Bacterial scission of ether bonds

New insights into the oxidative and cytogenotoxic effects of Tetraglyme on human peripheral blood cells

The present study investigated the oxidative and cytogenotoxic potential of Tetraethylene glycol dimethyl ether (known as Tetraglyme) on healthy human peripheral blood lymphocytes, widely used as an in vitro model for assessing the human health risk posed by different chemical compounds. In a first step, Nuclear Magnetic Resonance (1H NMR) spectroscopy, and Ultra-High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) were employed to estimate Tetraglyme's stability under a wide range of pH values (4-12), and thus to identify potential by-products. Thereafter, isolated lymphocytes were treated with different concentrations of Tetraglyme (0.02-20 mg L-1) for assessing its oxidative (using the DCFH-DA staining), and cytogenotoxic potential (using the trypan blue exclusion test for estimating cell viability, Comet assay, as well as the cytokinesis-block micronucleus assay, with or without the addition of S9 metabolic activation system). According to the results, Tetraglyme remains stable at pH 4, but two additional derivatives (i.e. 1-[2-(2-ethoxyethoxy)ethoxy]-2-methoxyethane [C9H20O4] and 1-ethoxy-2-(2-ethoxyethoxy)ethane (Diethylene glycol diethyl ether) [C8H18O3]) were found in traces, under alkaline conditions (pH ≥7). Moreover, although Tetraglyme (and/or its derivatives) showed negligible alterations of cell viability (>92 %) in all cases, the pronounced ROS formation, DNA damage, cell proliferation arrest, and MN frequencies in challenged cells are indicative of its oxidative and cytogenotoxic potential. The significant alterations of Cytokinesis-Block Proliferation Index (CBPI) and Micronucleus (MN) frequencies in S9 challenged cells give further evidence for the potential involvement of Tetraglyme's metabolites in the observed cytogenotoxic mode of action. Although not conclusive, the present findings give rise to further research, utilizing different cell types and biological models, for elucidating Tetraglyme's toxic mode of action, as well as its environmental and human risk.

The biochemical mechanisms of plastic biodegradation

Since the invention of the first synthetic plastic, an estimated 12 billion metric tons of plastics have been manufactured, 70% of which was produced in the last 20 years. Plastic waste is placing new selective pressures on humans and the organisms we depend on, yet it also places new pressures on microorganisms as they compete to exploit this new and growing source of carbon. The limited efficacy of traditional recycling methods on plastic waste, which can leach into the environment at low purity and concentration, indicates the utility of this evolving metabolic activity. This review will categorize and discuss the probable metabolic routes for each industrially relevant plastic, rank the most effective biodegraders for each plastic by harmonizing and reinterpreting prior literature, and explain the experimental techniques most often used in plastic biodegradation research, thus providing a comprehensive resource for researchers investigating and engineering plastic biodegradation.

A review on co-metabolic degradation of organic micropollutants during anaerobic digestion: Linkages between functional groups and digestion stages

The emerging presence of organic micropollutants (OMPs) in water bodies produced by human activities is a source of growing concern due to their environmental and health issues. Biodegradation is a widely employed treatment method for OMPs in wastewater owing to its high efficiency and low operational cost. Compared to aerobic degradation, anaerobic degradation has numerous advantages, including energy efficiency and superior performance for certain recalcitrant compounds. Nonetheless, the low influent concentrations of OMPs in wastewater treatment plants (WWTPs) and their toxicity make it difficult to support the growth of microorganisms. Therefore, co-metabolism is a promising mechanism for OMP biodegradation in which co-substrates are added as carbon and energy sources and stimulate increased metabolic activity. Functional microorganisms and enzymes exhibit significant variations at each stage of anaerobic digestion affecting the environment for the degradation of OMPs with different structural properties, as these factors substantially influence OMPs' biodegradability and transformation pathways. However, there is a paucity of literature reviews that explicate the correlations between OMPs' chemical structure and specific metabolic conditions. This study provides a comprehensive review of the co-metabolic processes which are favored by each stage of anaerobic digestion and attempts to link various functional groups to their favorable degradation pathways. Furthermore, potential co-metabolic processes and strategies that can enhance co-digestion are also identified, providing directions for future research.

Aerobic Biotransformation and Defluorination of Fluoroalkylether Substances (ether PFAS): Substrate Specificity, Pathways, and Applications

Fluoroalkylether substances (ether PFAS) constitute a large group of emerging PFAS with uncertain environmental fate. Among them, GenX is the well-known alternative to perfluorooctanoic acid and one of the six proposed PFAS to be regulated by the U.S. Environmental Protection Agency. This study investigated the structure-biodegradability relationship for 12 different ether PFAS with a carboxylic acid headgroup in activated sludge communities. Only polyfluorinated ethers with at least one -CH2- moiety adjacent to or a C=C bond in the proximity of the ether bond underwent active biotransformation via oxidative and hydrolytic O-dealkylation. The bioreactions at ether bonds led to the formation of unstable fluoroalcohol intermediates subject to spontaneous defluorination. We further demonstrated that this aerobic biotransformation/defluorination could complement the advanced reduction process in a treatment train system to achieve more cost-effective treatment for GenX and other recalcitrant perfluorinated ether PFAS. These findings provide essential insights into the environmental fate of ether PFAS, the design of biodegradable alternative PFAS, and the development of cost-effective ether PFAS treatment strategies.

Meta-omics elucidates key degraders in a bacterial tris(2-butoxyethyl) phosphate (TBOEP)-degrading enrichment culture

Organophosphate esters (OPEs) are emerging contaminants of growing concern, and there is limited information about the bacterial transformation of OPEs. In this study, we investigated the biotransformation of tris(2-butoxyethyl) phosphate (TBOEP), a frequently detected alkyl-OPE by a bacterial enrichment culture under aerobic conditions. The enrichment culture degraded 5 mg/L TBOEP following the first-order kinetics with a reaction rate constant of 0.314 h^-1. TBOEP was mainly degraded via ether bond cleavage, evidenced by the production of bis(2-butoxyethyl) hydroxyethyl phosphate, 2-butoxyethyl bis(2-hydroxyethyl) phosphate, and 2-butoxyethyl (2-hydroxyethyl) hydrogen phosphate. Other transformation pathways include terminal oxidation of the butoxyethyl group and phosphoester bond hydrolysis. Metagenomic sequencing generated 14 metagenome-assembled genomes (MAGs), showing that the enrichment culture primarily consisted of Gammaproteobacteria, Bacteroidota, Myxococcota, and Actinobacteriota. One MAG assigned to Rhodocuccus ruber strain C1 was the most active in the community, showing upregulation of various monooxygenase, dehydrogenase, and phosphoesterase genes throughout the degradation process, and thus was identified as the key degrader of TBOEP and the metabolites. Another MAG affiliated with Ottowia mainly contributed to TBOEP hydroxylation. Our results provided a comprehensive understanding of the bacterial TBOEP degradation at community level.

Effectiveness of tetrahydrofuran at enhancing the 1,4-dioxane degradation ability of activated sludge lacking prior exposure to 1,4-dioxane

1,4-dioxane (DX) is a contaminant of emerging concern in water environments. The enrichment of DX-degrading bacteria indigenous to activated sludge is key for the efficient biological removal of DX in wastewater. To identify an effective substrate, which enables the selective enrichment of DX-degrading bacteria and has lower toxicity and persistence than DX, this study explored the effectiveness of tetrahydrofuran (THF) at enhancing the DX degradation ability of activated sludge without historical exposure to DX. Although the activated sludge initially exhibited negligible ability to degrade DX (100 mg-C/L) as the sole carbon source, the repeated batch cultivation on THF could enrich bacterial populations capable of degrading DX, inducing the DX degradation ability in activated sludge as effectively as DX did. The THF-enrichment culture after 4 weeks degraded 100 mg-C/L DX almost completely within 21 d. Sequencing analyses revealed that soluble di-iron monooxygenase group 5C, including THF/DX monooxygenase, would play a dominant role in the initial oxidation of DX in THF-enrichment culture, which completely differed from the enrichment culture cultivated on DX. The results indicate that THF can be applied as an effective substrate to enhance the DX degradation ability of microbial consortia, irrespective of the intrinsic ability.

