Biodegradation of phthalate isomers by Pseudomonas aeruginosa PP4, Pseudomonas sp. PPD and Acinetobacter lwoffii ISP4

Characterization of three novel dimethyl disulfide degrading bacteria and their potential degradation pathways

Dimethyl disulfide (DMDS) is an odor compound characterized by the lowest olfactory threshold and high toxicity. It is indispensable to explore the bacteria with high resistance and degradation efficiency to DMDS. Acinetobacter lwoffii, Pseudomonas mendocina, and Myroides odoratus were isolated from kitchen waste. After 6 days of individual treatment, the removal rates were 34.22 %, 40.95 %, and 41.94 % respectively. The DMDS metabolic pathways based on metagenomic assays were discovered to be incomplete due to the insufficient annotation of some key genes in the current database. Following 3 days of treatment with bacterial consortia at ratios of 5:1 for A. lwoffii C2/ M. odoratus C7 and 1:1:1 for the three strains achieved 100 % DMDS removal. Additionally, the consortia reduced hydrogen sulfide (H2S) and dimethyl sulfide (DMS).This discovery broadens the spectrum of bacteria exhibiting high tolerance and efficient degradation of DMDS, with significant implications for DMDS removal and odor treatment.

Biodegradation of phthalic acid and terephthalic acid by Comamonas testosteroni strains

Phthalic acid isomers are the monomers of phthalate molecules, also known as phthalic acid esters, widely employed in the plastics industry. This study aims to investigate the biodegradation of phthalic acid (PA) and terephthalic acid (TPA) by five industry-borne Comamonas testosteroni strains: 3APTOL, 3ABBK, 2B, 3A1, and C8. To assess the ability of C. testosteroni strains to biodegrade phthalic acid isomers in fermentation media, an analytical method was employed, consisting of high-performance liquid chromatography (HPLC) analyses. Subsequently, molecular screening of the genomic and plasmid DNA was conducted to identify the degradative genes responsible for the breakdown of these chemicals. The genes of interest, including ophA2, tphA2, tphA3, pmdA, and pmdB, were screened by real-time PCR. The five C. testosteroni strains effectively degraded 100% of 100 mg/L PA (p = 0.033) and TPA (p = 0.0114). Molecular analyses indicated that all C. testosteroni strains contained the pertinent genes at different levels within their genomes and plasmids, as reflected in the threshold cycle (Ct) values. Additionally, DNA temperature of melting (Tm) analyses uncovered minor differences between groups of genes in genomic and plasmid DNA. C. testosteroni strains could be excellent candidates for the removal of phthalic acid isomers from environmental systems.

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.

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.

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.

Biodegradation of diethyl phthalate and phthalic acid by a new indigenous Pseudomonas putida

Diethyl phthalate (DEP) is one of the extensively used plasticizers which has been considered a priority hazardous pollutant due to its carcinogenic, endocrine disrupter, and multi-toxic effects on humans. The identification of DEP in different parts of the ecosphere has increased the global community's attention to the elimination of this pollutant in a bio-eco-friendly way. In this research, a novel aerobic bacterial strain nominates as ShA (GenBank accession number: MN298858) capable of consuming DEP as carbon and energy sources, was isolated from the upper phase (0-10 cm) of Anzali international wetland sediments by enrichment culture method. Morphological characteristics and 16S rRNA gene sequence analysis demonstrated that strain ShA belonged to Pseudomonas putida. The substrate utilization test demonstrated that strain ShA was able to grow in mineral salt medium containing dimethyl phthalate (DMP) and phthalic acid (PA) isomers including terephthalic and isophthalic acid. Degradation assay showed strain ShA completely degraded 200 mg/L DEP within 22 h (pH 7.0, 30 °C). Surprisingly, PA as the main intermediate of DEP biodegradation was identified by GC-FID. Moreover, the rapid degradation of 2000 mg/L PA to CO₂ and H₂O was viewed in 22 h by strain ShA. The possible route of DEP degradation was DEP directly to PA and then PA consumption for growth. This study obtained results that provide a great contribution to applying strain ShA in the biodegradation of low molecular weight of PAEs and PA isomers in natural ecosystems. This is the first report of a P. putida strain able to degrade DEP and PA.

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.

