Biodegradation Pathway Research Articles

Aerobic bacterial degradation of polychlorinated biphenyls and their hydroxy and methoxy derivatives

Polychlorinated biphenyls are persistent organic pollutants hazardous to humans and to the environment. The products of biotransformation of these compounds can exist in natural objects as hydroxy and methoxy derivatives. This review summarizes the biodegradation pathways of polychlorinated biphenyls under the action of aerobic bacterial strains. The possibility of complete biodegradation of polychlorinated biphenyls and their derivatives under laboratory conditions is demonstrated. This information is valuable for researchers specializing in the biotransformations and toxicity of polychloroarene derivatives and would be useful for the development of remediation processes of natural objects contaminated with polychlorinated biphenyls.<br> The bibliography includes 253 references.

The potential role of gut microbiota in the occurrence and development of endometriosis

Endometriosis (EMT) has a significant impact on women’s physical and mental health. In this study, high-throughput sequencing technology was employed to detect differences in gut microbiota between EMT patients and healthy individuals (CTL). Additionally, Spearman correlation analysis was utilized to analyze the correlation between different bacterial genera and EMT biomarkers (CA125 and CA199). The results demonstrated that at the phylum level, the relative abundances of Proteobacteria and Desulfobacterota_G_459546 in the EMT group were significantly higher than those in the CTL group, while the relative abundances of Bacteroidota and Firmicutes_A in the EMT group were significantly lower than those in the CTL group. At the genus level, the relative abundances of Burkholderiales and Sphingomonadales in the EMT group were significantly higher than those in the CTL group, while the relative abundances of Bacteroidales and Roseburia in the EMT group were significantly lower than those in the CTL group. The correlation analysis results show that CA125 and CA199 are significantly positively correlated with Burkholderiales and Sphingomonadales, and significantly negatively correlated with Bacteroidales, Oscillospirales, and Roseburia. The PICRUSt2 results show that the relative abundance in the cell motility and xenobiotics biodegradation and metabolism pathways in the EMT group was higher than that in the CTL group, while the relative abundance in the translation, replication and repair, folding, sorting and degradation, metabolism of terpenoids and polyketides and metabolism of cofactors and vitamins pathways in the EMT group was lower than that in the CTL group. In brief, there is a close correlation between the imbalance of gut microbiota and the onset of EMT. The intestinal microbiota has great significance broad prospects for the prevention, diagnosis and treatment of EMT.

Arctic's hidden hydrocarbon degradation microbes: investigating the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on microbial communities and hydrocarbon biodegradation pathways in high-Arctic beaches

BackgroundCanadian Arctic summer sea ice has dramatically declined due to global warming, resulting in the rapid opening of the Northwest Passage (NWP), slated to be a major shipping route connecting the Atlantic and Pacific Oceans by 2040. This development elevates the risk of oil spills in Arctic regions, prompting growing concerns over the remediation and minimizing the impact on affected shorelines.ResultsThis research aims to assess the viability of nutrient and a surface washing agent addition as potential bioremediation methods for Arctic beaches. To achieve this goal, we conducted two semi-automated mesocosm experiments simulating hydrocarbon contamination in high-Arctic beach tidal sediments: a 32-day experiment at 8 °C and a 92-day experiment at 4 °C. We analyzed the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on the microbial community and its functional capacity using 16S rRNA gene sequencing and metagenomics. Hydrocarbon removal rates were determined through total petroleum hydrocarbon analysis. Biostimulation is commonly considered the most effective strategy for enhancing the bioremediation process in response to oil contamination. However, our findings suggest that nutrient addition has limited effectiveness in facilitating the biodegradation process in Arctic beaches, despite its initial promotion of aliphatic hydrocarbons within a constrained timeframe. Alternatively, our study highlights the promise of a surface washing agent as a potential bioremediation approach. By implementing advanced -omics approaches, we unveiled highly proficient, unconventional hydrocarbon-degrading microorganisms such as Halioglobus and Acidimicrobiales genera.ConclusionsGiven the receding Arctic sea ice and the rising traffic in the NWP, heightened awareness and preparedness for potential oil spills are imperative. While continuously exploring optimal remediation strategies through the integration of microbial and chemical studies, a paramount consideration involves limiting traffic in the NWP and Arctic regions to prevent beach oil contamination, as cleanup in these remote areas proves exceedingly challenging and costly.

