Cascading Pathways Regulate the Biotransformations of Eight Fluorotelomer Acids Performed by Wastewater Microbial Communities

Polyfluoroalkyl substances can be biotransformed in natural or engineered environmental systems to generate perfluoroalkyl acids (PFAAs). Data are needed to support the development of biotransformation pathway prediction tools that simulate biotransformation pathways of polyfluoroalkyl substances in specific environmental systems. The goal of this study was to experimentally evaluate the biotransformation of eight structurally similar fluorotelomer acids to identify biotransformation products and propose biotransformation pathways. We selected six fluorotelomer carboxylic acids and two fluorotelomer sulfonic acids and employed a biotransformation test system in which batch reactors are seeded with aerobic wastewater microbial communities. We identified 111 biotransformation products among the eight parent compounds, 58 of which represent unique chemical structures. Many of the biotransformation products are the result of apparent dehydrogenation, monohydroxylation, alcohol oxidation, decarboxylation, HF-elimination, and reductive defluorination biotransformations. We use these data to propose cascading biotransformation pathways that are regulated by integrated and synergistic α-oxidation-like, β-oxidation-like, and defluorination biotransformations that result in the formation of terminal PFAAs of varying chain length. Our data provide a comprehensive view on the aerobic biotransformation of fluorotelomer acids and our results can be used to support the ongoing development of biotransformation pathway prediction tools.

Nexus of Soil Microbiomes, Genes, Classes of Carbon Substrates, and Biotransformation of Fluorotelomer-Based Precursors

The unpredictable biodegradation of fluorotelomer (FT)-based per- and polyfluoroalkyl substances (PFAS) causes complicated risk management of PFAS-impacted sites. Here, we have successfully used redundancy analysis to link FT-based precursor biodegradation to key microbes and genes of soil microbiomes shaped by different classes of carbon sources: alcohols (C2-C4), alkanes (C6 and C8), an aromatic compound (phenol), or a hydrocarbon surfactant (cocamidopropyl betaine [CPB]). All the enrichments defluorinated fluorotelomer alcohols (n:2 FtOH; n = 4, 6, 8) effectively and grew on 6:2 fluorotelomer sulfonate (6:2 FtS) as a sulfur source. The butanol-enriched culture showed the highest defluorination extent for FtOHs and 6:2 FtS due to the high microbial diversity and the abundance of desulfonating and defluorinating genes. The CPB-enriched culture accumulated more 5:3 fluorotelomer carboxylic acid, suggesting unique roles of Variovorax and Pseudomonas. Enhanced 6:2 FtOH defluorination was observed due to a synergism between two enrichments with different carbon source classes except for those with phenol- and CPB-enriched cultures. While the 6:2 fluorotelomer sulfonamidoalkyl betaine was not degraded, trace levels of 6:2 fluorotelomer sulfonamidoalkyl amines were detected. The identified species and genes involved in desulfonation, defluorination, and carbon source metabolism are promising biomarkers for assessing precursor degradation at the sites.

Enzyme Catalyzed Formation of CoA Adducts of Fluorinated Hexanoic Acid Analogues using a Long-Chain acyl-CoA Synthetase from Gordonia sp. Strain NB4-1Y

Per and polyfluoroalkyl substances (PFAS) are a large family of anthropogenic fluorinated chemicals of increasing environmental concern. Over recent years, numerous microbial communities have been found to be capable of metabolizing some polyfluoroalkyl substances, generating a range of low-molecular-weight PFAS metabolites. One proposed pathway for the microbial breakdown of fluorinated carboxylates includes β-oxidation, this pathway is initiated by the formation of a CoA adduct. However, until recently no PFAS-CoA adducts had been reported. In a previous study, we were able to use a bacterial medium-chain acyl-CoA synthetase (mACS) to form CoA adducts of fluorinated adducts of propanoic acid and pentanoic acid but were not able to detect any products of fluorinated hexanoic acid analogues. Herein, we expressed and purified a long-chain acyl-CoA synthetase (lACS) and a A461K variant of mACS from the soil bacterium Gordonia sp. strain NB4-1Y and performed an analysis of substrate scope and enzyme kinetics using fluorinated and nonfluorinated carboxylates. We determined that lACS can catalyze the formation of CoA adducts of 1:5 fluorotelomer carboxylic acid (FTCA), 2:4 FTCA and 3:3 FTCA, albeit with generally low turnover rates (<0.02 s-1) compared with the nonfluorinated hexanoic acid (5.39 s-1). In addition, the A461K variant was found to have an 8-fold increase in selectivity toward hexanoic acid compared with wild-type mACS, suggesting that Ala-461 has a mechanistic role in selectivity toward substrate chain length. This provides further evidence to validate the proposed activation step involving the formation of CoA adducts in the enzymatic breakdown of PFAS.

