Transcriptional and metabolic response against hydroxyethane-(1,1-bisphosphonic acid) on bacterial denitrification by a halophilic Pannonibacter sp. strain DN

Direct ammonia oxidation (Dirammox) is favored over cell growth in Alcaligenes ammonioxydans HO-1 to deal with the toxicity of ammonium

Bacteria capable of direct ammonia oxidation (Dirammox) play important roles in global nitrogen cycling and nutrient removal from wastewater. Dirammox process, NH3  → NH2 OH → N2 , first defined in Alcaligenes ammonioxydans HO-1 and encoded by dnf gene cluster, has been found to widely exist in aquatic environments. However, because of multidrug resistance in Alcaligenes species, the key genes involved in the Dirammox pathway and the interaction between Dirammox process and the physiological state of Alcaligenes species remain unclear. In this work, ammonia removal via the redistribution of nitrogen between Dirammox and microbial growth in A. ammonioxydans HO-1, a model organism of Alcaligenes species, was investigated. The dnfA, dnfB, dnfC, and dnfR genes were found to play important roles in the Dirammox process in A. ammonioxydans HO-1, while dnfH, dnfG, and dnfD were not essential genes. Furthermore, an unexpected redistribution phenomenon for nitrogen between Dirammox and cell growth for ammonia removal in HO-1 was revealed. After the disruption of the Dirammox in HO-1, more consumed NH4 + was recovered as biomass-N via rapid metabolic response and upregulated expression of genes associated with ammonia transport and assimilation, tricarboxylic acid cycle, sulfur metabolism, ribosome synthesis, and other molecular functions. These findings deepen our understanding of the molecular mechanisms for Dirammox process in the genus Alcaligenes and provide useful information about the application of Alcaligenes species for ammonia-rich wastewater treatment.

Biotransformation of benzo[a]pyrene by Pannonibacter sp. JPA3 and the degradation mechanism through the initially oxidized benzo[a]pyrene-4,5-dihydrodiol to downstream metabolites

Owing to its adverse effects on the environment and human health, benzo[a]pyrene (BaP) has attracted considerable attention and has been used as a model compound in ecotoxicology. In this study, Pannonibacter sp. JPA3 as a BaP-degrading strain was isolated from the production water of an oil well. The strain could remove 80% of BaP at an initial concentration of 100 mg L^-1 after 35 d culture. The BaP-4,5-dihydrodiol, BaP-4,5-epoxide, 5-hydroxychrysene, and 2-hydroxy-1-naphthoic acid metabolites were identified in the biodegradation process. Simultaneously, the gene sequence coding for dioxygenase in the strain was amplified and a dioxygenase model was built by homology modeling. Combined with the identification of the metabolites, the interaction mechanism of BaP with dioxygenase was investigated using molecular docking. It was assumed that BaP was initially oxidized at the C₄-C₅ positions in the active cavity of dioxygenase. Moreover, a hypothesis for the progressive degradation mechanism of BaP by this strain was proposed via the identification of the downstream metabolites. In conclusion, our study provided an efficient BaP degrader and a comprehensive reference for the study of the degradation mechanism in terms of the degrading metabolites and theoretical research at the molecular level.

Employing conductive carrier for establishing spontaneous microbial galvanic cell and accelerating denitrification

It is well-known that metal corrosion is accelerated by formation of galvanic cell. In this study, we reported the acceleration of denitrification by using conductive carrier through formation of microbial galvanic cell (MGC). Electrically conductive graphite plate (GP) was used as biofilm carrier and compared with the non-conductive polypropylene (PP) plate carrier. Cyclic voltametric analyses showed that biofilms with bidirectional electron transfer functions of bioelectrochemical denitrification (BEDN) and acetate oxidation could be enriched spontaneously onto the GP carrier, hinting the establishment of MGC. Further analysis using differential pulse voltammetry revealed that the redox mediator related to extracellular electron transfer was detected in both media of the GP and PP carrier. Microbial community analysis showed that the biofilms in both GP and PP carrier had identical microbial composition but varied in abundance. The genus of Comamonas, Pseudomonas, Paracoccus and Thauera were the dominance of electroactive denitrifiers responsible for BEDN in both the GP and PP carrier. The GP carrier had a 75.9% higher abundant enrichment of electroactive denitrifiers than the PP carrier. Denitrification performance analyses showed that the GP carrier had a denitrification rate constant (k_DN) of 1.25 and 2.66 h^-1 at 15 °C and 30 °C, respectively, which was nearly 76.1% and 92.7% higher than the non-conductive PP carrier with corresponding values of about 0.71 and 1.38 h^-1. Further, the result of conductive carrier accelerating denitrification was confirmed in scaled-up denitrification bioreactors with volume of 104 L using brush-like biofilm carriers. The acceleration of denitrification was attributed to the spontaneously established MGC, which promoted the direct and mediated electron transfer of the electroactive denitrifiers grown onto the conductive carriers and speeded up the BEDN. The result of this study demonstrated that the BEDN could be integrated to traditional biological denitrification system to accelerate denitrification in the form of MGC by simply employment of conductive carrier.