Novel insights into revealing the intrinsic degradation mechanism of ciprofloxacin by Chlorella sorokiniana: Removal efficiency, pathways and metabolism

Microalgae-mediated biodegradation of antibiotics has attracted increasing interest. However, the exact degradation mechanism behind it remains elusive, which is crucial for improving its efficiency and large-scale implementation. Therefore, this study aims to thoroughly investigate how Chlorella sorokiniana (C.sorokiniana) degrades ciprofloxacin (CIP) from the molecular level to elucidate its complicated degradation mechanism. Results show that C.sorokiniana exhibited an impressive removal rate of 38.05–74.29 % for CIP, the synergistic effect of biosorption and biodegradation was the main removal mechanism of CIP. The content of EPS increased by 11.84–103.31 %, acting as a carrier to increase the bioavailability of CIP. Enzyme activity analysis identified POD, CYP450, and GST as the major catalytic enzymes responsible for the biotransformation process of CIP with increases of 6–41.2 %, 18.78–102.1 % and 3.53–58.15 %, respectively. Molecular docking further revealed that the binding affinity of 146.24 μM, 27.71 μM and 16.33 μM was observed for POD,CYP450, and GST, respectively, indicating the high metabolic efficiency of CIP by CYP450. Finally, DFT calculations elucidated the enzyme-mediated biodegradation pathway of CIP, including hydroxylation, decarboxylation, and ring opening. These findings are expected to further fill the knowledge gap on the catalysis mechanism of CIP degradation by enzymes and improve the practical application of microalgae to antibiotic wastewater.

Seasonal dynamics of bacterial composition and functions in biological treatment of coking wastewater

Seasonal dynamics of bacterial composition and functions were demonstrated for the biological fluidized-bed bioreactors combined in the anoxic/aerobic1/aerobic2 (AOO) coking wastewater (CWW) treatment sequences. The bacterial composition and functions in the CWW activated sludge samples were revealed by 16S rRNA genes amplicon sequencing. Thiobacillus, Cloacibacterium, Alkaliphilus and Pseudomonas were determined as core genera with seasonal changes. Mutable microbial community composition fluctuated in different seasons in same bioreactor. Distributions of predicted KEGG pathways along four seasons consistently demonstrated enrichment in biodegradation of carbon- and nitrogen-containing compounds. The major contaminants were removed from CWW by biochemical pathway of xenobiotics biodegradation and metabolism. This Level 2 pathway mainly owned the Level 3 pathways of benzoate degradation, drug metabolism-other enzymes, drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450, and aminobenzoate degradation. The RDA results showed that dissolved oxygen with seasonal fluctuation was the main parameter shaping the microbial community. The observed dynamics within the microbial community composition, coupled with the maintained stability of CWW treatment efficiencies and a consistent profile of microbial functional pathways, underscore the presence of functional redundancy in the AOO bioreactors. The study underscored stable and effective operational performances of bioreactors in the AOO sequences, contributing the knowledge of microbiological basics to the advancement of CWW biological treatment.Key points• Seasonal fluctuations of bacterial composition described for the AOO system.• Seasonal distributions of metabolic functions focused on carbon and nitrogen removal.• Functional redundancy was revealed in the AOO microbial community.

Anaerobic Degradation of Aromatic and Aliphatic Biodegradable Plastics: Potential Mechanisms and Pathways.

Biodegradable plastics (BDPs) have been widely used as substitutes for traditional plastics, and their environmental fate is a subject of intense research interest. Compared with the aerobic degradation of BDPs, their biodegradability under anaerobic conditions in environmental engineering systems remains poorly understood. This study aimed to investigate the degradability of BDPs composed of poly(butylene adipate-co-terephthalate) (PBAT), poly(lactide acid) (PLA), and their blends, and explore the mechanism underlying their microbial degradation under conditions of anaerobic digestion (AD). The BDPs readily depolymerized under thermophilic conditions but were hydrolyzed at a slow rate under conditions of mesophilic AD. After 45 days of thermophilic AD, a decrease in the molecular weight and significant increase in the production of methane and carbon dioxide production were observed. Network and metagenomics analyses identified AD as reservoirs of plastic-degrading bacteria that produce multiple plastic-degrading enzymes. PETase was identified as the most abundant plastic-degrading enzyme. A potential pathway for the anaerobic biodegradation of BDPs was proposed herein. The polymers of high molecular weight were subjected to abiotic hydrolysis to form oligomers and monomers, enabling subsequent microbial hydrolysis and acetogenesis. Ultimately, complete degradation was achieved predominantly via the pathway involved in the conversion of acetic acid to methane. These findings provide novel insight into the mechanism underlying the anaerobic degradation of BDPs and the microbial resources crucial for the efficient degradation of BDPs.

