultures, the mechanisms of nitrogen metabolism, growth regulation, and cell communication remain unclear. This review highlights the unique physiological structures of AnAOB, current techniques for isolating and enriching planktonic AnAOB, and the associated challenges. A deeper understanding of these aspects offers guidance for improving planktonic AnAOB enrichment and incubation.

Scavenging of reactive oxygen species in Candidatus Brocadia fulgida through nanocompartments

The antioxidant defense mechanisms for anaerobic ammonia oxidation (anammox) bacteria are still unclear. In this study, the potential antioxidant ability of nanocompartments in Candidatus Brocadia fulgida to typical reactive oxygen species (ROS) was investigated. The results showed that the copies of genes involved in anammox central metabolism were inhibited with hydrogen peroxide (H2O2), while the genes encoded putative anti-oxidative protein (nanocompartments and cargo HAO) up-regulated. The genetically engineered bacteria grew better and maintained the lower ROS levels (65.60 %-78.07 %) and higher electron transport activities (∼5-21 times) than the wild bacteria under H2O2 stimulus. Molecular docking confirmed that nanocompartment proteins could provide diverse sites to bind with H2O2 based on heme as the redox center. Additionally, the nanocompartments induced up-regulation of multiple protective pathways for coping with oxidative stress from H2O2, including antioxidant enzymes and other non-enzymatic pathways. Thus, the heme-containing nanocompartments presented great potential in preventing and relieving oxidative stress.

Multi-dimensional perspectives into the pervasive role of microbial extracellular polymeric substances in electron transport processes

During the process of biological treatment, most microorganisms are encapsulated in extracellular polymeric substances (EPS), which protect the cell from adverse environments and aid in microbial attachment. Microorganisms utilize extracellular electron transfer (EET) for energy and information interchange with other cells and the outside environment. Understanding the role of steric EPS in EET is critical for studying microbiology and utilizing microorganisms in biogeochemical processes, pollutant transformation, and bioenergy generation. However, the current study shows that understanding the roles of EPS in the EET processes still needs a great deal of research. In view of recent research, this work aims to systematically summarize the production and functional group composition of microbial EPS. Additionally, EET pathways and the role of EPS in EET processes are detailed. Then factors impacting EET processes in EPS are then discussed, with a focus on the spatial structure and composition of EPS, conductive materials and environmental pollution, including antibiotics, pH and minerals. Finally, strategies to enhance EET, as well as current challenges and future prospects are outlined in detail. This review offers novel insights into the roles of EPS in biological electron transport and the application of microorganisms in pollutant transformation.

A survey of the Desulfuromonadia "cytochromome" provides a glimpse of the unexplored diversity of multiheme cytochromes in nature

BACKGROUND

Multiheme cytochromes c (MHC) provide prokaryotes with a broad metabolic versatility that contributes to their role in the biogeochemical cycling of the elements and in energy production in bioelectrochemical systems. However, MHC have only been isolated and studied in detail from a limited number of species. Among these, Desulfuromonadia spp. are particularly MHC-rich. To obtain a broad view of the diversity of MHC, we employed bioinformatic tools to study the cytochromome encoded in the genomes of the Desulfuromonadia class.

RESULTS

We found that the distribution of the MHC families follows a different pattern between the two orders of the Desulfuromonadia class and that there is great diversity in the number of heme-binding motifs in MHC. However, the vast majority of MHC have up to 12 heme-binding motifs. MHC predicted to be extracellular are the least conserved and show high diversity, whereas inner membrane MHC are well conserved and show lower diversity. Although the most prevalent MHC have homologues already characterized, nearly half of the MHC families in the Desulforomonadia class have no known characterized homologues. AlphaFold2 was employed to predict their 3D structures. This provides an atlas of novel MHC, including examples with high beta-sheet content and nanowire MHC with unprecedented high numbers of putative heme cofactors per polypeptide.

CONCLUSIONS

This work illuminates for the first time the universe of experimentally uncharacterized cytochromes that are likely to contribute to the metabolic versatility and to the fitness of Desulfuromonadia in diverse environmental conditions and to drive biotechnological applications of these organisms.

