A critical review of aerobic denitrification: Insights into the intracellular electron transfer

Simultaneous nitrification and denitrification of hypersaline wastewater by a robust bacterium Halomonas salifodinae from a repeated-batch acclimation

Biotreatment of hypersaline wastewater requires robust strains with high resistance to activity inhibition and even bacterium death, which remains a worldwide challenge. Here Halomonas salifodinae, a simultaneous nitrification and denitrification (SND) bacterium, was isolated by performing repeated-batch acclimation, showing efficient nitrogen removal at 0-15% salinity and low activity inhibition prominently superior to that of other strains such as Pseudomonas sp. and Acinetobacter sp. Community analysis as well as comparison of microbial activity at different salinities revealed an increased relative abundance of halotolerant populations by stimulating their salt tolerance during the repeated-batch process. For single or mixed nitrogen sources at 15% salinity, the SND efficiencies of the isolated strain reached above 95%. The high activities were attributed to the key enzymes AMO and HAO for nitrification as well as NAP and NIR for denitrification. The findings provide a promising acclimation pathway to obtain robust bacteria for biotreatment of hypersaline wastewater.

Involvement of the metabolically active bacteria in the organic matter degradation during olive mill waste composting

RNA-based high-throughput sequencing is a valuable tool in the discernment of the implication of metabolically active bacteria during composting. In this study, "alperujo" composting was used as microbial model for the elucidation of structure-function relationships with physicochemical transformation of the organic matter. DNA and RNA, subsequently retrotranscribed into cDNA, were isolated at the mesophilic, thermophilic and maturation phases. 16S rRNA gene was amplified by quantitative PCR (qPCR) and Illumina MiSeq platform to assess bacterial abundance and diversity, respectively. The results showed that the abundance of active bacteria assessed by qPCR was maximum at thermophilic phase, which confirm it as the most active stage of the process. Concerning diversity, Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the main phyla presented in composts. Concomitantly, three different behaviours were observed for bacterial dynamics: some genera decreased during the whole process meanwhile others proliferated only at thermophilic or maturation phase. Statistical correlation between physicochemical transformations of the organic matter and bacterial diversity revealed bacterial specialisation. This result indicated that specific groups of bacteria were only involved in the organic matter degradation during bio-oxidative phase or humification at maturation. Metabolic functions predictions confirmed that active bacteria were mainly involved in carbon (C) and nitrogen (N) cycles transformations, and pathogen reduction.

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.

Evaluation of NOx removal from flue gas and Fe(II)EDTA regeneration using a novel BTF-ABR integrated system

A promising process is under development for the removal of NOx and regeneration of Fe(II)EDTA in a novel biotrickling filter-anaerobic baffled reactor (BTF-ABR) integrated system at 50 ± 0.5 ℃. In this work, we investigated the NOx removal capacity of a BTF under different O₂ concentrations (7.0 vol%, 5.25 vol% and 3.5 vol%), and tested the effect of an ABR on NOx removal and regeneration of Fe(II)EDTA. The results showed that the NOx removal capacity was significantly increased with the O₂ concentration reduced from 7.0% to 3.5%. The microoxygen environment produced by the BTF-ABR integrated system was more conducive to the removal of NOx and regeneration of Fe(II)EDTA compared with that in the BTF. Real-time polymerase chain reaction (PCR) analysis showed that the coordinated expression of denitrification genes was the major reason for no N₂O emission, along with no nitrate and nitrite accumulation. The 16S rRNA gene amplicon sequencing analysis showed that the cooperation of denitrifying bacteria (Klebsiella, Petrimonas, Rhodococcus and Ochrobactium) and iron-reducing bacteria (Klebsiella, Geobacter and Petrimonas) in the system was the key to the stable and efficient removal of NOx and the regeneration of Fe(II)EDTA simultaneously.

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.