Characterization of an Esterase Producing Bacterium from the Gut of Chironomus circumdatus (Bloodworms) and its Ability to Use Modified Phthalates

Insects harbor bacteria that are a rich source of enzymes that can be utilized for various industrial and biotechnological applications. It is predicted that during evolution these detoxifying enzymes have been acquired by insects through bacteria. However, the role of host insect detoxification enzymes has already been extensively studied but only a few resistance development studies have been focused on the enzymes derived from gut bacteria. Thus in this study, two bacterial isolates were found in the gut of Chironomous circumdatus larvae having esterase activity, out of which one bacterium was molecular characterized and it was found to be Enterobacter mori designated as strain BI1245. Further, crude extract from the bacterium was characterized and it was observed that it showed maximum activity at pH 8 and temperature 60 °C. Moreover, the crude extract showed 0.26 mM and 290 U/mg of protein as K_m and V_max value when p-nitrophenyl acetate was used as a substrate. Thereafter, the bacterial isolate was incubated in minimal salts medium containing modified phthalates and it was found that bacterium could utilize shorter alkyl-chain phthalic acid esters faster as compared to long alkyl chains thereby indicating that side chain of the substrates has a significant effect on the utilization of phthalic acid esters. Thus the gut flora present in insects may play an important role in providing resistance to the host to live in phthalate polluted water.

Complete biodegradation of di-n-butyl phthalate (DBP) by a novel Pseudomonas sp. YJB6

Phthalate acid esters (PAEs) are environmentally ubiquitous and have aroused a worldwide concern due to their threats to environment and human health. Di-n-butyl phthalate (DBP) is one of the most frequently observed PAEs in the environment. In this study, a novel bacterium identified as Pseudomonas sp. YJB6 that isolated from PAEs-contaminated soil was determined to have strong DBP-degrading activity. A complete degradation of DBP in 200 mg/L was achieved within 3 days when YJB6 was cultivated at 31.4 °C with an initial inoculation size of 0.6 (OD600) in basic mineral salts liquid medium (MSM), pH 7.6. The degradation curves of DBP (50-2000 mg/L) fitted well the first-order kinetics model, with a half-life (t_1/2) ranging from 0.86 to 1.88 d. The main degradation intermediates were identified as butyl-ethyl phthalate (BEP), mono-butyl phthalate (MBP), phthalic acid (PA) and benzoic acid (BA), indicating a new complex and complete biodegradation pathway presented by YJB6. DBP might be metabolized through de-esterification, β-oxidation, and hydrolysis, followed by entering the Krebs cycle of YJB6 as a final step. Strain YJB6 was successfully immobilized with sodium alginate (SA), polyvinyl alcohol (PVA), and SA-PVA. The immobilization significantly improved the stability and adaptability of the cells thus resulting in high volumetric DBP-degrading rates compared to that of the freely suspended cells. In addition, these immobilized cells can be reused for many cycles with well conserved in DBP-degrading activity. The ideal DBP degrading ability of the free and immobilized YJB6 cells suggests that strain YJB6, especially the SA-PVA+ YJB6 promises great potential to remove hazardous PAEs.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Biodegradation of diethyl-phthalate (DEP) by halotolerant bacteria isolated from an estuarine environment

Phthalates are widely used as plasticizers in many industrial products due to their chemical properties that confer flexibility and durability to building materials, lubricants, solvents, insect repellents, clothing, cosmetics, being widely distributed in the environment. Besides persistent, they are also considered endocrine-disrupting compounds (EDCs), causing a global concern about their release into the environment, once they can alter the reproductive and endocrine health of humans systems. Under natural conditions, photodegradation and hydrolysis rates of phthalates are often very slow; therefore, microbial degradation is a natural way to treat these pollutants. In this context, three bacterial consortia (CMS, GMS and GMSS) were isolated from environmental samples from the Santos Estuarine System (SES) and were able to grow on diethyl-phthalate (DEP) as an only carbon source. From the GMSS consortium, three different strains were isolated and identified as Burkholderia cepacia, Pseudomonas koreensis and Ralstonia pickettii by molecular and mass spectrometry (MALDI-TOF-Biotyper) techniques. Considering there are no reports about Ralstonia genus on phthalates degradation, this strain was chosen to proceed the kinetics experiments. Ralstonia pickettii revealed a great ability to degrade DEP (300 mg/L) in less than 24 h. This is the first report implicating R. pickettii in DEP degradation.