Monitoring the Biochemical Activity of Single Anammox Granules with Microbarometers

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

Copper sulfide mineral performs non-enzymatic anaerobic ammonium oxidation through a hydrazine intermediate

Anaerobic ammonium oxidation (anammox)-the biological process that activates ammonium with nitrite-is responsible for a significant fraction of N2 production in marine environments. Despite decades of biochemical research, however, no synthetic models capable of anammox have been identified. Here we report that a copper sulfide mineral replicates the entire biological anammox pathway catalysed by three metalloenzymes. We identified a copper-nitrosonium {CuNO}10 complex, formed by nitrite reduction, as the oxidant for ammonium oxidation that leads to heterolytic N-N bond formation from nitrite and ammonium. Similar to the biological process, N2 production was mediated by the highly reactive intermediate hydrazine, one of the most potent reductants in nature. We also found another pathway involving N-N bond heterocoupling for the formation of hybrid N2O, a potent greenhouse gas with a unique isotope composition. Our study represents a rare example of non-enzymatic anammox reaction that interconnects six redox states in the abiotic nitrogen cycle.

Recovery strategies and mechanisms of anammox reaction following inhibition by environmental factors: A review

Anaerobic ammonium oxidation (anammox) is a promising biological method for treating nitrogen-rich, low-carbon wastewater. However, the application of anammox technology in actual engineering is easily limited by environmental factors. Considerable progress has been investigated in recent years in anammox restoration strategies, significantly addressing the challenge of poor reaction performance following inhibition. This review systematically outlines the strategies employed to recover anammox performance following inhibition by conventional environmental factors and emerging pollutants. Additionally, comprehensive summaries of strategies aimed at promoting anammox activity and enhancing nitrogen removal performance provide valuable insights into the current research landscape in this field. The review contributes to a comprehensive understanding of restoration strategies of anammox-based technologies.

Ferroheme/Ferriheme Directly Involved in the Synthesis and Decomposition of Hydrazine as an Electron Carrier during Anammox

Anammox bacteria performed the reaction of NH4+ and NO with hydrazine synthase to produce N2H4, followed by the decomposition of N2H4 with hydrazine dehydrogenase to generate N2. Ferroheme/ferriheme, which serves as the active center of both hydrazine synthase and hydrazine dehydrogenase, is thought to play a crucial role in the synthesis and decomposition of N2H4 during Anammox due to its high redox activity. However, this has yet to be proven and the exact mechanisms by which ferroheme/ferriheme is involved in the Anammox process remain unclear. In this study, abiotic and biological assays confirmed that ferroheme participated in NH4+ and NO reactions to generate N2H4 and ferriheme, and the produced N2H4 reacted with ferriheme to generate N2 and ferroheme. In other words, the ferroheme/ferriheme cycle drove the continuous reaction between NH4+ and NO. Raman, ultraviolet-visible spectroscopy, and X-ray absorption fine structure spectroscopy confirmed that ferroheme/ferriheme is involved in the synthesis and decomposition of N2H4 via the core FeII/FeIII cycle. The mechanism of ferroheme/ferriheme participation in the synthesis and decomposition of N2H4 was proposed by density functional theory calculations. These findings revealed for the first time the heme electron transfer mechanisms, which are of great significance for deepening the understanding of Anammox.

Improving anammox activity and reactor start-up speed by using CO2/NaHCO3 buffer

Anammox bacteria grow slowly and can be affected by large pH fluctuations. Using suitable buffers could make the start-up of anammox reactors easy and rapid. In this study, the effects of three kinds of buffers on the nitrogen removal and growth characteristics of anammox sludge were investigated. Reactors with CO2/NaHCO3 buffer solution (CCBS) performed the best in nitrogen removal, while 4-(2-hydroxyerhyl)piperazine-1-ethanesulfonic acid (HEPES) and phosphate buffer solution (PBS) inhibited the anammox activity. Reactors with 50 mmol/L CCBS could start up in 20 days, showing the specific anammox activity and anammox activity of 1.01±0.10 gN/(gVSS·day) and 0.83±0.06 kgN/(m3·day), respectively. Candidatus Kuenenia was the dominant anammox bacteria, with a relative abundance of 71.8%. Notably, anammox reactors could also start quickly by using 50 mmol/L CCBS under non-strict anaerobic conditions. These findings are meaningful for the quick start-up of engineered anammox reactors and prompt enrichment 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.

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.

