Cysteine reduced the inhibition of CO2 on heterotrophic denitrification: Restoring redox balance, facilitating iron acquisition and carbon metabolism

Photoaffinity probe-enabled discovery of sennoside A reductase in Bifidobacterium pseudocatenulatum

Sennoside A (SA), a typical prodrug, exerts its laxative effect only after its transformation into rheinanthrone catalyzed by gut microbial hydrolases and reductases. Hydrolases have been identified, but reductases remain unknown. By linking a photoreactive group to the SA scaffold, we synthesized a photoaffinity probe to covalently label SA reductases and identified SA reductases using activity-based protein profiling (ABPP). From lysates of an active strain, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum), 397 proteins were enriched and subsequently identified using mass spectrometry (MS). Among these proteins, chromate reductase/nicotinamide adenine dinucleotide (NADH) phosphate (NADPH)-dependent flavin mononucleotide (FMN) reductase/oxygen-insensitive NADPH nitroreductase (nfrA) was identified as a potent SA reductase through further bioinformatic analysis and The Universal Protein Resource (UniProt) database screening. We also determined that recombinant nfrA could reduce SA. Our study contributes to further illuminating mechanisms of SA transformation to rheinanthrone and simultaneously offers an effective method to identify gut bacterial reductases.

The Effect of Cysteine on the Removal of Cadmium in Paddy Soil by Combination with Bioremediation and the Response of the Soil Microbial Community

Bioremediation is widely recognized as a promising and efficient approach for the elimination of Cd from contaminated paddy soils. However, the Cd removal efficacy achieved through this method remains unsatisfactory and is accompanied by a marginally higher cost. Cysteine has the potential to improve the bioleaching efficiency of Cd from soils and decrease the use cost since it is green, acidic and has a high Cd affinity. In this study, different combination modes of cysteine and microbial inoculant were designed to analyze their effects on Cd removal and the soil microbial community through the sequence extraction of Cd fraction and high-throughput sequencing. The results demonstrate that the mixture of cysteine and the microbial inoculant was the best mode for increasing the Cd removal efficiency. And a ratio of cysteine to microbial inoculant of 5 mg:2 mL in a 300 mL volume was the most economically efficient matching. The Cd removal rate increased by 7.7-15.1% in comparison with the microbial inoculant treatment. This could be ascribed to the enhanced removal rate of the exchangeable and carbonate-bound Cd, which achieved 94.6% and 96.1%, respectively. After the treatment, the contents of ammonium nitrogen (NH3-N), total phosphorus (TP), available potassium (AK), and available phosphorus (AP) in the paddy soils were increased. The treatment of combinations of cysteine and microbial inoculant had an impact on the soil microbial diversity. The relative abundances of Alicyclobacillus, Metallibacterium, and Bacillus were increased in the paddy soils. The microbial metabolic functions, such as replication and repair and amino acid metabolism, were also increased after treatment, which benefitted the microbial survival and adaptation to the environment. The removal of Cd was attributed to the solubilizing, complexing, and ion-exchanging effects of the cysteine, the intra- and extracellular adsorption, and the production of organic acids of functional microorganisms. Moreover, cysteine, as a carbon, nitrogen, and sulfur source, promoted the growth and metabolism of microorganisms to achieve the effect of the synergistic promotion of microbial Cd removal. Therefore, this study underscored the potential of cysteine to enhance the bioremediation performance in Cd-contaminated paddy soils, offering valuable theoretical and technical insights for this field.

How denitrifiers defense ciprofloxacin: Insights from intracellular and extracellular stress response

Overuse of antibiotics has led to their existence in nitrogen-containing water. The impacts of antibiotics on bio-denitrification and the metabolic response of denitrifiers to antibiotics are unclear. We systematically analyzed the effect of ciprofloxacin (CIP) on bio-denitrification and found that 5 mg/L CIP greatly inhibited denitrification with a model denitrifier (Paracoccus denitrificans). Nitrate reduction decreased by 32.89 % and nitrous oxide emission increased by 75.53 %. The balance analysis of carbon and nitrogen metabolism during denitrification showed that CIP exposure blocked electron transfer and reduced the flow of substrate metabolism used for denitrification. Proteomics results showed that CIP exposure induced denitrifiers to use the pentose phosphate pathway more for substrate metabolism. This caused a substrate preference to generate NADPH to prevent cellular damage rather than NADH for denitrification. Notably, despite denitrifiers having antioxidant defenses, they could not completely prevent oxidative damage caused by CIP exposure. The effect of CIP exposure on denitrifiers after removal of extracellular polymeric substances (EPS) demonstrated that EPS around denitrifiers formed a barrier against CIP. Fluorescence and infrared spectroscopy revealed that the binding effect of proteins in EPS to CIP prevented damage. This study shows that denitrifiers resist antibiotic stress through different intracellular and extracellular defense strategies.

Insights into the Acceleration Mechanism of Intracellular N and Fe Co-doped Carbon Dots on Anaerobic Denitrification Using Proteomics and Metabolomics Techniques

Bulk carbon-based materials can enhance anaerobic biodenitrification when they are present in extracellular matrices. However, little information is available on the effect of nitrogen and iron co-doped carbon dots (N, Fe-CDs) with sizes below 10 nm on this process. This work demonstrated that Fe-NX formed in N, Fe-CDs and their low surface potentials facilitated electron transfer. N, Fe-CDs exhibited good biocompatibility and were effectively absorbed by Pseudomonas stutzeri ATCC 17588. Intracellular N, Fe-CDs played a dominant role in enhancing anaerobic denitrification. During this process, the nitrate removal rate was significantly increased by 40.60% at 11 h with little nitrite and N2O accumulation, which was attributed to the enhanced activities of the electron transport system and various denitrifying reductases. Based on proteomics and metabolomic analysis, N, Fe-CDs effectively regulated carbon/nitrogen/sulfur metabolism to induce more electron generation, less nitrite/N2O accumulation, and higher levels of nitrogen removal. This work reveals the mechanism by which N, Fe-CDs enhance anaerobic denitrification and broaden their potential application in nitrogen removal.

Simultaneously enhanced autotrophic-heterotrophic denitrification in iron-based ecological floating bed by plant biomass: Metagenomics insights into microbial communities, functional genes and nitrogen metabolic pathways

In this study, the ecological floating bed supporting with zero-valent iron (ZVI) and plant biomass (EFB-IB) was constructed to improve nitrogen removal from low-polluted water. The effects of ZVI coupling with plant biomass on microbial community structure, metabolic pathways and functional genes were analyzed by metagenomic sequencing, and the mechanism for nitrogen removal was revealed. Results showed that compared with mono-ZVI system (EFB-C), the denitrification efficiencies of EFB-IB were effectively enhanced, with the higher average NO3--N removal efficiencies of 22.60-59.19%. Simultaneously, the average NH4+-N removal efficiencies were 73.08-91.10%. Metagenomic analyses showed that EFB-IB enriched microbes that involved in iron cycle, lignocellulosic degradation and nitrogen metabolism. Plant biomass addition simultaneously increased the relative abundances of autotrophic and heterotrophic denitrifying bacteria. Network analysis showed the cooperation between autotrophic and heterotrophic denitrifying bacteria in EFB-IB. Moreover, compared with EFB-C, plant biomass addition increased the relative abundances of genes related to iron cycle, lignocellulose degradation and glycolysis processes, ensuring the production of autotrophic and heterotrophic electron donors. Therefore, the relative abundances of key enzymes and functional genes related to denitrification were higher in EFB-IB, being beneficial to the NO3--N removal. Additionally, the correlation analysis of nitrogen removal and functional genes verified the synergistic mechanism of iron-based autotrophic denitrification and plant biomass-mediated heterotrophic denitrification in EFB-IB. In summary, plant biomass has excellent potential to improve the nitrogen removal of iron-based EFB from low-polluted water.

CO2 uptake in ethanol-driven chain elongation system: Microbial metabolic mechanisms

CO2 as a byproduct of organic waste/wastewater fermentation has an important impact on the carboxylate chain elongation. In this study, a semi-continuous flow reactor was used to investigate the effects of CO2 loading rates (Low = 0.5 LCO2·L-1·d-1, Medium = 1.0 LCO2·L-1·d-1, High = 2.0 LCO2·L-1·d-1) on chain elongation system Ethanol and acetate were utilized as the electron donor and electron acceptor, respectively. The results demonstrate that low loading rate of CO2 has a positive effect on chain elongation. The maximum production of caproate and CH4 were observed at a low CO2 loading rate. Caproate production reached 1.88 g COD·L-1·d-1 with a selectivity of 62.55 %, while CH4 production reached 129.7 ml/d, representing 47.4 % of the total. Metagenomic analysis showed that low loading rate of CO2 favored the enrichment of Clostridium kluyveri, with its abundance being 3.8 times higher than at of high CO2 loading rate. Metatranscriptomic analysis revealed that high CO2 loading rate induced oxidative stress in microorganisms, as evidenced by increased expression of heat shock proteins and superoxide dismutase genes. Further investigation suggested that genes associated with the reverse β-oxidation pathway, CO2 uptake pathway and hydrogenotrophic methanogenesis pathway were reduced at high CO2 loading rate. These findings provide insight into the underlying mechanisms of how CO2 affects chain elongation, and it could be a crucial reason for the poor performance of chain elongation systems with high endogenous CO2 production.

Attenuation effects of ZVI/PDS pretreatment on propagation of antibiotic resistance genes in bioreactors: Driven by antibiotic residues and sulfate assimilation

Sulfate radical-based advanced oxidation processes (AOPs) combined biological system was a promising technology for treating antibiotic wastewater. However, how pretreatment influence antibiotic resistance genes (ARGs) propagation remains largely elusive, especially the produced by-products (antibiotic residues and sulfate) are often ignored. Herein, we investigated the effects of zero valent iron/persulfate pretreatment on ARGs in bioreactors treating sulfadiazine wastewater. Results showed absolute and relative abundance of ARGs reduced by 59.8%- 81.9% and 9.1%- 52.9% after pretreatments. The effect of 90-min pretreatment was better than that of the 30-min. The ARGs reduction was due to decreased antibiotic residues and stimulated sulfate assimilation. Reduced antibiotic residues was a major factor in ARGs attenuation, which could suppress oxidative stress, inhibit mobile genetic elements emergence and resistant strains proliferation. The presence of sulfate in influent supplemented microbial sulfur sources and facilitated the in-situ synthesis of antioxidant cysteine through sulfate assimilation, which drove ARGs attenuation by alleviating oxidative stress. This is the first detailed analysis about the regulatory mechanism of how sulfate radical-based AOPs mediate in ARGs attenuation, which is expected to provide theoretical basis for solving concerns about by-products and developing practical methods to hinder ARGs propagation.

How β-Cyclodextrin-Functionalized Biochar Enhanced Biodenitrification in Low C/N Conditions via Regulating Substrate Metabolism and Electron Utilization

Biodenitrification plays a vital role in the remediation of nitrogen-contaminated water. However, influent with a low C/N ratio limits the efficiency of denitrification and causes the accumulation/emission of noxious intermediates. In this study, β-cyclodextrin-functionalized biochar (BC@β-CD) was synthesized and applied to promote the denitrification performance of Paracoccus denitrificans when the C/N was only 4, accompanied by increased nitrate reduction efficiency and lower nitrite accumulation and nitrous oxide emission. Transcriptomic and enzymatic activity analyses showed BC@β-CD enhanced glucose degradation by promoting the activities of glycolysis (EMP), the pentose phosphate pathway (PPP), and the tricarboxylic acid (TCA) cycle. Notably, BC@β-CD drove a great generation of electron donors by stimulating the TCA cycle, causing a greater supply of substrate metabolism to denitrification. Meanwhile, the promotional effect of BC@β-CD on oxidative phosphorylation accelerates electron transfer and ATP synthesis. Moreover, the presence of BC@β-CD increased the intracellular iron level, causing further improved electron utilization in denitrification. BC@β-CD helped to remove metabolites and induced positive feedback on the metabolism of P. denitrificans. Collectively, these effects elevated the glucose utilization for supporting denitrification from 36.37% to 51.19%. This study reveals the great potential of BC@β-CD for enhancing denitrification under low C/N conditions and illustrates a potential application approach for β-CD in wastewater bioremediation.

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

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

Responses of soil fertility and microbiomes of atrazine contaminated soil to remediation by hydrochar and persulfate

Peroxydisulfate (PDS) is widely used in field-scale remediation of organically polluted soil, yet PDS is detrimental to the soil microbiome. In this work, sludge-derived hydrochar was used to alleviate the oxidative damage of PDS to the soil ecosystem and simultaneously improve atrazine (ATZ) degradation. Response surfaces showed that ATZ degradation was enhanced with an increased dosage of PDS (regression slope of 24.09) and hydrochar (regression slope of 4.19). In contrast, bacterial abundance was negatively related to PDS dosage but positively to hydrochar dosage. At the optimum dosage of PDS (2.21% dry weight of soil) and hydrochar (5% dry weight of soil), ATZ degradation reached 95.31%, and bacterial abundance recovered to 7.72 log gene copy number g^-1 soil (versus 8.44 in raw soil). Hydrochar alleviated the negative impacts of PDS on soil fertility such as urease activity. High PDS dosages (3% dry weight of soil) facilitated the proliferation of Halomonas, while moderate dosages (1.5% dry weight of soil) stimulated Alicyclobacillus. Hydrochar facilitated the growth of functional genera like Comamonas, Cloacibacterium, and Terrabacter. ATZ degradation pathway was positively correlated with Bacillus and nitrogen metabolism pathway. Hydrochar mediated intracellular reactive oxidative species scavenger reactions in catalase activity, allowing microbial survival under harsh oxidative conditions due to PDS addition.