Microbial Enzymes for the Biodegradation of Polylactic Acid (PLA): Molecular Docking Simulation and Biodegradation Pathway Proposal

Polylactic acid (PLA), as a biodegradable polymer, finds widespread utility across diverse sectors, encompassing transportation, agriculture, biomedicine, textiles, electronics, and food packaging. Nonetheless, its degradation kinetics exhibit significant environmental sensitivity, necessitating the development of novel biotechnological methodologies to investigate the microbial and enzymatic constituents implicated in PLA biodegradation. In this review, molecular docking simulations are discussed to analyze the enzymatic degradation of PLA using specific enzymes: proteinase K, PLA depolymerase, and lipase. The binding energy, binding affinity, and dimensions of PLA-binding sites within the enzyme cavities have been examined for each enzyme. The binding amino acid residues mainly include serine, histidine, and aspartate for all plastics, while the interactions involve Van der Waals forces, conventional hydrogen bonding, carbon-hydrogen bonding, and Pi-interactions. Based on our synthesis of the literature, a theoretical PLA biodegradation pathway that illustrates the interaction pattern between PLA and the enzymes, as well as the degradation mechanism is proposed. Our review indicates that in natural environments, enzymes work synergistically, utilizing their unique properties to facilitate an efficient sequential catalytic process for PLA degradation. This integrative approach elucidates the mechanistic underpinnings and metabolic cascades governing PLA degradation, enriching insights into enzymatic catalysis and microbial enzyme-mediated plastic biotransformation. Consequently, a comprehensive understanding of these processes is paramount in optimizing biodegradation kinetics and enhancing the environmental performance of biodegradable polymers. This review provides a detailed framework for refining PLA management strategies and advancing sustainable polymer utilization.

Mechanisms of efficient polyacrylamide degradation: From multi-omics analysis to structural characterization of two amidohydrolases

Polyacrylamide (PAM) is a high molecular weight polymer with extensive applications. However, inefficient natural degradation of PAM results in its environmental accumulation. Here, using multi-omics analysis, we constructed the PAM biodegradation pathway in Klebsiella sp. PCX, an efficient PAM-degrading bacterium. Subsequently, two unclassified amidohydrolases (PCX00451 and PCX04581) were identified as key factors for rapid PAM biodegradation, both of which possessed much higher hydrolysis efficiency for PAM than for small molecule amide compounds. Besides, crystal structures of PCX00451 and PCX04581 were solved. Both two amidohydrolases were consisted with a twisted triosephosphateisomerase (TIM)-barrel and a smaller β-sandwich domain. And their binding pockets were in the conserved metal center of TIM-barrel domain. Moreover, Asp267 of PCX00451 and Asp282 of PCX04581 were examined as active sites for acid/base catalysis. Our research characterized the molecular mechanisms of two efficient amidohydrolases, providing theoretical basis and valuable tools for PAM bioremediation.

Isolation and Identification of Four Strains of Bacteria with Potential to Biodegrade Polyethylene and Polypropylene from Mangrove.

