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

Ferroheme/Ferriheme Directly Involved in the Synthesis and Decomposition of Hydrazine as an Electron Carrier during Anammox

Anammox bacteria performed the reaction of NH4+ and NO with hydrazine synthase to produce N2H4, followed by the decomposition of N2H4 with hydrazine dehydrogenase to generate N2. Ferroheme/ferriheme, which serves as the active center of both hydrazine synthase and hydrazine dehydrogenase, is thought to play a crucial role in the synthesis and decomposition of N2H4 during Anammox due to its high redox activity. However, this has yet to be proven and the exact mechanisms by which ferroheme/ferriheme is involved in the Anammox process remain unclear. In this study, abiotic and biological assays confirmed that ferroheme participated in NH4+ and NO reactions to generate N2H4 and ferriheme, and the produced N2H4 reacted with ferriheme to generate N2 and ferroheme. In other words, the ferroheme/ferriheme cycle drove the continuous reaction between NH4+ and NO. Raman, ultraviolet-visible spectroscopy, and X-ray absorption fine structure spectroscopy confirmed that ferroheme/ferriheme is involved in the synthesis and decomposition of N2H4 via the core FeII/FeIII cycle. The mechanism of ferroheme/ferriheme participation in the synthesis and decomposition of N2H4 was proposed by density functional theory calculations. These findings revealed for the first time the heme electron transfer mechanisms, which are of great significance for deepening the understanding of Anammox.

Anammox activity improved significantly by the cross-fed NO from ammonia-oxidizing bacteria and denitrifying bacteria to anammox bacteria

Nitric oxide (NO) has been suggested as an obligate intermediate in anaerobic ammonium oxidation (anammox), nitrification and denitrification. At the same time, ammonia-oxidizing bacteria (AOB) and denitrifying bacteria (DNB) are always existed in anammox flora, so what is the role of NO produced from AOB and DNB? Could it accelerate nitrogen removal via the anammox pathway with NO as an electron acceptor? To investigate this hypothesis, nitrogen transforming of an anammox biofilter was analyzed, functional gene expression of anammox bacteria (AnAOB), AOB and DNB were compared, and NO source was verified. For anammox biofilter, anammox contributed to 91.3 % nitrogen removal with only 14.4 % of AnAOB being enriched, while DNB was dominant. Meta-omics analysis and batch test results indicated that AOB could provide NO to AnAOB, and DNB also produced NO via up-regulating nirS/K and down-regulating nor. The activation of the anammox pathway of NH4++NO→N2 caused the downregulation of nirS and nxr in Ca. Kuenenia stuttgartiensis. Additionally, changes in nitrogen transforming pathways affected the electron generation and transport, limiting the carbon metabolism of AnAOB. This study provided new insights into improving nitrogen removal of the anammox system.

Global variations and controlling factors of anammox rates

Soil anammox is an environmentally friendly way to eliminate reactive nitrogen (N) without generating nitrous oxide. Nevertheless, the current earth system models have not incorporated the anammox due to the lack of parameters in anammox rates on a global scale, limiting the accurate projection for N cycling. A global synthesis with 1212 observations from 89 peer-reviewed papers showed that the average anammox rate was 1.60 ± 0.17 nmol N g-1  h-1 in terrestrial ecosystems, with significant variations across different ecosystems. Wetlands exhibited the highest rate (2.17 ± 0.31 nmol N g-1  h-1 ), followed by croplands at 1.02 ± 0.09 nmol N g-1  h-1 . The lowest anammox rates were observed in forests and grasslands. The anammox rates were positively correlated with the mean annual temperature, mean annual precipitation, soil moisture, organic carbon (C), total N, as well as nitrite and ammonium concentrations, but negatively with the soil C:N ratio. Structural equation models revealed that the geographical variations in anammox rates were primarily influenced by the N contents (such as nitrite and ammonium) and abundance of anammox bacteria, which collectively accounted for 42% of the observed variance. Furthermore, the abundance of anammox bacteria was well simulated by the mean annual precipitation, soil moisture, and ammonium concentrations, and 51% variance of the anammox bacteria was accounted for. The key controlling factors for soil anammox rates differed from ecosystem type, for example, organic C, total N, and ammonium contents in croplands, versus soil C:N ratio and nitrite concentrations in wetlands. The controlling factors in soil anammox rate identified by this study are useful to construct an accurate anammox module for N cycling in earth system models.