Electron bifurcation and fluoride efflux systems implicated in defluorination of perfluorinated unsaturated carboxylic acids by Acetobacterium spp

Enzymatic cleavage of C─F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. The microbial defluorination products were structurally confirmed and showed regiospecificity and stereospecificity, consistent with their formation by enzymatic reactions. A comparison of defluorination activities among several Acetobacterium species indicated that a functional fluoride exporter was required for the detoxification of the released fluoride. Results from both in vivo inhibition tests and in silico enzyme modeling suggested the involvement of enzymes of the flavin-based electron-bifurcating caffeate reduction pathway [caffeoyl-CoA reductase (CarABCDE)] in the reductive defluorination. This is a report on specific microorganisms carrying out enzymatic reductive defluorination of PFAS, which could be linked to electron-bifurcating reductases that are environmentally widespread.

A review of the occurrence and microbial transformation of per- and polyfluoroalkyl substances (PFAS) in aqueous film-forming foam (AFFF)-impacted environments

Aqueous film-forming foams (AFFFs) have been extensively used for extinguishing hydrocarbon-fuel fires at military sites, airports, and fire-training areas. Despite being a significant source of per- and polyfluoroalkyl substances (PFAS), our understanding of PFAS occurrence in AFFF formulations and AFFF-impacted environments is limited, as is the impact of microbial transformation on the environment fate of AFFF-derived PFAS. This literature review compiles PFAS concentrations in electrochemical fluorination (ECF)- and fluorotelomer (FT)-based AFFFs and provides an overview of PFAS occurrence in AFFF-impacted environments. Our analysis reveals that AFFF use is a predominant point source of PFAS contamination, including primary precursors (polyfluoroalkyl substances as AFFF components), secondary precursors (polyfluoroalkyl transformation products of primary precursors), and perfluoroalkyl acids (PFAAs). Moreover, there are discrepancies between PFAS concentration profiles in AFFFs and those measured in AFFF-impacted media. For example, primary precursors constitute 52.6 % and 99.5 % of PFAS mass in ECF- and FT-based AFFFs, respectively, whereas they represent only 0.7 % total mass in AFFF-impacted groundwater. Conversely, secondary precursors, which constitute <1 % of PFAS in AFFFs, represent 4.0-27.8 % of PFAS in AFFF-impacted environments. The observed differences in PFAS levels between AFFFs and environmental samples are likely due to in-situ biotransformation processes. Biotransformation rates and pathways reported for AFFF-derived primary and secondary precursors varied among different classes of precursors, consistent with the PFAS occurrence in AFFF-impacted environments. For example, readily biodegradable primary precursors, N-dimethyl ammonio propyl perfluoroalkane sulfonamide (AmPr-FASA) and n:2 fluorotelomer thioether amido sulfonate (n:2 FtTAoS), were rarely detected in AFFF-impacted environments. In contrast, key secondary precursors, perfluoroalkane sulfonamides (FASAs) and n:2 fluorotelomer sulfonate (n:2 FTS), were widely detected, which was attributed to their resistance to biotransformation. Key knowledge gaps and future research priorities are presented to better understand the occurrence, fate, and transport of AFFF-derived PFAS in the environment and to design more effective remediation strategies.

Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances

Per- and polyfluoroalkyl substances (PFAS) are highly fluorinated synthetic organic compounds that have been used extensively in various industries owing to their unique properties. The PFAS family encompasses diverse classes, with only a fraction being commercially relevant. These substances are found in the environment, including in water sources, soil, and wildlife, leading to human exposure and fueling concerns about potential human health impacts. Although PFAS degradation is challenging, biodegradation offers a promising, eco-friendly solution. Biodegradation has been effective for a variety of organic contaminants but is yet to be successful for PFAS due to a paucity of identified microbial species capable of transforming these compounds. Recent studies have investigated PFAS biotransformation and fluoride release; however, the number of specific microorganisms and enzymes with demonstrable activity with PFAS remains limited. This review discusses enzymes that could be used in PFAS metabolism, including haloacid dehalogenases, reductive dehalogenases, cytochromes P450, alkane and butane monooxygenases, peroxidases, laccases, desulfonases, and the mechanisms of microbial resistance to intracellular fluoride. Finally, we emphasize the potential of enzyme and microbial engineering to advance PFAS degradation strategies and provide insights for future research in this field.