K fertilizer alleviates N2O emissions by regulating the abundance of nitrifying and denitrifying microbial communities in the soil-plant system

Potassium (K) fertilizer additions can result in high crop yields of good quality and low nitrogen (N) loss; however, the interaction between K and N fertilizer and its effect on N₂O emissions and associated microbes remain unclear. We investigated this in a pot experiment with six fertilizer treatments involving K and two sources of N, using agricultural soil from the suburbs of Wuhan, central China. The aim was to determine the effects of the interaction between K and different forms of N on the N₂O flux and the abundance of nitrifying and denitrifying microbial communities, using static chamber-gas chromatography and high-throughput sequencing methods. Compared with no fertilizer control (CK), the addition of nitrate fertilizer (NN) or ammonia fertilizer (AN) or K fertilizer significantly increased N₂O emissions. However, the combined application (NNK) of K and NN significantly reduced the average N₂O emissions by 28.3%, while the combined application (ANK) of K and AN increased N₂O emissions by 22.7%. The abundance of nitrifying genes amoA in ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) changed in response to N and/or K fertilization, but the denitrifying genes narG, nirK and norl were strongly correlated with N₂O emissions. This suggests that N or K fertilizer and their interaction affect N₂O emissions mainly by altering the abundance of functional genes of denitrifying microbes in the soil-plant system. The genera Paracoccus, Rubrivivax and Geobacter as well as Streptomyces and Hyphomicrobium play an important role in N₂O emissions during denitrification with the combined application of N and K.

High Dimension Granite Pavement Bio-Desalination Practical Implementation

Biocleaning technology is based on the use of safe environmental microorganisms for green cultural heritage (CH) restoration. Compared with traditional cleaning products, this biological technique is very specific, effective, and nontoxic. This innovative biotechnological application has been used for recovering diverse monuments and artworks. Most CH in situ surfaces that are treated with microorganisms are small areas; however, some important pathologies, such as salt contamination, can affect high dimension artistic surfaces. The purpose of this study is to analyze and overcome the problems and limitations of scaling up the bio-desalination protocol for in situ applications. Three water-based gel delivery systems and three heating systems were tested in situ and evaluated in terms of performance difficulty, efficacy, and costs. The tests were carried out on the salt contaminated granite pavement of Cristo Chapel of Sta Ma de Conxo in Santiago de Compostela (Spain). Ground agar 2% and a heating electric mat were selected as the best performing systems. The implemented protocol was applied for the bio-desalination of the 233 m2 Chapel pavement. Conductivity, nitrate–nitrite measurements, biological monitoring, and digital image analysis were performed to determine the efficacy of the treatment. This research allowed for the development of an innovative and optimized in situ, high dimension bio-desalination application protocol transferable to other large scale, in situ biocleaning strategies.

Biological stimulation with Fe(III) promotes the growth and aerobic denitrification of Pseudomonas stutzeri T13

Certain metal ions can contribute to the functional microorganisms becoming dominant by stimulating their metabolism and activity. Therefore, Pseudomonas stutzeri T13 was used to investigate the impacts of biological stimulation with certain metal ions on aerobic denitrifying bacteria. Results showed that with the addition of 0.036 mmol/L Fe³⁺ ions, the nitrogen-assimilation capacity of P. stutzeri T13 significantly increased by 43.99% when utilizing ammonium as the sole nitrogen source. Kinetic models were applied to analyze the role of Fe³⁺ ions in the growth, and results indicated that increasing Fe³⁺ ion concentrations decreased the decay rate. The maximum nitrate reduction rate increased from 9.55 mg-N L^-1 h^-1 to 19.65 mg-N L^-1 h^-1 with Fe³⁺ ion concentrations increasing from 0.004 to 0.036 mmol/L, which was due to the increased level of napA gene transcription and activity of nitrate reductase. This study provides a theoretical foundation for further understanding of the mechanism of Fe³⁺ ion stimulation of aerobic denitrification, benefiting the practicable application of aerobic denitrifiers.

