Deciphering the Inhibition of Ethane on Anaerobic Ammonium Oxidation

Potent and Selective Inhibition of Sulfate-Reducing Bacteria by Neutral Red

Sulfate-reducing bacteria (SRB) are anaerobic microorganisms that use sulfate as a terminal electron acceptor for the oxidation of organic compounds or H2. These organisms can cause a serious problem in, for example, the offshore oil industry, due to the production of sulfide. Thus, it is of fundamental and practical importance to identify potent and selective inhibitors of SRB. In this study, neutral red was identified as a previously unrecognized selective inhibitor of SRB, with several orders of magnitude higher potency than most commonly used industrial biocides and inorganic oxyanions. Neutral red remained a potent inhibitor of SRB growth under fermentative conditions and was tolerated by nitrate-reducing bacteria. After 30 days of exposure to 14.2 μM neutral red, the sulfidogenesis activity of SRB-enriched biomass was reduced by 98.3%, and the abundance of SRB populations declined from 25.5% to 0.76%. Transcriptomic analysis revealed that the inhibition of the central sulfate reduction pathway was implicated in the mechanism of neutral red toxicity against SRB growth. Furthermore, downregulation of two electron transport complexes (QmoABC and DsrMKJOP), ATP synthase, as well as cytoplasmic/periplasmic hydrogenase suggested the collapse of the proton gradient. These findings have implications for environmental control of SRB and may enhance economic benefits in industrial operations.

Transcriptional and molecular simulation analysis of the response mechanism of anammox bacteria to 3,4-dimethylpyrazole phosphate stress

Anaerobic ammonium oxidation (anammox) and nitrification are two vital biological pathways for ammonium oxidation, pivotal in microbial nitrogen cycling. 3,4-Dimethylpyrazole phosphate (DMPP) is commonly used as inhibitors in agricultural soils to reduce nitrogen losses from farmland, while whether it affect anammox is an open question. Acute inhibition tests revealed that 53.5 mg·L-1 DMPP caused 50 % reduction in anammox bacteria. After 36 days of prolonged exposure to 5 mg·L-1 DMPP, the ammonium(nitrite) removal rate of endnote decreased from 78.39(94.78) to 13.57(15.28) mgN·gVSS-1·d-1. Additionally, the abundance of Ca. Kuenenia decreased from 36.5 % to 6.06 %. Transcriptomic analysis revealed that the mRNA levels of ammonium transport genes (amt_1 and amt_4), and hydrazine synthase (hzs) were significantly downregulated. Molecular docking simulations indicated that DMPP bound with ammonium transport and hydrazine synthesis. This interaction hindered the transcriptional levels of genes encoding ammonium transporters and hzs. The study has guiding value to reduce the nitrogen loss involved in anammox bacteria in agricultural soils under the application of DMPP.

A comprehensive review of antibiotics stress on anammox systems: Mechanisms, applications, and challenges

Anaerobic ammonia oxidation (anammox), an energy-efficient technology for treating ammonium-rich wastewater, faces the challenge of antibiotic stress in sewage. This paper systematically evaluated the impact of antibiotics on anammox by considering both inhibitory effects and recovery duration. This review focused on cellular responses, including extracellular polymeric substances (EPS), quorum sensing (QS), and enzymes. Then, the physiological properties of cells and the interactions between nitrogen and carbon metabolism under antibiotic stress were discussed, particularly within the anammoxosome. The microbial community evolution and the development and transfer of antibiotic resistance genes (ARGs) were further analyzed to reveal the resistance mechanisms of anammox. To address the limitations imposed by antibiotics, the development of bio-augmentation and combined processes based on molecular biology techniques, such as bio-electrochemical systems (BES), has been suggested. This review offered new insights into the mechanisms of antibiotic inhibition during the anammox process and aimed to advance their engineering applications.

An overlooked nanofluids effect from Fe3O4 nanoparticles enhances mass transfer in anammox granular sludge

Magnetite (Fe3O4) particles have been widely reported to enhance the anammox's activity in anammox granular sludge (AnGS), yet the underlying mechanisms remain unclear. This study demonstrates that both Fe3O4 microparticles (MPs) and nanoparticles (NPs) at a dosage of 200 mg Fe3O4/L significantly increased the specific anammox activity (SAA) of AnGS. Additionally, the transcriptional activities of the hzs and hdh genes involved in the anammox process, as well as the heme c content in AnGS, were also notably enhanced. Notably, Fe3O4 NPs were more effective than MPs in boosting anammox activity within AnGS. Mechanistically, Fe3O4 MPs released free iron, which anammox bacteria utilized to promote the synthesis of key enzymes, thereby enhancing their activity. Compared to MPs, Fe3O4 NPs not only elevated the synthesis of these key enzymes to a higher level but also induced a nanofluids effect on the surface of AnGS, improving substrate permeability and accessibility to intragranular anammox bacteria. Moreover, the nanofluids effect was identified as the primary mechanism through which Fe3O4 NPs enhanced anammox activity within AnGS. These findings provide new insights into the effects of nanoparticles on granular sludge systems, extending beyond AnGS.

