Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions

Chemoorganotrophic electrofermentation by Cupriavidus necator using redox mediators

The non-pathogenic β-proteobacterium Cupriavidus necator has the ability to switch between chemoorganotrophic, chemolithoautotrophic and electrotrophic growth modes, making this microorganism a widely used host for cellular bioprocesses. Oxygen usually acts as the terminal electron acceptor in all growth modes. However, several challenges are associated with aeration, such as foam formation, oxygen supply costs, and the formation of an explosive gas mixture in chemolithoautotrophic cultivation with H2, CO2 and O2. Bioelectrochemical systems in which O2 is replaced by an electrode as a terminal electron acceptor offer a promising solution to these problems. The aim of this study was to establish a mediated electron transfer between the anode and the metabolism of living cells, i.e. anodic respiration, using fructose as electron and carbon source. Since C. necator is not able to transfer electrons directly to an electrode, redox mediators are required for this process. Based on previous observations on the extracellular electron transfer enabled by a polymeric mediator, we tested 11 common biological and non-biological redox mediators for their functionality and inhibitory effect for anodic electron transfer in a C. necator-based bioelectrochemical system. The use of ferricyanide at a concentration of 15 mM resulted in the highest current density of 260.75µAcm-2 and a coulombic efficiency of 64.1 %.

Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway

Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this review, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.

Nitrate reduction to ammonium: a phylogenetic, physiological, and genetic aspects in Prokaryotes and eukaryotes

The microbe-mediated conversion of nitrate (NO3-) to ammonium (NH4+) in the nitrogen cycle has strong implications for soil health and crop productivity. The role of prokaryotes, eukaryotes and their phylogeny, physiology, and genetic regulations are essential for understanding the ecological significance of this empirical process. Several prokaryotes (bacteria and archaea), and a few eukaryotes (fungi and algae) are reported as NO3- reducers under certain conditions. This process involves enzymatic reactions which has been catalysed by nitrate reductases, nitrite reductases, and NH4+-assimilating enzymes. Earlier reports emphasised that single-cell prokaryotic or eukaryotic organisms are responsible for this process, which portrayed a prominent gap. Therefore, this study revisits the similarities and uniqueness of mechanism behind NO3- -reduction to NH4+ in both prokaryotes and eukaryotes. Moreover, phylogenetic, physiological, and genetic regulation also shed light on the evolutionary connections between two systems which could help us to better explain the NO3--reduction mechanisms over time. Reports also revealed that certain transcription factors like NtrC/NtrB and Nit2 have shown a major role in coordinating the expression of NO3- assimilation genes in response to NO3- availability. Overall, this review provides a comprehensive information about the complex fermentative and respiratory dissimilatory nitrate reduction to ammonium (DNRA) processes. Uncovering the complexity of this process across various organisms may further give insight into sustainable nitrogen management practices and might contribute to addressing global environmental challenges.

Organoselenium Compounds in Medicinal Chemistry

The chemical and biological interest in this element and the molecules bearing selenium has been exponentially growing over the years. Selenium, formerly designated as a toxin, becomes a vital trace element for life that appears as selenocysteine and its dimeric form, selenocystine, in the active sites of selenoproteins, which catalyze a wide variety of reactions, including the detoxification of reactive oxygen species and modulation of redox activities. From the point of view of drug developments, organoselenium drugs are isosteres of sulfur-containing and oxygen-containing drugs with the advantage that the presence of the selenium atom confers antioxidant properties and high lipophilicity, which would increase cell membrane permeation leading to better oral bioavailability. This statement is the paramount relevance considering the big number of clinically employed compounds bearing sulfur or oxygen atoms in their structures including nucleosides and carbohydrates. Thus, in this article we have focused on the relevant features of the application of selenium in medicinal chemistry. With the increasing interest in selenium chemistry, we have attempted to highlight the most significant published data on this subject, mainly concentrating the analysis on the last years. In consequence, the recent advances of relevant pharmacological organoselenium compounds are discussed.

Tuning Local Atomic Structures in MoS2 Based Catalysts for Electrochemical Nitrate Reduction

In recent years, there has been a substantial surge in the investigation of transition-metal dichalcogenides such as MoS2 as a promising electrochemical catalyst. Inspired by denitrification enzymes such as nitrate reductase and nitrite reductase, the electrochemical nitrate reduction catalyzed by MoS2 with varying local atomic structures is reported. It is demonstrated that the hydrothermally synthesized MoS2 containing sulfur vacancies behaves as promising catalysts for electrochemical denitrification. With copper doping at less than 9% atomic ratio, the selectivity of denitrification to dinitrogen in the products can be effectively improved. X-ray absorption characterizations suggest that two sulfur vacancies are associated with one copper dopant in the MoS2 skeleton. DFT calculation confirms that copper dopants replace three adjacent Mo atoms to form a trigonal defect-enriched region, introducing an exposed Mo reaction center that coordinates with Cu atom to increase N2 selectivity. Apart from the higher activity and selectivity, the Cu-doped MoS2 also demonstrates remarkably improved tolerance toward oxygen poisoning at high oxygen concentration. Finally, Cu-doped MoS2 based catalysts exhibit very low specific energy consumption during the electrochemical denitrification process, paving the way for potential scale-up operations.

Mechanisms of nanoscale zero-valent iron mediating aerobic denitrification in Pseudomonas stutzeri by promoting electron transfer and gene expression

Aerobic denitrification and its mechanism by P. stutzeri was investigated in the presence of nanoscale zero-valent iron (nZVI). The removal of nitrate and ammonia was accelerated and the nitrite nitrogen accumulation was reduced by nZVI. The particle size and dosage of nZVI were key factors for enhancing aerobic denitrification. nZVI reduced the negative effects of low carbon/nitrogen, heavy metals, surfactants and salts to aerobic denitrification. nZVI and its dissolved irons were adsorbed into the bacteria cells, enhancing the transfer of electrons from nicotinamide adenine dinucleotide (NADH) to nitrate reductase. Moreover, the activities of NADH-ubiquinone reductase involved in the respiratory system, and the denitrifying enzymes were increased. The expression of denitrifying enzyme genes napA and nirS, as well as the iron metabolism gene fur, were promoted in the presence of nZVI. This work provides a strategy for enhancing the biological denitrification of wastewater using the bio-stimulation of nanomaterials.

High-efficient nutrient removal in a single-stage electrolysis-integrated sequencing batch biofilm reactor (E-SBBR) for low C/N sanitary sewage treatment

To efficiently remove nutrients from low C/N sanitary sewage by conventional biological process is challenging due to the lack of sufficient electron donors. A novel electrolysis-integrated sequencing batch biofilm reactor (E-SBBR) was established to promote nitrogen and phosphorus removal for sanitary sewage with low C/N ratios (3.5-1.5). Highly efficient removal of nitrogen (>79%) and phosphorus (>97%) was achieved in the E-SBBR operating under alternating anoxic/electrolysis-anoxic/aerobic conditions. The coexistence of autotrophic nitrifiers, electron transfer-related bacteria, and heterotrophic and autohydrogenotrophic denitrifiers indicated synergistic nitrogen removal via multiple nitrogen-removing pathways. Electrolysis application induced microbial anoxic ammonia oxidation, autohydrogenotrophic denitrification and electrocoagulation processes. Deinococcus enriched on the electrodes were likely to mediate the electricity-driven ammonia oxidation which promoted ammonia removal. PICRUSt2 indicated that the relative abundances of key genes (hyaA and hyaB) associated with hydrogen oxidation significantly increased with the decreasing C/N ratios. The high autohydrogenotrophic denitrification rates during the electrolysis-anoxic period could compensate for the decreased heterotrophic rates resulting from insufficient carbon sources and nitrate removal was dramatically enhanced. Electrocoagulation with iron anode was responsible for phosphorus removal. This study provides insights into mechanisms by which electrochemically assisted biological systems enhance nutrient removal for low C/N sanitary sewage.