Effective degradation of Di-n-butyl phthalate by reusable, magnetic Fe3O4 nanoparticle-immobilized Pseudomonas sp. W1 and its application in simulation

Di-n-butyl phthalate (DBP), one of the most widely used plasticizers, has been listed as a priority pollutant because of its toxicity to both humans and animals. In this study, Pseudomonas sp. W1, isolated from activated sludge, was capable of degrading 99.88% of DBP (1000 mg L^-1) within 8 days. We immobilized the W1 strain using Fe₃O₄ iron nanoparticles (IONPs) coated with poly-dopamine (PDA), and further evaluated its DBP degradation efficiency. The DBP degradation performance of W1 was improved by immobilization, exhibiting 99.69% of DBP degradation efficiency on the 6th day, which was 25.68% higher than un-immobilized W1. After three cycles of magnetic recycling and utilization, W1-PDA-IONPs retained 99.6% of their original efficiency. W1-PDA-IONPs were then used to degrade DBP in landfill leachate. When the proportion of raw leachate was ≤50%, DBP could be all degraded by W1-PDA-IONPs within 6 days. In 100% landfill leachate, DBP degradation efficiency after 10 days of incubation reached 66.40%. Furthermore, W1-PDA-IONPs cells in a simulated aeration system could be effectively magnetically separated at aeration rates from 60 to 600 mL min^-1. These results highlight the potential of W1-PDA-IONPs in the bioremediation of DBP-contaminated waste water.

Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria

As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.

Microbial degradation of phthalates: biochemistry and environmental implications

The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.

Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration

Theories in soil biology, such as plant-microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below-ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above-ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost-effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature-based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.

Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans

Syntrophorhabdus aromaticivorans is a syntrophically fermenting bacterium that can degrade isophthalate (3-carboxybenzoate). It is a xenobiotic compound which has accumulated in the environment for more than 50 years due to its global industrial usage and can cause negative effects on the environment. Isophthalate degradation by the strictly anaerobic S. aromaticivorans was investigated to advance our understanding of the degradation of xenobiotics introduced into nature, and to identify enzymes that might have ecological significance for bioremediation. Differential proteome analysis of isophthalate- vs benzoate-grown cells revealed over 400 differentially expressed proteins of which only four were unique to isophthalate-grown cells. The isophthalate-induced proteins include a phenylacetate:CoA ligase, a UbiD-like decarboxylase, a UbiX-like flavin prenyltransferase, and a hypothetical protein. These proteins are encoded by genes forming a single gene cluster that putatively codes for anaerobic conversion of isophthalate to benzoyl-CoA. Subsequently, benzoyl-CoA is metabolized by the enzymes of the anaerobic benzoate degradation pathway that were identified in the proteomic analysis. In vitro enzyme assays with cell-free extracts of isophthalate-grown cells indicated that isophthalate is activated to isophthalyl-CoA by an ATP-dependent isophthalate:CoA ligase (IPCL), and subsequently decarboxylated to benzoyl-CoA by a UbiD family isophthalyl-CoA decarboxylase (IPCD) that requires a prenylated flavin mononucleotide (prFMN) cofactor supplied by UbiX to effect decarboxylation. Phylogenetic analysis revealed that IPCD is a novel member of the functionally diverse UbiD family (de)carboxylases. Homologs of the IPCD encoding genes are found in several other bacteria, such as aromatic compound-degrading denitrifiers, marine sulfate-reducers, and methanogenic communities in a terephthalate-degrading reactor. These results suggest that metabolic strategies adapted for degradation of isophthalate and other phthalate are conserved between microorganisms that are involved in the anaerobic degradation of environmentally relevant aromatic compounds.

