Nitric oxide-dependent anaerobic ammonium oxidation

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

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

A nitric oxide-eluting and REDV peptide-conjugated coating promotes vascular healing

Drug-eluting stents (DESs) placement remarkably reduces the over-proliferation of smooth muscle cells (SMCs) and thus neointimal hyperplasia. However, the pharmacological agent also slows down the re-endothelization, delays injury vascular healing and increases the risk of in-stent restenosis (ISR). Here, inspired by mussel foot proteins (Mfps), a mimicking endothelium functional stent coating was efficiently fabricated by thiol-ene "click" reaction, consisting of catechol grafted chitosan (CS-C), zinc sulfate, and Arg-Glu-Asp-Val (REDV) peptide. The mimicking endothelium coating could continuously catalyze endogenous nitric oxide (NO) gas and maintain the bioactivity of REDV peptide. Compared with bare stents, the mimicking coatings significantly inhibited the acute thrombosis for the first 1-week, accelerated re-endothelization and decreased in-stent restenosis for 1- and 3-month after implantation. In addition, the synergistic effect of NO and REDV peptide also regulated inflammation response and promoted the expression of muscle fiber.

Unraveling Nitrogen, Sulfur, and Carbon Metabolic Pathways and Microbial Community Transcriptional Responses to Substrate Deprivation and Toxicity Stresses in a Bioreactor Mimicking Anoxic Brackish Coastal Sediment Conditions

Microbial communities are key drivers of carbon, sulfur, and nitrogen cycling in coastal ecosystems, where they are subjected to dynamic shifts in substrate availability and exposure to toxic compounds. However, how these shifts affect microbial interactions and function is poorly understood. Unraveling such microbial community responses is key to understand their environmental distribution and resilience under current and future disturbances. Here, we used metagenomics and metatranscriptomics to investigate microbial community structure and transcriptional responses to prolonged ammonium deprivation, and sulfide and nitric oxide toxicity stresses in a controlled bioreactor system mimicking coastal sediment conditions. Ca. Nitrobium versatile, identified in this study as a sulfide-oxidizing denitrifier, became a rare community member upon ammonium removal. The ANaerobic Methanotroph (ANME) Ca. Methanoperedens nitroreducens showed remarkable resilience to both experimental conditions, dominating transcriptional activity of dissimilatory nitrate reduction to ammonium (DNRA). During the ammonium removal experiment, increased DNRA was unable to sustain anaerobic ammonium oxidation (anammox) activity. After ammonium was reintroduced, a novel anaerobic bacterial methanotroph species that we have named Ca. Methylomirabilis tolerans outcompeted Ca. Methylomirabilis lanthanidiphila, while the anammox Ca. Kuenenia stuttgartiensis outcompeted Ca. Scalindua rubra. At the end of the sulfide and nitric oxide experiment, a gammaproteobacterium affiliated to the family Thiohalobacteraceae was enriched and dominated transcriptional activity of sulfide:quinone oxidoreductases. Our results indicate that some community members could be more resilient to the tested experimental conditions than others, and that some community functions such as methane and sulfur oxidation coupled to denitrification can remain stable despite large shifts in microbial community structure. Further studies on complex bioreactor enrichments are required to elucidate coastal ecosystem responses to future disturbances.

The marine nitrogen cycle: new developments and global change

The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.

Sandwiching Phosphorene with Iron Porphyrin Monolayer for High Stability and Its Biomimetic Sensor to Sensitively Detect Living Cell Released NO

Instability of 2D phosphorene material is the major obstacle for its broad applications. Herein phosphorene is sandwiched with self-assembled iron porphyrin monolayers on both sides (I-Phene) to significantly enhance stability. Iron porphyrin has strong interaction with phosphorene through formation of PFe bonds. The sandwich structure offers excellent stability of phosphorene by both-sided monolayer protections for an intact phosphorene structure more than 40 days under ambient conditions. Meanwhile, the electron transfer between iron porphyrin and phosphorene result in a high oxidation state of Fe, making I-Phene biomimetic sensitivity toward oxidation of nitric oxide (NO) for 2.5 and 4.0 times higher than phosphorene and iron-porphyrin alone, respectively. Moreover, I-Phene exhibits excellent selectivity, a wide detection range, and a low detection limit at a low oxidation potential of 0.82 V, which is comparable with the reported noble metal based biomimetic sensors while ranking the best among all non-noble biomimetic ones. I-Phene is further used for real-time monitoring NO released from cells. This work provides effective approach against phosphorene degrading for outstanding stability, which has universal significance for its various important applications, and holds a great promise for a highly sensitive biomimetic sensor in live-cell assays.

