Genome analysis and heterologous expression of acetate-activating enzymes in the anammox bacterium Kuenenia stuttgartiensis

Anaerobic ammonium-oxidizing bacteria were recently shown to use short-chain organic acids as additional energy source. The AMP-forming acetyl-CoA synthetase gene (acs) of Kuenenia stuttgartiensis, encoding an important enzyme involved in the conversion of these organic acids, was identified and heterologously expressed in Escherichia coli to investigate the activation of several substrates, that is, acetate, propionate and butyrate. The heterologously expressed ACS enzyme could complement an E. coli triple mutant deficient in all pathways of acetate activation. Activity was observed toward several short-chain organic acids, but was highest with acetate. These properties are in line with a mixotrophic growth of anammox bacteria. In addition to acs, the genome of K. stuttgartiensis contained the essential genes of an acetyl-CoA synthase/CO dehydrogenase complex and genes putatively encoding two isoenzymes of archaeal-like ADP-forming acetyl-CoA synthetase underlining the importance of acetyl-CoA as intermediate in the carbon assimilation metabolism of anammox bacteria.     

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.Subject terms: Environmental microbiology, Metabolism     

Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria

Recently, two fresh water species, "Candidatus Brocadia anammoxidans" and "Candidatus Kuenenia stuttgartiensis", and one marine species, "Candidatus Scalindua sorokinii", of planctomycete anammox bacteria have been identified. "Candidatus Scalindua sorokinii" was discovered in the Black Sea, and contributed substantially to the loss of fixed nitrogen. All three species contain a unique organelle—the anammoxosome—in their cytoplasm. The anammoxosome contains the hydrazine/hydroxylamine oxidoreductase enzyme, and is thus the site of anammox catabolism. The anammoxosome is surrounded by a very dense membrane composed almost exclusively of linearly concatenated cyclobutane-containing lipids. These so-called 'ladderanes' are connected to the glycerol moiety via both ester and ether bonds. In natural and man-made ecosystems, anammox bacteria can cooperate with aerobic ammonium-oxidising bacteria, which protect them from harmful oxygen, and provide the necessary nitrite. The cooperation of these two groups of ammonium-oxidising bacteria is the microbial basis for a sustainable one reactor system, CANON (completely autotrophic nitrogen-removal over nitrite) to remove ammonia from high strength wastewater.     

Biochemistry and molecular biology of anammox bacteria

Anaerobic ammonium-oxidizing (anammox) bacteria are one of the latest additions to the biogeochemical nitrogen cycle. These bacteria derive their energy for growth from the conversion of ammonium and nitrite into dinitrogen gas in the complete absence of oxygen. These slowly growing microorganisms belong to the order Brocadiales and are affiliated to the Planctomycetes. Anammox bacteria are characterized by a compartmentalized cell architecture featuring a central cell compartment, the “anammoxosome”. Thus far unique “ladderane” lipid molecules have been identified as part of their membrane systems surrounding the different cellular compartments. Nitrogen formation seems to involve the intermediary formation of hydrazine, a very reactive and toxic compound. The genome of the anammox bacterium Kuenenia stuttgartiensis was assembled from a complex microbial community grown in a sequencing batch reactor (74% enriched in this bacterium) using a metagenomics approach. The assembled genome allowed the in silico reconstruction of the anammox metabolism and identification of genes most likely involved in the process. The present anammox pathway is the only one consistent with the available experimental data, thermodynamically and biochemically feasible, and consistent with Ockham’s razor: it invokes minimum biochemical novelty and requires the fewest number of biochemical reactions. The worldwide presence of anammox bacteria has now been established in many oxygen-limited marine and freshwater systems, including oceans, seas, estuaries, marshes, rivers and large lakes. In the marine environment over 50% of the N₂ gas released may be produced by anammox bacteria. Application of the anammox process offers an attractive alternative to current wastewater treatment systems for the removal of ammonia-nitrogen. Currently, at least five full scale reactor systems are operational.     

Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria

Bacterial aerobic ammonium oxidation and anaerobic ammonium oxidation (anammox) are important processes in the global nitrogen cycle. Key enzymes in both processes are the octahaem cytochrome c (OCC) proteins, hydroxylamine oxidoreductase (HAO) of aerobic ammonium-oxidizing bacteria (AOB), which catalyses the oxidation of hydroxylamine to nitrite, and hydrazine oxidoreductase (HZO) of anammox bacteria, which converts hydrazine to N(2). While the genomes of AOB encode up to three nearly identical copies of hao operons, genome analysis of Candidatus'Kuenenia stuttgartiensis' showed eight highly divergent octahaem protein coding regions as possible candidates for the HZO. Based on their phylogenetic relationship and biochemical characteristics, the sequences of these eight gene products grouped in three clusters. Degenerate primers were designed on the basis of available gene sequences with the aim to detect hao and hzo genes in various ecosystems. The hao primer pairs amplified gene fragments from 738 to 1172 bp and the hzo primer pairs amplified gene fragments from 289 to 876 bp in length, when tested on genomic DNA isolated from a variety of AOB and anammox bacteria. A selection of these primer pairs was also used successfully to amplify and analyse the hao and hzo genes in community DNA isolated from different ecosystems harbouring both AOB and anammox bacteria. We propose that OCC protein-encoding genes are suitable targets for molecular ecological studies on both aerobic and anaerobic ammonium-oxidizing bacteria.     

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.     

Theoretical insight into the hydroxylamine oxidoreductase mechanism

The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the conversion of hydroxylamine to nitrite, with a complicate arrangement of heme groups in three subunits. As a distinctive feature, the protein has a covalent linkage between a tyrosyl residue of one subunit and a meso carbon atom of the heme active site of another. We studied the influence of this bond in the catalysis from a theoretical perspective through electronic structure calculations at the density functional theory level, starting from the crystal structure of the protein. Geometry optimizations of proposed reaction intermediates were used to calculate the dissociation energy of different nitrogen containing ligands, considering the presence and absence of the meso tyrosyl residue. The results indicate that the tyrosine residue enhances the binding of hydroxylamine, and increases the stability of a Fe^IIINO intermediate, while behaving indifferently in the Fe^IINO form. The calculations performed on model systems including neighboring aminoacids revealed the probable formation of a bidentate hydrogen bond between the Fe^IIIH₂O complex and Asp 257, in a high-spin aquo complex as the resting state. Characterization of non-planar heme distortions showed that the meso-substituent induces significant ruffling in the evaluated intermediates.     

Metabolism of Inorganic N Compounds by Ammonia-Oxidizing Bacteria

ABSTRACT

Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N₂O, NO₂, and N₂ can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N₂O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO₂ can serve as an alternative oxidant in place of O₂ in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.     

Biases in community structures of ammonia/ammonium-oxidizing microorganisms caused by insufficient DNA extractions from Baijiang soil revealed by comparative analysis of coastal wetland sediment and rice paddy soil

Repetitive extraction of DNAs from surface sediments of a coastal wetland in Mai Po Nature Reserve (MP) of Hong Kong and surface Baijiang soils from a rice paddy (RP) in Northeast China was conducted to compare the microbial diversity in this study. Community structures of ammonia/ammonium-oxidizing microorganisms in these samples were analyzed by PCR-DGGE technique. The diversity and abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonium-oxidizing (anammox) bacteria were also analyzed based on archaeal and bacterial ammonia monooxygenase subunit A encoding (amoA) and anammox bacterial 16S rRNA genes, respectively. DGGE profiles of archaeal and bacterial amoA and anammox bacterial 16S rRNA genes showed a similar pattern among all five repetitively extracted DNA fractions from both MP and RP, except the anammox bacteria in RP, indicating a more diverse anammox community retrieved in the second to the fifth fractions than the first one. Both soil and marine group AOA were detected while soil and coastal group AOB and Scalindua-anammox bacteria were dominant in MP. Soil group AOA and marine group AOB were dominant in RP, while both Scalindua and Kuenenia species were detected in RP. Pearson correlation analysis showed that the abundance of archaeal and bacterial amoA and anammox bacterial 16S rRNA genes was significantly correlated with the DNA concentrations of the five DNA fractions from MP, but not from RP (except the archaeal amoA gene). Results suggest that anammox bacteria diversity may be biased by insufficient DNA extraction of rice paddy soil samples.     