Engineered Living Hydrogels

Living biological systems, ranging from single cells to whole organisms, can sense, process information, and actuate in response to changing environmental conditions. Inspired by living biological systems, engineered living cells and nonliving matrices are brought together, which gives rise to the technology of engineered living materials. By designing the functionalities of living cells and the structures of nonliving matrices, engineered living materials can be created to detect variability in the surrounding environment and to adjust their functions accordingly, thereby enabling applications in health monitoring, disease treatment, and environmental remediation. Hydrogels, a class of soft, wet, and biocompatible materials, have been widely used as matrices for engineered living cells, leading to the nascent field of engineered living hydrogels. Here, the interactions between hydrogel matrices and engineered living cells are described, focusing on how hydrogels influence cell behaviors and how cells affect hydrogel properties. The interactions between engineered living hydrogels and their environments, and how these interactions enable versatile applications, are also discussed. Finally, current challenges facing the field of engineered living hydrogels for their applications in clinical and environmental settings are highlighted.

Valorization of Small Alkanes by Biocatalytic Oxyfunctionalization

The oxidation of alkanes into valuable chemical products is a vital reaction in organic synthesis. This reaction, however, is challenging, owing to the inertness of C-H bonds. Transition metal catalysts for C-H functionalization are frequently explored. Despite chemical alternatives, nature has also evolved powerful oxidative enzymes (e. g., methane monooxygenases, cytochrome P450 oxygenases, peroxygenases) that are capable of transforming C-H bonds under very mild conditions, with only the use of molecular oxygen or hydrogen peroxide as electron acceptors. Although progress in alkane oxidation has been reviewed extensively, little attention has been paid to small alkane oxidation. The latter holds great potential for the manufacture of chemicals. This Minireview provides a concise overview of the most relevant enzyme classes capable of small alkanes (C_<6 ) oxyfunctionalization, describes the essentials of the catalytic mechanisms, and critically outlines the current state-of-the-art in preparative applications.

Current insights into the microbial degradation for pyrethroids: strain safety, biochemical pathway, and genetic engineering

As a biologically inspired insecticide, pyrethroids (PYRs) exert evident toxic side effects on non-target organisms. PYRs and their general toxic intermediate 3-phenoxybenzoic acid (3-PBA) have shown high detection rates/levels in human beings recently, for which diet was identified as the major exposure route. Microbial mineralization has emerged as a versatile strategy in addressing such escalating concern. Herein, PYRs and 3-PBA biodegradation with regards to strain safety, application and surfactant were summarized. Numerous PYRs-degrading microbes have been reported yet with a minority focused on 3-PBA. Most isolates were from contaminated sites while several microbial food cultures (MFCs) have been investigated. MFCs such as Bacillus spp. and Aspergillus spp. that dominate in PYRs-degrading microbial pools are applicable candidates for agricultural by-products detoxification during the postharvest process. Subsequently, we discussed committed degradation steps, wherein hydrolase responsible for PYRs ester linkage cleavage and oxygenase for 3-PBA diphenyl ether bond rupture play vital roles. Finally, comprehensive information of the key enzyme genes is outlined along with methodologies concerning gene cloning. Cytochrome P450 monooxygenases (CYP) is competent for diphenyl ether scission. Newly-developed omics has become a feasible gene and enzyme mining technology. To achieve PYRs mineralization in feed and food commodities, the screening of MFCs rich in related enzymes and the construction of MFCs-derived genetically modified microbes (GMMs) exhibit great potential considering the safety issues.

Biodegradation of Functionalized Nanocellulose

Nanocellulose has attracted widespread interest for applications in materials science and biomedical engineering due to its natural abundance, desirable physicochemical properties, and high intrinsic mineralizability (i.e., complete biodegradability). A common strategy to increase dispersibility in polymer matrices is to modify the hydroxyl groups on nanocellulose through covalent functionalization, but such modification strategies may affect the desirable biodegradation properties exhibited by pristine nanocellulose. In this study, cellulose nanofibrils (CNFs) functionalized with a range of esters, carboxylic acids, or ethers exhibited decreased rates and extents of mineralization by anaerobic and aerobic microbial communities compared to unmodified CNFs, with etherified CNFs exhibiting the highest level of recalcitrance. The decreased biodegradability of functionalized CNFs depended primarily on the degree of substitution at the surface of the material rather than within the bulk. This dependence on surface chemistry was attributed not only to the large surface area-to-volume ratio of nanocellulose but also to the prerequisite surface interaction by microorganisms necessary to achieve biodegradation. Results from this study highlight the need to quantify the type and coverage of surface substituents in order to anticipate their effects on the environmental persistence of functionalized nanocellulose.

Ether Oxidation by an Evolved Fungal Heme-Peroxygenase: Insights into Substrate Recognition and Reactivity

Ethers can be found in the environment as structural, active or even pollutant molecules, although their degradation is not efficient under environmental conditions. Fungal unspecific heme-peroxygenases (UPO were reported to degrade low-molecular-weight ethers through an H₂O₂-dependent oxidative cleavage mechanism. Here, we report the oxidation of a series of structurally related aromatic ethers, catalyzed by a laboratory-evolved UPO (PaDa-I) aimed at elucidating the factors influencing this unusual biochemical reaction. Although some of the studied ethers were substrates of the enzyme, they were not efficiently transformed and, as a consequence, secondary reactions (such as the dismutation of H₂O₂ through catalase-like activity and suicide enzyme inactivation) became significant, affecting the oxidation efficiency. The set of reactions that compete during UPO-catalyzed ether oxidation were identified and quantified, in order to find favorable conditions that promote ether oxidation over the secondary reactions.

Thiols Act as Methyl Traps in the Biocatalytic Demethylation of Guaiacol Derivatives

Demethylating methyl phenyl ethers is challenging, especially when the products are catechol derivatives prone to follow-up reactions. For biocatalytic demethylation, monooxygenases have previously been described requiring molecular oxygen which may cause oxidative side reactions. Here we show that such compounds can be demethylated anaerobically by using cobalamin-dependent methyltransferases exploiting thiols like ethyl 3-mercaptopropionate as a methyl trap. Using just two equivalents of this reagent, a broad spectrum of substituted guaiacol derivatives were demethylated, with conversions mostly above 90 %. This strategy was used to prepare the highly valuable antioxidant hydroxytyrosol on a one-gram scale in 97 % isolated yield.

Thiols Act as Methyl Traps in the Biocatalytic Demethylation of Guaiacol Derivatives

Demethylating methyl phenyl ethers is challenging, especially when the products are catechol derivatives prone to follow-up reactions. For biocatalytic demethylation, monooxygenases have previously been described requiring molecular oxygen which may cause oxidative side reactions. Here we show that such compounds can be demethylated anaerobically by using cobalamin-dependent methyltransferases exploiting thiols like ethyl 3-mercaptopropionate as a methyl trap. Using just two equivalents of this reagent, a broad spectrum of substituted guaiacol derivatives were demethylated, with conversions mostly above 90 %. This strategy was used to prepare the highly valuable antioxidant hydroxytyrosol on a one-gram scale in 97 % isolated yield.

Synthetic pyrethroids common metabolite 3-phenoxybenzoic acid induces caspase-3 and Bcl-2 mediated apoptosis in human hepatocyte cells

Synthetic pyrethroids are a group of insecticides frequently used in public health and agriculture, and 3-PBA is a common metabolite of them. Although the liver is the primary organ responsible for metabolizing many compounds including pesticides, to the authors' knowledge there have been no studies on the direct hepatotoxic effects of 3-PBA. Therefore, this study aimed to investigate the possible hepatotoxic effects of 3-PBA on a Human Hepatoma Cell Line (HepG2) and the underlying apoptotic mechanisms. Firstly, an LC₅₀ of 1041.242 µM was calculated for 3-PBA by using the WST-1 test with concentrations ranging between 1 µM and 10 mM. Following that, the HepG2 cells in the experimental group were exposed to 3 different concentrations of 3-PBA (1/5 LC₅₀, 1/10 LC₅₀ and 1/20 LC₅₀) for 24 hours. The apoptotic mechanism was evaluated by using flow cytometry, and immunofluorescence assays for Caspase 3 and Bcl-2. In the flow cytometry assay, the total number of apoptotic cells increased in a dose dependent manner (p < 0.05). In the immunofluorescence assay, the Caspase 3 protein showed strong immunoreactivity in the experimental groups, while the reaction to the Bcl-2 protein was minimal. These results demonstrated that 3-PBA has a significant hepatotoxic effect on HepG2 cells and induces apoptosis via the regulation of Caspase-3 and Bcl-2. Furthermore, our results could further the understanding of the fundamental molecular mechanisms of 3-PBA hepatotoxicity. More studies are needed to determine the effects of long-term exposure to 3-PBA and also the molecular mechanisms underlying hepatotoxicity.

