Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture

Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.

Quinoline's influence on nitrogen removal performance and microbial community composition of the anammox process

This study aimed to evaluate the effects of quinoline on nitrogen removal performance and microbial community of an anaerobic biofilm reactor with anammox activity. Results showed that 20 mg L^-1 quinoline addition leading the ammonia and nitrite removal efficiency of the ABR reduced from about 90% to 40%. Illumina MiSeq sequencing study indicated that microbial community structure and composition varied with the additive of quinoline. Planctomycetes and Bacteroidetes, decreased in abundance, suggested that quinoline adversely affects the anammox metabolism within the anammox reactor. The distribution of the anammox bacteria was affected by quinoline addition. Ca. Jettenia prevailed over the other two anammox bacteria (Brodica and Kuenenia) in the recovered phase.

Nitritation-anammox process - A realizable and satisfactory way to remove nitrogen from high saline wastewater

In this study, acclimation of freshwater nitritation-anammox sludge to remove nitrogen in high saline and hypersaline wastewater was evaluated, during which the microbes activity and microbial community revolution were revealed to understand the fate of a nitritation-anammox process (SNAP) in response to increasing salt stress. By enhanced aeration, the SNAP system can treat saline (3%) ammonium-rich (185 mg/L) wastewater after gradual adaption. Hypersalinity (5%) caused final deterioration of the SNAP system due to a severe inhibition on anammox activity. Genera Kuenenia (anammox), Nitrosomonas (AOB) and Nitrosovibrio (AOB) bacteria were salt adaptable microbes, while genus Nitrospira (NOB) bacteria were sensitive to salinity. Under the enhanced aeration, AOB bacteria could bear 3% salinity with possible enriched ammonia monooxygenase to stimulate the conversion of ammonium to nitrite by producing more intermediate-hydroxylamine, which could alleviate the negative effect of insufficient hydroxylamine oxidase members in AOB bacteria.

Metagenomics Response of Anaerobic Ammonium Oxidation (anammox) Bacteria to Bio-Refractory Humic Substances in Wastewater

Anammox-based processes have been widely applied for the treatment of wastewater (e.g., wastewater irrigation systems and constructed wetland) which consists of bio-refractory humic substances. Nonetheless, the impacts of bio-refractory humic substances on anammox consortia are rarely reported. In the present study, three identical lab-scale anammox reactors (i.e., HS0, HS1 and HS10), two of which were dosed with humic substances at 1 and 10 mg·L−1, respectively, were operated for nearly one year. The long-term operation of the reactors showed that the presence of humic substances in influent had no significant influence on nitrogen removal rates. Despite this, comparative metagenomics showed changes in anammox microbiota structure during the exposure to humic substance; e.g., the relative abundance of Candidatus Kuenenia was lower in HS10 (18.5%) than that in HS0 (22.8%) and HS1 (21.7%). More specifically, a lower level of humic substances (1 mg·L−1) in influent led to an increase of genes responsible for signal transduction, likely due to the role of humic substances as electron shuttles. In contrast, a high level of humic substances (10 mg·L−1) resulted in a slight decrease of functional genes associated with anammox metabolism. This may partially be due to the biodegradation of the humic substances. In addition, the lower dosage of humic substances (1 mg·L−1) also stimulated the abundance of hzs and hdh, which encode two important enzymes in anammox reaction. Overall, this study indicated that the anammox system could work stably over a long period under humic substances, and that the process was feasible for leachate treatment.

Efficient step-feed partial nitrification, simultaneous Anammox and denitrification (SPNAD) equipped with real-time control parameters treating raw mature landfill leachate

An innovative step-feed partial nitrification, simultaneous Anammox and denitrification (SPNAD), equipped with real-time control parameters, achieved efficient nitrogen removal from raw mature landfill leachate. The variables pH and ORP served as real time on-line parameters to flexibly control the durations of aerobic and anoxic. A nitrogen removal efficiency (NRE) of 98.7% and nitrogen removal rate (NRR) of 0.23 kg m^-3d^-1 were obtained at the influent NH₄⁺ -N, SCOD and total nitrogen (TN) of 1000 ± 250 mg L^-1, 1100 ± 200 mg L^-1, and 1300 ± 75 mg L^-1, respectively. Mass balance research demonstrated that Anammox contributed 69.3% to nitrogen removal and denitrification contributed 15.7%. A significant change in the Anammox community structure occurred (ca. Brocadia from 0.26% to 2.13%, ca. Kuenenia from 0.29% to 0.02%). This change is mainly attributed to different kinetic strategies (R-strategist of ca. Brocadia and K-strategist of ca. Kuenenia). Further study revealed the co-existence of functional microorganisms Nitrosomonas (3.0%), Cadidatus-Brocadia (2.13%), and Thauera (25.3%).