Aerobic biotransformation of 6:2 fluorotelomer sulfonate in soils from two aqueous film-forming foam (AFFF)-impacted sites

Although 6:2 fluorotelomer sulfonate (6:2 FTS) is a common ingredient in aqueous film-forming foam (AFFF) formulations, its environmental fate at AFFF-impacted sites remains poorly understood. This study investigated the biotransformation of 6:2 FTS in microcosms prepared with soils collected from two AFFF-impacted sites; the former Loring Air Force Base (AFB) and Robins AFB. The half-life of 6:2 FTS in Loring soil was 43.3 days; while >60 mol% of initially spiked 6:2 FTS remained in Robins soil microcosms after a 224-day incubation. Differences in initial sulfate concentrations and the depletion of sulfate over the incubation likely contributed to the different 6:2 FTS biotransformation rates between the two soils. At day 224, stable transformation products, i.e., C4C7 perfluoroalkyl carboxylates, were formed with combined molar yields of 13.8 mol% and 1.2 mol% in Loring and Robins soils, respectively. Based on all detected transformation products, the biotransformation pathways of 6:2 FTS in the two soils were proposed. Microbial community analysis suggests that Desulfobacterota microorganisms may promote 6:2 FTS biotransformation via more efficient desulfonation. In addition, species from the genus Sphingomonas, which exhibited higher tolerance to elevated concentrations of 6:2 FTS and its biotransformation products, are likely to have contributed to 6:2 FTS biotransformation. This study demonstrates the potential role of biotransformation processes on the fate of 6:2 FTS at AFFF-impacted sites and highlights the need to characterize site biogeochemical properties for improved assessment of 6:2 FTS biotransformation behavior.

Electron-bifurcation and fluoride efflux systems in Acetobacterium spp. drive defluorination of perfluorinated unsaturated carboxylic acids

Enzymatic cleavage of C-F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. Two critical molecular features in Acetobacterium species enabling reductive defluorination are (i) a functional fluoride efflux transporter (CrcB) and (ii) an electron-bifurcating caffeate reduction pathway (CarABCDE). The fluoride transporter was required for detoxification of released fluoride. Car enzymes were implicated in defluorination by the following evidence: (i) only Acetobacterium spp. with car genes catalyzed defluorination; (ii) caffeate and PFAS competed in vivo ; (iii) models from the X-ray structure of the electron-bifurcating reductase (CarC) positioned the PFAS substrate optimally for reductive defluorination; (iv) products identified by 19 F-NMR and high-resolution mass spectrometry were consistent with the model. Defluorination biomarkers identified here were found in wastewater treatment plant metagenomes on six continents.

Formation of CoA Adducts of Short-Chain Fluorinated Carboxylates Catalyzed by Acyl-CoA Synthetase from Gordonia sp. Strain NB4-1Y

Perfluoroalkyl and polyfluoroalkyl substances (PFAS) make up a group of anthropogenic chemicals with a myriad of applications. However, some PFAS have been shown to negatively impact human health and the environment, leading to increased regulation, with some countries making efforts to phase out their use. PFAS fate in the environment is driven by physical, chemical, and biological processes, with microbial communities in matrices such as soil and sewage sludge being known to generate a range of low-molecular-weight PFAS metabolites. Proposed metabolic intermediates for both mixed and pure microbial cultures include fluorinated carboxylates that may be activated by CoA prior to β-oxidation and defluorination, although thus far, no PFAS-CoA adducts have been reported. Herein, we expressed and purified acyl-CoA synthetase (ACS) from the soil bacterium Gordonia sp. strain NB4-1Y and performed an analysis of substrate scope and enzyme kinetics using fluorinated and nonfluorinated carboxylates. We determined that ACS was able to catalyze the formation of CoA adducts of 3,3,3-trifluoropropionic acid, 5,5,5-trifluoropentanoic acid, 4,5,5-trifluoropent-4-enoic acid, and 4,4,5,5,5-pentafluoropentanoic acid. Kinetic analysis revealed a 90-98% decrease in kcat between nonfluorinated carboxylates and their fluorinated analogues. This provides evidence to validate proposed enzymatic pathways for microbial PFAS metabolism that proceed via an activation step involving the formation of CoA adducts.