Cationic lipids for gene delivery: many players, one goal

Lipid-based carriers represent the most widely used alternative to viral vectors for gene expression and gene silencing purposes. This class of non-viral vectors is particularly attractive for their ease of synthesis and chemical modifications to endow them with desirable properties. Despite combinatorial approaches have led to the generation of a large number of cationic lipids displaying different supramolecular structures and improved behavior, additional effort is needed towards the development of more and more effective cationic lipids for transfection purposes. With this review, we seek to highlight the great progress made in the design of each and every constituent domain of cationic lipids, that is, the chemical structure of the headgroup, linker and hydrophobic moieties, and on the specific effect on the assembly with nucleic acids. Since the complexity of such systems is known to affect their performances, the role of formulation, stability and phase behavior on the transfection efficiency of such assemblies will be thoroughly discussed. Our objective is to provide a conceptual framework for the development of ever more performing lipid gene delivery vectors.

Oxygen-Free Regioselective Biocatalytic Demethylation of Methyl-phenyl Ethers via Methyltransfer Employing Veratrol-O-demethylase

The cleavage of aryl methyl ethers is a common reaction in chemistry requiring rather harsh conditions; consequently, it is prone to undesired reactions and lacks regioselectivity. Nevertheless, O-demethylation of aryl methyl ethers is a tool to valorize natural and pharmaceutical compounds by deprotecting reactive hydroxyl moieties. Various oxidative enzymes are known to catalyze this reaction at the expense of molecular oxygen, which may lead in the case of phenols/catechols to undesired side reactions (e.g., oxidation, polymerization). Here an oxygen-independent demethylation via methyl transfer is presented employing a cobalamin-dependent veratrol-O-demethylase (vdmB). The biocatalytic demethylation transforms a variety of aryl methyl ethers with two functional methoxy moieties either in 1,2-position or in 1,3-position. Biocatalytic reactions enabled, for instance, the regioselective monodemethylation of substituted 3,4-dimethoxy phenol as well as the monodemethylation of 1,3,5-trimethoxybenzene. The methyltransferase vdmB was also successfully applied for the regioselective demethylation of natural compounds such as papaverine and rac-yatein. The approach presented here represents an alternative to chemical and enzymatic demethylation concepts and allows performing regioselective demethylation in the absence of oxygen under mild conditions, representing a valuable extension of the synthetic repertoire to modify pharmaceuticals and diversify natural products.

Biodegradation and fate of ethyl tert-butyl ether (ETBE) in soil and groundwater: A review

This review summarises the current state of knowledge on the biodegradation and fate of the gasoline ether oxygenate ethyl tert-butyl ether (ETBE) in soil and groundwater. Microorganisms have been identified in soil and groundwater with the ability to degrade ETBE aerobically as a carbon and energy source, or via cometabolism using alkanes as growth substrates. Aerobic biodegradation of ETBE initially occurs via hydroxylation of the ethoxy carbon by a monooxygenase enzyme, with subsequent formation of intermediates which include acetaldehyde, tert-butyl acetate (TBAc), tert-butyl alcohol (TBA), 2-hydroxy-2-methyl-1-propanol (MHP) and 2-hydroxyisobutyric acid (2-HIBA). Slow cell growth and low biomass yields on ETBE are believed to result from the ether structure and slow degradation kinetics, with potential limitations on ETBE metabolism. Genes known to facilitate transformation of ETBE include ethB (within the ethRABCD cluster), encoding a cytochrome P450 monooxygenase, and alkB-encoding alkane hydroxylases. Other genes have been identified in microorganisms but their activity and specificity towards ETBE remains poorly characterised. Microorganisms and pathways supporting anaerobic biodegradation of ETBE have not been identified, although this potential has been demonstrated in limited field and laboratory studies. The presence of co-contaminants (other ether oxygenates, hydrocarbons and organic compounds) in soil and groundwater may limit aerobic biodegradation of ETBE by preferential metabolism and consumption of available dissolved oxygen or enhance ETBE biodegradation through cometabolism. Both ETBE-degrading microorganisms and alkane-oxidising bacteria have been characterised, with potential for use in bioaugmentation and biostimulation of ETBE degradation in groundwater.

Sulfate Ester Detergent Degradation in Pseudomonas aeruginosa Is Subject to both Positive and Negative Regulation

Bacteria using toxic chemicals, such as detergents, as growth substrates face the challenge of exposing themselves to cell-damaging effects that require protection mechanisms, which demand energy delivered from catabolism of the toxic compound. Thus, adaptations are necessary for ensuring the rapid onset of substrate degradation and the integrity of the cells. Pseudomonas aeruginosa strain PAO1 can use the toxic detergent sodium dodecyl sulfate (SDS) as a growth substrate and employs, among others, cell aggregation as a protection mechanism. The degradation itself is also a protection mechanism and has to be rapidly induced upon contact to SDS. In this study, gene regulation of the enzymes initiating SDS degradation in strain PAO1 was studied. The gene and an atypical DNA-binding site of the LysR-type regulator SdsB1 were identified and shown to activate expression of the alkylsulfatase SdsA1 initiating SDS degradation. Further degradation of the resulting 1-dodecanol is catalyzed by enzymes encoded by laoCBA, which were shown to form an operon. Expression of this operon is regulated by the TetR-type repressor LaoR. Studies with purified LaoR identified its DNA-binding site and 1-dodecanoyl coenzyme A as the ligand causing detachment of LaoR from the DNA. Transcriptional studies revealed that the sulfate ester detergent sodium lauryl ether sulfate (SLES) induced expression of sdsA1 and the lao operon. Growth experiments revealed an essential involvement of the alkylsulfatase SdsA1 for SLES degradation. This study revealed that the genes for the enzymes initiating the degradation of toxic sulfate-ester detergents are induced stepwise by a positive and a negative regulator in P. aeruginosa strain PAO1.IMPORTANCE Bacterial degradation of toxic compounds is important not only for bioremediation but also for the colonization of hostile anthropogenic environments in which biocides are being used. This study with Pseudomonas aeruginosa expands our knowledge of gene regulation of the enzymes initiating degradation of sulfate ester detergents, which occurs in many hygiene and household products and, consequently, also in wastewater. As an opportunistic pathogen, P. aeruginosa causes severe hygienic problems because of its pronounced biocide resistance and its metabolic versatility, often combined with its pronounced biofilm formation. Knowledge about the regulation of detergent degradation, especially regarding the ligands of DNA-binding regulators, may lead to the rational development of specific inhibitors for restricting growth and biofilm formation of P. aeruginosa in hygienic settings. In addition, it may also contribute to optimizing bioremediation strategies not only for detergents but also for alkanes, which when degraded merge with sulfate ester degradation at the level of long-chain alcohols.