Responses of soil bacterial and fungal denitrification and associated N2O emissions to organochloride pesticide

The extensive application of organochloride pesticides in agriculture has raised concerns about their potential negative impacts on soil microbial denitrification and associated N2O emissions. However, most studies have primarily focused on bacteria, and the contribution of fungi to N2O emissions and their response to organochloride pesticides have often been overlooked. In this study, 15N tracing combined with the respiration inhibition method was applied to examine the impacts of chlorothalonil on both fungal and bacterial denitrification. The results demonstrated that fungal N2O emissions dominated in the absence of chlorothalonil, accounting for 73 % of total N2O emissions. Chlorothalonil inhibited fungal and bacterial denitrification via different mechanisms and altered the main pathways of soil N2O emissions. Amplicon sequencing analyses indicated that chlorothalonil significantly reduced the abundances of N2O-producing fungi owing to its fungicidal effect and fungal N2O emissions significantly dropped. Molecular biological analyses revealed that chlorothalonil induced lower electron generation, transport, and consumption efficiencies, which led to the inhibition of denitrifying enzymes in bacteria. Bacterial N2O emissions dramatically increased and became the dominant source. These findings provide insights into the mechanisms by which N2O emissions from fungal and bacterial denitrification are influenced by chlorothalonil.

Reveal molecular mechanism on the effects of silver nanoparticles on nitrogen transformation and related functional microorganisms in an agricultural soil

Silver nanoparticles (AgNPs) are widely present in aquatic and soil environment, raising significant concerns about their impacts on creatures in ecosystem. While the toxicity of AgNPs on microorganisms has been reported, their effects on biogeochemical processes and specific functional microorganisms remain relatively unexplored. In this study, a 28-day microcosmic experiment was conducted to investigate the dose-dependent effects of AgNPs (10 mg and 100 mg Ag kg-1 soil) on nitrogen transformation and functional microorganisms in agricultural soils. The molecular mechanisms were uncovered by examining change in functional microorganisms and metabolic pathways. To enable comparison, the toxicity of positive control with an equivalent Ag+ dose from CH3COOAg was also included. The results indicated that both AgNPs and CH3COOAg enhanced nitrogen fixation and nitrification, corresponding to increased relative abundances of associated functional genes. However, they inhibited denitrification via downregulating nirS, nirK, and nosZ genes as well as reducing nitrate and nitrite reductase activities. In contrast to high dose of AgNPs, low levels increased bacterial diversity. AgNPs and CH3COOAg altered the activities of associated metabolic pathways, resulting in the enrichment of specific taxa that demonstrated tolerance to Ag. At genus level, AgNPs increased the relative abundances of nitrogen-fixing Microvirga and Bacillus by 0.02 %-629.39 % and 14.44 %-30.10 %, respectively, compared with control group (CK). The abundances of denitrifying bacteria, such as Rhodoplanes, Pseudomonas, and Micromonospora, decreased by 19.03 % to 32.55 %, 24.73 % to 50.05 %, and 15.66 % to 76.06 %, respectively, compared to CK. CH3COOAg reduced bacterial network complexity, diminished the symbiosis mode compared to AgNPs. The prediction of genes involved in metabolic pathways related to membrane transporter and cell motility showed sensitive to AgNPs exposure in the soil. Further studies involving metabolomics are necessary to reveal the essential effects of AgNPs and CH3COOAg on biogeochemical cycle of elements in agricultural soil.

Comprehensive metagenomic and enzyme activity analysis reveals the inhibitory effects and potential toxic mechanism of tetracycline on denitrification in groundwater

The widespread use of tetracycline (TC) inevitably leads to its increasing emission into groundwater. However, the potential risks of TC to denitrification in groundwater remain unclear. In this study, the effects of TC on denitrification in groundwater were systematically investigated at both the protein and gene levels from the electron behavior aspect for the first time. The results showed that increasing TC from 0 to 10 µg·L-1 decreased the nitrate removal rate from 0.41 to 0.26 mg·L-1·h-1 while enhancing the residual nitrite concentration from 0.52 mg·L-1 to 50.60 mg·L-1 at the end of the experiment. From a macroscopic view, 10 µg·L-1 TC significantly inhibited microbial growth and altered microbial community structure and function in groundwater, which induced the degeneration of denitrification. From the electron behavior aspect (the electron production, electron transport and electron consumption processes), 10 µg·L-1 TC decreased the concentration of electron donors (nicotinamide adenine dinucleotide, NADH), electron transport system activity, and denitrifying enzyme activities at the protein level. At the gene level, 10 µg·L-1 TC restricted the replication of genes related to carbon metabolism, the electron transport system and denitrification. Moreover, discrepant inhibitory effects of TC on individual denitrification steps, which led to the accumulation of nitrite, were observed in this study. These results provide the information that is necessary for evaluating the potential environmental risk of antibiotics on groundwater denitrification and bring more attention to their effects on geochemical nitrogen cycles.

Evaluating the inhibitory effects of Nitrobenzene short-term stress on denitrification performance: Electron behaviors, bacterial and fungal community

Denitrifying system is a feasible way to remove nitro-aromatic compounds (NACs) in wastewater. However, the toxicity and mechanisms of NACs to denitrification remain unknown. This study investigated effects of nitrobenzene (NB, a typical NAC) on denitrification in short term. Results showed that NB in 10-50 mg/L groups decreased NO3--N removal efficiency by 9%-24%, but increased nitrous oxide (N2O) generation by 6-17fold. Mechanistic research indicated that NB could deteriorate electron behaviors and disturbed enzyme activities of microbial metabolism and denitrification, leading to a decline in denitrification performance. Structural equation modeling revealed that N2O reductase activity was the core factor in predicting denitrification performance at exposure of NB, with the indirect effects of NADH and electron transport system activity. High-throughput sequencing analysis demonstrated that NB had made an alteration on both bacterial and fungal community structure, as well as their interactions.

The regulation of carbon dioxide on food microorganisms: A review

This review presents a survey of two extremely important technologies about CO2 with the effectiveness of controlling microorganisms - atmospheric pressure CO2-based modified atmosphere packaging (MAP) and high pressure CO2 non-thermal pasteurization (HPCD). CO2-based MAP is effectively in delaying the lag and logarithmic phases of microorganisms by replacing the surrounding air, while HPCD achieved sterilization by subjecting food to either subcritical or supercritical CO2 for some time in a continuous, batch or semi-batch way. In addition to the advantages of healthy, eco-friendly, quality-preserving, effective characteristic, some challenges such as the high drip loss and packaging collapse associated with higher concentration of CO2, the fuzzy mechanisms of oxidative stress, the unproven specific metabolic pathways and biomarkers, etc., in CO2-based MAP, and the unavoidable extraction of bioactive compounds, the challenging application in solid foods with higher efficiency, the difficult balance between optimal sterilization and optimal food quality, etc., in HPCD still need more efforts to overcome. The action mechanism of CO2 on microorganisms, researches in recent years, problems and future perspectives are summarized. When dissolved in solution medium or cellular fluids, CO2 can form carbonic acid (H2CO3), and H2CO3 can further dissociate into bicarbonate ions (HCO3-), carbonate (CO32-) and hydrogen cations (H+) ionic species following series equilibria. The action mode of CO2 on microorganisms may be relevant to changes in intracellular pH, alteration of proteins, enzyme structure and function, alteration of cell membrane function and fluidity, and so on. Nevertheless, the effects of CO2 on microbial biofilms, energy metabolism, protein and gene expression also need to be explored more extensively and deeply to further understand the action mechanism of CO2 on microorganisms.

