Cloning, purification and characterization of novel Cu-containing nitrite reductase from the Bacillus firmus GY-49

The nitrogen removal characterization and ecological risk assessment of Bacillus sp. isolated from mariculture systems in China with spatiotemporal difference

The accumulation of nitrogen compounds may worsen the aquatic environment and cause serious economic losses in the aquaculture industry. In this study, the denitrification performance and ecological safety of 120 Bacillus sp. isolates with spatial and temporal differences were evaluated based on the aspects of hemolysis, drug resistance, denitrification performance, and purification effect for mariculture wastewater. Firstly, 55/120 safe strains with no hemolytic activity were detected through hemolysis testing. Then, based on selective denitrification medium and colorimetric reagent method, 34/55 Bacillus sp. with denitrification effect were screened. For these 34 Bacillus sp. isolates, the drug resistance phenotype and genotype, denitrification genes, and enzyme activities related to the nitrogen metabolizing (AMO, HAO, NAR, NIR) were examined. And the MARI was 0.00-0.25, with a multi-drug resistance rate of 17.6%. The drug resistance genes tetB, blaTEM, and cfr and the denitrification genes nap, nor, and narG were detected. Ultimately, 27/34 strains with denitrification function and ecological safety were obtained. In addition, eight Bacillus sp. showed certain denitrification effects on nitrogen-containing wastewater treatment. Among them, B. subtilis B24 has outstanding denitrification ability, with removal rates of 92%, 62%, 68%, and 30% for NH4 + -N, NO2--N, NO3--N, and TN in simulated wastewater, respectively. It also has a good denitrification effect in practical applications. This study provides candidate bacterial strains for the treatment of mariculture wastewater.

Heterologous expression, enzymatic properties, product analysis and molecular docking of assimilative nitrite reductase (NiR) in Bacillus velezensis GXMZU-B1 derived from mariculture

High concentrations of nitrite stress aquatic animals, leading to significant fish and shrimp deaths as well as environmental pollution. Reducing nitrite levels in high-density aquaculture is crucial for both aquaculture safety and environmental protection. Nitrite reductase (NiR) can rapidly reduce nitrite in water, offering potential applications in aquaculture and water treatment. In this study, a novel NiR gene (nasD) was isolated from Bacillus velezensis GXMZU-B1, a highly effective nitrite-degrading bacterium, and expressed heterologously in Escherichia coli. The recombinant NASD was purified using Ni-NTA affinity chromatography, and its physicochemical properties and reaction products were analyzed. The enzyme showed optimal activity at 30°C and pH 6.5. Metal ions such as Fe3+, Zn2+, and Ba2+ enhanced enzyme activity, whereas Cu2+, K+, Mg2+, and Mn2+ reduced it. The best electron donors was NADPH. NASD converts nitrite (NO2-) into ammonium (NH4+), making it environmentally friendly and potentially valuable for aquaculture and water pollution control. Bioinformatics analysis indicated that the enzyme is stable, with a conserved sequence and a Pyr_redox_2 domain. Using NADPH as a coenzyme, AlphaFold3 modeling and molecular docking with nitrite identified 14 potential catalytic sites. These findings highlight the potential of recombinant NASD as a promising candidate for nitrite degradation in aquaculture.

A Novel Nitrite Reductase from Acinetobacter haemolyticus for Efficient Degradation of Nitrite

Nitrite reductases play a crucial role in the nitrogen cycle, demonstrating significant potential for applications in the food industry and environmental remediation, particularly for nitrite degradation and detection. In this study, we identified a novel nitrite reductase (AhNiR) from a newly isolated denitrifying bacterium, Acinetobacter haemolyticus YD01. We constructed a heterologous expression system using E. coli BL21/pET28a-AhNir, which exhibited remarkable nitrite reductase enzyme activity of 29 U/mL in the culture broth, substantially higher than that reported for other strains. Structural analysis of AhNiR revealed the presence of [Fe-S] clusters, with molecular docking studies identifying Tyr-282 and Ala-289 as key catalytic sites. The enzymatic properties of AhNiR demonstrated an optimal pH of 7.5 and an optimal catalytic temperature of 30 °C. Its kinetic parameters, Km and vmax, were 1.53 mmol/L and 10.18 mmol/min, respectively, fitting with the Michaelis-Menten equation. This study represents the first report of a nitrite reductase from a denitrifying bacterium, providing a new enzyme source for nitrite degradation applications in the food industry and environmental remediation, as well as for biosensing technologies aimed at nitrite detection.