In Situ Activity and Spatial Organization of Anaerobic Ammonium-Oxidizing (Anammox) Bacteria in Biofilms

We investigated autotrophic anaerobic ammonium-oxidizing (anammox) biofilms for their spatial organization, community composition, and in situ activities by using molecular biological techniques combined with microelectrodes. Results of phylogenetic analysis and fluorescence in situ hybridization (FISH) revealed that “Brocadia”-like anammox bacteria that hybridized with the Amx820 probe dominated, with 60 to 92% of total bacteria in the upper part (<1,000 μm) of the biofilm, where high anammox activity was mainly detected with microelectrodes. The relative abundance of anammox bacteria decreased along the flow direction of the reactor. FISH results also indicated that Nitrosomonas-, Nitrosospira-, and Nitrosococcus-like aerobic ammonia-oxidizing bacteria (AOB) and Nitrospira-like nitrite-oxidizing bacteria (NOB) coexisted with anammox bacteria and accounted for 13 to 21% of total bacteria in the biofilms. Microelectrode measurements at three points along the anammox reactor revealed that the NH₄⁺ and NO₂⁻ consumption rates decreased from 0.68 and 0.64 μmol cm⁻² h⁻¹ at P2 (the second port, 170 mm from the inlet port) to 0.30 and 0.35 μmol cm⁻² h⁻¹ at P3 (the third port, 205 mm from the inlet port), respectively. No anammox activity was detected at P4 (the fourth port, 240 mm from the inlet port), even though sufficient amounts of NH₄⁺ and NO₂⁻ and a high abundance of anammox bacteria were still present. This result could be explained by the inhibitory effect of organic compounds derived from biomass decay and/or produced by anammox and coexisting bacteria in the upper parts of the biofilm and in the upstream part of the reactor. The anammox activities in the biofilm determined by microelectrodes reflected the overall reactor performance. The several groups of aerobic AOB lineages, Nitrospira-like NOB, and Betaproteobacteria coexisting in the anammox biofilm might consume a trace amount of O₂ or organic compounds, which consequently established suitable microenvironments for anammox bacteria.     

The bacterial diversity in an anaerobic ammonium-oxidizing (anammox) reactor community

An anaerobic ammonium-oxidation (anammox) reactor was operated for more than 500 days and the anammox activity of the biomass in the reactor reached 0.58 kg N_total/kg VSS d. The removal ratios of NO₂⁻-N to NH₄⁺-N in both reactor and activity tests were nearly 1.1. The bacterial diversity in the reactor was investigated by analysis of 16S rRNA gene clone libraries and quantitative real-time PCR (qPCR). The analysis showed that more than half of the clones in the library were affiliated to recognized filamentous bacteria. The previously recognized anammox bacterium (AnAOB) Candidatus Kuenenia stuttgartiensis was only detected by using a Planctomycetes-specific 16S rRNA gene primer set. However, at least two different types of AnAOB were detected by the primer set targeting the hydrazine-oxidizing enzyme gene (hzo). The aerobic ammonium-oxidizing bacteria (AAOB) Nitrosomonas europaea–eutropha group, which is widely detected in oxygen-limited environments, was also found in this reactor. The result of qPCR indicated that AnAOB comprised 16% of the community population while AAOB comprised less than 1% in the reactor.     

Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘Candidatus Brocadia sapporoensis’

We successfully enriched a novel anaerobic ammonium-oxidizing (anammox) bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and produced hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20–45 °C with a maximum activity at 37 °C. The maximum specific growth rate (μ_max) was 0.0082 h^?1 at 37 °C, corresponding to a doubling time of 3.5 days. The half-saturation constant (K_S) for nitrite was 5 ± 2.5 μM. The anammox activity was inhibited by nitrite (IC₅₀ = 11.6 mM) but not by formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). The enriched anammox bacterium shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The enriched bacterium showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its 16S rRNA gene sequence. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.     

Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China

The anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the oxygen-limited zone for nitrogen cycling, but their roles in agricultural ecosystems are still poorly understood. In this study, soil samples were taken from the rhizosphere and non-rhizosphere and from surface (0–5 cm) and subsurface (20–25 cm) layers with 1, 4, and 9 years of rice cultivation history on the typical albic soil of Northeast China to examine the diversity and distribution of anammox bacteria based on 16S rRNA gene and hydrazine oxidoreductase encoding gene (hzo). By comparing these soil samples, no obvious difference was observed in community composition between the rhizosphere and non-rhizosphere or the surface and subsurface layers. Surprisingly, anammox bacterial communities of these rice paddy soils were consisted of mainly Candidatus Scalindua species, which are best known to be dominant in marine and pristine environments. The highest diversity was revealed in the 4-year paddy soil based on clone library analysis. Phylogenetic analysis of 16S rRNA gene and deduced HZO from the corresponding encoding gene showed that most of the obtained clones are grouped together with Candidatus Scalindua sorokinii, Candidatus Scalindua brodae, and Candidatus Scalindua spp. of seawater. The obtained clone sequences from all samples are distributed in two subclusters that contain sequences from environmental samples only. Tentative new species were also discovered in this paddy soil. This study provides the first evidence on the existence of anammox bacteria with limited diversity in agricultural ecosystems in Northern China.     

Microbial and Physicochemical Characteristics of Compact Anaerobic Ammonium-Oxidizing Granules in an Upflow Anaerobic Sludge Blanket Reactor

Anaerobic ammonium oxidation (anammox) is a promising new process to treat high-strength nitrogenous wastewater. Due to the low growth rate of anaerobic ammonium-oxidizing bacteria, efficient biomass retention is essential for reactor operation. Therefore, we studied the settling ability and community composition of the anaerobic ammonium-oxidizing granules, which were cultivated in an upflow anaerobic sludge blanket (UASB) reactor seeded with aerobic granules. With this seed, the start-up period was less than 160 days at a NH₄⁺-N removal efficiency of 94% and a loading rate of 0.064 kg N per kg volatile suspended solids per day. The formed granules were bright red and had a high settling velocity (41 to 79 m h⁻¹). Cells and extracellular polymeric substances were evenly distributed over the anaerobic ammonium-oxidizing granules. The high percentage of anaerobic ammonium-oxidizing bacteria in the granules could be visualized by fluorescent in situ hybridization and electron microscopy. The copy numbers of 16S rRNA genes of anaerobic ammonium-oxidizing bacteria in the granules were determined to be 4.6 × 10⁸ copies ml⁻¹. The results of this study could be used for a better design, shorter start-up time, and more stable operation of anammox systems for the treatment of nitrogen-rich wastewaters.The anaerobic ammonia oxidation (anammox) process is a recently discovered biological nitrogen removal technology in which ammonia is oxidized to nitrogen gas with nitrite as the electron acceptor (5, 29, 32). In contrast to heterotrophic denitrification (6, 26), the anammox process does not require external electron donors (e.g., methanol) due to their chemolithoautotrophic lifestyle. Furthermore, if this process is combined with a partial nitrification step, only half of the ammonium needs to be nitrified to nitrite, which together with the remaining ammonium can subsequently be converted into nitrogen through the anammox process. This reduces the oxygen demand of the system and leads to further reduction in operational costs (27).The anaerobic ammonium-oxidizing bacteria (anammox bacteria) have a low growth rate (18), with a doubling time at best estimated as 7 to 11 days (18, 28). The yield of the anammox bacteria has been determined to be 0.066 mol C biomass mol⁻¹ ammonium consumed, and the maximum ammonium consumption rate is ∼45 nmol mg⁻¹ protein min⁻¹ (18). Given the low growth rate and low yield, very efficient biomass retention is essential to retain the anammox bacteria within the reactor systems during cultivation (19). The enrichment of anammox bacteria from a mixed inoculum requires the optimization of conditions favorable for the anammox bacteria and generally takes 200 to 300 days (5, 6, 27). Thus, conditions that would reduce the start-up time of anammox reactors would positively effect the implementation of the process. Several sources of inocula, such as activated sludge (4), nitrifying activated sludge (27), and anaerobic sludge (6), have been used for the start-up of anammox reactors with start-up times of as long as 1,000 days (27).Aerobic granules have been reported to have high microbial diversity (31) and compact structure with very good settling properties resulting in an efficient means of biomass retention. These properties, including interspecies competition and mass transfer, result in the stratification of microbial species with anoxic pockets in the interior of the granules that may be suitable to harbor anammox bacteria. Therefore, the main objective of this study was to investigate the feasibility of start-up of the anammox process by seeding the reactor with aerobic granular sludge by using an upflow anaerobic sludge blanket (UASB) reactor. After the successful start-up and the formation of anammox granules, the structure and physicochemical properties of the anammox granules and the reactor performance were characterized. Microbial community analysis revealed that the dominant anammox species was related to a species of anammox bacteria present in anammox biofilms.     

