The biodegradation vs. biotransformation of fluorosubstituted aromatics

Identification of transformation products from fluorinated lithium-ion battery additives TPFPB and TPFPP: forever chemicals of tomorrow?

Fluorinated organic compounds (FOCs) represent a class of synthetic chemicals distinguished by their resilient carbon-fluorine bonds, which demonstrate an ability to withstand environmental degradation over an extended period. The integration of FOCs into cutting-edge applications, including lithium-ion batteries (LiBs), presents considerable potential for environmental harm that has not yet been sufficiently addressed. This study focuses on the environmental fate of two fluorinated aromatics, tris(pentafluorophenyl)borane (TPFPB) and tris(pentafluorophenyl)phosphine (TPFPP), given their important role in improving the performance of LiBs. To achieve this, laboratory simulation methods including total oxidizable precursor assay, electrochemistry (EC), Fenton reaction, UV-C irradiation, and hydrolysis were employed. Liquid chromatography and gas chromatography coupled with high-resolution mass spectrometry were used for identification of transformation products (TPs) and prediction of their molecular formulae. Despite the structural similarity between TPFPB and TPFPP, distinct differences in electrochemical behavior and degradation pathways were observed. TPFPB readily underwent hydroxylation and hydrolysis, resulting in a wide range of 49 TPs. A total of 28 TPs were newly identified, including oligomers and highly toxic dioxins. In contrast, TPFPP degraded exclusively under harsh conditions, requiring the development of innovative conditioning protocols for EC. In total, the simulation experiments yielded nine structurally different compounds, including seven previously undescribed, partially defluorinated TPs. This study highlights the potential risks associated with the use of FOCs in LiBs and provides insight into the complex environmental behavior of FOCs.

Defluorination of monofluorinated alkane by Rhodococcus sp. NJF-7 isolated from soil

Microbial degradation of fluorinated compounds raised significant attention because of their widespread distribution and potential environmental impacts. Here, we report a bacterial isolate, Rhodococcus sp. NJF-7 capable of defluorinating monofluorinated medium-chain length alkanes. This isolate consumed 2.29 ± 0.13 mmol L- 1 of 1-fluorodecane (FD) during a 52 h incubation period, resulting in a significant release of inorganic fluoride amounting to 2.16 ± 0.03 mmol L- 1. The defluorination process was strongly affected by the initial FD concentration and pH conditions, with lower pH increasing fluoride toxicity to bacterial cells and inhibiting enzymatic defluorination activity. Stoichiometric conversion of FD to fluoride was observed at neutral pH with resting cells, while defluorination was significantly lower at reduced pH (6.5). The discovery of the metabolites decanoic acid and methyl decanoate suggests that the initial attack by monooxygenases may be responsible for the biological defluorination of FD. The findings here provide new insights into microbial defluorination processes, specifically aiding in understanding the environmental fate of organic semi-fluorinated alkane chemicals.

The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis

Fluorinated organic chemicals, such as per- and polyfluorinated alkyl substances (PFAS) and fluorinated pesticides, are both broadly useful and unusually long-lived. To combat problems related to the accumulation of these compounds, microbial PFAS and organofluorine degradation and biosynthesis of less-fluorinated replacement chemicals are under intense study. Both efforts are undermined by the substantial toxicity of fluoride, an anion that powerfully inhibits metabolism. Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite of detoxification mechanisms. In this perspective, we synthesize emerging ideas on microbial defluorination/fluorination and fluoride resistance mechanisms and identify best approaches for bioengineering new approaches for degrading and making organofluorine compounds.

Evolutionary obstacles and not C-F bond strength make PFAS persistent

The fate of organic matter in the environment, including anthropogenic chemicals, is largely predicated on the enzymatic capabilities of microorganisms. Microbes readily degrade, and thus recycle, most of the ~100,000 commercial chemicals used in modern society. Per- and polyfluorinated compounds (PFAS) are different. Many research papers posit that the general resistance of PFAS to microbial degradation is based in chemistry and that argument relates to the strength of the C-F bond. Here, I advance the opinion that the low biodegradability of PFAS is best formulated as a biological optimization problem, hence evolution. The framing of the problem is important. If it is framed around C-F bond strength, the major effort should focus on finding and engineering new C-F cleaving enzymes. The alternative, and preferred approach suggested here, is to focus on the directed evolution of biological systems containing known C-F cleaving systems. There are now reports of bacteria degrading and/or growing on multiply fluorinated arenes, alkenoic and alkanoic acids. The impediment to more efficient and widespread biodegradation in these systems is biological, not chemical. The rationale for this argument is made in the five sections below that follow the Introduction.

FluoroFusion: NHC-Catalyzed Nucleophilic Aromatic Substitution Reaction Unveils Functional Perfluorinated Diarylmethanones

A mild, facile, and metal-free approach via the N-heterocyclic carbene-catalyzed SNAr reaction between aryl aldehydes with perfluoroarenes to obtain the coveted functional perfluorinated diarylmethanones is disclosed. This method accommodates a diverse substrate range and exhibits notable tolerance toward various functional groups. Our success in modifying biologically relevant molecules, crafting a fully fluorinated bioisosteric analogue of drug candidate D1, and highlighting the potential of these ketones as valuable electrolyte additives for lithium-ion batteries (LIBs) underscores the versatility of our methodology.

Biotransformation of fluorinated drugs and xenobiotics by the model fungus Cunninghamella elegans

Some species of the genus Cunninghamella (C. elegans, C. echinulata and C. blaskesleeana) produce the same phase I and phase II metabolites when incubated with xenobiotics as mammals, and thus are considered microbial models of mammalian metabolism. This had made these fungi attractive for metabolism studies with drugs, pesticides and environmental pollutants. As a substantial proportion of pharmaceuticals and agrochemicals are fluorinated, their biotransformation has been studied in Cunninghamella fungi and C. elegans in particular. This article details the methods employed for cultivating the fungi in planktonic and biofilm cultures, and extraction and analysis of fluorinated metabolites. Furthermore, protocols for the heterologous expression of Cunninghamella cytochromes P450 (CYPs), which are the enzymes associated with phase I metabolism, are described.

Defluorination as the key trait to gauge the biodegradability of fluorinated pollutants in environmental microbial communities

Research on microbial defluorination is largely centred on controlled experiments using axenic or well defined microbial inocula. These approaches serve a relevant purpose in the field, offering fundamental biochemical and mechanistic insights on the intricacies of biological defluorination. However, they fail to account for the effective contribution of environmental microbial communities in the recycling of fluoroorganic pollutants, a highly relevant perspective from an environmental risk assessment standpoint, while also missing an important outlook on how community-wide dynamics can leverage the breakdown of C─F bonds in these recalcitrant compounds. With that in mind, this chapter provides experimental and methodological insights on the study of microbial defluorination in wild environmental communities, using this critical catabolic step as the de facto endpoint to evolve, select and cultivate microorganisms with improved defluorination performances.

Biodegradation Potential of C7-C10 Perfluorocarboxylic Acids and Data from the Genome of a New Strain of Pseudomonas mosselii 5(3)

The use of bacteria of the genus Pseudomonas-destructors of persistent pollutants for biotechnologies of environmental purification-is an interesting area of research. The aim of this work was to study the potential of Pseudomonas mosselii strain 5(3) isolated from pesticide-contaminated soil as a degrader of C7-C10 perfluorocarboxylic acids (PFCAs) and analyze its complete genome. The genome of the strain has been fully sequenced. It consists of a chromosome with a length of 5,676,241 b.p. and containing a total of 5134 genes, in particular, haloalkane dehalogenase gene (dhaA), haloacetate dehalogenase H-1 gene (dehH1), fluoride ion transporter gene (crcB) and alkanesulfonate monooxygenase gene (ssuE), responsible for the degradation of fluorinated compounds. The strain P. mosselii 5(3) for was cultivated for 7 days in a liquid medium with various C7-C10 PFCAs as the sole source of carbon and energy, and completely disposed of them. The results of LC-MS analysis showed that the transformation takes place due to perfluorohexanoic acid with the release of various levels of stoichiometry (depending on PFCA) of fluorine ion mineralization indicators determined by ion chromatography. Thus, Pseudomonas mosselii strain 5(3) demonstrates a genetically confirmed high potential for the decomposition of C7-C10 PFCA.

