Functional genomic analysis of phthalate acid ester (PAE) catabolism genes in the versatile PAE-mineralising bacterium Rhodococcus sp. 2G

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.

Exploring di (2-ethylhexyl) phthalate degradation by a synthetic marine bacterial consortium: Genomic insights, pathway and interaction prediction, and application in sediment microcosms

Di (2-ethylhexyl) phthalate (DEHP), a toxic phthalate ester (PAE) plasticizer, is often detected in marine sediment and biota. Our understanding of DEHP-degrading marine bacteria and the associated genetic mechanisms is limited. This study established a synthetic bacterial consortium (A02) consisting of three marine bacteria (OR05, OR16, and OR21). Consortium A02 outperformed the individual strains in DEHP degradation. Investigations into the degradation of DEHP intermediates revealed that OR05 and OR16 likely contributed to enhanced DEHP degradation by Consortium A02 via the utilization of DEHP intermediates, such as protocatechuic acid and mono (ethylhexyl) phthalate, with OR21 as the key DEHP degrader. A pathway of DEHP degradation by Consortium A02 was predicted based on genome analysis and experimental degradation. Bioaugmentation with Consortium A02 led to 80% DEHP degradation in 26 days in saline sediment (100 mg/kg), surpassing the 53% degradation by indigenous microbes, indicating the potential of A02 for treating DEHP-contaminated sediments. Meanwhile, bioaugmentation notably changed the bacterial community, with the exclusive presence of certain bacterial genera in the A02 bioaugmented microcosms, and was predicted to result in a more dynamic and active sediment bacterial community. This study contributes to the limited literature on DEHP degradation by marine bacteria and their associated genes.

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.

Study on the mechanism and degradation behavior of Encifer adhaerens DNM-S1 capturing dimethyl phthalate

The global concern surrounding pollution caused by phthalates is escalating, with dimethyl phthalate (DMP) emerging as one of the most prevalent contaminants within the phthalates (PAEs) category. Although the biodegradation of DMP is considered both safe and efficient, its underlying degradation mechanism is not yet fully elucidated, and the degradation performance can be somewhat inconsistent. To address this issue, our study isolated a DMP-degrading bacterium (DNM-S1) from a vegetable greenhouse. The resulting data revealed that DNM-S1 exhibited a remarkable degradation performance, successfully degrading 84.98% of a 2000 mg L-1 DMP solution within 72 h. Remarkably, it achieved complete degradation of a 50 mg L-1 DMP solution within just 3 h. DMP degradation by DNM-S1 was also found to be efficient even under low-temperature conditions (10 °C). Our research further indicates that DNM-S1 is capable of capturing DMP through the ester bond in the bacterium's cell wall fatty acids, forming hydrogen bonds through hydrophobic interactions. The DMP was then transported into the DNM-S1 protoplasm using an active transport mechanism. Interestingly, the secondary metabolites of DNM-S1 contained natural carotenoids, which could potentially counteract the damaging effects of PAEs on cell membrane permeability. In summary, these findings highlight the potential of DNM-S1 in addressing PAEs pollution and provide new insights into the metabolic mechanism of PAEs degradation.

Molecular insights into the catabolism of dibutyl phthalate in Pseudomonas aeruginosa PS1 based on biochemical and multi-omics approaches

A comprehensive understanding of the molecular mechanisms underlying microbial catabolism of dibutyl phthalate (DBP) is still lacking. Here, we newly isolated a bacterial strain identified as Pseudomonas aeruginosa PS1 with high efficiency of DBP degradation. The degradation ratios of DBP at 100-1000 mg/L by this strain reached 80-99 % within 72 h without a lag phase. A rare DBP-degradation pathway containing two monobutyl phthalate-catabolism steps was proposed based on intermediates identified by HPLC-TOF-MS/MS. In combination with genomic and transcriptomic analyses, we identified 66 key genes involved in DBP biodegradation and revealed the genetic basis for a new complete catabolic pathway from DBP to Succinyl-CoA or Acetyl-CoA in the genus Pseudomonas for the first time. Notably, we found that a series of homologous genes in Pht and Pca clusters were simultaneously activated under DBP exposure and some key intermediate degradation related gene clusters including Pht, Pca, Xyl, Ben, and Cat exhibited a favorable coexisting pattern, which contributed the high-efficient DBP degradation ability and strong adaptability to this strain. Overall, these results broaden the knowledge of the catabolic diversity of DBP in microorganisms and enhance our understanding of the molecular mechanism underlying DBP biodegradation.

Mechanisms of biochar assisted di-2-ethylhexyl phthalate (DEHP) biodegradation in tomato rhizosphere by metabolic and metagenomic analysis

The intensive accumulation of di-2-ethylhexyl phthalate (DEHP) in agricultural soils has resulted in severe environmental pollution that endangers ecosystem and human health. Biochar is an eco-friendly material that can help in accelerating organic pollutant degradation; nevertheless, its roles in enhancing DEHP removal in rhizosphere remain unclear. This work investigated the impacts of biochar dosage (0%-2.0%) on DEHP degradation performance in tomato rhizosphere by comprehensively exploring the change in DEHP metabolites, bacterial communities and DEHP-degrading genes. Our results showed a significant increase of rhizosphere pH, organic matter and humus by biochar amendment, which achieved a satisfactorily higher DEHP removal efficiency, maximally 77.53% in treatments with 1.0% of biochar. Biochar addition also remarkably changed rhizosphere bacterial communities by enriching some potential DEHP degraders of Nocardioides, Sphingomonas, Bradyrhizobium and Rhodanobacter. The abundance of genes encoding key enzymes (hydrolase, esterase and cytochrome P450) and DEHP-degrading genes (pht3, pht4, pht5, benC-xylZ and benD-xylL) were increased after biochar amendment, leading to the change in DEHP degradation metabolism, primarily from benzoic acid pathway to protocatechuic acid pathway. Our findings evidenced that biochar amendment could accelerate DEHP degradation by altering rhizosphere soil physicochemical variables, bacterial community composition and metabolic genes, providing clues for the mechanisms of biochar-assisted DEHP degradation in organic contaminated farmland soils.

Activated DBP degradation and relevant signal transduction path via quorum sensing autoinducers in Streptomyces sp. SH5

Microbe-mediated DBP (dibutyl phthalate) mineralization is acknowledged to be affected by diverse extracellular factors. However, little is known about the regulatory effects from quorum sensing (QS) signals. In this study, extracellularly applied QS signals A-like (hydroxymethyl dihydrofuran) was discovered to significantly enhance DBP degradation efficiency in Streptomyces sp. SH5. Monobutyl phthalate, protocatechuic acid and beta-ketoadipate were discovered as degradation intermediates by HPLC-TOF-MS/MS. Multi-omics analysis revealed the up-regulation of multiple hydrolases, transferases and decarboxylases that potentially contributed to A-like accelerated DBP degradation. Transcription of Orf2708, an orthologue of global transcriptional activator, was significantly induced by A-like. Orf2708 was demonstrated to interact specifically with the promoter of hydrolase orf2879 gene by EMSA, and the overexpression of orf2879 led to an enhanced DBP degradation in SH5. Taken together with the molecular docking studies showing the stability of ligand-receptor complex of A-like and its potential receptor Orf3712, a hierarchical regulatory cascade underlying the QS signal mediated DBP degradation was proposed as A-like/Orf3712 duplex formation, enhanced orf2708 expression and the downstream specific activation of hydrolase Orf2879. Our study presents the first evidence of GBLs-type promoted DBP degradation among bacteria, and the elucidated signal transduction path indicates a universal application potential of this activation strategy.

Complete degradation of di-n-butyl phthalate by Glutamicibacter sp. strain 0426 with a novel pathway

Di-n-butyl phthalate (DBP) is widely used as plasticizer that has potential carcinogenic, teratogenic, and endocrine effects. In the present study, an efficient DBP-degrading bacterial strain 0426 was isolated and identified as a Glutamicibacter sp. strain 0426. It can utilize DBP as the sole source of carbon and energy and completely degraded 300 mg/L of DBP within 12 h. The optimal conditions (pH 6.9 and 31.7 °C) for DBP degradation were determined by response surface methodology and DBP degradation well fitted with the first-order kinetics. Bioaugmentation of contaminated soil with strain 0426 enhanced DBP (1 mg/g soil) degradation, indicating the application potential of strain 0426 for environment DBP removal. Strain 0426 harbors a distinctive DBP hydrolysis mechanism with two parallel benzoate metabolic pathways, which may account for the remarkable performance of DBP degradation. Sequences alignment has shown that an alpha/beta fold hydrolase (WP_083586847.1) contained a conserved catalytic triad and pentapeptide motif (GX1SX2G), of which function is similar to phthalic acid ester (PAEs) hydrolases and lipases that can efficiently catalyze hydrolysis of water-insoluble substrates. Furthermore, phthalic acid was converted to benzoate by decarboxylation, which entered into two different pathways: one is the protocatechuic acid pathway under the role of pca cluster, and the other is the catechol pathway. This study demonstrates a novel DBP degradation pathway, which broadens our understanding of the mechanisms of PAE biodegradation.

Exploring the potential of a new marine bacterium associated with plastisphere to metabolize dibutyl phthalate and bis(2-ethylhexyl) phthalate by enrichment cultures combined with multi-omics analysis

Phthalic acid esters (PAEs) plasticizers are virulent endocrine disruptors that are mixed into plastics while fabricating and can filter out once they release into the surrounding environments. Plastic surfaces serve as new habitats for microorganisms, referred to as 'plastisphere'. Previous metagenomic investigations of the 'plastisphere' indicated that marine plastic surfaces may harbor microbes that degrade PAEs plasticizers. To our knowledge, the potential of microorganisms in the marine 'plastisphere' to metabolize PAEs is poorly understood. In this study, by screening the natural microbial community on plastic debris that had been deployed in situ for up to 20 months, a novel marine bacterium, Microbacterium esteraromaticum DEHP-1, was successfully isolated, which could degrade and mineralize 10-200 mg/L dibutyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP). According to the results of gas chromatography-mass spectrometry (GC-MS) and whole genome mining of strain DEHP-1, we found that strain DEHP-1 may metabolize DBP by successive removal of the ester side chain by esterase 2518 to produce mono-butyl phthalate (MBP) and phthalic acid (PA), whereas the degradation of DEHP may take place by the direct action of monooxygenase 0132 on the fatty acid side chain of the DEHP molecule to produce di-n-hexyl phthalate (DnHP) and DBP, and then the subsequent hydrolysis of DBP by de-esterification to PA and finally into the tricarboxylic acid (TCA) cycle. Non-targeted metabolomics results showed that intracellular degradation of PAEs did not happen. However, exposure to PAEs was found to significantly affect pathways such as arginine and proline, riboflavin, glutathione and lysine degradation. Therefore, the intracellular metabolic behavior of strain DEHP-1 exposed to PAEs was proposed for the first time. This study sheds light on the metabolic capacity and strategies of bacteria in the marine 'plastisphere' to effectively degrade PAEs and highlights the importance of marine microbes in mitigating plastic poisonousness.

Characterization and low-temperature biodegradation mechanism of 17β-estradiol-degrading bacterial strain Rhodococcus sp. RCBS9

Steroidal estrogens residues in the environment can be a serious hazard to humans and animals and has been listed as group 1 carcinogens by World Health Organization (WHO). Microbial degradation is one of the effective strategies for the removal of such contaminants. In this study, a low-temperature degrading bacterial strain (Rhodococcus sp. RCBS9) was isolated from the soil of a dairy farm for 17β-estradiol (E2) degradation. The strain RCBS9 exhibited an efficient degradation potential at low temperatures. To lean how different factors influence E2 degradation, we have found a major role of intracellular enzymes in E2 degradation. Genomic and metabolomic analyses have suggested potential degradation genes and four metabolic pathways. These findings provide valuable strain resources for the low temperature bioremediation of E2 contamination and insights into E2 biodegradation mechanism.

Effect of weak electrical stimulation on m-dichlorobenzene biodegradation in biotrickling filters: Insights from performance and microbial community analysis

The microbial electrolysis cell coupled with the biotrickling filters (MEC-BTF) was developed for enhancing the biodegradation of gaseous m-dichlorobenzene (m-DCB) through weak electrical stimulation. The maximum removal efficiency and elimination capacity in MEC-BTF were 1.48 and 1.65 times higher than those in open-circuit BTF (OC-BTF), respectively. Weak electrical stimulation had a positive impact on the characteristics of the biofilm. Additionally, microbial community analysis revealed that weak electrical stimulation increased the abundance of key functional genera (e.g., Rhodanobacter and Bacillus) and genes (e.g., catA/E and E1.3.1.32), thereby accelerating reductive dechlorination and ring-opening of m-DCB. Macrogenomic sequencing further revealed that electron transfer pathway in MEC-BTF might be mediated through extracellular electroactive mediators and cytochromes.

Isolation and characterization of Rhodococcus sp. GG1 for metabolic degradation of chloroxylenol

The coronavirus disease 2019 (COVID-19) pandemic has significantly increased the demand of disinfectant use. Chloroxylenol (para-chloro-meta-xylenol, PCMX) as the major antimicrobial ingredient of disinfectant has been widely detected in water environments, with identified toxicity and potential risk. The assessment of PCMX in domestic wastewater of Macau Special Administrative Region (SAR) showed a positive correlation between PCMX concentration and population density. An indigenous PCMX degrader, identified as Rhodococcus sp. GG1, was isolated and found capable of completely degrading PCMX (50 mg L-1) within 36 h. The growth kinetics followed Haldane's inhibition model, with maximum specific growth rate, half-saturation constant, and inhibition constant of 0.38 h-1, 7.64 mg L-1, and 68.08 mg L-1, respectively. The degradation performance was enhanced by optimizing culture conditions, while the presence of additional carbon source stimulated strain GG1 to alleviate inhibition from high concentrations of PCMX. In addition, strain GG1 showed good environmental adaptability, degrading PCMX efficiently in different environmental aqueous matrices. A potential degradation pathway was identified, with 2,6-dimethylhydroquinone as a major intermediate metabolite. Cytochrome P450 (CYP450) was found to play a key role in dechlorinating PCMX via hydroxylation and also catalyzed the hydroxylated dechlorination of other halo-phenolic contaminants through co-metabolism. This study characterizes an aerobic bacterial pure culture capable of degrading PCMX metabolically, which could be promising in effective bioremediation of PCMX-contaminated sites and in treatment of PCMX-containing waste streams.

Substrate-enzyme interactions and catalytic mechanism in a novel family VI esterase with dibutyl phthalate-hydrolyzing activity

Microbial degradation has been confirmed as effective and environmentally friendly approach to remediate phthalates from the environment, and hydrolase is an effective element for contaminant degradation. In the present study, a novel dibutyl phthalate (DBP)-hydrolyzing carboxylesterase (named PS06828) from Pseudomonas sp. PS1 was heterogeneously expressed in E. coli, which was identified as a new member of the lipolytic family VI. Purified PS06828 could efficiently degrade DBP with a wide range of temperature (25-37 °C) and pH (6.5-9.0). Multi-spectroscopy methods combined with molecular docking were employed to study the interaction of PS06828 with DBP. Fluorescence and UV-visible absorption spectra revealed the simultaneous presence of static and dynamic component in the fluorescence quenching of PS06828 by DBP. Synchronous fluorescence and circular dichroism spectra showed inconspicuous alteration in micro-environmental polarity around amino acid residues but obvious increasing of α-helix and reducing of β-sheet and random coil in protein conformation. Based on the information on exact binding sites of DBP on PS06828 provided by molecular docking, the catalytic mechanism mediated by key residues (Ser113, Asp166, and His197) was proposed and subsequently confirmed by site-directed mutagenesis. The results can strengthen our mechanistic understanding of family VI esterase involved in hydrolysis of phthalic acid esters, and provide a solid foundation for further enzymatic modification.

Rice genotypes and root-associated niches shifted bacterial community in response to pollution of di-(2-ethylhexyl) phthalate (DEHP) for promoting DEHP removal

Organic pollutants influenced root-associated bacterial community. However, the response variation of root-associated bacterial community among different rice genotypes exposed to phthalates (PAEs) and their removal mechanism remains unknown. Here, bacterial community and PAE-degrading genes in root-associated niches were analyzed between low (Fengyousimiao) and high (Hhang) PAE-accumulating rice cultivars exposed to di-(2-ethylhexyl) phthalate (DEHP). DEHP dissipation percentages in rhizosphere of Hhang were significantly higher than those of Fengyousimiao. The bacterial community diversities (including Chao1 and Shannon index) significantly decreased along bulk soil - rhizosphere - rhizoplane - endosphere. The bacterial community structures were shaped mainly by root-associated niches, DEHP pollution and rice genotypes, with significant differences in rhizosphere and rhizoplane between Fengyousimiao and Hhang. Rhizosphere enriched more PAE-degrading bacteria than in bulk soil, and exhibited significantly higher expression of PAE-degrading genes (hydrolase 65, phtab, phtC, pcaF and pcaI) than in bulk soil. Furthermore, rhizosphere of Hhang demonstrated significantly stronger bacterial functions related to xenobiotics biodegradation and higher expression of PAE-degrading genes than those of Fengyousimiao, leading to significantly higher DEHP dissipation percentages in rhizosphere of Hhang. The findings demonstrate that Hhang shaped specific root-associated bacterial community with higher abundances of PAE-degrading bacteria and genes than Fengyousimiao to promote DEHP degradation.

The occurrence, fate, toxicity, and biodegradation of phthalate esters: An overview

Phthalate esters (PAEs) are a class of emerging xenobiotic compounds that are extensively used as plasticizers. In recent times, there has been an increasing concern over the risk of this pervasive pollution exposure causing endocrine disruption and carcinogenicity in humans and animals. The widespread use of PAEs in home and industrial applications has resulted in their discharge in aquatic bodies via leaching, volatilization, and precipitation. In this overview, the current state of PAE pollution, its potential origins, its fate, as well as its effects on the aquatic environment are discussed. A state-of-the-art review of several studies in the literature that focus on the biological degradation of PAEs is included in this study. The paper aims to provide a comprehensive view of current research on PAEs in the environment, highlighting its fate and alleviated risks on the aquatic biotas, their challenges, future prospects, and the need for good management and policies for its remediation. PRACTITIONER POINTS: Occurrence of phthalate esters was summarized in various environmental matrices along with its serious ecotoxicological implications on biota. Wastewater is the prime source of PAEs contamination. Lack of species-specific effects on biota due to dose, exposure route, and susceptibility. The predominant route to mineralization in PAEs is biodegradation. A critical analysis of worldwide PAE production and consumption identifies the necessity for global PAE production, consumption, and release policies.

Health risks of phthalates: A review of immunotoxicity

Phthalates (PAEs) are known environmental endocrine disruptors that have been widely detected in several environments, and many studies have reported the immunotoxic effects of these compounds. Here, we reviewed relevant published studies, summarized the occurrence and major metabolic pathways of six typical PAEs (DMP, DEP, DBP, BBP, DEHP, and DOP) in water, soil, and the atmosphere, degradation and metabolic pathways under aerobic and anaerobic conditions, and explored the molecular mechanisms of the toxic effects of eleven PAEs (DEHP, DPP, DPrP, DHP, DEP, DBP, MBP, MBzP, BBP, DiNP, and DMP) on the immune system of different organisms at the gene, protein, and cellular levels. A comprehensive understanding of the mechanisms by which PAEs affect immune system function through regulation of immune gene expression and enzymes, increased ROS, immune signaling pathways, specific and non-specific immunosuppression, and interference with the complement system. By summarizing the effects of these compounds on typical model organisms, this review provides insights into the mechanisms by which PAEs affect the immune system, thus supplementing human immune experiments. Finally, we discuss the future direction of PAEs immunotoxicity research, thus providing a framework for the analysis of other environmental pollutants, as well as a basis for PAEs management and safe use.

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.

Elucidating the biodegradation pathway and catabolic genes of benzophenone-3 in Rhodococcus sp. S2-17

A new bacterium, Rhodococcus sp. S2-17, which could completely degrade an emerging organic pollutant, benzophenone-3 (BP-3), was isolated from contaminated sediment through an enrichment procedure, and its BP-3 catabolic pathway and genes were identified through metabolic intermediate and transcriptomic analyses and biochemical and genetic studies. Metabolic intermediate analysis suggested that strain S2-17 may degrade BP-3 using a catabolic pathway progressing via the intermediates BP-1, 2,4,5-trihydroxy-benzophenone, 3-hydroxy-4-benzoyl-2,4-hexadienedioic acid, 4-benzoyl-3-oxoadipic acid, 3-oxoadipic acid, and benzoic acid. A putative BP-3 catabolic gene cluster including cytochrome P450, flavin-dependent oxidoreductase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, and α/β hydrolase genes was identified through genomic and transcriptomic analyses. Genes encoding the cytochrome P450 complex that demethylates BP-3 to BP-1 were functionally verified through protein expression, and the functions of the other genes were also verified through knockout mutant construction and intermediate analysis. This study suggested that strain S2-17 might have acquired the ability to catabolize BP-3 by recruiting the cytochrome P450 complex and α/β hydrolase, which hydrolyzes 4-benzoyl-3-oxoadipic acid to benzoic acid and 3-oxoadipic acid, genes, providing insights into the recruitment of genes of for the catabolism of emerging organic pollutants.

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.

Mechanism for biodegradation of sulfamethazine by Bacillus cereus H38

Degradation of sulfonamides (SAs) by microorganisms has become a focus of current research. Sulfamethazine (SMZ) is a type of SA widely used in the livestock and poultry industry. However, understanding the intermediate products, degradation pathways and mechanism of SMZ biodegradation is limited at present. In this study, a SMZ degrading bacterium Bacillus cereus H38, which can use SMZ as its only carbon source, was isolated from farmland soil. The bacterium was gram-positive with rod-shaped cells. The effects of initial SMZ concentration, pH, temperature and amount of inoculation on the biodegradation of SMZ were investigated by a single factor experiment. The results showed that the maximum degradation rate of SMZ was achieved in the environmental conditions at an initial SMZ concentration of 5 mg/L, pH of 7.0, temperature of 25 °C and inoculation amount of 5%. Under these optimum degradation conditions, strain H38 can completely degrade SMZ within 3 days. The effects of intracellular enzymes, extracellular enzymes and periplasmic enzymes on the SMZ degradation process were compared. It was found that intracellular enzymes contributed the most to the biodegradation of SMZ, and the degradation rate approached 70%. Three possible intermediates were identified by LC-MS/MS, and two degradation pathways were proposed. Whole genome sequencing results showed that the genome size of strain H38 was 5,477,631 bp, including 5599 coding sequences (CDSs), and the GC content was 35.21%. In addition, functional annotation of CDSs was performed to analyze the metabolic pathways of nitrogen and sulfur in strain H38 combining genomics and bioinformatics. This study proposes new insights into the mechanism for biodegradation of SAs and will inform future research.

Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities

The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.

Remediation strategies for mitigation of phthalate pollution: Challenges and future perspectives

Phthalates are a group of emerging xenobiotic compounds commonly used as plasticizers. In recent times, there has been an increasing concern over the risk of phthalate exposure leading to adverse effects to human health and the environment. Therefore, it is necessary to not only understand the current status of phthalate pollution, their sources, exposure routes and health impacts, but also identify remediation technologies for mitigating phthalate pollution. Present review article aims to inform its readers about the ever increasing data on health burdens posed by phthalates and simultaneously highlights the recent advancements in research to alleviate phthalate contamination from environment. The article enumerates the major phthalates in use today, traces their environmental fate, addresses their growing health hazard concerns and largely focus on to provide an in-depth understanding of the different physical, chemical and biological treatment methods currently being used or under research for alleviating the risk of phthalate pollution, their challenges and the future research perspectives.

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.

An efficient phthalate ester-degrading Bacillus subtilis: Degradation kinetics, metabolic pathway, and catalytic mechanism of the key enzyme

Phthalate ester pollution in the environment and food chain is frequently reported. Microbial treatment is a green and efficient method for solving this problem. The isolation and systematic investigation of microorganisms generally recognized as safe (GRAS) will provide useful resources. A GRAS Bacillus subtilis strain, BJQ0005, was isolated from Baijiu fermentation starter and efficiently degraded phthalate esters (PAEs). The half-lives for di-isobutyl phthalate, di-butyl phthalate and di-(2-ethylhexyl) phthalate were 3.93, 4.28, and 25.49 h, respectively, from the initial amount of 10 mg per 10 mL reaction mixture, which are records using wild-type strains. Genome sequencing and metabolic intermediate analysis generated the whole metabolic pathway. Eighteen enzymes from the α/β hydrolase family were expressed. Enzymes GTW28_09400 and GTW28_13725 were capable of single ester bond hydrolysis of PAEs, while GTW28_17760 hydrolyzed di-ester bonds of PAEs. Using molecular docking, a possible mechanism affecting enzymatic ester bond hydrolysis of mono-butyl phthalate was proposed of GTW28_17760. The carboxyl group generated by the first hydrolysis step interacted with histidine in the catalytic active center, which negatively affected enzymatic hydrolysis. Isolation and systematic investigation of the PAE degradation characteristics of B. subtilis will promote the green and safe treatment of PAEs in the environment and food industry.

A Review of Current and Emerging Approaches for Water Pollution Monitoring

The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucleic acids. The latest technologies applied in wastewater and surface water mapped from these key players were reviewed and categorized into physicochemical and compound characterizations, biomonitoring, and molecular approaches in taxonomical and functional analyses. Overall, researchers are continuously rallying to enhance the detection of causal source for water pollution through either conventional or mostly advanced approaches focusing on spectrometry, high-throughput sequencing, and flow cytometry technology among others. From this review’s perspective, each pollution evaluation technology has its own advantages and it would be beneficial for several aspects of pollutants assessments to be combined and established as a complementary package for better aquatic environmental management in the long run.

Biodegradation of phthalate esters by Paracoccus kondratievae BJQ0001 isolated from Jiuqu (Baijiu fermentation starter) and identification of the ester bond hydrolysis enzyme

Phthalate ester (PAE) pollution is an increasing problem globally. Paracoccus kondratievae BJQ0001 was isolated from the fermentation starter of Baijiu and showed an efficient degradation capability toward PAEs. To our poor knowledge, this is the first report of a P. kondratievae strain capable of degrading PAEs. The first complete genome sequence of P. kondratievae was presented without gaps, and composed of two circular chromosomes and one plasmid. The species simultaneously degraded di-methyl phthalate (DMP), di-ethyl phthalate (DEP), di-butyl phthalate (DBP), di-isobutyl phthalate (DIBP) and di-(2-ethylhexyl) phthalate (DEHP), with DMP and DEP as the preferred substrates. The half-life (t_1/2) of DMP was only 6.34 h with an initial concentration of 200 mg/L. Combined with gene annotation and metabolic intermediate analysis, a metabolic pathway was proposed for the species. Benzoic acid, the intermediate of anaerobic PAE metabolism, was identified in the aerobic degradation process. Two key enzymes for alkyl ester bond hydrolysis were obtained, and belonged to families IV and VI of hydrolases, respectively. These results will promote the investigation of PAE degradation by P. kondratievae, and provide useful information for improving the quality control of food and environmental PAE treatment.

Insights into the binding interaction of substrate with catechol 2,3-dioxygenase from biophysics point of view

This study aims to clarify the interaction mechanism of substrate with catechol 2,3-dioxygenase (C23O) through multi-technique combination. A novel C23O (named C23O-2G) was cloned, heterogeneously expressed, and identified as a new member in subfamily I.2 of extradiol dioxygenases. Based on the simulations of molecular docking and dynamics, the exact binding sites of catechol on C23O-2G were identified, and the catalytic mechanism mediated by key residues was proposed. The roles of the predicted residues during catalysis were confirmed by site-directed mutagenesis, and the mutation of Thr254 could significantly increase catalytic efficiency and substrate specificity of C23O-2G. The binding and thermodynamic parameters obtained from fluorescence spectra suggested that catechol could effectively quench the intrinsic fluorescence of C23O-2G via static and dynamic quenching mechanisms and spontaneously formed C23O-2G/catechol complex by the binding forces of hydrogen bond and van der Waals force. The results of UV-vis spectra, synchronous fluorescence, and CD spectra revealed obvious changes in the microenvironment and conformation of C23O-2G, especially for the secondary structure. The atomic force microscope images further demonstrated the changes from an appearance point of view. This study could improve our mechanistic understanding of representative dioxygenases involved in aromatic compound degradation.

Metagenomic analysis exploring microbial assemblages and functional genes potentially involved in di (2-ethylhexyl) phthalate degradation in soil

Widespread use of di (2-ethylhexyl) phthalate (DEHP) as a plasticizer has caused considerable soil pollution; however, little is known about indigenous microbial communities involved in its degradation in soil. In this study, metagenomic sequencing combined with metabolite determination was used to explore microorganisms and genes potentially involved in DEHP degradation in aerobic and anaerobic soils. The results showed that under both dryland aerobic and flooded anaerobic conditions, DEHP was initially hydrolyzed into mono (2-ethylhexyl) phthalate which was then hydrolyzed into phthalic acid; benzoic acid was the central intermediate during further metabolism steps. Bacteria were more responsive to DEHP presence than fungi/archaea, and potential degradative genes stimulated by DEHP were predominantly associated with bacteria, reflecting the dominant role of bacteria in DEHP degradation. Members of the Actinomycetales seemed to be the dominant degraders under aerobic conditions, while a number of phyla i.e. Gemmatimonadetes, Proteobacteria, Acidobacteria and Bacteroidetes appeared to be involved under anaerobic conditions. Interestingly, ~50% of esterase/lipase/cytochrome P450 genes enriched by DEHP under aerobic conditions were from Nocardioides, a bacterial genus that has not been previously directly linked to phthalate ester degradation. The results indicate that novel degraders may play an important role in DEHP degradation in natural soil environments. This study provides a better understanding of the phthalate ester biodegradation processes occurring in soil.

Effects of bok choy on the dissipation of dibutyl phthalate (DBP) in mollisol and its possible mechanisms of biochemistry and microorganisms

Phytoremediation is an ecologically sustainable method for remediating contaminated soils, however, research on phytoremediation and its mechanisms are still rarely reported. The highest dibutyl phthalate (DBP) dissipation rate was 91% in 0-3mm bok choy rhizosphere via a 45-day rhizo-box experiment, and bok choy could regulate soil nutrients by increasing soil ammonia nitrogen (AN) and available phosphorus (AP). The biochemistry mechanism of interaction between dissolved organic matter (DOM) and DBP was also elucidated by various spectroscopy techniques. It was found that the alkyl ester in DBP produced the fastest response during the binding process, and the aromatic, hydroxyl and phenolic groups of the DOM humic-like substances preceded amide in DOM protein-like substance. It was found that DBP pollution reduced the Chao1 richness and Shannon index of bacteria in black soil via a pot experiment and high-throughput sequencing, which disturbed the metabolic activities and functional diversity of microorganisms in Mollisol. The microbial abundance increased in bok choy amendments, which has a specific microbial community structure and a high abundance of Actinobacteria and Acidobacteria. We concluded that some enriched genera were responsible for DBP dissipation, Alsobacter, Lacibacter, Myceligenerans, Schrenkiella parvula and Undibacterium. The findings of this study revealed that the possible biochemistry and microbial mechanisms of phytoremediation promoting the DBP dissipation in rhizosphere Mollisol and provided more useful information for phytoremediation of organic pollutants.

Bioaugmentation of Exogenous Strain Rhodococcus sp. 2G Can Efficiently Mitigate Di(2-ethylhexyl) Phthalate Contamination to Vegetable Cultivation

This work developed a bioaugmentation strategy that simultaneously reduced soil di(2-ethylhexyl) phthalate (DEHP) pollution and its bioaccumulation in Brassica parachinensis by inoculating the isolated strain Rhodococcus sp. 2G. This strain could efficiently degrade DEHP at a wide concentration range from 50 to 1600 mg/L and transformed DEHP through a unique biochemical degradation pathway that distinguished it from other Rhodococcus species. Besides, strain 2G colonized well in the rhizosphere soil of the inoculated vegetable without competition with indigenous microbes, resulting in increased removal of DEHP from soil (∼95%) and reduced DEHP bioaccumulation in vegetables (∼75% in the edible part) synchronously. Improved enzyme activities and DOC content in the rhizosphere of the planting vegetable and inoculating strain 2G were responsible for the high efficiency in mitigating DEHP contamination to vegetable cultivation. This work demonstrated a great potential application to grow vegetables in contaminated soil for safe food production.

In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2

Members of genus Gordonia are known to degrade various xenobitics and produce secondary metabolites. The genome of a halotorelant phthalic acid ester (PAEs) degrading actinobacterium Gordonia alkanivorans strain YC-RL2 was sequenced using Biosciences RS II platform and Single Molecular Real-Time (SMRT) technology. The reads were assembled de novo by hierarchical genome assembly process (HGAP) algorithm version 2. Genes were annotated by NCBI Prokaryotic Genome Annotation Pipeline. The generated genome sequence was 4,979,656 bp with an average G+C content of 67.45%. Calculation of ANI confirmed previous classification that strain YC-RL2 is G. alkanivorans. The sequences were searched against KEGG and COG databases; 3132 CDSs were assigned to COG families and 1808 CDSs were predicted to be involved in 111 pathways. 95 of the KEGG annotated genes were predicted to be involved in the degradation of xenobiotics. A phthalate degradation operon could not be identified in the genome indicating that strain YC-RL2 possesses a novel way of phthalate degradation. A total of 203 and 22 CDSs were annotated as esterase/hydrolase and dioxygenase genes respectively. A total of 53 biosynthetic gene clusters (BGCs) were predicted by antiSMASH (antibiotics & Secondary Metabolite Analysis Shell) bacterial version 4.0. The genome also contained putative genes for heavy metal metabolism. The strain could tolerate 1 mM of Cd²⁺, Co²⁺, Cu²⁺, Ni²⁺, Zn²⁺, Mn²⁺ and Pb²⁺ ions. These results show that strain YC-RL2 has a great potential to degrade various xenobiotics in different environments and will provide a rich genetic resource for further biotechnological and remediation studies.