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

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

Effective restoration of partial nitritation and anammox biofilm process by short-term hydroxylamine dosing: Mechanism and microbial interaction

The one-stage partial nitritation and anammox (PN-A) process frequently experiences deterioration from ammonium accumulation and nitrate build-up. In this study, hydroxylamine was dosed to restore the process from deterioration in a continuously aerated PN-A sequencing biofilm batch reactor, and the impact of hydroxylamine on the metabolism of PN-A process was studied. PN-A process was totally restored in 5 days via 10 mg N·L^-1 hydroxylamine dosing, reducing nitrate-produced/ammonium-removed ratio from 28.5% to less than 11.0%. hydroxylamine dosing promoted biological production of nitric oxide and nitrous oxide and reduced the production of nitrate in the PN-A process. This study advanced the understanding of the metabolism versatility of hydroxylamine and nitric oxide as well as their function in interaction between aerobic ammonium oxidation bacteria and anaerobic ammonium oxidation bacteria, and proposed the potential application of hydroxylamine dosing in ammonium-contained wastewater treatment.

Impact of organics, aeration and flocs on N2O emissions during granular-based partial nitritation-anammox

Partial nitration-anammox is a resource-efficient technology for nitrogen removal from wastewater. However, the advantages of this nitrogen removal technology are challenged by the emission of N₂O, a potent greenhouse gas. In this study, a granular sludge one-stage partial nitritation-anammox reactor comprising granules and flocs was run for 337 days in the presence of influent organics to investigate its effect on N removal and N₂O emissions. Besides, the effect of aeration control strategies and flocs removal was investigated as well. The interpretation of the experimental results was complemented with modelling and simulation. The presence of influent organics (1 g COD g^-1 N) helped to suppress NOB and significantly reduced the overall N₂O emissions while having no significant effect on anammox activity. Besides, long-term monitoring of the reactor indicated that constant airflow rate control resulted in more stable effluent quality and less N₂O emissions than DO control. Still, floc removal reduced N₂O emissions at DO control but increased N₂O emissions at constant airflow rate. Furthermore, anammox bacteria could significantly reduce N₂O production during heterotrophic denitrification, likely via competition for NO with heterotrophs. Overall, this study demonstrated that the presence of influent organics together with proper aeration control strategies and floc management could significantly reduce the N₂O emissions without compromising nitrogen removal efficiency during one-stage partial nitritation-anammox processes.

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.

Fast start-up and enhancement of partial nitritation and anammox process for treating synthetic wastewater in a sequencing bath biofilm reactor: Strategy and function of nitric oxide

In this study, the partial nitritation and anammox (PN-A) process was initiated within 30 days in a sequencing batch biofilm reactor (SBBR) by employing pre non-aeration and post non-aeration with fixed aeration rates. The average ammonia removal efficiency (ARE), total nitrogen removal efficiency (TNRE) of 98.5 ± 1.5% and 89.5 ± 1.6% were achieved. By doubling aeration rate and agitation rate and adopting pre non-aeration, the TNRR was promoted from 0.135 ± 0.013 kg N·m^-3·d^-1 to 0.285 ± 0.015 kg N·m^-3·d^-1, obtaining an average ARE and TNRE of 97.5 ± 1.5% and 85.5 ± 2.6%. Nitric oxide might induce anaerobic ammonia oxidation bacteria (AnAOB) during the start-up stage, and could be an indicator for synergetic state between ammonia oxidation bacteria (AOB) and AnAOB. Lower nitrous oxide emission factor of 0.51% was obtained. The abundance of AOB, AnAOB and nitrite oxidation bacteria (NOB) accounted for 1.6%, 19.3% and 0.3%, respectively.

Rethinking microbial infallibility in the metagenomics era

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

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

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

Bacterial nitric oxide metabolism: Recent insights in rhizobia

Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N₂-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.

Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments

Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.