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

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

Microbial divergence and evolution. The case of anammox bacteria

Species differentiation and the appearance of novel diversity on Earth is a major issue to understand the past and future of microbial evolution. Herein, we propose the analysis of a singular evolutive example, the case of microorganisms carrying out the process of anammox (anaerobic ammonium oxidation). Anammox represents a singular physiology active on Earth from ancient times and, at present, this group is still represented by a relatively limited number of species carrying out a specific metabolism within the Phylum Planctomycetota. The key enzyme on the anammox pathway is hydrazine dehydrogenase (HDH) which has been used as a model in this study. HDH and rRNA (16S subunit) phylogenies are in agreement suggesting a monophyletic origin. The diversity of this singular phylogenetic group is represented by a few enriched bacterial consortia awaiting to be cultured as monospecific taxa. The apparent evolution of the HDH genes in these anammox bacteria is highly related to the diversification of the anammox clades and their genomes as pointed by phylogenomics, their GC content and codon usage profile. This study represents a clear case where bacterial evolution presents a paralleled genome, gene and species diversification through time from a common ancestor; a scenario that most times is masked by a web-like phylogeny and the huge complexity within the prokaryotes. Besides, this contribution suggests that microbial evolution of the anammox bacteria has followed an ordered, vertical diversification through Earth history and will present a potentially similar speciation fate in the future.

Multipathway of Nitrogen Metabolism Revealed by Genome-Centered Metatranscriptomics from Pyrite-Guided Mixotrophic Partial Denitrification/Anammox Installations

Further reducing the organic requirements is essential for the sustainable development of partial denitrification/anammox technology. Here, an innovative mixotrophic partial denitrification/anammox (MPD/A) installation fed with pyrite and few organics was realized, and the average nitrogen and phosphorus removal rates were as high as 96.24 ± 0.11% and 79.23 ± 2.06%, respectively, with a C/N ratio of 0.5. To understand the nature by which MPD/A achieves efficient nitrogen removal and organic conservation, the electron transfer-dependent nitrogen escape and energy metabolism were first elucidated using multiomics analysis. Apart from heterotrophic denitrification and anammox, the results revealed some unexpected metabolic couplings of MPD/A systems, in particular, putative nitrate-dependent organic and pyrite oxidation among nominally heterotrophic Denitratisoma (PRO3) strains, which accelerated nitrate gasification with a low-carbon supply. Additionally, Candidatus Brocadia (AMX) employed extracellular solid-state electron acceptors as terminal electron sinks for high-rate ammonium removal. AMX transported ammonium electrons to extracellular γFeO(OH) (generated from pyrite oxidation) through the transient storage of menaquinoline pools, cytoplasmic migration via multiheme cytochrome(s), and OmpA protein/nanowires-mediated electron hopping on cell surfaces. Further investigation observed that extracellular electron flux resulted in the transfer of more energy from the increased oxidation of the electron donor to the ATP, supporting nitrite-independent ammonium removal.

Anodic ammonium oxidation in microbial electrolysis cell: Towards nitrogen removal in low C/N environment

Biological nitrogen removal in low C/N environment is challenging in wastewater treatment for a long time. Autotrophic ammonium oxidation is promising due to the no need of carbon source addition, but alternative electron acceptors other than oxygen has to be widely investigated. Recently, microbial electrolysis cell (MEC), which applies a polarized inert electrode as the electron harvester, has been proved effective to oxidize ammonium with electroactive biofilm. That is, anodic microbes stimulated by exogenous low power can extract electron from ammonium and transfer electron to electrodes. This review aims to consolidate the recent advances in anodic ammonium oxidation in MEC. Various technologies based on different functional microbes and mechanisms of these processes are reviewed. Thereafter, the crucial factors influencing the ammonium oxidation technology are discussed. Challenges and prospects of anodic ammonium oxidation in ammonium-containing wastewater treatment are also proposed to provide valuable insights on the technologic reference and potential value of MEC in ammonium-containing wastewater treatment.

Extracellular cytochrome nanowires appear to be ubiquitous in prokaryotes

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens, recently identified as extracellular cytochrome nanowires (ECNs), have received wide attention due to numerous potential applications. However, whether other organisms employ similar ECNs for electron transfer remains unknown. Here, using cryoelectron microscopy, we describe the atomic structures of two ECNs from two major orders of hyperthermophilic archaea present in deep-sea hydrothermal vents and terrestrial hot springs. Homologs of Archaeoglobus veneficus ECN are widespread among mesophilic methane-oxidizing Methanoperedenaceae, alkane-degrading Syntrophoarchaeales archaea, and in the recently described megaplasmids called Borgs. The ECN protein subunits lack similarities in their folds; however, they share a common heme arrangement, suggesting an evolutionarily optimized heme packing for efficient electron transfer. The detection of ECNs in archaea suggests that filaments containing closely stacked hemes may be a common and widespread mechanism for long-range electron transfer in both prokaryotic domains of life.