Study on the expanded culture and kinetics of anammox bacteria in the upper flow packed bed

Anaerobic ammonium oxidation (Anammox) technology has a unique advantage in the simultaneous treatment of ammonia nitrogen and nitrite nitrogen. Kinetics models were usually utilized to identify an expanded anammox reactor to be efficient and stable. And the high-throughput sequencing test had been utilized to identify different kinds of anammox bacteria for a long time. The Monod model showed that the theoretical maximum total nitrogen removal concentration was near 1700 mgN/(gVSS·d). Nitrite nitrogen was an obvious inhibitor of anammox bacteria based on the kinetics results of both Monod model and Haldane model. The Luong model indicated that there was still a great potential of improvement of total influent nitrogen concentration. And the Modified Stover-Kincannon Model and Grau second-order model were applicable to describe stable operation of the reactor. While, high-throughput sequencing test results indicated that the bacteria Candidatus Kuenenia was the dominant anammox bacteria of this reactor, which meant that Candidatus Kuenenia was more applicable for operation condition of the reactor. Interestingly, the original bacterium Candidatus Anammoxoglobus was gradually eliminated during the operation phase. The reactor still had a quite high potential for the removal of the substrate. In the process of culture expansion, the phenomenon of bacterial species alteration had emerged, which was relatively rare in previous papers.

Effect of temperature on nitrogen removal and biological mechanism in an up-flow microaerobic sludge reactor treating wastewater rich in ammonium and lack in carbon source

Previous study has demonstrated that microaerobic process is effective in nitrogen removal from the wastewater with high ammonium and low carbon to nitrogen ratio. In the microaerobic system, synergistic action of anammox, ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and denitrifiers was the key issues to remove nitrogen from the wastewater rich in ammonium. Temperature has a significant effect on specific growth rate and activity of various nitrogen removal functional bacteria. In this study, the effect of temperature (35 °C-15 °C) on nitrogen removal were investigated in an up-flow microaerobic sludge reactor (UMSR) at the HRT of 8 h and reflux ratio of 45. Above 71.2% of total nitrogen (TN) and 80.7% of NH₄⁺ removal efficiencies were observed at the temperature no less than 17 °C. With the temperature further decreasing to 15 °C, denitrifiers still dominant the UMSR, but AOB, NOB and Candidatus Brocadia as the predominant anammox bacteria were inhibited revealed by high throughput sequencing, resulting in the decrease of TN and NH₄⁺ removal to 39.7% and 61.8%, respectively. Fortunately, when the temperature rebounded to 20 °C, a higher TN and NH₄⁺ removal of 81.2% and 97.3% were obtained again in the UMSR.

Nitrogen cycling during wastewater treatment

Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.

Is anammox a promising treatment process for nitrogen removal from nitrogen-rich saline wastewater?

Rapidly growing discharge of nitrogen-rich saline wastewater has significantly affect environment. However, due to the inhibition resulting from high salinity on microbes, it is still a challenge to treat nitrogen-rich saline wastewater efficiently. Anammox process, as a cost-effective and environment-friendly nitrogen removal approach, has shown a potential in treating nitrogen-rich saline wastewater. This review is conducted from a critical perspective and provides a comprehensive overview on the performance of anammox process treating nitrogen-rich saline wastewater. Two strategies including freshwater-derived anammox bacteria acclimatization and marine anammox bacteria enrichment are evaluated. Second, effects resulting from salinity on the performance of anammox reactor, the microbial communities and sludge characteristics are discussed. Third, salinity-tolerant mechanism of anammox bacteria is analyzed. This review also reveals some critical knowledge gaps and future research needs, which benefits application of anammox process to treat nitrogen-rich saline wastewater.

Synergistic inhibition of anaerobic ammonium oxidation (anammox) activity by phenol and thiocyanate

Coke-oven wastewater discharged from the steel-manufacturing process is phenol and thiocyanate (SCN)-rich wastewater, which inhibits microbial activities in biological wastewater treatment processes. In the present study, synergistic inhibition of anaerobic ammonium oxidation (anammox) activity by phenol and SCN was examined by batch incubation and continuous operation of an anammox reactor. The comparison of anammox activities determined in the batch incubation, in which the anammox biomass was anoxically incubated with 10-250 mg L^-1 of i) phenol, ii) SCN, or iii) both phenol and SCN, showed that synergistic inhibition by phenol and SCN was greater than the inhibitions by phenol or SCN alone. The synergistic inhibition by phenol and SCN was further investigated by operating an up-flow column anammox reactor for 262 d. The removal efficiencies of NH₄⁺ and NO₂^- deteriorated when phenol and SCN concentrations in the influent increased to 16 and 32 mg L^-1, respectively, and the inhibition of anammox activity was further investigated by a¹⁵NO₂^- tracer experiment. Addition of phenol and SCN resulted in a population shift of anammox bacteria, and the dominant species changed from "Candidatus Kuenenia stuttgartiensis" to "Ca. Brocadia sinica". The relative abundance of Azoarcus and Thiobacillus 16S rRNA gene reads increased during the operation, suggesting that they were responsible for the anaerobic phenol and SCN degradation. The present study is the first to document the synergistic inhibition of anammox activity by phenol and SCN and the microbial consortia involved in the nitrogen removal as well as the phenol and SCN degradations.