Electron transfer mechanism of intracellular carbon-dependent DNRA inside anammox bacteria

Generally, anaerobic ammonium oxidation (anammox) converts nitrite (NO2-) and ammonium (NH4+) to nitrogen gas (N2) but generates some nitrate (NO3-) (equivalent to 11% of inlet total nitrogen (TN)). Although it reported that anammox bacteria could degrade NO3- via dissimilatory nitrate reduction to ammonium (DNRA) pathway using the intracellular carbon as the electron donor, it is still unclear the specific electron transfer mechanism in this intracellular carbon-dependent DNRA inside anammox bacteria, and whether the sole anammox bacteria could achieve higher TN removal efficiency more than the theoretical maximum of 89%. In this study, transcriptome analysis and metabolic inhibitor experiments demonstrated that NADH generated from the decomposition of the intracellular carbon (glycogen) supplied electrons for the NO3-conversion; the electrons were transferred from NADH to nitrate reductase (Nar) and nitrite reductase forming ammonium (NrfA) from ubiquinone (UQ) and complex III, respectively. Combining the intracellular carbon-dependent DNRA with normal anammox process, an average TN removal efficiency of 95% was achieved by the sole anammox bacteria in a sequencing batch reactor. Fluorescent in situ hybridization (FISH) images and real-time fluorescence quantitative PCR (qPCR) results illustrated anammox bacteria could survive and proliferate in the SBR. Our work improved the understanding of the electron transfer mechanism inside anammox bacteria, and further exploit its potential in nitrogen pollutants removal.

Promoting heterotrophic denitrification of Pseudomonas hunanensis strain PAD-1 using pyrite: A mechanistic study

Denitrification is critical for removing nitrate from wastewater, but it typically requires large amounts of organic carbon, which can lead to high operating costs and secondary environmental pollution. To address this issue, this study proposes a novel method to reduce the demand for organic carbon in denitrification. In this study, a new denitrifier, Pseudomonas hunanensis strain PAD-1, was obtained with properties for high efficiency nitrogen removal and trace N2O emission. It was also used to explore the feasibility of pyrite-enhanced denitrification to reduce organic carbon demand. The results showed that pyrite significantly improved the heterotrophic denitrification of strain PAD-1, and optimal addition amount was 0.8-1.6 g/L. The strengthening effect of pyrite was positively correlated with carbon to nitrogen ratio, and it could effectively reduce demand for organic carbon sources and enhance carbon metabolism of strain PAD-1. Meanwhile, the pyrite significantly up-regulated electron transport system activity (ETSA) of strain PAD-1 by 80%, nitrate reductase activity by 16%, Complex III activity by 28%, and napA expression by 5.21 times. Overall, the addition of pyrite presents a new avenue for reducing carbon source demand and improving the nitrate harmless rate in the nitrogen removal process.

Control of charge transport in electronically active systems towards integrated biomolecular circuits (IbC)

The miniaturization of traditional silicon-based electronics will soon reach its limitation as quantum tunneling and heat become serious problems at the several-nanometer scale. Crafting integrated circuits via self-assembly of electronically active molecules using a "bottom-up" paradigm provides a potential solution to these technological challenges. In particular, integrated biomolecular circuits (IbC) offer promising advantages to achieve this goal, as nature offers countless examples of functionalities entailed by self-assembly and examples of controlling charge transport at the molecular level within the self-assembled structures. To this end, the review summarizes the progress in understanding how charge transport is regulated in biosystems and the key redox-active amino acids that enable the charge transport. In addition, charge transport mechanisms at different length scales are also reviewed, offering key insights for controlling charge transport in IbC in the future.

Competitive and substrate limited environments drive metabolic heterogeneity for comammox Nitrospira

Nitrospira has been revealed as a high versatile genus. Although previously considered only responsible for the conversion of nitrite to nitrate, now we know that Nitrospira can perform complete ammonia oxidation to nitrate too (comammox). Comammox activity was firstly reported as dominant in extremely limited oxygen environments, where anaerobic ammonia oxidation was also occurring (anammox). To explain the comammox selection, we developed an Individual-based Model able to describe Nitrospira and anammox growth in suspended flocs assembled in a dynamic nitrogen and oxygen-limiting environment. All known and hypothesized nitrogen transformations of Nitrospira were considered: ammonia and nitrite oxidation, comammox, nitrate-reducing ammonia oxidation, and anaerobic nitrite-reducing ammonia oxidation. Through bioenergetics analysis, the growth yield associated to each activity was estimated. The other kinetic parameters necessary to describe growth were calibrated according to the reported literature values. Our modeling results suggest that even extremely low oxygen concentrations (~1.0 µM) allow for a proportional growth of anammox versus Nitrospira similar to the one experimentally observed. The strong oxygen limitation was followed by a limitation of ammonia and nitrite, because anammox, without strong competitors, were able to grow faster than Nitrospira depleting the environment in nitrogen. These substrate limitations created an extremely competitive environment that proved to be decisive in the community assembly of Nitrospira and anammox. Additionally, a diversity of metabolic activities for Nitrospira was observed in all tested conditions, which in turn, explained the transient nitrite accumulation observed in aerobic environments with higher ammonia availability.

Pollution abatement reducing the river N2O emissions although it is partially offset by a warming climate: Insights from an urbanized watershed study

Global nitrogen (N) pollution has resulted in increased river nitrous oxide (N₂O) emissions, which contribute to climate change. However, little is known about how pollution abatement conversely reduces river N₂O production in a warming climate. Here, field observations and microcosmic experiments were conducted in a coastal urbanized watershed (S.E. China) to explore the interactive effect of changing nitrate and temperature on river sediment denitrification (DNF) and N₂O production. The results showed that urban river reaches (UR) with higher organic carbon content and denitrifying gene abundance in sediments have a greater DNF rate, nitrate removal efficiency (NRE), and N₂O concentration than agricultural river reaches (AR). Microcosmic incubation suggested that the DNF rate and associated N₂O production decreased under low nitrate addition, wherein the NRE increased. The scenario simulation illustrated a nonlinear response of N₂O production to nitrate removal (i.e., ΔN₂O/ΔNO₃-N) from both UR and AR sediments at a given temperature, and the DNF rate and N₂O production increased with increasing temperature. An increase in temperature by 1 degree Celsius would offset 18.75% of the N₂O reduction by nitrate removal via DNF. These findings implied that watershed pollution abatement undoubtedly contributes to the reduction in global river N₂O emissions although it is partially offset by extra N₂O production caused by global warming.

The role of anthraquinone-2-sulfonate on intra/extracellular electron transfer of anaerobic nitrate reduction

To improve the electron (e^-) transfer efficiency, exogenous redox mediators (RMs) were usually employed to enhance the denitrification efficiency due to the electron shuttling. Previous studies were mainly focused on how to improve the extracellular electron transfer (EET) by exogenous RMs. However, the intracellular electron transfer (IET), another crucial e^- transfer pathway, of biological denitrification was scarcely reported, especially for the relationship between the denitrification and IET. In this study, Coenzyme Q, Complexes I, II and III were determined as the core components in the IET chain of denitrification by using four specific respiration chain inhibitors (RCIs). Anthraquinone-2-sulfonate (AQS) partially recovered the IET of denitrification from NO₃^--N to N₂ gas when the RCIs were added. Specifically, the generations of N₂ gas were improved by 9.68%-18.25% in the experiments with RCIs and AQS, comparing to that with RCIs. nrfA gene was not detected by reverse transcription-polymerase chain reaction, suggesting that Klebsiella oxytoca strain could not conduct dissimilatory nitrate reduction to ammonium. Nitrate assimilation was considered as the main NH₄⁺-N formation way of K. oxytoca strain. The two e^- transfer pathways of denitrification were constructed and the roles of AQS on the IET and EET of denitrification were specifically discussed. The results of this study provided a better understanding of the e^- transfer pathways of denitrification, and suggested a potential practical use of exogenous RM on bio-treatment of nitrate-containing wastewater.

