Bacterial degradation of chlorophenols and their derivatives

Computational Insights into the Catalysis of the pH Dependence of Bromite Decomposition Catalyzed by Chlorite Dismutase from Dechloromonas aromatica (DaCld)

The heme-containing chlorite dismutases catalyze the rapid and efficient decomposition of chlorite (ClO2-) to yield Cl- and O2, and the catalytic efficiency of chlorite dismutase from Dechloromonas aromatica (DaCld) in catalyzing the decomposition of bromite (BrO2-) was dependent on pH, which was supposed to be caused by the conversion of active Cpd I to the inactive Cpd II by proton-coupled electron transfer (PCET) from the pocket Tyr118 to the propionate side chain of heme at high pH. However, the direct evidence of PCET and how the pH affects the efficiency of DaCld, as well as whether Cpd II is really inactive, are still poorly understood. Here, on the basis of the high-resolution crystal structures, the computational models in both acidic (pH 5.0) and alkaline (pH 9.0) environments were constructed, and a series of quantum mechanical/molecular mechanical calculations were performed. On the basis of our calculation results, the O-Br bond cleavage of BrO2- always follows the homolytic mode to generate Cpd II rather than Cpd I. It is different from the O-O cleavage of O2/H2O2 or peracetic acid catalyzed by the other heme-containing enzymes. Thus, in the subsequent O-O rebound reaction, it is the Fe(IV)═O in Cpd II that combines with the O-Br radical. Because the porphyrin ring in Cpd II does not bear an unpaired electron, the previously suggested PCET from Tyr118 to the propionate side chain of heme was not theoretically recognized in an alkaline environment. In addition, the O-O rebound step in an alkaline solution corresponds to an energy barrier that is larger than that in an acidic environment, which can well explain the pH dependence of the activity of DaCld. In addition, the protonation state of the propionic acid side chains of heme and the surrounding hydrogen bond networks were calculated to have a significant impact on the barriers of the O-O rebound step, which is mainly achieved by affecting the reactivity of the Fe(IV)═O group in Cpd II. In an acidic environment, the relatively weaker coordination of the O2 atom to Fe leads to its higher reactivity toward the O-O rebound reaction. These observations may provide useful information for understanding the catalysis of chlorite dismutases.

Hydrothermally Synthesized Z-Scheme Nanocomposite of ZIF-9 Modified MXene for Photocatalytic Degradation of 4-Chlorophenol

4-Chlorophenol (4CP) is a well-known environmental contaminant often detected in wastewater, generally arising from industrial processes such as chemical manufacture, pharmaceutical production, and pesticide formulation. 4CP is a matter of great concern since it is persistent and has the potential to have harmful impacts on both aquatic ecosystems and human health, owing to its hazardous and mutagenic properties. Hence, degradation of 4CP is of utmost significance. This research investigates the photocatalytic degradation of 4CP using a novel Z-scheme heterojunction nanocomposite composed of MXene and ZIF-9. The nanocomposite is synthesized through a two-step hydrothermal method and thoroughly characterized by using XRD, SEM, UV-visible spectroscopy, zeta potential, and electrochemical impedance spectroscopy studies, confirming successful fabrication with improved surface properties. The comparative photocatalytic degradation studies between pristine materials and the nanocomposite were performed, and significant enhancement in performance was observed. The effect of pH on the degradation efficiency is also explored and correlated with the surface charge. The Z-scheme photocatalysis mechanism is proposed, which is supported by time-resolved photoluminescence studies and scavenger experiments. The reusability of the nanocomposite is also evaluated. The study contributes to the development of efficient and sustainable photocatalysts for wastewater treatment.

Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium

2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.

Degradation and metagenomic analysis of 4-chlorophenol utilizing multiple metal tolerant bacterial consortium

Chlorophenols are persistent environmental pollutants used in synthesizing dyes, drugs, pesticides, and other industrial products. The chlorophenols released from these processes seriously threaten the environment and human health. The present study describes 4-chlorophenol (4-CP) degradation activity and metagenome structure of a bacterial consortium enriched in a 4-CP-containing medium. The consortium utilized 4-CP as a single carbon source at a wide pH range, temperature, and in the presence of heavy metals. The immobilized consortium retained its degradation capacity for an extended period. The 4-aminoantipyrine colorimetric analysis revealed complete mineralization of 4-CP up to 200 mg/L concentration and followed the zero-order kinetics. The addition of glycerol and yeast extract enhanced the degradation efficiency. The consortium showed both ortho- and meta-cleavage activity of catechol dioxygenase. Whole genome sequence (WGS) analysis revealed the microbial compositions and functional genes related to xenobiotic degradation pathways. The identified genes were mapped on the KEGG database to construct the 4-CP degradation pathway. The results exhibited the high potential of the consortium for bioremediation of 4-CP contaminated sites. To our knowledge, this is the first report on WGS analysis of a 4-CP degrading bacterial consortium.

Associations of dichlorophenol with metabolic syndrome based on multivariate-adjusted logistic regression: a U.S. nationwide population-based study 2003-2016

BACKGROUND

Para-dichlorobenzene (p-DCB) exposure associated with oxidative stress has indeed raised public concerns. However, whether p-DCB is linked with metabolic syndrome (MetS) remains unclear. We hypothesized that higher exposure to p-DCB would be linked with a higher risk of MetS in the U.S population. This study aimed to examine the associations of exposure to p-DCB with MetS prevalence.

METHODS

We included 10,428 participants (5,084 men and 5,344 women), aged ≥ 20 years, from the National Health and Nutrition Examination Survey (2003-2016). The cases of MetS were diagnosed by NCEP/ATPIII. Logistic regression models were conducted to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) of MetS prevalence. Moreover, the mix associations of p-DCB metabolites were assessed using quantile sum (WQS) regression and quantile g-computation (qgcomp) methods.

RESULTS

We documented 2,861 (27.1%) MetS cases. After adjustment for the potential risk factors, the ORs (95% CI) of MetS prevalence across the quartile of urinary 2,5-dichlorophenol (2,5-DCP) were 1.09 (0.93-1.28), 1.22 (1.00-1.49), and 1.34 (1.04-1.73). Moreover, 2,5 DCP is significantly associated with a higher prevalence of abdominal obesity [ORQ4vsQ1 (95% CI): 1.23 (1.03-1.48)]. The WQS and qgcomp index also showed significant associations between p-DCB metabolites and MetS. Moreover, we further examined that 2,5 DCP was correlated with higher systolic blood pressure (r = 0.022, P = 0.027), waist circumference (r = 0.099, P < 0.001), and glycohemoglobin (r = 0.027, P = 0.008) and a lower high density cholesterol (r = -0.059, P < 0.001). In addition, the significant positive associations between 2,5 DCP and MetS were robust in the subgroup and sensitivity analyses.

CONCLUSION

These findings indicated that increased urinary p-DCB concentration, especially 2,5 DCP, had a higher MetS prevalence. These results should be interpreted cautiously and further research is warranted to validate our findings.