Light-driven ammonium oxidation to dinitrogen gas by self-photosensitized biohybrid anammox systems

The anaerobic ammonium oxidation (anammox) process exerts a very vital role in the global nitrogen cycle (estimated to contribute 30%-50% N₂ production in the oceans) and presents superiority in water/wastewater nitrogen removal performance. Until now, anammox bacteria can convert ammonium (NH₄⁺) to dinitrogen gas (N₂) with nitrite (NO₂^-), nitric oxide (NO), and even electrode (anode) as electron acceptors. However, it is still unclear whether anammox bacteria could utilize photoexcited holes as electron acceptors to directly oxide NH₄⁺ to N₂. Here, we constructed an anammox-cadmium sulfide nanoparticles (CdS NPs) biohybrid system. The photoinduced holes from the CdS NPs could be utilized by anammox bacteria to oxidize NH₄⁺ to N₂. ¹⁵N-isotope labeling experiments demonstrated that NH₂OH instead of NO was the real intermediate. Metatranscriptomics data further proved a similar pathway for NH₄⁺ conversion with anodes as electron acceptors. This study provides a promising and energy-efficient alternative for nitrogen removal from water/wastewater.

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.

Structural biology of proteins involved in nitrogen cycling

Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.

Carrier type affects anammox community assembly, species interactions and nitrogen conversion

The impacts of carrier type on anammox community assembly, species interactions and nitrogen conversion were studied in this work. It was found that in addition to shared species with higher abundance, different carrier types recruited rare species by imposing selection pressure. Results from co-occurrence networks revealed that carrier type strongly influenced interactions between keystone species inhabiting within anammox biofilm through potentially inducing niche differences. Overall, elastic cubic sponges would lead to closer cooperation between different populations, whereas plastic hollow cylinders would trigger fiercer competition. Meanwhile, the results based on metagenomics sequencing showed carrier type significantly affected nitrogen conversion related genes abundances, and higher reads number was detected on the elastic cubic sponges. The information obtained in this work could provide some valuable information for the selection and optimization of carrier type in the anammox process.

Effects of biochar on anaerobic treatment systems: Some perspectives

Many anaerobic activities involve carbon, nitrogen, iron, and sulfur cycles. As a well-developed porous material with abundant functional groups, pyrolytic biochar has been widely researched in efforts to promote microbial activities. However, the lack of consensus on the biochar mechanism has limited its practical application. This review summarizes the effects of different pyrolysis temperatures, particle sizes, and dosages of biochar on microbial activities and community in Fe(III) reduction, anaerobic digestion, nitrogen removal, and sulfate reduction systems. It was found that biochar could promote anaerobic activities by stimulating electron transfer, alleviating toxicity, and providing suitable habitats for microbes. However, it inhibits microbial activities by releasing heavy metal ions or persistent free radicals and adsorbing signaling molecules. Finding a balance between the promotion and inhibition of biochar is therefore essential. This review provides valuable perspectives on how to achieve efficient and stable use of biochar in anaerobic systems.

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.

Phylogenomic Evidence for the Origin of Obligate Anaerobic Anammox Bacteria Around the Great Oxidation Event

The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32-2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.

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

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

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.

Anaerobic ammonium oxidation (anammox) promoted by pyrogenic biochar: Deciphering the interaction with extracellular polymeric substances (EPS)