An NADH-Dependent Reductase from Eubacterium ramulus Catalyzes the Stereospecific Heteroring Cleavage of Flavanones and Flavanonols

The human intestinal anaerobe Eubacterium ramulus is known for its ability to degrade various dietary flavonoids. In the present study, we demonstrate the cleavage of the heterocyclic C-ring of flavanones and flavanonols by an oxygen-sensitive NADH-dependent reductase, previously described as enoate reductase, from E. ramulus This flavanone- and flavanonol-cleaving reductase (Fcr) was purified following its heterologous expression in Escherichia coli and further characterized. Fcr cleaved the flavanones naringenin, eriodictyol, liquiritigenin, and homoeriodictyol. Moreover, the flavanonols taxifolin and dihydrokaempferol served as substrates. The catalyzed reactions were stereospecific for the (2R)-enantiomers of the flavanone substrates and for the (2S,3S)-configured flavanonols. The enantioenrichment of the nonconverted stereoisomers allowed for the determination of hitherto unknown flavanone racemization rates. Fcr formed the corresponding dihydrochalcones and hydroxydihydrochalcones in the course of an unusual reductive cleavage of cyclic ether bonds. Fcr did not convert members of other flavonoid subclasses, including flavones, flavonols, and chalcones, the latter indicating that the reaction does not involve a chalcone intermediate. This view is strongly supported by the observed enantiospecificity of Fcr. Cinnamic acids, which are typical substrates of bacterial enoate reductases, were also not reduced by Fcr. Based on the presence of binding motifs for dinucleotide cofactors and a 4Fe-4S cluster in the amino acid sequence of Fcr, a cofactor-mediated hydride transfer from NADH onto C-2 of the respective substrate is proposed.IMPORTANCE Gut bacteria play a crucial role in the metabolism of dietary flavonoids, thereby contributing to their activation or inactivation after ingestion by the human host. Thus, bacterial activities in the intestine may influence the beneficial health effects of these polyphenolic plant compounds. While an increasing number of flavonoid-converting gut bacterial species have been identified, knowledge of the responsible enzymes is still limited. Here, we characterized Fcr as a key enzyme involved in the conversion of flavonoids of several subclasses by Eubacterium ramulus, a prevalent human gut bacterium. Sequence similarity of this enzyme to hypothetical proteins from other flavonoid-degrading intestinal bacteria in databases suggests a more widespread occurrence of this enzyme. Functional characterization of gene products of human intestinal microbiota enables the assignment of metagenomic sequences to specific bacteria and, more importantly, to certain activities, which is a prerequisite for targeted modulation of gut microbial functionality.

Quantification and biodegradability assessment of meso-2,3-dimercaptosuccinic acid adsorbed on iron oxide nanoparticles

Many interesting applications of magnetic iron oxide nanoparticles (IONPs) have recently been developed based on their magnetic properties and promising catalytic activity. Depending on their intended use, such nanoparticles (NPs) are frequently functionalized with proteins, polymers, or other organic molecules such as meso-2,3-dimercaptosuccinic acid (DMSA) to improve their colloidal stability or biocompatibility. Although the coating strongly affects the colloidal properties and environmental behaviour of NPs, quantitative analysis of the coating is often neglected. To address this issue, we established an ion chromatographic method for the quantitative analysis of surface-bound sulfur-containing molecules such as DMSA. The method determines the amount of sulfate generated by complete oxidation of sulfur present in the molecule. Quantification of the DMSA content of DMSA-coated IONPs showed that reproducibly approximately 38% of the DMSA used in the synthesis was adsorbed on the IONPs. Tests for the biodegradability of free and NP-bound DMSA using a microbial community from a wastewater treatment plant showed that both free and NP-bound DMSA was degraded to negligible extent, suggesting long-term environmental stability of DMSA-coated IONPs.

Suspect Screening of Hydrocarbon Surfactants in AFFFs and AFFF-Contaminated Groundwater by High-Resolution Mass Spectrometry

Aqueous film-forming foams (AFFFs) are proprietary mixtures containing hydrocarbon surfactants and per- and polyfluoroalkyl substances (PFASs) that are used to extinguish hydrocarbon-based fuel fires. There is limited information on hydrocarbon surfactants in AFFFs and AFFF-contaminated groundwater even though hydrocarbon surfactants are more abundant (5-10% w/w) than PFASs (0.9-1.5% w/w) in AFFFs. Eight commercial AFFFs manufactured between 1988 and 2012 and 10 AFFF-contaminated groundwaters collected from near source zones of fire-fighter training areas were analyzed for suspect hydrocarbon surfactants by liquid chromatography quadrupole time-of-flight mass spectrometry. A suspect list and a homologous series detection computational tool, enviMass, were combined to screen for hydrocarbon surfactants. Nine classes of hydrocarbon surfactants were detected in AFFFs including octylphenol polyethoxylates, linear alcohol ethoxylates, ethoxylated cocoamines, alkyl ether sulfates, alkyl amido dipropionates, linear alkyl benzenesulfonates, alkyl sulfates, and polyethylene glycols. Of those, six were also found in groundwater along with diethanolamines and alkyl amido betaines, which were not found in the eight archived AFFFs. This indicates that although aerobically biodegradable, hydrocarbon surfactants likely persist in groundwater due to anaerobic aquifer conditions. To the best of our knowledge, this is the first screening for hydrocarbon surfactants in AFFFs and in AFFF-contaminated groundwater.

The hydrolase LpqI primes mycobacterial peptidoglycan recycling

Growth and division by most bacteria requires remodelling and cleavage of their cell wall. A byproduct of this process is the generation of free peptidoglycan (PG) fragments known as muropeptides, which are recycled in many model organisms. Bacteria and hosts can harness the unique nature of muropeptides as a signal for cell wall damage and infection, respectively. Despite this critical role for muropeptides, it has long been thought that pathogenic mycobacteria such as Mycobacterium tuberculosis do not recycle their PG. Herein we show that M. tuberculosis and Mycobacterium bovis BCG are able to recycle components of their PG. We demonstrate that the core mycobacterial gene lpqI, encodes an authentic NagZ β-N-acetylglucosaminidase and that it is essential for PG-derived amino sugar recycling via an unusual pathway. Together these data provide a critical first step in understanding how mycobacteria recycle their peptidoglycan.

Bacterial growth and division require remodelling of the cell wall, which generates free peptidoglycan fragments. Here, Moynihan et al. show that Mycobacterium tuberculosis can recycle components of their peptidoglycan, and characterise a crucial enzyme required for this process.

Pyrethroid pesticide metabolite, 3-PBA, in soils: method development and application to real agricultural soils

3-Phenoxybenzoic acid (3-PBA) is a shared metabolite of several synthetic pyrethroid pesticides (SPs) resulting from environmental degradation of parent compounds and thus occurs frequently as a residue in samples. Hence, the importance of 3-PBA evaluation after pyrethroid application. There is a gap of analytical methods to determine 3-PBA in soil samples. Therefore, an analytical method that combines the solid-phase extraction (SPE) and gas chromatography-mass spectrometry (GC/MS) detection has been developed for the determination of 3-PBA in soil samples. The analytical method was validated in terms of linearity, sensitivity, intra- and inter-day batch precisions, recoveries, and quantification limits. An SPE method using a Strata X cartridge allows obtaining limits of detection and quantification equal to 4.0 and 13.3 ng g^-1, respectively. Under optimized conditions, the method average recovery levels ranged from 70.3 to 93.5% with a relative standard deviation below 3.4%. Method intra- and inter-day precision was under 5.0 and 4.8%, respectively. The developed method was applied to 11 agricultural soil samples in the north of Portugal. The developed methodology allowed for the determination of the pyrethroid metabolite, 3-PBA, in agricultural soil samples at levels of few ng g^-1. Graphical abstract ᅟ.

Identification of active and taxonomically diverse 1,4-dioxane degraders in a full-scale activated sludge system by high-sensitivity stable isotope probing

1,4-Dioxane is one of the most common and persistent artificial pollutants in petrochemical industrial wastewaters and chlorinated solvent groundwater plumes. Despite its possible biological treatment in natural environments, the identity and dynamics of the microorganisms involved are largely unknown. Here, we identified active and diverse 1,4-dioxane-degrading microorganisms from activated sludge by high-sensitivity stable isotope probing of rRNA. By rigorously analyzing 16S rRNA molecules in RNA density fractions of ¹³C-labeled and unlabeled 1,4-dioxane treatments, we discovered 10 significantly ¹³C-incorporating microbial species from the complex microbial community. 16S rRNA expression assays revealed that 9 of the 10 species, including the well-known degrader Pseudonocardia dioxanivorans, an ammonia-oxidizing bacterium and phylogenetically novel bacteria, increased their metabolic activities shortly after exposure to 1,4-dioxane. Moreover, high-resolution monitoring showed that, during a single year of operation of the full-scale activated sludge system, the nine identified species exhibited yearly averaged relative abundances of 0.001–1.523%, and yet showed different responses to changes in the 1,4-dioxane removal efficiency. Hence, the co-existence and individually distinct dynamics of various 1,4-dioxane-degrading microorganisms, including hitherto unidentified species, played pivotal roles in the maintenance of the biological system removing the recalcitrant pollutant.