Bacterial Nanocellulose/Copper as a Robust Laccase-Mimicking Bionanozyme for Catalytic Oxidation of Phenolic Pollutants

Industrial effluents containing phenolic compounds are a major public health concern and thus require effective and robust remediation technologies. Although laccase-like nanozymes are generally recognized as being catalytically efficient in oxidizing phenols, their support materials often lack resilience in harsh environments. Herein, bacterial nanocellulose (BNC) was introduced as a sustainable, strong, biocompatible, and environmentally friendly biopolymer for the synthesis of a laccase-like nanozyme (BNC/Cu). A native bacterial strain that produces nanocellulose was isolated from black tea broth fermented for 1 month. The isolate that produced BNC was identified as Bacillus sp. strain T15, and it can metabolize hexoses, sucrose, and less expensive substrates, such as molasses. Further, BNC/Cu nanozyme was synthesized using the in situ reduction of copper on the BNC. Characterization of the nanozyme by scanning electron microscopy (SEM) and X-ray diffraction (XRD) confirmed the presence of the copper nanoparticles dispersed in the layered sheets of BNC. The laccase-mimetic activity was assessed using the chromogenic redox reaction between 2,4-dichlorophenol (2,4-DP) and 4-aminoantipyrine (4-AP) with characteristic absorption at 510 nm. Remarkably, BNC/Cu has 50.69% higher catalytic activity than the pristine Cu NPs, indicating that BNC served as an effective biomatrix to disperse Cu NPs. Also, the bionanozyme showed the highest specificity toward 2,4-DP with a Km of 0.187 mM, which was lower than that of natural laccase. The bionanozyme retained catalytic activity across a wider temperature range with optimum activity at 85 °C, maintaining 38% laccase activity after 11 days and 46.77% activity after the fourth cycle. The BNC/Cu bionanozyme could efficiently oxidize more than 70% of 1,4-dichlorophenol and phenol in 5 h. Thereby, the BNC/Cu bionanozyme is described here as having an efficient ability to mimic laccase in the oxidation of phenolic compounds that are commonly released into the environment by industry.

Adaptive laboratory evolution of Rhodococcus rhodochrous DSM6263 for chlorophenol degradation under hypersaline condition

BACKGROUND

Normally, a salt amount greater than 3.5% (w/v) is defined as hypersaline. Large amounts of hypersaline wastewater containing organic pollutants need to be treated before it can be discharged into the environment. The most critical aspect of the biological treatment of saline wastewater is the inhibitory/toxic effect exerted on bacterial metabolism by high salt concentrations. Although efforts have been dedicated to improving the performance through the use of salt-tolerant or halophilic bacteria, the diversities of the strains and the range of substrate spectrum remain limited, especially in chlorophenol wastewater treatment.

RESULTS

In this study, a salt-tolerant chlorophenol-degrading strain was generated from Rhodococcus rhodochrous DSM6263, an original aniline degrader, by adaptive laboratory evolution. The evolved strain R. rhodochrous CP-8 could tolerant 8% NaCl with 4-chlorophenol degradation capacity. The synonymous mutation in phosphodiesterase of strain CP-8 may retard the hydrolysis of cyclic adenosine monophosphate (cAMP), which is a key factor reported in the osmoregulation. The experimentally verified up-regulation of intracellular cAMP level in the evolved strain CP-8 contributes to the improvement of growth phenotype under high osmotic condition. Additionally, a point mutant of the catechol 1,2-dioxygenase, CatAN211S, was revealed to show the 1.9-fold increment on activity, which the mechanism was well explained by molecular docking analysis.

CONCLUSIONS

This study developed one chlorophenol-degrading strain with extraordinary capacity of salt tolerance, which showed great application potential in hypersaline chlorophenol wastewater treatment. The synonymous mutation in phosphodiesterase resulted in the change of intracellular cAMP concentration and then increase the osmotic tolerance in the evolved strain. The catechol 1,2-dioxygenase mutant with improved activity also facilitated chlorophenol removal since it is the key enzyme in the degradation pathway.

Metabolic insights into the interaction between nitrogen removal and 4-chlorophenol reduction of anammox consortia

The response characteristic and performance stabilization of anammox process under the stress of the potential organic pollutants support the application of ammonia-nitrogen wastewater treatment. In the present study, nitrogen removal performance was significantly suppressed with the addition of 4-chlorophenol. The activity of anammox process was inhibited by 14.23% (0.1 mg/L), 20.54% (1 mg/L) and 78.15% (10 mg/L), respectively. Metagenomic analysis revealed a significant decrease in the abundance of KEGG pathways associated with carbohydrate and amino acid metabolism with increasing 4-chlorophenol concentration. Metabolic pathway profiles suggest that putrescine is down-regulated at high 4-chlorophenol stress due to inhibition of nitrogen metabolism processes, while it is up-regulated to reduce oxidative damage. In addition, the presence of 4-chlorophenol induced an enhancement of EPS and bacterial debris decomposition, and a partial conversion of 4-chlorophenol to p-nitrophenol. This study unravels the mechanism of effect on anammox consortia in response to 4-CP, which could provide supplementary to facilitate its full-scale application.

Deciphering ligninolytic enzymes in the secretome of Pycnoporus sp. and their potential in degradation of 2-chlorophenol

Chlorophenols and their derivatives are persistent environmental pollutants, posing a threat to terrestrial and aquatic life. The biological approach for eliminating toxic contaminants is an effective, sustainable, and environmental friendly method. In this study, the crude enzymes present in the secretome of white-rot fungus (Pycnoporus sp.) were explored for the degradation of 2-chlorophenol. The activity of ligninolytic enzymes in the secretome was analyzed and characterized for their kinetics and thermodynamic properties. Laccase and manganese peroxidase were prevalent ligninolytic enzymes and exhibited temperature stability in the range of 50-65 °C and pH 4-5, respectively. The kinetic parameters Michaelis constant (Km) and turnover number (Kcat) for Lac were 42.54 μM and 45 s-1 for 2,2'-azino-bis (3-ethylben- zothiazoline-6-sulfonic acid), and 93.56 μM and 48 s-1 towards 2,6-dimethoxyphenol whereas Km and Kcat for MnP were 2039 μM and 294 s-1 for guaiacol as substrate. Treatment with the crude enzymes laccase and manganese peroxidase results in the reduction of 2-chlorophenol concentration, confirmed by UV-visible absorption spectra and high-performance liquid chromatography analysis. The detoxification of 2-chlorophenol into less toxic forms was confirmed by the plate toxicity assay. This study demonstrated that crude enzymes produced by Pycnoporus sp. could potentially minimize the toxicity of phenolic compounds in a sustainable way.

A comprehensive review of chlorophenols: Fate, toxicology and its treatment

Chlorophenols represent one of the most abundant families of toxic pollutants emerging from various industrial manufacturing units. The toxicity of these chloroderivatives is proportional to the number and position of chlorine atoms on the benzene ring. In the aquatic environment, these pollutants accumulate in the tissues of living organisms, primarily in fishes, inducing mortality at an early embryonic stage. Contemplating the behaviour of such xenobiotics and their prevalence in different environmental components, it is crucial to understand the methods used to remove/degrade the chlorophenol from contaminated environment. The current review describes the different treatment methods and their mechanism towards the degradation of these pollutants. Both abiotic and biotic methods are investigated for the removal of chlorophenols. Chlorophenols are either degraded through photochemical reactions in the natural environment, or microbes, the most diverse communities on earth, perform various metabolic functions to detoxify the environment. Biological treatment is a slow process because of the more complex and stable structure of pollutants. Advanced Oxidation Processes are effective in degrading such organics with enhanced rate and efficiency. Based on their ability to generate hydroxyl radicals, source of energy, catalyst type, etc., different processes such as sonication, ozonation, photocatalysis, and Fenton's process are discussed for the treatment or remediation efficiency towards the degradation of chlorophenols. The review entails both advantages and limitations of treatment methods. The study also focuses on reclamation of chlorophenol-contaminated sites. Different remediation methods are discussed to restore the degraded ecosystem back in its natural condition.

