Kinetics of pure cultures of hydrogen-oxidizing denitrifying bacteria and modeling of the interactions among them in mixed cultures

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.

Modelling of hydrogenotrophic denitrification process in a venturi-integrated membrane bioreactor

The aim of this study is to model a hydrogenotrophic denitrification process in a venturi-integrated submerged membrane bioreactor (MBR) system. The MBR was operated in batch mode using feed concentrations of 100 and 150 mg NO3-N/L. In contrast to most of the denitrification process models that represent the mixed culture with one composite biomass parameter, the biomass was subdivided into two main categories in this modelling study: mainly nitrate-reducing biomass and mainly nitrite-reducing biomass. The determination coefficients (r2) in the range of 0.97-0.99 indicate that the model successfully simulates the concentrations of nitrate- and nitrite-nitrogen in the bioreactor. The maximum specific growth rate of nitrite-reducing biomass (0.06 h-1) was found to be higher than that of nitrate-reducing biomass (0.0002 h-1). Similarly, the growth yield coefficient of nitrite-reducing biomass was higher than that of nitrate-reducing biomass (0.44 vs. 0.31 g biomass/g substrate). The kinetic and stoichiometric coefficients obtained from this modelling study suggest that the limiting step determining the overall conversion rate of hydrogenotrophic denitrification process is the conversion of nitrite to nitrogen gas.

Groundwater denitrification using a continuous flow mode hybrid system combining a hydrogenotrophic biofilter and an electrooxidation cell

An attached-growth continuous flow hydrogenotrophic denitrification system was investigated for groundwater treatment. Two bench-scale packed-bed reactors were used in series, without external pH adjustment or carbon source addition, while inorganic carbonate salts already contained in the groundwater were the sole carbon source used by the denitrifying bacteria. The hydrogen was produced by water electrolysis using renewable energy sources thus minimizing resource-draining factors of the treatment process. The biofilter was subjected to a combination of three groundwater retention times (13.5, 27 and 54 min, corresponding to 20, 10 and 5 mL min^-1 inlet water flow rates) and two hydrogen flow values (10 and 20 mL min^-1) to evaluate its efficiency under different operating parameters. In all cases, significant nitrate percentage removals were achieved, ranged between 64.1% and 100%. The treatment process appears to slow down with lower retention times and H₂ flow rate values, although residual nitrate concentrations were always in the range of 0-5.1 mg L^-1, values below the maximum permitted limit of 11.3 mg L^-1. In cases where nitrite accumulation was detected, a continuous flow electrochemical oxidation process with three different current density values (5.0, 7.5 and 10.0 mA cm^-2) was examined as a post-treatment step aiming to completely remove the toxic nitrite anions. Finally, an advanced mathematical model of the attached growth hydrogenotrophic denitrification process was developed to predict concentrations of all the substrates examined in the bio-filter (nitrate, nitrite, inorganic carbon and hydrogen).

Characteristics of denitrification and microbial community in respect to various H2 pressures and distances to the gas supply end in H2-based MBfR

The hydrogen-based hollow fiber membrane biofilm reactor (H2-based MBfR) has shown to be a promising technology for nitrate (NO₃^––N) reduction. Hollow fiber membranes (HFM) operating in a closed mode in an H₂-based MBfR often suffer from reverse gas diffusion, taking up space for the effective gas substrate and resulting in a reduction in the HFM diffusion efficiency, which in turn affects denitrification performance. In this work, we developed a laboratory-scale H₂-based MBfR, which operated in a closed mode to investigate the dynamics of denitrification performance and biofilm microbial community analysis at different H₂ supply pressures. A faster formation of biofilm on the HFM and a shorter start-up period were found for a higher H₂ supply pressure. An increase in the H₂ pressure under 0.08 MPa could significantly promote denitrification, while a minor increase in denitrification was observed once the H₂ pressure was over 0.08 MPa. Sequencing analysis of the biofilm concluded that (i) the dominant phylum-level bacteria in the reactor during the regulated hydrogen pressure phase were Gammaproteobacteria and Alphaproteobacteria; (ii) when the hydrogen pressure was 0.04–0.06 MPa, the dominant bacteria in the MBfR were mainly enriched on the hollow fiber membrane near the upper location (Gas inlet). With a gradual increase in the hydrogen pressure, the enrichment area of the dominant bacteria in MBfR gradually changed from the upper location to the distal end of the inlet. When the hydrogen pressure was 0.10 MPa, the dominant bacteria were mainly enriched on the hollow fiber membrane in the down location of the MBfR.