A dihydrochalcone derivative and further steroidal saponins from Sansevieria trifasciata Prain

Phytochemical investigation of the aerial parts of Sansevieria trifasciata, one of the most common Dracaenaceae plants, has resulted in the isolation of a new dihydrochalcone derivative named trifasciatine C (1), four previously unreported steroidal saponins as two pairs of inseparable regioisomers: trifasciatosides K/L (2/3), M/N (4/5), together with the known 1,2-(dipalmitoyl)-3-O-β-D-galactopyranosylglycerol (6), aconitic acid (7), and 1-methyl aconitic acid (8). Their structures were elucidated mainly by extensive spectroscopic analysis (1D and 2D nuclear magnetic resonance) and high-resolution electronspray ionization-mass spectrometry, as well as chemical methods and comparison of their spectral data with those of related compounds. Compounds 2/3 and 4/5 were evaluated for their antiproliferative activity on Hela cells, and no significant effect was observed.

Sodium lauryl ether sulfate (SLES) degradation by nitrate-reducing bacteria

The surfactant sodium lauryl ether sulfate (SLES) is widely used in the composition of detergents and frequently ends up in wastewater treatment plants (WWTPs). While aerobic SLES degradation is well studied, little is known about the fate of this compound in anoxic environments, such as denitrification tanks of WWTPs, nor about the bacteria involved in the anoxic biodegradation. Here, we used SLES as sole carbon and energy source, at concentrations ranging from 50 to 1000 mg L⁻¹, to enrich and isolate nitrate-reducing bacteria from activated sludge of a WWTP with the anaerobic-anoxic-oxic (A²/O) concept. In the 50 mg L⁻¹ enrichment, Comamonas (50%), Pseudomonas (24%), and Alicycliphilus (12%) were present at higher relative abundance, while Pseudomonas (53%) became dominant in the 1000 mg L⁻¹ enrichment. Aeromonas hydrophila strain S7, Pseudomonas stutzeri strain S8, and Pseudomonas nitroreducens strain S11 were isolated from the enriched cultures. Under denitrifying conditions, strains S8 and S11 degraded 500 mg L⁻¹ SLES in less than 1 day, while strain S7 required more than 6 days. Strains S8 and S11 also showed a remarkable resistance to SLES, being able to grow and reduce nitrate with SLES concentrations up to 40 g L⁻¹. Strain S11 turned out to be the best anoxic SLES degrader, degrading up to 41% of 500 mg L⁻¹. The comparison between SLES anoxic and oxic degradation by strain S11 revealed differences in SLES cleavage, degradation, and sulfate accumulation; both ester and ether cleavage were probably employed in SLES anoxic degradation by strain S11.

Glycerol metabolism of haloarchaea

Haloarchaea are heterotrophic members of the Archaea that thrive in hypersaline environments, often feeding off the glycerol that is produced as an osmolyte by eucaryotic Dunaliella during primary production. In this study we analyzed glycerol metabolism genes in closed genomes of haloarchaea and examined published data describing the growth properties of haloarchaea and experimental data for the enzymes involved. By integrating the genomic data with knowledge from the literature, we derived an understanding of the ecophysiology and evolutionary properties of glycerol catabolic pathways in haloarchaea.

Transposon Mutagenesis Identifies Genes Critical for Growth of Pseudomonas nitroreducens TX1 on Octylphenol Polyethoxylates

Pseudomonas nitroreducens TX1 is of special interest because of its ability to utilize 0.05% to 20% octylphenol polyethoxylates (OPEO_n) as a sole source of carbon. In this study, a library containing 30,000 Tn5-insertion mutants of the wild-type strain TX1 was constructed and screened for OPEO_n utilization, and 93 mutants were found to be unable to grow on OPEO_n In total, 42 separate disrupted genes were identified, and the proteins encoded by the genes were then classified into various categories, namely, information storage and processing (14.3%), cellular processes and signaling (28.6%), metabolism (35.7%), and unknown proteins (21.4%). The individual deletion of genes encoding isocitrate lyase (aceA), malate synthase (aceB), and glycolate dehydrogenase (glcE) was carried out, and the requirement for aceA and aceB but not glcE confirmed the role of the glyoxylate cycle in OPEO_n degradation. Furthermore, acetaldehyde dehydrogenase and acetyl-coenzyme A (acetyl-CoA) synthetase activity levels were 13.2- and 2.1-fold higher in TX1 cells grown on OPEO_n than in TX1 cells grown on succinate, respectively. Growth of the various mutants on different carbon sources was tested, and based on these findings, a mechanism involving exoscission to liberate acetaldehyde from the end of the OPEO_n chain during degradation is proposed for the breakdown of OPEO_n IMPORTANCE: Octylphenol polyethoxylates belong to the alkylphenol polyethoxylate (APEO_n) nonionic surfactant family. Evidence based on the analysis of intermediate metabolites suggested that the primary biodegradation of APEO_n can be achieved by two possible pathways for the stepwise removal of the C₂ ethoxylate units from the end of the chain. However, direct evidence for these hypotheses is still lacking. In this study, we described the use of transposon mutagenesis to identify genes critical to the catabolism of OPEO_n by P. nitroreducens TX1. The exoscission of the ethoxylate chain leading to the liberation of acetaldehyde is proposed. Isocitrate lyase and malate synthase in glyoxylate cycle are required in the catabolism of ethoxylated surfactants. Our findings also provide many gene candidates that may help elucidate the mechanisms in stress responses to ethoxylated surfactants by bacteria.

Characterization of Three Tetrabromobisphenol-S Derivatives in Mollusks from Chinese Bohai Sea: A Strategy for Novel Brominated Contaminants Identification

Identification of novel brominated contaminants in the environment, especially the derivatives and byproducts of brominated flame retardants (BFRs), has become a wide concern because of their adverse effects on human health. Herein, we qualitatively and quantitatively identified three byproducts of tetrabromobisphenol-S bis(2,3-dibromopropyl ether) (TBBPS-BDBPE), including TBBPS mono(allyl ether) (TBBPS-MAE), TBBPS mono(2-bromoallyl ether) (TBBPS-MBAE) and TBBPS mono(2,3-dibromopropyl ether) (TBBPS-MDBPE) as novel brominated contaminants. Meanwhile, the mass spectra and analytical method for determination of TBBPS-BDBPE byproducts were presented for the first time. The detectable concentrations (dry weight) of TBBPS-MAE, TBBPS-MBAE and TBBPS-MDBPE were in the ranges 28-394 μg/g in technical TBBPS-BDBPE and 0.1-4.1 ng/g in mollusks collected from the Chinese Bohai Sea. The detection frequencies in mollusk samples were 5%, 39%, 95% for TBBPS-MAE, TBBPS-MBAE and TBBPS-MDBPE, respectively, indicating their prevailing in the environment. The results showed that they could be co-produced and leaked into the environment with production process, and might be more bioaccumulative and toxic than TBBPS-BDBPE. Therefore, the production and use of TBBPS derivatives lead to unexpected contamination to the surrounding environment. This study also provided an effective approach for identification of novel contaminants in the environment with synthesized standards and Orbitrap high resolution mass spectrometry.

Oxidation of the cyclic ethers 1,4-dioxane and tetrahydrofuran by a monooxygenase in two Pseudonocardia species

The bacterium Pseudonocardia dioxanivorans CB1190 grows on the cyclic ethers 1,4-dioxane (dioxane) and tetrahydrofuran (THF) as sole carbon and energy sources. Prior transcriptional studies indicated that an annotated THF monooxygenase (THF MO) gene cluster, thmADBC, located on a plasmid in CB1190 is upregulated during growth on dioxane. In this work, transcriptional analysis demonstrates that upregulation of thmADBC occurs during growth on the dioxane metabolite β-hydroxyethoxyacetic acid (HEAA) and on THF. Comparison of the transcriptomes of CB1190 grown on THF and succinate (an intermediate of THF degradation) permitted the identification of other genes involved in THF metabolism. Dioxane and THF oxidation activity of the THF MO was verified in Rhodococcus jostii RHA1 cells heterologously expressing the CB1190 thmADBC gene cluster. Interestingly, these thmADBC expression clones accumulated HEAA as a dead-end product of dioxane transformation, indicating that despite its genes being transcriptionally upregulated during growth on HEAA, the THF MO enzyme is not responsible for degradation of HEAA in CB1190. Similar activities were also observed in RHA1 cells heterologously expressing the thmADBC gene cluster from Pseudonocardia tetrahydrofuranoxydans K1.