Application, eco-physiology and biodiversity of anaerobic ammonium-oxidizing bacteria

The demand for new and sustainable systems for nitrogen removal has increased dramatically in the last decade. It is clear that the conventional systems cannot deal with the increasing nitrogen loads in a cost effective way. As an alternative, the implementation of the anammox (anaerobic ammonium oxidation) process in the treatment of wastewater with high ammonium concentrations has been started. The compact anammox reactors can sustain high nitrogen loads without any problems. The highest observed anammox capacity is 8.9 kg N removed m^-3 reactor day^-1. The first 75 m³ anammox reactor is operating in Rotterdam, the Netherlands, combined with the partial nitrification process Single reaction system for High Ammonium Removal Over Nitrite (SHARON). Partial nitrification and anammox can also be combined in one reactor systems like Completely Autotrophic Nitrogen removal Over Nitrite (CANON) or Oxygen Limited Ammonium removal via Nitrification Denitrification (OLAND) where aerobic ammonium-oxidizing bacteria (AOB) and anammox bacteria cooperate under oxygen-limitation. These systems remove about 1.5 kg N m^-3 reactor day^-1. In addition to ammonium, urea can also be converted in the CANON system after a two-week adaptation period. The ecophysiological properties of the anammox bacteria make them very well suited to convert ammonium and nitrite. The K_s values for ammonium and nitrite are below 5 M. However, nitrite above 10 mM is detrimental for the anammox process, and oxygen reversibly inhibits the process at concentrations as low as 1 M. Acetate and propionate can be used by the anammox bacteria to convert nitrite and nitrate, whereas methanol and ethanol severely inhibit the anammox reaction. The enzyme hydroxylamine/hydrazine oxidoreductase (HAO), one of the key enzymes, is located in the anammoxosome, which is a membrane bound organelle. The membranes of the anammox bacteria contain unique ladderane lipids and hopanoids. The bacteria responsible for the anammox reaction are related to the Planctomycetes. The first anammox bacteria were isolated via Percoll centrifugation and characterized as Candidatus Brocadia anammoxidans. Survey of different wastewater treatment plants using anammox specific 16S rRNA gene primers and anammox specific oligonucleotide probes has revealed the presence of at least three other anammox bacteria, which have been tentatively named Candidatus Kuenenia stuttgartiensis, Candidatus Scalindua wagneri and Candidatus Scalindua brodae. A close relative of the latter, Candidatus Scalindua sorokinii was found to be responsible for about 50% of the nitrogen conversion in the anoxic zone of the Black Sea, making the anammox bacteria an important player in the oceanic nitrogen cycle.     