Nitrogen removal through "Candidatus Brocadia sinica" treating high-salinity and low-temperature wastewater with glycine addition: Enhanced performance and kinetics

Freshwater-derived anaerobic ammonia oxidation (anammox) bacteria ("Candidatus Brocadia sinica") were investigated to remove nitrogen from high-salinity and low-temperature wastewater with glycine addition. The reactor was operated at 15 ± 0.5 °C with influent pH of 7.5 ± 0.1. When glycine were 0.2, 0.4, and 0.6 mM, respectively, nitrite removal rate (NRR) increased by 27.7%, 47.3%, and 70.4% accordingly. Optimal ammonia removal rate (0.32 kg/(m³·d)) and NRR (0.45 kg/(m³·d)) were achieved at 0.8 mM glycine. Effect resulting from glycine on nitrite reductase was higher than hydrazine synthase. Moreover, ΔNO₂^--N/ΔNH₄⁺-N increased with glycine addition while ΔNO₃^--N/ΔNH₄⁺-N first increased and then decreased. The remodified Logistic model and modified Boltzmann model were appropriate to describe nitrogen removal with glycine addition. Kinetic parameter λ achieved through the remodified Logistic model revealed that "Candidatus Brocadia sinica" had a shorter lag phase than that of marine anammox bacteria.

High-resolution mapping and modeling of anammox recovery from recurrent oxygen exposure

Oxygen inhibits anammox, a bioconversion executed by anoxic ammonium oxidizing bacteria (AnAOB). Nonetheless, oxygen is mostly found in the proximity of AnAOB in nitrogen removal applications, being a substrate for nitritation. The experiments performed to date were mostly limited to batch activity tests where AnAOB activity is estimated during oxygen exposure. However, little attention has been paid to the recovery and reversibility of activity following aerobic conditions, of direct relevance for bioreactor operation. In this work, anoxic and autotrophic reactor cultivation at 20 °C yielded an enriched microbial community in AnAOB, consisting for 75% of a member of the genus Brocadia. High-resolution kinetic data were obtained with online ammonium measurements and further processed with a newly developed Python data pipeline. The experimentally obtained AnAOB response showed complete inhibition until micro-aerobic conditions were reached again (<0.02 mg O₂ L^-1). After oxygen inhibition, AnAOB recovered gradually, with recovery times of 5-37 h to reach a steady-state activity, dependent on the perceived inhibition. The recovery immediately after inhibition was lowest when exposed to higher oxygen concentrations (range: 0.5-8 mg O₂ L^-1) with long contact times (range: 9-24 h). The experimental data did not fit well with a conventional 'instant recovery' Monod-type inhibition model. Yet, the fit greatly improved by incorporating a dynamic growth rate formula accurately describing gradual activity recovery. With the upgraded model, long-term kinetic simulations for partial nitritation/anammox (PN/A) with intermittent aeration showed a decrease in growth rate compared to the instant recovery mode. These results indicate that recovery of AnAOB after oxygen exposure was previously overlooked. It is recommended to account for this effect in the intensification of partial nitritation/anammox.

Aggregation ability of three phylogenetically distant anammox bacterial species

Anaerobic ammonium-oxidizing (anammox) bacteria are well known for their aggregation ability. However, very little is known about cell surface physicochemical properties of anammox bacteria and thus their aggregation abilities have not been quantitatively evaluated yet. Here, we investigated the aggregation abilities of three different anammox bacterial species: "Candidatus Brocadia sinica", "Ca. Jettenia caeni" and "Ca. Brocadia sapporoensis". Planktonic free-living enrichment cultures of these three anammox species were harvested from the membrane bioreactors (MBRs). The physicochemical properties (e.g., contact angle, zeta potential, and surface thermodynamics) were analyzed for these anammox bacterial species and used in the extended DLVO theory to understand the force-distance relationship. In addition, their extracellular polymeric substances (EPSs) were characterized by X-ray photoelectron spectroscopy and nuclear magnetic resonance. The results revealed that the "Ca. B. sinica" cells have the most hydrophobic surface and less hydrophilic functional groups in EPS than other anammox strains, suggesting better aggregation capability. Furthermore, aggregate formation and anammox bacterial populations were monitored when planktonic free-living cells were cultured in up-flow column reactors under the same conditions. Rapid development of microbial aggregates was observed with the anammox bacterial population shifts to a dominance of "Ca. B. sinica" in all three reactors. The dominance of "Ca. B. sinica" could be explained by its better aggregation ability and the superior growth kinetic properties (higher growth rate and affinity to nitrite). The superior aggregation ability of "Ca. B. sinica" indicates significant advantages (efficient and rapid start-up of anammox reactors due to better biomass retention as granules and consequently stable performance) in wastewater treatment application.

Autofluorescent characteristics of Candidatus Brocadia fulgida and the consequences for FISH and microscopic detection

An enrichment culture of Candidatus Brocadia fulgida was identified by three independent methods: analysis of autofluorescence using different microscope filter blocks and a fluorescence spectrometer, fluorescence in situ hybridization (FISH) with anammox-specific probes and partial sequencing of the 16S rDNA, hydrazine synthase hzsA and hydrazine oxidoreductase hzo. The filter block BV-2A (400-440, 470 LP, Nikon) was suitable for preliminary detection of Ca. B. fulgida. An excitation-emission matrix revealed three pairs of excitation-emission maxima: 288-330 nm, 288-478 nm and 417-478 nm. Several autofluorescent cell clusters could not be stained with DAPI or by FISH, suggesting empty but intact cells (ghost cells) or inhibited permeability. Successful staining of autofluorescent cells with the FISH probes Ban162 and Bfu613, even at higher formamide concentrations, suggested insufficient specificity of Ban162. Under certain conditions, Ca. B. fulgida lost its autofluorescence, which reduced the reliability of autofluorescence for identification and detection. Non-fluorescent Ca. Brocadia cells could not be stained with Ban162, but with Bfu613 at higher formamide concentrations, suggesting a dependency between both parameters. The phylogenetic analysis showed only good taxonomical clustering of the 16S rDNA and hzsA. In conclusion, careful consideration of autofluorescent characteristics is recommended when analysing and presenting FISH observations of Ca. B. fulgida to avoid misinterpretations and misidentifications.

