Expression of a putative nitrite reductase and the reversible inhibition of nitrite-dependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255

Global patterns in gene content of soil microbiomes emerge from microbial interactions

Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH; nar gene abundances increase while nap abundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.

Improving nutrients removal of Anaerobic-Anoxic-Oxic process via inhibiting partial anaerobic mixture with nitrite in side-stream tanks: role of nitric oxide

A side-stream tank which was in parallel with the anoxic tank was used to improve the performance of the Anaerobic-Anoxic-Oxic process. The partial mixtures from the anaerobic tank were injected into the side-stream tank with the initial nitrite nitrogen (NO₂^--N) concentrations of 10 mg/L and 20 mg/L. When the initial NO₂^--N concentration in the tank was 20 mg/L, total nitrogen and total phosphorus removal efficiencies of the A²/O process increased from 72% and 48% to 90% and 89%, respectively. 2.23 mg/L of nitric oxide (NO) were observed in the side-stream tank. The abundance of Nitrosomonas sp. and Nitrospira sp. were varied from 0.98% and 6.13% to 2.04% and 1.13%, respectively. The abundances of Pseudomonas sp. and Acinetobacter sp. were increased from 0.81% and 0.74% to 6.69% and 5.48%, respectively. NO plays an important role for improving the nutrients removal of the A²/O process in the side-stream nitrite-enhanced strategy.

Metaproteomics, Heterotrophic Growth, and Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi after Long-Term Operation of an Autotrophic Nitrifying Biofilm Reactor

Bioregenerative life support systems (BLSS) are currently in development to tackle low recovery efficiencies, high energy demands, as well as food, water, and oxygen production challenges through the regeneration of nutrients from waste streams. The MELiSSA pilot plant has been developed as a testbed for regenerative life support system bioreactor operation and characterization. As nitrogen is a vital resource in such systems, we studied the functional composition of a new packed-bed nitrifying bioreactor inoculated with a co-culture of Nitrosomonas europaea (ATCC 25978) and Nitrobacter winogradskyi (ATCC 25391). After 840 days of autotrophic continuous cultivation, the packed-bed was sampled at five vertical positions, each with three horizontal positions, and the biomass at each position was characterized via qPCR, 16S amplicon sequencing, and liquid chromatography tandem mass spectrometry. The total number of cells within the different sections fluctuated around 8.95 ± 5.10 × 107 cells/mL of beads. Based on 16S amplicons and protein content, N. europaea and N. winogradskyi constituted overall 44.07 ± 11.75% and 57.53 ± 12.04% of the nitrifying bioreactor, respectively, indicating the presence of a heterotrophic population that, even after such a long operation time, did not affect the nitrification function of the bioreactor. In addition, DNA-based abundance estimates showed that N. europaea was slightly more abundant than N. winogradskyi, whereas protein-based abundance estimates indicated a much higher abundance of N. europaea. This highlights that single-method approaches need to be carefully interpreted in terms of overall cell abundance and metabolic activity.

Improvement of the performance of simultaneous nitrification denitrification and phosphorus removal (SNDPR) system by nitrite stress

This study investigated a new way to improve the performance of simultaneous nitrification denitrification and phosphorus removal (SNDPR) system by regularly changing the anaerobic/micro-aerobic/anoxic mode to the anaerobic/anoxic mode with 30 mg/L of nitrite dosing. The results indicated that the removal efficiency of total inorganic nitrogen and PO₄^3--P was improved from 75.44% and 85.14% to 98.89% and 98.17%, respectively. And the good performance of the SNDPR showed a long-time sustainability when the C/N ratio was 5. The results of microbial community illustrated that the abundance of the main nitrite-oxidizing bacteria (NOB), Nitrospira sp., dropped from 5.71% to 0.85% and the abundance of denitrifying polyphosphate-accumulating organisms (DPAOs), Pseudomonas sp. and Acinetobacter sp., increased by 5 times after nitrite stress. The high level of nitric oxide (NO) and free nitrite acid produced by addition of nitrite strongly suppressed the undesired organisms NOB and ordinary heterotrophic denitrifying organisms, and promoted the enrichment of DPAOs. The NO accumulated in the nitrite denitrification process could inhibit NOB and promote AOB. This study revealed that NO plays an important role in regulating the microbial community in the SNDPR system.