Mechanistic insights into CO2 pressure regulating microbial competition in a hydrogen-based membrane biofilm reactor for denitrification

CO₂ is a proven pH regulator in hydrogen-based membrane biofilm reactor (H₂-MBfR) but how its pressure regulates microbial competition in this system remains unclear. This work evaluates the CO₂ pressure dependent system performance, CO₂ allocation, microbial structure and activity of CO₂ source H₂-MBfR. The optimum system performance was reached at the CO₂ pressure of 0.008 MPa, and this pressure enabled 0.18 g C/(m²·d) of dissolved inorganic carbon (DIC) allocated to denitrifying bacteria (DNB) for carbon source anabolism and denitrification-related proton compensation, while inducing a bulk liquid pH (pH 7.4) in favor of DNB activity by remaining 0.21 g C/(m²·d) of DIC as pH buffer. Increasing CO₂ pressure from 0.008 to 0.016 MPa caused the markedly changed DNB composition, and the diminished DNB population was accompanied by the enrichment of sulfate-reducing bacteria (SRB). A high CO₂ pressure of 0.016 MPa was estimated to induce the enhanced SRB activity and weakened DNB activity.

Development of Bio-Electrochemical Reactor for Groundwater Denitrification: Effect of Electric Current and Water Hardness

Nitrate-nitrogen (NO3-N) contaminating groundwater is an environmental issue in many areas, and is difficult to treat by simple processes. A bio-electrochemical reactor (BER) using copper wire and graphite plate was developed to purify the NO3-N-contaminated groundwater. The low (of 10 mA) and high (of 20 mA) electric currents were applied to the BERs, and various influent hardness levels from 20 to 80 mg/L as CaCO3 due to groundwater characteristics were supplied to clarify the total nitrogen removal efficiency and NO3-N removal mechanisms. In the BER-10, the bio-electrochemical reactions caused 85% of total nitrogen to be removed through heterotrophic and autohydrogenotrophic denitrification in the suspended sludge and biofilm. However, the chemical deposit occurring at the cathode from water hardness affected the decreasing denitrification performance; 12.6% of Mg and 8.8% of Ca elements were observed in the biofilm. The enhancement of electrochemical reactions in the BER-20 caused integrating electrochemical and bio-electrochemical reactions; the NO3-N was electrochemically reduced to NO2-N, and it was further biologically reduced to N2. A better total nitrogen removal of 95% was found; although, a larger deposit of Mg (22.8%) and Ca (10.8%) was observed. The relatively low dissolved H2 in the BER-20 confirmed that the deposit affected the decreasing gaseous H2 transfer and inhibition of autohydrogenotrophic denitrification in the suspended sludge. According to the microbial analysis, both heterotrophic and autohydrogenotrophic denitrification were obtained in the suspended sludge of both BERs; Nocadia (26.8%) was the most abundant genus in the BER-10, whereas Flavobacterium (27.1%) and Nocadia (25.0%) were the dominant genera in the BER-20.

Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers

Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO₃ ^- , but it often entails accumulation of the cytotoxic intermediate NO₂ ^- and the greenhouse gas N₂ O. To explore if these high NO₂ ^- and N₂ O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO₂ ^- , NO, N₂ O, N₂ and O₂ as they depleted O₂ and transitioned to denitrification with NO₃ ^- as the only electron acceptor and hydrogen as the electron donor. Isolates with a complete denitrification pathway, although differing intermediate accumulation, were closely related to Dechloromonas denitrificans, Ferribacterium limneticum or Hydrogenophaga taeniospiralis. High NO₂ ^- accumulation was associated with the reductases' kinetics. While available, electrons only flowed towards NO₃ ^- in the narG-containing H. taeniospiralis but flowed concurrently to all denitrification intermediates in the napA-containing D. denitrificans and F. limneticum. The denitrification regulator RegAB, present in the napA strains, may further secure low intermediate accumulation. High N₂ O accumulation only occurred during the transition to denitrification and is thus likely caused by delayed N₂ O reductase expression.

Various electron donors for biological nitrate removal: A review

Nitrate (NO₃^-) pollution in water and wastewater has become a serious global issue. Biological denitrification, which reduces NO₃^- to N₂ (nitrogen gas) by denitrifying microorganisms, is an efficient and economical process for the removal of NO₃^- from water and wastewater. During the denitrification process, electron donor is required to provide electrons for reduction of NO₃^-. A variety of electron donors, including organic and inorganic compounds, can be used for denitrification. This paper reviews the state of the art of various electron donors used for biological denitrification. Depending on the types of electron donors, denitrification can be classified into heterotrophic and autotrophic denitrification. Heterotrophic denitrification utilizes organic compounds as electron donors, including low-molecular-weight organics (e.g. acetate, methanol, glucose, benzene, methane, etc.) and high-molecular-weight organics (e.g. cellulose, polylactic acid, polycaprolactone, etc.); while autotrophic denitrification utilizes inorganic compounds as electron donors, including hydrogen (H₂), reduced sulfur compounds (e.g. sulfide, element sulfur and thiosulfate), ferrous iron (Fe²⁺), iron sulfides (e.g. FeS, Fe_1-xS and FeS₂), arsenite (As(Ш)) and manganese (Mn(II)). The biological denitrification processes and the representative denitrifying microorganisms are summarized based on different electron donors, and their denitrification performance, operating costs and environmental impacts are compared and discussed. The pilot- or full-scale applications were summarized. The concluding remarks and future prospects were provided. The biodegradable polymers mediated heterotrophic denitrification, as well as H₂ and sulfur mediated autotrophic denitrification are promising denitrification processes for NO₃^- removal from various types of water and wastewater.