Cyclic Conversions in the Nitrogen Cycle

The cyclic nature of specific conversions in the nitrogen cycle imposes strict limitations to the conversions observed in nature and explains for example why anaerobic ammonium oxidation (anammox) bacteria can only use nitrite – and not nitrate – as electron acceptor in catabolism, and why nitrite is required as additional electron donor for inorganic carbon fixation in anabolism. Furthermore, the biochemistry involved in nitrite-dependent anaerobic methane oxidation excludes the feasibility of using nitrate as electron acceptor. Based on the cyclic nature of these nitrogen conversions, we propose two scenarios that may explain the ecological role of recently discovered complete ammonia-oxidizing (comammox) Nitrospira spp., some of which were initially found in a strongly oxygen limited environment: (i) comammox Nitrospira spp. may actually catalyze an anammox-like metabolism using a biochemistry similar to intra-oxic nitrite-dependent methane oxidation, or (ii) scavenge all available oxygen for ammonia activation and use nitrate as terminal electron acceptor. Both scenarios require the presence of the biochemical machinery for ammonia oxidation to nitrate, potentially explaining a specific ecological niche for the occurrence of comammox bacteria in nature.

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.

Coupled nitrification and N2 gas production as a cryptic process in oxic riverbeds

The coupling between nitrification and N₂ gas production to recycle ammonia back to the atmosphere is a key step in the nitrogen cycle that has been researched widely. An assumption for such research is that the products of nitrification (nitrite or nitrate) mix freely in the environment before reduction to N₂ gas. Here we show, in oxic riverbeds, that the pattern of N₂ gas production from ammonia deviates by ~3- to 16-fold from that predicted for denitrification or anammox involving nitrite or nitrate as free porewater intermediates. Rather, the patterns match that for a coupling through a cryptic pool, isolated from the porewater. A cryptic pool challenges our understanding of a key step in the nitrogen cycle and masks our ability to distinguish between sources of N₂ gas that 20 years’ research has sought to identify. Our reasoning suggests a new pathway or a new type of coupling between known pathways in the nitrogen cycle.

The N cycle involves complex, microbially-mediated shuttling between ammonium, nitrite and nitrate, with climatically important greenhouse gas byproducts. Here the authors use isotope labeling experiments in river sediments and find a cryptic new step in the N cycle between nitrification and the removal of fixed N through N₂ gas production.

Phanerozoic radiation of ammonia oxidizing bacteria

The modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to nitrite, an obligately aerobic process performed by a limited number of lineages of bacteria (AOB) and archaea (AOA). As this process has an absolute requirement for O2, the timing of its evolution-especially as it relates to the Great Oxygenation Event ~ 2.3 billion years ago-remains contested and is pivotal to our understanding of nutrient cycles. To estimate the antiquity of bacterial ammonia oxidation, we performed phylogenetic and molecular clock analyses of AOB. Surprisingly, bacterial ammonia oxidation appears quite young, with crown group clades having originated during Neoproterozoic time (or later) with major radiations occurring during Paleozoic time. These results place the evolution of AOB broadly coincident with the pervasive oxygenation of the deep ocean. The late evolution AOB challenges earlier interpretations of the ancient nitrogen isotope record, predicts a more substantial role for AOA during Precambrian time, and may have implications for understanding of the size and structure of the biogeochemical nitrogen cycle through geologic time.

Learning from microorganisms: using new insights in microbial physiology for sustainable nitrogen management

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To reduce nitrate to N₂ distinct nitrogen-oxide-reducing microorganisms function together.

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Detecting nirS, nirK or narG genes cannot be directly linked to NO and N₂O emission.

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Nitrogen-oxide-reducing specialists can be exploited to reduce NO and N₂O emission from wwtp.

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Aerobic methanotrophs and methane stripping must be considered for the application of N-DAMO.

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Ammonium recovery could be a more sustainable alternative to nitrogen removal.

Diverse nitrogen-transforming microorganisms with a wide variety of physiological properties are employed for biological nitrogen removal from wastewater. There are many technologies that achieve the required nitrogen discharge standards; however, greenhouse gas emissions and energy consumption constitute the bulk of the environmental footprint of wastewater treatment plants. In this review, we highlight current and proposed approaches aiming to achieve more energy-efficient and environment-friendly biological nitrogen removal, discuss whether new discoveries in microbial physiology of nitrogen-transforming microorganisms could be used to reduce greenhouse gas emissions, and summarize recent advances in ammonium recovery from wastewater.