A review of microbial degradation of per- and polyfluoroalkyl substances (PFAS): Biotransformation routes and enzymes

Since the 1950s, copious amounts of per- and polyfluoroalkyl substances (PFAS) (dubbed "forever chemicals") have been dumped into the environment, causing heavy contamination of soil, surface water, and groundwater sources. Humans, animals, and the environment are frequently exposed to PFAS through food, water, consumer products, as well as waste streams from PFAS-manufacturing industries. PFAS are a large group of synthetic organic fluorinated compounds with widely diverse chemical structures that are extremely resistant to microbial degradation. Their persistence, toxicity to life on earth, bioaccumulation tendencies, and adverse health and ecological effects have earned them a "top priority pollutant" designation by regulatory bodies. Despite that a number of physicochemical methods exist for PFAS treatment, they suffer from major drawbacks regarding high costs, use of high energy and incomplete mineralization (destruction of the CF bond). Consequently, microbial degradation and enzymatic treatment of PFAS are highly sought after as they offer a complete, cheaper, sustainable, and environmentally friendly alternative. In this critical review, we provide an overview of the classification, properties, and interaction of PFAS within the environment relevant to microbial degradation. We discuss latest developments in the biodegradation of PFAS by microbes, transformation routes, transformation products and degradative enzymes. Finally, we highlight the existing challenges, limitations, and prospects of bioremediation approaches in treating PFAS and proffer possible solutions and future research directions.

Aerobic biotransformation of 6:2 fluorotelomer sulfonate by Dietzia aurantiaca J3 under sulfur-limiting conditions

The polyfluorinated alkyl substance 6:2 fluorotelomer sulfonate (6:2 FTS) has been detected in diverse environments impacted by aqueous film-forming foams used for firefighting. In this study, a bacterial strain (J3) using 6:2 FTS as a sulfur source was isolated from landfill leachate previously exposed to polyfluoroalkyl substances in New South Wales, Australia. Strain J3 shares 99.9% similarity with the 16S rRNA gene of Dietzia aurantiaca CCUG 35676^T. Genome sequencing yielded a draft genome sequence of 37 contigs with a G + C content of 69.7%. A gene cluster related to organic sulfur utilisation and assimilation was identified, that included an alkanesulfonate monooxygenase component B (ssuD), an alkanesulfonate permease protein (ssuC), an ABC transporter (ssuB), and an alkanesulfonate-binding protein (ssuA). Proteomic analyses comparing strain J3 cultures using sulfate and 6:2 FTS as sulfur source indicated that the ssu gene cluster was involved in 6:2 FTS biodegradation. Upregulated proteins included the SsuD monooxygenase, the SsuB transporter, the ABC transporter permease (SsuC), an alkanesulfonate-binding protein (SsuA), and a nitrilotriacetate monooxygenase component B. 6:2 Fluorotelomer carboxylic acid (6:2 FTCA) and 6:2 fluorotelomer unsaturated acid (6:2 FTUA) were detected as early degradation products in cultures (after 72 h) while 5:3 fluorotelomer acid (5:3 FTCA), perfluorohexanoic acid (PFHxA) and perfluoropentanoic acid (PFPeA) were detected as later degradation products (after 168 h). This work provides biochemical and metabolic insights into 6:2 FTS biodegradation by the Actinobacterium D. aurantiaca J3, informing the fate of PFAS in the environment.

Development of a PFAS reaction library: identifying plausible transformation pathways in environmental and biological systems

Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are used in many consumer applications due to their stain repellency, surfactant properties, ability to form water-proof coatings and use in fire suppression. The production, application, transport, use and disposal of PFAS and PFAS-treated products have resulted in their wide-spread occurrence in environmental and biological systems. Concern over exposure to PFAS and their transformation products and metabolites has necessitated the development of tools to predict the transformation of PFAS in environmental systems and metabolism in biological systems. We have developed reaction libraries for predicting transformation products and metabolites in a variety of environmental and biological reaction systems. These reaction libraries are based on generalized reaction schemes that encode the process science of PFAS reported in the peer-reviewed literature. The PFAS reaction libraries will be executed through the Chemical Transformation Simulator, a web-based tool that is available to the public. These reaction libraries are intended for predicting the environmental transformation and metabolism of PFAS only.