Efficient biological nitrogen removal (BNR) by anaerobic ammonium oxidation (anammox) can be achieved with presence of redox-active pyrogenic biochar that potentially acting as an insoluble electron acceptor. Anammox bacteria and other symbiotic consortia are surrounded by extracellular polymeric substances (EPS) forming aggregate architecture, which also contains electrochemical-active biomolecules such as aromatic proteins and humic substances. Therefore, understanding the role of EPS is necessary in biochar-promoting anammox process. Herein, we investigated the influence of biochar with granular-sized (GP) and micrometer-sized (MP) particle sizes on microbiology and characteristics of EPS in anammox sludge. Addition of GP and MP biochar not only improved the BNR efficiency by 17.5% and 34.6%, respectively, but also increased the relative abundance of Candidatus Brocadia. The bulk and bound EPS contents substantially decreased in biochar-amended groups, while more slime EPS was produced. Spectroscopic (FTIR, Raman, and circular dichroism) and electrochemical (voltammetry and impedance spectrum) analyses revealed that biochar addition enhanced the structural integrity and electron-transfer capability of anammox sludge. EPS depletion led to a steep decrease in BNR efficiency (21.5% vs 83.0% with EPS-retained sludge), whereas it resumed to 42.1% in the presence of MP biochar. Electron transport system activity data showed that biochar replenished the loss of anaerobic respiration metabolism due to EPS depletion. In summary, these results suggested that EPS possibly work as transient mediator for shuttling electrons from ammonium oxidation to soluble (nitrite) and insoluble electron acceptors (redox-active biochar).

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen

Since the characterization of cytochrome c₅₅₂ as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH₄⁺ produced from NO₂^- is released as NH₃ leading to nitrogen loss, similar to denitrification which generates NO, N₂O, and N₂. NH₄⁺ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO₂^- to NH₄⁺, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.

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.

Specificity of Small c-Type Cytochromes in Anaerobic Ammonium Oxidation

Anaerobic ammonium oxidation (anammox) is a bacterial process in which ammonium and nitrite are combined into dinitrogen gas and water, yielding energy for the cell. This process relies on a series of redox reactions catalyzed by a set of enzymes, with electrons being shuttled to and from these enzymes, likely by small cytochrome c proteins. For this system to work productively, these electron carriers require a degree of specificity toward the various possible redox partners they encounter in the cell. Here, we compare two cytochrome c proteins from the anammox model organism Kuenenia stuttgartiensis. We show that they are highly homologous, are expressed at comparable levels, share the same fold, and display highly similar redox potentials, yet one of them accepts electrons from the metabolic enzyme hydroxylamine oxidase (HAO) efficiently, whereas the other does not. An analysis of the crystal structures supplemented by Monte Carlo simulations of the transient redox interactions suggests that this difference is at least partly due to the electrostatic field surrounding the proteins, illustrating one way in which the electron carriers in anammox could attain the required specificity. Moreover, the simulations suggest a different "outlet" for electrons on HAO than has traditionally been assumed.

The Steady March toward Biomimetic Nanoelectronics

Steady progress is being made in unveiling nature's long-range charge transport mechanisms in redox proteins and in the development of versatile self-assembling scaffolds and de novo proteins by design-two separate fields that soon may intersect to yield the first artificial bioelectronic wires. Here, we summarize compelling developments in these areas that put a spotlight on the prospect of their convergence, featuring, in particular, work by Dai et al. in this issue of ACS Nano that illustrates success in intentional design with nuanced control, binding multiple c-type hemes into a specific ordered array bearing the essential hallmarks of heme chains in bacterial multiheme cytochromes.

Protein-Embedded Metalloporphyrin Arrays Templated by Circularly Permuted Tobacco Mosaic Virus Coat Proteins

Bioenergetic processes in nature have relied on networks of cofactors for harvesting, storing, and transforming the energy from sunlight into chemical bonds. Models mimicking the structural arrangement and functional crosstalk of the cofactor arrays are important tools to understand the basic science of natural systems and to provide guidance for non-natural functional biomaterials. Here, we report an artificial multiheme system based on a circular permutant of the tobacco mosaic virus coat protein (cpTMV). The double disk assembly of cpTMV presents a gap region sandwiched by the two C₂-symmetrically related disks. Non-native bis-his coordination sites formed by the mutation of the residues in this gap region were computationally screened and experimentally tested. A cpTMV mutant Q101H was identified to create a circular assembly of 17 protein-embedded hemes. Biophysical characterization using X-ray crystallography, cyclic voltammetry, and electron paramagnetic resonance (EPR) suggested both structural and functional similarity to natural multiheme cytochrome c proteins. This protein framework offers many further engineering opportunities for tuning the redox properties of the cofactors and incorporating non-native components bearing varied porphyrin structures and metal centers. Emulating the electron transfer pathways in nature using a tunable artificial system can contribute to the development of photocatalytic materials and bioelectronics.