Deciphering retention effect of extracellular polymeric substances to typical heavy metals and their interaction with key inner enzymes of Candidatus Kuenenia

This study employed spectroscopy, metagenomics, and molecular simulation to investigate the inhibitory effects of Cd(II) and Cu(II) on the anammox system, examining both intracellular and extracellular effects. At concentrations of 5 mg/L, Cd(II) and Cu(II) significantly reduced nitrogen removal efficiency by 41.46 % and 62.03 %, respectively. Additionally, elevated metal concentrations were correlated with decreased extracellular polymeric substances (EPS), thereby reducing their capacity to absorb heavy metals, particularly Cu(II), which decreased from 76.47 % to 14.67 %. Spectral analysis revealed alterations in the secondary structures of EPS induced by Cd(II) and Cu(II), decreasing the ratio of extracellular protein α-helix to (β-sheet + random coil), which resulted in looser extracellular protein configurations. The results of the metagenomics study showed that the abundance of Candidatus Kuenenia and its genes encoding nitrogen removal-related enzymes was reduced. The abundance of hzs-γ was reduced by 35.09 % at a concentration of 5 mg/L Cu(II). Conversely, genes associated with metal efflux enzymes, like czcR, increased by 54.86 % at 2 mg/L Cd(II). Molecular docking revealed robust bindings of Cd(II) to HZS-α (-342.299 ± 218.165 kJ/mol) and Cu(II) to HZS-γ (-880.934 ± 55.526 kJ/mol). This study elucidated the inhibitory mechanisms of Cd(II) and Cu(II) on the anammox system, providing insights into the resistance of anammox bacteria to heavy metals.

Coupling Nitrate-Dependent Anaerobic Ethane Degradation with Anaerobic Ammonium Oxidation

The microbial oxidation of short-chain gaseous alkanes (SCGAs, consisting of ethane, propane, and butane) serves as an efficient sink to mitigate these gases' emission to the atmosphere, thus reducing their negative impacts on air quality and climate. "Candidatus Alkanivorans nitratireducens" are recently found to mediate nitrate-dependent anaerobic ethane oxidation (n-DAEO). In natural ecosystems, anaerobic ammonium-oxidizing (anammox) bacteria may consume nitrite generated from nitrate reduction by "Ca. A. nitratireducens", thereby alleviating the inhibition caused by nitrite accumulation on the metabolism of "Ca. A. nitratireducens". Here, we demonstrate the coupling of n-DAEO with anammox in a laboratory-scale model system to prevent nitrite accumulation. Our results suggest that a high concentration of ethane (6.9-7.9%) has acute inhibition on anammox activities, thus making the coupling process a significant challenge. By maintaining ethane concentrations within the range of 1.7-5.5%, stable ethane and ammonium oxidation, nitrate reduction, and dinitrogen gas generation without nitrite accumulation were finally achieved. After the accomplished coupling of n-DAEO with anammox, nitrate reduction rates increased by 8.1 times compared to the rate observed with n-DAEO alone. Microbial community profiling via 16S rRNA gene amplicon sequencing showed "Ca. A. nitratireducens" (6.6-12.9%) and anammox bacteria "Candidatus Kuenenia" (3.4-5.6%) were both dominant in the system, indicating they potentially form a syntrophic partnership to jointly contribute to nitrogen removal. Our findings offer insights into the cross-feeding interaction between "Ca. A. nitratireducens" and anammox bacteria in anoxic environments.

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.