Enhancing cation and anion exchange capacity of rice straw biochar by chemical modification for increased plant nutrient retention

Biochar, a potential alternative of infield crop residue burning, can prevent nutrient leaching from soil and augment soil fertility. However, pristine biochar contains low cation (CEC) and anion (AEC) exchange capacity. This study developed fourteen engineered biochar by treating a rice straw biochar (RBC-W) first separately with different CEC and AEC enhancing chemicals, and then with their combined treatments to increase CEC and AEC in the novel biochar composites. Following a screening experiment, promising engineered biochar, namely RBC-W treated with O₃-HCl-FeCl₃ (RBC-O-Cl), H₂SO₄-HNO₃-HCl-FeCl₃ (RBC-A-Cl), and NaOH-Fe(NO₃)₃(RBC-OH-Fe), underwent physicochemical characterization and soil leaching-cum nutrient retention studies. RBC-O-Cl, RBC-A-Cl, and RBC-OH-Fe recorded a spectacular rise in CEC and AEC over RBC-W. All the engineered biochar remarkably reduced the leaching of NH₄⁺-N, NO₃^- -N, PO₄^3--P and K⁺ from a sandy loam soil and increased retention of these nutrients. RBC-O-Cl at 4.46 g kg^-1 dosage emerged as the most effective soil amendment increasing the retention of above ions by 33.7, 27.8, 15.0, and 5.74 % over a comparable dose of RBC-W. The engineered biochar could thus enhance plants' nutrient use efficiency and reduce the use of costly chemical fertilizers that are harmful to environmental quality.

An unusual active site architecture in cytochrome c nitrite reductase NrfA-1 from Geobacter metallireducens

Dissimilatory nitrate reduction to ammonia (DNRA) is a central pathway in the biogeochemical nitrogen cycle, allowing for the utilization of nitrate or nitrite as terminal electron acceptors. In contrast to the competing denitrification to N2, a major part of the essential nutrient nitrogen in DNRA is retained within the ecosystem and made available as ammonium to serve as a nitrogen source for other organisms. The second step of DNRA is mediated by the pentahaem cytochrome c nitrite reductase NrfA that catalyzes the six-electron reduction of nitrite to ammonium and is widely distributed among bacteria. A recent crystal structure of an NrfA ortholog from Geobacter lovleyi was the first characterized representative of a novel subclass of NrfA enzymes that lacked the canonical Ca2+ ion close to the active site haem 1. Here, we report the structural and functional characterization of NrfA from the closely related G. metallireducens. We established the recombinant production of catalytically active NrfA with its unique, lysine-coordinated active site haem heterologously in Escherichia coli and determined its three-dimensional structure by X-ray crystallography to 1.9 Å resolution. The structure confirmed GmNrfA as a further calcium-independent NrfA protein, and it also shows an altered active site that contained an unprecedented aspartate residue, D80, close to the substrate-binding site. This residue formed part of a loop that also caused a changed arrangement of the conserved substrate/product channel relative to other NrfA proteins and rendered the protein insensitive to the inhibitor sulphate. To elucidate the relevance of D80, we produced and studied the variants D80A and D80N that showed significantly reduced catalytic activity.

Mechanistic insights into polyhydroxyalkanoate-enhanced denitrification capacity of microbial community: Evolution of community structure and intracellular electron transfer of nitrogen metabolism

Denitrification is the key driving force of nitrogen cycle in surface water and plays an important role in eutrophication water remediation. Compared with some other common carbon sources, such as glucose and sodium acetate, polyhydroxyalkanoates (PHAs) were found to have the distinguished advantages in screening specific denitrifying bacteria of natural surface water bodies. In this study, the large ensembles of taxa were obtained from surface water samples and then sub-cultured with PHA or glucose as the sole carbon source. The microbial community that could be screened by PHA was identified, and the environmental functions of these bacteria were analyzed. At the genus level, the main communities regulated by PHA included Pseudomonas (56.30 %), Acinetobacter (27.75 %), Flavobacterium (10.19 %) and Comamonas (3.14 %), which all had good denitrification ability. The changes in carbon source, nitrogen source and biomass (expressed by DNA) were simultaneously monitored when culturing the model strain (P. stuzeri) with PHA or glucose. Compared with the glucose group, less PHA was consumed to remove the same amount of nitrate within a shorter incubation time, and there was no significant difference in bacterial growth with PHA or glucose as the carbon source (glucose:ΔN:ΔC:ΔDNA = 1:18:0.072; PHA:ΔN:ΔC:ΔDNA = 1:11:0.063). PHA improved the denitrification efficiency by increasing the expression of NarGHI, NirB, NirK and NorB, i.e., the key enzymes in the denitrification process. In addition, PHA accelerated the assimilating rate of extracellular nitrate by bacteria through increasing the expression of NarK. Finally, PHA-regulated electron transfer during denitrification was studied by observing the changes in NADH and NAD⁺. PHA could use a large proportion of NADH to offer electrons for denitrification, which increased the rate of denitrification. Improved mechanistic insights into the PHA-enhanced denitrification capacity of the microbial community can provide novel options for the in-situ remediation of eutrophic surface water.

A hormesis-like effect of FeS on heterotrophic denitrification and its mechanisms

To alleviate the insufficiency of carbon source in sewage, many sulfur-containing inorganic electron donors were added into traditional heterotrophic denitrification process. However, the effects of extraneous inorganic electron donors on heterotrophic denitrification were still largely unknown. In this study, a hormesis-like effect of ferrous sulfide (FeS, a representative inorganic electron donors) on Paracoccus denitrificans was observed. Total nitrogen (TN) removal efficiency of P. denitrificans rose by 15% with the increase of FeS dosage from 0 to 0.3 g L^-1 (low level), whereas the TN removal significantly decreased to 53% as the dosage of FeS mounted up to 5.0 g L^-1 (high level). Furthermore, the impacts of FeS on glucose utilization and bacterial growth exhibited hormesis-like effects. A subsequent mechanistic study revealed that above influences were caused by its released ions (Fe²⁺, Fe³⁺, and S^2-) rather than particle size. Further study illustrated that low dosage of FeS released a small amount of Fe²⁺ and Fe³⁺, which provided sufficient electrons via promoting glucose utilization, then improved denitrification. Conversely, FeS with high dosage inhibited denitrification via its released S^2-, which suppressed the activity of key denitrifying enzymes rather than influenced glucose metabolism and electron provision. Our results provide an insight into improving denitrification efficiency of the mixotrophic process coexisting with autotrophic and heterotrophic denitrifiers.

The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies

Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO₃, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.

Sludge decay kinetics and metagenomic analysis uncover discrepant metabolic mechanisms in two different sludge in situ reduction systems

A comparative study was conducted between an anaerobic side-stream reactor (ASSR) process and a sludge process reduction (SPR) activated sludge (SPRAS) process for uncovering crucial metabolic mechanisms governing sludge reduction. Both of two processes were efficient in removing pollutants, while the SPRAS (62.3 %) obtained much higher sludge reduction than the ASSR (27.9 %). The highest rate coefficients of sludge decay, heterotroph lysis and particles hydrolysis were 0.106, 0.219 and 0.054 d^-1 in the SPR module, followed by ASSR with coefficients of 0.060, 0.135 and 0.047 d^-1. The SPR module achieved an 81.9 % higher sludge decay mass with a 32.8 % smaller volume than the ASSR module. The SPR module preferentially enriched hydrolytic/fermentative and slow-growing bacteria. Metagenomic analysis revealed that SPR strengthened the key hydrolases and L-lactate dehydrogenase in the glycolysis pathways and weakened the citrate cycle, inducing metabolic uncoupling due to the reduced biosynthesis of ATP. Inserting ASSR only altered the ATP biosynthesis pathway, but maintenance metabolism was dominant for sludge reduction, with a long sludge retention time prolonging the food chain for predation.