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.

Heme P460: A (Cross) Link to Nitric Oxide

Ammonia-oxidizing bacteria (AOB) convert ammonia (NH₃) to nitrite (NO₂^-) as their primary metabolism and thus provide a blueprint for the use of NH₃ as a chemical fuel. The first energy-producing step involves the homotrimeric enzyme hydroxylamine oxidoreductase (HAO), which was originally reported to oxidize hydroxylamine (NH₂OH) to NO₂^-. HAO uses the heme P460 cofactor as the site of catalysis. This heme is supported by seven other c hemes in each monomer that mediate electron transfer. Heme P460 cofactors are c-heme-based cofactors that have atypical protein cross-links between the peptide backbone and the porphyrin macrocycle. This cofactor has been observed in both the HAO and cytochrome (cyt) P460 protein families. However, there are differences; specifically, HAO uses a single tyrosine residue to form two covalent attachments to the macrocycle whereas cyt P460 uses a lysine residue to form one. In Nitrosomonas europaea, which expresses both HAO and cyt P460, these enzymes achieve the oxidation of NH₂OH and were both originally reported to produce NO₂^-. Each can inspire means to effect controlled release of chemical energy.Spectroscopically studying the P460 cofactors of HAO is complicated by the 21 non-P460 heme cofactors, which obscure the active site. However, monoheme cyt P460 is more approachable biochemically and spectroscopically. Thus, we have used cyt P460 to study biological NH₂OH oxidation. Under aerobic conditions substoichiometric production of NO₂^- was observed along with production of nitrous oxide (N₂O). Under anaerobic conditions, however, N₂O was the exclusive product of NH₂OH oxidation. We have advanced our understanding of the mechanism of this enzyme and have showed that a key intermediate is a ferric nitrosyl that can dissociate the bound nitric oxide (NO) molecule and react with O₂, thus producing NO₂^- abiotically. Because N₂O was the true product of one P460 cofactor-containing enzyme, this prompted us to reinvestigate whether NO₂^- is enzymatically generated from HAO catalysis. Like cyt P460, we showed that HAO does not produce NO₂^- enzymatically, but unlike cyt P460, its final product is NO, establishing it as an intermediate of nitrification. More broadly, NO can be recognized as a molecule common to the primary metabolisms of all organisms involved in nitrogen "defixation".Delving deeper into cyt P460 yielded insights broadly applicable to controlled biochemical redox processes. Studies of an inactive cyt P460 from Nitrosomonas sp. AL212 showed that this enzyme was unable to oxidize NH₂OH because it lacked a glutamate residue in its secondary coordination sphere that was present in the active N. europaea cyt P460 variant. Restoring the Glu residue imbued activity, revealing that a second-sphere base is Nature's key to controlled oxidation of NH₂OH. A key lesson of bioinorganic chemistry is reinforced: the polypeptide matrix is an essential part of dictating function. Our work also exposed some key functional contributions of noncanonical heme-protein cross-links. The heme-Lys cross-link of cyt P460 enforces the relative position of the cofactor and second-sphere residues. Moreover, the cross-link prevents the dissociation of the axial histidine residue, which stops catalysis, emphasizing the importance of this unique post-translational modification.

Genome-based analysis to understanding rapid resuscitation of cryopreserved anammox consortia via sequential supernatant addition

Simple cryopreservation of anaerobic ammonium-oxidation (anammox) consortia has become a promising preservation technology for the fast start-up of the anammox process. Here, we use genome-resolved metagenomics and metatranscriptomics to understand of the microbial interaction in a simple and effective resuscitation process for long-term cryopreserved anammox consortia by sequential addition of anammox SBR supernatant. Performance results showed that sequential addition of anammox supernatant significantly reduced the resuscitation time of the granule-based anammox process from 40 to 20 days. Genome-centric metagenomics were used to recover 19 high-quality draft genomes of anammox and heterotrophic bacteria. Comparative metatranscriptomic analysis was conducted to examine the gene expression of Candidatus Kuenenia stuttgartiensis, the dominant anammox bacterium, and heterotrophic bacteria to better understand their potential interactions. Proteobacteria-affiliated bacteria found in the supernatant were highly active in producing the secondary metabolites molybdopterin cofactor and folate which are needed for growth of the auxotrophic anammox bacteria. In addition, the significantly higher expression levels of hzsA and CO₂-fixtion genes in the Candidatus Kuenenia genome indicated the anammox bacteria were likely more active and growing faster after sequential anammox supernatant addition during the resuscitation process. The resuscitation treatment pulse assays confirmed that sequential addition of supernatant was an effective way for the rapid resuscitation of anammox consortia. Our findings offer the first evidence of cross-feeding during the rapid resuscitation of cryopreserved anammox consortia.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Flocs are the main source of nitrous oxide in a high-rate anammox granular sludge reactor: insights from metagenomics and fed-batch experiments