Effect of Nitric Oxide on Anammox Bacteria

The effects of nitrogen oxides on anammox bacteria are not well known. Therefore, anammox bacteria were exposed to 3,500 ppm nitric oxide (NO) in the gas phase. The anammox bacteria were not inhibited by the high NO concentration but rather used it to oxidize additional ammonium to dinitrogen gas under conditions relevant to wastewater treatment.Nitric oxide (NO) has several different roles in bacteria, fungi, and mammals (24). In nitrogen cycle bacteria, it acts as an intermediate and cell communication/signal transduction molecule. On the other hand, NO is a highly reactive and toxic compound that contributes to ozone depletion and air pollution (5). Due to its reactive nature, many bacteria employ an arsenal of proteins (those encoded by norVW, as well as bacterial globins, heme proteins, etc.) that are used to detoxify NO to the less-reactive and more-stable nitrous oxide (N₂O) (24). Still, N₂O is a very effective greenhouse gas and an unfavorable constituent in the off-gases from nitrification/denitrification nitrogen removal systems (4). The presence of gene(s) encoding cytochrome cd₁ nitrite reductase (EMBL accession no. {"type":"entrez-protein","attrs":{"text":"CAJ74898","term_id":"91201838","term_text":"CAJ74898"}}CAJ74898), flavorubredoxin NorVW (accession no. {"type":"entrez-protein","attrs":{"text":"CAJ73918","term_id":"91200863","term_text":"CAJ73918"}}CAJ73918 and {"type":"entrez-protein","attrs":{"text":"CAJ73688","term_id":"91200638","term_text":"CAJ73688"}}CAJ73688), and bacterial hemoglobin (accession no. {"type":"entrez-protein","attrs":{"text":"CAJ72702","term_id":"91203063","term_text":"CAJ72702"}}CAJ72702) in the genome of Kuenenia stuttgartiensis led to the proposal that NO also plays this dual role (metabolic versus toxic) in anammox bacteria (Fig. ​(Fig.1)1) (10, 20). This has ramifications for both application and metabolism of anammox bacteria. The source of NO in an anammox reactor could be the activity of other community members (ammonium-oxidizing or denitrifying bacteria) or high concentrations of nitrite in the influent wastewater stream. Full-scale anammox reactors typically contain a significant population of ammonium-oxidizing bacteria (AOB). In the single nitritation-anammox reactors, these carry out the conversion of 50% of the ammonium in the wastewater to nitrite (6). It has been shown that AOB may produce significant amounts of NO (2, 7), and recently it was reported that NO and N₂O could be emitted from these reactors up to 0.005 and 1.2% of the total nitrogen load to the reactor, respectively (6, 23). NO may inhibit the anammox bacteria and could also be further reduced to N₂O in these reactors (6, 23). It is presently unknown whether anammox bacteria contribute to the NO or N₂O emissions, although it has been suggested previously that anammox bacteria do not produce N₂O under physiologically relevant conditions (10). Nevertheless, if conversion of NO could be coupled to anaerobic ammonium oxidation, the toxic air pollutant NO would facilitate further removal of ammonium in full-scale anammox bioreactors. In the present study, we investigated the effect of very high NO fluxes on anammox bacteria.Open in a separate windowFIG. 1.The hypothetical anammox pathway with possible routes of NO removal. Solid black arrows: anammox pathway, including nitrite oxidation to nitrate; gray arrow, possible detoxification pathway to N₂O (not observed in the bioreactor); dashed gray arrow, NO oxidation to nitrite/nitrate (not possible under anoxic conditions).NO has been described many times as a potent inhibitor of nitrogen cycle bacteria; aerobic ammonium oxidizers, nitrite oxidizers, and denitrifiers were all inhibited by concentrations as low as a few micromolar units (1, 18, 24). In a previous study, it was suggested that “Candidatus Brocadia anammoxidans” could tolerate up to 600 ppm NO (approximately 1 mg NO·day⁻¹ NO load) (16). In the reported experiments, without direct measurement of nitrous oxide (N₂O) in the effluent gas stream, it was postulated that NO was reduced to N₂O (16). In the present study, we used a carefully monitored sequencing batch reactor (SBR) to further our understanding of the effect and fate of NO in a laboratory-scale anammox reactor under conditions which are relevant in wastewater treatment plants.An SBR (working volume, 3.5 liters) consisting of approximately 80% of the anammox bacterium “Candidatus Brocadia fulgida” and no detectable aerobic ammonium oxidizers (determined by fluorescence in situ hybridization (FISH) as described previously [15]) was used in the present study. Before the first introduction of NO into the reactor, the influent (synthetic wastewater) (21) was supplied to the reactor at a flow rate of 1.4 ml·min⁻¹ with nitrite and ammonium concentrations (assayed as previously described [9]) at 45 and 39 mM, respectively (corresponding to a total of 2,370 mg N·day⁻¹). All nitrite was consumed in the reactor, while 2 mM ammonium was still present in the effluent. For every 1 mol of ammonium, 1.22 mol of nitrite was consumed, similar to the previously determined anammox stoichiometry (19). NO was first introduced at a concentration of 400 to 600 ppm in the gas phase at a flow rate of 10 ml/min (CLD 700EL chemiluminescence NOx analyzer, detection limit of 0.1 ppm NO, with 15 ml/min Ar/CO₂ as the dilution gas [a load of 25 to 28 mg NO·day⁻¹]; EcoPhysics, Michigan). During this period, 45% (±6%) of the supplied NO was removed from the system. Initially, there was no detectable change in the ammonium and nitrite removal efficiencies and no detectable nitrous oxide (N₂O) in the flue gas (analyzed with an Agilent 6890 gas chromatograph). It is most likely that NO was converted