Dechloromonas and close relatives prevail during hydrogenotrophic denitrification in stimulated microcosms with oxic aquifer material

Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with a 15.3-fold increase in relative abundance of Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific.

Strategies to Overcome Intermediate Accumulation During in situ Nitrate Remediation in Groundwater by Hydrogenotrophic Denitrification

Bioremediation of polluted groundwater is one of the most difficult actions in environmental science. Nonetheless, the clean-up of nitrate polluted groundwater may become increasingly important as nitrate concentrations frequently exceed the EU drinking water limit of 50 mg L-1, largely due to intensification of agriculture and food production. Denitrifiers are natural catalysts that can reduce increasing nitrogen loading of aquatic ecosystems. Porous aquifers with high nitrate loading are largely electron donor limited and additionally, high dissolved oxygen concentrations are known to reduce the efficiency of denitrification. Therefore, denitrification lag times (time prior to commencement of microbial nitrate reduction) up to decades were determined for such groundwater systems. The stimulation of autotrophic denitrifiers by the injection of hydrogen into nitrate polluted regional groundwater systems may represent a promising remediation strategy for such environments. However, besides high costs other drawbacks, such as the transient or lasting accumulation of the cytotoxic intermediate nitrite or the formation of the potent greenhouse gas nitrous oxide, have been described. In this article, we detect causes of incomplete denitrification, which include environmental factors and physiological characteristics of the underlying bacteria and provide possible mitigation approaches.

Shift of bacterial community and denitrification functional genes in biofilm electrode reactor in response to high salinity

High salinity suppresses denitrification by inhibiting microorganism activities. The shift of microbial community and denitrification functional genes under salinity gradient was systematically investigated in a biofilm electrode reactor (BER) and biofilm reactor (BR) systems. Denitrification efficiency of both BER and BR was not significantly inhibited during the period of low salinity (0-2.0%). As the salinity increased to 2.5%, BER could overcome the impact of high salinity and maintained a relatively stable denitrification performance, and the effluent NO₃^--N was lower than 1.5 mg/L. High salinity (>2.5%) impoverished microbial diversity and altered the microbial community in both BER and BR. However, two genera Methylophaga and Methyloexplanations were enriched in BER due to electrochemical stimulation, which can tolerate high salinity (>3.0%). The relative abundance of Methylophaga in BER was almost 10 times as much as in BR. Paracoccus is a hydrogen autotrophic denitrifier, which was obviously inhibited with 1.0% NaCl. The hetertrophic denitrifiers were primarily responsible for the nitrate removal in the BER compared to the autotrophic denitrifiers. The abundance and proportion of denitrifying functional genes confirmed that main denitrifiers shift to salt-tolerant species (nirK-type denitrifiers) to reduce the toxic effects. The napA (2.2 × 10⁸ to 6.5 × 10⁸ copies/g biofilm) and nosZ (2.2 × 10⁷ to 4.4 × 10⁷ copies/g biofilm) genes were more abundant in BER compared to BR's, which was attributed to the enrichment of Methylophaga alcalica and Methyloversatilis universalis FAM5 in the BER. The results proved that BER had greater denitrification potential under high salinity (>2.0%) stress at the molecular level.

Metagenomic analysis reveals enhanced nutrients removal from low C/N municipal wastewater in a pilot-scale modified AAO system coupling electrolysis

The conventional biological nutrients removal process is challenged by insufficient organic carbon in influent. To cross such an organic-dependent barrier, a pilot-scale electrolysis-integrated anaerobic/anoxic/oxic (AAO) process was developed for enhanced removal of nitrogen (N) and phosphorus (P) from low carbon/nitrogen (C/N) municipal wastewater. Average removal efficiencies of total nitrogen (TN) and total phosphorus (TP) in the electrolysis-AAO reached to 77.24% and 95.08% respectively, showing increases of 13.88% and 21.87%, as compared to the control reactor. Spatial variations of N and P showed that NH₄⁺-N removal rate was promoted in aerobic zone of electrolysis-AAO. The intensified TN elimination, which was mostly reflected by abatement of NO₃^--N with the concomitant slight accumulation of NH₄⁺-N and NO₂^--N, mainly occurred in anoxic2 compartment as the electrons supplied by electrolysis. Furthermore, minor P contents were measured and remained almost unchanged along the reaction units, indicating that chemical precipitation should be the dominant mechanism of P-removal in electrolysis-AAO. From the metagenomic-based taxonomy, phylum Actinobacteria was dramatically inhibited, and phylum Proteobacteria dominated the electrolysis-AAO. Particularly, nitrifying bacteria and multifarious autotrophic denitrifiers were enriched, meanwhile, a significant evolution of heterotrophic denitrifiers was found in electrolysis-AAO compared to control, which was mostly reflected by the inhibition of genus Candidatus Microthrix. Batch tests further confirmed that autotrophic denitrifiers using H₂ and Fe²⁺ as essential electron sinks were mainly responsible for the electrolysis-induced denitrification. Differential metabolic capacities were revealed from the perspectives of functional enzymes and genes, and network analysis allowed insight of microbial taxa-functional genes associations and shed light on stronger relevance between autotrophic denitrifiers and denitrification-associated genes in the electrolysis-AAO system.