Microbial degradation of organochlorine pesticide: 2,4-Dichlorophenoxyacetic acid by axenic and mixed consortium

The presence of 2,4-dichlorophenoxyacetic acid (2,4-D), an organochlorine herbicide, in the environment has raised public concern as it poses hazard to both humans and the ecosystem. Three potential strains having the capability to degrade 2,4-D were isolated from on site agricultural soil and identified as Arthrobacter sp. SVMIICT25, Sphingomonas sp. SVMIICT11 and Stenotrophomonas sp. SVMIICT13. Over 12 days of incubation, 81-90% of 100 mg/L of 2,4-D degradation was observed at 2% inoculum. A shorter lag phase with 80% of degradation efficiency was observed within 5 days when the inoculum size was increased to 10%. Six microbial consortia were prepared by combining the isolates along with in-house strains, Bacillus sp. and Pseudomonas sp. Consortia R3 (Arthrobacter sp. + Sphingomonas sp.), operated with 10% of inoculum, showed 85-90% degradation within 4 days and 98-100% in 9 days. Further, targeted exo-metabolite analysis confirmed the presence and catabolism of intermediate 2,4-dichlorophenol and 4-chlorophenol compounds.

Phenol Degradation Performance in Batch and Continuous Reactors with Immobilized Cells of Pseudomonas putida

Phenol is a highly persistent environmental pollutant and is toxic to living organisms. The main objective of this study is to observe the phenol degradation performance by free and immobilized Pseudomonas putida (P. putida) in batch and continuous reactors, respectively. Batch experiments were evaluated to determine the maximum specific growth rate, saturation constant, inhibition constant, and cell yield. These kinetic parameters were used as the input values for the continuous-flow immobilized cells model. The immobilized cells model was validated by experimental results obtained from an immobilized cells continuous reactor. The model-predicted and experimental results showed good agreement for phenol effluent concentration in the continuous mode. In the steady-state condition, high phenol removal was achieved under various hydraulic retention times. The corresponding removal of phenol ranged from 93.3 to 95.9%, while the hydraulic retention times were maintained at 3.1–10.5 h. Furthermore, polyvinyl alcohol-immobilized cells with nanoscale particles were also prepared. The polyvinyl alcohol-immobilized P. putida cells with nanoscale Fe3O4 enhanced the ability of phenol degradation. The experimental results revealed that immobilized cells with nano-Fe3O4 had the highest phenol degradation performance at a low salinity of 1%. However, the advantage of the addition of nano-Fe3O4 was insignificant for phenol degradation at a higher salinity of 5%. The approaches of the batch and continuous column tests were practical in the treatment of actual phenol-containing wastewater.

Simultaneous bioremediation of phenol and tellurite by Lysinibacillus sp. EBL303 and characterization of biosynthesized Te nanoparticles

Aromatic compounds and metalloid oxyanions are abundant in the environment due to natural resources and industrial wastes. The high toxicity of phenol and tellurite poses a significant threat to all forms of life. A halotolerant bacterium was isolated and identified as Lysinibacillus sp. EBL303. The remediation analysis shows that 500 mg/L phenol and 0.5 mM tellurite can be remediated entirely in separate cultures within 74 and 56 h, respectively. In addition, co-remediation of pollutants resulted in the same phenol degradation and 27% less tellurite reduction within 98 h. Since phenol and tellurite exhibited inhibitory behavior, their removal kinetics fitted well with the first-order model. In the characterization of biosynthesized tellurium nanoparticles (TeNPs), transmission electron microscopy, dynamic light scattering, FE-SEM, and dispersive X-ray (EDX) showed that the separated intracellular TeNPs were spherical and consisted of only tellurium with 22-148 nm in size. Additionally, investigations using X-ray diffraction and Fourier-transform infrared spectroscopy revealed proteins and lipids covering the surface of these amorphous TeNPs. Remarkably, this study is the first report to demonstrate the simultaneous bioremediation of phenol and tellurite and the biosynthesis of TeNPs, indicating the potential of Lysinibacillus sp. EBL303 in this matter, which can be applied to environmental remediation and the nanotechnology industry.

Formation and stabilization of C4a-hydroperoxy-FAD by the Arg/Asn pair in HadA monooxygenase

HadA monooxygenase catalyses the detoxification of halogenated phenols and nitrophenols via dehalogenation and denitration respectively. C4a-hydroperoxy-FAD is a key reactive intermediate wherein its formation, protonation and stabilization reflect enzyme efficiency. Herein, transient kinetics, site-directed mutagenesis and pH-dependent behaviours of HadA reaction were employed to identify key features stabilizing C4a-adducts in HadA. The formation of C4a-hydroperoxy-FAD is pH independent, whereas its decay and protonation of distal oxygen are associated with pK_a values of 8.5 and 8.4 respectively. These values are correlated with product formation within a pH range of 7.6-9.1, indicating the importance of adduct stabilization to enzymatic efficiency. We identified Arg101 as a key residue for reduced FAD (FADH^- ) binding and C4a-hydroperoxy-FAD formation due to the loss of these abilities as well as enzyme activity in HadA_R101A and HadA_R101Q . Mutations of the neighbouring Asn447 do not affect the rate of C4a-hydroperoxy-FAD formation; however, they impair FADH^- binding. The disruption of Arg101/Asn447 hydrogen bond networking in HadA_N447A increases the pK_a value of C4a-hydroperoxy-FAD decay to 9.5; however, this pK_a was not altered in HadA_N447D (pK_a of 8.5). Thus, Arg101/Asn447 pair should provide important interactions for FADH^- binding and maintain the pK_a associated with H₂ O₂ elimination from C4a-hydroperoxy-FAD in HadA. In the presence of substrate, the formation of C4a-hydroxy-FAD at the hydroxylation step is pH insensitive, and it dehydrates to form the oxidized FAD with pK_a of 7.9. This structural feature might help elucidate how the reactive intermediate was stabilized in other flavin-dependent monooxygenases.

Biochemical characterization of hydroquinone hydroxylase from Phanerochaete chrysosporium

The white-rot fungus Phanerochaete chrysosporium can degrade lignin polymers using extracellular, non-specific, one-electron oxidizing enzymes. This results in the formation of guaiacyl (G), syringyl (S), and hydroxyphenyl (H) units, such as vanillic acid, syringic acid, and p-hydroxybenzoic acid (p-HBA) and the corresponding aldehydes, which are further metabolized intracellularly. Therefore, the aim of this study was to identify proteins involved in the hydroxylation of H-unit fragments such as p-HBA and its decarboxylated product hydroquinone (HQ) in P. chrysosporium. A flavoprotein monooxygenase (FPMO), PcFPMO2, was identified and its activity was characterized. Recombinant PcFPMO2 with an N-terminal polyhistidine tag was produced in Escherichia coli and purified. In the presence of NADPH, PcFPMO2 used six phenolic compounds as substrates. PcFPMO2 catalyzed the hydroxylation of the H-unit fragments such as p-HBA and HQ, and the G-unit derivative methoxyhydroquinone (MHQ). The highest catalytic efficiency (k_cat/K_m) was observed with HQ, indicating that PcFPMO2 could be involved in HQ hydroxylation in vivo. Additionally, PcFPMO2 converted MHQ to 3-, 5-, and 6-methoxy-1,2,4-trihydroxybenzene (3-, 5-, and 6-MTHB), respectively, suggesting that PcFPMO2 might partially be involved in MHQ degradation, following aromatic ring fission, via three MTHBs. FPMOs are divided into eight groups (groups A to H). This is the first study to show MHQ hydroxylase activity of a FPMO-group A superfamily member. These findings highlight the unique substrate spectrum of PcFPMO2, making it an attractive candidate for biotechnological applications.

Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae

Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 18.7% of bacteria. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Candidatus Sororchlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Based on gene content, sponge-associated chlamydiae resemble members from the same family more than sponge-associated chlamydiae of other families, and have greater metabolic versatility than known chlamydial animal pathogens. Sponge-associated chlamydiae are also enriched in genes for degrading diverse compounds found in sponges. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an unexplored source of novel natural products. This finding suggests that Chlamydiae members may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of the Chlamydiae phylum on marine ecosystems.

Kinetic Study of 4-Chlorophenol Biodegradation by Acclimated Sludge in a Packed Bed Reactor

In this study, batch experiments were conducted to evaluate the degradation of 4-CP using acclimated sludge. The Monod and Haldane models were employed to fit the specific growth rate with various initial 4-CP concentrations of 67–412 mg/L in the batch experiments. Haldane kinetics showed a better fit to experimental results than Monod kinetics. The kinetic parameters were obtained from a comparison of Monod and Haldane kinetics with batch experimental data. The values of μm and KS were found to be 0.691 d−1 and 5.62 mg/L, respectively, for Monod kinetics. In contrast, the values of μm, KS, and KI were 1.30 d−1, 8.38 mg/L, and 279.4 mg/L, respectively, for Haldane kinetics. The kinetic parameters in Haldane kinetics were used as input parameters for the kinetic model system of the packed bed reactor (PBR). The continuous flow PBR was conducted to validate the kinetic model system. The model-simulated results agreed well with experimental data in the PBR performance operation. At the steady-state stage, the removal efficiency of 4-CP was 70.8–96.1%, while the hydraulic retention time (HRT) was 2.5 to 12.4 h. The corresponding removal of 4-CP was assessed to be 94.6 and 96.1% when the inlet 4-CP loading rate was increased from 0.11 to 0.51 kg/m3-d. The approaches of kinetic models and experiments presented in this study can be applied to design a PBR for 4-CP treatment in wastewater from the effluents of various industries.

Cometabolic biodegradation system employed subculturing photosynthetic bacteria: A new degradation pathway of 4-chlorophenol in hypersaline wastewater

4-chlorophenol (4-CP) as a toxic persistent pollutant is quite difficult treatment by using traditional biological processes. Herein, photosynthetic bacteria (PSB) driven cometabolic biodegradation system associated with exogeneous carbon sources (e.g., sodium acetate) has been demonstrated as an effective microbial technique. The biodegradation rate (r_i) can be at 0.041 d^-1 with degradation efficiency of 93% in 3094 lx. Through the study of subculturing PSB in absence of NaCl, it was found that 50% inoculation time can be saved but keeping a similar 4-CP biodegradation efficiency in scale-up salinity system. A new plausible biodegradation pathway for 4-CP in 4th G PSB cometabolic system is proposed based on the detected cyclohexanone generation followed by ring opening. It is probably ascribed to the increasement of Firmicutes and Bacteroidetes at phyla level classified based on microbial community. This study contributes to a new insight into cometabolic technology for chlorophenol treatment in industrial hypersaline wastewater.

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Characterization of two 1,2,4-trihydroxybenzene 1,2-dioxygenases from Phanerochaete chrysosporium

Lignin is the most abundant aromatic compound in nature, and it plays an important role in the carbon cycle. White-rot fungi are microbes that are capable of efficiently degrading lignin. Enzymes from these fungi possess exceptional oxidative potential and have gained increasing importance for improving bioprocesses, such as the degradation of organic pollutants. The aim of this study was to identify the enzymes involved in the ring cleavage of the lignin-derived aromatic 1,2,4-trihydroxybenzene (THB) in Phanerochaete chrysosporium, a lignin-degrading basidiomycete. Two intradiol dioxygenases (IDDs), PcIDD1 and PcIDD2, were identified and produced as recombinant proteins in Escherichia coli. In the presence of O₂, PcIDD1 and PcIDD2 acted on eight and two THB derivatives, respectively, as substrates. PcIDD1 and PcIDD2 catalyze the ring cleavage of lignin-derived fragments, such as 6-methoxy-1,2,4-trihydroxybenzene (6-MeOTHB) and 3-methoxy-1,2-catechol. The current study also revealed that syringic acid (SA) was converted to 5-hydroxyvanillic acid, 2,6-dimethoxyhydroquinone, and 6-MeOTHB by fungal cells, suggesting that PcIDD1 and PcIDD2 may be involved in aromatic ring fission of 6-MeOTHB for SA degradation. This is the first study to show 6-MeOTHB dioxygenase activity of an IDD superfamily member. These findings highlight the unique and broad substrate spectra of PcIDDs, rendering it an attractive candidate for biotechnological application. KEY POINTS: • Novel intradiol dioxygenases (IDD) in lignin degradation were characterized. • PcIDDs acted on lignin-derived fragments and catechol derivatives. • Dioxygenase activity on 6-MeOTHB was identified in IDD superfamily enzymes.

Pseudomonas phenolilytica sp. nov., a novel phenol-degrading bacterium

This study describes a bacterium strain RBPA9 isolated from a municipality waste dumping area capable of degrading phenol, proposed as a novel species of Pseudomonas. Cells are Gram-negative, rod shaped, aerobic and motile. The genome is 3.92 Mb, and the G + C content is 64.64%. The overall genome relatedness indices such as in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) values were below 70% and 95-96%, respectively. Phylogenetic analysis based on genome-wide core genes and 16S rRNA gene sequences revealed that strain RBPA9 clustered with Pseudomonas stutzeri ATCC 17588 ^T in both the phylogenetic trees. Maximum growth was recorded at 200 mg /L concentration of phenol which was consumed within 24 h. A gene cluster of phenol degradation pathway was detected. The quantitative real-time PCR (RT-PCR) demonstrated the expression of all the genes required in the meta-cleavage pathway of phenol in RBPA9. Our results reveal that strain RBPA9 represents a novel species for which Pseudomonas phenolilytica sp. nov. is proposed. The type strain is RBPA9^T (= TBRC 15231 ^T = NBRC 115284 ^T).