Purification of the key enzyme complexes of the anammox pathway from DEMON sludge

Anaerobic Ammonium Oxidation ("anammox") is a bacterial process in which nitrite and ammonium are converted into nitrogen gas and water, yielding energy for the cell. Anammox is an important branch of the global biological nitrogen cycle, being responsible for up to 50% of the yearly nitrogen removal from the oceans. Strikingly, the anammox process uniquely relies on the extremely reactive and toxic compound hydrazine as a free intermediate. Given its global importance and biochemical novelty, there is considerable interest in the enzymes at the heart of the anammox pathway. Unfortunately, obtaining these enzymes in sufficiently large amounts for biochemical and structural studies is problematic, given the slow growth of pure cultures of anammox bacteria when high cell densities are required. However, the anammox process is being applied in wastewater treatment to remove nitrogenous waste in processes like DEamMONification (DEMON). In plants using such processes, which rely on a combination of aerobic ammonia-oxidizers and anammox organisms, kilogram amounts of anammox bacteria-containing sludge are readily available. Here, we report a protein isolation protocol starting from anammox cells present in DEMON sludge from a wastewater treatment plan that readily yields pure preparations of key anammox proteins in the tens of milligrams, including hydrazine synthase HZS and hydrazine dehydrogenase (HDH), as well as hydroxylamine oxidoreductase (HAO). HDH and HAO were active and of sufficient quality for biochemical studies and for HAO, the crystal structure could be determined. The method presented here provides a viable way to obtain materials for the study of proteins not only from the central anammox metabolism but also for the study of other exciting aspects of anammox bacteria, such as for example, their unusual ladderane lipids.

Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module

In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.

Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link

The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.

Unraveling the capability of graphene nanosheets and γ-Fe2O3 nanoparticles to stimulate anammox granular sludge

In this study, we investigated the potentials of nanomaterials to enhance anaerobic ammonium oxidation (anammox) process, in terms of nitrogen removal, microbial enrichment, and activity of key enzymes. Graphene nanosheets (GNs) and γ-Fe₂O₃ nanoparticles (NPs) were selected due to their catalytic functions as conductive material and electron shuttles, respectively. The obtained results revealed that the optimum dosage of GNs (10 mg/L) boosted the nitrogen removal rate (NRR) by 46 ± 3.1% compared to the control, with maximum NH₄⁺-N and NO₂^--N removal of 86.5 ± 2.7% and 97.1 ± 0.5%, respectively. Moreover, hydrazine dehydrogenase (HDH) enzyme activity was augmented by 1.1-fold when using 10 mg/L GNs. The presence of GNs promoted the anammox granulation via enhancement of hydrophobic interaction of extracellular polymeric substances (EPS). Regarding the use of γ-Fe₂O₃ NPs, 100 mg/L dose increased NRR by 55 ± 3.8%; however, no contribution to HDH enzyme activity and a decrease in EPS compositions were observed. Given that the abiotic use of γ-Fe₂O₃ NPs further resulted in high adsorption efficiency (~92%), we conclude that the observed promotion due to γ-Fe₂O₃ NPs was mainly abiotic. Moreover, the 16S rRNA analysis revealed that the relative abundance of genus C. Jettenia (anammox related bacteria) increased from 11.9% to 12.3% when using 10 mg/L GNs, while declined to 8.3% at 100 mg/L γ-Fe₂O₃ NPs. Eventually, nanomaterials could stimulate the efficiency of anammox process, and this promotion and associated mechanism depend on their dose and composition.

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.

