Degradation of Di(2-Ethylhexyl) Phthalate by a Novel Gordonia alkanivorans Strain YC-RL2

Recent advances in occurrence, biotreatment, and integrated insights into bacterial degradation of phthalic acid esters in aquatic environments

Phthalic acid esters (PAEs) are prevalent as emerging contaminants owing to their widespread use as plasticizers in industry. Despite their environmental and health risks, a limited understanding of PAE contamination in aquatic environments hinders the practical implementation of biotreatment strategies for their removal. This paper reviews the advances in occurrence, biotreatment, and relevant integrative analysis of bacterial PAE degradation over the past decade. In various aquatic environments, dibutyl phthalate (DBP) and di(2-ethylhexyl) phthalate (DEHP) are the predominant PAE pollutants across different regions, with alarming levels reported in Eastern China. PAEs in water usually inhibit the growth and metabolism of surrounding organisms. Meanwhile, various biotreatment techniques have proven effective in removing PAEs from leachate and wastewater. The treatment efficiency can be further enhanced by incorporating suitable physicochemical processes and optimizing key factors, such as the initial pollutant concentration, PAE type, and reaction time. Additionally, a K-means machine learning algorithm and 16S rRNA gene-based evolutionary analysis were employed to reveal that soil is a preferred source for isolating strains, with Gordonia and Pseudomonas being the dominant genera of PAE-degrading bacteria exhibiting high degradation efficiency. Moreover, most PAE hydrolase genes were discovered in these two genera. Different gene clusters facilitated the subsequent degradation pathways under aerobic or anaerobic conditions. This paper presents the latest updates on PAE biotreatment and offers an integrated analysis of the bacterial degradation involved. Future research should apply these insights to enhance the overall effectiveness of PAE removal in water.

Characterization of modified rape straw biochar in immobilizing Aspergillus sydowii W1 pellets and evaluation on its role as a novel composite for di(2-ethylhexyl) phthalate degradation

Di(2-ethylhexyl) phthalate (DEHP) is one of the most widely used plasticizers, which has harmful biological effects and poses a serious threat to ecological environments and human health. In this study, a novel strain Aspergillus sydowii W1 was reported with DEHP degradation ability. Under the optimal conditions of 35°C and pH 6.0, strain W1 degraded 68.48 % of 50 mg/L DEHP within 120 h, while the biochar immobilized W1 can enhance the removal efficiency by 15.33 %. The immobilized W1 also showed excellent performance in DEHP polluted wastewater with concentration of 50 mg/L, and its removal rate reached 85.72 % within 144 h. Interestingly, the fermented broth of strain W1 has the activity of hydrolyzing DEHP, and the highest value of crude enzyme activity was at 35°C and pH 8.5. In addition, nine metabolic products of DEHP degraded by strain W1 were identified by HPLC-MS/MS and GC-MS. In combination with these intermediates and related enzymatic analysis, two possible catabolism pathways of DEHP degradation by strain W1 were concluded. This study confirmed that immobilized W1 is an effective composite for removing DEHP in water environment and also strengthened our understanding on the DEHP degradation process of A. sydowii.

Screening, identification, metabolic pathway of di-n-butyl phthalate degrading Priestia megaterium P-7 isolated from long-term film mulched cotton field soil in Xinjiang

Introduction

Di-n-butyl phthalate (DBP) is one of the most widely used phthalate esters (PAEs) and is considered an emerging global pollutant. It may pose a significant threat to ecosystem and human health due to its residual hazards and accumulation in the environment. Bacteria-driven PAE biodegradation is considered an economical and effective strategy for remediating such polluted environments.

Methods

A DBP-degrading bacterium (P-7), was isolated from long-term film mulched cotton field soil. Its identity was confirmed via physiological, biochemical, and 16S rRNA gene analyses. The degradation conditions were optimized through single-factor experiments and response surface methodology (RSM).Furthermore, the whole-genome sequencing coupled with metabolomics was employed to elucidate metabolic mechanisms.

Results

Priestia megaterium P-7 (P. megaterium P-7) achieved 100% DBP removal within 20 h under optimal conditions and exhibited broad substrate specificity for other PAEs. Genomic analysis identified key genes (lip, aes, ybfF, estA, and yvaK) encoding esterases/hydrolases that initiate DBP catabolism, converting it to phthalic acid (PA). Subsequent decarboxylation (pdc, bsdCD, mdcACDH, and lysA) and dioxygenase-mediated steps integrated PA into the TCA cycle. Metabolomics revealed three degradation pathways: decarboxylation (DBP → MBP → BB → BA→Catechol), hydrolysis (DBP → MBP → PA → PCA → Catechol) and direct β-oxidation (DBP → DEP → MEP → PA → Catechol).

Conclusion

P. megaterium P-7 demonstrates exceptional degradation efficiency, substrate versatility, and environmental stress tolerance, making it a promising candidate for bioremediation of organic pollutants in contaminated soil.

Mangrove consortium resistant to the emerging contaminant DEHP: Composition, diversity, and ecological function of bacteria

The continuous use of Di(2-ethylhexyl) phthalate (DEHP) in plastic products turns it into a ubiquitous contaminant in the environment. However, DEHP can cause harm to human beings, wildlife, and ecosystems due to its estrogenicity and toxicity. Thus, finding an efficient approach to removing this contaminant from the environment is crucial. The present study aimed to prospect and characterize a bacterial consortium (MP001) isolated from a neotropical mangrove for DEHP bioremediation. A laboratory experiment was performed with environmentally relevant DEHP concentrations (0.05, 0.09, 0.19, 0.38, 0.75, 1.50, 3.00, and 6.00 mg L-1) to determine the consortium resistance to this contaminant and high-throughput sequencing was accomplished to assess the bacterial composition, diversity, and potential ecological function of consortium MP001. The consortium MP001 presented a significant biomass increase throughout short-term incubations with increasing concentrations of DEHP (GLMs, p< 0.001). MP001 was constituted by Paraclostridium sp. (78.99%) and Bacillus sp. (10.73%). After 48 h of consortia exposure to DEHP, the bacterial population changed to Paraclostridium (50.00%), Staphylococcus sp. (12.72%), Staphylococcus epidermidis (10.40%) and Bacillus sp. (17.63%). In the negative control, the bacteria community was composed of Paraclostridium sp. (54.02%), Pseudomonas stutzeri (19.44%), and Staphylococcus sp. (11.97%). The alpha diversity of the MP001 consortium was not significant (Kruskall-Wallis; p > 0.05), and no significant difference was found between the DEHP treatment and the negative control. Furthermore, the potential ecological function found in the consortium MP001 with higher potential for application in bioremediation purposes was fermentation. The results found in this study highlight the potential of a bacterial consortium to be used in the bioremediation of DEHP-contaminated aquatic environments.

LC-MS-based untargeted metabolomics reveals benzoic acid as a predictive biomarker for embryo implantation potential

Evaluating the quality of embryos and implantation potential is a critical determinant of in vitro fertilization and embryo transfer, and it is also one of the main challenges of assisted reproductive technology. A reliable non-invasive method to choose the best candidate with real implantation potential for transfer from two day-3 embryos with equal morphological quality is still lacking clinically. In this article, a sensitive LC-MS method was developed and metabolomic profiling analysis in a 3-day embryo culture medium was performed. Differential metabolites were analysed in two kinds of commercial culture media, and a total of 66 common metabolites were obtained from 106 independent samples in 5 batches. The relationship between changes in key metabolite, benzoic acid, concentration and the embryo implantation result was discovered. This work improved coverage through conditional optimization, enhanced the reliability of omics data through multi-batch validation, and provided a potential biomarker for evaluating the implantation potential of day-3 embryos.