to N₂, but the increase in the N₂ concentrations in the off-gas was below the detection limit (1,000 ppm).At day 49, the influent NO concentration was increased to 3,500 ppm (640 mg NO·day⁻¹ load). Simultaneously, the stirring speed of the reactor was increased from 200 to 600 rpm to enable better mass transfer to the flocculent anammox biomass. The increase in the stirring speed did not result in any disturbance in the floc size and settling ability of the biomass but did lead to a much higher level of NO removal (128 mg NO·day⁻¹) by the anammox bacteria. The converted NO could theoretically be converted to N₂O via detoxification enzymes or coupled to ammonium oxidation (Fig. ​(Fig.1).1). Surprisingly, there was no change in the nitrite removal capacity of the bioreactor, suggesting that NO was not a substrate preferred over nitrite. Nitrate concentrations (assayed according to the method in reference 9) were stable around 7.2 mM (±0.7 mM). Theoretically, as anammox bacteria reduce NO, they could oxidize a larger proportion of nitrite to nitrate (Fig. ​(Fig.1)1) to increase their capacity for CO₂ fixation; however, such an increase in nitrate production was not observed (or could not be discriminated by the method used [sensitivity, 100 μM]). During this phase of the experiment, the effluent ammonium concentration gradually decreased to below the detection limit (Fig. ​(Fig.2).2). There was only a minimal N₂O (0.6 ppm) emission from the system, and the total N₂ production increased from 3,060 to 3,680 mg N₂·day⁻¹. This indicated that NO reduction was coupled to the catabolism of the anammox bacteria rather than being detoxified by anammox or other community members. To the best of our knowledge, this was the first time that such a high load of NO was not found to be toxic to the nitrogen cycle bacteria. In a previous study, an NO load of 1 mg NO·day⁻¹ was reported to be toxic to anammox bacteria, most probably due to the fact that the experiments were conducted with biomass that had a 100-fold lower cell density and 10-fold lower activity compared to the current enrichment cultures. Furthermore, the NO conversion in the current experiments was stoichiometrically coupled to ammonium oxidation and not converted to N₂O, indicating that the previously reported N₂O emissions from full-scale anammox bioreactors originated not with the anammox bacteria but rather with other community members as hypothesized previously (8).Open in a separate windowFIG. 2.Ammonium concentration in the effluent of the anammox bioreactor. Dashed lines indicate the trend of effluent ammonium concentration during different phases of the reactor operation. Black arrows indicate the manipulations to influent NO stream, and the gray arrow points to an increase in the influent ammonium concentration. d, day.To determine if there could be more NO-dependent ammonium removal, the influent ammonium concentration was first increased to 41 mM (day 80) and then to 43 mM (day 81). This resulted in a slow but gradual increase in the effluent ammonium concentration, and additional ammonium did not appear to be completely converted, most probably due to NO mass transfer limitations. As a result of the higher level of ammonium removal, the observed anammox stoichiometry in the reactor decreased from 1.22 to 0.91 (nitrite/ammonium). Between days 95 and 131, the NO supply to the reactor was turned off, which resulted in an average ammonium concentration of 3.3 mM (±0.9 mM) in the effluent. Following this period, on day 132, the NO load on the reactor was increased back to 640 mg NO·day⁻¹ (Fig. ​(Fig.2).2). As a result, the effluent ammonium concentration gradually decreased again to an average of 1.5 mM (±0.36 mM). The highest level of NO removal achieved in this period was 371 mg NO·day⁻¹. When the NO supply was turned off on day 165, ammonium concentrations increased back to 3.5 mM (±0.71 mM).During the course of the experiment, the biodiversity of the reactor was monitored using FISH and 16S rRNA gene sequence analysis as described previously (15) with probes specific to eubacteria (3), Planctomycetes (13), anammox bacteria (15), “Ca. Brocadia fulgida” (11), and a variety of aerobic ammonium-oxidizing bacteria (12, 22). Before the experiments started and throughout the cultivation of the anammox bacteria with NO, the only detectable anammox species (with FISH and 16S rRNA gene sequence analysis) was “Candidatus Brocadia fulgida.”In the present study, we showed that 2 mM ammonium (4.5% of the influent concentration) could be removed by anammox bacteria via direct coupling to NO reduction. These observations support the proposal of NO as an intermediate of the anammox reaction and have two consequences for application of the anammox process for nitrogen removal. First, we obtained strong indications that previously reported N₂O emissions (6, 8) from full-scale anammox reactors were not generated by anammox bacteria. In our experiments, even under a very high load of NO, there was hardly any detectable N₂O in the effluent gas stream. The competition for nitrogen oxides by denitrifying and anammox bacteria needs further study but may ultimately be used to design operational conditions that would reduce or even prevent NO and N₂O emissions from full-scale nitritation-anammox reactors. Second, by implementing the results of this study, in the future the anammox process could be designed to remove NO from flue gases. Since NO is mostly emitted together with O₂, this could be achieved by the combination of anammox and aerobic ammonium-oxidizing bacteria, for example, with CANON (completely autotrophic nitrogen removal over nitrite)- or OLAND (oxygen-limited autotrophic nitrification-denitrification)-type reactor systems (14, 17).     