Effects of sliver nanoparticles on nitrogen removal by the heterotrophic nitrification-aerobic denitrification bacteria Zobellella sp. B307 and their toxicity mechanisms

Due to the widespread use of sliver nanoparticles (AgNPs), a large amount of AgNPs has inevitably been released into the environment, and there is growing concern about the toxicity of AgNPs to nitrogen-functional bacteria. In addition to traditional anaerobic denitrifying bacteria, heterotrophic nitrification-aerobic denitrification (HNAD) bacteria are also important participants in the nitrogen cycle. However, the mechanisms by which AgNPs influence HNAD bacteria have yet to be explicitly demonstrated. In this study, the inhibitory effects of different concentrations of AgNPs on a HNAD bacteria Zobellella sp. B307 were investigated, and the underlying mechanism was explored by analyzing the antioxidant system and the activities of key denitrifying enzymes. Results showed that AgNPs could inhibit the growth and the HNAD ability of Zobellella sp. B307. AgNPs could accumulate on the surface of bacterial cells and significantly destroyed the cell membrane integrity. Further studies demonstrated that the presence of high concentration of AgNPs could result in the overproduction of reactive oxygen species (ROS) and related oxidative stress in the cells. Furthermore, the catalytic activities of key denitrifying enzymes (nitrate reductase (NAR), nitrite reductase (NIR), and nitrous oxide reductase (N2OR)) were significantly suppressed under exposure to a high concentration of AgNPs (20 mg·L-1), which might be responsible for the inhibited nitrogen removal performance of strain B307. This work could improve our understanding of the inhibitory effect and underlying mechanism of AgNPs on HNAD bacteria.

Strong suppression of silver nanoparticles on antibiotic resistome in anammox process

This study comprehensively deciphered the effect of silver nanoparticles (AgNPs) on anammox flocculent sludge, including nitrogen removal performance, microbial community structure, functional enzyme abundance, antibiotic resistance gene (ARGs) dissemination, and horizontal gene transfer (HGT) mechanisms. After long-term exposure to 0-2.5 mg/L AgNPs for 200 cycles, anammox performance significantly decreased (P < 0.05), while the relative abundances of dominant Ca. Kuenenia and anammox-related enzymes (hzsA, nirK) increased compared to the control (P < 0.05). For antibiotic resistome, ARG abundance hardly changed with 0-0.5 mg/L AgNPs but decreased by approximately 90% with 1.5-2.5 mg/L AgNPs. More importantly, AgNPs effectively inhibited MGE-mediated HGT of ARGs. Additionally, structural equation model (SEM) disclosed the underlying relationship between AgNPs, the antibiotic resistome, and the microbial community. Overall, AgNPs suppressed the anammox-driven nitrogen cycle, regulated the microbial community, and prevented the spread of ARGs in anammox flocs. This study provides a theoretical baseline for an advanced understanding of the ecological roles of nanoparticles and resistance elements in engineered ecosystems.

Nitrate removal by anammox bacteria utilizing photoexcited electrons via inward extracellular electron transfer channel

Dissimilatory nitrate reduction to ammonium (DNRA) has been found to occur in some anammox bacteria species, and the DNRA metabolites (nitrite and ammonium) can further be removed to nitrogen from water. However, the activation of DNRA pathway of anammox bacteria is usually limited by the access to electron donors. Herein, we constructed a photosensitized hybrid system combining anammox bacteria (Candidatus Kuenenia stuttgartiensis and Candidatus Brocadia anammoxidans) with CdS nanoparticles semiconductor for energy-efficient NO3- removal. Such photosensitized anammox-CdS hybrid systems achieved NO3- removal with an average efficiency of 88% (the maximum of 91%) and a N2 selectivity of 72%, only with photoexcited electrons as donors. The DNRA-anammox metabolism of anammox bacteria was proved to responsible for NO3- removal via inward extracellular electron transfer channel. The greatly up-regulated genes encoding c-type cytochrome proteins (5 or 11 hemes) in the outer membrane, c-type cytochrome protein (4 hemes) and electron transport protein RnfA-E in the inner membrane, ferredoxin (2Fe-2S) in the cytoplasm and c-type cytochrome bc1 in anammoxosome membrane were supposed to play key roles in the inward extracellular electron transfer pathway. This work provides a novel insight into the design of the biotic-abiotic hybrid photosynthetic systems, and opens a new strategy for light-driven NO3- removal from the perspective of light energy input.