Propionibacterium freudenreichii-Assisted Approach Reduces N2O Emission and Improves Denitrification via Promoting Substrate Uptake and Metabolism

N₂O emission is often encountered during biodenitrification. In this paper, a new approach of using microorganisms to promote substrate uptake and metabolism to reduce denitrification intermediate accumulation was reported. With the introduction of Propionibacterium freudenreichii to a biodenitrification system, N₂O and nitrite accumulation was, respectively, decreased by 74 and 60% and the denitrification efficiency was increased by 150% at the time of 24 h with P. freudenreichii/groundwater denitrifier of 1/5 (OD₆₀₀). Propionate, produced by P. freudenreichii, only accelerated nitrate removal and was not the main reason for the decreased intermediate accumulation. The proteomic and enzyme analyses revealed that P. freudenreichii stimulated biofilm formation by upregulating proteins involved in porin forming, putrescine biosynthesis, spermidine/putrescine transport, and quorum sensing and upregulated transport proteins, which facilitated the uptake of the carbon source, nitrate, and Fe and Mo (the required catalytic sites of denitrification enzymes). Further investigation revealed that P. freudenreichii activated the methylmalonyl-CoA pathway in the denitrifier and promoted it to synthesize heme/heme d1, the groups of denitrification enzymes and electron transfer proteins, which upregulated the expression of denitrifying enzyme proteins and enhanced the ratio of NosZ to NorB, resulting in the increase of generation, transfer, and consumption of electrons in biodenitrification. Therefore, a significant reduction in the denitrification intermediate accumulation and an improvement in the denitrification efficiency were observed.

Characteristics of sludge-based pyrolysis biochar and its application of enhancing denitrification

A modified biochar for enhanced denitrification was developed through a facile pyrolysis method using sewage sludge as raw material and melamine as nitrogen source. Through electrochemical analysis, sludge-based pyrolysis biochar (SPBC) has superior electrical conductivity and poor redox activity. SPBC can increase the electron transfer through the geoconductor mechanism. The effect and the mechanism of SPBC on denitrification were studied. The nitrate treatment efficiency increased with the increase of SPBC dosage. From the perspective of molecular biology, the activities of NAR and NIR enzymes, the degradation efficiency of glucose and the ETSA of bacteria were all promoted with the increase of SPBC, thereby promoting the removal of NO₃^-. In addition, SPBC had a certain screening effect on microbial communities, and biodiversity decreased with the increase of SPBC dosage. Although the biodiversity decreased, the relative abundance of microorganisms conducive to denitrification increased with the increase of SPBC dosage. The transformation strategy of SPBC proposed in this paper provides a technical solution for sludge recycling and application for strengthening denitrification.

Photocatalytic Removal of the Greenhouse Gas Nitrous Oxide by Liposomal Microreactors

Nitrous oxide (N₂ O) is a potent greenhouse and ozone-reactive gas for which emissions are growing rapidly due to increasingly intensive agriculture. Synthetic catalysts for N₂ O decomposition typically contain precious metals and/or operate at elevated temperatures driving a desire for more sustainable alternatives. Here we demonstrate self-assembly of liposomal microreactors enabling catalytic reduction of N₂ O to the climate neutral product N₂ . Photoexcitation of graphitic N-doped carbon dots delivers electrons to encapsulated N₂ O Reductase enzymes via a lipid-soluble biomolecular wire provided by the MtrCAB protein complex. Within the microreactor, electron transfer from MtrCAB to N₂ O Reductase is facilitated by the general redox mediator methyl viologen. The liposomal microreactors use only earth-abundant elements to catalyze N₂ O removal in ambient, aqueous conditions.

Photocatalytic Removal of the Greenhouse Gas Nitrous Oxide by Liposomal Microreactors

Nitrous oxide (N2O) is a potent greenhouse and ozone-reactive gas for which emissions are growing rapidly due to increasingly intensive agriculture. Synthetic catalysts for N2O decomposition typically contain precious metals and/or operate at elevated temperatures driving a desire for more sustainable alternatives. Here we demonstrate self-assembly of liposomal microreactors enabling catalytic reduction of N2O to the climate neutral product N2. Photoexcitation of graphitic N-doped carbon dots delivers electrons to encapsulated N2O Reductase enzymes via a lipid-soluble biomolecular wire provided by the MtrCAB protein complex. Within the microreactor, electron transfer from MtrCAB to N2O Reductase is facilitated by the general redox mediator methyl viologen. The liposomal microreactors use only earth-abundant elements to catalyze N2O removal in ambient, aqueous conditions.

The NtrYX Two-Component System of Paracoccus denitrificans Is Required for the Maintenance of Cellular Iron Homeostasis and for a Complete Denitrification under Iron-Limited Conditions

Denitrification consists of the sequential reduction of nitrate to nitrite, nitric oxide, nitrous oxide, and dinitrogen. Nitrous oxide escapes to the atmosphere, depending on copper availability and other environmental factors. Iron is also a key element because many proteins involved in denitrification contain iron-sulfur or heme centers. The NtrYX two-component regulatory system mediates the responses in a variety of metabolic processes, including denitrification. A quantitative proteomic analysis of a Paracoccus denitrificans NtrY mutant grown under denitrifying conditions revealed the induction of different TonB-dependent siderophore transporters and proteins related to iron homeostasis. This mutant showed lower intracellular iron content than the wild-type strain, and a reduced growth under denitrifying conditions in iron-limited media. Under iron-rich conditions, it releases higher concentrations of siderophores and displayes lower nitrous oxide reductase (NosZ) activity than the wild-type, thus leading to nitrous oxide emission. Bioinformatic and qRT-PCR analyses revealed that NtrYX is a global transcriptional regulatory system that responds to iron starvation and, in turn, controls expression of the iron-responsive regulators fur, rirA, and iscR, the denitrification regulators fnrP and narR, the nitric oxide-responsive regulator nnrS, and a wide set of genes, including the cd₁-nitrite reductase NirS, nitrate/nitrite transporters and energy electron transport proteins.

Electroactive Biofilms of Activated Sludge Microorganisms on a Nanostructured Surface as the Basis for a Highly Sensitive Biochemical Oxygen Demand Biosensor

The possibility of the developing a biochemical oxygen demand (BOD) biosensor based on electroactive biofilms of activated sludge grown on the surface of a graphite-paste electrode modified with carbon nanotubes was studied. A complex of microscopic methods controlled biofilm formation: optical microscopy with phase contrast, scanning electron microscopy, and laser confocal microscopy. The features of charge transfer in the obtained electroactive biofilms were studied using the methods of cyclic voltammetry and electrochemical impedance spectroscopy. The rate constant of the interaction of microorganisms with the extracellular electron carrier (0.79 ± 0.03 dm³(g s)^-1) and the heterogeneous rate constant of electron transfer (0.34 ± 0.02 cm s^-1) were determined using the cyclic voltammetry method. These results revealed that the modification of the carbon nanotubes' (CNT) electrode surface makes it possible to create electroactive biofilms. An analysis of the metrological and analytical characteristics of the created biosensors showed that the lower limit of the biosensor based on an electroactive biofilm of activated sludge is 0.41 mgO₂/dm³, which makes it possible to analyze almost any water sample. Analysis of 12 surface water samples showed a high correlation (R² = 0.99) with the results of the standard method for determining biochemical oxygen demand.

Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria

Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.