Influence of Hydrogen Electron Donor, Alkaline pH, and High Nitrate Concentrations on Microbial Denitrification: A Review

Bacterial respiration of nitrate is a natural process of nitrate reduction, which has been industrialized to treat anthropic nitrate pollution. This process, also known as “microbial denitrification”, is widely documented from the fundamental and engineering points of view for the enhancement of the removal of nitrate in wastewater. For this purpose, experiments are generally conducted with heterotrophic microbial metabolism, neutral pH and moderate nitrate concentrations (<50 mM). The present review focuses on a different approach as it aims to understand the effects of hydrogenotrophy, alkaline pH and high nitrate concentration on microbial denitrification. Hydrogen has a high energy content but its low solubility, 0.74 mM (1 atm, 30 °C), in aqueous medium limits its bioavailability, putting it at a kinetic disadvantage compared to more soluble organic compounds. For most bacteria, the optimal pH varies between 7.5 and 9.5. Outside this range, denitrification is slowed down and nitrite (NO₂⁻) accumulates. Some alkaliphilic bacteria are able to express denitrifying activity at pH levels close to 12 thanks to specific adaptation and resistance mechanisms detailed in this manuscript, and some bacterial populations support nitrate concentrations in the range of several hundred mM to 1 M. A high concentration of nitrate generally leads to an accumulation of nitrite. Nitrite accumulation can inhibit bacterial activity and may be a cause of cell death.

pH control of an upflow pyrite-oxidizing denitrifying bioreactor via electrohydrogenesis

Maintenance of stable pH during pyrite-oxidizing denitrification process is important. Here, we demonstrated effective pH control (7.80 ± 0.20-8.40 ± 0.30) in an electrochemical-H₂ and pyrite-oxidizing denitrifying bioreactor (HPR) through in situ electrohydrogenesis. HPR achieved a higher nitrate removal activity (maximum:19.66 ± 0.63 mg NO₃^--N/(L·h)) with excellent resistance to high nitrate loading (up to 400 mg/L NO₃^--N) compared to that of the control groups. Nitrate removal rate of HPR fitted the Michaelis-Menten kinetic model (R² = 0.98, p < 0.01) well, and the denitrification followed the zero-order rate law. The results of the biofilm community analyses suggested that Thauera was the dominant bacteria in the cathode biofilm of HPR and may prefer hydrogen as an electron donor for autotrophic denitrification, while the relative abundance of Pseudomonas were similar in the cathode biofilm and pyrite biofilm. This study provides a new alternative for effective pH control in denitrifying bioreactors with pyrite as a packing material.

Nitrogen Removal and N2O Accumulation during Hydrogenotrophic Denitrification: Influence of Environmental Factors and Microbial Community Characteristics

Hydrogenotrophic denitrification is regarded as an efficient alternative technology of removing nitrogen from nitrate-polluted water that has insufficient organics material. However, the biochemical process underlying this method has not been completely characterized, particularly with regard to the generation and reduction of nitrous oxide (N₂O). In this study, the effects of key environmental factors on hydrogenotrophic denitrification and N₂O accumulation were investigated in a series of batch tests. The results show that nitrogen removal was efficient with a specific denitrification rate of 0.66 kg N/(kg MLSS·d), and almost no N₂O accumulation was observed when the dissolved hydrogen (DH) concentration was approximately 0.40 mg/L, the temperature was 30 °C, and the pH was 7.0. The reduction of nitrate was significantly affected by the pH, temperature, inorganic carbon (IC) content, and DH concentration. A considerable accumulation of N₂O was only observed when the pH decreased to 6.0 and the temperature decreased to 15 °C, where little N₂O accumulated under various IC and DH concentrations. To determine the microbial community structure, the hydrogenotrophic denitrifying enrichment culture was analyzed by Illumina high-throughput sequencing, and the dominant species were found to belong to the genera Paracoccus (26.1%), Azoarcus (24.8%), Acetoanaerobium (11.4%), Labrenzia (7.4%), and Dysgonomonas (6.0%).