Simultaneous removal of aromatic pollutants and nitrate at high concentrations by hypersaline denitrification:Long-term continuous experiments investigation

If we can use toxic aromatic compounds as supplementary carbon source, the simultaneous removal of nitrate (NO₃^-) and aromatic compounds may be achieved at much lower chemical costs. This study uses the expanded granular sludge bed (EGSB) reactors to investigate the hypersaline (> 3%) denitrification performance, the removal of aromatic compounds, i.e., aniline, phenol, and their mixture, and the mechanisms involved in. The four reactors exhibit high removal efficiency of NO₃^- (> 92.8%) and aromatic compounds (> 73.9%) at 0-1200 mg/L of aromatic compounds. The formation of toxic intermediates such as catechol and azo dyes is revealed by gas chromatography mass spectrometry (GC-MS) with and without N,O-Bis(trimethylsilyl) trifluoroacetamide (BSTFA) derivation, and their toxic effects lead to the lower cell survival ratios after exposing to phenol (64.2% ∼ 68.9%) than to aniline and mixture (72.7% ∼ 78.0%). The stable performance is associated with the more secretion of extracellular polymeric substances (EPS) and the adsorption of pollutants on EPS, and this was indicated from the higher fluorescence intensity in three-dimensional excitation-emission matrix (3D-EEM). Moreover, the Halomonas and Azoarcus show high abundance and play important roles in the removal of both NO₃^- and aromatic compounds. Besides, quantitative real time PCR (RT-qPCR) results demonstrate the key role of highly abundant nosZ and nirS genes in denitrification. The toxic organics in industrial wastewaters are potentially feasible carbon sources for denitrification even under high-salinity stress.

Response of the aerobic denitrifying phosphorus accumulating bacteria Pseudomonas psychrophila HA-2 to low temperature and zinc oxide nanoparticles stress

Performance and molecular changes of an aerobic denitrifying phosphorus accumulating bacteria Pseudomonas psychrophila HA-2 have been investigated under different temperatures and ZnO nanoparticles (NPs) exposures. Strain HA-2 removed 95.7% of total nitrogen (TN) and 24.6% of phosphorus at 10 °C, which was attributed to the joint up-regulation of intracellular energy metabolism and ribosome. Moreover, with the increase of ZnO NPs from 0 to 100 mg/L, TN and phosphurs removal efficiencies decreased from 95.7% to 44.5% and 24.6% to 6.8% at 10 °C, respectively, whereas phosphorus removal rate increased from 10.5% to 24.5% at 20 °C. Further transcriptomics and proteomics revealed that significant down-regulation of purine and amino acid metabolisms was the main reason for the inhibitory effect at 10 °C, while the up-regulation of antioxidant pathways and functional genes expressions was responsible for the promoted phosphorus accumulation at 20 °C. This study provides a potential solution for improving biological nutrients removal processes in winter months.

Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification

Aerobic denitrification has been proved to be profoundly affected by temperature and antibiotics, but little is known about how aerobic denitrifiers respond to temperature and antibiotic stress. In this study, the nitrate reduction performance and the intracellular metabolism by a psychrotolerant aerobic denitrifying bacteria, named Pseudomonas psychrophila RNC-1, were systematically investigated at different temperatures (10 °C, 20 °C, 30 °C) and different sulfamethoxazole (SMX) concentrations (0 mg/L, 0.1 mg/L, 0.5 mg/L, 1.0 mg/L, and 5.0 mg/L). The results showed that strain RNC-1 performed satisfactory nitrate removal at 10 °C and 20 °C, but its growth was significantly inhibited at 30 °C. Nitrate removal by strain RNC-1 was slightly promoted in the presence of 0.5 mg/L SMX, whereas it was significantly suppressed with 5.0 mg/L SMX. Nitrogen balance analysis indicated that assimilatory nitrate reduction and dissimilatory aerobic denitrification jointly dominated in the nitrate removal process of strain RNC-1, in which the inhibition effected on assimilation process was much higher than that on the aerobic denitrification process under SMX exposure. Further transcriptomics and proteomics analysis revealed that the psychrotolerant mechanism of strain RNC-1 could be attributed to the up-regulation of RNA translation, energy metabolism, ABC transporters and the over-expression of cold shock proteins, while the down-regulation of oxidative phosphorylation pathway was the primary reason for the deteriorative cell growth at 30 °C. The promotion of nitrate reduction with 0.5 mg/L SMX was related to the up-regulation of amino acid metabolism pathways, while the down-regulation of folate cycle, glycolysis/gluconeogenesis and bacterial chemotaxis pathways were responsible for the inhibition effect at 5.0 mg/L SMX. This work provides a mechanistic understanding of the metabolic adaption of strain RNC-1 under different stress, which is of significance for its application in nitrogen contaminated wastewater treatment processes.