Nitrous oxide (N₂O) emissions from anammox-based processes are well documented but insight into source of the N₂O emission in high-rate anammox granular sludge reactors (AGSR) is limited. In this study, metagenomics and fed-batch experiments were applied to investigate the relative contributions of anammox granules and flocs to N₂O production in a high-rate AGSR. Flocs, which constitute only ~10% of total biomass contributed about 60% of the total N₂O production. Granules, the main contributor of nitrogen removal (~95%), were responsible for the remaining ~40% of N₂O production. This result is inconsistent with reads-based analysis that found the gene encoding clade II type nitrous oxide reductase (nosZ_II) had similar abundances in both granules and flocs. Another notable trend observed was the relatively higher abundance of the gene for NO-producing nitrite reductase (nir) in comparison to the gene for the nitric oxide reductase gene (nor) in both granules and flocs, indicating nitric oxide (NO) may accumulate in the AGSR. This is significant since NO and N₂O pulse assays demonstrated that NO could lead to N₂O production from both granules and flocs. However, since anammox bacteria, which were shown to be in higher abundance in granules than in flocs, have the capacity to scavenge NO this provides a mechanism by which its inhibitory effects can be mitigated, limiting N₂O release from the granules, consistent with experimental observation. These results demonstrate flocs are the main source of N₂O emission in AGSR and provide lab-scale evidence that NO-dependent anammox can mitigate N₂O emission.

Unclassified Anammox bacterium responds to robust nitrogen removal in a sequencing batch reactor fed with landfill leachate

Treatment of landfill leachate was conducted in a lab-scale sequencing batch reactor (SBR). The SBR was started through inoculating activated sludge with controlling dissolved oxygen of 0.5-1.0 mg/L. Anammox reaction took place within around three months. The SBR established robust nitrogen removal with incremental NLRs of 0.25-2.17 kg N/m³/d. At the final phase, it achieved elevated nitrogen removals of 1.68-1.91 kg N/m³/d. 16S rRNA gene amplicon sequencing analysis revealed Nitrosomonas, unclassified Anammox bacterium, and diverse denitrifying populations coexisted and accounted for 4.02%, 20.05% and 34.69%, respectively. Phylogenic analysis and average nucleotide identity comparison jointly suggested the unclassified Anammox bacterium potentially pertained to a novel Anammox lineage. The functional profiles' prediction suggested sulfate reduction, arsenate reduction and eliminations of antibiotics and drugs likely occurred in the SBR. The finding from this study suggests contribution of unclassified Anammox bacteria in influencing nitrogen budget in natural and engineering systems is currently being underestimated.

Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping

Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and use of different carbon and energy substrates beyond genome-based predictions. Here, we experimentally resolved the central carbon metabolism of the anammox bacterium Candidatus ‘Kuenenia stuttgartiensis’ using time-series ¹³C and ²H isotope tracing, metabolomics, and isotopically nonstationary metabolic flux analysis. Our findings confirm predicted metabolic pathways used for CO₂ fixation, central metabolism, and amino acid biosynthesis in K. stuttgartiensis, and reveal several instances where genomic predictions are not supported by in vivo metabolic fluxes. This includes the use of the oxidative branch of an incomplete tricarboxylic acid cycle for alpha-ketoglutarate biosynthesis, despite the genome not having an annotated citrate synthase. We also demonstrate that K. stuttgartiensis is able to directly assimilate extracellular formate via the Wood–Ljungdahl pathway instead of oxidizing it completely to CO₂ followed by reassimilation. In contrast, our data suggest that K. stuttgartiensis is not capable of using acetate as a carbon or energy source in situ and that acetate oxidation occurred via the metabolic activity of a low-abundance microorganism in the bioreactor’s side population. Together, these findings provide a foundation for understanding the carbon metabolism of anammox bacteria at a systems-level and will inform future studies aimed at elucidating factors governing their function and niche differentiation in natural and engineered ecosystems.

Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462T Improved Environmental Adaptability

Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO₂^-) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462^T were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462^T. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.

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.

Diversity, enrichment, and genomic potential of anaerobic methane- and ammonium-oxidizing microorganisms from a brewery wastewater treatment plant

Anaerobic wastewater treatment offers several advantages; however, the effluent of anaerobic digesters still contains high levels of ammonium and dissolved methane that need to be removed before these effluents can be discharged to surface waters. The simultaneous anaerobic removal of methane and ammonium by denitrifying (N-damo) methanotrophs in combination with anaerobic ammonium-oxidizing (anammox) bacteria could be a potential solution to this challenge. After a molecular survey of a wastewater plant treating brewery effluent, indicating the presence of both N-damo and anammox bacteria, we started an anaerobic bioreactor with a continuous supply of methane, ammonium, and nitrite to enrich these anaerobic microorganisms. After 14 months of operation, a stable enrichment culture containing two types of 'Candidatus Methylomirabilis oxyfera' bacteria and two strains of 'Ca. Brocadia'-like anammox bacteria was achieved. In this community, anammox bacteria converted 80% of the nitrite with ammonium, while 'Ca. Methylomirabilis' contributed to 20% of the nitrite consumption. The analysis of metagenomic 16S rRNA reads and fluorescence in situ hybridization (FISH) correlated well and showed that, after 14 months, 'Ca. Methylomirabilis' and anammox bacteria constituted approximately 30 and 20% of the total microbial community. In addition, a substantial part (10%) of the community consisted of Phycisphaera-related planctomycetes. Assembly and binning of the metagenomic sequences resulted in high-quality draft genome of two 'Ca. Methylomirabilis' species containing the marker genes pmoCAB, xoxF, and nirS and putative NO dismutase genes. The anammox draft genomes most closely related to 'Ca. Brocadia fulgida' included the marker genes hzsABC, hao, and hdh. Whole-reactor and batch anaerobic activity measurements with methane, ammonium, nitrite, and nitrate revealed an average anaerobic methane oxidation rate of 0.12 mmol h^-1 L^-1 and ammonium oxidation rate of 0.5 mmol h^-1 L^-1. Together, this study describes the enrichment and draft genomes of anaerobic methanotrophs from a brewery wastewater treatment plant, where these organisms together with anammox bacteria can contribute significantly to the removal of methane and ammonium in a more sustainable way. KEY POINTS: • An enrichment culture containing both N-damo and anammox bacteria was obtained. • Simultaneous consumption of ammonia, nitrite, and methane under anoxic conditions. • In-depth metagenomic biodiversity analysis of inoculum and enrichment culture.

Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria

Anaerobic ammonium oxidation (anammox) bacteria contribute significantly to the global nitrogen cycle and play a major role in sustainable wastewater treatment. Anammox bacteria convert ammonium (NH₄⁺) to dinitrogen gas (N₂) using intracellular electron acceptors such as nitrite (NO₂⁻) or nitric oxide (NO). However, it is still unknown whether anammox bacteria have extracellular electron transfer (EET) capability with transfer of electrons to insoluble extracellular electron acceptors. Here we show that freshwater and marine anammox bacteria couple the oxidation of NH₄⁺ with transfer of electrons to insoluble extracellular electron acceptors such as graphene oxide or electrodes in microbial electrolysis cells. ¹⁵N-labeling experiments revealed that NH₄⁺ was oxidized to N₂ via hydroxylamine (NH₂OH) as intermediate, and comparative transcriptomics analysis revealed an alternative pathway for NH₄⁺ oxidation with electrode as electron acceptor. Complete NH₄⁺ oxidation to N₂ without accumulation of NO₂⁻ and NO₃⁻ was achieved in EET-dependent anammox. These findings are promising in the context of implementing EET-dependent anammox process for energy-efficient treatment of nitrogen.

Bacteria capable of anaerobic ammonium oxidation (anammox) produce half of the nitrogen gas in the atmosphere, but much of their physiology is still unknown. Here the authors show that anammox bacteria are capable of a novel mechanism of ammonium oxidation using extracellular electron transfer.