Biological removal of pharmaceutical compounds using white-rot fungi with concomitant FAME production of the residual biomass

The efficiency of two white-rot fungi (WRF), Trametes versicolor and Ganoderma lucidum, to eliminate thirteen pharmaceutical pollutants with concomitant biodiesel production from the accumulating lipid content after treatment, was examined. The removal efficiency was studied using both individual and combined strains. The results of individual and combined strains showed a total removal (100%) of diclofenac (DCF), gemfibrozil (GFZ), ibuprofen (IBP), progesterone (PGT) and ranitidine (RNT). Lower removals were achieved for 4-acetamidoantipyrin (AAA), clofibric acid (ACF), atenolol (ATN), caffeine (CFN), carbamazepine (CZP), hydrochlorothiazide (HCT), sulfamethoxazole (SMX) and sulpiride (SPD), although the combination of both strains enhanced the system's efficiency, with removals ranging from 15 to 41%. This increase of the removal efficiency when combining both strains was attributed to the interactions developed between them (i.e., competition). Results from enzymatic and cytochrome P450 examination suggested that both extracellular (laccase, MnP, LiP) and intracellular oxidation mechanisms participate in the biological removal of pharmaceuticals. On the other hand, the "green" potential of the fungal sludge generated during the biological removal process was assessed for biodiesel production by means of one-step direct (in-situ) transformation. This process consists of the simultaneous extraction and conversion of lipids contained in the sludge by catalytic esterification/transesterification using a robust acid heterogeneous Zr-SBA-15 catalyst. This catalytic system provided conversions close to 80% of the saponifiable fraction (including free fatty acids and glycerides) in the presence of high amount of impurities. The overall weight FAME yield, based on the initial dried mass, was close to 30% for both strains.

Performance and microbial communities of Mn(II)-based autotrophic denitrification in a Moving Bed Biofilm Reactor (MBBR)

In this study, Mn(II) as electron donor was tested for the effects on denitrification in the MBBR under the conditions of initial nitrate concentration (10mgL(-1), 30mgL(-1), 50mgL(-1)), pH (5, 6, 7) and hydraulic retention time (HRT) (4h, 8h, 12h) which conducted by response surface methodology (RSM), the results demonstrated that the highest nitrate removal efficiency was occurred under the conditions of initial nitrate concentration of 47.64mgL(-1), HRT of 11.96h and pH 5.21. Analysis of SEM and flow cytometry suggested that microorganisms were immobilized on the Yu Long plastic carrier media successfully before the reactor began to operate. Furthermore, high-throughput sequencing was employed to characterize and compare the community compositions and structures of MBBR under the optimum conditions, the results showed that Pseudomonas sp. SZF15 was the dominant contributor for effective removal of nitrate in the MBBR.

Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes

Denitrifying bacteria accumulate NO2−, NO, and N₂O, the amounts depending on transcriptional regulation of core denitrification genes in response to O₂-limiting conditions. The genes include nar, nir, nor and nosZ, encoding NO3−-, NO2−-, NO- and N₂O reductase, respectively. We previously constructed a dynamic model to simulate growth and respiration in batch cultures of Paracoccus denitrificans. The observed denitrification kinetics were adequately simulated by assuming a stochastic initiation of nir-transcription in each cell with an extremely low probability (0.5% h^-1), leading to product- and substrate-induced transcription of nir and nor, respectively, via NO. Thus, the model predicted cell diversification: after O₂ depletion, only a small fraction was able to grow by reducing NO2−. Here we have extended the model to simulate batch cultivation with NO3−, i.e., NO2−, NO, N₂O, and N₂ kinetics, measured in a novel experiment including frequent measurements of NO2−. Pa. denitrificans reduced practically all NO3− to NO2− before initiating gas production. The NO2− production is adequately simulated by assuming stochastic nar-transcription, as that for nirS, but with a higher probability (0.035 h^-1) and initiating at a higher O₂ concentration. Our model assumes that all cells express nosZ, thus predicting that a majority of cells have only N₂O-reductase (A), while a minority (B) has NO2−-, NO- and N₂O-reductase. Population B has a higher cell-specific respiration rate than A because the latter can only use N₂O produced by B. Thus, the ratio BA is low immediately after O₂ depletion, but increases throughout the anoxic phase because B grows faster than A. As a result, the model predicts initially low but gradually increasing N₂O concentration throughout the anoxic phase, as observed. The modelled cell diversification neatly explains the observed denitrification kinetics and transient intermediate accumulations. The result has major implications for understanding the relationship between genotype and phenotype in denitrification research.

Denitrifiers generally respire O₂, but if O₂ becomes limiting, they may switch to anaerobic respiration (denitrification) by producing NO3−-, NO2−-, NO- and/or N₂O reductase, encoded by nar, nir, nor, and nosZ genes, respectively. Denitrification causes transient accumulation of NO2− and NO/N₂O emissions, depending on the activity of the four reductases. Denitrifiers lacking nosZ produce ~100% N₂O, whereas organisms with only nosZ are net consumers of N₂O. Full-fledged denitrifiers are equipped with all four reductases, genetic regulation of which determines NO2− accumulation and NO/N₂O emissions. Paracoccus denitrificans is a full-fledged denitrifying bacterium, and here we present a modelling approach to understand its gene regulation. We found that the observed transient accumulation of NO2− and N₂O can be neatly explained by assuming cell diversification: all cells expressing nosZ, while a minority expressing nar and nir+nor. Thus, the model predicts that in a batch culture of this organism, only a minor sub-population is full-fledged denitrifier. The cell diversification is a plausible outcome of stochastic initiation of nar- and nir transcription, which then becomes autocatalytic by NO2−and NO, respectively. The findings are important for understanding the regulation of denitrification in bacteria: product-induced transcription of denitrification genes is common, and we surmise that diversification in response to anoxia is widespread.