Constitutive expression of the cytochrome P450 EthABCD monooxygenase system enables degradation of synthetic dialkyl ethers in Aquincola tertiaricarbonis L108

In Rhodococcus ruber IFP 2001, Rhodococcus zopfii IFP 2005, and Gordonia sp. strain IFP 2009, the cytochrome P450 monooxygenase EthABCD catalyzes hydroxylation of methoxy and ethoxy residues in the fuel oxygenates methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME). The expression of the IS3-type transposase-flanked eth genes is ETBE dependent and controlled by the regulator EthR (C. Malandain et al., FEMS Microbiol. Ecol. 72:289-296, 2010). In contrast, we demonstrated by reverse transcription-quantitative PCR (RT-qPCR) that the betaproteobacterium Aquincola tertiaricarbonis L108, which possesses the ethABCD genes but lacks ethR, constitutively expresses the P450 system at high levels even when growing on nonether substrates, such as glucose. The mutant strain A. tertiaricarbonis L10, which is unable to degrade dialkyl ethers, resulted from a transposition event mediated by a rolling-circle IS91-type element flanking the eth gene cluster in the wild-type strain L108. The constitutive expression of Eth monooxygenase is likely initiated by the housekeeping sigma factor σ(70), as indicated by the presence in strain L108 of characteristic -10 and -35 binding sites upstream of ethA which are lacking in strain IFP 2001. This enables efficient degradation of diethyl ether, diisopropyl ether, MTBE, ETBE, TAME, and tert-amyl ethyl ether (TAEE) without any lag phase in strain L108. However, ethers with larger residues, n-hexyl methyl ether, tetrahydrofuran, and alkyl aryl ethers, were not attacked by the Eth system at significant rates in resting-cell experiments, indicating that the residue in the ether molecule which is not hydroxylated also contributes to the determination of substrate specificity.

Using DNA-Stable Isotope Probing to Identify MTBE- and TBA-Degrading Microorganisms in Contaminated Groundwater

Although the anaerobic biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) has been documented in the laboratory and the field, knowledge of the microorganisms and mechanisms involved is still lacking. In this study, DNA-stable isotope probing (SIP) was used to identify microorganisms involved in anaerobic fuel oxygenate biodegradation in a sulfate-reducing MTBE and TBA plume. Microorganisms were collected in the field using Bio-Sep® beads amended with ¹³C₅-MTBE, ¹³C₁-MTBE (only methoxy carbon labeled), or¹³C₄-TBA. ¹³C-DNA and ¹²C-DNA extracted from the Bio-Sep beads were cloned and 16S rRNA gene sequences were used to identify the indigenous microorganisms involved in degrading the methoxy group of MTBE and the tert-butyl group of MTBE and TBA. Results indicated that microorganisms were actively degrading ¹³C-labeled MTBE and TBA in situ and the ¹³C was incorporated into their DNA. Several sequences related to known MTBE- and TBA-degraders in the Burkholderiales and the Sphingomonadales orders were detected in all three¹³C clone libraries and were likely to be primary degraders at the site. Sequences related to sulfate-reducing bacteria and iron-reducers, such as Geobacter and Geothrix, were only detected in the clone libraries where MTBE and TBA were fully labeled with ¹³C, suggesting that they were involved in processing carbon from the tert-butyl group. Sequences similar to the Pseudomonas genus predominated in the clone library where only the methoxy carbon of MTBE was labeled with ¹³C. It is likely that members of this genus were secondary degraders cross-feeding on ¹³C-labeled metabolites such as acetate.

Micropollutant biotransformation kinetics associate with WWTP process parameters and microbial community characteristics

The objective of this work was to identify relevant wastewater treatment plant (WWTP) parameters and underlying microbial processes that influence the biotransformation of a diverse set of micropollutants. To do this, we determined biotransformation rate constants for ten organic micropollutants in batch reactors seeded with activated sludge from ten diverse WWTPs. The estimated biotransformation rate constants for each compound ranged between one and four orders of magnitude among the ten WWTPs. The biotransformation rate constants were tested for statistical associations with various WWTP process parameters, amoA transcript abundance, and acetylene-inhibited monooxygenase activity. We determined that (i) ammonia removal associates with oxidative micropollutant biotransformation reaction rates; (ii) archaeal but not bacterial amoA transcripts associate with both ammonia removal and oxidative micropollutant biotransformation reaction rates; and (iii) the activity of acetylene-inhibited monooxygenases (including ammonia monooxygenase) associates with ammonia removal and the biotransformation rate of isoproturon, but does not associate with all oxidative micropollutant biotransformations. In combination, these results lead to the conclusion that ammonia removal and amoA transcript abundance can potentially be predictors of oxidative micropollutant biotransformation reactions, but that the biochemical mechanism is not necessarily linked to ammonia monooxygenase activity.

Glyoxylate metabolism is a key feature of the metabolic degradation of 1,4-dioxane by Pseudonocardia dioxanivorans strain CB1190

The groundwater contaminant 1,4-dioxane (dioxane) is transformed by several monooxygenase-expressing microorganisms, but only a few of these, including Pseudonocardia dioxanivorans strain CB1190, can metabolize the compound as a sole carbon and energy source. However, nothing is yet known about the genetic basis of dioxane metabolism. In this study, we used a microarray to study differential expression of genes in strain CB1190 grown on dioxane, glycolate (a previously identified intermediate of dioxane degradation), or pyruvate. Of eight multicomponent monooxygenase gene clusters carried by the strain CB1190 genome, only the monooxygenase gene cluster located on plasmid pPSED02 was upregulated with dioxane relative to pyruvate. Plasmid-borne genes for putative aldehyde dehydrogenases, an aldehyde reductase, and an alcohol oxidoreductase were also induced during growth with dioxane. With both dioxane and glycolate, a chromosomal gene cluster encoding a putative glycolate oxidase was upregulated, as were chromosomal genes related to glyoxylate metabolism through the glyoxylate carboligase pathway. Glyoxylate carboligase activity in cell extracts from cells pregrown with dioxane and in Rhodococcus jostii strain RHA1 cells expressing the putative strain CB1190 glyoxylate carboligase gene further demonstrated the role of glyoxylate metabolism in the degradation of dioxane. Finally, we used (13)C-labeled dioxane amino acid isotopomer analysis to provide additional evidence that metabolites of dioxane enter central metabolism as three-carbon compounds, likely as phosphoglycerate. The routing of dioxane metabolites via the glyoxylate carboligase pathway helps to explain how dioxane is metabolized as a sole carbon and energy source for strain CB1190.

Selective hydroxylation of alkanes by an extracellular fungal peroxygenase

Fungal peroxygenases are novel extracellular heme-thiolate biocatalysts that are capable of catalyzing the selective monooxygenation of diverse organic compounds, using only H(2)O(2) as a cosubstrate. Little is known about the physiological role or the catalytic mechanism of these enzymes. We have found that the peroxygenase secreted by Agrocybe aegerita catalyzes the H(2)O(2)-dependent hydroxylation of linear alkanes at the 2-position and 3-position with high efficiency, as well as the regioselective monooxygenation of branched and cyclic alkanes. Experiments with n-heptane and n-octane showed that the hydroxylation proceeded with complete stereoselectivity for the (R)-enantiomer of the corresponding 3-alcohol. Investigations with a number of model substrates provided information about the route of alkane hydroxylation: (a) the hydroxylation of cyclohexane mediated by H(2)(18)(2) resulted in complete incorporation of (18)O into the hydroxyl group of the product cyclohexanol; (b) the hydroxylation of n-hexane-1,1,1,2,2,3,3-D(7) showed a large intramolecular deuterium isotope effect [(k(H)/k(D))(obs)] of 16.0 ± 1.0 for 2-hexanol and 8.9 ± 0.9 for 3-hexanol; and (c) the hydroxylation of the radical clock norcarane led to an estimated radical lifetime of 9.4 ps and an oxygen rebound rate of 1.06 × 10(11) s(-1). These results point to a hydrogen abstraction and oxygen rebound mechanism for alkane hydroxylation. The peroxygenase appeared to lack activity on long-chain alkanes (> C(16)) and highly branched alkanes (e.g. tetramethylpentane), but otherwise exhibited a broad substrate range. It may accordingly have a role in the bioconversion of natural and anthropogenic alkane-containing structures (including alkyl chains of complex biomaterials) in soils, plant litter, and wood.

Biodegradation of polyether algal toxins--isolation of potential marine bacteria

Marine algal toxins such as brevetoxins, okadaic acid, yessotoxin, and ciguatoxin are polyether compounds. The fate of polyether toxins in the aqueous phase, particularly bacterial biotransformation of the toxins, is poorly understood. An inexpensive and easily available polyether structural analog salinomycin was used for enrichment and isolation of potential polyether toxin degrading aquatic marine bacteria from Florida bay area, and from red tide endemic sites in the South Florida Gulf coast. Bacterial growth on salinomycin was observed in most of the enrichment cultures from both regions with colony forming units ranging from 0 to 6×10(7) per mL. The salinomycin biodegradation efficiency of bacterial isolates determined using LC-MS ranged from 22% to 94%. Selected bacterial isolates were grown in media with brevetoxin as the sole carbon source to screen for brevetoxin biodegradation capability using ELISA. Out of the two efficient salinomycin biodegrading isolates MB-2 and MB-4, maximum brevetoxin biodegradation efficiency of 45% was observed with MB-4, while MB-2 was unable to biodegrade brevetoxin. Based on 16S rRNA sequence similarity MB-4 was found have a match with Chromohalobacter sp.

Biosynthesis of ethers: unusual or common natural events?

Ether bonds are found in a wide variety of natural products--mainly secondary metabolites--including lipids, oxiranes, terpenoids, flavonoids, polyketides, and carbohydrate derivatives, to name some representative examples. To furnish such a biodiversity of structures, a large number of different enzymes are involved in several different biosynthetic pathways. Depending on the compound and on the (micro) environment in which the reaction is performed, ethers are produced by very different (enzymatic) reactions, thus providing an impressive display of how Nature has combined evolution and thermodynamics to be able to produce a vast number of compounds. In addition, many of these compounds possess different biological activities of pharmacological interest. Moreover, some of these ethers (i.e., epoxides) have high chemical reactivity, and can be useful starting materials for further synthetic processes. This review aims to provide an overview of the different strategies that are found in Nature for the formation of these "bioethers". Both fundamental and practical insights of the biosynthetic processes will be discussed.

Oxidative cleavage of diverse ethers by an extracellular fungal peroxygenase

Many litter-decay fungi secrete heme-thiolate peroxygenases that oxidize various organic chemicals, but little is known about the role or mechanism of these enzymes. We found that the extracellular peroxygenase of Agrocybe aegerita catalyzed the H2O2-dependent cleavage of environmentally significant ethers, including methyl t-butyl ether, tetrahydrofuran, and 1,4-dioxane. Experiments with tetrahydrofuran showed the reaction was a two-electron oxidation that generated one aldehyde group and one alcohol group, yielding the ring-opened product 4-hydroxybutanal. Investigations with several model substrates provided information about the route for ether cleavage: (a) steady-state kinetics results with methyl 3,4-dimethoxybenzyl ether, which was oxidized to 3,4-dimethoxybenzaldehyde, gave parallel double reciprocal plots suggestive of a ping-pong mechanism (K(m)((peroxide)), 1.99 +/- 0.25 mM; K(m)((ether)), 1.43 +/- 0.23 mM; k(cat), 720 +/- 87 s(-1)), (b) the cleavage of methyl 4-nitrobenzyl ether in the presence of H2(18)O2 resulted in incorporation of 18O into the carbonyl group of the resulting 4-nitrobenzaldehyde, and (c) the demethylation of 1-methoxy-4-trideuteromethoxybenzene showed an observed intramolecular deuterium isotope effect [(k(H)/k(D))(obs)] of 11.9 +/- 0.4. These results suggest a hydrogen abstraction and oxygen rebound mechanism that oxidizes ethers to hemiacetals, which subsequently hydrolyze. The peroxygenase appeared to lack activity on macromolecular ethers, but otherwise exhibited a broad substrate range. It may accordingly have a role in the biodegradation of natural and anthropogenic low molecular weight ethers in soils and plant litter.

Conversion of dehydrodiferulic acids by human intestinal microbiota

Plant cell wall associated dehydrodiferulic acids (DFA) are abundant components of cereal insoluble dietary fibers ingested by humans. The ability of human intestinal microbiota to convert DFA was studied in vitro by incubating 8-O-4- and 5-5-coupled DFA with fecal suspensions. 8-O-4-DFA was completely degraded by the intestinal microbiota of the majority of donors, yielding homovanillic acid, 3-(3,4-dihydroxyphenyl)propionic acid, and 3,4-dihydroxyphenylacetic acid as the main metabolites. The transient formation of ferulic acid and presumably 3-(3-hydroxy-4-methoxyphenyl)pyruvic acid suggests an initial cleavage of the ether bond. In contrast to 8-O-4-DFA, the 5-5-coupled DFA was not cleaved into monomers by any of the fecal suspensions. Only the side chains were hydrogenated and the methoxy groups were demethylated. The cleavage of DFA by human intestinal microbiota, which depended on their coupling type, may affect both the bioavailability of DFA and the degradability of DFA-coupled fiber in the gut.

Long term studies on the anaerobic biodegradability of MTBE and other gasoline ethers

Anaerobic biodegradation of methyl tert-butyl ether (MTBE) using electron acceptors such as nitrate, Fe(III), sulfate and bicarbonate, may be more cost effective and feasible compared to aerobic treatment methods, for dealing with the MTBE problem. Currently, there are a few reports in the literature which have documented anaerobic biodegradation of MTBE in batch studies. However, some of the reports have been controversial, additionally many other studies have failed to document anaerobic biodegradation. Experiments were conducted over a long term period in both batch and continuous reactors to investigate the anaerobic biodegradability of MTBE and other gasoline ethers. Inoculums collected from various environments were used, along with different electron acceptors. Only one set of the batch experiments showed a 30-60% conversion of MTBE to tert-butyl alcohol under Fe(III)-reducing conditions, using complexed Fe(III). The use of complexed Fe(III) created an initial low pH of 1-2 in these batches due to its acidic nature, therefore, the removal may be due to acid hydrolysis rather than biological processes. Based on the findings obtained, caution should be applied in the interpretation of experimental data in which complexed Fe(III) is used for bioremediation of MTBE.

Mechanistic studies on N-acetylmuramic acid 6-phosphate hydrolase (MurQ): an etherase involved in peptidoglycan recycling

Peptidoglycan recycling is a process in which bacteria import cell wall degradation products and incorporate them back into either peptidoglycan biosynthesis or basic metabolic pathways. The enzyme MurQ is an N-acetylmuramic acid 6-phosphate (MurNAc 6-phosphate) hydrolase (or etherase) that hydrolyzes the lactyl side chain from MurNAc 6-phosphate and generates GlcNAc 6-phosphate. This study supports a mechanism involving the syn elimination of lactate to give an alpha,beta-unsaturated aldehyde with (E)-stereochemistry, followed by the syn addition of water to give product. The observation of both a kinetic isotope effect slowing the reaction of [2-(2)H]MurNAc 6-phosphate and the incorporation of solvent-derived deuterium into C2 of the product indicates that the C2-H bond is cleaved during catalysis. The observation that the solvent-derived (18)O isotope is incorporated into the C3 position of the product, but not the C1 position, provides evidence of the cleavage of the C3-O bond and argues against imine formation. The finding that 3-chloro-3-deoxy-GlcNAc 6-phosphate serves as an alternate substrate is also consistent with an elimination-addition mechanism. Upon extended incubations of MurQ with GlcNAc 6-phosphate, the alpha,beta-unsaturated aldehydic intermediate accumulates in solution, and (1)H NMR analysis indicates it exists as the ring-closed form of the (E)-alkene. A structural model is developed for the Escherichia coli MurQ and is compared to that of the structural homologue glucosamine-6-phosphate synthase. Putative active site acid/base residues are probed by mutagenesis, and Glu83 and Glu114 are found to be crucial for catalysis. The Glu83Ala mutant is essentially inactive as an etherase yet is capable of exchanging the C2 proton of substrate with solvent-derived deuterium. This suggests that Glu83 may function as the acidic residue that protonates the departing lactate.

Landfill cover soil, soil solution, and vegetation responses to municipal landfill leachate applications

Municipal solid waste landfill leachate must be removed and treated to maintain landfill cover integrity and to prevent contamination of surface and ground waters. From 2003 to 2007, we studied an onsite disposal system in Ottawa County, Michigan, where leachate was spray irrigated on the vegetated landfill cover. We established six 20-m-diameter circular experimental plots on the landfill; three were spray irrigated as part of the operational system, and three remained as untreated control plots. We quantified the effects of leachate application on soil properties, soil solution chemistry, vegetative growth, and estimated solute leaching. The leachate had high mean levels of electrical conductivity (0.6-0.7 S m(-1)), Cl (760-900 mg L(-1)), and NH(4)-N (290-390 mg L(-1)) but was low in metals and volatile organic compounds. High rates of leachate application in 2003 (32 cm) increased soil electrical conductivity and NO(3)-N leaching, so a sequential rotation of spray areas was implemented to limit total leachate application to <9.6 cm yr(-1) per spray area. Concentrations of NO(3)-N and leaching losses remained higher on irrigated plots in subsequent years but were substantially reduced by spray area rotation. Leachate irrigation increased plant biomass but did not significantly affect soil metal concentrations, and plant metal concentrations remained within normal ranges. Rotating spray areas and timing irrigation to conform to seasonal capacities for evapotranspiration reduced the localized impacts of leachate application observed in 2003. Careful monitoring of undiluted leachate applications is required to avoid adverse impacts to vegetation or soils and elevated solute leaching losses.

Biodegradation of bis(2-chloroethyl) ether by Xanthobacter sp. strain ENV481

Degradation of bis(2-chloroethyl) ether (BCEE) was observed to occur in two bacterial strains. Strain ENV481, a Xanthobacter sp. strain, was isolated by enrichment culturing of samples from a Superfund site located in the northeastern United States. The strain was able to grow on BCEE or 2-chloroethylethyl ether as the sole source of carbon and energy. BCEE degradation in strain ENV481 was facilitated by sequential dehalogenation reactions resulting in the formation of 2-(2-chloroethoxy)ethanol and diethylene glycol (DEG), respectively. 2-Hydroxyethoxyacetic acid was detected as a product of DEG catabolism by the strain. Degradation of BCEE by strain ENV481 was independent of oxygen, and the strain was not able to grow on a mixture of benzene, ethylbenzene, toluene, and xylenes, other prevalent contaminants at the site. Another bacterial isolate, Pseudonocardia sp. strain ENV478 (S. Vainberg et al., Appl. Environ. Microbiol. 72:5218-5224, 2006), degraded BCEE after growth on tetrahydrofuran or propane but was not able to grow on BCEE as a sole carbon source. BCEE degradation by strain ENV478 appeared to be facilitated by a monooxygenase-mediated O-dealkylation mechanism, and it resulted in the accumulation of 2-chloroacetic acid that was not readily degraded by the strain.

Measurement of polybrominated diphenyl ethers and metabolites in mouse plasma after exposure to a commercial pentabromodiphenyl ether mixture

BACKGROUND

Previous studies have shown that polybrominated diphenyl ethers (PBDEs) behave as weak estrogens in animal and cell culture bioassays. In vivo metabolites of PBDEs are suspected to cause these effects.

OBJECTIVES

To identify candidate metabolites, mouse plasma samples were collected after continuous oral and subcutaneous exposure to DE-71, a widely used commercial pentabromodiphenyl ether product, for 34 days.

METHODS

Samples were extracted, separated into neutral and phenolic fractions, and analyzed by gas chromatographic mass spectrometry.

RESULTS

In the plasma samples of orally treated animals, 2,2',4,4',5,5'-hexabromodiphenyl ether (BDE-153) represented 52% of total measurable PBDEs, whereas it represented only 4.3% in the DE-71 mixture. This suggested that BDE-153 was more persistent than other congeners in mice. Several metabolites were detected and quantitated: 2,4-dibromophenol, 2,4,5-tribromophenol, and six hydroxylated PBDEs. The presence of the two phenols suggested cleavage of the ether bond of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) and 2,2',4,4',5-pentabromodiphenyl ether (BDE-99), respectively. The hydroxylated (HO)-PBDEs might come from hydroxylation or debromination/hydroxylation. Among the quantitated hydroxylated metabolites, the most abundant was 4-HO-2,2',3,4'-tetra-BDE, which suggested that there was a bromine shift during the hydroxylation process. para-HO-PBDEs have been proposed to behave as endocrine disruptors.

CONCLUSIONS

THERE SEEM TO BE THREE METABOLIC PATHWAYS: cleavage of the diphenyl ether bond, hydroxylation, and debromination/hydroxylation. The cleavage of the diphenyl ether bond formed bromophenols, and the other two pathways formed hydroxylated PBDEs, of which para-HO-PBDEs are most likely formed from BDE-47. These metabolites may be the most thyroxine-like and/or estrogen-like congeners among the HO-PBDEs.

Analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from Sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants

Polyethylene glycol dehydrogenase (PEGDH) from Sphingopyxis terrae (formerly Sphingomonas terrae) is composed of 535 amino acid residues and one flavin adenine dinucleotide per monomer protein in a homodimeric structure. Its amino acid sequence shows 28.5 to 30.5% identity with glucose oxidases from Aspergillus niger and Penicillium amagasakiense. The ADP-binding site and the signature 1 and 2 consensus sequences of glucose-methanol-choline oxidoreductases are present in PEGDH. Based on three-dimensional molecular modeling and kinetic characterization of wild-type PEGDH and mutant PEGDHs constructed by site-directed mutagenesis, residues potentially involved in catalysis and substrate binding were found in the vicinity of the flavin ring. The catalytically important active sites were assigned to His-467 and Asn-511. One disulfide bridge between Cys-379 and Cys-382 existed in PEGDH and seemed to play roles in both substrate binding and electron mediation. The Cys-297 mutant showed decreased activity, suggesting the residue's importance in both substrate binding and electron mediation, as well as Cys-379 and Cys-382. PEGDH also contains a motif of a ubiquinone-binding site, and coenzyme Q10 was utilized as an electron acceptor. Thus, we propose several important amino acid residues involved in the electron transfer pathway from the substrate to ubiquinone.

Catabolism of 1,5-anhydro-D-fructose in Sinorhizobium morelense S-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-D-fructose reductase and its application in sugar analysis and rare sugar synthesis

The bacterium Sinorhizobium morelense S-30.7.5 was isolated by a microbial screening using the sugar 1,5-anhydro-D-fructose (AF) as the sole carbon source. This strain metabolized AF by a novel pathway involving its reduction to 1,5-anhydro-D-mannitol (AM) and the further conversion of AM to D-mannose by C-1 oxygenation. Growth studies showed that the AF metabolizing capability is not confined to S. morelense S-30.7.5 but is a more common feature among the Rhizobiaceae. The AF reducing enzyme was purified and characterized as a new NADPH-dependent monomeric reductase (AFR, EC 1.1.1.-) of 35.1 kDa. It catalyzed the stereoselective reduction of AF to AM and also the conversion of a number of 2-keto aldoses (osones) to the corresponding manno-configurated aldoses. In contrast, common aldoses and ketoses, as well as nonsugar aldehydes and ketones, were not reduced. A database search using the N-terminal AFR sequence retrieved a putative 35-kDa oxidoreductase encoded by the open reading frame Smc04400 localized on the chromosome of Sinorhizobium meliloti 1021. Based on sequence information for this locus, the afr gene was cloned from S. morelense S-30.7.5 and overexpressed in Escherichia coli. In addition to the oxidoreductase of S. meliloti 1021, AFR showed high sequence similarities to putative oxidoreductases of Mesorhizobium loti, Brucella suis, and B. melitensis but not to any oxidoreductase with known functions. AFR could be assigned to the GFO/IDH/MocA family on the basis of highly conserved common structural features. His6-tagged AFR was used to demonstrate the utility of this enzyme for AF analysis and synthesis of AM, as well as related derivatives.