The Biodegradation of Acrylic-Coated Woven Fabrics by Gordonia alkanivorans S7: A Novel Approach for Sustainable Textile Waste Management

The increasing environmental issue related to textile waste, especially synthetic fibers treated with acrylic resins, demands the creation of sustainable recycling techniques. Biotechnological methods, such as microbial degradation, present a viable solution for the elimination of these coatings and the recovery of important fibers. This study investigates the potential of a biotechnological approach for the removal of acrylic resins from coated woven textile wastes. The biodegradation process of coated woven fabric after the pretreatment at a high temperature (121 °C) or 6% H2O2 was performed using the hydrocarbon-degrading bacterial strain Gordonia alkanivorans S7. Over a 72 h biodegradation period, an increase in emulsifying and esterase activities was observed. A reduction mass of the coated textile waste by up to 7 wt% was achieved, and the elimination of acrylic resin was confirmed through FTIR analysis. The findings indicate the usefulness of the biotechnological method in eliminating acrylic resin from textile waste, presenting a viable strategy for polyester fiber recovery and substantially mitigating its environmental impact.

Algae- and bacteria-based biodegradation of phthalic acid esters towards the sustainable green solution

Phthalic acid esters are widely used worldwide as plasticizers. The high consumption of phthalates in China makes it the world's largest plasticizer market. The lack of phthalic acid ester's chemical bonding with the polymer matrix facilitates their detachment from plastic products and subsequent release into the environment and causes serious threats to the health of living organisms. Thus, environmentally friendly and sustainable solutions for their removal are urgently needed. In this context, both natural and engineered bacterial and algal communities have played a crucial role in the degradation of various phthalic acid esters present in water and soil. When algae-bacteria co-culture is compared to a singular algae or bacteria system, this symbiotic system shows superior performance in the removal of dibutyl phthalates and diethyl phthalates from synthetic wastewater. This review provides an optimistic outlook for co-culture systems by in-depth examining single microorganisms, namely bacteria and algae, as well as algae-bacterial consortiums for phthalates degradation, which will draw attention to species co-existence for the removal of various pollutants from the environment. In addition, further development and research, particularly on the mechanisms, genes involved in the degradation of phthalic acid esters, and interactions between bacterial and algal species, will lead to the discovery of more adaptable species as well as the production of targeted species to address the environmental pollution crisis and provide a green, efficient, and sustainable approach to environmental protection. Discrepancies in knowledge and potential avenues for exploration will enhance the existing body of literature, enabling researchers to investigate this field more comprehensively.

Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste

Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman's correlation analysis suggested that Myxococcales, Methyloligellaceae, Mycobacterium, and Micromonospora were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through catC, pcaD, pcaI, pcaF, and fadA. Efficient bacterial isolates from the mangrove sediment, identified as Gordonia sp. and Gordonia polyisoprenivorans, were able to degrade DEHP (65-97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).

Biodegradation of PAEs in contaminated soil by immobilized bacterial agent and the response of indigenous bacterial community

Phthalic acid esters (PAEs) are common hazardous organic contaminants in agricultural soil. Microbial remediation is an effective and eco-friendly method for eliminating PAEs. Nevertheless, the operational mode and potential application of immobilized microorganisms in PAEs-contaminated soil are poorly understood. In this study, we prepared an immobilized bacterial agent (IBA) using a cedar biochar carrier to investigate the removal efficiency of PAEs by IBA in the soil. We found that IBA degraded 88.35% of six optimal-control PAEs, with 99.62% biodegradation of low-molecular-weight PAEs (DMP, DEP, and DBP). The findings demonstrated that the IBA achieved high efficiency and a broad-spectrum in degrading PAEs. High-throughput sequencing revealed that IBA application altered the composition of the soil bacterial community, leading to an increase in the relative abundance of PAEs-degrading bacteria (Rhodococcus). Furthermore, co-occurrence network analysis indicated that IBA promoted microbial interactions within the soil community. This study introduces an efficient method for the sustainable remediation of PAEs-contaminated soil.

Bacterial Catabolism of Phthalates With Estrogenic Activity Used as Plasticisers in the Manufacture of Plastic Products

Phthalic acid esters (PAEs), the pervasive and ubiquitous endocrine-disrupting chemicals of environmental concern, generated annually on a million-ton scale, are primarily employed as plasticisers in the production of a variety of plastic products and as additives in a large number of commercial supplies. The increased awareness of various adverse effects on the ecosystem and human health including reproductive and developmental disorders has led to a striking increase in research interest aimed at managing these man-made oestrogenic chemicals. In these circumstances, microbial metabolism appeared as the major realistic process to neutralise the toxic burdens of PAEs in an ecologically accepted manner. Among a wide variety of microbial species capable of degrading/transforming PAEs reported so far, bacteria-mediated degradation has been studied most extensively. The main purpose of this review is to provide current knowledge of metabolic imprints of microbial degradation/transformation of PAEs, a co-contaminant of plastic pollution. In addition, this communication illustrates the recent advancement of the structure-functional aspects of the key metabolic enzyme phthalate hydrolase, their inducible regulation of gene expression and evolutionary relatedness, besides prioritising future research needs to facilitate the development of new insights into the bioremediation of PAE in the environment.

Biodegradation of phthalic acid esters by a novel marine bacterial strain RL-BY03: Characterization, metabolic pathway, bioaugmentation and genome analysis

Biodegradation is recognized as the main route for the decomposition of phthalic acid esters (PAEs) in nature, but the fate of PAEs in marine ecosystems is not well understood. Herein, a novel marine bacterium, Gordonia sihwaniensis RL-BY03, was identified and analyzed for its ability to degrade PAEs. Furthermore, the metabolic mechanism of di-(2-ethylhexyl) phthalate (DEHP) was examined through UPLC-MS/MS and genomic analysis. RL-BY03 could rely solely on several types of PAEs as its sole carbon source. Initial pH and temperature for DEHP degradation were optimized as 8.0 and 30 °C, respectively. Surprisingly, RL-BY03 could simultaneously degrade ethyl acetate and DEHP and they could increase the cell surface hydrophobicity. DEHP degradation kinetics fitted well with the first-order decay model. The metabolic pathway of DEHP was deduced following the detection of five metabolic intermediates. Further, genes that are related to DEHP degradation were identified through genomic analysis and their expression levels were validated through RT-qPCR. A co-related metabolic pathway at biochemical and molecular level indicated that DEHP was turned into DBP and DEP by β-oxidation, which was further hydrolyzed into phthalic acid. Phthalic acid was utilized through catechol branch of β-ketoadipate pathway. Additionally, RL-BY03 exhibited excellent bioremediation potential for DEHP-contaminated marine samples. In general, these findings have the potential to enhance our understanding of the fate of PAEs in marine ecosystems.