Microbial Defluorination of Unsaturated Per- and Polyfluorinated Carboxylic Acids under Anaerobic and Aerobic Conditions: A Structure Specificity Study

The recently discovered microbial reductive defluorination of two C₆ branched and unsaturated fluorinated carboxylic acids (FCAs) provided valuable insights into the environmental fate of per- and polyfluoroalkyl substances (PFASs) and potential bioremediation strategies. However, a systematic investigation is needed to further demonstrate the role of C═C double bonds in the biodegradability of unsaturated PFASs. Here, we examined the structure-biodegradability relationships of 13 FCAs, including nine commercially available unsaturated FCAs and four structurally similar saturated ones, in an anaerobic defluorinating enrichment and an activated sludge community. The anaerobic and aerobic transformation/defluorination pathways were elucidated. The results showed that under anaerobic conditions, the α,β-unsaturation is crucial for FCA biotransformation via reductive defluorination and/or hydrogenation pathways. With sp² C-F bonds being substituted by C-H bonds, the reductive defluorination became less favorable than hydrogenation. Moreover, for the first time, we reported enhanced degradability and defluorination capability of specific unsaturated FCA structures with trifluoromethyl (-CF₃) branches at the α/β-carbon. Such FCA structures can undergo anaerobic abiotic defluorination in the presence of reducing agents and significant aerobic microbial defluorination. Given the diverse applications and emerging concerns of fluorochemicals, this work not only advances the fundamental understanding of the fate of unsaturated PFASs in natural and engineered environments but also may provide insights into the design of readily degradable fluorinated alternatives to existing PFAS compounds.

Desulfonation and defluorination of 6:2 fluorotelomer sulfonic acid (6:2 FTSA) by Rhodococcus jostii RHA1: Carbon and sulfur sources, enzymes, and pathways

6:2 fluorotelomer sulfonic acid (6:2 FTSA) is one per- and poly-fluoroalkyl substances commonly detected in the environment. While biotransformation of 6:2 FTSA has been reported, factors affecting desulfonation and defluorination of 6:2 FTSA remain poorly understood. This study elucidated the effects of carbon and sulfur sources on the gene expression of Rhodococcus jostii RHA1 which is responsible for the 6:2 FTSA biotransformation. While alkane monooxygenase and cytochrome P450 were highly expressed in ethanol-, 1-butanol-, and n-octane-grown RHA1 in sulfur-rich medium, these cultures only defluorinated 6:2 fluorotelomer alcohol but not 6:2 FTSA, suggesting that the sulfonate group in 6:2 FTSA hinders enzymatic defluorination. In sulfur-free growth media, alkanesulfonate monooxygenase was linked to desulfonation of 6:2 FTSA; while alkane monooxygenase, haloacid dehalogenase, and cytochrome P450 were linked to defluorination of 6:2 FTSA. The desulfonation and defluorination ability of these enzymes toward 6:2 FTSA were validated through heterologous gene expression and in vitro assays. Four degradation metabolites were confirmed and one was identified as a tentative metabolite. The results provide a new understanding of 6:2 FTSA biotransformation by RHA1. The genes encoding these desulfonating- and defluorinating-enzymes are potential markers to be used to assess 6:2 FTSA biotransformation in the environment.

Environmental Sources, Chemistry, Fate, and Transport of Per- and Polyfluoroalkyl Substances: State of the Science, Key Knowledge Gaps, and Recommendations Presented at the August 2019 SETAC Focus Topic Meeting

A Society of Environmental Toxicology and Chemistry (SETAC) Focused Topic Meeting (FTM) on the environmental management of per- and polyfluoroalkyl substances (PFAS) convened during August 2019 in Durham, North Carolina (USA). Experts from around the globe were brought together to critically evaluate new and emerging information on PFAS including chemistry, fate, transport, exposure, and toxicity. After plenary presentations, breakout groups were established and tasked to identify and adjudicate via panel discussions overarching conclusions and relevant data gaps. The present review is one in a series and summarizes outcomes of presentations and breakout discussions related to (1) primary sources and pathways in the environment, (2) sorption and transport in porous media, (3) precursor transformation, (4) practical approaches to the assessment of source zones, (5) standard and novel analytical methods with implications for environmental forensics and site management, and (6) classification and grouping from multiple perspectives. Outcomes illustrate that PFAS classification will continue to be a challenge, and additional pressing needs include increased availability of analytical standards and methods for assessment of PFAS and fate and transport, including precursor transformation. Although the state of the science is sufficient to support a degree of site-specific and flexible risk management, effective source prioritization tools, predictive fate and transport models, and improved and standardized analytical methods are needed to guide broader policies and best management practices. Environ Toxicol Chem 2021;40:3234-3260. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Biodesulfurization Induces Reprogramming of Sulfur Metabolism in Rhodococcus qingshengii IGTS8: Proteomics and Untargeted Metabolomics

