Nitrification and Anammox with Urea as the Energy Source

Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches

Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.

"Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces

Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.

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

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

The benefits of autotrophic nitrogen removal from high concentration of urea wastewater through a process of urea hydrolysis and partial nitritation in sequencing batch reactor

For the sake of high efficiency and saving operational cost for high-concentration urea wastewater treatment, a novel two-stage partial nitritation (PN)-anammox process containing simultaneous urea hydrolysis and PN in sequencing batch reactor (SBR) was investigated. Although the influent urea concentration increased from 500 to 1200 mg/L, the SBR simultaneously achieved urea removal efficiency higher than 98% and stable PN with effluent NO₂^--N/NH₄⁺-N ratio of 1.0-1.3 without any extra alkalinity addition. The intracellular hydrolysis was the dominant mechanism for urea removal and persistent free ammonia inhibition on nitrite-oxidizing bacteria was the main reason for nitrite accumulation of 97.92% in SBR. The subsequent anammox reactor showed efficient nitrogen removal performance with average ammonium removal efficiency, nitrogen removal efficiency and maximum nitrogen removal loading rate of 98.08%, 81.45% and 1.05 kg N·m^-3·d^-1 respectively. High-throughput sequencing results indicated Gemmatimonadetes became the most abundant bacterial phylum related to potential intracellular urea hydrolysis and displayed obvious ammonium-oxidizing bacteria enrichment and nitrite-oxidizing bacteria inhibition in SBR, and the dominant anammox bacteria (Candidatus_Kuenenia) in anammox reactor. The proposed process was proven to be promising for high-concentration urea wastewater treatment, facilitating the sustainable development of the urea industry in the future.

The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons

In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.

Performance and mechanism of urea hydrolysis in partial nitritation system based on SBR

Urea hydrolysis in partial nitritation process forming nitrite and ammonia is advantageous to subsequent treatment with ANAMMOX for total nitrogen removal. In this study, stable partial nitritation for urea wastewater with urea increasing from 250 to 2000 mg L^-1 were achieved in an aerobic SBR. Urea removal efficiency and nitrite accumulation percentage both kept above 98%, with nitrite production rate about 0.985 kg N·m^-3·d^-1. Urea hydrolysis mechanism in this aerobic system was described as, (1) massive urea in the bulk was absorbed into cell, (2) urea was hydrolyzed by intracellular urease inside cell, (3) produced ammonia then slowly diffused into the bulk through membrane, which is later converted by ammonia-oxidizing bacteria (AOB) into nitrite. Due to this mechanism, the activity of AOB could not be inhibited by high FA (free ammonia) value under high urea concentration condition while nitrite-oxidizing bacteria (NOB) remained to be inhibited. An uncultured genus belonging to poorly characterized phylum Gemmatimonadetes was found enriched in this process and became dominant genus. This genus was speculated to have same energy pathway like ureaplasma, by absorbing excessive urea from environment and utilize urea hydrolysis to generate energy. So it was believed to be responsible for urea hydrolysis mechanism mentioned above. This SBR showed stable partial nitritation and high urea removal efficiency for treating urea wastewater, which was obviously feasible as the pretreatment process for subsequent ANAMMOX.

A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.

Comparative study of activated sludge with different individual nitrogen sources at a low temperature: Effluent dissolved organic nitrogen compositions, metagenomic and microbial community

The objective of this study was to explore nitrogen removal, especially effluent dissolved organic nitrogen (DON) composition, relative genes and microbial community structures with four individual nitrogen sources at 5°C. Results show that effluent DON did not have dependent relationship with the TN removal rate (urea>ammonia chloride>L-Alanine>D-Alanine). With the same influent TN, the highest effluent DON was formed with urea; the lowest DON was fed with ammonia chloride. The main DON composition was the product of cell metabolism excluding urea, rather than the original substrate. Glutamic acid synthesizing process was of great importance to DON accumulation at 5°C. The nitrogen source type was important to the diversity and heterogeneity of the nitrogen removal genes. Bacterial population structure using redundancy analysis (RDA) showed Simplicispira occupied a higher abundance remarkably in the reactors feeding with urea, and Dyadobacter occupied higher feeding with l-Alanine.