In-silico characterization of a hypothetical protein of Sulfobacillus sp. hq2 for degradation of phthalate diesters

Phthalate plasticizers are hazardous compounds capable of causing endocrine disruption, cancers, and developmental disorders. Phthalate diesters are commonly used plasticizers in plastic products (PVC pipes) that leach out into the environment due to changes in temperature, pressure, and pH, posing harmful effects on different life forms. Bioremediation of phthalate diesters utilizing bacterial esterase has been recognized as an efficient approach but few effective esterases capable of degrading a wide range of phthalate diesters have been identified. Further, the thermostability of these esterases is a highly desirable property for their applications in diverse in-situ conditions. In this present in-silico study a hypothetical protein (POB10642.1) as a high-potential esterase from a thermostable strain of Sulfobacillus sp. hq2 has been characterized. Analysis revealed a significant sequence identity of 42.67 % and structural similarity (RMSD 0.557) with known phthalate diester degrading EstS1 esterase and a high Tm range of 55-66 °C. Structural analysis revealed the presence of two cavities on the surface mediating toward the catalytic site forming a catalytic tunnel. The enzyme POB10642.1 has significant molecular docking binding energies in the range of -5.4 to -7.5 kcal/mol with several phthalate diesters, including Diethyl phthalate, Dipropyl phthalate, Dibutyl phthalate, Dipentyl phthalate, Dihexyl phthalate, Benzyl butyl phthalate, Dicyclohexyl phthalate, and Bis(2-ethylhexyl) phthalate. High stability of binding during 100 ns molecular dynamics simulations revealed efficient and stable binding of the enzyme with a wide range of phthalate diesters at its active site, demonstrating the ability of the identified esterase to interact with and degrade diverse phthalate diesters. Therefore, POB10642.1 esterase can be an efficient candidate to be utilized in the development of enzyme-based bioremediation technologies to reduce the toxic levels of phthalate diesters.

Microbial degradation of contaminants of emerging concern: metabolic, genetic and omics insights for enhanced bioremediation

The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication etc., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. "Omics" and "Meta-omics" techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.

Simultaneously degradation of various phthalate esters by Rhodococcus sp. AH-ZY2: Strain, omics and enzymatic study

Phthalate esters (PAEs) are widely used as plasticizers and cause serious complex pollution problem in environment. Thus, strains with efficient ability to simultaneously degrade various PAEs are required. In this study, a newly isolated strain Rhodococcus sp. AH-ZY2 can degrade 500 mg/L Di-n-octyl phthalate completely within 16 h and other 500 mg/L PAEs almost completely within 48 h at 37 °C, 180 rpm, and 2 % (v/v) inoculum size of cultures with a OD600 of 0.8. OD600 = 0.8, 2 % (v/v). Twenty genes in its genome were annotated as potential esterase and four of them (3963, 4547, 5294 and 5359) were heterogeneously expressed and characterized. Esterase 3963 and 4547 is a type I PAEs esterase that hydrolyzes PAEs to phthalate monoesters. Esterase 5294 is a type II PAEs esterase that hydrolyzes phthalate monoesters to phthalate acid (PA). Esterase 5359 is a type III PAEs esterase that simultaneously degrades various PAEs to PA. Molecular docking results of 5359 suggested that the size and indiscriminate binding feature of spacious substrate binding pocket may contribute to its substrate versatility. AH-ZY2 is a potential strain for efficient remediation of PAEs complex pollution in environment. It is first to report an esterase that can efficiently degrade mixed various PAEs.

Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria

Phthalate isomers are key intermediates in the biodegradation of pollutants including waste polyethylene terephthalate (PET) plastics and plasticizers. So far, an increasing number of phthalate isomer-degrading strains have been isolated, and their degradation pathways show significant diversity. In this paper, we comprehensively review the current status of research on the degrading bacteria, degradation characteristics, aerobic and anaerobic degradation pathways, and degradation genes (clusters) of phthalate isomers, and discuss the current shortcomings and challenges. Moreover, the degradation process of phthalate isomers produces many important aromatic precursor molecules, which can be used to produce higher-value derivative chemicals, and the modification of their degradation pathways holds good prospects. Therefore, this review also highlights the current progress made in modifying the phthalate isomer degradation pathway and explores its potential for high-value applications.

Assimilation of phthalate esters in bacteria

The massive usage of phthalate esters (PAEs) has caused serious pollution. Bacterial degradation is a potential strategy to remove PAE contamination. So far, an increasing number of PAE-degrading strains have been isolated, and the catabolism of PAEs has been extensively studied and reviewed. However, the investigation into the bacterial PAE uptake process has received limited attention and remains preliminary. PAEs can interact spontaneously with compounds like peptidoglycan, lipopolysaccharides, and lipids on the bacterial cell envelope to migrate inside. However, this process compromises the structural integrity of the cells and causes disruptions. Thus, membrane protein-facilitated transport seems to be the main assimilation strategy in bacteria. So far, only an ATP-binding-cassette transporter PatDABC was proven to transport PAEs across the cytomembrane in a Gram-positive bacterium Rhodococcus jostii RHA1. Other cytomembrane proteins like major facilitator superfamily (MFS) proteins and outer membrane proteins in cell walls like FadL family channels, TonB-dependent transporters, and OmpW family proteins were only reported to facilitate the transport of PAEs analogs such as monoaromatic and polyaromatic hydrocarbons. The functions of these proteins in the intracellular transport of PAEs in bacteria await characterization and it is a promising avenue for future research on enhancing bacterial degradation of PAEs. KEY POINTS: • Membrane proteins on the bacterial cell envelope may be PAE transporters. • Most potential transporters need experimental validation.

Comparing the removal efficiency of diisobutyl phthalate by Bacillariophyta, Cyanophyta and Chlorophyta

The utilization of microalgae for both removing phthalate esters (PAEs) from wastewater and producing bioenergy has become a popular research topic. However, there is a lack of studies comparing the effectiveness of different types of microalgae in removing these harmful compounds. Therefore, the present study aimed to evaluate and compare the efficiency of various processes, such as hydrolysis, photolysis, adsorption, and biodegradation, in removing diisobutyl phthalate (DiBP) using six different species of microalgae. The study indicated that the average removal efficiency of DiBP (initial concentrations of 5, 0.5, and 0.05 mg L-1) by all six microalgae (initial cell density of 1 × 106 cells mL-1) was in the order of Scenedesmus obliquus (95.39 %) > Chlorella vulgaris (94.78 %) > Chroococcus sp. (91.16 %) > Cyclotella sp. (89.32 %) > Nitzschia sp. (88.38 %) > Nostoc sp. (84.33 %). The results of both hydrolysis and photolysis experiments revealed that the removal of DiBP had minimal impact, with respective removal efficiencies of only 0.89 % and 1.82 %. The adsorption efficiency of all six microalgae decreased significantly with increasing initial DiBP concentrations, while the biodegradation efficiency was elevated. Chlorella vulgaris and Chroococcus sp. demonstrated the highest adsorption and biodegradation efficiencies among the microalgae tested. Scenedesmus obliquus was chosen for the analysis of the degradation products of DiBP due to its exceptional ability to remove DiBP. The analysis yielded valuable results, identifying monoisobutyl phthalate (MiBP), phthalic acid (PA), and salicylic acid (SA) as the possible degradation products of DiBP. The possible degradation pathways mainly included dealkylation, the addition of hydroxyl groups, and decarboxylation. This study lays a theoretical foundation for the elimination of PAEs in the aquatic environment.

Biodegradation of di-2-ethylhexyl phthalate by Bacillus firmus MP04 strain: parametric optimization using full factorial design

Di-2-ethylhexyl phthalate (DEHP) is used as a plasticizer in making plastics and released from landfills. This study attempted to degrade DEHP using microbial isolates. Isolates of Bacillus spp. were tested for their efficacy in degrading DEHP. Degradation was assessed using liquid chromatography-mass spectrometry (LC-MS). The most efficient DEHP degradation was achieved by Bacillus firmus MP04, which has been identified as Bacillus firmus MP04. This strain was found to use DEHP as the sole source of carbon without carbon source supplementation. Full factorial design was used to optimize the conditions for DEHP degradation which revealed the suitability of pH 7, 5% salt concentration, 20 to 37 °C temperature, and yeast extract as a nitrogen source. LC-MS elucidated the possible degradation mechanism via benzoic acid formation. However, prolonged incubation formed a typical compound denatonium benzoate due to reactions with other compounds. As maximum degradation was achieved in 4 days, prolonged incubation is not suggested. It can be concluded that new strain Bacillus firmus MP04 is the most efficient strain among all the tested strains for DEHP degradation.