Nitric oxide removal from flue gas with ammonium using AnammoxDeNOx process and its application in municipal sewage treatment

A novel AnammoxDeNOx process was designed to simultaneously remove NOx in flue gas and ammonium wastewater, with the aim of exploring the possibility of using NO as a long-term and stable electron acceptor for anammox bacteria. The performance of the AnammoxDeNOx process indicated a NOx removal efficiency from simulated flue gas (including CO₂, SO₂, O₂ and NO₂) of 87-96% using simulated ammonium wastewater. With municipal wastewater, the removal efficiencies for NOx were 70-90%, total nitrogen 40-70%, and COD 80-90% (NO concentration: 100-500 ppm). The anammox genus underwent considerable changes from the dominant Candidatus Kuenenia in the stage of domestication to the predominant Candidatus Brocadia, which then became the dominant species in the simulated flue gas and actual municipal wastewater stages.

Negligible seeding source effect on the final ANAMMOX community under steady and high nitrogen loading rate after enrichment using poly(vinyl alcohol) gel carriers

This study investigated the effect of seeding source on the mature anaerobic ammonia oxidation (ANAMMOX) bacterial community niche in continuous poly(vinyl alcohol) (PVA) gel systems operated under high nitrogen loading rate (NLR) condition. Four identical column reactors packed with PVA gels were operated for 182 d using different seeding sources which had distinct community structures. The ANAMMOX reaction was achieved in all the bioreactors with comparable total and ANAMMOX bacterial 16S rRNA gene quantities. The bacterial community structure of the bioreactors became similar during operation; some major bacteria were commonly found. Interestingly, one ANAMMOX species, "Candidatus Brocadia sinica", was conclusively predominant in all the bioreactors, even though different seeding sludges were used as inoculum source, possibly due to the unique physiological characteristics of "Ca. Brocadia sinica" and the operating conditions (i.e., PVA gel-based continuous system and 1.0 kg-N/(m³·d) of NLR). The results clearly suggest that high NLR condition is a more significant factor determining the final ANAMMOX community niche than is the type of seeding source.

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples

Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH₄⁺ and NO₂^- biochemically to form N₂ gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.

Experimental Evidence for in Situ Nitric Oxide Production in Anaerobic Ammonia-Oxidizing Bacterial Granules

Although nitric oxide (NO) emissions from anaerobic ammonium oxidation (anammox)-based processes were reported previously, the NO production pathways are poorly understood. Here, we investigated the NO production pathways in anammox granules in detail by combining ¹⁵N-stable isotope tracer experiments with various inhibitors, microsensor measurements, and transcriptome analysis for key genes of NO₂^- reduction. NO was emitted from the anammox granules, which account for 0.07% of the N₂ emission. ¹⁵N-stable isotope-tracer experiments indicated that most of the N₂ was produced by anammox bacteria, whereas NO was produced from NO₂^- reduction by anammox and denitrifying bacteria. The NO emission rate was highest at pH 8.0 and accelerated by increasing NH₄⁺ and NO₂^- concentrations in the culture media. The microsensor analyses showed the in situ NO production rate was highest in the outer layer of the anammox granule where anammox activity was also highest. The detected in situ NO concentrations of up to 2.7 μM were significantly above physiological thresholds known to affect a wide range of microorganisms present in wastewater. Hence, NO likely plays pivotal roles in the microbial interactions in anammox granules, which needs to be further investigated.

Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes

Various microorganisms play key roles in the nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR amplicon sequencing of N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible for N-transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive, especially when we analyze multiple samples and try to detect N cycle functional genes present at a relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named the nitrogen cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine the abundance and diversity of N cycle functional genes in wastewater samples. Although nonspecific amplification was detected on the NiCE chip, this can be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples.IMPORTANCE We report a novel approach, namely, the nitrogen cycle evaluation (NiCE) chip, by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess the diversities of N cycle functional genes. The NiCE chip technology is applicable to analysis of the temporal dynamics of N cycle gene transcription in wastewater treatment bioreactors. The NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes. While there is room for future improvement, this tool should significantly advance our ability to explore the N cycle in various environmental samples.

Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes

Various microorganisms play key roles in the nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR amplicon sequencing of N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible for N-transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive, especially when we analyze multiple samples and try to detect N cycle functional genes present at a relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named the nitrogen cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine the abundance and diversity of N cycle functional genes in wastewater samples. Although nonspecific amplification was detected on the NiCE chip, this can be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples.IMPORTANCE We report a novel approach, namely, the nitrogen cycle evaluation (NiCE) chip, by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess the diversities of N cycle functional genes. The NiCE chip technology is applicable to analysis of the temporal dynamics of N cycle gene transcription in wastewater treatment bioreactors. The NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes. While there is room for future improvement, this tool should significantly advance our ability to explore the N cycle in various environmental samples.

Deterioration of the anammox process at decreasing temperatures and long SRTs

The implementation of autotrophic nitrogen removal in the mainstream of a municipal wastewater treatment plant is currently pursued. Among the crucial unknown factors are the kinetic properties of anaerobic ammonium oxidising (anammox) bacteria at low temperatures. In this study we investigated the adaptation of a fast-growing anammox culture to a lower temperature. In a membrane bioreactor a highly enriched anammox community was obtained at 30°C, 25°C and 20°C. This culture was exposed to long- and short-term temperature changes. In short-term experiments the decrease in biomass-specific activity due to decrease in temperature can be described by an activation energy of 64 ± 28 kJ mol^-1. Prolonged cultivation (months) implies that cultivation at low temperatures resulted in deterioration of biomass-specific activity (Ea^LT 239 kJ mol^-1). The growth rate and specific anammox activity in the system decreased from 0.33 d^-1 and 4.47 g NO₂-N g VSS^-1 d^-1 at 30°C to 0.0011 d^-1 and 0.037 g NO₂-N g VSS^-1 d^-1 at 20°C. The reason for the deterioration of the system was related to the required long SRT in the system. The long SRT leads to an increase of non-active and non-anammox cells in the reactor, thereby decreasing the biomass-specific activity.

Enhanced nitrogen removal from piggery wastewater with high NH4+ and low COD/TN ratio in a novel upflow microaerobic biofilm reactor

To enhance nutrient removal more cost-efficiently in microaerobic process treating piggery wastewater characterized by high ammonium (NH₄⁺-N) and low chemical oxygen demand (COD) to total nitrogen (TN) ratio, a novel upflow microaerobic biofilm reactor (UMBR) was constructed and the efficiency in nutrient removal was evaluated with various influent COD/TN ratios and reflux ratios. The results showed that the biofilm on the carriers had increased the biomass in the UMBR and enhanced the enrichment of slow-growth-rate bacteria such as nitrifiers, denitrifiers and anammox bacteria. The packed bed allowed the microaerobic biofilm process perform well at a low reflux ratio of 35 with a NH₄⁺-N and TN removal as high as 93.1% and 89.9%, respectively. Compared with the previously developed upflow microaerobic sludge reactor, the UMBR had not changed the dominant anammox approach to nitrogen removal, but was more cost-efficiently in treating organic wastewater with high NH₄⁺-N and low COD/TN ratio.

Microbial dynamics of biofilm and suspended flocs in anammox membrane bioreactor: The effect of non-woven fabric membrane

Membrane bioreactor with non-woven fabric membranes (NWMBR) is developing into a suitable method for anaerobic ammonium oxidation (anammox). As a carrier, non-woven fabric membrane divided total biomass into biofilm and suspended flocs gradually. Total nitrogen removal efficiency was maintained around 82.6% under nitrogen loading rate of 567.4mgN/L/d after 260days operation. Second-order substrate removal and Stover-Kincannon models were successfully used to simulate the nitrogen removal performance in NWMBR. High-throughput sequence was employed to elucidate the underlying microbial community dynamics. Candidatus Brocadia, Kuenenia, Jettenia were detected to affirm the dominant status of anammox microorganisms and 98.2% of anammox microorganisms distributed in biofilm. In addition, abundances of functional genes (hzs, nirK) in biofilm and suspended flocs were assessed by quantitative PCR to further investigate the coexistence of anammox and other microorganisms. Potential nitrogen removal pathways were established according to relevant nitrogen removal performance and microbial community.

High-throughput analysis of anammox bacteria in wetland and dryland soils along the altitudinal gradient in Qinghai-Tibet Plateau

This study investigated the diversity, community composition, and abundance of anaerobic ammonium oxidation (anammox) bacteria along the altitudinal gradient in Qinghai–Tibet Plateau. Two types of soil samples (wetland and dryland soils, n = 123) were collected from 641 m to 5,033 m altitudes. Polymerase chain reaction (PCR) screening showed that anammox were not widespread, and were only detected in 9 sampling sites of the 50 sites tested by amplifying the 16S rRNA genes. Then, only samples collected from Linzhi (2,715 m), Rikaze (4,030 m), and Naqu (5,011 m), which were positive for the presence of anammox, were further processed to explore the biogeography of anammox bacteria in Qinghai–Tibet Plateau. Results of high‐throughput sequencing targeting the hydrazine synthesis β‐subunit (hzsB) gene revealed the presence of three known anammox genera (Candidatus Brocadia, Candidatus Jettenia, and Candidatus Kuenenia) in both soil types. Their diversity, community composition, and abundance did not show significant variation with altitude at large scale. However, it was the small‐scale environmental heterogeneities between wetland and dryland soils that determined their biogeographical distribution. Specifically, the dryland soils had higher diversity of anammox bacteria than the wetland soils, but their abundance patterns varied. The community composition of anammox bacteria were found to be influenced by soil nitrate content.