A Novel Regulator Participating in Nitrogen Removal Process of Bacillus subtilis JD-014

Aerobic denitrification is considered as a promising biological method to eliminate the nitrate contaminants in waterbodies. However, the molecular mechanism of this process varies in different functional bacteria. In this study, the nitrogen removal characteristics for a newly isolated aerobic denitrifier Bacillus subtilis JD-014 were investigated, and the potential functional genes involved in the aerobic denitrification process were further screened through transcriptome analysis. JD-014 exhibited efficient denitrification performance when having sodium succinate as the carbon source with the range of nitrate concentration between 50 and 300 mg/L. Following the transcriptome data, most of the up-regulated differentially expressed genes (DEGs) were associated with cell motility, carbohydrate metabolism, and energy metabolism. Moreover, gene nirsir annotated as sulfite reductase was screened out and further identified as a regulator participating in the nitrogen removal process within JD-014. The findings in present study provide meaningful information in terms of a comprehensive understanding of genetic regulation of nitrogen metabolism, especially for Bacillus strains.

Nitrogen species control the interaction between NO3--N reduction and aniline degradation and microbial community structure in the oxic-anoxic transition zone

Contrary to the fact that NO₃^--N can serve as electron acceptor to promote organics degradation, it was also found NO₃^--N reduction does not necessarily promote organics degradation. We speculate nitrogen (N) species may control the interaction between NO₃^--N reduction and organics degradation via shifting related microbial community structure. To prove the hypothesis, oxic-anoxic transition zone (OATZ) microcosms simulated by lake water and sediment were conducted with the addition of N species (NO₃^--N, NO₂^--N, and NH₄⁺-N) and aniline as typical organics. High-throughput sequencing was used to analyze the microbial community structure and functional enzyme in the microcosms. Results show that, NO₂^--N inhibited NO₃^--N reduction while enhanced aniline degradation. For NH₄⁺-N, it promoted NO₃^--N reduction when NH₄⁺-N/NO₃^--N concentration ratio ≤ 2 and inhibited aniline degradation when NH₄⁺-N/aniline concentration ratio ≥ 0.5. The presence of NO₂^--N or NH₄⁺-N weakened the interaction between NO₃^--N reduction and aniline degradation, which might be caused by significant changes in the diversity and abundance of microbial communities controlled by N species. The microbial mechanism indicates that NO₂^--N weakened the interaction by affecting both denitrification enzyme activity and electron transfer capability, while NH₄⁺-N weakened the interaction mainly by affecting electron transfer capability. These results imply that N species, as well as other electron acceptors and donors, in the contaminated OATZ should be fully considered, when performing in situ remediation technology of NO₃^--N reduction.

Effects of C/N ratio and dissolved oxygen on aerobic denitrification process: A mathematical modeling study

COD to ammonium nitrogen (C/N) ratio and dissolved oxygen (DO) concentration are the most important factors affecting aerobic denitrification process, however, the effects of those on the mix-cultured aerobic denitrification process are still ambiguous. A mathematical model based on the framework of activated sludge model No. 3 (ASM3) was proposed for simulating nitrogen removal in an aerobic denitrification SBR process via anoxic/aerobic denitrification. AQUASIM 2.1G was employed for parameter estimation, sensitivity analysis and model calibration, as well as model validation. Ultimately, the impacts of the C/N ratio and the DO concentration on the aerobic denitrification process were revealed by the validated model. The model proposed well described nitrogen removal in an aerobic denitrification SBR process. The total nitrogen (TN) removal efficiency of the process increased with the increasing of C/N ratio and the decreasing of DO concentration. C/N ratio impacted the synthesis of cell internal storage products (X_STO), and the effects of DO concentration on the process resulted from the competition with substrate between heterotrophs and aerobic denitrifiers. High C/N ratio was preferred, however, the DO concentration should be maintained at a relatively lower level under the premise of ensuring the aerobic condition.

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.