Insights into molecular mechanism of plasticizer biodegradation in Dietzia kunjamensis IITR165 and Brucella intermedia IITR166 isolated from a solid waste dumpsite

AIMS

Isolation of phthalate esters (PAEs) degrading bacteria from a solid waste dumpsite could degrade many plasticizers efficiently and to investigate their degrading kinetics, pathways, and genes.

METHODS AND RESULTS

Based on their 16S rRNA gene sequence the strains were identified as Dietzia kunjamensis IITR165 and Brucella intermedia IITR166, which showed a first-order degradation kinetic model under lab conditions. The quantification of phthalates and their intermediate metabolites identification were done by using ultra-high-performance liquid chromatography (UHPLC) and gas chromatography-tandem mass-spectrometry (GC-MS/MS), respectively. Both the bacteria utilized >99% dibutyl phthalate at a high concentration of 100-400 mg L-1 within 192 h as monitored by UHPLC. GC-MS/MS revealed the presence of metabolites dimethyl phthalate (DMP), phthalic acid (PA), and benzoic acid (BA) during DBP degradation by IITR165 while monobutyl phthalate (MBP) and PA were identified in IITR166. Phthalate esters degrading gene cluster in IITR165 comprised two novel genes coding for carboxylesterase (dkca1) and mono-alkyl phthalate hydrolase (maph), having only 37.47% and 47.74% homology, respectively, with reported phthalate degradation genes, along with the terephthalate dioxygenase system (tphA1, A2, A3, and B). However, IITR166 harbored different gene clusters comprising di-alkyl phthalate hydrolase (dph_bi), and phthalate dioxygenase (ophA, B, and C) genes.

CONCLUSIONS

Two novel bacterial strains, Dietzia kunjamensis IITR165 and Brucella intermedia IITR166, were isolated and found to efficiently degrade DBP at high concentrations. The degradation followed first-order kinetics, and both strains exhibited a removal efficiency of over 99%. Metabolite analysis revealed that both bacteria utilized de-methylation, de-esterification, and decarboxylation steps during degradation.

Whole-genome analysis of Comamonas sp. USTBZA1 for biodegrading diethyl phthalate

Extensive use of phthalic acid esters (PAEs) as plasticizer causes diffusion into the environment, which posed a great threat to mankind. It was reported that Comamonas sp. was a potentially robust aromatic biodegrader. Although the biodegradation of several PAEs by Comamonas sp. was studies, the comprehensive genomic analysis of Comamonas sp. was few reported. In the present study, one promising bacterial strain for biodegrading diethyl phthalate (DEP) was successfully isolated from activated sludge and characterized as Comamonas sp. USTBZA1 based on the 16S rRNA sequence analysis. The results showed that pH 7.5, 30 °C and inoculum volume ratio of 6% were optimal for biodegradation. Initial DEP of 50 mg/L could be completely biodegrade by strain USTBZA1 within 24 h which conformed to the Gompertz model. Based on the Q-TOF LC/MS analysis, monoethyl phthalate (MEP) and phthalic acid (PA) were identified as the metabolic products of DEP biodegradation by USTBZA1. Furthermore, the whole genome of Comamonas sp. USTBZA1 was analyzed to clarify the molecular mechanism for PAEs biodegradation by USTBZA1. There were 3 and 41 genes encoding esterase/arylesterase and hydrolase, respectively, and two genes regions (pht34512 and pht4253) were responsible for the conversion of PA to protocatechuate (PCA), and two genes regions (ligCBAIKJ) were involved in PCA metabolism in USTBZA1. These results substantiated that Comamonas sp. USTBZA1 has potential application in the DEP bioremediation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03736-3.

Nonbacterial Microflora in Wastewater Treatment Plants: an Underappreciated Potential Source of Pathogens

Wastewater treatment plants (WWTPs) receive and treat large volumes of domestic, industrial, and urban wastewater containing pathogenic and nonpathogenic microorganisms, chemical compounds, heavy metals, and other potentially hazardous substances. WWTPs play an essential role in preserving human, animal, and environmental health by removing many of these toxic and infectious agents, particularly biological hazards. Wastewater contains complex consortiums of bacterial, viral, archaeal, and eukaryotic species, and while bacteria in WWTP have been extensively studied, the temporal and spatial distribution of nonbacterial microflora (viruses, archaea, and eukaryotes) is less understood. In this study, we analyzed the viral, archaeal, and eukaryotic microflora in wastewater throughout a treatment plant (raw influent, effluent, oxidation pond water, and oxidation pond sediment) in Aotearoa (New Zealand) using Illumina shotgun metagenomic sequencing. Our results suggest a similar trend across many taxa, with an increase in relative abundance in oxidation pond samples compared to influent and effluent samples, except for archaea, which had the opposite trend. Additionally, some microbial families, such as Podoviridae bacteriophages and Apicomplexa alveolates, appeared largely unaffected by the treatment process, with their relative abundance remaining stable throughout. Several groups encompassing pathogenic species, such as Leishmania, Plasmodium, Toxoplasma, Apicomplexa, Cryptococcus, Botrytis, and Ustilago, were identified. If present, these potentially pathogenic species could be a threat to human and animal health and agricultural productivity; therefore, further investigation is warranted. These nonbacterial pathogens should be considered when assessing the potential for vector transmission, distribution of biosolids to land, and discharge of treated wastewater to waterways or land. IMPORTANCE Nonbacterial microflora in wastewater remain understudied compared to their bacterial counterparts despite their importance in the wastewater treatment process. In this study, we report the temporal and spatial distributions of DNA viruses, archaea, protozoa, and fungi in raw wastewater influent, effluent, oxidation pond water, and oxidation pond sediments by using shotgun metagenomic sequencing. Our study indicated the presence of groups of nonbacterial taxa which encompass pathogenic species that may have potential to cause disease in humans, animals, and agricultural crops. We also observed higher alpha diversity in viruses, archaea, and fungi in effluent samples than in influent samples. This suggests that the resident microflora in the wastewater treatment plant may be making a greater contribution to the diversity of taxa observed in wastewater effluent than previously thought. This study provides important insights to better understand the potential human, animal, and environmental health impacts of discharged treated wastewater.

Evaluation of distinct molecular architectures and coordinated regulation of the catabolic pathways of oestrogenic dioctyl phthalate isomers in Gordonia sp

Bacterial strain GONU, belonging to the genus Gordonia, was isolated from a municipal waste-contaminated soil sample and was capable of utilizing an array of endocrine-disrupting phthalate diesters, including di-n-octyl phthalate (DnOP) and its isomer di(2-ethylhexyl) phthalate (DEHP), as the sole carbon and energy sources. The biochemical pathways of the degradation of DnOP and DEHP were evaluated in strain GONU by using a combination of various chromatographic, spectrometric and enzymatic analyses. Further, the upregulation of three different esterases (estG2, estG3 and estG5), a phthalic acid (PA)-metabolizing pht operon and a protocatechuic acid (PCA)-metabolizing pca operon were revealed based on de novo whole genome sequence information and substrate-induced protein profiling by LC-ESI-MS/MS analysis followed by differential gene expression by real-time PCR. Subsequently, functional characterization of the differentially upregulated esterases on the inducible hydrolytic metabolism of DnOP and DEHP revealed that EstG5 is involved in the hydrolysis of DnOP to PA, whereas EstG2 and EstG3 are involved in the metabolism of DEHP to PA. Finally, gene knockout experiments further validated the role of EstG2 and EstG5, and the present study deciphered the inducible regulation of the specific genes and operons in the assimilation of DOP isomers.

Bioremediation of PAEs-contaminated saline soil: The application of a marine bacterial strain isolated from mangrove sediment

Phthalic acid esters (PAEs) are known as the most widely used plasticizer as well as one of the ubiquitously distributed emerging pollutants. Biodegradation and bioremediation via application of PAEs-degrading microbes is promising. In this study, a novel marine microbe, Gordonia hongkongensis RL-LY01, was isolated from mangrove sediment showing high di-(2-ethylhexyl) phthalate (DEHP) degradation capacity. Strain RL-LY01 could degrade a wide range of PAEs and the degradation kinetics of DEHP followed the first-order decay model. Meanwhile, good environmental adaptability, preference to alkaline conditions and good tolerance to salinity and metal ions was shown. Further, metabolic pathway of DEHP in strain RL-LY01 was proposed, with di-ethyl phthalate, phthalic acid, benzoic acid and catechol as intermediates. Additionally, one known mono-alkyl phthalate hydrolase gene (mehpH) was identified. Finally, the excellent performance during bioremediation of artificial DEHP-contaminated saline soil and sediment indicated strain RL-LY01 employs great application potential for the bioremediation of PAE-contaminated environments.

Whole Genome Analysis and Assessment of the Metabolic Potential of Gordonia rubripertincta Strain 112, a Degrader of Aromatic and Aliphatic Compounds

The application of Gordonia strains in biotechnologies of environmental purification as degraders of pollutants of different chemical structures is an interesting research topic. The strain Gordonia rubripertincta 112 (IEGM112) is capable of utilizing diesel fuel, alkanes, and aromatic compounds. The aim of this work was to study the potential of G. rubripertincta 112 as a degrader of aromatic and aliphatic compounds and analyze its complete genome in comparison with other known G. rubripertincta strains. The genome had a total length of 5.28 Mb and contained 4861 genes in total, of which 4799 were coding sequences (CDS). The genome contained 62 RNA genes in total, of which 50 were tRNAs, three were ncRNAs, and nine were rRNAs. The strain bears plasmid elements with a total length of 189,570 nucleotides (plasmid p1517). The strain can utilize 10.79 ± 1.17% of hexadecane and 16.14 ± 0.16% of decane over 3 days of cultivation. In the genome of the strain, we have found metabolic pathways of alkane (cytochrome P450 hydroxylases) and catechol (ortho- and meta-pathways) degradation. These results will help us to further approach the fundamental study of the processes occurring in the strain cells and to enrich our knowledge of the catabolic capabilities of G. rubripertincta.

Enzyme catalyzes ester bond synthesis and hydrolysis: The key step for sustainable usage of plastics

Petro-plastic wastes cause serious environmental contamination that require effective solutions. Developing alternatives to petro-plastics and exploring feasible degrading methods are two solving routes. Bio-plastics like polyhydroxyalkanoates (PHAs), polylactic acid (PLA), polycaprolactone (PCL), poly (butylene succinate) (PBS), poly (ethylene furanoate) s (PEFs) and poly (ethylene succinate) (PES) have emerged as promising alternatives. Meanwhile, biodegradation plays important roles in recycling plastics (e.g., bio-plastics PHAs, PLA, PCL, PBS, PEFs and PES) and petro-plastics poly (ethylene terephthalate) (PET) and plasticizers in plastics (e.g., phthalate esters, PAEs). All these bio- and petro-materials show structure similarity by connecting monomers through ester bond. Thus, this review focused on bio-plastics and summarized the sequences and structures of the microbial enzymes catalyzing ester-bond synthesis. Most of these synthetic enzymes belonged to α/β-hydrolases with conserved serine catalytic active site and catalyzed the polymerization of monomers by forming ester bond. For enzymatic plastic degradation, enzymes about PHAs, PBS, PCL, PEFs, PES and PET were discussed, and most of the enzymes also belonged to the α/β hydrolases with a catalytic active residue serine, and nucleophilically attacked the ester bond of substrate to generate the cleavage of plastic backbone. Enzymes hydrolysis of the representative plasticizer PAEs were divided into three types (I, II, and III). Type I enzymes hydrolyzed only one ester-bond of PAEs, type II enzymes catalyzed the ester-bond of mono-ester phthalates, and type III enzymes hydrolyzed di-ester bonds of PAEs. Divergences of catalytic mechanisms among these enzymes were still unclear. This review provided references for producing bio-plastics, and degrading or recycling of bio- and petro-plastics from an enzymatic point of view.

Major biotransformation of phthalic acid esters in Eisenia fetida: Mechanistic insights and association with catalytic enzymes and intestinal symbionts

Phthalic acid esters (PAEs) are an important group of organic pollutants that are widely used as plasticizers in the environment. The PAEs in soil organisms are likely to be biotransformed into a variety of metabolites, and the combined toxicity of PAEs and their metabolites might be more serious than PAEs alone. However, there are only a few studies on PAE biotransformation by terrestrial animals, e.g. earthworms. Herein, the key biotransformation pathways of PAEs and their association with catalytic enzymes and intestinal symbionts in earthworms were studied using in vivo and in vitro incubation approaches. The widely distributed PAE in soil, dibutyl phthalate (DBP), was proven to be biotransformed rapidly together with apparent bioaccumulation in earthworms. The biotransformation of PAE congeners with medium or long side chains appeared to be faster compared with those with short side chains. DBP was biotransformed into butyl methyl phthalate (BMP), monobutyl phthalate (MBP), and phthalic acid (PA) through esterolysis and transesterification. Besides, the generation of small quantities of low-molecular weight metabolites via β-oxidation, decarboxylation or ring-cleavage, was also observed, especially when the appropriate proportion of NADPH coenzyme was applied to transfer electrons for oxidases. Interestingly, the esterolysis of PAEs was mainly regulated by the cytoplasmic carboxylesterase (CarE) in earthworms, with a Michaelis constant (K_m) of 0.416 mM in the catalysis of DBP. The stronger esterolysis in non-intestinal tissues indicated that the CarE was primarily secreted by non-intestinal tissues of earthworms. Additionally, the intestinal symbiotic bacteria of earthworms could respond to PAE stress, leading to the changes in their diversity and composition. The enrichment of some genera e.g. Bacillus and Paracoccus, and the enhancement of metabolism function, e.g. amino acids, energy, lipids biosynthesis and oxidase secretion, indicated their important role in the degradation of PAEs.

Transcriptome analysis and cytochrome P450 monooxygenase reveal the molecular mechanism of Bisphenol A degradation by Pseudomonas putida strain YC-AE1

BACKGROUND

Bisphenol A (BPA) is a rapid spreading organic pollutant that widely used in many industries especially as a plasticizer in polycarbonate plastic and epoxy resins. BPA reported as a prominent endocrine disruptor compound that possesses estrogenic activity and fulminant toxicity. Pseudomonas putida YC-AE1 was isolated in our previous study and exerted a strong degradation capacity toward BPA at high concentrations; however, the molecular degradation mechanism is still enigmatic.

RESULTS

We employed RNA sequencing to analyze the differentially expressed genes (DEGs) in the YC-AE1 strain upon BPA induction. Out of 1229 differentially expressed genes, 725 genes were positively regulated, and 504 genes were down-regulated. The pathways of microbial metabolism in diverse environments were significantly enriched among DEGs based on KEGG enrichment analysis. qRT-PCR confirm the involvement of BPA degradation relevant genes in accordance with RNA Seq data. The degradation pathway of BPA in YC-AE1 was proposed with specific enzymes and encoded genes. The role of cytochrome P450 (CYP450) in BPA degradation was further verified. Sever decrease in BPA degradation was recorded by YC-AE1 in the presence of CYP450 inhibitor. Subsequently, CYP450bisdB deficient YC-AE1 strain △ bisdB lost its ability toward BPA transformation comparing with the wild type. Furthermore, Transformation of E. coli with pET-32a-bisdAB empowers it to degrade 66 mg l-1 of BPA after 24 h. Altogether, the results showed the role of CYP450 in biodegradation of BPA by YC-AE1.

CONCLUSION

In this study we propose the molecular basis and the potential role of YC-AE1cytochrome P450 monooxygenase in BPA catabolism.

Analysis of the performance of the efficient di-(2-ethylhexyl) phthalate-degrading bacterium Rhodococcus pyridinovorans DNHP-S2 and associated catabolic pathways

The widespread use of plastic has led to the global occurrence of phthalate esters (PAEs) pollution. PAEs can be effectively removed from polluted environments by microbe-mediated degradation. Di-(2-ethylhexyl) phthalate (DEHP) has the highest residual concentration in agricultural soil-contaminated areas compared to other PAEs in most of China. The Rhodococcus pyridinovorans DNHP-S2 microbial isolate identified was found to efficiently degrade DEHP. Within a 72 h period, the bacteria were able to degrade 52.47% and 99.75% of 500 mg L^-1 DEHP at 10 °C and 35 °C, respectively. Dimethyl phthalate (DMP) was first identified as an intermediate metabolite of DEHP, which is different from the previously reported DEHP catabolic pathway. Genomic sequencing of DNHP-S2 identified benzoate 1,2-dioxygenase and catechol 2,3/1,2-dioxygenase as potential mediators of DEHP degradation, consistent with the existence of two downstream metabolic pathways governing DEHP degradation. Three targets DEHP metabolism-related enzymes were found to be DEHP-inducible at the mRNA level, and DNHP-S2 was able to mediate the complete degradation of DEHP at lower temperatures, as confirmed via RT-qPCR. DNHP-S2 was also found to readily break down other PAEs including DMP, di-n-butyl phthalate (DBP), di-n-octyl phthalate (DnOP), and n-butyl benzyl phthalate (BBP). Together, these results thus highlight DNHP-S2 as a bacterial strain with great promise as a tool for the remediation of PAE pollution. In addition to providing new germplasm and genetic resources for use in the context of PAE degradation, these results also offer new insight into the potential mechanisms whereby PAEs undergo catabolic degradation, making them well-suited for use in PAE-contaminated environments.

Phthalates - A family of plasticizers, their health risks, phytotoxic effects, and microbial bioaugmentation approaches

Phthalates are a family of reprotoxicant compounds, predominantly used as a plasticizer to improve the flexibility and longevity of consumable plastic goods. After their use these plastic products find their way to the waste disposal sites where they leach out the hazardous phthalates present within them, into the surrounding environment, contaminating soil, groundwater resources, and the nearby water bodies. Subsequently, phthalates move into the living system through the food chain and exhibit the well-known phenomenon of biological magnification. Phthalates as a primary pollutant have been classified as 1B reprotoxicants and teratogens by different government authorities and they have thus imposed restrictions on their use. Nevertheless, the release of these compounds in the environment is unabated. Bioremediation has been suggested as one of the ways of mitigating this menace, but studies regarding the field applications of phthalate utilizing microbes for this purpose are limited. Through this review, we endeavor to make a deeper understanding of the cause and concern of the problem and to find out a possible solution to it. The review critically emphasizes the various aspects of phthalates toxicity, including their chemical nature, human health risks, phytoaccumulation and entry into the food chain, microbial role in phthalate degradation processes, and future challenges.

Composting and green technologies for remediation of phthalate (PAE)-contaminated soil: Current status and future perspectives

Phthalate esters (PAEs) are hazardous organic compounds that are widely added to plastics to enhance their flexibility, temperature, and acidic tolerance. The increase in global consumption and the corresponding environmental pollution of PAEs has caused broad public concerns. As most PAEs accumulate in soil due to their high hydrophobicity, composting is a robust remediation technology for PAE-contaminated soil (efficiency 25%-100%), where microbial activity plays an important role. This review summarized the roles of the microbial community, biodegradation pathways, and specific enzymes involved in the PAE degradation. Also, other green technologies, including biochar adsorption, bioaugmentation, and phytoremediation, for PAE degradation were also presented, compared, and discussed. Composting combined with these technologies significantly enhanced removal efficiency; yet, the properties and roles of each bacterial strain in the degradation, upscaling, and economic feasibility should be clarified in future research.

Efficient biodegradation of di-(2-ethylhexyl) phthalate by a novel strain Nocardia asteroides LMB-7 isolated from electronic waste soil

The di-2-ethylhexyl phthalate (DEHP) degrading strain LMB-7 was isolated from electronic waste soil. According to its biophysical/biochemical characteristics and 16S rRNA gene analysis, the strain was identified as Nocardia asteroides. Optimal pH and temperature for DEHP degradation were 8.0 and 30 °C, respectively, and DEHP removal reached 97.11% after cultivation for 24 h at an initial concentration of 400 mg/L. As degradation intermediates, di-butyl phthalates, mono-2-ethylhexyl phthalate and 2-ethylhexanol could be identified, and it could be confirmed that DEHP was completely degraded by strain LMB-7. To our knowledge, this is a new report of DEHP degradation by a strain of Nocardia asteroides, at rates higher than those reported to date. This finding provides a new way for DEHP elimination from environment.

Phthalate hydrolase: distribution, diversity and molecular evolution

The alpha/beta-fold superfamily of hydrolases is rapidly becoming one of the largest groups of structurally related enzymes with diverse catalytic functions. In this superfamily of enzymes, esterase deserves special attention because of their wide distribution in biological systems and importance towards environmental and industrial applications. Among various esterases, phthalate hydrolases are the key alpha/beta enzymes involved in the metabolism of structurally diverse estrogenic phthalic acid esters, ubiquitously distributed synthetic chemicals, used as plasticizer in plastic manufacturing processes. Although they vary both at the sequence and functional levels, these hydrolases use a similar acid-base-nucleophile catalytic mechanism to catalyse reactions on structurally different substrates. The current review attempts to present insights on phthalate hydrolases, describing their sources, structural diversities, phylogenetic affiliations and catalytically different types or classes of enzymes, categorized as diesterase, monoesterase and diesterase-monoesterase, capable of hydrolysing phthalate diester, phthalate monoester and both respectively. Furthermore, available information on in silico analyses and site-directed mutagenesis studies revealing structure-function integrity and altered enzyme kinetics have been highlighted along with the possible scenario of their evolution at the molecular level.

Phthalate Esters Metabolic Strain Gordonia sp. GZ-YC7, a Potential Soil Degrader for High Concentration Di-(2-ethylhexyl) Phthalate

As commonly used chemical plasticizers in plastic products, phthalate esters have become a serious ubiquitous environmental pollutant, such as in soil of plastic film mulch culture. Microbial degradation or transformation was regarded as a suitable strategy to solve the phthalate esters pollution. Thus, a new phthalate esters degrading strain Gordonia sp. GZ-YC7 was isolated in this study, which exhibited the highest di-(2-ethylhexyl) phthalate degradation efficiency under 1000 mg/L and the strongest tolerance to 4000 mg/L. The comparative genomic analysis results showed that there exist diverse esterases for various phthalate esters such as di-(2-ethylhexyl) phthalate and dibutyl phthalate in Gordonia sp. GZ-YC7. This genome characteristic possibly contributes to its broad substrate spectrum, high degrading efficiency, and high tolerance to phthalate esters. Gordonia sp. GZ-YC7 has potential for the bioremediation of phthalate esters in polluted soil environments.