Evaluation on the Nanoscale Zero Valent Iron Based Microbial Denitrification for Nitrate Removal from Groundwater

Nanoscale zero valent iron (NZVI) based microbial denitrification has been demonstrated to be a promising technology for nitrate removal from groundwater. In this work, a mathematical model is developed to evaluate the performance of this new technology and to provide insights into the chemical and microbial interactions in the system in terms of nitrate reduction, ammonium accumulation and hydrogen turnover. The developed model integrates NZVI-based abiotic reduction of nitrate, NZVI corrosion for hydrogen production and hydrogen-based microbial denitrification and satisfactorily describes all of the nitrate and ammonium dynamics from two systems with highly different conditions. The high NZVI corrosion rate revealed by the model indicates the high reaction rate of NZVI with water due to their large specific surface area and high surface reactivity, leading to an effective microbial nitrate reduction by utilizing the produced hydrogen. The simulation results further suggest a NZVI dosing strategy (3–6 mmol/L in temperature range of 30–40 °C, 6–10 mmol/L in temperature range of 15–30 °C and 10–14 mmol/L in temperature range of 5–15 °C) during groundwater remediation to make sure a low ammonium yield and a high nitrogen removal efficiency.

Low probability of initiating nirS transcription explains observed gas kinetics and growth of bacteria switching from aerobic respiration to denitrification

In response to impending anoxic conditions, denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides (NO_x) to N₂ (denitrification). Since denitrifying bacteria are non-fermentative, the initial production of denitrification proteome depends on energy from aerobic respiration. Thus, if a cell fails to synthesise a minimum of denitrification proteome before O₂ is completely exhausted, it will be unable to produce it later due to energy-limitation. Such entrapment in anoxia is recently claimed to be a major phenomenon in batch cultures of the model organism Paracoccus denitrificans on the basis of measured e⁻-flow rates to O₂ and NO_x. Here we constructed a dynamic model and explicitly simulated actual kinetics of recruitment of the cells to denitrification to directly and more accurately estimate the recruited fraction (). Transcription of nirS is pivotal for denitrification, for it triggers a cascade of events leading to the synthesis of a full-fledged denitrification proteome. The model is based on the hypothesis that nirS has a low probability (, h⁻¹) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification. We assume that the recruitment is initiated as [O₂] falls below a critical threshold and terminates (assuming energy-limitation) as [O₂] exhausts. With  = 0.005 h⁻¹, the model robustly simulates observed denitrification kinetics for a range of culture conditions. The resulting (fraction of the cells recruited to denitrification) falls within 0.038–0.161. In contrast, if the recruitment of the entire population is assumed, the simulated denitrification kinetics deviate grossly from those observed. The phenomenon can be understood as a ‘bet-hedging strategy’: switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia turns out to be a ‘false alarm’.

In response to oxygen-limiting conditions, denitrifying bacteria produce a set of enzymes to convert / to N₂ via NO and N₂O. The process (denitrification) helps generate energy for survival and growth during anoxia. Denitrification is imperative for the nitrogen cycle and has far-reaching consequences including contribution to global warming and destruction of stratospheric ozone. Recent experiments provide circumstantial evidence for a previously unknown phenomenon in the model denitrifying bacterium Paracoccus denitrificans: as O₂ depletes, only a marginal fraction of its population appears to switch to denitrification. We hypothesise that the low success rate is due to a) low probability for the cells to initiate the transcription of genes (nirS) encoding a key denitrification enzyme (NirS), and b) a limited time-window in which NirS must be produced. Based on this hypothesis, we constructed a dynamic model of denitrification in Pa. denitrificans. The simulation results show that, within the limited time available, a probability of 0.005 h⁻¹ for each cell to initiate nirS transcription (resulting in the recruitment of 3.8–16.1% cells to denitrification) is sufficient to adequately simulate experimental data. The result challenges conventional outlook on the regulation of denitrification in general and that of Pa. denitrificans in particular.

Reconstructing a Thauera genome from a hydrogenotrophic-denitrifying consortium using metagenomic sequence data

Here, shotgun metagenomic sequencing was conducted to reveal the hydrogen-oxidizing autotrophic-denitrifying metabolism in an enriched Thauera-dominated consortium. A draft genome named Thauera R4 of over 90 % completeness (3.8 Mb) was retrieved mainly by a coverage-defined binning method from 3.5 Gb paired-end Illumina reads. We identified 1,263 genes (accounting for 33 % of total genes in the finished genome of Thauera aminoaromatica MZ1T) with average nucleotide identity of 87.6 % shared between Thauera R4 and T. aminoaromatica MZ1T. Although Thauera R4 and T. aminoaromatica shared quite similar nitrogen metabolism and a high nucleotide similarity (98.8 %) in their 16S ribosomal RNA genes, they showed different functional potentials in several important environmentally relevant processes. Unlike T. aminoaromatica MZ1T, Thauera R4 carries an operon of [NiFe]-hydrogenase (EC 1.12.99.6) catalyzing molecular hydrogen oxidation in nitrate-rich solution. Moreover, Thauera R4 is a mixtrophic bacterium possessing key enzymes for autotrophic CO2-fixation and heterotrophic acetate assimilation metabolism. This Thauera R4 bin provides another genetic reference to better understand the niches of Thauera and demonstrates a model pipeline to reveal functional profiles and reconstruct novel and dominant genomes from a simplified mixed culture in environmental studies.