Simultaneous partial nitrification, anaerobic ammonium oxidation and denitrification (SNAD) in a full-scale landfill-leachate treatment plant

The occurrence of simultaneous partial nitrification, anaerobic ammonium oxidation and denitrification (SNAD) observed in a single partially aerated full-scale bioreactor treating landfill-leachate is reported in this paper. At present, the full-scale bioreactor is treating an average leachate flow of 304 m(3)d(-1) with a sludge retention time between 12 and 18d. The average COD, NH(4)(+)-N and NO(3)(-)-N concentrations at the upstream end of the bioreactor, i.e., influent, are 554, 634 and 3 mg L(-1), respectively; whereas no NO(2)(-)-N is detected in the influent. The percentage removals of COD and NH(4)(+)-N in the bioreactor were 28% and 80%, respectively. A nitrogen mass balance approach was adopted to analyze the performance of SNAD in the full-scale bioreactor. The total nitrogen (TN) removal by combined partial nitrification and anaerobic ammonium oxidation is 68% and the heterotrophic denitrification contributes to 8% and 23% of TN and COD removals, respectively. The red granule in the bioreactor was analyzed by using fluorescence in situ hybridization and polymerase chain reaction. The results of both analytical methods confirm the presence of anaerobic ammonium oxidizing bacteria as the predominant species along with other Planctomycete-like bacteria. Overall, the SNAD process offers the simultaneous removals of nitrogen and COD in the wastewater.

Effect of alum treatment on the concentration of total and ureolytic microorganisms in poultry litter

Microbial mineralization of urea and uric acid in poultry litter results in the production of ammonia, which can lead to decreased poultry performance, malodorous emissions, and loss of poultry litter value as a fertilizer. Despite the fact that this is a microbial process, little is known about how the microbial populations, especially ammonia-producing (ureolytic) organisms in poultry litter, respond to litter amendments such as aluminum sulfate (Al(2)(SO(4))(3).14H(2)O; alum). The goal of this study was to measure the temporal changes in total bacterial and fungal populations and urease-producing microorganisms in nontreated litter or litter treated with 10% alum. Quantitative real-time polymerase chain reaction was used to target the bacterial 16S rRNA gene, the fungal 18S rRNA gene, or the urease gene of bacterial and fungal ammonia producers in a poultry litter incubation study. Nontreated poultry litter had relatively high total (2.8 +/- 0.8 x 10(10) cells g(-1) litter) and ureolytic (2.8 +/- 1.3 x 10(8) cells g(-1) litter) bacterial populations. Alum treatment reduced the total bacterial population by 50% and bacterial urease producers by 90% within 4 wk. In contrast, at 16 wk after alum treatment, the fungal population was three orders of magnitude higher in alum-treated litter than in nontreated litter (3.5 +/- 0.8 x 10(7) cells g(-1) litter and 5.5 +/- 2.5 x 10(4) cells g(-1) litter, respectively). The decrease in pH produced by alum treatment is believed to inhibit bacterial populations and favor growth of fungi that may be responsible for the mineralization of organic nitrogen in alum-treated litters.

Combined process of urea nitrogen removal in anaerobic Anammox co-culture reactor

In this study, the feasibility of biological urea nitrogen removal in anaerobic Anammox co-culture was investigated. After 100 days of operation, complete urea nitrogen removal of 0.35 g (NH(2))(2)CO-N L(-1) d(-1) was achieved. The pure Anammox bacteria were obtained by percoll density-gradient centrifugation and found to be of incapable to hydrolyze urea. The ureolytic bacteria were isolated from the Anammox co-culture by the spread plate and streak. Comparative analysis of partial 16S rDNA sequence presented it belongs to Bacillus sp., and so named as Bacillus sp. LST-1. Fluorescence in situ hybridization was applied to identify the ratio of Bacillus sp. and Anammox in the reactor and the value was approximately 1:4. Urea nitrogen removal was realized in this autotrophic, anoxic reactor via the combined process of urea hydrolysis by Bacillus sp. LST-1 and ammonium oxidizing by Anammox. The investigation of this combined process might have an actual significance in engineering application for its low operational cost.