Genome-Wide Expression Analysis Unravels Fluoroalkane Metabolism in Pseudomonas sp. Strain 273

Pseudomonas sp. strain 273 grows with medium-chain terminally fluorinated alkanes under oxic conditions, releases fluoride, and synthesizes long-chain fluorofatty acids. To shed light on the genes involved in fluoroalkane metabolism, genome, and transcriptome sequencing of strain 273 grown with 1,10-difluorodecane (DFD), decane, and acetate were performed. Strain 273 harbors three genes encoding putative alkane monooxygenases (AlkB), key enzymes for initiating alkane degradation. Transcripts of alkB-2 were significantly more abundant in both decane- and DFD-grown cells compared to acetate-grown cells, suggesting AlkB-2 catalyzes the attack on terminal CH3 and CH2F groups. Coordinately expressed with alkB-2 was an adjacent gene encoding a fused ferredoxin-ferredoxin reductase (Fd-Fdr). Phylogenetic analysis distinguished AlkB that couples with fused Fd-Fdr reductases from AlkB with alternate architectures. A gene cluster containing an (S)-2-haloacid dehalogenase (had) gene was up-regulated in cells grown with DFD, suggesting a possible role in the removal of the ω-fluorine. Genes involved in long-chain fatty acid biosynthesis were not differentially expressed during growth with acetate, decane, or DFD, suggesting the bacterium's biosynthetic machinery does not discriminate against monofluoro-fatty acid intermediates. The analysis sheds first light on genes and catalysts involved in the microbial metabolism of fluoroalkanes.

The wide presence of fluorinated compounds in common chemical products and the environment: a review

The C-F bonds, due to their many unique features, have been incorporated into numerous compounds in countless products and applications. These fluorinated compounds eventually are disposed of and released into the environment through different pathways. In this review, we analyzed the occurrence of these fluorinated compounds in seven types of products (i.e., refrigerants/propellants, aqueous film-forming foam, cosmetics, food packaging, agrochemicals, pharmaceuticals, coating materials) and discussed their fate in the environment. This is followed by describing the quantity of fluorinated compounds from each source based on available data. Total on- and off-site disposal or other releases of 536 fluorinated compounds in 2021 were analyzed using the data sourced from the U.S. EPA Toxics Release Inventory (TRI). Among the chemicals examined, chlorofluorocarbons (CFCs) and hydrochlorofluorocarbons (HCFCs) were the primary contributors in terms of total mass. Upon examining the seven sources of fluorinated compounds, it became evident that additional contributors are also responsible for the presence of organofluorine compounds in the environment. Although various toxic degradation products of fluorinated compounds could form in the environment, trifluoroacetic acid (TFA) was specifically highlighted in this review given the fact that it is a common dead-end degradation product of > 1 million chemicals. This paper ended with a discussion of several questions raised from this study. The path forward was elaborated as well for the purpose of protecting the environment and human health.

Impact of per- and polyfluorinated alkyl substances (PFAS) on the marine environment: Raising awareness, challenges, legislation, and mitigation approaches under the One Health concept

Per- and polyfluorinated alkyl substances (PFAS) have long been known for their detrimental effects on the ecosystems and living organisms; however the long-term impact on the marine environment is still insufficiently recognized. Based on PFAS persistence and bioaccumulation in the complex marine food network, adverse effects will be exacerbated by global processes such as climate change and synergies with other pollutants, like microplastics. The range of fluorochemicals currently included in the PFAS umbrella has significantly expanded due to the updated OECD definition, raising new concerns about their poorly understood dynamics and negative effects on the ocean wildlife and human health. Mitigation challenges and approaches, including biodegradation and currently studied materials for PFAS environmental removal are proposed here, highlighting the importance of ongoing monitoring and bridging research gaps. The PFAS EU regulations, good practices and legal frameworks are discussed, with emphasis on recommendations for improving marine ecosystem management.

A proposed approach to defining per- and polyfluoroalkyl substances (PFAS) based on molecular structure and formula

Various groups and researchers, including the authors of this work, have proposed different definitions of what constitutes per- and polyfluoroalkyl substances (PFAS). The different definitions are all based on a structural definition. Although a structural definition is reasonable, such an approach is difficult to execute if the intent is to narrow or refine the definition. This approach can also lead to inexplicable demarcations of what are and what are not PFAS. Our objective was to create a narrow, simple PFAS definition that allows interested groups to communicate with a common understanding and will also serve as a starting point to focus on substances that are of real environmental concern. Our studies have demonstrated that numerous highly fluorinated complex structures exist that make a structure-based definition difficult. We suggest that a definition based on fractional fluorination expressed as the percentage of fluorine of a molecular formula using atom counting offers advantages. Using a combination of a structure-based definition and a definition based on the fractional percentage of the molecular formula that is fluorine can provide a more inclusive and succinct definition. Thus, we propose a new definition based on four substructures along with any structures where the molecular formula is 30% fluorine by atom count. Integr Environ Assess Manag 2023;19:1333-1347. Published 2023. This article is a U.S. Government work and is in the public domain in the USA. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Distribution and transformation of organophosphate esters in moving bed biofilm reactor

A moving bed biofilm reactor (MBBR) process in wastewater treatment plants (WWTPs) uses plastic carriers, called biofilm carrier, to increase their treatment efficiency. Biofilm carrier is made up of plastic, containing the OPEs as flame retardants or plasticizers, so OPEs in biofilm carrier are possible to release from WWTPs to the river. This study investigated the effect of the MBBR process in WWTP on aquatic environments, focusing on OPEs. OPE eluted from the biofilm carrier by leaching test was tris(2-chloroethyl) phosphate (TCEP), and the concentration of the effluent compared to the influent was increased in the WWTP of the MBBR process. 3609 mg/day of TCEP would be discharged into the water using the second-order model with rate constant [Formula: see text] = 0.000451 (ng L-1)-1 h-1, which is the most suitable for the leaching concentration of TCEP. It was identified that TCEP in biofilm carrier was transformed into oxidative dechlorinated compounds and oxidative compounds by microorganisms in the bioreactor. As a result of the study, it was confirmed that not only TCEP but also transformation products of TCEP emitted into the water from the MBBR process of WWTP.

Fluorotelomer alcohols are efficiently biotransformed by Cunninghamella elegans

Cunninghamella elegans is a well-studied fungus that biotransforms a range of xenobiotics owing to impressive cytochrome P450 (CYP) activity. In this paper, we report the biotransformation of 6:2 fluorotelomer alcohol (6:2 FTOH) by the fungus, yielding a range of fluorinated products that were detectable by fluorine-19 nuclear magnetic resonance spectroscopy (¹⁹F NMR), gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). Upon incubation with the pre-grown cultures, the substrate (100 mg/L) was completely consumed within 48 h, which is faster biotransformation than other fungi that have hitherto been studied. The main metabolite formed was the 5:3 fluorotelomer carboxylic acid (5:3 FTCA), which accumulated in the culture supernatant. When the cytochrome P450 inhibitor 1-aminobenzotriazole was included in the culture flasks, there was no biotransformation of 6:2 FTOH, indicating that these enzymes are key to the catalysis. Furthermore, when exogenous 5:3 FTCA was added to the fungus, the standard biotransformation of the drug flurbiprofen was inhibited, strongly suggesting that the main fluorotelomer alcohol biotransformation product inhibits CYP activity and accounts for its accumulation.

