Molecular characterization of the alpha subunit of multicomponent phenol hydroxylase from 4-chlorophenol-degrading Pseudomonas sp. strain PT3

A review of enhancement of chlorophenol bioremediation using synergistic effects between zero-valent iron and microorganisms

Chlorophenols (CPs) are a class of synthetic organic chemicals that are widely distributed in soil and groundwater, posing significant risks to human health and the environment due to persistence, acute toxicity, and potential carcinogenicity. Zero-valent iron (ZVI) has emerged as a promising remediation technique for CPs, but its efficacy is often hindered by surface passivation, non-target competition, and limited mobility in the subsurface. While CPs are inherently biodegradable, their high toxicity and the lack of functional enzymes in indigenous microbial systems restrict the effectiveness of bioremediation. Recently, a hybrid system integrating ZVI with microbial degradation draws increasingly research interests, paving out a new path for sustainable degradation of CPs. These systems leverage the synergistic interactions between ZVI and microorganisms to enhance CP biodegradation. This review provides a comprehensive analysis of the advancement. Key topics include the enhancement of electron transfer, alterations to microbial communities, mitigation of toxicity, and the interplay between other processes. Operation modes, ZVI dosage, and interactions with naturally occurring iron minerals, are also discussed in the context of applications in soil and groundwater remediation. Despite research efforts and successful implementations, critical knowledge gaps remain, particularly in regard to the characterization of microbial processes in natural systems, highlighting the need for future research.

An investigation of soil and groundwater metagenomes for genes encoding soluble and particulate methane monooxygenase, toluene-4-monoxygenase, propane monooxygenase and phenol hydroxylase

Soil and groundwater were investigated for the genes encoding soluble and particulate methane monooxygenase/ammonia monooxygenase (sMMO, pMMO/AMO), toluene 4-monooxygenase (T4MO), propane monooxygenase (PMO) and phenol hydroxylase (PH). The objectives were (1) to determine which subunits were present, (2) to examine the diversity of the phylotypes associated with the biomarkers and (3) to identify which metagenome associated genomes (MAGs) contained these subunits. All T4MO and PH subunits were annotated in the groundwater metagenomes, while few were annotated in the soil metagenomes. The majority of the soil metagenomes included only four sMMO subunits. Only two groundwater metagenomes contained five sMMO subunits. Gene counts for the pMMO subunits varied between samples. The majority of the soil metagenomes were annotated for all four PMO subunits, while three out of eight groundwater metagenomes contained all four PMO subunits. A comparison of the blast alignments for the sMMO alpha chain (mmoX) indicated the phylotypes differed between the soil and groundwater metagenomes. For the pMMO/AMO alpha subunit (pmoA/amoA), Nitrosospira was important for the soil metagenomes, while Methylosinus and Methylocystis were dominant for the groundwater metagenomes. The majority of pmoA alignments from both metagenomes were from uncultured bacteria. High quality MAGs were obtained from the groundwater data. Four MAGs (Methylocella and Cypionkella) contained sMMO subunits. Another three MAGs, within the order Pseudomonadales, contained all three pMMO subunits. All PH subunits were detected in seven MAGs (Azonexus, Rhodoferax, Aquabacterium). In those seven, all contained catechol 2,3-dioxagenase, and Aquabacterium also contained catechol 1,2-dioxygenase. T4MO subunits were detected in eight MAGs (Azonexus, Rhodoferax, Siculibacillus) and all, except one, contained all six subunits. Four MAGs (Rhodoferax and Azonexus) contained all subunits for PH and T4MO, as well as catechol 2,3-dixoygenase. The detection of T4MO and PH in groundwater metagenomes and MAGs has important implications for the potential oxidation of groundwater contaminants.

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.

Phenol hydroxylase from Pseudomonas sp. KZNSA: Purification, characterization and prediction of three-dimensional structure

A 61.3 kDa Phenol hydroxylase (PheA) was purified and characterized from Pseudomonas sp. KZNSA (PKZNSA). Cell free extract of the isolate grown in mineral salt medium supplemented with 600 ppm phenol showed 21.58 U/mL of PheA activity with a specific activity of 7.67 U/mg of protein. The enzyme was purified to 1.6-fold with a total yield of 33.6%. The purified PheA was optimally active at pH 8 and temperature 30 °C, with ≈95% stability at pH 7.5 and temperature 30 °C after 2 h. The Lineweaver-Burk plot showed the v_max and K_m values of 4.04 µM/min and 4.03 µM, respectively, for the substrate phenol. The ES-MS data generated from the tryptic digested fragments of pure protein and PCR amplification of a ≈600 bp gene from genomic DNA of PKZNSA lead to the determination of complete amino acid and nucleotide sequence of PheA. Bioinformatics tools and homology modelling studies indicated that PheA from PKZNSA is likely a probable protein kinase UbiB (2-octaprenylphenol hydroxylase) involving Lys and Asp at positions 153 and 288 for binding and active site, respectively. Characterization and optimization of PheA activity may be useful for a better understanding of 2,4-dichlorophenol degradation by this organism and for potential industrial application of the enzyme.