Phthalate Release from Plastic Fragments and Degradation in Seawater

Plastic debris in the environment contains plasticizers, such as phthalates (PAEs), that can be released during plastic aging. Here, two common plastic materials, an insulation layer of electric cables (polyvinyl chloride, PVC-cables) and plastic garbage bag (polyethylene, PE-bags), were incubated in natural seawater under laboratory conditions, and the PAE migration to the seawater phase was studied with varying light and bacterial conditions over a 90-day time course. Free PAEs diluted in seawater were also studied for bacterial degradation. Our results showed that, within the first month of incubation, both plastic materials significantly leached out PAEs into the surrounding water. We found that di-isobutyl phthalate (DiBP) and di- n-butyl phthalate (DnBP) were the main PAEs released from the PE-bags, with the highest values of 83.4 ± 12.5 and 120.1 ± 18.0 ng g^-1 of plastic, respectively. Furthermore, dimethyl phthalate (DMP) and diethyl phthalate (DEP) were the main PAEs released from PVC-cables, with mass fractions as high as 9.5 ± 1.4 and 68.9 ± 10.3 ng g^-1, respectively. Additionally, we found that light and bacterial exposure increased the total amount of PAEs released from PVC-cables by a factor of up to 5, whereas they had no influence in the case of PE-bags.

Biodegradation of phthalic acid esters (PAEs) and in silico structural characterization of mono-2-ethylhexyl phthalate (MEHP) hydrolase on the basis of close structural homolog

Three bacterial strains capable of degrading phthalates namely Pseudomonas sp. PKDM2, Pseudomonas sp. PKDE1 and Pseudomonas sp. PKDE2 were isolated and characterized for their degradative potential. These strains efficiently degraded 77.4%-84.4% of DMP, 75.0%-75.7% of DEP and 71.7%-74.7% of DEHP, initial amount of each phthalate is 500mgL^-1 of each phthalate, after 44h of incubation. GC-MS results reveal the tentative DEHP degradation pathway, where hydrolases mediate the breakdown of DEHP to phthalic acid (PA) via an intermediate MEHP. MEHP hydrolase is a serine hydrolase which is involved in the reduction of the MEHP to PA. The predicted 3D model of MEHP hydrolase from Pseudomonas mosselii was docked with phthalate monoesters (PMEs) such as MEHP, mono-n-hexyl phthalate (MHP), mono-n-butyl phthalate (MBP) and mono-n-ethyl phthalate (MEP), respectively. Docking results show the distance between the carbonyl carbon of respective phthalate monoester and the hydroxyl group of catalytic serine lies in the range of 2.9 to 3.3Å, which is similar to the ES complex of other serine hydrolases. This structural study highlights the interaction and the role of catalytic residues of MEHP hydrolase involved in the biodegradation of PMEs to phthalate.

Comparative study on the degradation of dibutyl phthalate by two newly isolated Pseudomonas sp. V21b and Comamonas sp. 51F

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Comparative degradation of DBP by Pseudomonas sp. V21b and Comamonas sp. 51F.

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Degradation in MSM and contaminated samples.

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Kinetics of DBP degradation.

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Stoichiometry of DBP degradation and biomass formation.

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Phthalate esters genes identification.

Dibutyl phthalate is (DBP) the top priority toxicant responsible for carcinogenicity, teratogenicity and endocrine disruption. This study demonstrates the DBP degradation capability of the two newly isolated bacteria from municipal solid waste leachate samples. The isolated bacteria were designated as Pseudomonas sp. V21b and Comamonas sp. 51F after scanning electron microscopy, transmission electron microscopy, Gram-staining, antibiotic sensitivity tests, biochemical characterization, 16S-rRNA gene identification and phylogenetic studies. They were able to grow on DBP, benzyl butyl phthalate, monobutyl phthalate, diisodecyl phthalate, dioctyl phthalate, and protocatechuate. It was observed that Pseudomonas sp. V21b was more efficient in DBP degradation when compared with Comamonas sp. 51F. It degraded 57% and 76% of the initial DBP in minimal salt medium and in DBP contaminated samples respectively. Kinetics for the effects of DBP concentration on Pseudomonas sp. V21b and Comamonas sp. 51F growth was also evaluated. Stoichiometry for DBP degradation and biomass formation were compared for both the isolates. Two major metabolites diethyl phthalate and monobutyl phthalates were identified using GC–MS in the extracts. Key genes were amplified from the genomes of Pseudomonas sp. V21b and Comamonas sp. 51F. DBP degradation pathway was also proposed.