Enhanced Bioremediation of 4-Chlorophenol by Electrically Neutral Reactive Species Generated from Nonthermal Atmospheric-Pressure Plasma

4-Chlorophenol (4-CP) is a chlorinated aromatic compound with broad industrial applications. It is released into the environment as an industrial byproduct and is highly resistant to biodegradation. Pseudomonas sp. in the environment and activated sludge are used for 4-CP bioremediation; however, the degradation of 4-CP takes a long time. Consequently, the toxicity of 4-CP is a major barrier to its bioremediation. In this study, we investigated the synergistic effect of electrically neutral reactive species on the bacterial bioremediation of 4-CP. Our results showed that the concentration of 4-CP decreased from 2.0 to 0.137 mM and that it was converted to 4-chlorocatechol (4-CC; 0.257 mM), 4-chlororesorcinol (0.157 mM), hydroquinone (0.155 mM), and trihydroxy chlorobenzene and their respective ring-cleaved products following irradiation of neutral reactive species. These compounds were less toxic than 4-CP, except for 4-CC, which reduced the toxicity of 4-CP to Pseudomonas putida. When the neutral reactive species-treated 4-CP fraction was added to P. putida cultured in a synthetic sewage medium for 48 h, the 4-CP concentration was reduced to 0.017 mM, whereas nontreated 4-CP (2.0 mM) was hardly degraded by P. putida. These results suggest that the biodegradation of 4-CP can be efficiently improved by combining irradiation of neutral reactive species with microbial treatment. The irradiation of neutral reactive species of environmental pollutants may additionally lead to further improvements in bioremediation processes.

Actinobacteria isolated from wastewater treatment plants located in the east-north of Algeria able to degrade pesticides

The pollution of water resources by pesticides poses serious problems for public health and the environment. In this study, Actinobacteria strains were isolated from three wastewater treatment plants (WWTPs) and were screened for their ability to degrade 17 pesticide compounds. Preliminary screening of 13 of the isolates of Actinobacteria allowed the selection of 12 strains with potential for the degradation of nine different pesticides as sole carbon source, including aliette, for which there are no previous reports of biodegradation. Evaluation of the bacterial growth and degradation kinetics of the pesticides 2,4-dichlorophenol (2,4-DCP) and thiamethoxam (tiam) by selected Actinobacteria strains was performed in liquid media. Strains Streptomyces sp. ML and Streptomyces sp. OV were able to degrade 45% of 2,4-DCP (50 mg/l) as the sole carbon source in 30 days and 84% of thiamethoxam (35 mg/l) in the presence of 10 mM of glucose in 18 days. The biodegradation of thiamethoxam by Actinobacteria strains was reported for the first time in this study. These strains are promising for use in bioremediation of ecosystems polluted by this type of pesticides.

Biodegradation Kinetics of Phenol and 4-Chlorophenol in the Presence of Sodium Salicylate in Batch and Chemostat Systems

The biodegradation of phenol, sodium salicylate (SA), and 4-chlorophenol (4-CP) by Pseudomonas putida (P. putida) was evaluated by batch and chemostat experiments in single and binary substrate systems. The Haldane kinetics model for cell growth was chosen to describe the batch kinetic behavior to determine kinetic parameters in the single or binary substrates system. In the single phenol and SA system, the kinetic constants of μm,P = 0.423 h−1, μm,A = 0.247 h−1, KS,P = 48.1 mg/L, KS,A = 71.7 mg/L, KI,P = 272.5 mg/L, and KI,A = 3178.2 mg/L were evaluated. Experimental results indicate that SA was degraded more rapidly by P. putida cells compared to phenol because SA has a much larger KI value than phenol, which makes the cells less sensitive to substrate inhibition even though the μm,P value is larger compared to μm,A. The ratio of inhibition of phenol degradation due to the presence of SA (IA1) to the inhibition of SA degradation due to the presence of phenol (IA2) is 2.3, indicating that SA has a higher uncompetitive inhibition on phenol biodegradation compared to that of phenol on SA biodegradation in the binary substrate system. In the ternary substrate system, the time required for the complete degradation of SA and phenol was 14 and 11.5 d and an approximately 90% removal efficiency for 4-CP was achieved within 14 d. In the chemostat system, the removal rates of phenol and SA were 96.6 and 97.0%, while those of SA and 4-CP were 91.4% and 95.2%, respectively. The model prediction agreed satisfactorily with the experimental results of the chemostat system.

Fenton-Mediated Chlorophenol Degradation by Iron-Reducing Compounds Isolated from Endophytic Fungi in Atacama Puna Plateau Lecanicillium ATA01

Low-molecular-mass iron-reducing compounds (IRCs) were produced by entomopathogenic endophytic fungi Lecanicillium sp. ATA01 in liquid cultures. The extracellular hydrophilic extract contained three IRCs formed by peptides, iron and phenolate structures with molecular masses of 1207, 567 and 550 Da. These compounds were able to chelate and mediate the reduction of Fe+3 to Fe+2 and oxidized recalcitrant lignin-model substrates such as veratryl alcohol (VA), 2,6-dimethoxyphenol (DMP), and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS) with or without hydrogen peroxide. Besides, IRCs can promote the degradation of chlorophenols. The maximal degradation of p-chlorophenol, 2,4-dichlorophenol, 2,4,6-trichlorophenol, and pentachlorophenol was conducted at optimal degradation conditions for IRCs (pH 3.5, iron 100 mM, and H2O2 10 mM). Furthermore, Fenton-like reactions using the synthetic iron chelates DTPA and EDTA and free Fe+2 and Fe+3 were also carried out in order to compare with the reaction mediated by IRCs. The ferric IRCs displayed the ability to enhance the hydroxylation of chlorophenols as a part of a degradation mechanism of the IRC-assisted Fenton reaction. The complexed iron was more efficient than free iron in the Fenton-like reaction, and between them, the fungal chelates were more efficient than the synthetic mill chelates.

Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6

Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = -1.0 ± 0.5‰ in chemostats (D = 0.090 h^-1, 88 mg L^-1) and ε(C) = -2.1 ± 0.5‰ in batch (c₀ = 220 mg L^-1) to ε(C) = -4.1 ± 0.2‰ in chemostats at 90 μg L^-1. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h^-1. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.

Degradation of 2,6-dicholorophenol by Trichoderma longibraciatum Isolated from an industrial Soil Sample in Dammam, Saudi Arabia

2,6-Dichlorophenol (2,6-DCP) is an aromatic compound with industrial importance in making insecticides, herbicides, and other organic compounds. However, it poses serious health and ecological problems. Microbial degradation of 2,6-DCP has been widely applied due to its effectiveness and eco-friendly characteristics. In this study, Trichoderma longibraciatum was isolated from an industrial soil sample in Dammam, Saudi Arabia using the enrichment method of mineral salt's medium (MSM) amended with 2,6-DCP. Morphological and molecular identification (using the internal transcribed spacer rRNA gene sequencing) of the 2,6-DCP tolerating fungal isolate were charactraized. The fungal isolate has demonstrated a tolerance to 2,6-DCP up to 300 mg/L. Mycelial growth and fungal sporulation were reduced with increasing 2,6-DCP concentrations up to 96 h incubation period. However, after 168 h incubation period, the fungal isolate recorded maximum growth at all the tested 2,6-DCP concentrations up to 150 mg/L. Carboxy methyl cellulase production by tested fungus was decreased by increasing 2,6-DCP concentration up to 75 mg/L. The biodegradation pattern of 2,6-DCP in GM liquid medium using GC–mass analysis as well as the degradation pathway was presented. This study provides a promising fungal isolate that could be used in the bioremediation process for chlorinated phenols in soil.