Enhanced thermophilic denitrification performance and potential microbial mechanism in denitrifying granular sludge system

Thermophilic biological nitrogen removal will provide low-cost strategies for the treatment of high-temperature nitrogenous wastewater (greater than 45 ℃). In this study, a thermophilic denitrifying granular sludge system was established at 50 ℃ and compared with mesophilic systems (30 ℃ and 40 ℃). The results showed a significant increase in COD and nitrate removal rate with the elevating temperature. Besides, the microbial community analysis indicated an obvious succession of key functional bacteria at different temperatures. Enriched thermophiles including Truepera, Azoarcus, and Elioraea were the dominant denitrifiers in the thermophilic denitrifying granular sludge system, which ensured the high nitrate removal at 50 ℃. Moreover, the functional gene prediction also denoted an enrichment of nitrate reduction genes and carbon metabolism pathways at 50 ℃, which could explain the enhancement of thermophilic denitrification. These findings could provide new insight into the application of denitrifying granular sludge in thermophilic wastewater treatment.

Effects of Malic Acid and Sucrose on the Fermentation Parameters, CNCPS Nitrogen Fractions, and Bacterial Community of Moringa oleifera Leaves Silage

The present study investigated the effects of malic acid, sucrose, and their mixture on the fermentation parameters, Cornell Net Carbohydrate and Protein System (CNCPS) nitrogen fractions, and bacterial community of Moringa oleifera leaves (MOL) silages. The trial was divided into four treatments and labeled as CON (control group) and MLA, SUC, and MIX (respectively denoting the addition of 1% malic acid, 1% sucrose, and 1% malic acid + 1% sucrose to the fresh weight basis). The silage packages were opened on the 2nd, 5th, 10th, 20th, and 40th days of ensiling for subsequent determination. Malic acid and sucrose increased the lactic acid content (p < 0.05) and pH value, and the acetic acid contents of MLA and MIX were lower than those in CON (p < 0.05). Compared with sucrose, malic acid had a better capacity to preserve nutrients and inhibit proteolysis, and thus exerted better effects on the CNCPS nitrogen fractions. The results of 16S rRNA showed that the dominant phyla were Firmicutes and Proteobacteria and that the dominant genera were Lactobacillus and Weissella. With the application of silage additives and the processing of fermentation, there was a remarkable change in the composition and function of the bacterial community. The variation of the fermentation parameters and CNCPS nitrogen fractions in the MOL silages caused by malic acid and sucrose might be attributed to the dynamic and dramatic changes of the bacterial community.

Response characteristics of nirS-type denitrifier Paracoccus denitrificans under florfenicol stress

Florfenicol (FF) is widely used in aquaculture and can interfere with denitrification when released into natural ecosystems. The aim of this study was to analyze the response characteristics of nirS-type denitrifier Paracoccus denitrificans under FF stress and further mine antibiotic-responsive factors in aquatic environment. Phenotypic analysis revealed that FF delayed the nitrate removal with a maximum inhibition value of 82.4% at exponential growth phase, leading to nitrite accumulation reached to 21.9-fold and biofilm biomass decreased by ~38.6%, which were due to the lower bacterial population count (P < 0.01). RNA-seq transcriptome analyses indicated that FF treatment decreased the expression of nirS, norB, nosD and nosZ genes that encoded enzymes required for NO₂^- to N₂ conversion from 1.02- to 2.21-fold (P < 0.001). Furthermore, gene associated with the flagellar system FlgL was also down-regulated by 1.03-fold (P < 0.001). Moreover, 10 confirmed sRNAs were significantly induced, which regulated a wide range of metabolic pathways and protein expression. Interestingly, different bacteria contained the same sRNAs means that sRNAs can spread between them. Overall, this study suggests that the denitrification of nirS-type denitrifiers can be hampered widely by FF and the key sRNAs have great potential to be antibiotic-responsive factors.

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.