Sulfur metabolism in fuel-biodesulfurizing bacteria and the underlying physiological adaptations are not understood, which has impeded the development of a commercially viable bioprocess for fuel desulfurization. To fill these knowledge gaps, we performed comparative proteomics and untargeted metabolomics in cultures of the biodesulfurization reference strain Rhodococcus qingshengii IGTS8 grown on either inorganic sulfate or the diesel-borne organosulfur compound dibenzothiophene as a sole sulfur source. Dibenzothiophene significantly altered the biosynthesis of many sulfur metabolism proteins and metabolites in a growth phase-dependent manner, which enabled us to reconstruct the first experimental model for sulfur metabolism in a fuel-biodesulfurizing bacterium. All key pathways related to assimilatory sulfur metabolism were represented in the sulfur proteome, including uptake of the sulfur sources, sulfur acquisition, and assimilatory sulfate reduction, in addition to biosynthesis of key sulfur-containing metabolites such as S-adenosylmethionine, coenzyme A, biotin, thiamin, molybdenum cofactor, mycothiol, and ergothioneine (low-molecular weight thiols). Fifty-two proteins exhibited significantly different abundance during at least one growth phase. Sixteen proteins were uniquely detected and 47 proteins were significantly more abundant in the dibenzothiophene culture during at least one growth phase. The sulfate-free dibenzothiophene-containing culture reacted to sulfate starvation by restricting sulfur assimilation, enforcing sulfur-sparing, and maintaining redox homeostasis. Biodesulfurization triggered alternative pathways for sulfur assimilation different from those operating in the inorganic sulfate culture. Sulfur metabolism reprogramming and metabolic switches in the dibenzothiophene culture were manifested in limiting sulfite reduction and biosynthesis of cysteine, while boosting the production of methionine via the cobalamin-independent pathway, as well as the biosynthesis of the redox buffers mycothiol and ergothioneine. The omics data underscore the key role of sulfur metabolism in shaping the biodesulfurization phenotype and highlight potential targets for improving the biodesulfurization catalytic activity via metabolic engineering.

IMPORTANCE For many decades, research on biodesulfurization of fossil fuels was conducted amid a large gap in knowledge of sulfur metabolism and its regulation in fuel-biodesulfurizing bacteria, which has impeded the development of a commercially viable bioprocess. In addition, lack of understanding of biodesulfurization-associated metabolic and physiological adaptations prohibited the development of efficient biodesulfurizers. Our integrated omics-based findings reveal the assimilatory sulfur metabolism in the biodesulfurization reference strain Rhodococcus qingshengii IGTS8 and show how sulfur metabolism and oxidative stress response were remodeled and orchestrated to shape the biodesulfurization phenotype. Our findings not only explain the frequently encountered low catalytic activity of native fuel-biodesulfurizing bacteria but also uncover unprecedented potential targets in sulfur metabolism that could be exploited via metabolic engineering to boost the biodesulfurization catalytic activity, a prerequisite for commercial application.

Fate and transport of per- and polyfluoroalkyl substances (PFASs) in the vadose zone

Per- and polyfluoroalkyl substances (PFASs) are a heterogeneous group of persistent organic pollutants that have been detected in various environmental compartments around the globe. Emerging research has revealed the preferential accumulation of PFASs in shallow soil horizons, particularly at sites impacted by firefighting activities, agricultural applications, and atmospheric deposition. Once in the vadose zone, PFASs can sorb to soil, accumulate at interfaces, become volatilized, be taken up in biota, or leach to the underlying aquifer. At the same time, polyfluorinated precursor species may transform into highly recalcitrant perfluoroalkyl acids, changing their chemical identity and thus transport behavior along the way. In this review, we critically discuss the current state of the knowledge and aim to interconnect the complex processes that control the fate and transport of PFASs in the vadose zone. Furthermore, we identify key challenges and future research needs. Consequently, this review may serve as an interdisciplinary guide for the risk assessment and management of PFAS-contaminated sites.