Microbial competition among anammox bacteria in nitrite-limited bioreactors

Phylogenetically diverse anammox bacteria have been detected in most of anoxic natural and engineered ecosystems and thus regarded as key players in the global nitrogen cycle. However, ecological niche differentiation of anammox bacteria remains unresolved despite its ecological and practical importance. In this study, the microbial competitions for a common substrate (nitrite) among three anammox species (i.e. "Candidatus Brocadia sinica", "Candidatus Jettenia caeni" and "Candidatus Kuenenia stuttgartiensis") were systematically investigated in nitrite-limited gel-immobilized column reactors (GICR) and membrane bioreactors (MBRs) under different nitrogen loading rates (NLRs). 16 S rRNA gene-based population dynamics revealed that "Ca. J. caeni" could proliferate only at low NLRs, whereas "Ca. B. sinica" outcompeted other two species at higher NLRs in both types of reactors. Furthermore, FISH analysis revealed that "Ca. J. caeni" was mainly present as spherical microclusters at the inner part (low NO₂^- environment), whereas "Ca. B. sinica" was present throughout the gel beads and granules. This spatial distribution supports the outcomes of the competition experiments. However, the successful competition of "Ca. J. caeni" at low NLR could not be explained with the Monod model probably due to inaccuracy of kinetic parameters such as half saturation constant (K_s) for nitrite and a difference in the maintenance rate (m). In addition, the growth of "Ca. K. stuttgartiensis" could not be observed in any experimental conditions, suggesting possible unknown factor(s) is missing. Taken together, NLR was one of factors determining ecological niche differentiation of "Ca. B. sinica" and "Ca. J. caeni".

Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes

Despite the high relevance of anaerobic ammonium oxidation (anammox) for nitrogen loss from marine systems, its relative importance compared to denitrification has less been studied in freshwater ecosystems, and our knowledge is especially scarce for groundwater. Surprisingly, phospholipid fatty acids (PLFA)-based studies identified zones with potentially active anammox bacteria within two superimposed pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory (CZE; Germany). We found anammox to contribute an estimated 83% to total nitrogen loss in suboxic groundwaters of these aquifer assemblages at rates of 3.5–4.7 nmol L⁻¹ d⁻¹, presumably favored over denitrification by low organic carbon availability. Transcript abundances of hzsA genes encoding hydrazine synthase exceeded nirS and nirK transcript abundances encoding denitrifier nitrite reductase by up to two orders of magnitude, providing further support of a predominance of anammox. Anammox bacteria, dominated by groups closely related to Cand. Brocadia fulgida, constituted up to 10.6% of the groundwater microbial community and were ubiquitously present across the two aquifer assemblages with indication of active anammox bacteria even in the presence of 103 μmol L⁻¹ oxygen. Co-occurrence of hzsA and amoA gene transcripts encoding ammonia mono-oxygenase suggested coupling between aerobic and anaerobic ammonium oxidation under suboxic conditions. These results clearly demonstrate the relevance of anammox as a key process driving nitrogen loss from oligotrophic groundwater environments, which might further be enhanced through coupling with incomplete nitrification.

A pilot-scale study on the start-up of partial nitrification-anammox process for anaerobic sludge digester liquor treatment

Treatment of sludge digester liquor was successfully accomplished using a pilot-scale partial nitrification-anammox (PN/A) reactor with a nitrogen removal rate (NRR) of 1.23kgN/m³/d. A stable and efficient PN process was attained by controlling the concentration of free ammonia (0.7-8.4mg/L) and free nitrous acid (0.02-1.0mg/L). The application of hydroxylamine played a vital role in the reactivation of anammox bacteria. The bacteria exhibited improved granule properties at a specific input power between 0.065 and 0.097kW/m³, and achieved a specific anammox activity (SAA) of 1.01kgN/kgVSS/d on day 148. From day 0 to 120, the heme c content in the granules increased from 0.42±0.1 to 5.77±1.0µmol/gVSS, with a corresponding increase in NRRs and SAAs. High-throughput sequencing techniques revealed that the dominant anammox bacterial genus was Candidatus Brocadia. These conclusions provide valuable information for the full-scale treatment of sludge digester liquor.

Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA and functional genes

Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd ₁-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples. WWTP had the lowest diversity with Candidatus Kuenenia dominating while the SCS was dominated by Candidatus Scalindua. MP showed the highest diversity of anammox bacteria including C. Scalindua, C. Kuenenia, and Candidatus Brocadia. Comparing different primer sets, no significant differences in specificity for 16S rRNA gene could be distinguished. Primer set CL1 showed relatively high efficiency in detecting the anammox bacterium hzo gene from all samples, while CL2 showed greater selectivity for WWTP samples. The recently reported primer sets of the hzsA gene resulted in high efficiencies in detecting anammox bacteria while nirS primer sets were more selective for specific samples. Results collectively indicate that the distribution of anammox bacteria is niche-specific within different ecosystems and primer specificity may cause biases on the diversity detected.