Biodegradation of endocrine disruptor dibutyl phthalate (DBP) by a newly isolated Methylobacillus sp. V29b and the DBP degradation pathway

Bacteria of the genus Methylobacillus are methanotrophs, a metabolic feature that is widespread in the phylum Proteobacteria. The study demonstrates the isolation and characterization of a newly isolated Methylobacillus sp. V29b. which grows on methanol, protocatechuate, monobutyl phthalate, dibutyl phthalate, diethyl phthalate, benzyl butyl phthalate, dioctyl phthalate and diisodecyl phthalate. Methylobacillus sp. V29b was characterized with scanning electron microscopy, transmission electron microscopy, Gram staining, antibiotics sensitivity tests and biochemical characterization. It degrades 70 % of the initial DBP in minimal salt medium and 65 % of the initial DBP in samples contaminated with DBP. DBP biodegradation kinetics was explained by the Monod growth inhibition model. Values for maximum specific growth rate (µ_max) and half-velocity constant (K_s) are 0.07 h⁻¹ and 998.2 mg/l, respectively. Stoichiometry for DBP degradation was calculated for Methylobacillus sp. V29b. Four metabolic intermediates, dibutyl phthalate (DBP), monobutyl phthalate, phthalic acid and pyrocatechol, were identified. Based on the metabolic intermediates identified, a chemical pathway for DBP degradation was proposed. Six genes for phthalic acid degradation were identified from the genome of Methylobacillus sp. V29b.

Enzymes involved in the anaerobic degradation of ortho-phthalate by the nitrate-reducing bacterium Azoarcus sp. strain PA01

The pathway of anaerobic degradation of o-phthalate was studied in the nitrate-reducing bacterium Azoarcus sp. strain PA01. Differential two-dimensional protein gel profiling allowed the identification of specifically induced proteins in o-phthalate-grown compared to benzoate-grown cells. The genes encoding o-phthalate-induced proteins were found in a 9.9 kb gene cluster in the genome of Azoarcus sp. strain PA01. The o-phthalate-induced gene cluster codes for proteins homologous to a dicarboxylic acid transporter, putative CoA-transferases and a UbiD-like decarboxylase that were assigned to be specifically involved in the initial steps of anaerobic o-phthalate degradation. We propose that o-phthalate is first activated to o-phthalyl-CoA by a putative succinyl-CoA-dependent succinyl-CoA:o-phthalate CoA-transferase, and o-phthalyl-CoA is subsequently decarboxylated to benzoyl-CoA by a putative o-phthalyl-CoA decarboxylase. Results from in vitro enzyme assays with cell-free extracts of o-phthalate-grown cells demonstrated the formation of o-phthalyl-CoA from o-phthalate and succinyl-CoA as CoA donor, and its subsequent decarboxylation to benzoyl-CoA. The putative succinyl-CoA:o-phthalate CoA-transferase showed high substrate specificity for o-phthalate and did not accept isophthalate, terephthalate or 3-fluoro-o-phthalate whereas the putative o-phthalyl-CoA decarboxylase converted fluoro-o-phthalyl-CoA to fluoro-benzoyl-CoA. No decarboxylase activity was observed with isophthalyl-CoA or terephthalyl-CoA. Both enzyme activities were oxygen-insensitive and inducible only after growth with o-phthalate. Further degradation of benzoyl-CoA proceeds analogous to the well-established anaerobic benzoyl-CoA degradation pathway of nitrate-reducing bacteria.

A monograph on the remediation of hazardous phthalates

Phthalates or phthalic acid esters are a group of xenobiotic and hazardous compounds blended in plastics to enhance their plasticity and versatility. Enormous quantities of phthalates are produced globally for the production of plastic goods, whose disposal and leaching out into the surroundings cause serious concerns to the environment, biota and human health. Though in silico computational, in vitro mechanistic, pre-clinical animal and clinical human studies showed endocrine disruption, hepatotoxic, teratogenic and carcinogenic properties, usage of phthalates continues due to their cuteness, attractive chemical properties, low production cost and lack of suitable alternatives. Studies revealed that microbes isolated from phthalate-contaminated environmental niches efficiently bioremediate various phthalates. Based upon this background, this review addresses the enumeration of major phthalates used in industry, routes of environmental contamination, evidences for health hazards, routes for in situ and ex situ microbial degradation, bacterial pathways involved in the degradation, major enzymes involved in the degradation process, half-lives of phthalates in environments, etc. Briefly, this handy module would enable the readers, environmentalists and policy makers to understand the impact of phthalates on the environment and the biota, coupled with the concerted microbial efforts to alleviate the burden of ever increasing load posed by phthalates.

Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01(T)

Azoarcus sp. strain PA01(T) belongs to the genus Azoarcus, of the family Rhodocyclaceae within the class Betaproteobacteria. It is a facultatively anaerobic, mesophilic, non-motile, Gram-stain negative, non-spore-forming, short rod-shaped bacterium that was isolated from a wastewater treatment plant in Constance, Germany. It is of interest because of its ability to degrade o-phthalate and a wide variety of aromatic compounds with nitrate as an electron acceptor. Elucidation of the o-phthalate degradation pathway may help to improve the treatment of phthalate-containing wastes in the future. Here, we describe the features of this organism, together with the draft genome sequence information and annotation. The draft genome consists of 4 contigs with 3,908,301 bp and an overall G + C content of 66.08 %. Out of 3,712 total genes predicted, 3,625 genes code for proteins and 87 genes for RNAs. The majority of the protein-encoding genes (83.51 %) were assigned a putative function while those remaining were annotated as hypothetical proteins.

Degradation of di-n-butyl phthalate by newly isolated Ochrobactrum sp

A gram negative isolate designated JDC-41 was obtained from river sludge using mixtures of phthalate esters as the sole source and energy. The isolate was identified as Ochrobactrum sp. based on its 16S rRNA gene sequence. Over 87% of supplied di-n-butyl phthalate (DBP) was degraded by JDC-41 in a pH neutral mineral salts medium at 30 degrees C within 48 h. Increased DBP (50-500 mg/L) in the culture correspondingly increased degradation half-life from 3.83 to 18.12 h. DBP induced cells more rapidly degraded DBP.

Bypassing isophthalate inhibition by modulating glutamate dehydrogenase (GDH): purification and kinetic characterization of NADP-GDHs from isophthalate-degrading Pseudomonas aeruginosa strain PP4 and Acinetobacter lwoffii strain ISP4

Pseudomonas aeruginosa strain PP4 and Acinetobacter lwoffii strain ISP4 metabolize isophthalate as a sole source of carbon and energy. Isophthalate is known to be a competitive inhibitor of glutamate dehydrogenase (GDH), which is involved in C and N metabolism. Strain PP4 showed carbon source-dependent modulation of NADP-GDH; GDH(I) was produced when cells were grown on isophthalate, while GDH(II) was produced when cells were grown on glucose. Strain ISP4 produced a single form of NADP-GDH, GDH(P), when it was grown on either isophthalate or rich medium (2YT). All of the forms of GDH were purified to homogeneity and characterized. GDH(I) and GDH(II) were found to be homotetramers, while GDH(P) was found to be a homohexamer. GDH(II) was more sensitive to inhibition by isophthalate (2.5- and 5.5-fold more sensitive for amination and deamination reactions, respectively) than GDH(I). Differences in the N-terminal sequences and electrophoretic mobilities in an activity-staining gel confirmed the presence of two forms of GDH, GDH(I) and GDH(II), in strain PP4. In strain ISP4, irrespective of the carbon source, the GDH(P) produced showed similar levels of inhibition with isophthalate. However, the specific activity of GDH(P) from isophthalate-grown cells was 2.5- to 3-fold higher than that of GDH(P) from 2YT-grown cells. Identical N-terminal sequences and electrophoretic mobilities in the activity-staining gel suggested the presence of a single form of GDH(P) in strain ISP4. These results demonstrate the ability of organisms to modulate GDH either by producing an entirely different form or by increasing the level of the enzyme, thus enabling strains to utilize isophthalate more efficiently as a sole source of carbon and energy.

Biodegradation of phenanthrene by Pseudomonas sp. strain PPD: purification and characterization of 1-hydroxy-2-naphthoic acid dioxygenase