Ecological niche differentiation among anammox bacteria

Anaerobic ammonium oxidizing (anammox) bacteria can directly convert ammonium and nitrite to nitrogen gas anaerobically and were responsible for a substantial part of the fixed nitrogen loss and re-oxidation of nitrite to nitrate in freshwater and marine ecosystems. Although a wide variety of studies have been undertaken to investigate the abundance and biodiversity of anammox bacteria so far, ecological niche differentiation of anammox bacteria is still not fully understood. To assess their growth behavior and consequent population dynamics at a given environment, the Monod model is often used. Here, we summarize the Monod kinetic parameters such as the maximum specific growth rate (μ_max) and the half-saturation constant for nitrite (K_NO2-) and ammonium (K_NH4+) of five known candidatus genera of anammox bacteria. We also discuss potential pivotal environmental factors and metabolic flexibility that influence the community compositions of anammox bacteria. Particularly biodiversity of the genus "Scalindua" might have been largely underestimated. Several anammox bacteria have been successfully enriched from various source of biomass. We reevaluate their enrichment methods and culture medium compositions to gain a clue of niche differentiation of anammox bacteria. Furthermore, we formulate the current issues that must be addressed. Overall this review re-emphasizes the importance of enrichment cultures (preferably pure cultures), physiological characterization and direct microbial competition studies using enrichment cultures in laboratories.

New perspectives on microbial communities and biological nitrogen removal processes in wastewater treatment systems

Biological nitrogen removal (BNR) is a critical process in wastewater treatment. Recently, there have new microbial communities been discovered to be capable of performing BNR with novel metabolic pathways. This review presents the up-to-date status on these microorganisms, including ammonia oxidizing archaea (AOA), complete ammonia oxidation (COMAMMOX) bacteria, anaerobic ammonium oxidation coupled to iron reduction (FEAMMOX) bacteria, anaerobic ammonium oxidation (ANAMMOX) bacteria and denitrifying anaerobic methane oxidation (DAMO) microorganism. Their metabolic pathways and enzymatic reactions in nitrogen cycle are demonstrated. Generally, these novel microbial communities have advantages over canonical nitrifiers or denitrifiers, such as higher substrate affinities, better physicochemical tolerances and/or less greenhouse gas emission. Also, their recent development and/or implementation in BNR is discussed and outlook. Finally, the key implications of coupling these microbial communities for BNR are identified. Overall, this review illustrates novel microbial communities that could provide new possibilities for high-performance and energy-saving nitrogen removal from wastewater.

Genome of a Novel Bacterium "Candidatus Jettenia ecosi" Reconstructed From the Metagenome of an Anammox Bioreactor

The microbial community of a laboratory-scale bioreactor based on the anammox process was investigated by using metagenomic approaches and fluorescent in situ hybridization (FISH). The bioreactor was initially inoculated with activated sludge from the denitrifying bioreactor of a municipal wastewater treatment station. By constantly increasing the ammonium and nitrite load, a microbial community containing the novel species of anammox bacteria "Candidatus Jettenia ecosi" developed in the bioreactor after 5 years when the maximal daily nitrogen removal rate reached 8.5 g/L. Sequencing of the metagenome of anammox granules and the binning of the contigs obtained, allowed a high quality draft genome of the dominant anammox bacterium, "Candidatus Jettenia ecosi" to be assembled. Annotation of the 3.9 Mbp long genome revealed 3970 putative protein-coding genes, 45 tRNA genes, and genes for 16S/23S rRNAs. Analysis of the genome of "Candidatus Jettenia ecosi" revealed genes involved in anammox metabolism, including nitrite and ammonium transporters, copper-containing nitrite reductase, a nitrate reductase complex, hydrazine synthase, and hydrazine dehydrogenase. Autotrophic carbon fixation could be accomplished through the Wood Ljungdahl pathway. The composition of the community was investigated through a search of 16S rRNA sequences in the metagenome and FISH analysis of the anammox granules. The presence of the members of Ignavibacteriae, Betaproteobacteria, Chloroflexi and other microbial lineages reflected the complexity of the microbial processes in the studied bioreactor performed by anammox Planctomycetes, fermentative bacteria, and denitrifiers.

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.