Droplet digital microfluidic system for screening filamentous fungi based on enzymatic activity

Fungal cell-wall-degrading enzymes have great utility in the agricultural and food industries. These cell-wall-degrading enzymes are known to have functions that can help defend against pathogenic organisms. The existing methods used to discover these enzymes are not well adapted to fungi culture and morphology, which prevents the proper evaluation of these enzymes. We report the first droplet-based microfluidic method capable of long-term incubation and low-voltage conditions to sort filamentous fungi inside nanoliter-sized droplets. The new method was characterized and validated in solid-phase media based on colloidal chitin such that the incubation of single spores in droplets was possible over multiple days (2-4 days) and could be sorted without droplet breakage. With long-term culture, we examined the activity of cell-wall-degrading enzymes produced by fungi during solid-state droplet fermentation using three highly sensitive fluorescein-based substrates. We also used the low-voltage droplet sorter to select clones with highly active cell-wall-degrading enzymes, such as chitinases, β-glucanases, and β-N-acetylgalactosaminidases, from a filamentous fungi droplet library that had been incubated for >4 days. The new system is portable, affordable for any laboratory, and user-friendly compared to classical droplet-based microfluidic systems. We propose that this system will be useful for the growing number of scientists interested in fungal microbiology who are seeking high-throughput methods to incubate and sort a large library of fungal cells.

Strategies for the Biodegradation of Polyfluorinated Compounds

Many cite the strength of C-F bonds for the poor microbial biodegradability of polyfluorinated organic compounds (PFCs). However, commercial PFCs almost invariably contain more functionality than fluorine. The additional functionality provides a weak entry point for reactions that activate C-F bonds and lead to their eventual cleavage. This metabolic activation strategy is common in microbial biodegradation pathways and is observed with aromatic hydrocarbons, chlorinated compounds, phosphonates and many other compounds. Initial metabolic activation precedes critical bond breakage and assimilation of nutrients. A similar strategy with commercial PFCs proceeds via initial attack at the non-fluorinated functionalities: sulfonates, carboxylates, chlorines, phenyl rings, or phosphonates. Metabolic transformation of these non-fluorinated groups can activate the C-F bonds, allowing more facile cleavage than a direct attack on the C-F bonds. Given that virtually all compounds denoted as "PFAS" are not perfluorinated and are not alkanes, it is posited here that considering their individual chemical classes is more useful for both chemical and microbiological considerations of their fate.

Metabolic engineering of Escherichia coli for efficient degradation of 4-fluorophenol

As a kind of refractory organic pollutant, 4-fluorophenol (4-FP) can be degraded by only a few microorganisms with low efficiency because of the great electron-withdrawing ability of fluorine atoms. So it is necessary to artificially construct engineered strain to improve the degradation efficiency and meet the requirements of pollutant degradation. In this study, four genes (fpdA2, fpdB, fpdC, and fpdD) for 4-FP degradation from Arthrobacter sp. strain IF1 were optimized and synthesized and then reconstructed into Escherichia coli by a multi-monocistronic vector to obtain recombinant BL-fpd that could degrade 4-FP efficiently. Under optimized induction conditions (inducing the strain by 2 g/L L-arabinose and 1 mM IPTG at 37 ℃), BL-fpd could completely degrade 2 mM 4-FP, 4-chlorophenol, 4-bromophenol, and 4-nitrophenol into β-ketoadipate, which could be further metabolized by the bacteria. FpdA2 showed the highest activity towards 4-bromophenol. The strain could completely degrade 1 mM 4-FP in industrial wastewater within 3 h. This study provided a promising strain for the degradation of 4-FP and some other 4-substituted phenols. The construction technologies of multi-monocistronic expression vector may also be used to construct other organic pollutants degrading bacteria.

Microwell Fluoride Screen for Chemical, Enzymatic, and Cellular Reactions Reveals Latent Microbial Defluorination Capacity for -CF3 Groups

The capacity to defluorinate polyfluorinated organic compounds is a rare phenotype in microbes but is increasingly considered important for maintaining the environment. New discoveries will be greatly facilitated by the ability to screen many natural and engineered microbes in a combinatorial manner against large numbers of fluorinated compounds simultaneously. Here, we describe a low-volume, high-throughput screening method to determine defluorination capacity of microbes and their enzymes. The method is based on selective binding of fluoride to a lanthanum chelate complex that gives a purple-colored product. It was miniaturized to determine biodefluorination in 96-well microtiter plates by visual inspection or robotic handling and spectrophotometry. Chemicals commonly used in microbiological studies were examined to define usable buffers and reagents. Base-catalyzed, purified enzyme and whole-cell defluorination reactions were demonstrated with fluoroatrazine and showed correspondence between the microtiter assay and a fluoride electrode. For discovering new defluorination reactions and mechanisms, a chemical library of 63 fluorinated compounds was screened in vivo with Pseudomonas putida F1 in microtiter well plates. These data were also calibrated against a fluoride electrode. Our new method revealed 21 new compounds undergoing defluorination. A compound with four fluorine substituents, 4-fluorobenzotrifluoride, was shown to undergo defluorination to the greatest extent. The mechanism of its defluorination was studied to reveal a latent microbial propensity to defluorinate trifluoromethylphenyl groups, a moiety that is commonly incorporated into numerous pharmaceutical and agricultural chemicals. IMPORTANCE Thousands of organofluorine chemicals are known, and a number are considered to be persistent and toxic environmental pollutants. Environmental bioremediation methods are avidly being sought, but few bacteria biodegrade fluorinated chemicals. To find new organofluoride biodegradation, a rapid screening method was developed. The method is versatile, monitoring chemical, enzymatic, and whole-cell biodegradation. Biodegradation of organofluorine compounds invariably releases fluoride anions, which was sensitively detected. Our method uncovered 21 new microbial defluorination reactions. A general mechanism was delineated for the biodegradation of trifluoromethylphenyl groups that are increasingly being used in drugs and pesticides.

New 19F NMR methodology reveals structures of molecules in complex mixtures of fluorinated compounds

Although the number of natural fluorinated compounds is very small, fluorinated pharmaceuticals and agrochemicals are numerous. 19F NMR spectroscopy has a great potential for the structure elucidation of fluorinated organic molecules, starting with their production by chemical or chemoenzymatic reactions, through monitoring their structural integrity, to their biotic and abiotic transformation and ultimate degradation in the environment. Additionally, choosing to incorporate 19F into any organic molecule opens a convenient route to study reaction mechanisms and kinetics. Addressing limitations of the existing 19F NMR techniques, we have developed methodology that uses 19F as a powerful spectroscopic spy to study mixtures of fluorinated molecules. The proposed 19F-centred NMR analysis utilises the substantial resolution and sensitivity of 19F to obtain a large number of NMR parameters, which enable structure determination of fluorinated compounds without the need for their separation or the use of standards. Here we illustrate the 19F-centred structure determination process and demonstrate its power by successfully elucidating the structures of chloramination disinfectant by-products of a single mono-fluorinated phenolic compound, which would have been impossible otherwise. This novel NMR approach for the structure elucidation of molecules in complex mixtures represents a major contribution towards the analysis of chemical and biological processes involving fluorinated compounds.