Unraveling potential mechanism of different metal ions effect on anammox through big data analysis, molecular docking and molecular dynamics simulation

Heavy metals (HMs) have been widely reported to pose an adverse effect on anaerobic ammonia oxidation (anammox) bacteria, yet the underlying mechanisms remain unclear. This study provides new insights into the potential mechanisms of interaction between HMs and functional enzymes through big date analysis, molecular docking and molecular dynamics simulation. The statistical analysis indicated that 10 mg/L Cu(II) and Cd(II) reduced nitrogen removal rate (NRR) by 85% and 43%, while 5 mg/L Fe(II) enhanced NRR by 29%. Additionally, the results of molecular simulations provided a microscopic interpretation for these macroscopic data. Molecular docking revealed that Hg(II) formed a distinctive binding site on ferritin, while other HMs resided at iron oxidation sites. Furthermore, HMs exhibited distinct binding sites on hydrazine dehydrogenase. Concurrently, the molecular dynamics simulation results further substantiated their capacity to form complexes. Cu(II) displayed the strongest binding affinity with ferritin for -1576 ± 79 kJ/mol in binding free energy calculation. Moreover, Cd(II) bound to ferritin and HDH for -1052.67 ± 58.49 kJ/mol, -290.02 ± 49.68 kJ/mol, respectively. This research addressed a crucial knowledge gap, shedding light on potential applications for remediating heavy metal-laden industrial wastewater.

How to Provide Nitrite Robustly for Anaerobic Ammonium Oxidation in Mainstream Nitrogen Removal

Innovation in decarbonizing wastewater treatment is urgent in response to global climate change. The practical implementation of anaerobic ammonium oxidation (anammox) treating domestic wastewater is the key to reconciling carbon-neutral management of wastewater treatment with sustainable development. Nitrite availability is the prerequisite of the anammox reaction, but how to achieve robust nitrite supply and accumulation for mainstream systems remains elusive. This work presents a state-of-the-art review on the recent advances in nitrite supply for mainstream anammox, paying special attention to available pathways (forward-going (from ammonium to nitrite) and backward-going (from nitrate to nitrite)), key controlling strategies, and physiological and ecological characteristics of functional microorganisms involved in nitrite supply. First, we comprehensively assessed the mainstream nitrite-oxidizing bacteria control methods, outlining that these technologies are transitioning to technologies possessing multiple selective pressures (such as intermittent aeration and membrane-aerated biological reactor), integrating side stream treatment (such as free ammonia/free nitrous acid suppression in recirculated sludge treatment), and maintaining high activity of ammonia-oxidizing bacteria and anammox bacteria for competing oxygen and nitrite with nitrite-oxidizing bacteria. We then highlight emerging strategies of nitrite supply, including the nitrite production driven by novel ammonia-oxidizing microbes (ammonia-oxidizing archaea and complete ammonia oxidation bacteria) and nitrate reduction pathways (partial denitrification and nitrate-dependent anaerobic methane oxidation). The resources requirement of different mainstream nitrite supply pathways is analyzed, and a hybrid nitrite supply pathway by combining partial nitrification and nitrate reduction is encouraged. Moreover, data-driven modeling of a mainstream nitrite supply process as well as proactive microbiome management is proposed in the hope of achieving mainstream nitrite supply in practical application. Finally, the existing challenges and further perspectives are highlighted, i.e., investigation of nitrite-supplying bacteria, the scaling-up of hybrid nitrite supply technologies from laboratory to practical implementation under real conditions, and the data-driven management for the stable performance of mainstream nitrite supply. The fundamental insights in this review aim to inspire and advance our understanding about how to provide nitrite robustly for mainstream anammox and shed light on important obstacles warranting further settlement.

Effect of free ammonia on partial denitrification: Long-term performance, mechanism, and feasibility of PD/Anammox-FBBR for mature landfill leachate treatment

As a stable and effective approach for NO2--N accumulation, partial denitrification (PD) could significantly cut down operation cost, and PD/Anammox (PD/A) is a promising nitrogen removal process in wastewater treatment. The biotoxicity of free ammonia (FA) to nitrifying bacteria and anammox bacteria has been demonstrated, while whether FA affects PD bacteria is an open question. Here, long-term operation of PD-fixed bed biofilm reactor (PD-FBBR) treating synthetic wastewater and mature landfill leachate was conducted to reveal the mechanism concerning the effect of FA on PD bacteria. Stable NO2--N accumulation was achieved with NO3--N to NO2--N transformation ratio (NTR) of 60-70% during 280-day operation with FA ranged from 0 to 20.71 ± 0.23 mg/L, while NTR decreased and maintained at ∼30% when FA reached 40.59 ± 0.19 mg/L. Specific NOx--N reduction rate improved at low FA concentration (< 12 mg/L), while high FA level (> 25 mg/L) had inhibitory effect on PD bacteria. Under FA stress, more extracellular polymeric substances (EPS) were secreted, and the glnA gene abundance, glutamine synthase concentration, and glutamine concentration in cell and EPS significantly increased, indicating the enhancement of glutamine biosynthesis in PD bacteria for ammonia assimilation played an important role in response to FA stress. Metagenomic sequencing showed that FA stimulated the upregulation of narK (NO3--N/NO2--N antiporter) gene abundance and enhanced uptake of NO3--N and extrusion of NO2--N. Comamonas, unclassified_f__Comamonadaceae and Thauera were highly enriched in biofilm, which played a key role in the stable NO2--N accumulation. Furthermore, a novel two stage PD/A-FBBR was applied to mature landfill leachate treatment, and satisfactory total inorganic nitrogen removal efficiency ranged from 81.38 ± 3.56% to 89.16 ± 1.57% was obtained at relatively low COD/NO3--N of 2.57-2.84. Overall, these findings demonstrated how PD bacteria respond to FA stress and confirmed the feasibility of PD/A process in high FA wastewater treatment.