Pseudomonas sp. strain PPD can metabolize phenanthrene as the sole source of carbon and energy via the 'phthalic acid' route. The key enzyme, 1-hydroxy-2-naphthoic acid dioxygenase (1-HNDO, EC 1.13.11.38), was purified to homogeneity using a 3-hydroxy-2-naphthoic acid (3-H2NA)-affinity matrix. The enzyme was a homotetramer with a native molecular mass of 160 kDa and subunit molecular mass of approximately 39 kDa. It required Fe(II) as the cofactor and was specific for 1-hydroxy-2-naphthoic acid (1-H2NA), with K(m) 13.5 microM and V(max) 114 micromol min(-1) mg(-1). 1-HNDO failed to show activity with gentisic acid, salicylic acid and other hydroxynaphthoic acids tested. Interestingly, the enzyme showed substrate inhibition with a K(i) of 116 microM. 1-HNDO was found to be competitively inhibited by 3-H2NA with a K(i) of 24 microM. Based on the pH-dependent spectral changes, the enzyme reaction product was identified as 2-carboxybenzalpyruvic acid. Under anaerobic conditions, the enzyme failed to convert 1-H2NA to 2-carboxybenzalpyruvic acid. Stoichiometric studies showed the incorporation of 1 mol O(2) into the substrate to yield 1 mol product. These results suggest that 1-HNDO from Pseudomonas sp. strain PPD is an extradiol-type ring-cleaving dioxygenase.

Carbon source-dependent modulation of NADP-glutamate dehydrogenases in isophthalate-degrading Pseudomonas aeruginosa strain PP4, Pseudomonas strain PPD and Acinetobacter lwoffii strain ISP4

Acinetobacter lwoffii strain ISP4 metabolizes isophthalate rapidly compared with Pseudomonas aeruginosa strain PP4 and Pseudomonas strain PPD. Isophthalate has been reported to be a potent competitive inhibitor of glutamate dehydrogenase (GDH). Exogenous supplementation of isophthalate with glutamate or alpha-ketoglutarate at 1 mM concentration caused strains PP4 and PPD to grow faster than in the presence of isophthalate alone; however, no such effect was observed in strain ISP4. When grown on isophthalate, all strains showed activity of NADP-dependent GDH (NADP-GDH), while cells grown on glucose, 2x yeast extract-tryptone broth (2YT) or glutamate showed activities of both NAD-dependent GDH (NAD-GDH) and NADP-GDH. Activity staining, inhibition and thermal stability studies indicated the carbon source-dependent presence of two (GDH(I) and GDH(II)), three (GDH(A), GDH(B) and GDH(C)) and one (GDH(P)) forms of NADP-GDH in strains PP4, PPD and ISP4, respectively. The results demonstrate the carbon source-dependent modulation of different forms of NADP-GDH in these bacterial strains. This modulation may help the efficient utilization of isophthalate as a carbon source by overcoming the inhibitory effect on GDH.

Bacterial degradation of phthalate isomers and their esters

Phthalate isomers and their esters are used heavily in various industries. Excess use and leaching from the product pose them as major pollutants. These chemicals are toxic, teratogenic, mutagenic and carcinogenic in nature. Various aspects like toxicity, diversity in the aerobic bacterial degradation, enzymes and genetic organization of the metabolic pathways from various bacterial strains are reviewed here. Degradation of these esters proceeds by the action of esterases to form phthalate isomers, which are converted to dihydroxylated intermediates by specific and inducible phthalate isomer dioxygenases. Metabolic pathways of phthalate isomers converge at 3,4-dihydroxybenzoic acid, which undergoes either ortho- or meta- ring cleavage and subsequently metabolized to the central carbon pathway intermediates. The genes involved in the degradation are arranged in operons present either on plasmid or chromosome or both, and induced by specific phthalate isomer. Understanding metabolic pathways, diversity and their genetic regulation may help in constructing bacterial strains through genetic engineering approach for effective bioremediation and environmental clean up.

Effects of enrichment with phthalate on polycyclic aromatic hydrocarbon biodegradation in contaminated soil

The effect of enrichment with phthalate on the biodegradation of polycyclic aromatic hydrocarbons (PAH) was tested with bioreactor-treated and untreated contaminated soil from a former manufactured gas plant (MGP) site. Soil samples that had been treated in a bioreactor and enriched with phthalate mineralized (14)C-labeled phenanthrene and pyrene to a greater extent than unenriched samples over a 22.5-h incubation, but did not stimulate benzo[a]pyrene mineralization. In contrast to the positive effects on (14)C-labeled phenanthrene and pyrene, no significant differences were found in the extent of biodegradation of native PAH when untreated contaminated soil was incubated with and without phthalate amendment. Denaturing-gradient gel electrophoresis (DGGE) profiles of bacterial 16S rRNA genes from unenriched and phthalate-enriched soil samples were substantially different, and clonal sequences matched to prominent DGGE bands revealed that beta-Proteobacteria related to Ralstonia were most highly enriched by phthalate addition. Quantitative real-time PCR analyses confirmed that, of previously determined PAH-degraders in the bioreactor, only Ralstonia-type organisms increased in response to enrichment, accounting for 89% of the additional bacterial 16S rRNA genes resulting from phthalate enrichment. These findings indicate that phthalate amendment of this particular PAH-contaminated soil did not significantly enrich for organisms associated with high molecular weight PAH degradation or have any significant effect on overall degradation of native PAH in the soil.