Biodegradation of 3-Chloronitrobenzene and 3-Bromonitrobenzene by Diaphorobacter sp. Strain JS3051

Halonitrobenzenes are toxic chemical intermediates used widely for industrial synthesis of dyes and pesticides. Bacteria able to degrade 2- and 4-chloronitrobenzene have been isolated and characterized; in contrast, no natural isolate has been reported to degrade meta-halonitrobenzenes. In this study, Diaphorobacter sp. strain JS3051, previously reported to degrade 2,3-dichloronitrobenzene, grew readily on 3-chloronitrobenzene and 3-bromonitrobenzene, but not on 3-fluoronitrobenzene, as sole sources of carbon, nitrogen, and energy. A Rieske nonheme iron dioxygenase (DcbAaAbAcAd) catalyzed the dihydroxylation of 3-chloronitrobenzene and 3-bromonitrobenzene, resulting in the regiospecific production of ring-cleavage intermediates 4-chlorocatechol and 4-bromocatechol. The lower activity and relaxed regiospecificity of DcbAaAbAcAd toward 3-fluoronitrobenzene is likely due to the higher electronegativity of the fluorine atom, which hinders it from interacting with E204 residue at the active site. DccA, a chlorocatechol 1,2-dioxygenase, converts 4-chlorocatechol and 4-bromocatechol into the corresponding halomuconic acids with high catalytic efficiency, but with much lower K_cat/K_m values for fluorocatechol analogues. The results indicate that the Dcb and Dcc enzymes of Diaphorobacter sp. strain JS3051 can catalyze the degradation of 3-chloro- and 3-bromonitrobenzene in addition to 2,3-dichloronitrobenzene. The ability to utilize multiple substrates would provide a strong selective advantage in a habitat contaminated with mixtures of chloronitrobenzenes. IMPORTANCE Halonitroaromatic compounds are persistent environmental contaminants, and some of them have been demonstrated to be degraded by bacteria. Natural isolates that degrade 3-chloronitrobenzene and 3-bromonitrobenzene have not been reported. In this study, we report that Diaphorobacter sp. strain JS3051 can degrade 2,3-dichloronitrobenzene, 3-chloronitrobenzene, and 3-bromonitrobenzene using the same catabolic pathway, whereas it is unable to grow on 3-fluoronitrobenzene. Based on biochemical analyses, it can be concluded that the initial dioxygenase and lower pathway enzymes are inefficient for 3-fluoronitrobenzene and even misroute the intermediates, which is likely responsible for the failure to grow. These results advance our understanding of how the broad substrate specificities of catabolic enzymes allow bacteria to adapt to habitats with mixtures of xenobiotic contaminants.

19F-centred NMR analysis of mono-fluorinated compounds

Addressing limitations of the existing NMR techniques for the structure determination of mono-fluorinated compounds, we have developed methodology that uses 19F as the focal point of this process. The proposed 19F-centred NMR analysis consists of a complementary set of broadband, phase-sensitive NMR experiments that utilise the substantial sensitivity of 19F and its far reaching couplings with 1H and 13C to obtain a large number of NMR parameters. The assembled 1H, 13C and 19F chemical shifts, values of J HF, J HH, and J FC coupling constants and the size of 13C induced 19F isotopic shifts constitute a rich source of information that enables structure elucidation of fluorinated moieties and even complete structures of molecules. Here we introduce the methodology, provide a detailed description of each NMR experiment and illustrate their interpretation using 3-fluoro-3-deoxy-d-glucose. This novel approach performs particularly well in the structure elucidation of fluorinated compounds embedded in complex mixtures, eliminating the need for compound separation or use of standards to confirm the structures. It represents a major contribution towards the analysis of fluorinated agrochemicals and (radio)pharmaceuticals at any point during their lifetime, including preparation, use, biotransformation and biodegradation in the environment. The developed methodology can also assist with the investigations of the stability of fluoroorganics and their pharmacokinetics. Studies of reaction mechanisms using fluorinated molecules as convenient reporters of these processes, will also benefit.

Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances

Poly- and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today's society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called 'forever chemicals' due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.

Multilayered solid phase extraction and ultra performance liquid chromatographic method for suspect screening of halogenated pharmaceuticals and photo-transformation products in freshwater - comparison between data-dependent and data-independent acquisition mass spectrometry

Since conventional biological wastewater treatments are not admittedly effective to convert pharmaceutical active compounds (PhACs) into nontoxic products, natural abiotic mechanisms such as solar photolysis arises as an important degradation process, especially for halogenated molecules. In the present work, photolysis simulation was carried out in-lab for precursors and their respective photo-transformation products (photo-TPs), which were analyzed through reversed-phase ultra-high performance liquid chromatography coupled to high resolution mass spectrometry (RP-UHPLCHRMS). An in-house library was created in order to provide reference information for target (precursors) and suspect screening (photo-TPs) analysis of freshwater samples from impacted aquatic environments. Strategies in the use of data-dependent acquisition (DDA) and data-independent acquisition (DIA), as well as the data processing software are discussed here for the identification of 6 PhACs and photo-TPs. Because no standards of photo-TPs were available, only the target compounds, i.e. sitagliptin (398 ± 2 ng L^-1), iohexol (209 ± 5 ng L^-1), lamotrigine (103 ± 10 ng L^-1), losartan (43 ± 10 ng L^-1), ofloxacin (28 ± 7 ng L^-1), and sertraline (25 ± 7 ng L^-1) could be quantified through multiple standard additions.

Revisiting pesticide pollution: The case of fluorinated pesticides

Fluorinated pesticides acquired a significant market share in the agrochemical sector due to the surge of new fluoroorganic ingredients approved in the last two decades. This growing trend has not been accompanied by a comprehensive scientific and regulatory framework entailing all their potential negative impacts for the environment, especially when considering the hazardous properties that may result from the incorporation of fluorine into organic molecules. This review aims to address the safe/hazardous dichotomy associated with fluorinated pesticides by providing an updated outlook on their relevancy in the agrochemical sector and how it leads to their role as environmental pollutants. Specifically, the environmental fate and distribution of these pesticides in the ecosystems is discussed, while also analysing their potential to act as toxic substances for non-target organisms.

Combinatorial pathway balancing provides biosynthetic access to 2-fluoro-cis,cis-muconate in engineered Pseudomonas putida

The wealth of bio-based building blocks produced by engineered microorganisms seldom include halogen atoms. Muconate is a platform chemical with a number of industrial applications that could be broadened by introducing fluorine atoms to tune its physicochemical properties. The soil bacterium Pseudomonas putida naturally assimilates benzoate via the ortho-cleavage pathway with cis,cis-muconate as intermediate. Here, we harnessed the native enzymatic machinery (encoded within the ben and cat gene clusters) to provide catalytic access to 2-fluoro-cis,cis-muconate (2-FMA) from fluorinated benzoates. The reactions in this pathway are highly imbalanced, leading to accumulation of toxic intermediates and limited substrate conversion. By disentangling regulatory patterns of ben and cat in response to fluorinated effectors, metabolic activities were adjusted to favor 2-FMA biosynthesis. After implementing this combinatorial approach, engineered P. putida converted 3-fluorobenzoate to 2-FMA at the maximum theoretical yield. Hence, this study illustrates how synthetic biology can expand the diversity of nature's biochemical catalysis.

Bacterial degradation of the anti-depressant drug fluoxetine produces trifluoroacetic acid and fluoride ion

Fluoxetine (FLX) is a blockbuster drug with annual sales in the billions of dollars. Its widespread use has resulted in its detection in water courses, where it impacts aquatic life. Investigations on the biodegradation of FLX by microorganisms are important, since augmentation of secondary wastewater treatment by an effective degrader may be one method of improving the drug's removal. In this paper, we demonstrate that common environmental bacteria can use FLX as a sole carbon and energy source. Investigations into the metabolites formed using fluorine-19 nuclear magnetic resonance spectroscopy (¹⁹F NMR) and gas chromatography-mass spectrometry indicated that the drug was initially hydrolysed to yield 4-(trifluoromethyl)phenol (TFMP) and 3-(methylamino)-1-phenylpropan-1-ol. Since the fluorometabolite accumulated, the bacteria presumably used the latter compound for carbon and energy. Further growth studies revealed that TFMP could also be used as a sole carbon and energy source and was most likely catabolised via meta-cleavage, since semialdehyde products were detected in culture supernatants. The final products of the degradation pathway were trifluoroacetate and fluoride ion; the former is a dead-end product and was not further catabolised. Fluoride ion most likely arises owing to spontaneous defluorination of the meta-cleavage products that were shown to be photolabile.Key points• Bacteria can use FLX and TFMP as sole carbon and energy sources for their growth.• Biodegradation produces fluorometabolites that were detected by ¹⁹F NMR and GC-MS.• Trifluoroacetic acid and fluoride ion were identified as end products.