Effects of sulfoxaflor on greenhouse vegetable soil N2O emissions and its microbial driving mechanism

The wide application of pesticides ensures the safety of food production, but it also has a serious impact on soil ecosystem. Although sulfoxaflor as a pesticide has great potential for application due to its excellent insecticidal activity and low crossresistance, little is known about its soil environmental safety risks. In this study, the effects of sulfoxaflor on N₂O emissions and microorganisms in greenhouse vegetable soils were studied by indoor simulation culture experiments. Dynamic changes of soil main inorganic N and N₂O emission rate were tested, and the abundance and community of total bacteria and microorganisms related to N cycle were analyzed. The results indicated that soil microorganisms rapidly degraded sulfoxaflor, and the N₂O emissions rate and ammonium nitrogen (NH₄⁺-N) content significantly increased, while nitrate nitrogen (NO₃^--N) content was significantly decreased. Sulfoxaflor significantly changed the abundance and community of total bacteria, nitrite reducing and nitrous oxide reducing bacteria, but had no significant effect on ammoxidation microorganisms. The N₂O emission rate was positively correlated with gene abundance of denitrifying microorganisms. Under 65% soil maximum water holding capacity, sulfoxaflor may broke the dynamic balance of N₂O production and consumption in the denitrification process, which caused a significant increase in N₂O emission. Therefore, the application of sulfoxaflor had a certain effect on N cycling and utilization in greenhouse vegetable soil.

The nitrogen removal characterization of a cold-adapted bacterium: Bacillus simplex H-b

The removal efficacy of biological nitrogen removal process is inhibited by low temperatures. Herein, a psychrotrophic bacterium strain, Bacillus simplex H-b, was isolated and identified with the potential to conduct heterotrophic nitrification and aerobic denitrification in the temperature range from 5 to 37 °C. At 10 °C, the removal efficiencies of initial nitrate-N (63 mg/L), nitrite-N (10 mg/L) and ammonium-N (60 mg/L) were 67.29%, 78.69% and 82.16%, with the maximum removal rate of 0.56, 0.18 and 0.74 mg/L/h, respectively. Additionally, both the accumulation level of ATP (adenosine triphosphate) and the formation of extracellular polymeric substances was found to increase with the decrease of temperature from 37 °C to 10 °C, indicating strain H-b might resist low temperature stress through its cellular extreme environment resistant mechanism and further suggesting the newly isolated strain could serve as a promising candidate for nitrogen contaminated wastewater treatment, especially under low-temperature condition.

Complete genome sequence of a denitrifying bacterium Halomonas sp. SS10-MC5 isolated from hydrothermal vent of Indian Ocean

A denitrifying bacterium Halomonas sp. SS10-MC5, was isolated from a deep-sea hydrothermal vent chimney sample of the Indian Ocean. Here we described the complete genome of strain SS10-MC5 which has one circular chromosome of 4,441,120 bp with a mean G + C content of 66.12 mol%. The complete genome harbors 4094 predicted protein-encoding genes, 65 tRNA genes as well as four 16S-23S-5S rRNA operons. Genes involved in denitrification, assimilation, PHA synthesis, stress response, and so on, were identified in this genome. These metabolic features and related genes revealed genetic basis for the adaptation to the marine environment, which help to further understand its adaptive evolution and ecological role in submarine hydrothermal environments.

Characteristics of microbial denitrification under different aeration intensities: Performance, mechanism, and co-occurrence network