Competition and coexistence of aerobic ammonium- and nitrite-oxidizing bacteria at low oxygen concentrations

In natural and man-made ecosystems nitrifying bacteria experience frequent exposure to oxygen-limited conditions and thus have to compete for oxygen. In several reactor systems (retentostat, chemostat and sequencing batch reactors) it was possible to establish co-cultures of aerobic ammonium- and nitrite-oxidizing bacteria at very low oxygen concentrations (2-8 microM) provided that ammonium was the limiting N compound. When ammonia was in excess of oxygen, the nitrite-oxidizing bacteria were washed out of the reactors, and ammonium was converted to mainly nitrite, nitric oxide and nitrous oxide by Nitrosomonas-related bacteria. The situation could be rapidly reversed by adjusting the oxygen to ammonium ratio in the reactor. In batch and continuous tests, no inhibitory effect of ammonium, nitric oxide or nitrous oxide on nitrite-oxidizing bacteria could be detected in our studies. The recently developed oxygen microsensors may be helpful to determine the kinetic parameters of the nitrifying bacteria, which are needed to make predictive kinetic models of their competition.

1994-2004: 10 years of research on the anaerobic oxidation of ammonium

The obligately anaerobic ammonium oxidation (anammox) reaction with nitrite as primary electron acceptor is catalysed by the planctomycete-like bacteria Brocadia anammoxidans, Kuenenia stuttgartiensis and Scalindua sorokinii. The anammox bacteria use a complex reaction mechanism involving hydrazine as an intermediate. They have a unique prokaryotic organelle, the anammoxosome, surrounded by ladderane lipids, which exclusively contains the hydrazine oxidoreductase as the major protein to combine nitrite and ammonia in a one-to-one fashion. In addition to the peculiar microbiology, anammox was shown to be very important in the oceanic nitrogen cycle, and proved to be a very good alternative for treatment of high-strength nitrogenous waste streams. With the assembly of the K. stuttgartiensis genome at Genoscope, Evry, France, the anammox reaction has entered the genomic and proteomic era, enabling the elucidation of many intriguing aspects of this fascinating microbial process.

Enrichment of anammox from activated sludge and its application in the CANON process

A microbial culture capable of actively oxidizing ammonium to dinitrogen gas in the absence of oxygen, using nitrite as the electron acceptor, was enriched from local activated sludge (Western Australia) in <14 weeks. The maximum anaerobic ammonium oxidation (i.e., anammox) activity achieved by the anaerobic culture was 0.26 mmol NH (4) (+) (g biomass)(-1) h(-1) (0.58 kg total-N m(-3) day(-1)). Qualitative FISH analysis (fluorescence in situ hybridization) confirmed the phylogenetic position of the enriched microorganism as belonging to the order Planctomycetales, in which all currently identified anammox strains fall. Preliminary FISH analysis suggests the anammox strain belongs to the same phylogenetic group as the Candidatus 'Brocadia anammoxidans' strain discovered in the Netherlands. However, there are quite a few differences in the target sites for the more specific probes of these organisms and it is therefore likely to represent a new species of anammox bacteria. A small amount of aerobic ammonium-oxidizing biomass was inoculated into the anammox reactor (10% v/v) to initiate completely autotrophic nitrogen removal over nitrite (the CANON process) in chemostat culture. The culture was always under oxygen limitation and no organic carbon was added. The CANON reactor was operated as an intermittently aerated system with 20 min aerobiosis and 30 min anaerobiosis, during which aerobic and anaerobic ammonium oxidation were performed in sequential fashion, respectively. Anammox was not inhibited by repeated intermittent exposure to oxygen, allowing sustained, completely autotrophic ammonium removal (0.08 kg N m(-3) day(-1)) for an extended period of time.