The individual and combined effects of polystyrene and silver nanoparticles on nitrogen transformation and bacterial communities in an agricultural soil

The effects of emerging contaminants micro/nanoplastics (MPs/NPs) and silver nanoparticles (Ag NPs) on health have attracted universal concern throughout the world. However, it is unclear on the combined effects of MPs/NPs and Ag NPs on the biogeochemistry cycle such as nitrogen transformation and functional microorganism in the soil. In the present study, we conducted a 45-day soil microcosm experiment with polystyrene (PS) MPs/NPs and Ag NPs to investigate their combined impact on nitrogen cycling and the bacterial community. The results showed that MPs or NPs exerted limited effects on nitrogen transformation in the soil. The combined effects of PS MPs/NPs and Ag NPs were mainly caused by the presence of Ag NPs. However, PS NPs alleviated the inhibition of anammox and denitrification induced by Ag NPs via upregulating anammox-related genes and elevating nitrate and nitrite reductase activities. PS MPs + Ag NPs treatment significantly reduced bacterial diversity. PS MPs/NPs + Ag NPs increased the relative abundances of denitrifying Cupriavidus by 0.32% and 0.06% but decreased nitrogen-fixing functional microorganisms of Microvirga (by 2.05% and 2.24%), Bacillus (by 0.16% and 0.22%), and Herbaspirillum (by 0.14% and 0.07%) at the genus level compared with Ag NPs alone. The significant downregulation of nitrogen-fixing genes (K02586, K02588, and K02591) was observed in PS MPs/NPs + Ag NPs treatment compared to Ag NPs in the nitrogen metabolism pathway. Moreover, g-Lysobacter and g-Aquimonas were identified as biomarkers in PS MPs + Ag NPs and PS NPs + Ag NPs by LEfSe analysis. Our study sheds the light that changes of functional microorganism abundances contributed to the alteration of nitrogen transformation. Taking the particle size of plastics into account will be helpful to accurately assess the combined ecological risks of plastics and nanomaterial contaminants.

The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress

Previously characterized nitrite reductases fall into three classes: siroheme-containing enzymes (NirBD), cytochrome c hemoproteins (NrfA and NirS), and copper-containing enzymes (NirK). We show here that the di-iron protein YtfE represents a physiologically relevant new class of nitrite reductases. Several functions have been previously proposed for YtfE, including donating iron for the repair of iron–sulfur clusters that have been damaged by nitrosative stress, releasing nitric oxide (NO) from nitrosylated iron, and reducing NO to nitrous oxide (N₂O). Here, in vivo reporter assays confirmed that Escherichia coli YtfE increased cytoplasmic NO production from nitrite. Spectroscopic and mass spectrometric investigations revealed that the di-iron site of YtfE exists in a mixture of forms, including nitrosylated and nitrite-bound, when isolated from nitrite-supplemented, but not nitrate-supplemented, cultures. Addition of nitrite to di-ferrous YtfE resulted in nitrosylated YtfE and the release of NO. Kinetics of nitrite reduction were dependent on the nature of the reductant; the lowest K_m, measured for the di-ferrous form, was ∼90 μM, well within the intracellular nitrite concentration range. The vicinal di-cysteine motif, located in the N-terminal domain of YtfE, was shown to function in the delivery of electrons to the di-iron center. Notably, YtfE exhibited very low NO reductase activity and was only able to act as an iron donor for reconstitution of apo-ferredoxin under conditions that damaged its di-iron center. Thus, YtfE is a high-affinity, low-capacity nitrite reductase that we propose functions to relieve nitrosative stress by acting in combination with the co-regulated NO-consuming enzymes Hmp and Hcp.

Insights into amoxicillin degradation in water by non-thermal plasmas

Antibiotics have been extensively used as pharmaceuticals for diverse applications. However, their overuse and indiscriminate discharge to water systems have led to increased antibiotic levels in our aquatic environments, which poses risks to human and livestock health. Non-thermal plasma water. However, the issues of process scalability and the mechanisms towards understanding the plasma-induced degradation remain. This study addresses these issues by coupling a non-thermal plasma jet with a continuous flow reactor to reveal the effective mechanisms of amoxicillin degradation. Four industry-relevant feeding gases (nitrogen, air, argon, and oxygen), discharge voltages, and frequencies were assessed. Amoxicillin degradation efficiencies achieved using nitrogen and air were much higher compared to argon and oxygen and further improved by increasing the applied voltage and frequency. The efficiency of plasma-induced degradation depended on the interplay of hydrogen peroxide (H₂O₂) and nitrite (NO₂^-), validated by mimicked chemical solutions tests. Insights into prevailing degradation pathways were elucidated through the detection of intermediate products by advanced liquid chromatography-mass spectrometry.

Role of chemical reactions in the nitrogenous trace gas emissions and nitrogen retention: A meta-analysis

Increasing evidence has been found that chemical reactions affect significantly the terrestrial nitrogen (N) cycle, which was previously assumed to be mainly dominated by biological processes. Due to the limitation of knowledge and analytical techniques, it is currently challenging to discern the contribution of biotic and abiotic processes to the terrestrial N cycle for geobiologists and biogeochemists alike. To better understand the role of abiotic reactions in the terrestrial N cycle, it is necessary to comprehend the chemical controls on nitrogenous trace gas emissions and N retention in soil under various environmental conditions. In this manuscript, we assess the role of abiotic reactions in nitrous oxide (N₂O) and nitric oxide (NO) emissions as well as N retention through a meta-analysis using all related peer-reviewed publications before August 2020. Results show that abiotic reactions contributed 29.3-37.7% and 44.0-57.0% to the total N₂O emission and N retention, representing 3.7-4.7 and 4.0-6.0 Tg year^-1 of global terrestrial N₂O emission and N retention, respectively. Much higher NO production was observed in sterilized soils than that in unsterilized treatments indicating the major contribution of chemical reactions to NO emission and rapid microbial reduction of NO to N₂O and N₂. Chemical hydroxylamine oxidation accounts for the largest abiotic contribution to N₂O emission, while chemical nitrite reduction and fixation represent for the largest contribution to abiotic NO production and soil N retention, respectively. Factors influencing the abiotic processes include pH, total organic carbon (TOC), total nitrogen (TN), the ratio of carbon to nitrogen (C/N), and transition metals. These results broadened our knowledge about the mechanisms involved in chemical N reactions and provided a simplified estimation about their contribution to nitrogenous trace gas emission and N retention, which is meaningful to further study interactions of biologically and chemically mediated reactions in biogeochemical N cycle.

Short- and long-term effects of decabromodiphenyl ether (BDE-209) on sediment denitrification using a semi-continuous microcosm

The widespread use of decabromodiphenyl ether (BDE-209) resulted in its deposition in environmental media and biological matrices. However, to date, few studies focused on the effect of BDE-209 on microorganisms, and those available were investigated via an enclosed system completely cutting off the communication between testing system and its native environment. Herein, 4.0 mg/g BDE-209 acute exposure induced a 20% decline of NO_X-N (the sum of NO₃^--N and NO₂^--N) removal efficiency and a significant accumulation of NO₂^--N and N₂O. These inhibitory effects presented in a BDE-209 concentration-dependent manner. Using a semi-continuous microcosm, the inhibitory effects of BDE-209 on denitrification were observed to be significantly enhanced with the extending of exposure duration. Denitrifying genes assay illustrated that BDE-209 has an insignificant effect on the global abundance of denitrifying bacteria because of microbial exchange with its overlying water. But the utilization of electron donor (carbon substrate), the activity of electron transport system and denitrifying enzymes were significantly inhibited by BDE-209 exposure in a exposure-duration-dependent manner. Finally, insufficient electron donor and lower efficiency of electron transport and utilization on denitrifying enzymes deteriorated the denitrification performance. These results provided a new insight into BDE-209 influence on denitrification in the natural environment.

Application of bioelectrochemical systems to regulate and accelerate the anaerobic digestion processes

Anaerobic digestion (AD) serves as a potential bioconversion process to treat various organic wastes/wastewaters, including sewage sludge, and generate renewable green energy. Despite its efficiency, AD has several limitations that need to be overcome to achieve maximum energy recovery from organic materials while regulating inhibitory substances. Hence, bioelectrochemical systems (BESs) have been widely investigated to treat inhibitory compounds including ammonia in AD processes and improve the AD operational efficiency, stability, and economic viability with various integrations. The BES operations as a pretreatment process, inside AD or after the AD process aids in the upgradation of biogas (CO₂ to methane) and residual volatile fatty acids (VFAs) to valuable chemicals and fuels (alcohols) and even directly to electricity generation. This review presents a comprehensive summary of BES technologies and operations for overcoming the limitations of AD in lab-scale applications and suggests upscaling and future opportunities for BES-AD systems.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen

Since the characterization of cytochrome c₅₅₂ as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH₄⁺ produced from NO₂^- is released as NH₃ leading to nitrogen loss, similar to denitrification which generates NO, N₂O, and N₂. NH₄⁺ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO₂^- to NH₄⁺, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.