Cometabolism of 17α-ethynylestradiol by nitrifying bacteria depends on reducing power availability and leads to elevated nitric oxide formation

17α-ethynylestradiol (EE2) is a priority emerging contaminant (EC) in diverse environments that can be cometabolized by ammonia oxidizing bacteria (AOB). However, its transformation kinetics and the underlying molecular mechanism are unclear. In this study, kinetic parameters, including maximum specific EE2 transformation rate, EE2 half-saturation coefficient, and EE2transformation capacity of AOBwere obtained by using the model AOB strain, Nitrosomonas europaea 19718. The relationship between EE2 cometabolism and ammonia oxidation was divided into three phases according to reducing power availability, namely "activation", "coupling", and "saturation". Specifically, there was a universal lag of EE2 transformation after ammonia oxidation was initiated, suggesting that sufficient reducing power (approximately 0.95 ± 0.06 mol NADH/L) was required to activate EE2 cometabolism. Interestingly, nitric oxide emission increased by 12 ± 2% during EE2 cometabolism, along with significantly upregulated nirK cluster genes. The findings are of importance to understanding the cometabolic behavior and mechanism of EE2 in natural and engineered environments. Maintaining relatively high and stable reducing power supply from ammonia oxidation can potentially improve the cometabolic removal of EE2 and other ECs during wastewater nitrification processes.

Comparative metatranscriptome analysis revealed broad response of microbial communities in two soil types, agriculture versus organic soil

BACKGROUND

Studying expression of genes by direct sequencing and analysis of metatranscriptomes at a particular time and space can disclose structural and functional insights about microbial communities. The present study reports comparative analysis of metatranscriptome from two distinct soil ecosystems referred as M1 (agriculture soil) and O1 (organic soil).

RESULTS

Analysis of sequencing reads revealed Proteobacteria as major dominant phyla in both soil types. The order of the top 3 abundant phyla in M1 sample was Proteobacteria > Ascomycota > Firmicutes, whereas in sample O1, the order was Proteobacteria > Cyanobacteria > Actinobacteria. Analysis of differentially expressed genes demonstrated high expression of transcripts related to copper-binding proteins, proteins involved in electron carrier activity, DNA integration, endonuclease activity, MFS transportation, and other uncharacterized proteins in M1 compared to O1. Of the particular interests, several transcripts related to nitrification, ammonification, stress response, and alternate carbon fixation pathways were highly expressed in M1. In-depth analysis of the sequencing data revealed that transcripts of archaeal origin had high expression in M1 compared to O1 indicating the active role of Archaea in metal- and pesticide-contaminated environment. In addition, transcripts encoding 4-hydroxyphenylpyruvate dioxygenase, glyoxalase/bleomycin resistance protein/dioxygenase, metapyrocatechase, and ring hydroxylating dioxygenases of aromatic hydrocarbon degradation pathways had high expression in M1. Altogether, this study provided important insights about the transcripts and pathways upregulating in the presence of pesticides and herbicides.

CONCLUSION

Altogether, this study claims a high expression of microbial transcripts in two ecosystems with a wide range of functions. It further provided clue about several molecular markers which could be a strong indicator of metal and pesticide contamination in soils. Interestingly, our study revealed that Archaea are playing a significant role in nitrification process as compared to bacteria in metal- and pesticide-contaminated soil. In particular, high expression of transcripts related to aromatic hydrocarbon degradation in M1 soil indicates their important role in biodegradation of pollutants, and therefore, further investigation is needed.

Controls and Adaptive Management of Nitrification in Agricultural Soils

Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.

Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions

Nitrite-oxidizing bacteria (NOB) are vital players in the global nitrogen cycle that convert nitrite to nitrate during the second step of nitrification. Within this functional guild, members of the genus Nitrospira are most widespread, phylogenetically diverse, and physiologically versatile, and they drive nitrite oxidation in many natural and engineered ecosystems. Despite their ecological and biotechnological importance, our understanding of their energy metabolism is still limited. A major bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing and fastidious microorganisms. In this study, we cultivated Nitrospira moscoviensis under nitrite-oxidizing conditions in a continuous stirred tank reactor (CSTR) system. This cultivation setup enabled accurate control of physicochemical parameters and avoided fluctuating levels of their energy substrate nitrite, thus ensuring constant growth conditions and furthermore allowing continuous biomass harvesting. Transcriptomic analyses under these conditions supported the predicted core metabolism of N. moscoviensis, including expression of all proteins required for carbon fixation via the reductive tricarboxylic acid cycle, assimilatory nitrite reduction, and the complete respiratory chain. Here, simultaneous expression of multiple copies of respiratory complexes I and III suggested functional differentiation. The transcriptome also indicated that the previously assumed membrane-bound nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation, is formed by three soluble subunits. Overall, the transcriptomic data greatly refined our understanding of the metabolism of Nitrospira. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of these fascinating microorganisms.

Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata

Nitrous oxide (N2O) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of N2O and NO globally. However, nothing is known about N2O and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to N2O, and emits N2O at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that N2O formed by N. inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Our findings indicate that comammox microbes may produce less N2O during nitrification than AOB.

Metatranscriptomic Investigation of Adaptation in NO and N2O Production From a Lab-Scale Nitrification Process Upon Repeated Exposure to Anoxic-Aerobic Cycling

The molecular mechanisms of microbial adaptation to repeated anoxic-aerobic cycling were investigated by integrating whole community gene expression (metatranscriptomics) and physiological responses, including the production of nitric (NO) and nitrous (N2O) oxides. Anoxic-aerobic cycling was imposed for 17 days in a lab-scale full-nitrification mixed culture system. Prior to cycling, NO and N2O levels were sustained at 0.097 ± 0.006 and 0.054 ± 0.019 ppmv, respectively. Once the anoxic-aerobic cycling was initiated, peak emissions were highest on the first day (9.8 and 1.3 ppmv, respectively). By the end of day 17, NO production returned to pre-cycling levels (a peak of 0.12 ± 0.007 ppmv), while N2O production reached a new baseline (a peak of 0.32 ± 0.05 ppmv), one order of magnitude higher than steady-state conditions. Concurrently, post-cycling transcription of norBQ and nosZ returned to pre-cycling levels after an initial 5.7- and 9.5-fold increase, while nirK remained significantly expressed (1.6-fold) for the duration of and after cycling conditions. The imbalance in nirK and nosZ mRNA abundance coupled with continuous conversion of NO to N2O might explain the elevated post-cycling baseline for N2O. Metatranscriptomic investigation notably indicated possible NO production by NOB under anoxic-aerobic cycling through a significant increase in nirK expression. Opposing effects on AOB (down-regulation) and NOB (up-regulation) CO2 fixation were observed, suggesting that nitrifying bacteria are differently impacted by anoxic-aerobic cycling. Genes encoding the terminal oxidase of the electron transport chain (ccoNP, coxBC) were the most significantly transcribed, highlighting a hitherto unexplored pathway to manage high electron fluxes resulting from increased ammonia oxidation rates, and leading to overall, increased NO and N2O production. In sum, this study identified underlying metabolic processes and mechanisms contributing to NO and N2O production through a systems-level interrogation, which revealed the differential ability of specific microbial groups to adapt to sustained operational conditions in engineered biological nitrogen removal processes.

The draft genome sequence of "Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge

The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of "Nitrospira lenta" strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of "N. lenta" has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the "N. lenta" core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and "N. defluvii", despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of "N. lenta" provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.

Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands

Nitrogen dynamics and its association to metabolically active microbial populations were assessed in two vertical subsurface vertical flow (VF) wetlands treating urban wastewater. These VF wetlands were operated in parallel with unsaturated (UVF) and partially saturated (SVF) configurations. The SVF wetland exhibited almost 2-fold higher total nitrogen removal rate (5 g TN m^-2 d^-1) in relation to the UVF wetland (3 g TN m^-2 d^-1), as well as a low NO_x-N accumulation (1 mg L^-1 vs. 26 mg L^-1 in SVF and UVF wetland effluents, respectively). After 6 months of operation, ammonia oxidizing prokaryotes (AOP) and nitrite oxidizing bacteria (NOB) displayed an important role in both wetlands. Oxygen availability and ammonia limiting conditions promoted shifts on the metabolically active nitrifying community within 'nitrification aggregates' of wetland biofilms. Ammonia oxidizing archaea (AOA) and Nitrospira spp. overcame ammonia oxidizing bacteria (AOB) in the oxic layers of both wetlands. Microbial quantitative and diversity assessments revealed a positive correlation between Nitrobacter and AOA, whereas Nitrospira resulted negatively correlated with Nitrobacter and AOB populations. The denitrifying gene expression was enhanced mainly in the bottom layer of the SVF wetland, in concomitance with the depletion of NO_x-N from wastewater. Functional gene expression of nitrifying and denitrifying populations combined with the active microbiome diversity brought new insights on the microbial nitrogen-cycling occurring within VF wetland biofilms under different operational conditions.

Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi

Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH₄⁺). Up to 60% of NH₄⁺-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO₃⁻), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO₂], and nitrous oxide [N₂O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, emits nitrogen (N) oxide gases (NO, NO₂, and N₂O), which are potentially hazardous compounds that contribute to global warming. To better understand the dynamics of nitrification-derived N oxide production, we conducted culturing experiments and used an integrative genome-scale, constraint-based approach to model N oxide gas sources and sinks during complete nitrification in an aerobic coculture of two model nitrifying bacteria, the ammonia-oxidizing bacterium Nitrosomonas europaea and the nitrite-oxidizing bacterium Nitrobacter winogradskyi. The model includes biotic genome-scale metabolic models (iFC578 and iFC579) for each nitrifier and abiotic N oxide reactions. Modeling suggested both biotic and abiotic reactions are important sources and sinks of N oxides, particularly under microaerobic conditions predicted to occur in coculture. In particular, integrative modeling suggested that previous models might have underestimated gross NO production during nitrification due to not taking into account its rapid oxidation in both aqueous and gas phases. The integrative model may be found at https://github.com/chaplenf/microBiome-v2.1.

IMPORTANCE Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH₄⁺). Up to 60% of NH₄⁺-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO₃⁻), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO₂], and nitrous oxide [N₂O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification

Nitrification plays a crucial role in global nitrogen cycling and treatment processes. However, the relationships between the nitrifier guilds of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) are still poorly understood, especially in freshwater habitats. This study examined the physiological interactions between the AOB and NOB present in a freshwater aquarium biofilter by culturing them, either together or separately, in a synthetic medium. Metagenomic and 16S rRNA gene sequencing revealed the presence and the draft genomes of Nitrosomonas-like AOB as well as Nitrobacter-like NOB in the cultures, including the first draft genome of Nitrobacter vulgaris. The nitrifiers exhibited different growth rates with different ammonium (NH₄⁺) or nitrite concentrations (50-1,500 μM) and the growth rates were elevated under a high bicarbonate (HCO₃^-) concentration. The half-saturation constant (K_s for NH₄⁺), the maximum growth rate (μ_max), and the lag duration indicated a strong dependence on the synergistic relationships between the two guilds. Overall, the ecophysiological and metagenomic results in this study provided insights into the phylogeny of the key nitrifying players in a freshwater biofilter and showed that interactions between the two nitrifying guilds in a microbial community enhanced nitrification.

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus

Nitrite-oxidizing bacteria (NOB) have conventionally been regarded as a highly specialized functional group responsible for the production of nitrate in the environment. However, recent culture-based studies suggest that they have the capacity to lead alternative lifestyles, but direct environmental evidence for the contribution of marine nitrite oxidizers to other processes has been lacking to date. We report on the alternative biogeochemical functions, worldwide distribution, and sometimes high abundance of the marine NOB Nitrococcus. These largely overlooked bacteria are capable of not only oxidizing nitrite but also reducing nitrate and producing nitrous oxide, an ozone-depleting agent and greenhouse gas. Furthermore, Nitrococcus can aerobically oxidize sulfide, thereby also engaging in the sulfur cycle. In the currently fast-changing global oceans, these findings highlight the potential functional switches these ubiquitous bacteria can perform in various biogeochemical cycles, each with distinct or even contrasting consequences.

Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification

Quorum sensing (QS) is a widespread process in bacteria used to coordinate gene expression with cell density, diffusion dynamics, and spatial distribution through the production of diffusible chemical signals. To date, most studies on QS have focused on model bacteria that are amenable to genetic manipulation and capable of high growth rates, but many environmentally important bacteria have been overlooked. For example, representatives of proteobacteria that participate in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, produce QS signals called acyl-homoserine lactones (AHLs). Nitrification emits nitrogen oxide gases (NO, NO₂, and N₂O), which are potentially hazardous compounds that contribute to global warming. Despite considerable interest in nitrification, the purpose of QS in the physiology/ecology of nitrifying bacteria is poorly understood. Through a quorum quenching approach, we investigated the role of QS in a well-studied AHL-producing nitrite oxidizer, Nitrobacter winogradskyi We added a recombinant AiiA lactonase to N. winogradskyi cultures to degrade AHLs to prevent their accumulation and to induce a QS-negative phenotype and then used mRNA sequencing (mRNA-Seq) to identify putative QS-controlled genes. Our transcriptome analysis showed that expression of nirK and nirK cluster genes (ncgABC) increased up to 19.9-fold under QS-proficient conditions (minus active lactonase). These data led to us to query if QS influenced nitrogen oxide gas fluxes in N. winogradskyi Production and consumption of NO_x increased and production of N₂O decreased under QS-proficient conditions. Quorum quenching transcriptome approaches have broad potential to identify QS-controlled genes and phenotypes in organisms that are not genetically tractable.

IMPORTANCE

Bacterial cell-cell signaling, or quorum sensing (QS), is a method of bacterial communication and gene regulation that is well studied in bacteria. However, little is known about the purpose of QS in many environmentally important bacteria. Here, we demonstrate quorum quenching coupled with mRNA-Seq to identify QS-controlled genes and phenotypes in Nitrobacter winogradskyi, a nitrite-oxidizing bacterium. Nitrite oxidizers play an important role in the nitrogen cycle though their participation in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite. Our quorum quenching approach revealed that QS influences production and consumption of environmentally important nitrogen oxide gases (NO, NO₂, and N₂O) in N. winogradskyi This study demonstrated a novel technique for studying QS in difficult-to-work-with microorganisms and showed that nitrite oxidizers might also contribute to nitrification-dependent production of nitrogen oxide gases that contribute to global warming.

Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach

Biofilms are widely used in wastewater treatment for their particular enhancement of nitrogen removal and other significant advantages. In this study, the diversity and potential functions of nitrogen removal bacteria in suspended activated sludge (AS) and biofilm of a full-scale hybrid reactor were uncovered by metagenomes (∼34 Gb), coupled with PCR-based 454 reads (>33 K reads). The results indicated that the diversity and abundance of nitrifiers and denitrifiers in biofilm did not surpass that in AS, while more nitrification and denitrification genes were indeed found in biofilm than AS, suggesting that the increased nitrogen removal ability by applying biofilm might be attributed to the enhancement of removal efficiency, rather than the biomass accumulation of nitrogen removal bacteria. The gene annotation and phylogenetic analysis results revealed that AS and biofilm samples consisted of 6.0 % and 9.4 % of novel functional genes for nitrogen removal and 18 % and 30 % of new Nitrospira species for nitrite-oxidizing bacteria, respectively. Moreover, the identification of Nitrospira-like amoA genes provided metagenomic evidence for the presence of complete ammonia oxidizer (comammox) with the functional potential to perform the complete oxidation of ammonia to nitrate. These findings have significant implications in expanding our knowledge of the biological nitrogen transformations in wastewater treatment.

A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is in contrast to new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate) and this finding will have far-reaching implications for nitrification research. We review recent work that has changed our perspective on NOB and provides a new basis for future studies on these enigmatic organisms.

A New Acyl-homoserine Lactone Molecule Generated by Nitrobacter winogradskyi

It is crucial to reveal the regulatory mechanism of nitrification to understand nitrogen conversion in agricultural systems and wastewater treatment. In this study, the nwiI gene of Nitrobacter winogradskyi was confirmed to be a homoserine lactone synthase by heterologous expression in Escherichia coli that synthesized several acyl-homoserine lactone signals with 7 to 11 carbon acyl groups. A novel signal, 7, 8-trans-N-(decanoyl) homoserine lactone (C10:1-HSL), was identified in both N. winogradskyi and the recombined E. coli. Furthermore, this novel signal also triggered variances in the nitrification rate and the level of transcripts for the genes involved in the nitrification process. These results indicate that quorum sensing may have a potential role in regulating nitrogen metabolism.

Assessment of nitric oxide (NO) redox reactions contribution to nitrous oxide (N2 O) formation during nitrification using a multispecies metabolic network model

Over the coming decades nitrous oxide (N2O) is expected to become a dominant greenhouse gas and atmospheric ozone depleting substance. In wastewater treatment systems, N2O is majorly produced by nitrifying microbes through biochemical reduction of nitrite (NO2(-)) and nitric oxide (NO). However it is unknown if the amount of N2O formed is affected by alternative NO redox reactions catalyzed by oxidative nitrite oxidoreductase (NirK), cytochromes (i.e., P460 [CytP460] and 554 [Cyt554 ]) and flavohemoglobins (Hmp) in ammonia- and nitrite-oxidizing bacteria (AOB and NOB, respectively). In this study, a mathematical model is developed to assess how N2O formation is affected by such alternative nitrogen redox transformations. The developed multispecies metabolic network model captures the nitrogen respiratory pathways inferred from genomes of eight AOB and NOB species. The performance of model variants, obtained as different combinations of active NO redox reactions, was assessed against nine experimental datasets for nitrifying cultures producing N2O at different concentration of electron donor and acceptor. Model predicted metabolic fluxes show that only variants that included NO oxidation to NO2(-) by CytP460 and Hmp in AOB gave statistically similar estimates to observed production rates of N2O, NO, NO2(-) and nitrate (NO3(-)), together with fractions of AOB and NOB species in biomass. Simulations showed that NO oxidation to NO2(-) decreased N2O formation by 60% without changing culture's NO2(-) production rate. Model variants including NO reduction to N2O by Cyt554 and cNor in NOB did not improve the accuracy of experimental datasets estimates, suggesting null N2O production by NOB during nitrification. Finally, the analysis shows that in nitrifying cultures transitioning from dissolved oxygen levels above 3.8 ± 0.38 to <1.5 ± 0.8 mg/L, NOB cells can oxidize the NO produced by AOB through reactions catalyzed by oxidative NirK.

The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer

In marine systems, nitrate is the major reservoir of inorganic fixed nitrogen. The only known biological nitrate-forming reaction is nitrite oxidation, but despite its importance, our knowledge of the organisms catalyzing this key process in the marine N-cycle is very limited. The most frequently encountered marine NOB are related to Nitrospina gracilis, an aerobic chemolithoautotrophic bacterium isolated from ocean surface waters. To date, limited physiological and genomic data for this organism were available and its phylogenetic affiliation was uncertain. In this study, the draft genome sequence of N. gracilis strain 3/211 was obtained. Unexpectedly for an aerobic organism, N. gracilis lacks classical reactive oxygen defense mechanisms and uses the reductive tricarboxylic acid cycle for carbon fixation. These features indicate microaerophilic ancestry and are consistent with the presence of Nitrospina in marine oxygen minimum zones. Fixed carbon is stored intracellularly as glycogen, but genes for utilizing external organic carbon sources were not identified. N. gracilis also contains a full gene set for oxidative phosphorylation with oxygen as terminal electron acceptor and for reverse electron transport from nitrite to NADH. A novel variation of complex I may catalyze the required reverse electron flow to low-potential ferredoxin. Interestingly, comparative genomics indicated a strong evolutionary link between Nitrospina, the nitrite-oxidizing genus Nitrospira, and anaerobic ammonium oxidizers, apparently including the horizontal transfer of a periplasmically oriented nitrite oxidoreductase and other key genes for nitrite oxidation at an early evolutionary stage. Further, detailed phylogenetic analyses using concatenated marker genes provided evidence that Nitrospina forms a novel bacterial phylum, for which we propose the name Nitrospinae.

Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.

Cultivation, growth physiology, and chemotaxonomy of nitrite-oxidizing bacteria

Lithoautotrophic nitrite-oxidizing bacteria (NOB) are known as fastidious microorganisms, which are hard to maintain and not many groups are trained to keep them in culture. They convert nitrite stoichiometrically to nitrate and growth is slow due to the poor energy balance. NOB are comprised of five genera, which are scattered among the phylogenetic tree. Because NOB proliferate in a broad range of environmental conditions (terrestrial, marine, acidic) and have diverse lifestyles (lithoautotrophic, mixotrophic, and heterotrophic), variation in media composition is necessary to match their individual growth requirements in the laboratory. From Nitrobacter and Nitrococcus relatively high cell amounts can be achieved by consumption of high nitrite concentrations, whereas accumulation of cells belonging to Nitrospira, Nitrospina, or the new candidate genus Nitrotoga needs prolonged feeding procedures. Isolation is possible for planktonic cells by dilution series or plating techniques, but gets complicated for strains with a tendency to develop microcolonies like Nitrospira. Physiological experiments including determination of the temperature or pH-optimum can be conducted with active laboratory cultures of NOB, but the attainment of reference values like cell protein content or cell numbers might be hard to realize due to the formation of flocs and the low cell density. Monitoring of laboratory enrichments is necessary especially if several species or genera coexist within the same culture and due to population shifts over time. Chemotaxonomy is a valuable method to identify and quantify NOB in biofilms and pure cultures alike, since fatty acid profiles reflect their phylogenetic heterogeneity. This chapter focusses on methods to enrich, isolate, and characterize NOB by various cultivation-based techniques.

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.

A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are, according to molecular data, among the most diverse and widespread nitrifiers in natural ecosystems and biological wastewater treatment. Here, environmental genomics was used to reconstruct the complete genome of "Candidatus Nitrospira defluvii" from an activated sludge enrichment culture. On the basis of this first-deciphered Nitrospira genome and of experimental data, we show that Ca. N. defluvii differs dramatically from other known nitrite oxidizers in the key enzyme nitrite oxidoreductase (NXR), in the composition of the respiratory chain, and in the pathway used for autotrophic carbon fixation, suggesting multiple independent evolution of chemolithoautotrophic nitrite oxidation. Adaptations of Ca. N. defluvii to substrate-limited conditions include an unusual periplasmic NXR, which is constitutively expressed, and pathways for the transport, oxidation, and assimilation of simple organic compounds that allow a mixotrophic lifestyle. The reverse tricarboxylic acid cycle as the pathway for CO2 fixation and the lack of most classical defense mechanisms against oxidative stress suggest that Nitrospira evolved from microaerophilic or even anaerobic ancestors. Unexpectedly, comparative genomic analyses indicate functionally significant lateral gene-transfer events between the genus Nitrospira and anaerobic ammonium-oxidizing planctomycetes, which share highly similar forms of NXR and other proteins reflecting that two key processes of the nitrogen cycle are evolutionarily connected.

The microbial nitrogen cycle

This special issue highlights several recent discoveries in the microbial nitrogen cycle including the diversity of nitrogen-fixing bacteria in special habitats, distribution and contribution of aerobic ammonium oxidation by bacteria and crenarchaea in various aquatic and terrestrial ecosystems, regulation of metabolism in nitrifying bacteria, the molecular diversity of denitrifying microorganisms and their enzymes, the functional diversity of freshwater and marine anammox bacteria, the physiology of nitrite-dependent anaerobic methane oxidation and the degradation of recalcitrant organic nitrogen compounds. Simultaneously the articles in this issue show that many questions still need to be addressed, and that the microbes involved in catalyzing the nitrogen conversions still harbour many secrets that need to be disclosed to fully understand the biogeochemical nitrogen cycle, and make future predictions and global modelling possible.