Influence of temperature and pH on the anammox process: A review and meta-analysis

The anammox (anaerobic ammonium oxidation) process was considered a very efficient and economic wastewater treatment technology immediately after its discovery in 1995, thus research in this field was intensified. The anammox process is characterised by a high temperature optimum and is very sensitive to both temperature and pH fluctuations. The process can also be inhibited by many factors, including by its substrates, i.e. nitrite and ammonium (or its unionised forms: free ammonia and free nitrous acid). This paper presents a comprehensive study of the most important and recent findings on the influence of two parameters that are crucial in wastewater treatment, i.e. temperature and pH. Because both parameters may influence the anammox process simultaneously, a meta-analysis was conducted of the data from the literature. Although meta-analysis is commonly used in medical research, mathematical analysis of the literature data has become an interesting and important step in the environmental sciences. This paper presents information on the influence of both temperature and pH on process efficiency and microbial composition. Additionally, the responses of different operating systems on both temperature and pH changes are described. Moreover, the role of both adaptation to changed conditions and of pH control as well as indicated areas of process operation are discussed.

Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation

A draft genome sequence of a neutrophilic halophile capable of thiocyanate degradation, Thiohalobacter thiocyanaticus FOKN1, was determined using a PacBio RSII sequencer. A 3.23-Mb circular genome sequence was assembled, in which 3,026 gene-coding sequences, 45 tRNAs, and 1 rrn operon were annotated.

Startup and operating characteristics of an external air-lift reflux partial nitritation-ANAMMOX integrative reactor

The differences in the physiological characteristics between AOB and ANAMMOX bacteria lead to suboptimal performance when used in a single reactor. In this study, aerobic and anaerobic zones with different survival environments were constructed in a single reactor to realize partitioned culture of AOB and ANAMMOX bacteria. An external air-lift reflux system was formed which used the exhaust from the aeration zone as power to return the effluent to the aeration zone. The reflux system effectively alleviated the large pH fluctuations and promoted NO₂^--N to rapidly use by ANAMMOX bacteria, effectively inhibiting the activity of NOB. After 95d of running, the nitrogen removal rate increased from the initial 0.21kg/(m³·d) to 3.1kg/(m³·d). FISH analyses further demonstrated that AOB and ANAMMOX bacteria acquired efficient enrichment in the corresponding zone. Thus, this type of integrative reactor may create the environments needed for the partial nitritation-ANAMMOX processing.

Dual substrate limitation modeling and implications for mainstream deammonification

Substrate limitation occurs frequently in wastewater treatment and knowledge about microbial behavior at limiting conditions is essential for the use of biokinetic models in system design and optimization. Monod kinetics are well-accepted for modeling growth rates when a single substrate is limiting, but several models exist for treating two or more limiting substrates simultaneously. In this study three dual limitation models (multiplicative, minimum, and Bertolazzi) were compared based on experiments using nitrite-oxidizing bacteria (limited by dissolved oxygen and nitrite) and ANaerobic AMMonia-OXidizing bacteria or Aanammox (limited by ammonium and nitrite) within mixed liquor from deammonification pilots. A deterministic likelihood-based parameter estimation followed by Bayesian inference was used to estimate model-specific parameters. The minimum model outperformed the other two by a slight margin in three separate analyses. 1) Parameters estimated using the minimum model were closest to parameters estimated from single limitation batch tests. 2) Among simulations based on each model's own estimated parameters, the minimum model best described the experimental observations. 3) Among simulations based on parameters estimated from single limitation, the minimum model best described the experimental observations. The dual substrate model selected among the three studied can effect a 75% process performance variation based on simulations of a full-scale mainstream deammonification system.

Maximum specific growth rate of anammox bacteria revisited

Anammox bacteria have long been considered to be slow-growing bacteria. However, it has recently been reported that they could grow much faster than previously thought when they were cultivated in a membrane bioreactor (MBR) with a step-wise decrease in the solid retention time (SRT). Here, we reevaluated the maximum specific growth rates (μ_max) of three phylogenetically distant anammox bacterial species (i.e. "Ca. Brocadia sinica", "Ca. Jettenia caeni" and "Ca. Scalindua sp.") by directly measuring 16S rRNA gene copy numbers using newly developed quantitative polymerase chain reaction (qPCR) assays. When free-living planktonic "Ca. B. sinica" and "Ca. J. caeni" cells were immobilized in polyvinyl alcohol (PVA) and sodium alginate (SA) gel beads and cultivated in an up-flow column reactor with high substrate loading rates at 37 °C, the μ_max were determined to be 0.33 ± 0.02 d^-1 and 0.18 d^-1 (corresponding doubling time of 2.1 day and 3.9 day) from the exponential increases in 16S rRNA genes copy numbers, respectively. These values were faster than the fastest growth rates reported for these species so far. The cultivation of anammox bacteria in gel beads was achieved less than one month without special cultivation method and selection pressure, and the exponential increase in 16S rRNA gene numbers was directly measured by qPCR with high reproducibility; therefore, the resulting μ_max values were considered accurate. Taken together, the fast growth is, therefore, considered to be an intrinsic kinetic property of anammox bacteria.