Key carboxylate residues for iron transit through the prokaryotic ferritin SynFtn

Ferritins are proteins forming 24meric rhombic dodecahedral cages that play a key role in iron storage and detoxification in all cell types. Their function requires the transport of Fe²⁺ from the exterior of the protein to buried di-iron catalytic sites, known as ferroxidase centres, where Fe²⁺ is oxidized to form Fe³⁺-oxo precursors of the ferritin mineral core. The route of iron transit through animal ferritins is well understood: the Fe²⁺ substrate enters the protein via channels at the threefold axes and conserved carboxylates on the inner surface of the protein cage have been shown to contribute to transient binding sites that guide Fe²⁺ to the ferroxidase centres. The routes of iron transit through prokaryotic ferritins are less well studied but for some, at least, there is evidence that channels at the twofold axes are the major route for Fe²⁺ uptake. SynFtn, isolated from the cyanobacterium Synechococcus CC9311, is an atypical prokaryotic ferritin that was recently shown to take up Fe²⁺ via its threefold channels. However, the transfer site carboxylate residues conserved in animal ferritins are absent, meaning that the route taken from the site of iron entry into SynFtn to the catalytic centre is yet to be defined. Here, we report the use of a combination of site-directed mutagenesis, absorbance-monitored activity assays and protein crystallography to probe the effect of substitution of two residues potentially involved in this pathway. Both Glu141 and Asp65 play a role in guiding the Fe²⁺ substrate to the ferroxidase centre. In the absence of Asp65, routes for Fe²⁺ to, and Fe³⁺ exit from, the ferroxidase centre are affected resulting in inefficient formation of the mineral core. These observations further define the iron transit route in what may be the first characterized example of a new class of ferritins peculiar to cyanobacteria.

Comprehensive insights into core microbial assemblages in activated sludge exposed to textile-dyeing wastewater stress

Microorganisms in activated sludge are widely recognized for their roles in wastewater treatment. However, previous studies were mainly concerned with the diversity and driving factors of microbial communities within domestic wastewater treatment, and those of domestic wastewater treatment systems mixed with industrial wastewater are poorly understood. In this research, three different full-scale aerobic activated sludge (AS) wastewater treatment systems fed with municipal, textile-dyeing, and mixed wastewater, respectively, were monitored over the operation course of three months. 16S rRNA amplicon sequencing analysis revealed that the microbial communities in textile-dyeing wastewater activated sludge (AS) exhibited significantly lower richness and diversity (p < 0.01, Adonis) compared to those fed with municipal wastewater. In contrast, textile-dyeing derived AS selectively enriched microbial taxa with aromatic degradation and denitrification potentials. Further, FARPROTAX and metabolomics indicated the inhibition of 72.5% metabolic functions (p < 0.01) in AS from the system fed with textile-dyeing wastewater, including the pathways of pentose phosphate metabolism, purine metabolism, and glycerophospholipid metabolism. Overall, this study corroborates textile-dyeing wastewater is a novel microbial niche and could suppress sludge performance by inhibiting microbial activity and metabolism, raising concerns on AS-based systems for industrial wastewater treatment.

Insight into the role of extracellular polymeric substances in denitrifying biofilms under nitrobenzene exposure

Denitrifying biofilm promises to be very useful for remediation of nitro-aromatic compounds (NACs) and nitrates in wastewater. Little is known about the role of extracellular polymeric substances (EPS) in nitrobenzene (NB, a typical NAC) remediation, despite the indispensability of EPS for biofilm formation. Herein, the significance of the mechanistic role of EPS in the response of denitrifying biofilms to various levels of NB was investigated. The removal of NB was predominantly controlled via absorption, with little biodegradation during the short-term exposure. Specifically, NB was adsorbed by EPS, as shown by a total adsorption of 40.06% at the initial step, which declined to around 10.52% in the equilibrium stage, while sorption via cells gradually increased from 59.93% to 89.47% over the same period. The results suggested that EPS might act as an important reservoir for NB, which endows inner cells with increased adsorption ability. The presence of EPS might also alleviate the negative impacts of NB toxicity on inner cells, thus protecting microorganisms. This was indicated by the difference in denitrification performance and cell integrity between intact and EPS-free biofilms. High-throughput sequencing data demonstrated that EPS could maintain the stability of microbial communities under NB stress. The fluorescence quenching analysis further indicated that EPS formed stable complexes with NB mainly through hydrophobic interactions with protein-like fractions (tryptophan and tyrosine). Moreover, Fourier transform infrared spectroscopy identified that the hydroxyl, amino, carboxyl, and phosphate groups of EPS were the candidate functional groups binding with NB. Protein secondary structures were also significantly affected, resulting in a loose structure and enhanced hydrophobic performance for EPS. These results provide insights into the role of EPS in alleviating NB-caused cellular stress and the underlying binding mechanisms between NB and EPS.

Comprehensive metagenomic and enzyme activity analysis reveals the negatively influential and potentially toxic mechanism of polystyrene nanoparticles on nitrogen transformation in constructed wetlands

The widespread use of nanoplastics inevitably leads to their increasing emission into constructed wetlands (CWs). However, little is known about the impacts of nanoplastics on nitrogen transformation in CWs. In this study, the influence of polystyrene nanoparticles (PS NPs), one of the most widely used plastics, on the nitrogen transformation in CWs was comprehensively investigated, and the influential and toxic mechanism was evaluated through metagenomic analysis (DNA level) and key enzyme activities (protein level) related to N-transformation metabolism and antioxidant systems. The results showed that over 97% of PS NPs were retained in CWs, and the biofilm of sand was the main sink of PS NPs. Exposure to 1 and 10 mg/L PS NPs suppressed the nitrogen transformation, causing a certain degree of inhibition in TN removal, especially in the relatively short term of the exposure experiment (p < 0.05). At the protein level, 1 and 10 mg/L PS NPs negatively affect enzyme activities involved in denitrification (nitrate reductase and nitrite reductase) and electron transport system activity (ETSA). In contrast, 10 mg/L of PS NPs significantly suppressed the activities of nitrifying enzymes (ammonia monooxygenase, hydroxylamine dehydrogenase and nitrite oxidoreductase), whereas 1 mg/L PS NPs showed no impacts on nitrifying enzymes. Metagenomic analysis further certified that PS NPs restrained the relative abundances of genes involved in nitrogen transformation including nitrification and denitrification biochemical metabolisms (the electron production, electron transport and electron consumption processes). It also indicated that PS NPs could affect nitrogen transformation by reducing the abundance of genes for electron donor and ATP production involved in carbon metabolism (glycolysis and tricarboxylic acid cycle metabolism). In our study, the potential toxic mechanisms of PS NPs attributed to over production of reactive oxygen species and variations of antioxidant systems in macrophytes and microorganisms. These results provided valuable information for evaluating the impacts of PS NPs on CWs and arouse more attention to their impacts on the global geochemical nitrogen and carbon cycles.

Ionic copper strengthens the toxicity of tetrabromobisphenol A (TBBPA) to denitrification by decreasing substrate transport and electron transfer

Increasing electrical and electronic waste have raised concerns about the potential toxicity of brominated flame retardants (BFRs) and heavy metals (HMs). However, few studies have focused on the combined effect of BFRs and HMs on microorganisms, especially denitrifying bacteria, which have an essential role in N cycles and N₂O emission. Herein, we investigate the combined effect of tetrabromobisphenol A (TBBPA) and Cu on model denitrifying bacteria. A further 24.5% decline in N removal efficiency was observed when 0.05 mg/L Cu were added into a denitrifying system containing 0.75 mg/L TBBPA. Further study demonstrated that Cu heightened the toxicity of TBBPA to denitrification via following aspects: (1) Cu stimulated EPS secretion induced by TBBPA during denitrification, blocked the transmembrane transport of glucose, which caused insufficient carbon substrate for bacteria growth and electron provision; (2) Cu further suppressed key denitrifying enzymes' activity and down-regulated genes involving electron transport induced by TBBPA, led to the decrease of electron transport activity. Finally, the decrease of bacterial growth, insufficient electron donor, and lower electron transport activity caused the synergetic toxic effect of TBBPA and Cu on denitrification. Overall, the present study provides new insights into the combined effect of BFRs and HMs on microorganisms.