Novel strategy for membrane biofouling control in MBR with nano-MnO2 modified PVDF membrane by in-situ ozonation

In this study, ozonation catalyst nano-MnO₂ blended polyvinylidene fluoride (PVDF) membrane was fabricated via phase inversion method and applied to membrane bioreactors (MBR), and then coupled with in-situ ozonation to study the anti-biofouling performance and reveal its mechanism. Results showed that, compared with pristine PVDF membrane (MBR_M₀), 0.75 wt% and 1.00 wt% nano-MnO₂ modified PVDF membrane (MBR_M_0.75 and MBR_M_1.00) could mitigate the membrane biofouling rate. Meanwhile MBR_M_1.00 coupled with in-situ ozonation could increase the membrane cleaning cycle to 1.5 and 2.7 times, compared with MBR_M₀ and MBR_M_0.75 without in-situ ozonation. The possible mechanisms included that the nano-MnO₂ modification coupled with in-situ ozonation directly removed the biofouling on the membrane surface, improved the hydrophilicity of the membrane surface and enhanced the chemical oxidation and biodegradation of membrane biofouling contaminants in the sludge mixture. The results of this work provide a new strategy for the control of membrane biofouling in MBR to treat industrial wastewater.

Oxidative dehalogenation of halophenols by high-valent nonheme iron(IV)-oxo intermediates

Mononuclear high-valent iron(IV)-oxo intermediates are excellent oxidants towards oxygenation reactions by heme and nonheme metalloenzymes and their model systems. One of the most important functions of these intermediates in nature is to detoxify various environmental pollutants. Organic substrates, such as halogenated phenols, are known to be water pollutants which can be degraded to their less hazardous forms through an oxidation reaction by iron(IV)-oxo complexes. Metalloproteins in nature utilize various types of second-coordination sphere interactions to anchor the substrate in the vicinity of the active site. This concept of substrate-binding is well-known for natural enzymes, but is elusive for the relevant biomimetic model systems. Herein, we report the oxidative reactivity patterns of an iron(IV)-oxo intermediate, [Fe^IV(O)(2PyN2Q)]²⁺, (2PyN2Q = 1,1-di(pyridin-2yl)-N,N-bis(quinolin-2-ylmethyl)methanamine) with a series of mono-, di- and tri-halophenols. A detailed experimental study shows that the dehalogenation reactions of the halophenols by such iron(IV)-oxo intermediates proceed via an initial hydrogen atom abstraction from the phenolic O-H group. Furthermore, based on the size and nucleophilicity of the halophenol, an intermediate substrate-bound species forms that is a phenolate adduct to the ferric species, which thereafter leads to the formation of the corresponding products.

Modelling the cathodic reduction of 2,4-dichlorophenol in a microbial fuel cell

This work presents a simplified mathematical model able to predict the performance of a microbial fuel cell (MFC) for the cathodic dechlorination of 2,4-dichlorophenol (2,4-DCP) operating at different cathode pH values (7.0 and 5.0). Experimental data from previous work were utilized for the fitting of the model. The MFC modelled consisted of two chambers (bioanode and abiotic cathode), wherein the catholyte contained 300 mg L⁻¹ of 2,4-DCP and the anolyte 1000 mg L⁻¹ of sodium acetate. The model considered two mixed microbial populations in the anode compartment using sodium acetate as the carbon source for growth and maintenance: electrogenic and non-electrogenic biomass. 2,4-DCP, its intermediates of the reductive process (2-chlorophenol, 2-CP and 4-chlorophenol, 4-CP) and protons were considered in the model as electron acceptors in the electrogenic mechanism. The global process rate was assumed to be controlled by the biological mechanisms and modelled using multiplicative Monod-type equations. The formulation of a set of differential equations allowed to describe the simultaneous evolution of every component: concentration of sodium acetate in the anodic compartment; and concentration of 2,4-DCP, 2-CP, 4-CP, phenol and chloride in the cathode chamber. Current production and coulombic efficiencies were also estimated from the fitting. It was observed that most of the organic substrate was used by non-electrogenic mechanism. The influence of the Monod parameters was more important than the influence of the biomass yield coefficients. Finally, the model was employed to simulate different scenarios under distinct experimental conditions.

Computational Study of the Peroxygenase Mechanism Catalyzed by Hemoglobin Dehaloperoxidase Involved in the Degradation of Chlorophenols

The biochemical evidence showed that hemoglobin dehaloperoxidase (DHP B) from Amphitrite Ornata is a multifunctional hemoprotein that catalyzes both dehalogenation and hydroxylation of halophenols via the peroxidase and peroxygenase mechanism, respectively, which sets the basis for the degradation of halophenols. In the peroxygenase mechanism, the reaction was previously suggested to be triggered either by the hydrogen atom abstraction by the Fe═O center or by the proton abstraction by His55. To illuminate the peroxygenase mechanism of DHP B at the atomistic level, on the basis of the high-resolution crystal structure, computational models were constructed, and a series of quantum mechanical/molecular mechanical calculations have been performed. According to the calculation results, the pathway (Path a) initiated by the H-abstraction by the Fe═O center is feasible. In another pathway (Path b), His55 can abstract the proton from the hydroxyl group of the substrate (4-Cl-o-cresol) to initiate the reaction; however, its feasibility depends on the prior electron transfer from the substrate to the porphyrin group. The rate-limiting step of Path a is the OH-rebound, which corresponds to an energy barrier of 14.7 kcal/mol at the quartet state. His55 acts as an acid-base catalyst and directly involves in the catalysis. Our mutant study indicates that His55 can be replaced by other titratable residues. These findings may provide useful information for further understanding of the catalytic reaction of DHP B and for the design of enzymes in the degradation of pollutants, in particular, halophenols.

An RNA aptamer that shifts the reduction potential of metabolic cofactors

The discovery of ribozymes has inspired exploration of RNA's potential to serve as primordial catalysts in a hypothesized RNA world. Modern oxidoreductase enzymes employ differential binding between reduced and oxidized forms of redox cofactors to alter cofactor reduction potential and enhance the enzyme's catalytic capabilities. The utility of differential affinity has been underexplored as a chemical strategy for RNA. Here we show an RNA aptamer that preferentially binds oxidized forms of flavin over reduced forms and markedly shifts flavin reduction potential by -40 mV, similar to shifts for oxidoreductases. Nuclear magnetic resonance structural analysis revealed π-π and donor atom-π interactions between the aptamer and flavin that cause unfavorable contacts with the electron-rich reduced form, suggesting a mechanism by which the local environment of the RNA-binding pocket drives the observed shift in cofactor reduction potential. It seems likely that primordial RNAs could have used similar strategies in RNA world metabolisms.

Glucose Addition Enhanced the Advanced Treatment of Coking Wastewater

Biological processes have high removal efficiencies and low operational costs, but the secondary effluent of coking wastewater (CWW), even at a low concentration, is difficult for microorganisms to degrade directly. In this study, glucose was used as a carbon source and co-metabolic substrate for microbial acclimation in order to enhance the advanced treatment of coking wastewater (CWW). The removal performance of the pollutants, especially recalcitrant compounds, was studied and the changes in the microbial community structure after activated sludge acclimation were analyzed. The effect of glucose addition on the secondary biochemical effluent of coking wastewater (SBECW) treatment by the acclimated sludge was further studied by a comparison between the performance of two parallel reactors seeded with the acclimated sludge. Our results showed that the concentrations of chemical oxygen demand (COD), total organic carbon (TOC), and UV absorption at 254 nm (UV254) of the wastewater decreased in the acclimation process. Refractory organic matter, such as polycyclic aromatic hydrocarbons and nitrogen-containing heterocyclics, in the SBECW was effectively degraded by the acclimated sludge. High-throughput sequencing revealed that microbes with a strong ability to degrade recalcitrant compounds were enriched after acclimation, such as Thauera (8.91%), Pseudomonas (3.35%), and Blastocatella (10.76%). Seeded with the acclimated sludge, the reactor with the glucose addition showed higher COD removal efficiencies than the control system without glucose addition (p < 0.05). Collectively, glucose addition enhanced the advanced treatment of coking wastewater (CWW).

Optimization and reconstruction of two new complete degradation pathways for 3-chlorocatechol and 4-chlorocatechol in Escherichia coli

Chlorinated aromatic compounds are a serious environmental concern because of their widespread occurrence throughout the environment. Although several microorganisms have evolved to gain the ability to degrade chlorinated aromatic compounds and use them as carbon sources, they still cannot meet the diverse needs of pollution remediation. In this study, the degradation pathways for 3-chlorocatechol (3CC) and 4-chlorocatechol (4CC) were successfully reconstructed by the optimization, synthesis, and assembly of functional genes from different strains. The addition of a ¹³C-labeled substrate and functional analysis of different metabolic modules confirmed that the genetically engineered strains can metabolize chlorocatechol similar to naturally degrading strains. The strain containing either of these artificial pathways can degrade catechol, 3CC, and 4CC completely, although differences in the degradation efficiency may be noted. Proteomic analysis and scanning electron microscopy observation showed that 3CC and 4CC have toxic effects on Escherichia coli, but the engineered bacteria can significantly eliminate these inhibitory effects. As core metabolic pathways for the degradation of chloroaromatics, the two chlorocatechol degradation pathways constructed in this study can be used to construct pollution remediation-engineered bacteria, and the related technologies may be applied to construct complete degradation pathways for complex organic hazardous materials.

Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1

Phenol is a common environmental contaminant. The purpose of this study was to isolate phenol-degrading microorganisms from wastewater in the sections of the Chinese Medicine Manufactory. The phenol-degrading Acinetobacter lwoffii NL1 was identified based on a combination of biochemical characteristics and 16S rRNA genes. To analyze the molecular mechanism, the whole genome of A. lwoffii NL1 was sequenced, yielding 3499 genes on one circular chromosome and three plasmids. Enzyme activity analysis showed that A. lwoffii NL1 degraded phenol via the ortho-cleavage rather than the meta-cleavage pathway. Key genes encoding phenol hydroxylase and catechol 1,2-dioxygenase were located on a megaplasmid (pNL1) and were found to be separated by mobile genetic elements; their function was validated by heterologous expression in Escherichia coli and quantitative real-time PCR. A. lwoffii NL1 could degrade 0.5 g/L phenol within 12 h and tolerate a maximum of 1.1 g/L phenol, and showed resistance against multiple antibiotics and heavy metal ions. Overall, this study shows that A. lwoffii NL1 can be potentially used for efficient phenol degradation in heavy metal wastewater treatment.

Effect of metabolic uncouplers on the performance of toluene-degrading biotrickling filter

The biomass control potential of three metabolic uncouplers (carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP), carbonyl cyanide m-chlorophenylhydrazone (CCCP), and m-chlorophenol (m-CP)) was tested in biotrickling filters (BTFs) degrading toluene. The experiments employed two types of reactors: a traditional column design and a novel differential BTF (DBTF) reactor developed by De Vela and Gostomski (J Environ Eng 147:04020159, 2021). Uncouplers caused the toluene elimination capacity (EC) (~33 g/m3h for column reactors and ~600 g/m3h for DBTF) to decrease by 15-97% in a dose-dependent fashion. The EC completely recovered in the column reactor in 3 to 13 days, while only partial recovery happened in the DBTF. Short-term (1 to 3 days) true uncoupling was indicated by the 20-160% increase in %CO2 recovery, depending on concentration. FCCP and CCCP increased the pressure drop due to increased extracellular polymeric substances (EPS) production for protection against the uncouplers. The 4.0-mM m-CP weakened the biofilm in the BTF bed, as evidenced by the 130-500% increase in the total organic carbon in the liquid sump of the column and DBTF reactors. Moreover, a microbial shift led to the proliferation of genera that degrade uncouplers, further demonstrating that the uncouplers tested were not a sustainable biomass control strategy in BTFs.

Degradation of 2,4-DCP using persulfate and iron/E-carbon micro-electrolysis coupling system

The greenhouse gas carbon dioxide (CO₂) was converted to a novel CO₂ conversion material (electrolytic carbon, EC) by molten salt electrochemical conversion, which served as the carbon source to prepare an iron-carbon composite (Fe-EC). The composite was used to activate persulfate (PS) and degrade 2,4-dichlorophenol (2,4-DCP) in an aqueous solution. The effects of several essential operating parameters such as PS dosage and pH on 2,4-DCP degradation were investigated. The removal efficiency of 2,4-DCP (20 mg L^-1) was 97.8% in the presence of Fe-EC (50 mg L^-1) and PS (1 mmol L^-1). Moreover, the average % reaction stoichiometric efficiency (RSE) (calculated for all selected times 5-60 min) was maintained at 23.07%. Electron paramagnetic resonance (EPR), classical radical scavenging experiments, and density functional theory (DFT) calculations were integrated for a mechanistic study, which disclosed that the active species in the system were identified as SO₄^⦁-, •OH, and O₂^⦁-. Moreover, the iron-carbon micro-electrolysis/PS (ICE-PS) system had a high tolerance to a wide range of pH, which would provide theoretical guidance for the treatment of organic pollutants in practical industrial wastewater.

Biodegradation of Chloroxylenol by Cunninghamella elegans IM 1785/21GP and Trametes versicolor IM 373: Insight into Ecotoxicity and Metabolic Pathways

Chloroxylenol (PCMX) is applied as a preservative and disinfectant in personal care products, currently recommended for use to inactivate the SARS-CoV-2 virus. Its intensive application leads to the release of PCMX into the environment, which can have a harmful impact on aquatic and soil biotas. The aim of this study was to assess the mechanism of chloroxylenol biodegradation by the fungal strains Cunninghamella elegans IM 1785/21GP and Trametes versicolor IM 373, and investigate the ecotoxicity of emerging by-products. The residues of PCMX and formed metabolites were analysed using GC-MS. The elimination of PCMX in the cultures of tested microorganisms was above 70%. Five fungal by-products were detected for the first time. Identified intermediates were performed by dechlorination, hydroxylation, and oxidation reactions catalysed by cytochrome P450 enzymes and laccase. A real-time quantitative PCR analysis confirmed an increase in CYP450 genes expression in C. elegans cells. In the case of T. versicolor, spectrophotometric measurement of the oxidation of 2,20-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) showed a significant rise in laccase activity during PCMX elimination. Furthermore, with the use of bioindicators from different ecosystems (Daphtoxkit F and Phytotoxkit), it was revealed that the biodegradation process of PCMX had a detoxifying nature.

Challenges and opportunities for the biodegradation of chlorophenols: Aerobic, anaerobic and bioelectrochemical processes

Chlorophenols (CPs) are highly toxic and refractory contaminants which widely exist in various environments and cause serious harm to human and environment health and safety. This review provides comprehensive information on typical CPs biodegradation technologies, the most green and benign ones for CPs removal. The known aerobic and anaerobic degradative bacteria, functional enzymes, and metabolic pathways of CPs as well as several improving methods and critical parameters affecting the overall degradation efficiency are systematically summarized and clarified. The challenges for CPs mineralization are also discussed, mainly including the dechlorination of polychlorophenols (poly-CPs) under aerobic condition and the ring-cleavage of monochlorophenols (MCPs) under anaerobic condition. The coupling of functional materials and degraders as well as the operation of sequential anaerobic-aerobic bioreactors and bioelectrochemical system (BES) are promising strategies to overcome some current limitations. Future perspective and research gaps in this field are also proposed, including the further understanding of microbial information and the specific role of materials in CPs biodegradation, the potential application of innovative biotechnologies and new operating modes to optimize and maximize the function of the system, and the scale-up of bioreactors towards the efficient biodegradation of CPs.

Comparison of treatability of four different chlorophenol-containing wastewater by pyrite-Fenton process combined with aerobic biodegradation: Role of sludge acclimation

Aerobic biodegradation combined with pyrite-Fenton process was used for the treatment of wastewater containing different chlorophenols (4-CP, 2,3-DCP, 2,4-DCP, 2,4,6-TCP). Fenton degradation using pyrite as the low cost iron catalyst was used as a pre-treatment step to lower the toxicity of CPs prior to aerobic biodegradation. Synthetic wastewater spiked directly with either 100 mg/L CPs or pyrite-Fenton pre-treated CPs was fed to the batch bioreactors inoculated with unacclimated or acclimated activated sludge using glucose as the C-source. The results show that the CP biodegradation under aerobic conditions was highly dependent on the type of CP treated. Except for 2,4-DCP, all other CPs investigated caused severe sludge toxicity, and thus significantly hindered glucose degradation by unacclimated sludge. The CP toxicity decreased in the order of: 2,4,6-TCP > 2,3-DCP > 4-CP > 2,4-DCP. The toxic effect was explained through an interaction of CPs with the lipid fraction of cell membrane. While the pyrite-Fenton pre-treatment improved the COD removal efficiency using unacclimated sludge, the sCOD removal efficiency was still less than the control reactor operated with no CP addition. With sludge acclimation, however, the sCOD removal efficiencies increased, and approached 74% for 2,4-DCP, 61% for 4-CP, 56% for 2,4,6-TCP and 46% for 2,3-DCP, suggesting an enhanced biomass tolerance to CP toxicity. On the other hand, the sludge acclimation combined with pyrite Fenton pre-treatment provided the best bioreactor performance for all CPs with the sCOD removal efficiencies reaching 81% for 2,4,6-TCP, 78% for 2,4-DCP, 73% for 4-CP and 62% for 2,3-DCP. This suggests that the dechlorination of CPs with Fenton process, in conjunction with sludge acclimation, not only reduced the sludge toxicity, but also enhanced the bioavailability of CP-containing wastewater for microorganisms, especially for highly chlorinated toxic CPs such as 2,4,6-TCP. Overall, the findings highlight the need for sludge acclimation for effective treatment of chlorophenol-containing wastewater by a combined pyrite-Fenton and aerobic biodegradation system.

The performance and microbial communities of an anaerobic membrane bioreactor for treating fluctuating 2-chlorophenol wastewater

An anaerobic membrane bioreactor (AnMBR) was used to treat low to high (5-200 mg/L) concentrations of 2-chlorophenol (2-CP) wastewater. The AnMBR achieved high and stable chemical oxygen demand removal and 2-CP removal with an average value of 93.2% and 94.2% under long hydraulic retention times (HRTs, 48-96 h), respectively. 2-CP removal efficiency of 98.6 mg/L/d was achieved with 2-CP concentration of 200 mg/L, which was much higher than that of other anaerobic bioreactors. Furthermore, volatile fatty acids didn't accumulate under high 2-CP loading. Long HRTs significantly reduced the membrane fouling as the fouling rate (0.90 × 10⁹-5.44 × 10⁹ m^-1h^-1) was low. Spirochaetaceae and Methanosaeta were the dominant microbes responsible for dechlorination, methanogenesis, and shock resistance. All these results demonstrate that this AnMBR operated under long HRTs is good and robust for fluctuating chlorophenols wastewater treatment, which has high potential for treating fluctuating refractory organics wastewater with the low membrane fouling rate.

Taking Advantage of Promiscuity of Cold-Active Enzymes

Cold-active enzymes increase their catalytic efficiency at low-temperature, introducing structural flexibility at or near the active sites. Inevitably, this feat seems to be accompanied by lower thermal stability. These characteristics have made cold-active enzymes into attractive targets for the industrial applications, since they could reduce the energy cost in the reaction, attenuate side-reactions, and simply be inactivated. In addition, the increased structural flexibility could result in broad substrate specificity for various non-native substrates, which is called substrate promiscuity. In this perspective, we deal with a less addressed aspect of cold-active enzymes, substrate promiscuity, which has enormous potential for semi-synthesis or enzymatic modification of fine chemicals and drugs. Further structural and directed-evolutional studies on substrate promiscuity of cold-active enzymes will provide a new workhorse in white biotechnology.

Experimental and theoretical affinity and catalysis studies between halogenated phenols and peroxidases: Understanding the bioremediation potential

Halogenated phenols, such as 2,4-dichlorophenol (2,4-DCP) and 4-bromophenol (4-BP) are pollutants generated by a various industrial sectors like chemical, dye, paper bleaching, pharmaceuticals or in an agriculture as pesticides. The use of Horseradish peroxidase (HRP) in the halogenated phenols treatment has already been mentioned, but it is not well understood how the different phenolic substrates can bind in the peroxidase active site nor how these specific interactions can influence in the bioremediation potential. In this work, different removal efficiencies were obtained for phenolic compounds investigated using HRP as catalyst (93.87 and 59.19% to 4BP and 2,4 DCP, respectively). Thus, to rationalize this result based on the interactions of phenols with active center of HRP, we combine computational and experimental methodologies. The theoretical approaches utilized include density functional theory (DFT) calculations, docking simulation and quantum mechanics/molecular mechanics (QM/MM) technique. Michaelis Menten constant (Km) obtained through experimental methodologies were 2.3 and 0.95 mM to 2,4-DCP and 4-BP, respectively, while the specificity constant (K_cat/K_m) found was 1.44 mM^-1 s^-1 and 0.62 mM^-1 s^-1 for 4-BP and 2,4-DCP, respectively. The experimental parameters appointed to the highest affinity of HRP to 4-BP. According to the molecular docking calculations, both ligands have shown stabilizing intermolecular interaction energies within the HRP active site, however, the 4-BP showed more stabilizing interaction energy (-53.00 kcal mol^-1) than 2,4-dichlorophenol (-49.23 kcal mol^-1). Besides that, oxidative mechanism of 4-BP and 2,4-DCP was investigated by the hybrid QM/MM approach. This study showed that the lowest activation energy values for transition states investigated were obtained for 4-BP. Therefore, by theoretical approach, the compound 4-BP showed the more stabilizing interaction and activation energy values related to the interaction within the enzyme and the oxidative reaction mechanism, respectively, which corroborates with experimental parameters obtained. The combination between experimental and theoretical approaches was essential to understand how the degradation potential of the HRP enzyme depends on the interactions between substrate and the active center cavity of the enzyme.