This study aimed to explore how dissolved oxygen (DO) affected the characteristics and mechanisms of denitrification in mixed bacterial consortia. We analyzed denitrification efficiency, intracellular nicotinamide adenine dinucleotide (NADH), relative expression of functional genes, and potential co-occurrence network of microorganisms. Results showed that the total nitrogen (TN) removal rates at different aeration intensities (0.00, 0.25, 0.63, and 1.25 L/(L·min)) were 0.93, 1.45, 0.86, and 0.53 mg/(L·min), respectively, which were higher than previously reported values for pure culture. The optimal aeration intensity was 0.25 L/(L·min), at which the maximum NADH accumulation rate and highest relative abundance of napA, nirK, and nosZ were achieved. With increased aeration intensity, the amount of electron flux to nitrate decreased and nitrate assimilation increased. On one hand, nitrate reduction was primarily inhibited by oxygen through competition for electron donors of a certain single strain. On the other hand, oxygen was consumed rapidly by bacteria by stimulating carbon metabolism to create an optimal denitrification niche for denitrifying microorganisms. Denitrification was performed via inter-genus cooperation (competitive interactions and symbiotic relationships) between keystone taxa (Azoarcus, Paracoccus, Thauera, Stappia, and Pseudomonas) and other heterotrophic bacteria (OHB) in aeration reactors. However, in the non-aeration case, which was primarily carried out based on intra-genus syntrophy within genus Propionivibrio, the co-occurrence network constructed the optimal niche contributing to the high TN removal efficiency. Overall, this study enhanced our knowledge about the molecular ecological mechanisms of aerobic denitrification in mixed bacterial consortia and has theoretical guiding significance for further practical application.

Intra/extracellular electron transfer for aerobic denitrification mediated by in-situ biosynthesis palladium nanoparticles

The slow electron transfer rate is the bottleneck to the biological wastewater treatment process, and the nanoparticles (NPs) has been verified as a feasible strategy to improve the biological degradation efficiency by accelerating the electron transfer. Here, we employed the Gram-positive Bacillus megaterium Y-4, capable of synthetizing Pd(0), to investigate the intra/extracellular electron transfer (IET/EET) mechanisms mediated by NPs in aerobic denitrification for the first time. Kinetic and thermodynamic results showed that the bio-Pd(0) could significantly promote the removal of both nitrate and nitrite by improving affinity and decreasing activation energy. The enzymic activity and the respiration chain inhibition experiment indicated that the bio-Pd(0) could facilitate the nitrate biotic reduction by improving the Fe-S center activity and serving as parallel H carriers to replace coenzyme Q to selectively increase the electron flux toward nitrate in IET, while promoting the nitrite reduction by abiotic catalysis. Most importantly, the detection of DPV peak at -226~-287 mV proved that the one-electron EET via multiheme cytochrome-bound flavins also occurred in Gram-positive bacteria and enhanced in Pd-loaded cells. In addition, the remarkable increase of the formal charge in EPS indicated that the bio-Pd(0) could act as an electron shuttle to increase the redox site in EPS, eventually accelerating the electron hopping in long-distance electron transfer. Overall, this study expanded our understanding of the roles of bio-Pd(0) on the aerobic denitrification process and provided an insight into the IET/EET of Gram-positive strains.

Impacts of human disturbance on the biogeochemical nitrogen cycle in a subtropical river system revealed by nitrifier and denitrifier genes

Human activities have largely modified nitrogen (N) sources supply, cycling and export from land to ocean. Nitrification and denitrification are vital processes alleviating N pollution in aquatic ecosystems but the diverse responses and niche of microbial N retention to human disturbance are still understudied. Here we investigated the changes in N species and functional genes in the urban, agriculture and reservoir river sections of the Jiulong River (southeast China). Our results show that ammonia-oxidizing bacteria (AOB) (Nitrosomonas) were dominant in the urban river section receiving ammonium-rich sewage that enhanced nitrification and subsequent denitrification, while ammonia-oxidizing archaea (AOA) was more abundant than AOB in the river section flowing through areas of pomelo (Citrus maxima) agriculture with low pH, low ammonium and very high nitrate input. Warm temperatures and large total suspended matter (TSM) in the wet season promoted growth of nitrifiers and denitrifiers, which were mostly particle-attached. The potential river N retention through gaseous N removal (PR_N2O and PR_N2) in the agriculture section with huge N loading was among the lowest. Strong nitrification and denitrification were suspected to occur in the agricultural acid soil system rather than in the river network. In addition, the decreased TSM and N concentration promoted free-living microbes in the reservoir. The highest PR_N2 and N₂ production observed in the reservoir in the dry season implied that denitrification and anammox occurring in sediments was likely to increase N retention. This study suggests the diverse factors involved in processing of N pollution among diverse landscapes.