Biological nitrate removal processes from drinking water supply-a review

This paper reviews both heterotrophic and autotrophic processes for the removal of nitrate from water supplies. The most commonly used carbon sources in heterotrophic denitrification are methanol, ethanol and acetic acid. Process performance for each feed stock is compared with particular reference nitrate and nitrite residual and to toxicity potential. Autotrophic nitrate removal has the advantages of not requiring an organic carbon source; however the slow growth rate of autotrophic bacteria and low nitrate removal rate have contributed to the fact that relatively few full scale plants are in operation at the present time.

Characterization of Thauera-dominated hydrogen-oxidizing autotrophic denitrifying microbial communities by using high-throughput sequencing

The present study, for the first time, reported a Thauera-dominated hydrogen-oxidizing autotrophic denitrifying microbial community enriched from different seed sludges including activated sludge and anaerobic digestion sludge. After 244 days enrichment, nitrogen removal rates reached up to 0.2 mg N/mg VSS/d which were comparable to that of the model organism Paracoccus denitrificans under the same conditions. Furthermore, high-throughput sequencing was applied to characterize and compare the seed sludges and enriched cultures. Operational taxonomic units (OTU)-based analysis (97% similarity cutoff) of total 280,000 16S rRNA gene V6 region sequences from 7 sludge samples (40,000 sequences per sample) revealed that the microbial diversity decreased after the enrichment, indicated by OTU numbers drop of 55-60%. Thauera species in the class of β-Proteobacteria were enriched into the dominant populations with relative abundances of 47-62%, regardless of seed sludge sources.

Influence of external resistance on electrogenesis, methanogenesis, and anode prokaryotic communities in microbial fuel cells

The external resistance (R(ext)) of microbial fuel cells (MFCs) regulates both the anode availability as an electron acceptor and the electron flux through the circuit. We evaluated the effects of R(ext) on MFCs using acetate or glucose. The average current densities (I) ranged from 40.5 mA/m(2) (9,800 Ω) to 284.5 mA/m(2) (150 Ω) for acetate-fed MFCs (acetate-fed reactors [ARs]), with a corresponding anode potential (E(an)) range of -188 to -4 mV (versus a standard hydrogen electrode [SHE]). For glucose-fed MFCs (glucose-fed reactors [GRs]), I ranged from 40.0 mA/m(2) (9,800 Ω) to 273.0 mA/m(2) (150 Ω), with a corresponding E(an) range of -189 to -7 mV. ARs produced higher Coulombic efficiencies and energy efficiencies than GRs over all tested R(ext) levels because of electron and potential losses from glucose fermentation. Biogas production accounted for 14 to 18% of electron flux in GRs but only 0 to 6% of that in ARs. GRs produced similar levels of methane, regardless of the R(ext). However, total methane production in ARs increased as R(ext) increased, suggesting that E(an) might influence the competition for substrates between exoelectrogens and methanogens in ARs. An increase of R(ext) to 9,800 Ω significantly changed the anode bacterial communities for both ARs and GRs, while operating at 970 Ω and 150 Ω had little effect. Deltaproteobacteria and Bacteroidetes were the major groups found in anode communities in ARs and GRs. Betaproteobacteria and Gammaproteobacteria were found only in ARs. Bacilli were abundant only in GRs. The anode-methanogenic communities were dominated by Methanosaetaceae, with significantly lower numbers of Methanomicrobiales. These results show that R(ext) affects not only the E(an) and current generation but also the anode biofilm community and methanogenesis.

Autotrophic nitrogen-removing biofilms on porous and non-porous membranes

The effective removal of nitrogen compounds from wastewater has become a critical issue for treatment plants as the awareness of their negative impact on the environment increased. Autotrophic nitrogen removal has become an interesting alternative to the more conventional heterotrophic processes, as it eliminates the need for an organic carbon addition to the source water and reduces biomass yields. Gas transfer membrane biofilm reactors (MBfR) for nitrification and hydrogen driven denitrification are of special interest as they combine membrane diffusers and biofilms, provide an efficient supply of necessary electron donor for autotrophic removal of ammonia and nitrate, extend solids retention times and retain biomass within the reactor. Subsequently, a wide range of MBfR, which vary based on the type of membrane material and membrane module configuration, are being tested for this purpose. This paper reviews the research to date and also discusses the challenges that still lay ahead before MBfR can be used at treatment plants.