Oxidative stress and antioxidant mechanisms of obligate anaerobes involved in biological waste treatment processes: A review

In-depth understanding of the molecular mechanisms and physiological consequences of oxidative stress is still limited for anaerobes. Anaerobic biotechnology has become widely accepted by the wastewater/sludge industry as a better alternative to more conventional but costly aerobic processes. However, the functional anaerobic microorganisms used in anaerobic biotechnology are frequently hampered by reactive oxygen/nitrogen species (ROS/RNS)-mediated oxidative stress caused by exposure to stressful factors (e.g., oxygen and heavy metals), which negatively impact treatment performance. Thus, identifying stressful factors and understanding antioxidative defense mechanisms of functional obligate anaerobes are crucial for the optimization of anaerobic bioprocesses. Herein, we present a comprehensive overview of oxidative stress and antioxidant mechanisms of obligate anaerobes involved in anaerobic bioprocesses; as examples, we focus on anaerobic ammonium oxidation bacteria and methanogenic archaea. We summarize the primary stress factors in anaerobic bioprocesses and the cellular antioxidant defense systems of functional anaerobes, a consortia of enzymatic and nonenzymatic mechanisms. The dual role of ROS/RNS in cellular processes is elaborated; at low concentrations, they have vital cell signaling functions, but at high concentrations, they cause oxidative damage. Finally, we highlight gaps in knowledge and future work to uncover antioxidant and damage repair mechanisms in obligate anaerobes. This review provides in-depth insights and guidance for future research on oxidative stress of obligate anaerobes to boost the accurate regulation of anaerobic bioprocesses in challenging and changing operating conditions.

Micron-scale biogeography reveals conservative intra anammox bacteria spatial co-associations

Micron-scale resolution can help to reliably identify true taxon-taxon interactions in complex microbial communities. Despite widespread recognition of the critical role of metabolic interactions in anaerobic ammonium oxidation (anammox) system performance, no studies have examined microbial interactions at the micron-scale in anammox consortia. To fill this gap, we extensively sampled (totally 242 samples) the consortia of a lab-scale anammox reactor at different length scales, including bulk-scale (∼cm), macro-scale (300-500 µm) and micron-scale (70-100 µm). We firstly observed evident micron-scale heterogeneity in anammox consortia, with the relative abundance of anammox bacteria fluctuated greatly across individual clusters (2.0%-79.3%), indicating that the biotic interactions play a significant role in the assembly of anammox communities under well-controlled and well-mixed condition. Importantly, by mapping the spatial associations in anammox consortia at micron-scale, we demonstrated that the conserved co-associations for anammox bacteria were restricted to three different Brocadia species over time, and their co-associations with heterotrophs were random, implying that there was no statistically significant symbiotic interaction between anammox bacteria and other heterotrophic populations. Further metagenomic binning revealed that the quorum sensing with secondary messenger c-di-GMP potentially holding on the conservative metabolic cooperation among Brocadia species. These results shed new light on the social behavior of the anammox community. Overall, delineating of biological structures at micron-scale opens a new way of monitoring the microbial spatial structure and interactions, paving the way for improved community engineering of biotreatment systems.

Active assimilators of soluble microbial products produced by wastewater anammox bacteria and their roles revealed by DNA-SIP coupled to metagenomics

Heterotrophic bacteria grow on influent organics or soluble microbial products (SMP) in wastewater anammox processes, playing key roles in facilitating microbial aggregation and reducing excess nitrate. The overgrowth of heterotrophs represents one of the major causes of anammox process failure, while the metabolic functions of coexisting heterotrophs and their roles in anammox process remain vague. This study aimed at revealing metabolic interactions between AnAOB and active SMP assimilators by integrating ¹³C DNA-stable isotope probing, metabolomic and metagenomic approaches. Glycine, aspartate, and glutamate with low biosynthetic energy cost were the major SMP components produced by AnAOB (net yield: 44.8, 10.4, 8.1 mg·g NH₄⁺-N^-1). Glycine was likely synthesized by AnAOB via the reductive glycine pathway which is oxygen-tolerant, supporting heterotrophic growth. Fermentative Chloroflexi bacterium OLB13, denitrifying Gemmatimonadaceae and Burkholderiaceae bacterium JOSHI-001 were active SMP assimilators, which were prevalent in globally distributed wastewater anammox reactors as core taxa. They likely formed a mutualistic relationship with auxotrophic Ca. Kuenenia by providing necessities such as methionine, folate, 4'-phosphopantetheine, and molybdopterin cofactor, and receiving vitamin B₁₂ for methionine synthesis. For the first time, the identify and metabolic features of SMP assimilators in wastewater anammox communities were revealed. Supplying necessities secreted by heterotrophs could be helpful to the endeavor of AnAOB enrichment. Practically, maintaining active but not overgrown SMP assimilators is critical to efficient and stable operation of wastewater anammox processes.