With the rapid growth of global plastic production, the degradation of microplastics (MPs) has received widespread attention, and the search for efficient biodegradation pathways has become a hot topic. The aim of this study was to screen mangrove sediment and surface water for bacteria capable of degrading polyethylene (PE) and polypropylene (PP) MPs. In this study, two strains of PE-degrading bacteria and two strains of PP-degrading candidate bacteria were obtained from mangrove, named Pseudomonas sp. strain GIA7, Bacillus cereus strain GIA17, Acinetobacter sp. strain GIB8, and Bacillus cereus strain GIB10. The results showed that the degradation rate of the bacteria increased gradually with the increase in degradation time for 60 days. Most of the MP-degrading bacteria had higher degradation rates in the presence of weak acid. The appropriate addition of Mg2+ and K+ was favorable to improve the degradation rate of MPs. Interestingly, high salt concentration inhibited the biodegradation of MPs. Results of scanning electron microscopy (SEM), atomic force microscopy (AFM), and Fourier-transform infrared spectroscopy (FTIR) indicated the degradation and surface changes of PP and PE MPs caused by candidate bacteria, which may depend on the biodegradation-related enzymes laccase and lipase. Our results indicated that these four bacterial strains may contribute to the biodegradation of MPs in the mangrove environment.

Bacterial bioaugmentation for paracetamol removal from water and sewage sludge. Genomic approaches to elucidate biodegradation pathway

Wastewater treatment plants (WWTPs) are recognized as significant contributors of paracetamol (APAP) into the environment due to their limited ability to degrade it. This study used a bioaugmentation strategy with Pseudomonas extremaustralis CSW01 and Stutzerimonas stutzeri CSW02 to achieve APAP biodegradation in solution in wide ranges of temperature (10-40oC) and pH (5-9), reaching DT50 values < 1.5hours to degrade 500mgL-1 APAP. Bacterial strains also mineralized APAP in solution (<30%), but when forming consortia with Mycolicibacterium aubagnense HPB1.1, mineralization significantly increased (up to 74% and 58% for CSW01+HPB1.1 and CSW02+HPB1.1, respectively), decreasing DT50 values to only 1 and 9 days. Despite the complete degradation of APAP and its high mineralization, residual toxicity throughout the process was observed. Three APAP metabolites were identified (4-aminophenol, hydroquinone and trans-2-hexenoic acid) that quickly disappeared, but residual toxicity remained, indicating the presence of other non-detected intermediates. CSW01 and CSW02 degraded also 100% APAP (50mgkg-1) adsorbed on sewage sludge, with DT50 values of only 0.7 and 0.3 days, respectively, but < 15% APAP was mineralized. A genome-based analysis of CSW01 and CSW02 revealed that amidases, deaminases, hydroxylases, and dioxygenases enzymes were involved APAP biodegradation, and a possible metabolic pathway was proposed. Environmental ImplicationThe wide use of paracetamol (APAP) involves ecological risks, being considered an emerging pollutant. APAP excreted by humans ends up in WWTPs, where its elimination is not complete, remaining in part in the effluent treated waters (discharged into surface waters used for soil irrigation) and in part adsorbed on sewage sludge (used as fertilizer in agricultural soils). APAP bioremediation in WWTPs is the unique opportunity to remove it from both matrices before its dispersion in the environment.The novelty of this study is the isolation of two bacterial strains from sewage sludge, P. extremaustralis CSW01 and S. stutzeri CSW02, that could degrade very high concentrations of APAP and their main formed metabolites, both in water and, for the first time, in sewage sludge, in very short periods of time, and even reach high percentages of APAP mineralization in water. Moreover, CSW01 and CSW02 were active under wide ranges of temperature and pH, and are therefore excellent candidates for the chance to achieve a reduction of APAP toxicity in the environment. In addition, by a genome-based analysis, enzymes possibly involved in APAP biodegradation have been identified and a possible degradation pathway has been proposed.

Differential Effects of Sulfur Fertilization on Soil Microbial Communities and Maize Yield Enhancement