Deciphering correlation between chromaticity and activity of anammox sludge

The red color is the most striking character of anaerobic ammonium-oxidizing bacteria (AnAOB) which has been used to estimate the anammox activity roughly. However, the quantitative relationship between the color and activity of anammox sludge still remains unknown. In this study, the chromaticity, activity and their correlation were systematically investigated at different steady-state nitrogen loading rates. The chromaticity of anammox sludge was digitalized by the CIE L*a*b* color space. The results revealed that the average chroma value was found to be significantly correlated with specific anammox activity (r = 0.940, p < 0.01) and the cluster centers of chromaticity coordinates (a*, b*) of anammox sludge were established to define the typical working states of anammox system. The visible spectra of anammox sludge were proved to originate from the cytochrome c. The correlation between chroma and heme c concentration of anammox sludge was consistent with the fully-reduced cytochrome c and the chroma was determined by both content and redox ratio of cytochrome c. The chromaticity of anammox sludge was able to be linked with the anammox activity via reduced cytochrome c content. The gene abundance of cytochrome c synthetase linked the chromaticity with AnAOB quantity via total cytochrome c content, while the enzyme activity of octaheme hydrazine dehydrogenase linked the chromaticity with AnAOB activity via reduced cytochrome c ratio. Moreover, the redundancy analysis proved that heme c, as the key component of cytochrome c, was the most important explanatory variable accounting for the maximum 69.6% of the total variation of the anammox community, which correlated positively with the relative abundance of dominant AnAOB (Candidatus Kuenenia). This work aimed at demonstrating the chromaticity of anammox sludge could be developed as an alternative intuitive anammox activity indicator which will promote the monitoring and optimization of anammox process.

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.

Biological and Bioinspired Inorganic N-N Bond-Forming Reactions

The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.

A self-assembled nanocompartment in anammox bacteria for resisting intracelluar hydroxylamine stress

Anammox bacteria play an important role in the global nitrogen cycle, but research on anammoxosome structure is still in its initial stages. In particular, the anammox bacteria genome contains nanocompartments gene loci. However, the function and structure of the nanocompartments in anammox bacteria is poorly understood. We apply genetic engineering to demonstrate the self-assembled nanocompartments of anammox bacteria. The encapsulin shell protein (cEnc) and cargo protein hydroxylamine oxidoreductase (HAO) can self-assemble to form regular nanocompartments (about 128 nm in diameter) in vitro. Cell growth curve tests show that nanocompartments help model bacteria resist hydroxylamine (NH₂OH) stress. Batch test results and transcriptional data show that cEnc and HAO are highly expressed in response to the negative effects of NH₂OH on anammox efficiency, predicting a potential role of nanocompartments in helping anammox bacteria resist NH₂OH stress. These findings improve our understanding of the mechanisms by which anammox bacteria respond to harmful environmental metabolites.

Role of multiheme cytochromes involved in extracellular anaerobic respiration in bacteria

Heme containing proteins are involved in a broad range of cellular functions, from oxygen sensing and transport to catalyzing oxidoreductive reactions. The two major types of cytochrome (b-type and c-type) only differ in their mechanism of heme attachment, but this has major implications for their cellular roles in both localization and mechanism. The b-type cytochromes are commonly cytoplasmic, or are within the cytoplasmic membrane, while c-type cytochromes are always found outside of the cytoplasm. The mechanism of heme attachment allows for complex c-type multiheme complexes, having the capacity to hold multiple electrons, to be assembled. These are increasingly being identified as secreted into the extracellular environment. For organisms that respire using extracellular substrates, these large multiheme cytochromes allow for electron transfer networks from the cytoplasmic membrane to the cell exterior for the reduction of extracellular electron acceptors. In this review the structures and functions of these networks and the mechanisms by which electrons are transferred to extracellular substrates is described.

Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome

Anaerobic ammonium-oxidizing (anammox) bacteria convert nitrite and ammonium via nitric oxide (NO) and hydrazine into dinitrogen gas by using a diverse array of proteins, including numerous c-type cytochromes. Many new catalytic and spectroscopic properties of c-type cytochromes have been unraveled by studies on the biochemical pathways underlying the anammox process. The unique anammox intermediate hydrazine is produced by a multiheme cytochrome c protein, hydrazine synthase, through the comproportionation of ammonium and NO and the input of three electrons. It is unclear how these electrons are delivered to hydrazine synthase. Here, we report the discovery of a functional tetraheme c-type cytochrome from the anammox bacterium Kuenenia stuttgartiensis with a naturally-occurring contracted Cys-Lys-Cys-His (CKCH) heme-binding motif, which is encoded in the hydrazine synthase gene cluster. The purified tetraheme protein (named KsTH) exchanged electrons with hydrazine synthase. Complementary spectroscopic techniques revealed that this protein harbors four low-spin hexa-coordinated hemes with His/Lys (heme 1), His/Cys (heme 2), and two His/His ligations (hemes 3 and 4). A genomic database search revealed that c-type cytochromes with a contracted CXCH heme-binding motif are present throughout the bacterial and archaeal domains in the tree of life, suggesting that this heme recognition site may be employed by many different groups of microorganisms.