Nitric Oxide: A Neglected Driver for the Conjugative Transfer of Antibiotic Resistance Genes among Wastewater Microbiota

The dissemination of plasmid-borne antibiotic resistance genes (ARGs) in wastewater is becoming an urgent concern. Previous studies mainly focused on the effects of coexisting contaminants on plasmid conjugation, but ignored the potential contribution of some byproducts inevitably released from wastewater treatment processes. Herein, we demonstrate for the first time that nitric oxide (NO), an intermediate of the wastewater nitrogen cycle, can significantly boost the conjugative transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella typhimurium, and wastewater microbiota). Phenotypic and genotypic tests confirmed that NO-induced promotion was not attributed to the SOS response, a well-recognized driver for horizontal gene transfer. Instead, NO exposure increased the outer membrane permeability of both the donor and recipient by inhibiting the expression of key genes involved in lipopolysaccharide biosynthesis (such as waaJ), thereby lowering the membrane barrier for conjugation. On the other hand, NO exposure not only resulted in the accumulation of intracellular tryptophan but also triggered the deficiency of intracellular methionine, both of which were validated to play key roles in regulating the global regulatory genes (korA, korB, and trbA) of plasmid RP4, activating its encoding transfer apparatus (represented by trfAp and trbBp). Overall, our findings highlighted the risks of NO in spreading ARGs among wastewater microbiota and updated the regulation mechanism of plasmid conjugation.

Simultaneously autotrophic denitrification and organics degradation in low-strength coal gasification wastewater (LSCGW) treatment via microelectrolysis-triggered Fe(II)/Fe(III) cycle

The autotrophic iron-depended denitrification (AIDD), triggered by microelectrolysis, was established in the microelectrolysis-assistant up-flow anaerobic sludge blanket (MEA-UASB) with the purpose of low-strength coal gasification wastewater (LSCGW) treatment while control UASB operated in parallel. The results revealed that chemical oxygen demand (COD) removal efficiency and total nitrogen (TN) removal load at optimum current (2.5 A/m³) in MEA-UASB (83.2 ± 2.6% and 0.220 ± 0.010 kg N/m³·d) were 1.42-fold and 1.57-fold higher than those (58.5 ± 2.1% and 0.139 ± 0.011 kg N/m³·d) in UASB, verifying that AIDD and following dissimilatory iron reduction (DIR) process could offer the novel pathway to solve the electron donor-deficient and traditionally denitrification-infeasible problems. High-throughput 16S rRNA gene pyrosequencing shown that iron-oxidizing denitrifiers (Thiobacillus and Acidovorax species) and iron reducing bacteria (Geothrix and Ignavibacterium speices), acted as microbial iron cycle of contributors, were specially enriched at optimum operating condition. Additionally, the activities of microbial electron transfer chain, electron transporters (complex I, II, III and cytochrome c) and abundance of genes encoding important enzymes (narG, nirK/S, norB and nosZ) were remarkably promoted, suggesting that electron transport and consumption capacities were stimulated during denitrification process. This study could shed light on better understanding about microelectrolysis-triggered AIDD for treatment of refractory LSCGW and further widen its application potential in the future.

Metabolic potential of the imperfect denitrifier Candidatus Desulfobacillus denitrificans in an anammox bioreactor

The imperfect denitrifier, Candidatus (Ca.) Desulfobacillus denitrificans, which lacks nitric oxide (NO) reductase, frequently appears in anammox bioreactors depending on the operating conditions. We used genomic and metatranscriptomic analyses to evaluate the metabolic potential of Ca. D. denitrificans and deduce its functional relationships to anammox bacteria (i.e., Ca. Brocadia pituitae). Although Ca. D. denitrificans is hypothesized to supply NO to Ca. B. pituitae as a byproduct of imperfect denitrification, this microbe also possesses hydroxylamine oxidoreductase, which catalyzes the oxidation of hydroxylamine to NO and potentially the reverse reaction. Ca. D. denitrificans can use a range of electron donors for denitrification, including aromatic compounds, glucose, sulfur compounds, and hydrogen, but metatranscriptomic analysis suggested that the major electron donors are aromatic compounds, which inhibit anammox activity. The interrelationship between Ca. D. denitirificans and Ca. B. pituitae via the metabolism of aromatic compounds may govern the population balance of both species. Ca. D. denitrificans also has the potential to fix CO2 via an irregular Calvin cycle and couple denitrification to the oxidation of hydrogen and sulfur compounds under chemolithoautotrophic conditions. This metabolic versatility, which suggests a mixotrophic lifestyle, would facilitate the growth of Ca. D. denitrificans in the anammox bioreactor.

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

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

Redox stratification within cryoconite granules influences the nitrogen cycle on glaciers

Cryoconite granules are naturally occurring microbial structures on glacier surfaces worldwide. They play a key role in carbon and nitrogen cycling in glacier ecosystems and can accelerate the melting of snow and ice. However, detailed mechanism of nitrogen cycling in cryoconite granules remains unclear. Here, we demonstrate that redox stratification affects the spatial distribution of N cycling processes in cryoconite granules. Based on microsensor measurements for O2, NH4+, NO2- and NO3-, we identified the presence of fine-scale redox stratification within cryoconite granules. Cyanobacteria at the surface layer of the granules created oxic conditions, whereas the inner core of the granules was anoxic. Metatranscriptomic analyses indicated the active occurrences of nitrification in the inner core, whereas denitrification actively occurred both in the inner core and the surface layer of the granules. Cyanobacteria in the inner core of the granules were inactive, and likely dead and being degraded, providing carbon and nitrogen to support nitrifiers and denitrifiers. Quantities of nitrification genes/transcripts were greater in large cryoconite granules than small ones, most likely because nitrogen substrates were more abundantly present in the inner core of large granules due to distinct redox stratification. Our results suggest that the development of a granular structure of cryoconite granules can largely affect carbon and nitrogen cycling on glaciers.

Simple assay for colorimetric quantification of unamplified bacterial 16S rRNA in activated sludge using gold nanoprobes

Domestic and industrial wastewater treatment systems are vital in the protection of natural ecosystems and human health. Identification of microbial communities in the systems is essential to stable treatment performance. However, the current tools of microbial community analysis are labor intensive and time consuming, and require expensive equipment. Therefore, we developed a simple assay for colorimetric quantification of bacterial 16S rRNA extracted from environmental samples. The assay is based on RNA extraction with commercial kits, mixing the unamplified RNA sample with Au-nanoprobes and NaCl, and analyzing the absorbance spectra. Our experimental results confirmed that the assay format was valid. By analyzing the synthesized DNA, we optimized the operational parameters affecting the assay. We achieved adequate capture DNA density by setting the capture DNA probe concentration at 10 μM during the functionalization step. The required incubation time after NaCl addition was 30 min. The binding site of the target had negligible effect on DNA detection. Under the optimized condition, a calibration curve was created using 16S rRNA extracted from activated sludge. The curve was linear above 5.0 × 10⁷ copies/μL of bacterial 16S rRNA concentration, and the limit of detection was 1.17 × 10⁸ copies/μL. Using the calibration curve, the bacterial 16S rRNA concentration in activated sludge samples could be quantified with deviations between 48% and 208% against those determined by RT-qPCR. The findings of our study introduce an innovative tool for the quantification of 16S rRNA concentration as the activity of key bacteria in wastewater treatment processes, achieving stable treatment performance.

Larger Anammox Granules not only Harbor Higher Species Diversity but also Support More Functional Diversity

Granule-based partial nitritation and anammox (PN/A) represents one of the most energy-efficient biotechniques for ammonium removal from wastewater. The PN/A granules appear in a continuum of sizes, yet little is known about the extent to which microbial communities and microbial metabolisms are partitioned between size-fractionated granules. Here, we divided granules harvested from a pilot-scale PN/A reactor into five discrete size fractions (<0.2, 0.2-0.5, 0.5-0.8, 0.8-1.0, and >1.0 mm). The composition and functional attribute of five pools of the size-fractionated granules were characterized by 16S ribosomal RNA (rRNA) gene amplicon and metagenomic and metatranscriptomic sequencing to provide a comprehensive insight into the key microbial group in a PN/A system. Larger granules were shown to not only harbor higher microbial diversity but also support more diverse functions than smaller granules. De novo coassembly and binning of metagenomic reads yielded 22 draft genomes of dominant microorganisms, which allowed us to infer an ecological model of the microbial ecosystem in anammox-based granules. This genome-based ecological model indicates that nitrifying organisms in smaller granules feed nitrite to anammox bacteria in larger granules. The results improve our understanding of the PN/A system, especially for the metabolic interactions between small and large granules.

Nitric oxide reactivity accounts for N-nitroso-ciprofloxacin formation under nitrate-reducing conditions

The formation of N-nitroso-ciprofloxacin (CIP) was investigated both in wastewater treatment plants including nitrification/denitrification stages and in sludge slurry experiments under denitrifying conditions. The analysis of biological wastewater treatment plant effluents by Kendrick mass defect analysis and liquid chromatography - high resolution - mass spectrometry (LCHRMS) revealed the occurrence of N-nitroso-CIP and N-nitroso-hydrochlorothiazide at concentration levels of 34 ± 3 ng/L and 71 ± 6 ng/L, respectively. In laboratory experiments and dark conditions, produced N-nitroso-CIP concentrations reached a plateau during the course of biodegradation experiments. A mass balance was achieved after identification and quantification of several transformation products by LCHRMS. N-nitroso-CIP accounted for 14.3% of the initial CIP concentration (20 µg/L) and accumulated against time. The use of 4,5-diaminofluorescein diacetate and superoxide dismutase as scavengers for in situ production of nitric oxide and superoxide radical anion respectively, revealed that the mechanisms of formation of N-nitroso-CIP likely involved a nitrosation pathway through the formation of peroxynitrite and another one through codenitrification processes, even though the former one appeared to be prevalent. This work extended the possible sources of N-nitrosamines by including a formation pathway relying on nitric oxide reactivity with secondary amines under activated sludge treatment.

Impact of gas-water ratios on N2O emissions in biological aerated filters and analysis of N2O emissions pathways

Biological aerated filter (BAF) is a widely applied biofilm process for wastewater treatment. However, characteristics of nitrous oxide (N₂O) production in BAF are rarely reported. In this study, two tandem BAFs treating domestic wastewater were built up, and different gas-water ratios were controlled to explore N₂O production pathway. Results showed that N₂O production increased with increasing gas-water ratio in both BAFs; higher gas-water ratio promoted more N₂O releasing from hydroxylamine oxidation process. To improve nitrogen removal performance and reduce N₂O emission, the optimal gas-water ratios for BAF1 and BAF2 were 5:1 and 1.5:1, respectively. Most of N₂O was produced from ammonia oxidizing bacteria (AOB) denitrification and hydroxylamine oxidation in BAF1, and heterotrophic denitrification contributed to relieve N₂O emission. In BAF2, N₂O was emitted from AOB denitrification and hydroxylamine oxidation by 87.8% and 12.2%, respectively. Heterotrophic denitrification is a N₂O sink in BAF, causing BAF1 produced less N₂O than BAF2 with the same gas-water ratio. Enhancing heterotrophic denitrification and anaerobic ammonium oxidation (Anammox) activity could reduce the release of N₂O in BAFs.

Exclusive microbially driven autotrophic iron-dependent denitrification in a reactor inoculated with activated sludge

Autotrophic iron-dependent denitrification (AIDD) is arising as a promising process for nitrogen removal from wastewater with a low carbon to nitrogen ratio. However, there is still a debate about the existence of such a process in activated sludge systems. This work provides evidence and elucidated the feasibility of autotrophic Fe(II)-oxidizing nitrate-reducing culture for nitrogen removal by long-term reactor operation, batch experimental verification, unstructured kinetic modeling and microbial community analyses. A relatively stable nitrate removal rate was achieved coupled with the oxidation of ferrous ions in 3-month operation of reactor. The kinetic modeling suggests that the iron oxidation was a growth-associated process in AIDD. Utilization of extracellular polymeric substances (and/or soluble microbial products) as electron donor for denitrification by heterotrophic denitrifiers was not mainly responsible for nitrogen removal in the reactor. After long-term operation of the reactor with activated sludge as inoculum, the enrichment culture KS-like consortium, dominated by Fe(II) oxidizer, Gallionellaceae, was successfully acclimated for autotrophic Fe(II)-oxidizing nitrate reduction. This work extents our understanding about the existence of such an autotrophic Fe(II)-oxidizing nitrate-reducing culture in both natural and engineered systems, and opens a door for its potential application in wastewater treatment.

A nitric oxide-binding heterodimeric cytochrome c complex from the anammox bacterium Kuenenia stuttgartiensis binds to hydrazine synthase

Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochromes called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme-binding motifs upon complex formation, a finding that may be of functional relevance, because NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex.