Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

Characteristics of microplastics in typical poultry farms and the association of environment microplastics colonized-microbiota, waterfowl gut microbiota, and antibiotic resistance genes

Microplastics (MPs) pollution is a growing global environmental concern. MPs serve as ecological niches for microbial communities, which may accelerate the spread of antibiotic resistance genes (ARGs), posing risks to the breeding industry. While studies on MPs in aquatic organisms are common, research on farmed poultry is limited. This study investigates MPs in poultry farm environments and waterfowl intestines for the first time. MPs were isolated via density separation and analyzed for characterization in soil, pond water, and waterfowl intestines. Metagenomics was used to investigate the association between environment MPs colonized-microbiota and waterfowl gut microbiota. Our findings reveal that MPs are abundant in soil (6.75 ± 2.78 items/g d.w.), pond water (0.94 ± 0.28 items/g w.w.), and poultry intestines (45.35 ± 19.52 items/g w.w.), primarily appearing as fragmented particles sized 20-50 μm. MPs abundance in intestines correlates with environmental levels. Colonized-microbiota on MPs are linked to poultry intestinal microbiota, with greater diversity and microbial functions. Network analysis reveals that Corynebacterium plays a key role in MPs and poultry intestinal. Polymyxin resistance exhibits high clustering. Procrustes analysis reveals correlations between MPs, bacteria, and ARGs in the farming environment. Overall, MPs in poultry farms may facilitate pathogen and ARGs transmission, posing risks to animal gut health.

Metagenome-Assembled Genomes and Metatranscriptome Analysis of Perfluorooctane Sulfonate-Reducing Bacteria Enriched From Activated Sludge

Per- and polyfluoroalkyl substances (PFAS) exhibit a widespread distribution across diverse global ecosystems throughout their lifecycle, posing substantial risks to human health. The persistence of PFAS makes biodegradation a challenging yet environmentally friendly solution for their treatment. In the authors' previous study, a bacterial consortium capable of reducing perfluorooctane sulfonate (PFOS) was successfully enriched from activated sludge. This study aimed to investigate the array of genes associated with PFOS reduction via biosorption and biotransformation to elucidate the metabolic pathways. Two metagenome-assembled genomes (MAGs) based on 16S rRNA sequences that share 99.86% and 97.88% similarity with Hyphomicrobium denitrificans and Paracoccus yeei, respectively were obtained. They were found to contain several genes encoding enzymes that potentially regulate biofilm formation of biosorption and facilitate the desulfonation and defluorination processes of biotransformation. Transcriptomic analysis demonstrated the high expression levels of these genes, including alkanesulfonate monooxygenase, catechol dioxygenase, (S)-2-haloacid dehalogenase and putative cytochrome P450, suggesting their involvement in PFOS biotransformation. The expression of these genes supports the presence of candidate metabolites of PFOS biotransformation detected in the previous study. These findings emphasise the significant potential of bacterial consortia and the crucial role played by genes encoding enzymes in facilitating the remediation of PFOS contaminants.

Development of multifunctional immobilized bacterial agents for multi-pesticides degradation and environment remediation

The proliferation of weeds, pests, and plant diseases in crop cultivation has driven the increased application of herbicide lactofen, insecticide acetamiprid, and fungicide carbendazim, contributing to environmental pollution. Microorganisms are requently employed to remove pesticide residues from the environment. However, Liquid bacterial agents encounter difficulties in transportation and preservation during application and the current immobilized bacterial agents have a single degradation function. This study developed immobilized bacterial agents containing the lactofen-degrading strain Bacillus sp. Za, the acetamiprid-degrading strain Pigmentiphaga sp. D-2, and the carbendazim-degrading strain Rhodococcus sp. djl-6. Preparation conditions, including activated carbon concentration, sodium alginate (SA), CaCl2, and immobilization time, were optimized using the response surface method (RSM). The degradation performance of the immobilized bacteria was evaluated, with degradation rates exceeding 70% for all three pesticides under conditions of 30 °C, pH 7.0, and 6% inoculation over 48 h. The immobilized bacterial agents were stored at pH 7.0 and 4 °C for 180 days, maintaining a preservation rate of 51.26% with a viable cell count of 1.04 × 108 CFU/g. These agents effectively remediated soil and water contaminated with multi-pesticides, achieving degradation rates of 92.50% and 98.50% for lactofen, 91.05% and 99.89% for acetamiprid, 88.43% and 98.99% for carbendazim within 21 in soil and 7 days in water, respectively. This study provides essential technical support for developing microbial agents capable of degrading multi-pesticides residues, with significant potential applications in agriculture and environmental protection.

Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs

Shifts in host-associated microbiomes can impact both host and microbes.1,2,3,4,5,6 It is of interest to understand how perturbations, like the introduction of exogenous chemicals,7,8,9,10,11,12,13 impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.14,15,16,17,18,19 These alkaloids are antimicrobial20,21,22; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.

Cooperation Between Rhodococcus qinshengii and Rhodococcus erythropolis for Carbendazim Degradation

Carbendazim (CBZ) is a fungicide widely used on different crops, including soybeans, cereals, cotton, tobacco, peanuts, and sugar beet. Excessive use of this xenobiotic causes environmental deterioration and affects human health. Microbial metabolism is one of the most efficient ways of carbendazim elimination. In this work, Rhodococcus qingshengii RC1 and Rhodococcus erythropolis RC9 were isolated from a bacterial community growing in a biofilm reactor acclimated with microbiota from carbendazim-contaminated soil. Sequencing analysis of genomes of both strains revealed the presence of cbmA, the gene coding for the enzyme that hydrolyses carbendazim to produce 2-aminobenzimidazole (2-AB). The alternative gene for the first catabolic step (mheI) was detected by PCR in strain RC9 but not in RC1. Metabolomic analysis by HPLC and LC-MS showed that both strains have the ability to metabolize carbendazim. R. qingshengii RC1 converts carbendazim to 2-AB, the first degradation intermediary, while R. erythropolis RC9 metabolizes the fungicide to its mineralization, probably because R. qingshengii RC1 lacks the hdx gene coding for 2-AB hydroxylase. HRESIMS-MS/MS results indicate that R. erythropolis RC9 metabolizes carbendazim by cleavage of the benzene ring and subsequent formation of 5-formyl-2-hydroxy-4,5-dihydro-1H-imidazole-4-carboxylic acid (X2 C5H6N2O4). The presence of carbendazim metabolites in culture supernatants of strains RC9 and RC1 suggests that both strains contribute to the efficient degradation of carbendazim in nature.

Construction of a synthetic anaerobic dechlorination microbiome to degrade chlorinated ethenes by application of metabolic interactions principle

Bioaugmentation is a bioremediation approach to treat groundwater contaminated with chlorinated ethenes, but currently it faces challenges such as poor microbiome stability and effectiveness, due to blind species integration and metabolic inhibition. The objective of this study was to create a controllable and functionally stable microbial community for dichlorination application. For this, we utilized targeted screening to identify dechlorinating bacteria from contaminated groundwater, that in combination would form an anaerobic dechlorination microbial community with stabilizing metabolic interactions between the constituents. The results showed that two organohalide-respiring bacterial (OHRB) species were isolated, and these were identified as Enterobacter bugandensis X4 and Enterobacter sichuanensis C4. Upon co-cultivation with lactic acid as the carbon source, the strains demonstrated metabolic interactions and synergistic dehalogenation ability towards trichloroethene (TCE). It was further demonstrated that the functional microbiome constructed with the strains was stable over time and exhibited a robust TCE degradation rate of 80.85% at 13.13 mg/L TCE within 10 days. Additionally, the complete conversion of TCE was achieved through microbiome bioaugmentation, this augmented microbiome increased the degradation rate towards 52.55 mg/L TCE by approximately 30% within 6 days. Additionally, bioaugmentation stimulated the growth of indigenous OHRB, such as Dehalobacter and Desulfovibrio. It also promoted a positive succession of the microbial community. These findings offer valuable insights into the microbial remediation of chlorinated ethenes-contaminated groundwater and offers novel ideas for the construction of an artificial functional microbiome.

Molecular Mechanism of Mok I Gene Overexpression in Enhancing Monacolin K Production in Monascus pilosus

Monascus species are capable of producing various active metabolites, including monacolin K (MK) and pigments. Studies have shown that the overexpression of the mok I gene from the MK synthesis gene cluster in Monascus species can significantly increase MK production; however, the molecular mechanism has not yet been fully elucidated. Therefore, this study focused on the mok I gene of Monascus pilosus to construct overexpression strains of the mok I gene, resulting in high-yield MK production. Sixteen positive transformants were obtained, seven of which produced 9.63% to 41.39% more MK than the original strain, with no citrinin detected in any of the transformants. The qRT-PCR results revealed that the expression levels of mok I in the transformed strains TI-13, TI-24, and TI-25 increased by more than 50% compared to the original strain at various fermentation times, with the highest increase being 10.9-fold. Furthermore, multi-omics techniques were used to analyze the molecular mechanisms underlying enhanced MK production in transformed strains. The results indicated that mok I overexpression may enhance MK synthesis in M. pilosus by regulating the expression of key genes (such as MAO, HPD, ACX, and PLC) and the synthesis levels of key metabolites (such as delta-tocopherol and alpha-linolenic acid) in pathways linked to the biosynthesis of cofactors, the biosynthesis of unsaturated fatty acids, tyrosine metabolism, ubiquinone and other terpenoid-quinone biosynthesis, alpha-linolenic acid metabolism, and glycerophospholipid metabolism. These findings provide a theoretical basis for further study of the metabolic regulation of MK in Monascus species and for effectively enhancing their MK production.

Removal of chlorimuron-ethyl from the environment: The significance of microbial degradation and its molecular mechanism

Chlorimuron-ethyl is a selective pre- and post-emergence herbicide, which is widely used to control broad-leaved weeds in soybean fields. However, herbicide residues have also increased as a result of the pervasive use of chlorimuron-ethyl, which has become a significant environmental concern. Consequently, the removal of chlorimuron-ethyl residues from the environment has garnered significant attention in recent decades. A variety of technologies have been developed to address this issue, including adsorption, aqueous chlorination, photodegradation, Fenton, photo-Fenton, ozonation, and biodegradation. After extensive studies, the biodegradation of chlorimuron-ethyl by microorganisms has now been recognized as an efficient and environmentally friendly degradation process. As research has progressed, a number of microbial strains associated with chlorimuron-ethyl degradation have been identified, such as Pseudomonas sp., Klebsiella sp., Rhodococcus sp., Stenotrophomonas sp., Aspergillus sp., Hansschlegelia sp., and Enterobacter sp. In addition, the enzymes and genes responsible for chlorimuron-ethyl biodegradation are also being investigated. These degradation genes include sulE, pnbA, carE, gst, Kj-CysJ, Kj-eitD-2267, Kj-kdpD-226, Kj-dxs-398, Kj-mhpC-2096, and Kj-mhpC-2289, among others. The degradation enzymes associated with chlorimuron-ethyl biodegradation includes esterases (SulE, PnbA, and E3), carboxylesterase (CarE), Cytochrome P450, flavin monooxygenase (FMO), and glutathione-S-transferase (GST). Regrettably, few reviews have focused on the microbial degradation and molecular mechanisms of chlorimuron-ethyl. Therefore, this review covers the microbial degradation of chlorimuron-ethyl and its degradation pathways, the molecular mechanism of the microbial degradation of chlorimuron-ethyl, and the outlook on the practical application of the microbial degradation of sulfonylurea herbicides are all covered in this review's overview of previous studies into the degradation of chlorimuron-ethyl.

Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains

Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm2 (or 1.68•105 CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm2 (± 2.46•104 CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.

Current insights into environmental acetochlor toxicity and remediation strategies

Acetochlor is a selective pre-emergent herbicide that is widely used to control annual grass and broadleaf weeds. However, due to its stable chemical structure, only a small portion of acetochlor exerts herbicidal activity in agricultural applications, while most of the excess remains on the surfaces of plants or enters ecosystems, such as soil and water bodies, causing harm to the environment and human health. In recent years, researchers have become increasingly focused on the repair of acetochlor residues. Compared with traditional physical and chemical remediation methods, microorganisms are the most effective way to remediate chemical pesticide pollution, such as acetochlor, because of their rich species, wide distribution, and diverse metabolic pathways. To date, researchers have isolated and identified many high-efficiency acetochlor-degrading strains, such as Pseudomonas oleovorans, Klebsiella variicola, Bacillus subtilus, Rhodococcus, and Methylobacillus, among others. The microbial degradation pathways of acetochlor include dechlorination, hydroxylation, N-dealkylation, C-dealkylation, and dehydrogenation. In addition, the microbial enzymes, including hydrolase (ChlH), debutoxylase (Dbo), and monooxygenase (MeaXY), responsible for acetochlor biodegradation are also being investigated. In this paper, we review the migration law of acetochlor in the environment, its toxicity to nontarget organisms, and the main metabolic methods. Moreover, we summarize the latest progress in the research on the microbial catabolism of acetochlor, including the efficient degradation of microbial resources, biodegradation metabolic pathways, and key enzymes for acetochlor degradation. At the end of the article, we highlight the existing problems in the current research on acetochlor biodegradation, provide new ideas for the remediation of acetochlor pollution in the environment, and propose future research directions.

Metagenome-assembled genomes from enrichment cultures grown on xenobiotic solvents

Microbes play a significant role in the cleanup of xenobiotic contaminants. Based on metagenomes derived from long-term enrichment cultures grown on xenobiotic solvents, we report 166 metagenome-assembled genomes, of which 137 are predicted to be more than 90% complete. These genomes broaden the representation of xenobiotic degraders.

Review of Explosive Contamination and Bioremediation: Insights from Microbial and Bio-Omic Approaches

Soil pollution by TNT(2,4,6-trinitrotoluene), RDX(hexahydro-1,3,5-trinitro-1,3,5-triazacyclohexane), and HMX(octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), resulting from the use of explosives, poses significant challenges, leading to adverse effects such as toxicity and alteration of microbial communities. Consequently, there is a growing need for effective bioremediation strategies to mitigate this damage. This review focuses on Microbial and Bio-omics perspectives within the realm of soil pollution caused by explosive compounds. A comprehensive analysis was conducted, reviewing 79 articles meeting bibliometric criteria from the Web of Science and Scopus databases from 2013 to 2023. Additionally, relevant patents were scrutinized to establish a comprehensive research database. The synthesis of these findings serves as a critical resource, enhancing our understanding of challenges such as toxicity, soil alterations, and microbial stress, as well as exploring bio-omics techniques like metagenomics, transcriptomics, and proteomics in the context of environmental remediation. The review underscores the importance of exploring various remediation approaches, including mycorrhiza remediation, phytoremediation, bioaugmentation, and biostimulation. Moreover, an examination of patented technologies reveals refined and efficient processes that integrate microorganisms and environmental engineering. Notably, China and the United States are pioneers in this field, based on previous successful bioremediation endeavors. This review underscores research's vital role in soil pollution via innovative, sustainable bioremediation for explosives.

Effects of regular zooplankton supplement on the bacterial communities and process performance of biofilm for wastewater treatment

Biofilm processing technologies were widely used for wastewater treatment due to its advantages of low cost and easy management. However, the aging biofilms inevitably decrease the purification efficiency and increase the sludge production, which limited the widely application of biofilms technologies in rural area. In this study, we proposed a novel strategy by introducing high-trophic organisms to prey on low-trophic organisms, and reduce the aged biofilms and enhance treatment efficiencies in rural wastewater treatment. The effect of three typical zooplankton (Paramecium, Daphnia, and Rotifer) supplement on the purification efficiency and biofilm properties in the contact oxidation process were investigated, and the reaction conditions were optimized by an orthogonal experiment. Under optimal conditions, the biofilms weight decreased 67.6%, the oxygen consumption rate of biofilms increased 9.4%, and wastewater treatment efficiency was obviously increased after zooplankton supplement. Microbial sequencing results demonstrated that the zooplankton optimize the contact oxidation process by altering the bacterial genera mainly Diaphorobacter, Thermomonas, Alicycliphilus and Comamonas. This research provides insight into mechanism of the zooplankton supplement in biological contact oxidation process and provides a feasible strategy for improving the rural sewage treatment technology.

Changes in sulfur in soybean rhizosphere soil and the response of microbial flora in a continuous cropping system mediated by Funneliformis mosseae

Soybean is an S-loving crop, and continuous cropping might cause soil sulfur shortage. The primary objectives of this study are to determine whether Funneliformis mosseae (F. mosseae) can enhance the content of available S in S-deficient soil and thereby improve the sulfur utilization rate in soybean. The experiment used Heinong 48 (HN48), a soybean variety with a vast planting area in Heilongjiang Province, and F. mosseae was inoculated in the soil of soybean that had been continuously cropped for 0 and 3 years. The results of the barium sulfur turbidimetric assay show that the sulfur content in the soil and soybean was reduced by continuous cropping and increased by inoculation with F. mosseae; the results of the macro-genome sequencing technology, show that the diversity and abundance of bacteria in the soil was decreased by continuous cropping and increased by inoculation with F. mosseae. The sulfur-oxidizing bacteria (SOB) activity and sulfur-related gene expression levels were lower in the continuous crop group compared to the control group and higher in the F.mosseae-inoculated group compared to the control group. Continuous cropping reduced the sulfur content and ratio of soybean rhizosphere soil, affecting soil flora activity and thus soybean growth; F. mosseae inoculation increased the sulfur content of soybean root-perimeter soil and plants, increased the diversity and abundance of rhizosphere soil microorganisms, increased the expression of genes for sulfur transport systems, sulfur metabolism, and other metabolic functions related to elemental sulfur, and increased the species abundance and metabolic vigor of most SOB. In summary, continuous cropping inhibits soil sulfur uptake and utilization in soybean while the inoculation with F. mosseae can significantly improve this situation. This study offers a theoretical research foundation for using AMF as a bio-fungal agent to enhance soil sulfur use. It also supports the decrease of chemical fertilizers, their substitution, and the protection of native soil.

High-efficiency degradation of methomyl by the novel bacterial consortium MF0904: Performance, structural analysis, metabolic pathways, and environmental bioremediation

Methomyl is a widely used carbamate pesticide, which has adverse biological effects and poses a serious threat to ecological environments and human health. Several bacterial isolates have been investigated for removing methomyl from environment. However, low degradation efficiency and poor environmental adaptability of pure cultures severely limits their potential for bioremediation of methomyl-contaminated environment. Here, a novel microbial consortium, MF0904, can degrade 100% of 25 mg/L methomyl within 96 h, an efficiency higher than that of any other consortia or pure microbes reported so far. The sequencing analysis revealed that Pandoraea, Stenotrophomonas and Paracoccus were the predominant members of MF0904 in the degradation process, suggesting that these genera might play pivotal roles in methomyl biodegradation. Moreover, five new metabolites including ethanamine, 1,2-dimethyldisulfane, 2-hydroxyacetonitrile, N-hydroxyacetamide, and acetaldehyde were identified using gas chromatography-mass spectrometry, indicating that methomyl could be degraded firstly by hydrolysis of its ester bond, followed by cleavage of the C-S ring and subsequent metabolism. Furthermore, MF0904 can successfully colonize and substantially enhance methomyl degradation in different soils, with complete degradation of 25 mg/L methomyl within 96 and 72 h in sterile and nonsterile soil, respectively. Together, the discovery of microbial consortium MF0904 fills a gap in the synergistic metabolism of methomyl at the community level and provides a potential candidate for bioremediation applications.

Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review

Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.

Insights into the Binding Interaction of Catechol 1,2-Dioxygenase with Catechol in Achromobacter xylosoxidans DN002

Microbial remediation has become one of the promising ways to eliminate polycyclic aromatic hydrocarbons (PAHs) pollution due to its efficient enzyme metabolism system. Catechol 1,2-dioxygenase (C12O) is a crucial rate-limiting enzyme in the degradation pathway of PAHs in Achromobacter xylosoxidans DN002 that opens the benzene ring through the ortho-cleavage pathway. However, little attention has been given to explore the interaction mechanism of relevant enzyme-substrate. This study aims to investigate the binding interaction between C12O of strain DN002 and catechol by means of a molecular biological approach combined with homology modeling, molecular docking, and multiple spectroscopies. The removal rate of catechol in the mutant strain of cat A deletion was only 12.03%, compared to the wild-type strain (54.21%). A Ramachandran plot of active site regions of the primary amino acid sequences in the native enzyme showed that 93.5% sequences were in the most favored regions on account of the results of homology modeling, while an additional 6.2% amino acid sequences were found in conditionally allowed regions, and 0.4% in generously allowed regions. The binding pocket of C12O with catechol was analyzed to obtain that the catalytic trimeric group of Tyr164-His224-His226 was proven to be great vital for the ring-opening reaction of catechol by molecular docking. In the native enzyme, binding complexes were spontaneously formed by hydrophobic interactions. Binding constants and thermodynamic potentials from fluorescence spectra indicated that catechol effectively quenched the intrinsic fluorescence of C12O in the C12O/catechol complex via conventional static and dynamic quenching mechanisms of C12O. The results of ultraviolet and visible (UV) spectra, synchronous fluorescence, and circular dichroism (CD) spectra revealed conspicuous changes in the local conformation, and site-directed mutagenesis confirmed the role of predicted key residues during catalysis, wherein His₂₂₆ had a significant effect on catechol utilization by C12O. This is the first report to reveal interactions of C12O with substrate from the molecular docking results, providing the mechanistic understanding of representative dioxygenases involved in aromatic compound degradation, and a solid foundation for further site modifications as well as strategies for the directed evolution of this enzyme.

Persulfate-based strategy for promoted acesulfame removal during sludge anaerobic fermentation: Combined chemical and biological effects

The acesulfame (ACE) degradation in waste activated sludge (WAS) via direct anaerobic fermentation is difficult and the efficient elimination techniques are imperative for the ultimate safe WAS disposal. Persulfate (PS)-based approach was developed to promote the ACE removal during WAS anaerobic fermentation. Results demonstrated the effectiveness of PS-based treatments on ACE degradation, and the ACE removal efficiency was respectively 48.2% and 96.2% in the PS and PS/Fe-treated reactors while it was only 6.0% in the control reactor. Mechanism explorations revealed that the active free radicals (i.e. OH• and SO₄^•-) generated in the PS-based reactors were the key oxidative species for the ACE degradation. However, such effects were interfered by the released soluble substrates (i.e. protein, carbohydrate and inorganic ions) during anaerobic fermentation by competing and/or quenching free radicals, which caused the deceleration of the ACE removal efficiency. Moreover, the PS-based treatment facilitated the enrichment of functional microorganisms (i.e. Phyllobacteriaceae and Bradyrhizobiaceae) and upregulated the critical genes (i.e. pncB and nadE) involved in the ACE degradation. Based on the density functional theory (DFT) and metabolic intermediates analysis, the hydroxylation and oxidative ring-opening were the two main proposed metabolic pathways for ACE degradation. Overall, the combined chemical and biological metabolism effects collectively contributed to the efficient ACE degradation, and it provided a novel and effective strategy for refractory pollutants removal during WAS anaerobic fermentation.