Effect and potential mechanism of nitrite reductase B on nitrite degradation by Limosilactobacillus fermentum RC4

Nitrite has the potential risk of hypoxic poisoning or cancer in pickled food. In our previous study, Limosilactobacillus fermentum (L. fermentum) RC4 is effective in nitrite degradation by producing nitrite reductase B (NirB). To investigate the detailed mechanism from the genome, response, and regulation of NirB, the whole-genome sequence of L. fermentum RC4 was analyzed, the L. fermentum-EGFP-nirB with enhanced green fluorescent protein (EGFP) labeled the nitrite reductase large subunit nirB, and the recombined L. fermentum-NirB with overexpression NirB strain was conducted. The key genes within the dominant metabolism pathways may be involved in stress tolerance to regulate the degrading process. The green fluorescence density of EGFP indicated that NirB activity has a threshold and peaked under 300 mg/L nitrite concentration. NirB overexpressed in L. fermentum RC4 boosted the enzyme activity by 39.6% and the degradation rate by 10.5%, when fermented in 300 mg/L for 40 h, compared to the control group. RNA-seq detected 248 differential genes mainly enriched in carbohydrate, amino acid, and energy metabolism. The ackA gene for pyruvate metabolism and the mtnN gene for cysteine metabolism were up-regulated. NirB regulates these genes to produce acid and improve stress resistance for L. fermentum RC4 to accelerate nitrite degradation.

Optimization of degradation conditions and analysis of degradation mechanism for nitrite by Bacillus aryabhattai 47

Excessive nitrite levels cause significant damage to aquaculture, making it crucial to explore green and reliable nitrite removal technologies. In this study, A Bacillus aryabhattai (designated as the strain 47) isolated from aquaculture wastewater was used as the experimental strain. The nitrite degradation conditions of the strain 47 were optimized, and the optimal conditions are: glucose was 12.74 g/L, fermented special soybean meal was 21.27 g/L, MgCl2 369 mg/L, pH 7.0, incubated at 30 °C with the inoculum size of 2 % and the rotation speed of 170 rpm. Under the optimal conditions, the nitrite concentration of the culture solution was 200 mg/L, and the nitrite removal rate reached 91.4 %. Meanwhile, the mechanism by which Mg2+ enhanced the nitrite degradation ability of the strain 47 was investigated by transcriptomics. An operon structure directed cellular trafficking of Mg2+, and then, the Mg2+-mediated catalytic reaction of multiple enzymes enhanced and improved cellular metabolic processes (e.g. the transport and metabolism of nitrite, central carbohydrate metabolism oxidative phosphorylation). At the same time, with the progress of cell metabolism, cells secreted a series of enzymes related to nitrite transport and metabolism to promote the metabolism of nitrite. And the process of the assimilated nitrate reduction pathway of nitrite degradation in the strain 47 was elaborated at the transcriptome level. This study provided a new insight into nitrite treatment mediated by microbial organisms.

Nitrite is reduced by nitrite reductase NirB without small subunit NirD in Escherichia coli

The assimilatory nitrite reductase enzyme NirB and small subunit NirD genes encoded in nir operon in Escherichia coli were cloned into the pET28a vector, and the recombinant enzyme was characterized for the first time. Docking of NirB with NirD, NADH, NO₂^-, NO₃^-, and CHO₂^- was performed using docking modeling programs. Methyl viologen and sodium dithionite were used as electron couples, and the amount of reduced nitrite was measured to calculate enzyme activity. NirB is the main enzyme and shows high activity with or without NirD. However, the inclusion of NirD into the enzyme solution at a ratio of 1NirD:2NirB resulted in 10% higher nitrite reductase activity. The enzyme tends to aggregate in the absence of β-mercaptoethanol, which causes the conversion of tetrameric NirB to monomeric form, and the NirB enzyme shows its highest activity in monomeric form. The optimum temperature for enzyme activity was 37 °C and the optimum pH was found to be 7.0. K_m and V_max values of NirB were calculated as 9833 μM and 416.67 μmol NO₂^- reduced min^-1 mg^-1. Enzyme activity decreased by 55% and 50% in the presence of 100 mM nitrate and formate, respectively. The presence of 25 mM Cd²⁺ protected the enzyme at room temperature and the enzyme showed 10% higher activity in the presence of cadmium.