Sulfur (S) is an essential nutrient for plant growth, influencing not only crop yields but also the composition and function of soil microbial communities. However, the differential effects of S fertilization on abundant and rare taxa in agricultural soils remain poorly understood. This study investigates the impact of different S fertilizer types on maize yield and the structure and stability of soil microbial communities, with a particular focus on abundant and rare taxa. S fertilization led to significant increases maize yield on two typical soils (black soil and sandy soil) (5.3–24.3%) and altered soil properties, including reducing pH (0.04–0.20) and increasing the available sulfur (AS) content (3.8–8.0 mg kg−1), with ammonium sulfate having a more pronounced effect than elemental sulfur. Microbial analysis revealed distinct impacts on the diversity and community structure of both abundant and rare taxa. Elemental sulfur reduced the alpha diversity of abundant taxa more than ammonium sulfate, while NMDS indicated significant shifts in community structures, particularly among abundant taxa. Network analysis showed that S fertilization decreased the complexity of microbial interactions among rare taxa, with ammonium sulfate leading to simpler networks and elemental sulfur resulting in higher modularity. SEM highlighted that the diversity of rare taxa played a crucial role in influencing maize yield, alongside direct effects from soil properties such as AS and SAR (aryl sulfatase). Functional predictions demonstrated that amino acid metabolism and xenobiotic biodegradation and metabolism pathways were enriched in rare taxa, suggesting significant implications for soil health and crop productivity. This study provides new insights into the roles of abundant and rare bacterial taxa under S fertilization, emphasizing their importance in optimizing fertilization strategies for enhanced crop yield in specific soil types.

Biodegradation of thermoplastic starch by a newly isolated active microbial community: Deciphering the biochemical mechanisms controlling bioprocess robustness

Defining sustainable end-of-life routes for bioplastics comprises a task of outmost importance, while biological recycling constitutes the most favorable option for several biopolymers, such as thermoplastic starch (TPS). To our knowledge, this is the first study to assess the biodegradation of TPS pellets and films in aqueous cultures employing an acclimated microbial community. Biological treatment of bioplastics displayed a two-phase pattern that included different biodegradation rates, where TPS removal in the first phase remained high and decelerated in the second phase reaching a plateau. Thus, TPS weight reduction of 14.8 % was observed using pellets following 10 d of incubation, while although films exhibited higher reduction (slightly over 30 % in 15 d), the biodegradation rate was significantly reduced thereafter. Several changes of starch related bands were detected (using FTIR) in the surface of both pellets and films during the bioprocess, indicating induction of a common biodegradation pathway. Distinct bacterial assemblages were formed during the TPS biodegradation process and statistically significant differences were detected in the abundance of several genera between the two degradation phases. Fungal communities were more stable (Fusarium and Neocosmospora were dominant at all times) and there was no effect of biofilm or degradation phase on fungal community composition. Overall, a more diverse community incorporating lower catalytic activity was gradually formed, as confirmed by the shift between k-stategist and r-stategist taxa monitored, while crystalline over amorphous regions were enhanced in the biopolymer during TPS biodegradation, responses consistent with the biodegradation rate reduction observed in the plateau stage. The study highlighted the biochemical mechanism limiting TPS biodegradation processes and the significant potential of the newly isolated community in the development of TPS waste treatment technologies.

Metformin hydrolase is a recently evolved nickel-dependent heteromeric ureohydrolase

The anti-diabetic drug metformin is one of the most widely prescribed medicines in the world. Together with its degradation product guanylurea, it is a major pharmaceutical pollutant in wastewater treatment plants and surface waters. An operon comprising two genes of the ureohydrolase family in Pseudomonas and Aminobacter species has recently been implicated in metformin degradation. However, the corresponding proteins have not been characterized. Here we show that these genes encode a Ni2+-dependent enzyme that efficiently and specifically hydrolyzes metformin to guanylurea and dimethylamine. The active enzyme is a heteromeric complex of α- and β- subunits in which only the α-subunits contain the conserved His and Asp residues for the coordination of two Ni2+ ions in the active site. A crystal structure of metformin hydrolase reveals an α2β4 stoichiometry of the hexameric complex, which is unprecedented in the ureohydrolase family. By studying a closely related but more widely distributed enzyme, we find that the putative predecessor specifically hydrolyzes dimethylguanidine instead of metformin. Our findings establish the molecular basis for metformin hydrolysis to guanylurea as the primary pathway for metformin biodegradation and provide insight into the recent evolution of ureohydrolase family proteins in response to an anthropogenic compound.