Atlas of the microbial degradation of fluorinated pesticides

Fluorine-based agrochemicals have been benchmarked as the golden standard in pesticide development, prompting their widespread use in agriculture. As a result, fluorinated pesticides can now be found in the environment, entailing serious ecological implications due to their harmfulness and persistence. Microbial degradation might be an option to mitigate these impacts, though environmental microorganisms are not expected to easily cope with these fluoroaromatics due to their recalcitrance. Here, we provide an outlook on the microbial metabolism of fluorinated pesticides by analyzing the degradation pathways and biochemical processes involved, while also highlighting the central role of enzymatic defluorination in their productive metabolism. Finally, the potential contribution of these microbial processes for the dissipation of fluorinated pesticides from the environment is also discussed.

Biodegradation of 4-hydroxybenzoic acid by Acinetobacter johnsonii FZ-5 and Klebsiella oxytoca FZ-8 under anaerobic conditions

4-Hydroxybenzoic acid (4-HBA) is a common organic compound that is prevalent in the environment, and the persistence of 4-HBA residues results in exertion of pollution-related detrimental effects. Bioremediation is an effective method for the removal of 4-HBA from the environment. In this study, two bacterial strains FZ-5 and FZ-8 capable of utilizing 4-HBA as the sole carbon and energy source under anaerobic conditions were isolated from marine sediment samples. Phylogenetic analysis identified the two strains FZ-5 and FZ-8 as Acinetobacter johnsonii and Klebsiella oxytoca, respectively. The strains FZ-5 and FZ-8 degraded 2000 mg·L^-1 4-HBA in 72 h with degradation rates of 71.04% and 80.10%, respectively. The optimum culture conditions for degradation by the strains and crude enzymes were also investigated. The strains FZ-5 and FZ-8 also exhibited the ability to degrade other lignin-derived compounds, such as protocatechuic acid, cinnamic acid, and vanillic acid. Immobilization of the two strains showed that they could be used for the bioremediation of 4-HBA in an aqueous environment. Soils inoculated with the strains FZ-5 and FZ-8 showed higher degradation of 4-HBA than the uninoculated soil, and the strains could survive efficiently in anaerobic soil. This is the first report of 4-HBA-degrading bacteria, belonging to the two genera, which showed degradation ability under anaerobic conditions. This study expound the strains could efficiently degrade 4-HBA in anaerobic soil and will help in the development of 4-HBA anaerobic bioremediation systems.

Comprehensive Understanding of Fluoroacetate Dehalogenase-Catalyzed Degradation of Fluorocarboxylic Acids: A QM/MM Approach

Fluorochemicals are persistent, bioaccumulative, and toxic compounds that are widely tributed in the environment. Developing efficient biodegradation strategies to decompose the fluorochemicals via breaking the inert C-F bonds presents a holistic challenge. As a promising biodegradation enzyme candidate, fluoroacetate dehalogenase (FAcD) has been reported as the only non-metallic enzyme to catalyze the cleavage of the strong C-F bond. Here, we systematically investigated the catalytic actions of FAcD toward its natural substrate fluoroacetate using molecular dynamics simulations and quantum mechanism/molecular mechanism calculations. We propose that the enzymatic transformation involves four elementary steps, (I) C-F bond activation, (II) nucleophilic attack, (III) C-O bond cleavage, and (IV) proton transfer. Our results show that nucleophilic attack is the rate-determining step. However, for difluoroacetate and trifluoroacetate, C-F bond activation, instead of nucleophilic attack, becomes the rate-determining step. We show that FAcD, originally recognized as α-fluorocarboxylic acid degradation enzyme, can catalyze the defluorination of difluoroacetate to glyoxylate, which is captured by our high-resolution mass spectrometry experiments. In addition, we employed amino acid electrostatic analysis method to screen potential mutation hotspots for tuning FAcD's electrostatic environment to favor substrate conversion. The comprehensive understanding of catalytic mechanism will inform a rational enzyme engineering strategy to degrade fluorochemicals for benefits of environmental sustainability.

Aerobic degradation of 4-fluoroaniline and 2,4-difluoroaniline: performance and microbial community in response to the inocula

In this study, a distinct inoculum was investigated as an isolated variable within sequencing batch reactors via a comparison of the 4-fluoroaniline (4-FA) or 2,4-difluoroaniline (2,4-DFA) removal amounts. The inocula were derived from a treatment plant for treating pharmaceutical wastewater plus a small amount of municipal sewage (PMS), a treatment plant for treating fluoridated hydrocarbon wastewater (FHS), and a treatment plant for treating the comprehensive wastewater in an industrial park (CIS). There were slight differences among the degradation patterns of the 4-FA for the three inocula, whether during the enrichment period or the high concentration shock period. In contrast, it was observed that the degradation efficiency of 2,4-DFA initially varied with the inocula. The FHS-derived inoculum was determined to be optimal, exhibiting the earliest degradation reaction only after an acclimation of 7 days had the highest degradation rate constant of 0.519 h^-1, and had the fastest recovery time of three weeks after high concentration shock. Additionally, compared with the PMS-derived inoculum, the CIS-derived inoculum exhibited an earlier degradation reaction within three weeks, and a higher microbial diversity, but a lower shock resistance and degradation rate constant of 0.257 h^-1. High-throughput sequencing demonstrated that each final consortium was different in composition, and the microbial consortia developed well on the inoculum and substrate. In comparison of the similarity among the three 2,4-DFA enrichment cultures, the higher similarity (63.9-70.0%) among three final consortia enriching with 4-FA was observed. The results indicated that the inoculum played an important role in the degradation of FAs and the microbial bacterial communities of final consortia, and the effect extent might well depend on the fluorinated level of FAs.

Current Status of and Future Perspectives in Bacterial Degradation of Benzo[a]pyrene

Benzo[a]pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important strategy for its removal from the environment. Extensive studies have been carried out on the isolation and characterisation of microorganisms that can actively degrade low-molecular-weight PAHs (LMW-PAHs), and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high chemical stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of "omics" approaches.

Pseudomonas sp. Strain 273 Degrades Fluorinated Alkanes

Fluorinated organic compounds have emerged as environmental constituents of concern. We demonstrate that the alkane degrader Pseudomonas sp. strain 273 utilizes terminally monofluorinated C₇-C₁₀ alkanes and 1,10-difluorodecane (DFD) as the sole carbon and energy sources in the presence of oxygen. Strain 273 degraded 1-fluorodecane (FD) (5.97 ± 0.22 mM, nominal) and DFD (5.62 ± 0.13 mM, nominal) within 7 days of incubation, and 92.7 ± 3.8 and 90.1 ± 1.9% of the theoretical maximum amounts of fluorine were recovered as inorganic fluoride, respectively. With n-decane, strain 273 attained (3.24 ± 0.14) × 10⁷ cells per μmol of carbon consumed, while lower biomass yields of (2.48 ± 0.15) × 10⁷ and (1.62 ± 0.23) × 10⁷ cells were measured with FD or DFD as electron donors, respectively. The organism coupled decanol and decanoate oxidation to denitrification, but the utilization of (fluoro)alkanes was strictly oxygen-dependent, presumably because the initial attack on the terminal carbon requires oxygen. Fluorohexanoate was detected as an intermediate in cultures grown with FD or DFD, suggesting that the initial attack on the fluoroalkanes can occur on the terminal methyl or fluoromethyl groups. The findings indicate that specialized bacteria such as Pseudomonas sp. strain 273 can break carbon-fluorine bonds most likely with oxygenolytic enzyme systems and that terminally monofluorinated alkanes are susceptible to microbial degradation. The findings have implications for the fate of components associated with aqueous film-forming foam (AFFF) mixtures.