Insights into heterotrophic denitrification diversity in wastewater treatment systems: Progress and future prospects based on different carbon sources

Nitrate, as the most stable form of nitrogen pollution, widely exists in aquatic environment, which has great potential threat to ecological environment and human health. Heterotrophic denitrification, as the most economical and effective method to treat nitrate wastewater, has been widely and deeply studied. From the perspective of heterotrophic denitrification, this review discusses nitrate removal in the aquatic environment, and the behaviors of different carbon source types were classified and summarized to explain the cyclical evolution of carbon and nitrogen in global biochemical processes. In addition, the denitrification process, electron transfer as well as denitrifying and hydrolyzing microorganisms among different carbon sources were analyzed and compared, and the commonness and characteristics of the denitrification process with various carbon sources were revealed. This study provides theoretical support and technical guidance for further improvement of denitrification technologies.

Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community

In recent years, the externalization of electrons as part of respiratory metabolic processes has been discovered in many different bacteria and some archaea. Microbial extracellular electron transfer (EET) plays an important role in many anoxic natural or engineered ecosystems. In this study, an anaerobic methane-converting microbial community was investigated with regard to its potential to perform EET. At this point, it is not well-known if or how EET confers a competitive advantage to certain species in methane-converting communities. EET was investigated in a two-chamber electrochemical system, sparged with methane and with an applied potential of +400 mV versus standard hydrogen electrode. A biofilm developed on the working electrode and stable low-density current was produced, confirming that EET indeed did occur. The appearance and presence of redox centers at −140 to −160 mV and at −230 mV in the biofilm was confirmed by cyclic voltammetry scans. Metagenomic analysis and fluorescence in situ hybridization of the biofilm showed that the anaerobic methanotroph ‘Candidatus Methanoperedens BLZ2’ was a significant member of the biofilm community, but its relative abundance did not increase compared to the inoculum. On the contrary, the relative abundance of other members of the microbial community significantly increased (up to 720-fold, 7.2% of mapped reads), placing these microorganisms among the dominant species in the bioanode community. This group included Zoogloea sp., Dechloromonas sp., two members of the Bacteroidetes phylum, and the spirochete Leptonema sp. Genes encoding proteins putatively involved in EET were identified in Zoogloea sp., Dechloromonas sp. and one member of the Bacteroidetes phylum. We suggest that instead of methane, alternative carbon sources such as acetate were the substrate for EET. Hence, EET in a methane-driven chemolithoautotrophic microbial community seems a complex process in which interactions within the microbial community are driving extracellular electron transfer to the electrode.

Metabolic Homeostasis in Life as We Know It: Its Origin and Thermodynamic Basis

Living organisms require continuous input of energy for their existence. As a result, life as we know it is based on metabolic processes that extract energy from the environment and make it available to support life (energy metabolism). This metabolism is based on, and regulated by, the underlying thermodynamics. This is important because thermodynamic parameters are stable whereas kinetic parameters are highly variable. Thermodynamic control of metabolism is exerted through near equilibrium reactions that determine. (1) the concentrations of metabolic substrates for enzymes that catalyze irreversible steps and (2) the concentrations of small molecules (AMP, ADP, etc.) that regulate the activity of irreversible reactions in metabolic pathways. The result is a robust homeostatic set point (−ΔG_ATP) with long term (virtually unlimited) stability. The rest of metabolism and its regulation is constrained to maintain this set point. Thermodynamic control is illustrated using the ATP producing part of glycolysis, glyceraldehyde-3-phosphate oxidation to pyruvate. Flux through the irreversible reaction, pyruvate kinase (PK), is primarily determined by the rate of ATP consumption. Change in the rate of ATP consumption causes mismatch between use and production of ATP. The resulting change in [ATP]/[ADP][Pi], through near equilibrium of the reactions preceding PK, alters the concentrations of ADP and phosphoenolpyruvate (PEP), the substrates for PK. The changes in ADP and PEP alter flux through PK appropriately for restoring equality of ATP production and consumption. These reactions appeared in the very earliest lifeforms and are hypothesized to have established the set point for energy metabolism. As evolution included more metabolic functions, additional layers of control were needed to integrate new functions into existing metabolism without changing the homeostatic set point. Addition of gluconeogenesis, for example, resulted in added regulation to PK activity to prevent futile cycling; PK needs to be turned off during gluconeogenesis because flux through the enzyme would waste energy (ATP), subtracting from net glucose synthesis and decreasing overall efficiency.

Bacterial iron detoxification at the molecular level

Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable "free" iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can also lead to the formation of reactive nitrogen species. To avoid iron-mediated oxidative stress, bacteria utilize iron-dependent global regulators to sense the iron status of the cell and regulate the expression of proteins involved in the acquisition, storage, and efflux of iron accordingly. Here, we survey the current understanding of the structure and mechanism of the important members of each of these classes of protein. Diversity in the details of iron homeostasis mechanisms reflect the differing nutritional stresses resulting from the wide variety of ecological niches that bacteria inhabit. However, in this review, we seek to highlight the similarities of iron homeostasis between different bacteria, while acknowledging important variations. In this way, we hope to illustrate how bacteria have evolved common approaches to overcome the dual problems of the insolubility and potential toxicity of iron.

Weak electricity stimulates biological nitrate removal of wastewater: Hypothesis and first evidences

Nitrate pollution in water is a worldwide health and environmental concern. Biological nitrate removal of wastewater is widely used countering eutrophication of water bodies; however it could be troublesome and expensive when influent carbon source is insufficient. Here we present a novel process, the microbial fuel cell (MFC)-resistance-type electrical stimulation denitrification process (RtESD) using microbial weak electricity originated from the wastewater, to enhance nitrate removal. Results show that the optimal nitrate dependent denitrification rate (0.027 mg N/L·h) and nitrate removal efficiency (98.1%) can be achieved; partial autotrophic denitrification was enhanced in RtESD under stimulation of 0.2 V of microbial weak electricity (MWE). Aromatic proteins also increased in the presence of 0.2 V MWE stimulation according to three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy profiles, indicating that electron transfer could be improved in the case of MWE stimulation. Furthermore, the microbial community structure and diversity analysis results demonstrated that MWE stimulation inhibited the heterotrophic denitrifying bacteria and activated the autotrophic denitrifying bacteria in RtESD. Two hypotheses, enhancement of electron transfer and improvement of microorganism activity, were proposed regarding to the MWE stimulated pathways. This study provided a promising method utilizing MWE derived from wastewater to improve the denitrification rate and removal efficiency of nitrate-containing wastewater treatment processes.

Competition for electrons favours N2 O reduction in denitrifying Bradyrhizobium isolates

Bradyrhizobia are common members of soil microbiomes and known as N₂ -fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N₂ O. Inoculation with compatible rhizobia is often needed for optimal N₂ -fixation, but the choice of inoculant may have consequences for N₂ O emission. Here, we determined the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. Analyses of genomes and denitrification end-points showed that all were denitrifiers, but only ~1/3 could reduce N₂ O. The N₂ O-reducing isolates had strong preference for N₂ O- over NO₃ ^- -reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO₃ ^- reductase) and Nos (N₂ O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO₃ ^- reductase (Nar), reduced N₂ O and NO₃ ^- simultaneously. We propose that the control at the metabolic level, favouring N₂ O reduction over NO₃ ^- reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar.