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

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.

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.

Adsorption Characterization of Lactobacillus sp. for Di-(2-ethylhexyl) phthalate

Di-(2-ethylhexyl) phthalate (DEHP) is the widely detected plasticizer in foods whose exposure is associated with a myriad of human disorders. The present study focused on identifying Lactobacillus strains with high adsorption potential towards DEHP and further elucidating the mechanism of binding using HPLC, FTIR and SEM. Two strains, Lactobacillus rhamnosus GG and Lactobacillus plantarum MTCC 25,433, were found to rapidly adsorb more than 85% of DEHP in 2 h. Binding potential remained unaffected by heat treatment. Moreover, acid pre-treatment enhanced the DEHP adsorption. Chemical pre-treatments, such as NaIO4, pronase E or lipase, caused reduction in DEHP adsorption to 46% (LGG), 49% (MTCC 25,433) and 62% (MTCC 25,433), respectively, attributing it to cell wall polysaccharides, proteins and lipids. This was also corroborated by stretching vibrations of C = O, N-H, C-N and C-O functional groups. Furthermore, SDS and urea pre-treatment, demonstrated the crucial role of hydrophobic interactions in DEHP adsorption. The extracted peptidoglycan from LGG and MTCC 25,433 adsorbed 45% and 68% of DEHP, respectively, revealing the imperative role of peptidoglycan and its integrity in DEHP adsorption. These findings indicated that DEHP removal was based on physico-chemical adsorption and cell wall proteins, polysaccharides or peptidoglycan played a primary role in its adsorption. Owing to the high binding efficiency, L. rhamnosus GG and L. plantarum MTCC 25,433 were considered to be a potential detoxification strategy to mitigate the risk associated with the consumption of DEHP-contaminated foods.

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.

Optimizing concentration and interaction mechanism of Demodesmus sp. and Achromobacter pulmonis sp. consortium to evaluate their potential for dibutyl phthalate removal from synthetic wastewater

A green approach of Desmodesmus sp. to Achromobacter pulmonis (1:1) coculture ratios was optimized to improve the removal efficiency of dibutyl phthalate (DBP) from simulated wastewater. High DBP resistance bacterial strains and microalgae was optimized from plastic contaminated water and acclimation process respectively. The influence of various factors on DBP removal performance was comprehensively investigated. Highest DBP removal 93 % was recorded, when the ratios algae-bacteria 1:1, with sodium acetate, pH-6, shaking speed-120 rpm and lighting periods L:D-12:12. Enough nutrient (TN/TP/TOC) availability and higher protein-108 mg/L and sugar-40 mg/L were observed in presences of 50 mg/L DBP. The degradation and sorption were calculated 81,12; 27,39 & 43,12 % in algae-bacteria, only algae and only bacteria system respectively. The degradation kinetics t1/2 3.74,22.15,12.86 days were evaluated, confirming that algae-bacteria effectively degrade the DBP. This outcome leading to promote a green sustainable approach to remove the emerging contamination from wastewater.

Improved sea rice yield and accelerated di-2-ethylhexyl phthalate (DEHP) degradation by straw carbonization returning in coastal saline soils

Di-2-ethylhexyl phthalate, a persistent organic contaminant, is widely distributed in the environment and poses substantial threats to human health; however, there have been few investigations regarding the risks and remediation of DEHP in coastal saline soils. In this work, we studied the influences of straw carbonization returning on sea rice yield and DEHP degradation. Straw carbonization returning significantly increased soil nutrients and reduced salt stress to improve sea rice yield. DEHP degradation efficiency was enhanced to a maximum of 78.27% in straw carbonized return with 60% sea rice, mainly attributed to the high pH value, high soil organic matter and enriched potential DEHP degraders of Nocardioides, Mycobacterium and Bradyrhizobium. Some key genes related to metabolism (esterase and cytochrome P450) and DEHP-degradation (pht4, pht5, pcaG, dmpB, catA and fadA) were elevated and explained the accelerated DEHP degradation, shifting from the benzoic acid pathway to the protocatechuate pathway in straw carbonization returning. The results obtained in this study provide a deep and comprehensive understanding of sea rice yield improvement and DEHP degradation mechanisms in coastal paddy soil by a straw carbonization returning strategy.

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.

Molecular evaluation of the metabolism of estrogenic di(2-ethylhexyl) phthalate in Mycolicibacterium sp

BACKGROUND

Di(2-ethylhexyl) phthalate (DEHP) is a widely detected plasticizer and a priority pollutant of utmost concern for its adverse impact on humans, wildlife and the environment. To eliminate such toxic burden, biological processes are the most promising ways to combat rampant environmental insults under eco-friendly conditions. The present study investigated the biochemical and molecular assessment of the catabolic potential of Mycolicibacterium sp. strain MBM in the assimilation of estrogenic DEHP.

RESULTS

A detailed biochemical study revealed an initial hydrolytic pathway of degradation for DEHP followed by the assimilation of hydrolyzed phthalic acid and 2-ethylhexanol to TCA cycle intermediates. Besides the inducible nature of DEHP-catabolic enzymes, strain MBM can efficiently utilize various low- and high-molecular-weight phthalate diesters and can grow under moderately halotolerant conditions. Whole genome sequence analysis exhibited a genome size of 6.2 Mb with a GC content of 66.51% containing 6,878 coding sequences, including multiple genes, annotated as relevant to the catabolism of phthalic acid esters (PAEs). Substantiating the annotated genes through transcriptome assessment followed by RT-qPCR analysis, the possible roles of upregulated genes/gene clusters in the metabolism of DEHP were revealed, reinforcing the biochemical pathway of degradation at the molecular level.

CONCLUSIONS

A detailed co-relation of biochemical, genomic, transcriptomic and RT-qPCR analyses highlights the PAE-degrading catabolic machineries in strain MBM. Further, due to functional attributes in the salinity range of both freshwater and seawater, strain MBM may find use as a suitable candidate in the bioremediation of PAEs.

Remediation of phthalate acid esters from contaminated environment—Insights on the bioremedial approaches and future perspectives

Phthalates are well-known emerging pollutants that are toxic to the environment and human health. Phthalates are lipophilic chemicals used as plasticizers in many of the items for improving their material properties. These compounds are not chemically bound and are released to the surroundings directly. Phthalate acid esters (PAEs) are endocrine disruptors and can interfere with hormones, which can cause issues with development and reproduction, thus there is a huge concern over their existence in various ecological surroundings. The purpose of this review is to explore the occurrence, fate, and concentration of phthalates in various environmental matrices. This article also covers the phthalate degradation process, mechanism, and outcomes. Besides the conventional treatment technology, the paper also aims at the recent advancements in various physical, chemical, and biological approaches developed for phthalate degradation. In this paper, a special focus has been given on the diverse microbial entities and their bioremedial mechanisms executes the PAEs removal. Critically, the analyses method for determining intermediate products generated during phthalate biotransformation have been discussed. Concluisvely, the challenges, limitations, knowledge gaps and future opportunities of bioremediation and their significant role in ecology have also been highlighted.

Exploring Potent Fungal Isolates from Sanitary Landfill Soil for In Vitro Degradation of Dibutyl Phthalate

Di-n-butyl phthalate (DBP) is one of the most extensively used plasticizers for providing elasticity to plastics. Being potentially harmful to humans, investigating eco-benign options for its rapid degradation is imperative. Microbe-mediated DBP mineralization is well-recorded, but studies on the pollutant's fungal catabolism remain scarce. Thus, the present investigation was undertaken to exploit the fungal strains from toxic sanitary landfill soil for the degradation of DBP. The most efficient isolate, SDBP4, identified on a molecular basis as Aspergillus flavus, was able to mineralize 99.34% dibutyl phthalate (100 mg L^-1) within 15 days of incubation. It was found that the high production of esterases by the fungal strain was responsible for the degradation. The strain also exhibited the highest biomass (1615.33 mg L^-1) and total soluble protein (261.73 µg mL^-1) production amongst other isolates. The DBP degradation pathway scheme was elucidated with the help of GC-MS-based characterizations that revealed the formation of intermediate metabolites such as benzyl-butyl phthalate (BBP), dimethyl-phthalate (DMP), di-iso-butyl-phthalate (DIBP) and phthalic acid (PA). This is the first report of DBP mineralization assisted with A. flavus, using it as a sole carbon source. SDBP4 will be further formulated to develop an eco-benign product for the bioremediation of DBP-contaminated toxic sanitary landfill soils.

Biodegradation of high di-(2-Ethylhexyl) phthalate (DEHP) concentration by food waste composting and its toxicity assessment using seed germination test

Di-(2-ethylhexyl) phthalate (DEHP), a plasticizer derived from phthalate ester, is used as an additive in industrial products such as plastics, paints, and medical devices. However, DEHP is known as an endocrine-disrupting chemical, causing cancers and adverse effects on human health. This study evaluated DEHP biodegradation efficiency via food waste composting during 35 days of incubation. At high DEHP concentrations (2167 mg kg^-1) in food waste compost mixture, the DEHP biodegradation efficiency was 99% after 35 days. The highest degradation efficiency was recorded at the thermophilic phase (day 3 - day 11) with the biodegradation rate reached 187 mg kg^-1 day^-1. DEHP was metabolized to dibutyl phthalate (DBP) and dimethyl phthalate (DMP) and would be oxidized to benzyl alcohol (BA) and mineralized into CO₂ and water via various metabolisms. Finally, the compost's quality with residual DEHP was evaluated using Brassica chinensis L. seeds via 96 h of germination tests. The compost (at day 35) with a trace amount of DEHP as the end product showed no significant effect on the germination rate of Brassica chinensis L. seeds (88%) compared to that without DEHP (94%), indicating that the compost can be reused as fertilizer in agricultural applications. These results provide an improved understanding of the DEHP biodegradation via food waste composting without bioaugmentation and hence facilitating its green remediation and conversion into value-added products. Nevertheless, further studies are needed on DEHP biodegradation in large-scale food waste composting or industrial applications.

Rhodococcus: A promising genus of actinomycetes for the bioremediation of organic and inorganic contaminants

Rhodococcus is a genus of actinomycetes that has been explored by the scientific community for different purposes, especially for bioremediation uses. However, the mechanisms governing Rhodococcus-mediated bioremediation processes are far from being fully elucidated. In this sense, this work aimed to compile the recent advances in the use of Rhodococcus for the bioremediation of organic and inorganic contaminants present in different environmental compartments. We reviewed the bioremediation capacity and mechanisms of Rhodococcus spp. in the treatment of polycyclic aromatic hydrocarbons, phenolic substances, emerging contaminants, heavy metals, and dyes given their human health risks and environmental concern. Different bioremediation techniques were discussed, including experimental conditions, treatment efficiencies, mechanisms, and degradation pathways. The use of Rhodococcus strains in the bioremediation of several compounds is a promising approach due to their features, primarily the presence of appropriate enzyme systems, which result in high decontamination efficiencies; but that vary according to experimental conditions. Besides, the genus Rhodococcus contains a small number of opportunistic species and pathogens, representing an advantage from the point of view of safety. Advances in analytical detection techniques and Molecular Biology have been collaborating to improve the understanding of the mechanisms and pathways involved in bioremediation processes. In the context of using Rhodococcus spp. as bioremediation agents, there is a need for more studies that 1) evaluate the role of these actinomycetes on a pilot and field scale; 2) use genetic engineering tools and consortia with other microorganisms to improve the bioremediation efficiency; and 3) isolate new Rhodococcus strains from environments with extreme and/or contaminated conditions aiming to explore their adaptive capabilities for bioremediation purposes.

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.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

Use of soil actinomycetes for pharmaceutical, food, agricultural, and environmental purposes

In this article, we reviewed the international scientific production of the last years on actinomycetes isolated from soil aiming to report recent advances in using these microorganisms for different applications. The most promising genera, isolation conditions and procedures, pH, temperature, and NaCl tolerance of these bacteria were reported. Based on the content analysis of the articles, most studies have focused on the isolation and taxonomic description of new species of actinomycetes. Regarding the applications, the antimicrobial potential (antibacterial and antifungal) prevailed among the articles, followed by the production of enzymes (cellulases and chitinases, etc.), agricultural uses (plant growth promotion and phytopathogen control), bioremediation (organic and inorganic contaminants), among others. Furthermore, a wide range of growth capacity was verified, including temperatures from 4 to 60 °C (optimum: 28 °C), pH from 3 to 13 (optimum: 7), and NaCl tolerance up to 32% (optimum: 0-1%), which evidence a great tolerance for actinomycetes cultivation. Streptomyces was the genus with the highest incidence among the soil actinomycetes and the most exploited for different uses. Besides, the interest in isolating actinomycetes from soils in extreme environments (Antarctica and deserts, for example) is growing to explore the adaptive capacities of new strains and the secondary metabolites produced by these microorganisms for different industrial interests, especially for pharmaceutical, food, agricultural, and environmental purposes.