Degradation of nitrocellulose film under aerobic conditions by a newly isolated Rhodococcus pyridinivorans strain

The explosive and biorefractory nature of nitrocellulose (NC) poses major risks to both humans and the environment. Expanding the range of microorganisms capable of degrading NC is essential, though the most effective known microorganisms, Desulfovibrio genera and Fusarium solani, achieve degradation rates of 5%-25%. Here, a novel strain, Rhodococcus pyridinivorans LZ1 was isolated, demonstrating the ability to degrade NC, with its growth potentially enhanced by the presence of NC. The degradation process was monitored by assessing changes in nitrate, nitrite, and ammonium. Notably, the –OH strength of NC increased over time, whereas the energetic functional groups (–NO2 and O-NO2) diminished. Furthermore, the presence of NC enhanced nitrate esterase activity 1–2-fold, indicating that ammonification was the primary pathway for NC biodegradation. By converting the nitrate ester of NC into hydroxyl, R. pyridinivorans LZ1 mitigates the harmful effects of NC, offering a promising approach for the treatment of NC waste and wastewater.

Adaptation towards catabolic biodegradation of trace organic contaminants in activated sludge

Trace organic contaminants (TrOCs) are omnipresent in wastewater treatment plants (WWTPs), yet, their removal during wastewater treatment is oftentimes incomplete and underlying biotransformation mechanisms are not fully understood. In this study, we elucidate how different factors, including pre-exposure levels and duration, influence microbial adaptation towards catabolic TrOC biodegradation and its potential role in biological wastewater treatment. Four sequencing batch reactors (SBRs) were operated in parallel in three succeeding phases, adding and removing a selection of 26 TrOCs at different concentration levels. After each phase of SBR operation, a series of batch experiments was conducted to monitor biotransformation kinetics of those same TrOCs across various spike concentrations. For half of our test TrOCs, we detected increased biotransformation in sludge pre-exposed to TrOC concentrations ≥5 µg L−1 over a 30-day period, with most significant differences observed for the insect repellent DEET and the artificial sweetener saccharin. Accordingly, 16S rRNA amplicon sequencing revealed enrichment of taxa that have previously been linked to catabolic biodegradation of several test TrOCs, e.g., Bosea sp. and Shinella sp. for acesulfame degradation, and Pseudomonas sp. for caffeine, cyclamate, DEET, metformin, paracetamol, and isoproturon degradation. We further conducted shotgun metagenomics to query for gene products previously reported to be involved in the TrOCs’ biodegradation pathways. In the future, directed microbial adaptation may be a solution to improve bioremediation of TrOCs in contaminated environments or in WWTPs.

Biodecolorization and Biodegradation of Sulfur Black by the Strain Aspergillus sp. DS-28

The textile industry significantly contributes to environmental pollution through its use of synthetic dyes, especially sulfur black, known for its toxicity and resistance to degradation. This research focuses on a fungal strain, Aspergillus sp. strain DS-28, isolated from activated sludge, which exhibits an exceptional ability to biodegrade sulfur black dye. This study systematically assessed the biodegradation capacity of this strain through a series of experiments conducted over a 7-day period. Analytical techniques including high-performance liquid chromatography time-of-flight mass spectrometry (HPLC-TOF/MS), scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FTIR) were employed to monitor the degradation process. SEM showed a significant reduction in particle size, with surfaces becoming smoother and flatter post treatment. XRD indicated a decrease in the intensity of several chemical bonds, and FTIR analysis demonstrated the enhanced vibrational absorption peaks of benzene ring bonds, with the disappearance of -C-S- and -C-S-S-C- groups. The results demonstrate that Aspergillus sp. DS-28 degrades sulfur black by initiating the oxidative breakdown of its complex structures into simpler forms. This study not only elucidates the biodegradation pathway facilitated by Aspergillus sp. DS-28, but also highlights its potential application in developing eco-friendly waste management strategies for treating dye-contaminated wastewater.

Toxicity, degradation and metabolic pathway of 4-chlorinephenol in Chlorella vulgaris