Effects of allylthiourea,salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms

Anaerobic ammonium-oxidizing (anammox) bacteria, aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB) are three groups of ammonia/ammonium-oxidizing prokaryotes (AOPs) involved in the biochemical nitrogen cycling. In this study, the effects of allylthiourea (ATU), pH, and salinity on these three groups from mangrove sediment were investigated through microcosm incubation in laboratory. ATU treatments (50, 100, and 500 mg L^?1) obviously affected the community structure of anammox bacteria and AOB, but only slightly for AOA. ATU began to inhibit anammox bacteria growth slightly from day 10, but had an obvious inhibition on AOA growth from the starting of the study. At 100 mg L^?1 of ATU or higher, AOB growth was inhibited, but only lasted for 5 days. The pH treatments showed that acidic condition (pH 5) had a slight effect on the community structure of anammox bacteria and AOA, but an obvious effect on AOB. Acidic condition promoted the growth of all groups of AOPs in different extent, but alkaline condition (pH 9) had a weak effect on AOB community structure and a strong effect on both anammox bacteria and AOA. Alkaline condition obviously inhibited anammox bacteria growth, slightly promoted AOA, and slightly promoted AOB in the first 20 days, but inhibited afterward. Salinity treatment showed that higher salinity (20 and 40?‰) resulted in higher anammox bacteria diversity, and both AOA and AOB might have species specificity to salinity. High salinity promoted the growth of both anammox bacteria and AOB, inhibited AOA between 5 and 10 days, but promoted afterward. The results help to understand the role of these microbial groups in biogeochemical nitrogen cycling and their responses to the changing environments.     

Nitrogen removal with the anaerobic ammonium oxidation process

Anaerobic ammonium-oxidizing (anammox) bacteria convert ammonium to N₂ with nitrite as the terminal electron acceptor in the absence of O₂. Nitritation–anammox bioreactors provide a cost-effective and environment-friendly alternative to conventional nitrification/denitrification nitrogen removal systems. Currently, this process is only applied for ammonium removal from wastewater with high ammonium load and temperature. Nevertheless, recent results obtained with laboratory-scale bioreactors suggest new possible routes of application of the Nitritation–anammox technology including (1) municipal wastewater treatment, removal of (2) methane in combination with nitrite-reducing methane-oxidizing bacteria, (3) nitrate coupled to organic acid oxidation and (4) nitrogen oxides. The current review summarizes the state-of-the-art of the application of Nitritation–anammox systems and discusses the possibilities of utilizing these recent results for wastewater treatment.