Insights into heavy metals shock on anammox systems: Cell structure-based mechanisms and new challenges

Anaerobic ammonium oxidation (anammox) as a low-carbon and energy-saving technology, has shown unique advantages in the treatment of high ammonia wastewater. However, wastewater usually contains complex heavy metals (HMs), which pose a potential risk to the stable operation of the anammox system. This review systematically re-evaluates the HMs toxicity level from the inhibition effects and the inhibition recovery process, which can provide a new reference for engineering. From the perspective of anammox cell structure (extracellular, anammoxosome membrane, anammoxosome), the mechanism of HMs effects on cellular substances and metabolism is expounded. Furthermore, the challenges and research gaps for HMs inhibition in anammox research are also discussed. The clarification of material flow, energy flow and community succession under HMs shock will help further reveal the inhibition mechanism. The development of new recovery strategies such as bio-accelerators and bio-augmentation is conductive to breaking through the engineered limitations of HMs on anammox. This review provides a new perspective on the recognition of toxicity and mechanism of HMs in the anammox process, as well as the promotion of engineering applicability.

Novel synergistic metabolic processes for phenanthrene biodegradation by a nitrate-reducing phenanthrene-degrading culture and an anammox culture

The synergistic metabolism by anammox cultures and nitrate-reducers for anaerobic PAH biodegradation is largely unknown, including whether anammox culture and which kind of anammox bacterium can perform nitrogen metabolism in the anaerobic PAH biodegradation processes, the inhibitory effect of PAH on anammox activity and nitrite on PAH-degrading nitrate-reducers activity, and the synergistic metabolic processes. Herein, an anammox culture that can eliminate nitrite accumulation and decrease inorganic carbon emission during anaerobic phenanthrene (a model of PAH in this study) biodegradation, the synergistic mechanism for phenanthrene biodegradation by a nitrate-reducer and such anammox culture, and the inhibition effect of phenanthrene on such anammox culture and nitrite on a phenanthrene-degrading nitrate-reducer were newly discussed. The results showed that nitrite largely accumulated during anaerobic phenanthrene biodegradation (nitrate accumulation is a common phenomenon for the biodegradation of refractory matter, including PAHs, by nitrate-reducers) by a nitrate-reducer, PheN2, which mineralizes phenanthrene to inorganic carbon, and nitrite was verified as an inhibiting factor for further biodegradation. Anaerobic phenanthrene biodegradation rates and nitrite concentrations (0-7 mM) appeared to have a negative linear correlation. The anammox culture that mainly contained Candidatus Kuenenia was newly found to efficiently reduce nitrite accumulation and inorganic carbon emissions and significantly promote biodegradation efficiency by ∼1.94-fold. Our results showed that phenanthrene absorbed in and on anammox cells had a more direct relationship with the inhibitory effect on anammox activity than phenanthrene in the environment, and 15.2 mg/gVSS phenanthrene absorbed in and on the cells (4 mM concentration in the culture) showed nearly complete inhibition of anammox culture in this study. In addition, few (less than 2% abundance) anammox bacteria were found to be enough for the removal of nitrite produced from anaerobic phenanthrene biodegradation. In an ideal world, co-pollutants of ammonia, nitrate, phenanthrene, and nitrite could be converted to nitrogen gas and biomass by the synergistic metabolism of anammox cultures and nitrate reducers. Our study reveals a new synergistic process that may exist in our environments for PAH elimination by an anammox culture and a nitrate-reducer, which provides a new strategy for the bioremediation of PAH-polluted anoxic zones.