Fabrication of covalent organic frameworks and its selective extraction of fluoronitrobenzenes from environmental samples

In this study, porous covalent organic frameworks (COFs, named as COFs-SWMU) were synthesized for the first time via a facile approach by using 4,4',4''-methylidynetri-anilin and 2,5-dihydroxy-1,4-benzenedicarboxaldehyde as precursors under ambient temperature. The COFs-SWMU were characterized by scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffraction and X-ray photoelectron spectroscopy, thermogravimetric analysis, etc. The COFs-SWMU exhibited a relatively high specific surface area and desirable thermal stability. The adsorption performance of COFs-SWMU towards fluoronitrobenzenes (FNBs, including 1-fluoro-2-nitrobenzene, 1-fluoro-3-nitrobenzene, 1-fluoro-4-nitrobenzene, 2,4-difluoronitrobenzene, 3,4-difluoronitrobenzene, and 3,4-dinitrofluorobenzene) was investigated on the basis of adsorption capacity and partition coefficient (PC). The adsorption kinetics and isotherm of COFs-SWMU for FNBs were studied in detail. Further, a simple, fast and sensitive method which combined COFs-SWMU based extraction with high-performance liquid chromatography-diode array detection, was proposed for the analysis of FNBs in environmental samples. Desirable linearity (R²>0.9998) in the range of 0.1-100 μg•mL^-1, low limits of detection (LODs; 0.1‒0.15 μg•mL^‒1), low limits of quantitation (LOQs; 0.28‒0.40 μg•mL^‒1), and desirable precision (RSDs, 0.24-2.83% for intraday and 1.13-6.92% for interday) are obtained. Finally, the COFs-SWMU were applied to the effective extraction of FNBs from environmental samples, and desirable recovery results were obtained.

The ever-expanding limits of enzyme catalysis and biodegradation: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds

Biodegradation is simply the metabolism of anthropogenic, or otherwise unwanted, chemicals in our environment, typically by microorganisms. The metabolism of compounds commonly found in living things is limited to several thousand metabolites whereas ∼100 million chemical substances have been devised by chemical synthesis, and ∼100 000 are used commercially. Since most of those compounds are not natively found in living things, and some are toxic or carcinogenic, the question arises as to whether there is some organism somewhere with the enzymes that can biodegrade them. Repeatedly, anthropogenic chemicals have been denoted 'non-biodegradable,' only to find they are reactive with one or more enzyme(s). Enzyme reactivity has been organized into categories of functional group transformations. The discovery of new functional group transformations has continually expanded our knowledge of enzymes and biodegradation. This expansion of new-chemical biodegradation is driven by the evolution and spread of newly evolved enzymes. This review describes the biodegradation of widespread commercial chemicals with a focus on four classes: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds. Polyaromatic hydrocarbons include some of the most carcinogenic compounds known. Polychlorinated compounds include polychlorinated biphenyls (PCBs) and many pesticides of the twentieth century. Polyfluorinated compounds are a major focus of bioremediation efforts today. Polymers are clogging landfills, killing aquatic species in the oceans and increasingly found in our bodies. All of these classes of compounds, each thought at one time to be non-biodegradable, have been shown to react with natural enzymes. The known limits of enzyme catalysis, and hence biodegradation, are continuing to expand.

Carbon-fluorine bond cleavage mediated by metalloenzymes

Fluorochemicals are a widely distributed class of compounds and have been utilized across a wide range of industries for decades. Given the environmental toxicity and adverse health threats of some fluorochemicals, the development of new methods for their decomposition is significant to public health. However, the carbon-fluorine (C-F) bond is among the most chemically robust bonds; consequently, the degradation of fluorinated hydrocarbons is exceptionally difficult. Here, metalloenzymes that catalyze the cleavage of this chemically challenging bond are reviewed. These enzymes include histidine-ligated heme-dependent dehaloperoxidase and tyrosine hydroxylase, thiolate-ligated heme-dependent cytochrome P450, and four nonheme oxygenases, namely, tetrahydrobiopterin-dependent aromatic amino acid hydroxylase, 2-oxoglutarate-dependent hydroxylase, Rieske dioxygenase, and thiol dioxygenase. While much of the literature regarding the aforementioned enzymes highlights their ability to catalyze C-H bond activation and functionalization, in many cases, the C-F bond cleavage has been shown to occur on fluorinated substrates. A copper-dependent laccase-mediated system representing an unnatural radical defluorination approach is also described. Detailed discussions on the structure-function relationships and catalytic mechanisms provide insights into biocatalytic defluorination, which may inspire drug design considerations and environmental remediation of halogenated contaminants.

Microbial degradation of two highly persistent fluorinated fungicides - epoxiconazole and fludioxonil

Biodegradation of two highly persistent fluorinated fungicides, epoxiconazole (EPO) and fludioxonil (FLU), by microbial consortia enriched from estuarine sediment and agricultural soil is reported. After an enrichment period of 6 months, four microbial consortia were able to completely remove and defluorinate the fungicides in co-metabolic conditions. Defluorination was biologically mediated and results suggest it is not a primary catabolic step, as fungicide removal was always faster than its defluorination. Three of the four enriched consortia had similar biodegradation performances in the absence of a co-substrate. Biodegradation kinetics revealed that microbial degradation followed a first-order kinetics, with cultures being capable of biodegrading concentrations up to 10 mg L^-1 of EPO or FLU, in a maximum of 21 days. Estimated half-life values for these compounds were significantly lower than those reported in literature, highlighting the unique metabolic performance of the obtained consortia. Analysis of their microbial composition revealed that they integrate several bacterial species belonging to the Proteobacteria phylum, with the most common genera being Pseudomonas, Ochrobactrum and Comamonas. This is the first study providing clear evidence on the biodegradation of EPO and FLU, opening doors for the design of bioremediation technologies for the recovery of ecosystems polluted with such recalcitrant compounds.

Isolation and Characterization of a Novel Bacterium from the Marine Environment for Trichloroacetic Acid Bioremediation

Halogenated compounds are an important class of environmental pollutants that are widely used in industrial chemicals such as solvents, herbicides, and pesticides. Many studies have been carried out to explore the biodegradation of these chemicals. Trichloroacetic acid (TCA) is one of the main halogenated compounds that are carcinogenic to humans and animals. The bacterium was isolated from the northern coastline of Johor Strait. In this study, the ability of strain MH2 to biodegrade TCA was evaluated by a growth experiment and dehalogenase enzyme assay. The growth profile of the isolated strain was examined. The doubling time for L. boronitolerans MH2 was found to be 32 h. The release of chloride ion in the degradation process was measured at 0.33 × 10−3 ± 0.03 mol∙L−1 after 96 h when the growth curve had reached its maximum within the late bacterial exponential phase. The results showed that the strain had a promising ability to degrade TCA by producing dehalogenase enzyme when cell-free extracts were prepared from growth on TCA as the sole carbon source with enzyme-specific activity, 1.1 ± 0.05 µmolCl−min−1∙mg−1 protein. Furthermore, the morphological, and biochemical aspects of the isolated bacterium were studied to identify and characterize the strain. The morphological observation of the isolated bacterium was seen to be a rod-shaped, Gram-positive, motile, heterotrophic, and spore-forming bacterium. The amplification of the 16S rRNA and gene analysis results indicated that the isolated bacterium had 98% similarity to Lysinibacillus boronitolerans. The morphological and biochemical tests supported the 16S rRNA gene amplification. To the best of the authors’ knowledge, this is the first reported case of this genus of bacteria to degrade this type of halogenated compound.