First identification and characterization of detoxifying plastic-degrading DBP hydrolases in the marine diatom Cylindrotheca closterium

Diatoms are photosynthetic organisms with potential biotechnological applications in the bioremediation sector, having shown the capacity to reduce environmental concentrations of different pollutants. The diatom Cylindrotheca closterium is known to degrade di-n-butyl phthalate (DBP), one of the most abundant phthalate esters in aquatic environments and a known endocrine-disrupting chemical. In this study, we present for the first time the in silico identification of two putative DBP hydrolases (provisionally called DBPH1 and DBPH2) in the transcriptome of C. closterium. We modeled the structure of both DBPH1-2 and their proposed interactions with the substrate to gain insights into their mechanism of action. Finally, we analyzed the expression levels of the two putative hydrolases upon exposure of C. closterium to different concentrations of DBP (5 and 10 mg/l) for 24 and 48 h. The data showed a DBP concentration-dependent increase in expression levels of both dbph1 and 2 genes, further highlighting their potential involvement in phthalates degradation. This is the first identification of phthalate-degrading enzymes in microalgae, providing new insights into the possible use of diatoms in bioremediation strategies targeting phthalates.

Biodegradation of di-(2-ethylhexyl) phthalate by novel Rhodococcus sp. PFS1 strain isolated from paddy field soil

Di-(2-ethylhexyl)-phthalate (DEHP) is the phthalate ester frequently utilized as a plasticizer, commonly found in cosmetics, packaging materials; moreover, it has carcinogenic and mutagenic effects on humans. In the current study, we isolated the soil bacterium Rhodococcus sp. PFS1 and to assess its DEHP degradation ability in various environmental conditions. The strain PFS1 was isolated from paddy field soil and identified by the 16S rRNA sequencing analyses. The strain PFS1 was examined for its biodegradation ability of DEHP at various pH, temperature, salt concentration, glucose concentration, and high and low concentrations of DEHP. Moreover, the biodegradation of DEHP at a contaminated soil environment by strain PFS1 was assessed. Further, the metabolic pathway of DEHP degradation by PFS1 was analyzed by HPLC-MS analysis. The results showed that the strain PFS1 effectively degraded the DEHP at neutral pH and temperature 30 °C; moreover, expressed excellent DEHP degradation at the high salt concentration (up to 50 g/L). The strain PFS1 was efficiently degraded the different tested phthalate esters (PAEs) up to 90%, significantly removed the DEHP contamination in soil along with native organisms which are present in soil up to 94.66%; nevertheless, the PFS1 alone degraded the DEHP up to 87.665% in sterilized soil. According to HPLC-MS analysis, DEHP was degraded into phthalate (PA) by PFS1 strain via mono(2-ethylehxyl) phthalate (MEHP); then PA was utilized for cell growth. These results suggest that Rhodococcus sp. PFS1 has excellent potential to degrade DEHP at various environmental conditions especially in contaminated paddy field soil.

Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y

A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30 ℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains.

Phthalic acid esters degradation by a novel marine bacterial strain Mycolicibacterium phocaicum RL-HY01: Characterization, metabolic pathway and bioaugmentation

Phthalic acid esters (PAEs) are one of the most widely used plasticizers and the well-studied environmental pollutants with endocrine disrupting properties. Investigation about PAEs in terrestrial ecosystem has been extensively conducted while the fate of PAEs in marine environment remains underexplored. In this study, a novel di-(2-ethylhexyl) phthalate (DEHP) degrading marine bacterial strain, Mycolicibacterium phocaicum RL-HY01, was isolated and characterized from intertidal sediments. Strain RL-HY01 could utilize a range of PAE plasticizers as sole carbon source for growth. The effects of different environmental factors on the degradation of PAEs were evaluated and the results indicated that strain RL-HY01 could efficiently degrade PAEs under a wide range of pH (5.0 to 9.0), temperature (20 °C to 40 °C) and salinity (below 10%). Specifically, when Tween-80 was added as solubilizing agent, strain RL-HY01 could rapidly degrade DEHP and achieve complete degradation of DEHP (50 mg/L) in 48 h. The kinetics of DEHP degradation by RL-HY01 were well fitted with the modified Gompertz model. The metabolic intermediates of DEHP by strain RL-HY01 were identified by ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis and then the metabolic pathway of DEHP was deduced. DEHP was transformed into di-ethyl phthalate (DEP) via β-oxidation and then DEP was hydrolyzed into phthalic acid (PA) by de-esterification. PA was further transformed into gentisate via salicylic acid and further utilized for cell growth. Bioaugmentation of strain RL-HY01 with marine samples was performed to evaluate its application potential and the results suggested that strain RL-HY01 could accelerate the elimination of DEHP in marine samples. The results have advanced our understanding of the fate of PAEs in marine ecosystem and identified an efficient bioremediation strategy for PAEs-polluted marine sites.

Characterization of a novel carboxylesterase with catalytic activity toward di(2-ethylhexyl) phthalate from a soil metagenomic library

A novel carboxylesterase gene estyz5 was isolated from a soil metagenomic library. The recombinant enzyme EstYZ5 is 298 amino acids in length with a predicted molecular weight of 32 kDa. Sequence alignment and phylogenetic analysis revealed that EstYZ5 belongs to the hormone-sensitive lipase (HSL) family with a deduced catalytic triad of Ser144-Glu238-His268. EstYZ5 contains two conserved motifs, a pentapeptide motif GDSAG and a HGGG motif, which are typically found in members of the HSL family. Esterolytic activity of the recombinant enzyme was optimal at 30 °C and pH 8.0, and the kcat/Km value of the enzyme for the optimum substrate p-nitrophenyl butyrate was as high as 1272 mM-1·s-1. Importantly, EstYZ5 showed activity toward di(2-ethylhexyl) phthalate with complex side chains, which is rare for HSLs. Molecular docking simulations revealed that the catalytic triad and an oxyanion hole likely play vital roles in enzymatic activity and specificity. The phthalate-degrading activity of EstYZ5, combined with its high levels of esterolytic activity, render this new enzyme a candidate for biotechnological applications.

Microbial approaches for remediation of pollutants: Innovations, future outlook, and challenges

Environmental contamination with persistent organic pollutants has emerged as a serious threat of pollution. Bioremediation is a key to eliminate these harmful pollutants from the environment and has gained the interest of researchers during the past few decades. Scientific knowledge upon microbial interactions with individual pollutants over the past decades has helped to abate environmental pollution. Traditional bioremediation approaches have limitations for their applications; hence, it is essential to discover new bioremediation approaches with biotechnological interventions for best results. The developments in various methodologies are expected to increase the efficiency of bioremediation techniques and provide environmentally sound strategies. This paper deals with the profiling of microorganisms present in polluted sites using various techniques such as culture-based approaches and omics-based approaches. Besides this, it also provides up-to-date scientific literature on the microbial electrochemical technologies which are nowadays considered as the best approach for remediation of pollutants. Detailed information about future outlook and challenges to evaluate the effect of various treatment technologies for remediation of pollutants has been discussed.

Reducing the reproductive toxicity activity of Lactiplantibacillus plantarum: a review of mechanisms and prospects

Food pollution can cause a variety of negative effects on human health, especially reproductive toxicity. Common food contaminants include biological contaminants, chemical contaminants, and physical contaminants, among which endocrine disruptors, pesticides, and heavy metals have the greatest reproductive toxicity in chemical contaminants. Humans mainly solve food pollution through three aspects: decreasing the pollution of food raw materials, lowering the pollution in food processing, and reducing the harm to the human body after food pollutants enter the human body. With more and more research on probiotics, not only beneficial effects, but also the ability to reduce the toxicity of food contaminants is found. Thus, microbial treatment has been proved to be a more effective way to deal with food pollution. Recent research shows that several strains of Lactiplantibacillus plantarum can adsorb or degrade some chemical pollutants and relieve inflammation and oxidative stress caused by them. This review summarized the research to explore the possible role of Lactiplantibacillus plantarum in protecting human reproductive ability and maintaining food safety.

Biotechnology-based microbial degradation of plastic additives

Plastic additives are agents responsible to the flame resistance, durability, microbial resistance, and flexibility of plastic products. High demand for production and use of plastic additives is associated with environmental accumulation and various health hazards. One of the suitable methods of depleting plastic additive in the environment is bioremediation as it offers cost-efficiency, convenience, and sustainability. Microbial activity is one of the effective ways of detoxifying various compounds as microorganisms can adapt in an environment with high prevalence of pollutants. The present review discusses the use and abundance of these plastic additives, their health-related risks, the microorganisms capable of degrading them, the proposed mechanism of biodegradation, and current innovations capable of improving the efficiency of bioremediation.

Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments

Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide, with an annual global production of more than 8 million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at submillimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O₂-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl coenzyme A (benzoyl-CoA) pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side chains of DEHP. Interestingly, genes encoding DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase and phthaloyl-CoA decarboxylase—key enzymes for side chain hydrolysis and o-phthalic acid degradation, respectively—are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities.

IMPORTANCE Xenobiotic phthalate esters (PAEs) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O₂-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggested that the side chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O₂-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O₂-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.

Quantification, distribution, and effects of di (2-ethylhexyl) phthalate contamination: Risk analysis and mitigation strategies in urban environment

Phthalate acid ester, di (2-ethylhexyl) phthalate (DEHP) is ubiquitously detected contaminant of emerging concerns (CECs) in all the environmental samples. The present study attempted to understand the fate and transport of DEHP in urban areas by evaluating the quantities, distribution, risk, and effects in the Mysuru city, India. The study is anticipated to serve as a vital document for local and national regulators to frame a robust DEHP management plan and mitigate the risks associated. Liquid-liquid microextraction followed by gas chromatographic analysis was adopted to determine the concentrations of DEHP. The risk quotient method was adopted to assess potential risk, and a conceptual planning model framework was designed to mitigate the DEHP contamination. The municipal wastewater contained 115 ± 9.2 μg/L, whereas treated municipal wastewater showed 95 ± 7.6 μg/L DEHP that was attributed to the inefficiency of the treatment plant. Further, sediments in surface water, as well as groundwater samples of the study area, showed 8 ± 0.64 to 12 ± 0.96 μg/L and 32 ± 2.56 to 40 ± 3.2 μg/kg of DEHP, respectively. The risk quotient of 19.17 for samples in around treatment indicated highest risk, whereas groundwater samples had a risk quotient of 1-2 indicating relative risk to aquatic organisms. In addition, the study highlighted the source, possible entry pathways, and management strategies including treatment aspects to draw an understanding of the distribution and potential ecological imbalances with contamination of DEHP in the urban sector. PRACTITIONER POINTS: Understand the fate and transportation of DEHP in urban wastewater. Primary investigation and assessment to possible health and environmental risks of DEHP contamination in urban wastewater. Revealed the associated health risks and proposed possible management strategies.

Network-directed isolation of the cooperator Pseudomonas aeruginosa ZM03 enhanced the dibutyl phthalate degradation capacity of Arthrobacter nicotianae ZM05 under pH stress

Dibutyl phthalate (DBP), widely used as plasticizer, is a typical soil contaminant. A new isolate, Arthrobacter nicotianae ZM05, is efficient at degrading DBP but lacks stress resistance to adverse environments. In this study, to isolate effective cooperators of strain ZM05 under pH stress and explore the effects of DBP on the bacterial community structure and interaction between bacteria, a microcosm experiment was conducted by supplying the exogenous DBP-degrading bacteria ZM05. 16S rRNA gene sequencing analysis showed that DBP contamination decreased microbial community diversity and weakened potential interactions between microorganisms, evidenced by fewer links, lower average degree, and lower average clustering coefficients in the cooccurrence network. Furthermore, the subnetworks showed that DBP shifted the interactions between strain ZM05 and other microbes. Based on the prediction of the network, the nondegrading bacterium Pseudomonas aeruginosa ZM03 was isolated and proven through coculture experiments to have a positive interaction with strain ZM05 during DBP degradation under pH stress. Strain ZM03 could utilize downstream acidic metabolites to alleviate acid inhibition and accelerate degradation. This study provides solid evidence that bacterial communities adjust their interactions to adapt to DBP stress and provides new insight into the prediction of microbes that are cooperative with degrading bacteria.

Mechanistic insight into esterase-catalyzed hydrolysis of phthalate esters (PAEs) based on integrated multi-spectroscopic analyses and docking simulation

A novel PAE-hydrolyzing esterase (named Hyd) gene was screened from the genomic library of Rhodococcus sp. 2G and was successfully expressed in heterologous E. coli, which was defined as a new family of esterolytic enzymes. The purified Hyd could efficiently degrade various PAEs, displaying high activity and stability with a broad range of pH (4-10) and temperature (20-60 °C). Interaction mechanism of Hyd with dibutyl phthalate (DBP) was investigated by integrated multi-spectroscopic and docking simulation methods. Fluorescence and UV-vis spectra revealed that DBP could quench the fluorescence of Hyd through a static quenching mechanism. The results from synchronous fluorescence and CD spectra confirmed that the DBP binding to Hyd triggered conformational and micro-environmental changes of Hyd, which were characterized by increased stretching extent and random coil, and decreased α-helix and β-sheet. Molecular docking study showed that DBP could be bound to the cavity of Hyd with hydrogen bonding and hydrophobic interaction. A novel and distinctive catalytic mechanism was proposed: two key residues Thr¹⁹⁰ and Ser¹⁹¹ might catalyze the hydrolysis of DBP, instead of the conserved catalytic triad (Ser-His-Asp) reported elsewhere, which was confirmed by site-directed mutagenesis.

Biodegradation of phthalic acid esters (PAEs) by Cupriavidus oxalaticus strain E3 isolated from sediment and characterization of monoester hydrolases

Phthalic acid esters (PAEs) are teratogenic and carcinogenic and mainly metabolized by microorganisms in sediment. A novel strain, Cupriavidus oxalaticus strain E3, was isolated and characterized from sediment for PAEs degradation. The transformation of dibutyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP) as the sole carbon source by strain E3 was systematically studied in the darkness through the kinetic studies and analysis of intermediates. After the initial lag pause of 5 h-8 h, the strain efficiently degraded 87.4%-94.4% of DBP and 82.5%-85.6% of DEHP at an initial amount of each phthalate of 200 mg/L after 60 h of incubation. The biodegradation rate of DBP and DEHP followed a first-order kinetic model, and degradation rate constants (k) of them by E3 were 1.37 and 0.86 d^-1, respectively. Gas chromatography-mass spectrometry (GC-MS) results revealed that the tentative PAEs degradation pathway, included the transformation from PAEs to phthalic acid (PA) and the complete mineralization of PA. In the phase of PAEs to PA, DBP with short sides reduced the chain length via hydrolyzation, and DEHP with long sides reduced the chain length via hydrolyzation and β-oxidation. The 3D model of monoester hydrolase from C. oxalaticus was predicted and used for docking with mono-2-ethylhexyl phthalate (MEHP) and mono-n-butyl phthalate (MBP). The docking results showed that the conserved catalytic triplet structure (Ser140, His284, and Asp254) acted as active sites and participated in degrading PMEs. This study provided novel insights into the mechanisms of PAEs degradation at a molecular level and widened the scope of functional bacteria by isolating strain E3.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.