Biodiversity of air-borne microorganisms at Halley Station, Antarctica

A study of air-borne microbial biodiversity over an isolated scientific research station on an ice-shelf in continental Antarctica was undertaken to establish the potential source of microbial colonists. The study aimed to assess: (1) whether microorganisms were likely to have a local (research station) or distant (marine or terrestrial) origin, (2) the effect of changes in sea ice extent on microbial biodiversity and (3) the potential human impact on the environment. Air samples were taken above Halley Research Station during the austral summer and austral winter over a 2-week period. Overall, a low microbial biodiversity was detected, which included many sequence replicates. No significant patterns were detected in the aerial biodiversity between the austral summer and the austral winter. In common with other environmental studies, particularly in the polar regions, many of the sequences obtained were from as yet uncultivated organisms. Very few marine sequences were detected irrespective of the distance to open water, and around one-third of sequences detected were similar to those identified in human studies, though both of these might reflect prevailing wind conditions. The detected aerial microorganisms were markedly different from those obtained in earlier studies over the Antarctic Peninsula in the maritime Antarctic.

Molecular characterization and in situ quantification of anoxic arsenite-oxidizing denitrifying enrichment cultures

To explore the bacteria involved in the oxidation of arsenite (As(III)) under denitrifying conditions, three enrichment cultures (ECs) and one mixed culture (MC) were characterized that originated from anaerobic environmental samples. The oxidation of As(III) (0.5 mM) was dependent on NO(3) (-) addition and N(2) formation was dependent on As(III) addition. The ratio of N(2)-N formed to As(III) fed approximated the expected stoichiometry of 2.5. A 16S rRNA gene clone library analysis revealed three predominant phylotypes. The first, related to the genus Azoarcus from the division Betaproteobacteria, was found in the three ECs. The other two predominant phylotypes were closely related to the genera Acidovorax and Diaphorobacter within the Comamonadaceae family of Betaproteobacteria, and one of these was present in all of the cultures examined. FISH confirmed that Azoarcus accounted for a large fraction of bacteria present in the ECs. The Azoarcus clones had 96% sequence homology with Azoarcus sp. strain DAO1, an isolate previously reported to oxidize As(III) with nitrate. FISH analysis also confirmed that Comamonadaceae were present in all cultures. Pure cultures of Azoarcus and Diaphorobacter were isolated and shown to be responsible for nitrate-dependent As(III) oxidation. These results, taken as a whole, suggest that bacteria within the genus Azoarcus and the family Comamonadaceae are involved in the observed anoxic oxidation of As(III).

Kinetic studies on autohydrogenotrophic growth of Ralstonia eutropha with nitrate as terminal electron acceptor

Autohydrogenotrophic batch growth of Ralstonia eutropha H16 was studied in a stirred-tank reactor with nitrate and nitrite as terminal electron acceptors and the sole limiting substrates. Assuming product inhibition by nitrite, saturation kinetics with the two limiting substrates and a simple switching function, which allows growth on nitrite only at low nitrate concentrations, resulted in a kinetic growth model with nine model parameters. The data of two batch experiments were used to identify the kinetic model. The kinetic model was validated with two additional batch experiments. The model predictions are in very good agreement with the experimental data. The maximum nitrite concentration was estimated to be 30.7 mM (total inhibition of growth). After complete reduction of nitrate, the growth rate decreases almost to zero before it increases again because of the following nitrite respiration. The maximum autohydrogenotrophic growth rate of Ralstonia eutropha with nitrate as a final electron acceptor (0.509 d(-1)) was found to be reduced by 90-95% compared to the so far reported autohydrogenotrophic growth rates with oxygen.

Electron donor effect on nitrate reduction pathway and kinetics in a mixed methanogenic culture

The effect of different electron donors on the pathway and kinetics of nitrate reduction in a sulfide-acclimated mixed, mesophilic (35 degrees C) methanogenic culture was investigated. A mixture of dextrin and peptone, glucose, propionate, acetate, and H(2)/CO(2) were used as substrates at an initial chemical oxygen demand of 1,500 mg/L and the initial nitrate concentration ranged between 0 and 300 mg N/L. The fastest nitrate reduction was observed in the H(2)/CO(2) and acetate-fed cultures. In the case of propionate, nitrate reduction was the slowest followed by partial recovery of methanogenesis and accumulation of volatile fatty acids due to inhibition as a result of accumulation of denitrification intermediates. Similarly, accumulation of nitrite and nitric oxide and partial or complete inhibition of methanogenesis was observed in the H(2)/CO(2)-fed cultures. Methanogenesis completely recovered in the dextrin/peptone-, glucose-, and acetate-fed cultures at all nitrate levels. Denitrification was the dominant pathway of nitrate reduction in the propionate-, acetate-, and H(2)/CO(2)-fed cultures regardless of the COD/N value. However, both denitrification and dissimilatory nitrate reduction to ammonia (DNRA) were observed in the dextrin/peptone- and glucose-fed cultures and the degree of predominance of either of the two pathways was a function of the COD/N value. Therefore, the type of electron donor used affected both the nitrate reduction pathway and kinetics, as well as the recovery of fermentation and/or methanogenesis in the mixed methanogenic culture.