Degradation of 3-fluoroanilne by Rhizobium sp. JF-3

The interest of fluoroanilines in the environment is due to their extensive applications in industry and their low natural biodegradability. A pure bacterial strain capable of degrading 3-fluoroaniline (3-FA) as the sole source of carbon and energy was isolated from a sequencing batch reactor operating for the treatment of 3-FA. The strain (designated as JF-3) was identified by 16S rRNA gene analysis as a member of the genus Rhizobium. When grown in 3-FA medium at concentrations of 100-700 mg/L, strain JF-3 almost completely removed 3-FA within 72 h. However, the obvious cell growth inhibition was observed in cultures treated with 3-FA concentrations greater than 500 mg/L. The degradation kinetics of 3-FA were consistent with Haldane's model with the maximum degradation rate as 67.66 mg/(g dry cell h). The growth kinetics of strain JF-3 followed Andrew's model with the maximum growth rate as 30.87 h^-1. Also, strain JF-3 was able to degrade 4-fluoroaniline, aniline, and catechol, but hardly grew on 2-fluoroaniline, 2,4-dfluoroaniline, 2,3,4-trifluoroaniline, 3-fluorocatechol, and 4-fluorocatechol. Additionally, it was able to grow over a wide pH range (pH 6-10), and also showed tolerance to salinity with lower than 1.0%. This result, in combination with the enzyme assays and analysis of metabolite intermediates, indicated an unconventional pathway for 3-fluoroaniline metabolism that involved conversion to 3-aminophenol and resorcinol by monooxygenase, and which was subsequently metabolized via the ortho-cleavage pathway. To our knowledge, this is the first report on the utilization of 3-FA as a growth substrate by Rhizobium sp.

Co-metabolic degradation of the antibiotic ciprofloxacin by the enriched bacterial consortium XG and its bacterial community composition

Ciprofloxacin is a broad spectral and highly refractory antibiotic. It is an emerging pollutant. This study aimed to utilise co-metabolism as a means to degrade ciprofloxacin by a bacterial consortium. The stable bacterial consortium XG capable of efficiently degrading ciprofloxacin was successfully established through successive acclimation of indigenous microorganisms. The consortium XG was primarily consisted of Achromobacter, Bacillus, Lactococcus, Ochrobactrum, and Enterococcus as well as at least other five minor genera. A novel strain YJ17 with CIP-degrading ability was isolated from the consortium and identified as Ochrobactrum sp. The consortium XG utilised amino acids, carbohydrates, and carboxylic acids at a rate approximately 16.6-243-fold greater than the other carbon substrates, but only slow utilisation of ciprofloxacin as a sole carbon source. Ciprofloxacin can be co-metabolized along with many carbon sources, attaining degradation rates up to 63%. Glycyl-l-glutamic acid, d-cellobiose, and itaconic acid are among the substrates most favourable for co-metabolism. The metabolites of ciprofloxacin were identified by LC-QTOF-MS. Co-metabolic degradation of ciprofloxacin by consortium XG led to the removal of essential functional groups from parent compound, thus resulting in formation of metabolites with less bioactive potency. Finally, a possible biochemical pathway for the degradation of ciprofloxacin was proposed. Consortium XG possesses high potential for bioremediation of ciprofloxacin-contaminated environments in the presence of a co-substrate.

Biodegradation of enrofloxacin by microbial consortia obtained from rhizosediments of two estuarine plants

This study aimed to investigate the potential of microbial communities from the rhizosediment of two plants - Phragmites australis and Juncus maritimus - occurring in an estuarine area subjected to a high anthropogenic impact, to biodegrade ENR, a commonly used veterinary antibiotic. An enrichment process with 1 mgL^-1 of ENR was conducted during ca. 9 months, using acetate as a co-substrate. After this, the enriched microbial consortia were challenged with higher ENR concentrations of 2 and 3 mgL^-1. Microbial cultures enriched with 1 mgL^-1 of ENR were capable of biodegrading this antibiotic, though not completely. By the end of the enrichment phase, microbial cultures were defluorinating an average of 50% of the ENR supplemented. Higher ENR concentrations led to lower biodegradation performances, suggesting a possible toxic/inhibitory effect in the microbial cultures. Phylogenetic identification of the microorganisms isolated from microbial cultures enriched with ENR revealed a high taxonomical diversity, with microorganisms belonging mainly to Proteobacteria and Bacteroidetes phyla. Assemblage of the obtained isolated strains (according to the enriched cultures from which they were isolated) revealed that the resulting consortia were also capable of degrading ENR, indicating that the main microbial players in the biodegradation of this antibiotic were isolated. These consortia also showed to be more robust to degrade higher concentrations of ENR than the corresponding enriched cultures. This study shows that microorganisms derived from rhizosediments of the selected plants, exhibit capacity to biodegrade ENR, though not completely for the concentrations tested, and may be further explored for the development of bioremediation strategies for the treatment of this antibiotic.

In situ decay of polyfluorinated benzoic acids under anaerobic conditions

Polyfluorinated benzoic acids (PBAs) can be used as non-reactive tracers to characterize reactive mass transport mechanisms in groundwater. The use of PBAs as non-reactive tracers assumes that their reactivities are negligible. If this assumption is not valid, PBAs may not be appropriate to use as non-reactive tracers. In this study, the reactivity of two PBAs, 2,6-difluorobenzoic acid (2,6-DFBA) and pentafluorobenzoic acid (PFBA), was tested in situ. A series of two single-well push-pull tests were conducted in two hydrogeologically similar, yet spatially distinct, groundwater monitoring wells. Bromide, 2,6-DFBA, and PFBA were added to the injection fluid and periodically measured in the extraction fluid along with chloride, nitrate, sulfate, and fluoride. Linear regression of the dilution-adjusted breakthrough curves of both PBAs indicated zero-order decay accompanied by nitrate and subsequent sulfate removal. The dilution-adjusted breakthrough curves of chloride, a non-reactive halide similar to bromide, showed no evidence of reactivity. These results strongly suggested that biodegradation of both PBAs occurred under anaerobic conditions. The results of this study implied that PBAs may not be appropriate to use as non-reactive tracers in certain hydrogeologic settings, presumably those where they can serve as carbon and/or electron donors to stimulate microbial activity. Future studies would benefit from using ring-¹⁴C-labeled PBAs to determine the fate of carbon combined with microbial analyses to characterize the PBA-degrading members of the microbial community.

Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons under anaerobic conditions: Overview of studies, proposed pathways and future perspectives

The biodegradation of low- and high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) (LWM-PAHs and HMW-PAHs, respectively) has been studied extensively under aerobic conditions. Molecular O₂ plays 2 critical roles in this biodegradation process. O₂ activates the aromatic rings through hydroxylation prior to ring opening and serves as a terminal electron acceptor (TEA). However, several microorganisms have devised ways of activating aromatic rings, leading to ring opening (and thus biodegradation) when TEAs other than O₂ are used (under anoxic conditions). These microorganisms belong to the sulfate-, nitrate-, and metal-ion-reducing bacteria and the methanogens. Although the anaerobic biodegradation of monocyclic aromatic hydrocarbons and LWM-PAH naphthalene have been studied, little information is available about the biodegradation of HMW-PAHs. This manuscript reviews studies of the anaerobic biodegradation of HMW-PAHs and identifies gaps that limit both our understanding and the efficiency of this biodegradation process. Strategies that can be employed to overcome these limitations are also discussed.