Novel gene similar to nitrite reductase (NO forming) plays potentially important role in the latency of tuberculosis

The development of the latent phenotype of Mycobacterium tuberculosis (Mtb) in the human lungs is the major hurdle to eradicate Tuberculosis. We recently reported that exposure to nitrite (10 mM) for six days under in vitro aerobic conditions completely transforms the bacilli into a viable but non-cultivable phenotype. Herein, we show that nitrite (beyond 5 mM) treated Mtb produces nitric oxide (NO) within the cell in a dose-dependent manner. Our search for the conserved sequence of NO synthesizing enzyme in the bacterial system identified MRA2164 and MRA0854 genes, of which the former was found to be significantly up regulated after nitrite exposure. In addition, the purified recombinant MRA2164 protein shows significant nitrite dependent NO synthesizing activity. The knockdown of the MRA2164 gene at mRNA level expression resulted in a significantly reduced NO level compared to the wild type bacilli with a simultaneous return of its replicative capability. Therefore, this study first time reports that nitrite induces dormancy in Mtb cells through induced expression of the MRA2164 gene and productions of NO as a mechanism for maintaining non-replicative stage in Mtb. This observation could help to control the Tuberculosis disease, especially the latent phenotype of the bacilli.

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.

Isolation and Characterization of an Aerobic Denitrifier Bacillus sp. SC16 from an Intensive Aquaculture Pond

Overloading of ammonia and nitrite nitrogen in aquaculture can result in toxicity to aquatic animals. In order to eliminate the hazardous substances, a highly efficient denitrifying bacterium, Bacillus sp. SC16, was identified in a fishery pond and isolated subsequently. The strain SC16 could remove nitrate up to 97%, ammonia up to 36.6%, and nitrite up to 99.99% when incubated with nitrate at an initial concentration of 306.9 mg·L−1 for 72 h, ammonia at 165.49 mg·L−1 for 48 h, and nitrite at 200 mg·L−1 for 24 h under aerobic conditions. The nitrite reductase gene was identified as the nirK gene. The transcriptional levels of the nirK gene in strain SC16 incubated with ammonia, nitrate, and nitrite showed similar expression patterns. When the strain SC16 was used to treat the aquaculture water, the concentration of ammonia decreased significantly, from 8.35 mg·L−1 to 4.56 mg·L−1, and there was almost no accumulation of nitrite by the end of experiment. Therefore, the results indicated that Bacillus sp. SC16 could be a promising candidate for aquaculture water treatment.

Heterologous and Homologous Expression of Proteins from Haloarchaea: Denitrification as Case of Study

Haloarchaea (halophilic microbes belonging to the Archaea domain) are microorganisms requiring mid or even high salt concentrations to be alive. The molecular machinery of these organisms is adapted to such conditions, which are stressful for most life forms. Among their molecular adaptations, halophilic proteins are characterized by their high content of acidic amino acids (Aspartate (Asp) and glumate (Glu)), being only stable in solutions containing high salt concentration (between 1 and 4 M total salt concentration). Recent knowledge about haloarchaeal peptides, proteins, and enzymes have revealed that many haloarchaeal species produce proteins of interest due to their potential applications in biotechnology-based industries. Although proteins of interest are usually overproduced in recombinant prokaryotic or eukaryotic expression systems, these procedures do not accurately work for halophilic proteins, mainly if such proteins contain metallocofactors in their structures. This work summarizes the main challenges of heterologous and homologous expression of enzymes from haloarchaea, paying special attention to the metalloenzymes involved in the pathway of denitrification (anaerobic reduction of nitrate to dinitrogen), a pathway with significant implications in wastewater treatment, climate change, and biosensor design.

Characteristics of Heterotrophic Nitrifying and Aerobic Denitrifying Arthrobacter nicotianae D51 Strain in the Presence of Copper

A heterotrophic nitrification and aerobic denitrification bacterium, strain D51, was identified as Arthrobacter nicotianae based on morphological, phospholipid fatty acids (PLFAs), and 16S rRNA gene sequence analyses. Further tests demonstrated that strain D51 had the capability to use nitrite, nitrate, or ammonium as the sole nitrogen source in the presence of Cu2+. The maximum removal efficiencies of nitrite, nitrate and ammonium were 68.97%, 78.32%, and 98.70%, respectively. Additionally, the maximum growth rate and denitrification capacity of this strain occurred in the presence of 0.05 mg·L−1 of Cu2+.However, the growth and aerobic denitrification capacity were intensively inhibited by Cu2+ at ≥0.1 mg·L−1. Moreover, gas chromatography indicated that a portion of the nitrogen was transformed into N2O when the nitrite, nitrate, and ammonium were separately used as the sole nitrogen source. This is the first study of the nitrification and denitrification ability of Arthrobacter nicotianae under aerobic conditions, and the first experiment to investigate the impact of Cu2+ concentration on the growth and denitrification ability of this bacteria. The results presented herein extend the known varieties of heterotrophic nitrifying–aerobic denitrifying bacteria and provide useful information regarding the specific bacteria for nitrogen bioremediation of industrial wastewater containing Cu2+.