N-acyl homoserine lactone-degrading microbial enrichment cultures isolated from Penaeus vannamei shrimp gut and their probiotic properties in Brachionus plicatilis cultures

Three bacterial enrichment cultures (ECs) were isolated from the digestive tract of Pacific white shrimp Penaeus vannamei, by growing the shrimp microbial communities in a mixture of N-acyl homoserine lactone (AHL) molecules. The ECs, characterized by denaturing gradient gel electrophoresis analysis and subsequent rRNA sequencing, degraded AHL molecules in the degradation assays. Apparently, the resting cells of the ECs also degraded one of the three types of quorum-sensing signal molecules produced by Vibrio harveyi in vitro [i.e. harveyi autoinducer 1 (HAI-1)]. The most efficient AHL-degrading ECs, EC5, was tested in Brachionus experiments. EC5 degraded the V. harveyi HAI-1 autoinducer in vivo, neutralizing the negative effect of V. harveyi autoinducer 2 (AI-2) mutant, in which only the HAI-1- and CAI-1-mediated components of the quorum-sensing system are functional on the growth of Brachionus. This suggests that EC5 interferes with HAI-1-regulated metabolism in V. harveyi. These AHL-degrading ECs need to be tested in other aquatic systems for their probiotic properties, preferably in combination with specific AI-2-degrading bacteria.

Metabolic Diversity in Bacterial Degradation of Aromatic Compounds

Aromatic compounds pose a major threat to the environment, being mutagenic, carcinogenic, and recalcitrant. Microbes, however, have evolved the ability to utilize these highly reduced and recalcitrant compounds as a potential source of carbon and energy. Aerobic degradation of aromatics is initiated by oxidizing the aromatic ring, making them more susceptible to cleavage by ring-cleaving dioxygenases. A preponderance of aromatic degradation genes on plasmids, transposons, and integrative genetic elements (and their shuffling through horizontal gene transfer) have lead to the evolution of novel aromatic degradative pathways. This enables the microorganisms to utilize a multitude of aromatics via common routes of degradation leading to metabolic diversity. In this review, we emphasize the exquisiteness and relevance of bacterial degradation of aromatics, interlinked degradative pathways, genetic and metabolic regulation, carbon source preference, and biosurfactant production. We have also explored the avenue of metagenomics, which opens doors to a plethora of uncultured and uncharted microbial genetics and metabolism that can be used effectively for bioremediation.

Metabolism of 2-, 3- and 4-hydroxybenzoates by soil isolatesAlcaligenessp. strain PPH andPseudomonassp. strain PPD

Pseudomonas sp. strain PPD and Alcaligenes sp. strain PPH isolated from soil by enrichment culture technique utilize 2-, 3- and 4-hydroxybenzoates as the sole source of carbon and energy. The degradation pathways were elucidated by performing whole-cell O(2) uptake, enzyme activity and induction studies. Depending on the mixture of carbon source and the preculture condition, strain PPH was found to degrade 2-hydroxybenzoate either via the catechol or gentisate route and has both salicylate 1-hydroxylase and salicylate 5-hydroxylase. Strain PPD utilizes 2-hydroxybenzoate via gentisate. Both strains degrade 3- and 4-hydroxybenzoate via gentisate and protocatechuate, respectively. Enzymes were induced by respective hydroxybenzoate. Growth pattern, O(2) uptake and enzyme activity profiles on the mixture of three hydroxybenzoates as a carbon source suggest coutilization by both strains. When 3- or 4-hydroxybenzoate grown culture was used as an inoculum, strain PPH failed to utilize 2-hydroxybenzoate via catechol, indicating the modulation of the metabolic pathways, thus generating metabolic diversity.