Biodegradation of pentafluorosulfanyl-substituted aminophenol in Pseudomonas spp

The pentafluorosulfanyl (SF₅-) substituent conveys properties that are beneficial to drugs and agrochemicals. As synthetic methodologies improve the number of compounds containing this group will expand and these chemicals may be viewed as emerging pollutants. As many microorganisms can degrade aromatic xenobiotics, we investigated the catabolism of SF₅-substituted aminophenols by bacteria and found that some Pseudomonas spp. can utilise these compounds as sole carbon and energy sources. GC-MS analysis of the culture supernatants from cultures grown in 5-(pentafluorosulfanyl) 2-aminophenol demonstrated the presence of the N-acetylated derivative of the starting substrate and 4-(pentafluorosulfanyl)catechol. Biotransformation experiments with re-suspended cells were also conducted and fluorine-19 NMR analyses of the organic extract and aqueous fraction from suspended cell experiments revealed new resonances of SF₅-substituted intermediates. Supplementation of suspended cell cultures with yeast extract dramatically improved the degradation of the substrate as well as the release of fluoride ion. 4-(Pentafluorosulfanyl)catechol was shown to be a shunt metabolite and toxic to some of the bacteria. This is the first study to demonstrate that microorganisms can biodegrade SF₅-substituted aromatic compounds releasing fluoride ion, and biotransform them generating a toxic metabolite.

Promiscuous Defluorinating Enoyl-CoA Hydratases/Hydrolases Allow for Complete Anaerobic Degradation of 2-Fluorobenzoate

Biodegradation of the environmentally hazardous fluoroaromatics has mainly been associated with oxygenase-dependent defluorination reactions. Only very recently a novel mode of oxygen-independent defluorination was identified for the complete degradation of para-substituted fluoroaromatics in the denitrifying Thauera aromatica: a promiscuous class I benzoyl-coenzyme A (BzCoA) reductase (BCR) catalyzed the ATP-dependent defluorination of 4-F-BzCoA to BzCoA. Here, we studied the unknown enzymatic defluorination during the complete degradation of 2-F-benzoate to CO₂ and HF. We demonstrate that after activation of 2-F-benzoate by a promiscuous AMP-forming benzoate-CoA ligase, the 2-F-BzCoA formed is subsequently dearomatized by BCR to a mixture of 2-F- and 6-F-cyclohexa-1,5-diene-1-carboxyl-CoA (2-F-/6-F-1,5-dienoyl-CoA). This finding indicates that BCR is not involved in C–F-bond cleavage during growth with 2-F-benzoate. Instead, we identified defluorination of the two isomers by enoyl-CoA hydratases/hydrolases involved in down-stream reactions of the BzCoA degradation pathway. (i) The 1,5-dienoyl-CoA hydratase hydrated the F-1,5-dienoyl-CoA isomers to a mixture of the stable 2-F-6-OH-1-enoyl-CoA and the unstable α-fluorohydrin 6-F-6-OH-1-enoyl-CoA; the latter spontaneously decomposed to HF and 6-oxo-cyclohex-1-enoyl-CoA (6-oxo-1-enoyl-CoA), a common intermediate of the BzCoA degradation pathway. (ii) 6-Oxo-1-enoyl-CoA hydrolase/hydratase catalyzed the defluorination of 2-F-6-OH-1-enoyl-CoA to 2-oxo-6-OH-1-enoyl-CoA and HF again via water addition to an F-enoyl-CoA functionality. Based on these in vitro results, we demonstrate a previously overseen capability of 2-F-benzoate degradation for many but not all tested facultatively and obligately anaerobic bacteria that degrade aromatic compounds via the BzCoA degradation pathway. In conclusion, the newly identified enzymatic defluorination by enoyl-CoA hydratases via α-fluorohydrin formation represents an abundant, physiologically relevant principle of enzymatic defluorination.

Phenol Is the Initial Product Formed during Growth and Degradation of Bromobenzene by Tropical Marine Yeast, Yarrowia lipolytica NCIM 3589 via an Early Dehalogenation Step

Bromobenzene (BrB), a hydrophobic, recalcitrant organic compound, is listed by the environmental protection agencies as an environmental and marine pollutant having hepatotoxic, mutagenic, teratogenic, and carcinogenic effects. The tropical marine yeast Yarrowia lipolytica 3589 was seen to grow aerobically on BrB and displayed a maximum growth rate (μmax) of 0.04 h-1. Furthermore, we also observed an increase in cell size and sedimentation velocity for the cells grown on BrB as compared to the glucose grown cells. The cells attached to the hydrophobic bromobenzene droplets through its hydrophobic and acid-base interactions. The BrB (0.5%, 47.6 mM) was utilized by the cells with the release of a corresponding amount of bromide (12.87 mM) and yielded a cell mass of 1.86 g/L after showing 34% degradation in 96 h. Maximum dehalogenase activity of 16.16 U/mL was seen in the cell free supernatant after 24 h of growth. Identification of metabolites formed as a result of BrB degradation, namely, phenol, catechol, cis, cis muconic acid, and carbon dioxide were determined by LC-MS and GC-MS. The initial attack on bromobenzene by Y. lipolytica cells lead to the transient accumulation of phenol as an early intermediate which is being reported for the first time. Degradation of phenol led to catechol which was degraded by the ortho- cleavage pathway forming cis, cis muconic acid and then to Krebs cycle intermediates eventually leading to CO2 production. The study shows that dehalogenation via an extracellular dehalogenase occurs prior to ring cleavage with phenol as the preliminary degradative compound being produced. The yeast was also able to grow on the degradative products, i.e., phenol and catechol, to varying degrees which would be of potential relevance in the degradation and remediation of xenobiotic environmental bromoaromatic pollutants such as bromobenzene.

Biodegradation of the veterinary antibiotics enrofloxacin and ceftiofur and associated microbial community dynamics

Fluoroquinolones and cephalosporins are two classes of veterinary antibiotics arising as pollutants of emerging concern. In this work, the microbial degradation of two representative antibiotics of both these classes, enrofloxacin (ENR) and ceftiofur (CEF), is reported. Biodegradation of the target antibiotics was investigated by supplementing the culture medium with ENR and CEF, individually and in mixture. Microbial inocula were obtained from rhizosphere sediments of plants derived from experimental constructed wetlands designed for the treatment of livestock wastewaters contaminated with trace amounts of these antibiotics. Selected microbial inocula were acclimated during a period of 5months, where the antibiotics were supplemented every three weeks at the concentration of 1mgL^-1, using acetate as a co-substrate. After this period, the acclimated consortia were investigated for their capacity to biodegrade 2 and 3mgL^-1 of ENR and CEF. Complete removal of CEF from the inoculated culture medium was always observed within 21days, independently of its concentration or the concomitant presence of ENR. Biodegradation of ENR decreased with the increase in its concentration in the culture medium, with defluorination percentages decreasing from ca. 65 to 4%. Ciprofloxacin and norfloxacin were detected as biodegradation intermediates of ENR in the microbial cultures supplemented with this antibiotic, indicating that defluorination of at least part of ENR in these cultures is not an immediate catabolic step. Abiotic mechanisms showed high influence in the removal of CEF, affecting less ENR degradation. The acclimation process with the target antibiotics led to significant shifts in the structure and diversity of the microbial communities, predominantly selecting microorganisms belonging to the phyla Proteobacteria (e.g. Achromobacter, Variovorax and Stenotrophomonas genera) and Bacteroidetes (e.g. Dysgonomonas, Flavobacterium and Chryseobacterium genera). The results presented in this study indicate that biodegradation can be an important mechanism for the environmental removal of the tested compounds.