Environmental contamination by 4-chlorinephenol (4-CP) has received widespread attention due to its frequent detection and adverse environmental effects. The traditional water treatment approaches and equipment are relatively mature, making them easier to operate and maintain. However, 4-CP is particularly difficult to degrade using the technologies, often resulting in incomplete removal, secondary pollution, or high energy consumption. The present study explored the toxicity of 4-CP to Chlorella vulgaris and its removal mechanism in microalgae. The results revealed that the photosynthetic activity and the growth of C. vulgaris were inhibited at high-level 4-CP (≥ 60 mg/L) during the whole exposure period. The dry weight and Chlorophyll-a content of C. vulgaris in the 4-CP treatment at 90 mg/L were only 72.3 % and 72.1 % of the control group, respectively. The structure and function of C. vulgaris was dramatically impacted under 4-CP stress. Malondialdehyde content, superoxide dismutase and catalase activities were significantly increased under multiple 4-CP concentrations, rising by 217 %, 299 %, and 78 % at 90 mg/L 4-CP compared to the control. Additionally, the removal of 4-CP by C. vulgaris aligned more closely with the pseudo-first-order model than with the pseudo-second-order model. As 4-CP concentration rose from 10 to 90 mg/L, the 4-CP removal rate decreased from 86.0 % to 56.7 % and the half-life was increased from 5.419 to 7.673 d based on the pseudo-first-order kinetics of 4-CP removal by C. vulgaris. Biodegradation is the major pathway for 4-CP removal by C. vulgaris, accounting for 72.54 % of the total removal rate at 30 mg/L on the 6th day. A total of 5 metabolites were detected for 6-day cultivation, including 4-chlorocatechol, hydroquinone, pyrogallol, 1,4-benzoquinone and succinic acid. This work provided an insight into the removal mechanism and biodegradation pathway of 4-CP in C. vulgaris.

Discovery of the 1-naphthylamine biodegradation pathway reveals a broad-substrate-spectrum enzyme catalyzing 1-naphthylamine glutamylation.

1-Naphthylamine (1NA), which is harmful to human and aquatic animals, has been used widely in the manufacturing of dyes, pesticides, and rubber antioxidants. Nevertheless, little is known about its environmental behavior and no bacteria have been reported to use it as the growth substrate. Herein, we describe a pathway for 1NA degradation in the isolate Pseudomonas sp. strain JS3066, determine the structure and mechanism of the enzyme NpaA1 that catalyzes the initial reaction, and reveal how the pathway evolved. From genetic and enzymatic analysis, a five gene-cluster encoding a dioxygenase system was determined to be responsible for the initial steps in 1NA degradation through glutamylation of 1NA. The γ-glutamylated 1NA was subsequently oxidized to 1,2-dihydroxynaphthalene which was further degraded by the well-established pathway of naphthalene degradation via catechol. A glutamine synthetase-like (GS-like) enzyme (NpaA1) initiates 1NA glutamylation, and this enzyme exhibits a broad substrate selectivity toward a variety of anilines and naphthylamine derivatives. Structural analysis revealed that the aromatic residues in the 1NA entry tunnel and the V201 site in the large substrate-binding pocket significantly influence NpaA1's substrate preferences. The findings enhance understanding of degrading polycyclic aromatic amines, and will also enable the application of bioremediation at naphthylamine contaminated sites.

Biodegradation Pathway of Congo Red azo dye by Geotrichum candidum and Toxicity Assessment of Metabolites

Biodegradation Pathway of Congo Red azo dye by Geotrichum candidum and Toxicity Assessment of Metabolites

Aerobic phenol degradation using native bacterial consortium via ortho-and meta-cleavage pathways.

Effective bioremediation of a phenol-polluted environment harnesses microorganisms' ability to utilize hazardous compounds as beneficial degraders. In the present study, a consortium consisting of 15 bacterial strains was utilized. The current study aims to monitor the phenol biodegradation pathway. The tested consortium showed effective potential in the bioremediation of phenol-contaminated industrial wastewater. The enzymatic studies conducted brought to light that the bacterial consortium under test was proficient in degrading phenol under aerobic conditions while exhibiting the simultaneous expression of both ortho- and meta-cleavage pathways. It was observed that pheA, pheB, and C12O genes were maximally expressed, and the enzymes responsible for phenol degradation, namely, phenol hydroxylase, catechol 1,2-dioxygenase, and catechol 2,3-dioxygenase, reached maximum activity after 48 h of incubation with a 20-ppm phenol concentration. To gain a deeper understanding of the activation of both ortho- and meta-cleavage pathways involved in phenol degradation, a technique known as differential display reverse transcriptase polymerase chain reaction (DDRT-PCR) was applied. This method allowed for the specific amplification and detection of genes responsible for phenol degradation. The expression levels of these genes determined the extent to which both ortho- and meta-cleavage pathways were activated in response to the presence of phenol.