High-throughput sequencing-based microbial characterization of size fractionated biomass in an anoxic anammox reactor for low-strength wastewater at low temperatures

The microbial characterization of three size-fractionated sludge obtained from a suspended-growth anoxic anammox reactor treating low-strength wastewater at low temperatures were investigated by using high-throughput sequencing. Particularly, the spatial variability in relative abundance of microorganisms involved in nitrogen metabolism were analyzed in detail. Results showed that population segregation did occur in the reactor. It was found, for the first time, that the genus Nitrotoga was enriched only in large granules (>400μm). Three anammox genus including Candidatus Jettenia, Brocadia and Kuenenia were detected. Among them, Candidatus Brocadia and Kuenenia preferred to grow in large-sized granules (>400μm), whereas Candidatus Jettenia dominated in small- and moderate-sized sludge (<400μm). The members of genus Candidatus Jettenia appeared to play the vital role in nitrogen removal, since sludge with diameters smaller than 400μm accounted for 81.55% of the total biomass. However, further studies are required to identify the activity of different-size sludge.

The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors

Implementation of partial nitritation anammox (PNA) in the mainstream (municipal wastewater treatment) is still under investigation. Microbial community structure and reactor type can influence the performance of PNA reactor; yet, little is known about the role of the community composition of the inoculum and the reactor configuration under mainstream conditions. Therefore, this study investigated the community structure of inocula of different origin and their consecutive community dynamics in four different lab‐scale PNA reactors with 16S rRNA gene amplicon sequencing. These reactors were operated for almost 1 year and subjected to realistic seasonal temperature fluctuations as in moderate climate regions, that is, from 20°C in summer to 10°C in winter. The sequencing analysis revealed that the bacterial community in the reactors comprised: (1) a nitrifying community (consisting of anaerobic ammonium‐oxidizing bacteria (AnAOB), ammonia‐oxidizing bacteria (AOB), and nitrite‐oxidizing bacteria (NOB)); (2) different heterotrophic denitrifying bacteria and other putative heterotrophic bacteria (HB). The nitrifying community was the same in all four reactors at the genus level, although the biomasses were of different origin. Community dynamics revealed a stable community in the moving bed biofilm reactors (MBBR) in contrast to the sequencing batch reactors (SBR) at the genus level. Moreover, the reactor design seemed to influence the community dynamics, and reactor operation significantly influenced the overall community composition. The MBBR seems to be the reactor type of choice for mainstream wastewater treatment.

Municipal landfill leachate characteristics and feasibility of retrofitting existing treatment systems with deammonification - A full scale survey

Leachate characteristics, applied technologies and energy demand for leachate treatment were investigated through survey in different states of Germany. Based on statistical analysis of leachate quality data from 2010 to 2015, almost half of the contaminants in raw leachate satisfy direct discharge limits. Decrease in leachate pollution index of current landfills is mainly related to reduction in concentrations of certain heavy metals (Pb, Zn, Cd, Hg) and organics (biological oxygen demand (BOD₅), chemical oxygen demand (COD), and adsorbable organic halogen (AOX)). However, contaminants of concern remain COD, ammonium-nitrogen (NH₄N) and BOD₅ with average concentrations in leachate of about 1850, 640, and 120 mg/L respectively. Concentrations of COD and NH₄N vary seasonally, mainly due to temperature changes; concentrations during the first quarter of the year are mostly below the annual average value. Electrical conductivity (EC) of leachate may be used as a time and cost saving alternative to monitor sudden changes in concentration of these two parameters, due to high correlations of around 0.8 with both COD and NH₄N values which are possibly due to low heavy metal concentrations in leachate. The decreased concentrations of heavy metals and BOD₅ favor the retrofitting of an existing biological reactor (nitrification/denitrification) with the deammonification process and post denitrification, as this lowers average annual operational cost (in terms of energy and external carbon source) and CO₂ emission by €25,850 and 15,855 kg CO_2,eq respectively.

Nitrite inhibition and limitation - the effect of nitrite spiking on anammox biofilm, suspended and granular biomass

Anaerobic ammonium oxidation (anammox) has been studied extensively while no widely accepted optimum values for nitrite (both a substance and inhibitor) has been determined. In the current paper, nitrite spiking (abruptly increasing nitrite concentration in reactor over 20 mg NO^-₂-NL^-1) effect on anammox process was studied on three systems: a moving bed biofilm reactor (MBBR), a sequencing batch reactor (SBR) and an upflow anaerobic sludge blanket (UASB). The inhibition thresholds and concentrations causing 50% of biomass activity decrease (IC₅₀) were determined in batch tests. The results showed spiked biomass to be less susceptible to nitrite inhibition. Although the values of inhibition threshold and IC₅₀ concentrations were similar for non-spiked biomass (81 and 98 mg NO^-₂-NL^-1, respectively, for SBR), nitrite spiking increased IC₅₀ considerably (83 and 240 mg NO^-₂-NL^-1, respectively, for UASB). As the highest total nitrogen removal rate was also measured at the aforementioned thresholds, there is basis to suggest stronger limiting effect of nitrite on anammox process than previously reported. The quantitative polymerase chain reaction analysis showed similar number of anammox 16S rRNA copies in all reactors, with the lowest quantity in SBR and the highest in MBBR (3.98 × 10⁸ and 1.04 × 10⁹ copies g^-1 TSS, respectively).