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

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.

Evaluation of ecological impacts with ferrous iron addition in constructed wetland under perfluorooctanoic acid stress

In this study, ferrous ion (Fe(II)) had the potential to promote ecological functions in constructed wetlands (CWs) under perfluorooctanoic acid (PFOA) stress. Concretely, Fe(II) at 30 mg/L and 20-30 mg/L even led to 11.37% increase of urease and 93.15-243.61% increase of nitrite oxidoreductase respectively compared to the control. Fe(II) promotion was also observed on Nitrosomonas, Nitrospira, Azospira, and Zoogloea by 1.00-6.50 folds, which might result from higher expression of nitrogen fixation and nitrite redox genes. These findings could be explanation for increase of ammonium removal by 7.47-8.75% with Fe(II) addition, and reduction of nitrate accumulation with 30 mg/L Fe(II). Meanwhile, both Fe(II) stimulation on PAOs like Dechloromonas, Rhodococcus, Mesorhizobium, and Methylobacterium by 1.58-2.00 folds, and improvement on chemical phosphorus removal contributed to higher total phosphorus removal efficiency under high-level PFOA exposure. Moreover, Fe(II) raised chlorophyll content and reduced the oxidative damage brought by PFOA, especially at lower dosage. Nevertheless, combination of Fe(II) and high-level PFOA caused inhibition on microbial alpha diversity, which could result in decline of PFOA removal (by 4.29-12.83%). Besides, decrease of genes related to nitrate reduction demonstrated that enhancement on denitrification was due to nitrite reduction to N2 pathways rather than the first step of denitrifying process.

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.

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.

Direct fluoride monitoring using a fluorogenic RNA-based biosensor

Fluorinated compounds, whether naturally occurring or from anthropogenic origin, have been extensively exploited in the last century. Degradation of these compounds by physical or biochemical processes is expected to result in the release of fluoride. Several fluoride detection mechanisms have been previously described. However, most of these methods are not compatible with high- and ultrahigh-throughput screening technologies, lack the ability to real-time monitor the increase of fluoride concentration in solution, or rely on costly reagents (such as cell-free expression systems). Our group recently developed "FluorMango" as the first completely RNA-based and direct fluoride-specific fluorogenic biosensor. To do so, we merged and engineered the Mango-III light-up RNA aptamer and the fluoride-specific aptamer derived from a riboswitch, crcB. In this chapter, we explain how this RNA-based biosensor can be produced in large scale before providing examples of how it can be used to quantitatively detect (end-point measurement) or monitor in real-time fluoride release in complex biological systems by translating it into measurable fluorescent signal.

Microwell fluoride assay screening for enzymatic defluorination

There is intense interest in removing fluorinated compounds from the environment, environments are most efficiently remediated by microbial enzymes, and defluorinating enzymes are readily monitored by fluoride determination. Fluorine is the most electronegative element. Consequently, all mechanisms of enzymatic C-F bond cleavage produce fluoride anion, F-. Therefore, methods for the determination of fluoride are critical for C-F enzymology and apply to any fluorinated organic compounds, including PFAS, or per- and polyfluorinated alkyl substances. The biodegradation of most PFAS chemicals is rare or unknown. Accordingly, identifying new enzymes, or re-engineering the known defluorinases, will require rapid and sensitive methods for measuring fluoride in aqueous media. Most studies currently use ion chromatography or fluoride specific electrodes which are relatively sensitive but low throughput. The methods here describe refashioning a drinking water test to efficiently determine fluoride in enzyme and cell culture reaction mixtures. The method is based on lanthanum alizarin complexone binding of fluoride. Reworking the method to a microtiter well plate format allows detection of as little as 4 nmol of fluoride in 200 μL of assay buffer. The method is amenable to color imaging, spectrophotometric plate reading and automated liquid handling to expedite assays with thousands of enzymes and/or substrates for discovering and improving enzymatic defluorination.

FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride

Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid (RNA)-based biosensor specific for fluoride is introduced. The molecule consists of two RNA aptamer modules, a fluoride-specific sensor derived from the crcB riboswitch which changes its structure upon interaction with the target ion, and the light-up RNA Mango-III that emits fluorescence when complexed with a fluorogen. The two modules are connected by an optimized communication module identified by ultrahigh-throughput screening, which results in extremely high fluorescence of FluorMango in the presence of fluoride, and background fluorescence in its absence. The value and efficiency of this biosensor by direct monitoring of defluorinase activity in living bacterial cells is illustrated, and the use of this new tool in future screening campaigns aiming at discovering new defluorinase activities is discussed.

The fate and behavior of perfluorooctanoic acid (PFOA) in constructed wetlands: Insights into potential removal and transformation pathway

Although constructed wetland (CW) technology is widely used to eliminate emerging organic pollutants, the removal pathway of perfluoroalkyl and polyfluoroalkyl substances (PFASs) in CW system have not been fully understood yet. This study aims to deeply probe into the fate and behavior of perfluorooctanoic acid (PFOA) in CW system. Findings indicated that the removal efficiency of PFOA by CW system was 49.69-73.63 % with initial concentrations at 100-1000 μg/L. Substrate was the main "sink" of PFOA into the CWs (46.22-50.83 %), and the plant uptake (1.99-2.48 %) accounted for a small proportion. Transformation products in the effluent of CW systems included a series of short-chain perfluorinated carboxylic acids (PFCAs), hydrogen-containing perfluoroalkanes and other organic fluorides. Activated pathways of xenobiotics biodegradation suggested that enzyme-mediated biochemical reactions might be responsible for the PFOA transformation. The transformation pathway included enzymatic decarboxylation, hydroxylation, hydrolysis, dehydrogenation and dehalogenation, as well as non-enzymatic reactions. These discoveries provide new insights into the in-depth understanding environmental behavior of PFOA in ecosystem and lay the foundation for further ecological remediation.

Fluoro-recognition: New in vivo fluorescent assay for toluene dioxygenase probing induction by and metabolism of polyfluorinated compounds

The present study examined the regulatory and metabolic response of the aromatic degrader Pseudomonas putida F1 and its tod operon, controlling toluene degradation, to fluorinated aromatic and aliphatic compounds. The tod operon is upregulated by inducer binding to the TodS sensing domain of a two-component regulator. The induced enzymes include toluene dioxygenase that initiates catabolic assimilation of benzenoid hydrocarbons. Toluene dioxygenase was shown to oxidize 6-fluoroindole to a meta-stable fluorescent product, 6-fluoroindoxyl. The fluorescent output allowed monitoring relative levels of tod operon induction in whole cells using microtiter well plates. Mono- and polyfluorinated aromatic compounds were shown to induce toluene dioxygenase, in some cases to a greater extent than compounds serving as growth substrates. Compounds that are oxidized by toluene dioxygenase and undergoing defluorination were shown to induce their own metabolism. 1,2,4-Trifluorobenzene caused significant induction and computational modelling indicated productive binding to the TodS sensor domain of the TodST regulator. Toluene dioxygenase also showed preferential binding of 1,2,4-trifluorobenzene such that defluorination was favoured. Fluorinated aliphatic compounds were shown to induce toluene dioxygenase. An aliphatic ether with seven fluorine atoms, 1,1,1,2-tetrafluoro-2-trifluoromethoxy-4-iodobutane (TTIB), was an excellent inducer of toluene dioxygenase activity and shown to undergo transformation in cultures of P. putida F1.

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.