Transcriptomic response of Gordonia sp. strain NB4-1Y when provided with 6:2 fluorotelomer sulfonamidoalkyl betaine or 6:2 fluorotelomer sulfonate as sole sulfur source

Abstract

Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are environmental contaminants of concern. We previously described biodegradation of two PFAS that represent components and transformation products of aqueous film-forming foams (AFFF), 6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) and 6:2 fluorotelomer sulfonate (6:2 FTSA), by Gordonia sp. strain NB4-1Y. To identify genes involved in the breakdown of these compounds, the transcriptomic response of NB4-1Y was examined when grown on 6:2 FTAB, 6:2 FTSA, a non-fluorinated analog of 6:2 FTSA (1-octanesulfonate), or MgSO₄, as sole sulfur source. Differentially expressed genes were identified as those with ± 1.5 log₂-fold-differences (± 1.5 log₂FD) in transcript abundances in pairwise comparisons. Transcriptomes of cells grown on 6:2 FTAB and 6:2 FTSA were most similar (7.9% of genes expressed ± 1.5 log₂FD); however, several genes that were expressed in greater abundance in 6:2 FTAB treated cells compared to 6:2 FTSA treated cells were noted for their potential role in carbon–nitrogen bond cleavage in 6:2 FTAB. Responses to sulfur limitation were observed in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments, as 20 genes relating to global sulfate stress response were more highly expressed under these conditions compared to the MgSO₄ treatment. More highly expressed oxygenase genes in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments were found to code for proteins with lower percent sulfur-containing amino acids compared to both the total proteome and to oxygenases showing decreased expression. This work identifies genetic targets for further characterization and will inform studies aimed at evaluating the biodegradation potential of environmental samples through applied genomics.

Graphic Abstract

Electronic supplementary material

The online version of this article (10.1007/s10532-020-09917-8) contains supplementary material, which is available to authorized users.

Aerobic biotransformation of fluorotelomer compounds in landfill leachate-sediment

Consumer products containing fluorotelomer polymers are a source of fluorotelomer compounds to the environment following their disposal at landfills. The fate and transformation of fluorotelomer compounds are unknown in landfill leachates. This study investigates the aerobic biotransformation of 8:2 fluorotelomer alcohol (FTOH) and 6:2 fluorotelomer sulfonate (FTS) in landfill leachate-sediment microcosms using batch tests. Spiked 8:2 FTOH, 6:2 FTS and their known biotransformation products were quantified in sediment-leachate and headspace over 90 days under aerobic conditions. 8:2 FTOH and 6:2 FTS biotransformation was slow (half-life >>30 d) in landfill leachate-sediment microcosm, suggesting persistence of fluorotelomer compounds under the conditions investigated. Significant volatilization (>20%) of 8:2 FTOH was observed in the microcosm headspace after 90 days. C6 - C8 and C4 - C6 perfluorocarboxylic acids (PFCAs) were the most abundant products for 8:2 FTOH and 6:2 FTS, respectively. PFCAs accounted for 4-9 mol% of the initially spiked parent compounds at 90 days. Perfluorooctanoic acid (PFOA) was the single most abundant product of 8:2 FTOH (>2.8 mol% at 90 days). The unaccounted mass (20 to 35 mol%) of the initially spiked parent compounds indicated formation of fluorotelomer intermediates and sediment-bound residue. Overall the findings suggest that aerobic biotransformation of fluorotelomer compounds acts as a secondary source of long- and short-chain (≤C7) PFCAs in the environment. Partitioning of semi-volatile fluorotelomer compounds (e.g., 8:2 FTOH) to the gas-phase indicates possible long-range transport and subsequent release of PFCAs in pristine environments. Short-chain fluorotelomer replacements (e.g., 6:2 FTS) result in a higher abundance of short-chain PFCAs in landfill leachate. Future research is needed to understand the long-term exposure effects of short-chain PFCAs to humans, aquatic life and biota.

Formation of perfluorocarboxylic acids from 6:2 fluorotelomer sulfonate (6:2 FTS) in landfill leachate: Role of microbial communities

Fluorotelomer compounds in landfill leachate can undergo biotransformation under aerobic conditions and act as a secondary source of perfluorocarboxylic acids (PFCAs) to the environment. Very little is known about the role of various microbial communities towards fluorotelomer compounds biotransformation. Using an inoculum prepared from the sediment of a leachate collection ditch, 6:2 fluorotelomer sulfonate (6:2 FTS) biotransformation experiments were carried out. Specific substrates (i.e., glucose, ammonia) and ammonia-oxidizing inhibitor (allylthiourea) were used to produce two experimental runs with heterotrophic (HET) growth only and heterotrophic with ammonia-oxidizing and nitrite- oxidizing bacteria (HET + AOB + NOB). After 10 days, ∼20% of the spiked 6:2 FTS removal was observed in HET + AOB + NOB, compared to ∼7% under HET condition. Higher 6:2 FTS removal in HET + AOB + NOB likely resulted from ammonia monooxygenase enzyme that catalyzes the first step of ammonia oxidation. The HET + AOB + NOB condition also showed higher PFCA (C4-C6) formation (∼2% of initially spiked 6:2 FTS), possibly due to higher overall bioactivity. Microbial community analysis through 16s rRNA sequencing confirmed that Proteobacteria and Bacteroidetes were the most abundant phyla (>75% relative abundance) under all experimental conditions. High abundance of Actinobacteria (>17%) was observed under the HET + AOB + NOB condition on day 7. Since Actinobacteria can synthesize a wide range of enzymes including monooxygenases, they likely play an important role in 6:2 FTS biotransformation and PFCA production.

Biotransformation of polyfluoroalkyl substances by microbial consortia from constructed wetlands under aerobic and anoxic conditions

The wide application of 6:2 fluorotelomer sulfonate (6:2 FTS) and its precursors results in their ubiquitous occurrence in the environment. This study investigated the biotransformation of 6:2 FTS using fresh slurries collected from constructed wetland under aerobic and anoxic conditions. Biotransformation rates of 6:2 FTS was extremely slow under both aerobic and anoxic conditions. The analysis of transformation products showed that less than 0.7 mol% of initial concentration of 6:2 FTS was biotransformed under anoxic conditions. Effects of 6:2 FTS on the shifts in microbial community in wetland slurry during aerobic and anoxic transformation were evaluated using 16S rRNA gene amplicon sequencing. Under aerobic conditions, 6:2 FTS altered the microbial community structure, in which Methylocaldum (Gamma-proteobacteria) became the predominant genus after being exposed to 6:2 FTS. This means that Methylocaldum appears to have higher tolerance to 6:2 FTS and seems to be potential 6:2 FTS-degrading bacteria. Under anoxic transformation, only the genus Methanomethylovorans (Euryarchaeota) was increased remarkably in wetland slurry exposed to 6:2 FTS.

Degradation and defluorination of 6:2 fluorotelomer sulfonamidoalkyl betaine and 6:2 fluorotelomer sulfonate by Gordonia sp. strain NB4-1Y under sulfur-limiting conditions

6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) is a major component of aqueous film-forming foams (AFFFs) used for firefighting and is frequently detected, along with one of its suspected transformation products, 6:2 fluorotelomer sulfonate (6:2 FTSA), in terrestrial and aquatic ecosystems impacted by AFFF usage. Biochemical processes underlying bacterial biodegradation of these compounds remain poorly understood due to a lack of pure culture studies. Here, we characterized the water-soluble and volatile breakdown products of 6:2 FTSA and 6:2 FTAB produced using Gordonia sp. strain NB4-1Y cultures over seven days under sulfur-limited conditions. After 168 h, 99.9% of 60 μM 6:2 FTSA was degraded into ten major breakdown products, with a mol% recovery of 88.2, while 70.4% of 60 μM 6:2 FTAB was degraded into ten major breakdown products, with a mol% recovery of 84.7. NB4-1Y uses two pathways for 6:2 FTSA metabolism, with 55 mol% of breakdown products assigned to a major pathway and <1.0 mol% assigned to a minor pathway. This work indicates that rapid transformation of 6:2 FTSA and 6:2 FTAB can be achieved under controlled conditions and improves the bacterial metabolism of these compounds.

An insight into the ecology, diversity and adaptations of Gordonia species

The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.

Oligo(cis-1,4-isoprene) aldehyde-oxidizing dehydrogenases of the rubber-degrading bacterium Gordonia polyisoprenivorans VH2

The actinomycete Gordonia polyisoprenivorans strain VH2 is well-known for its ability to efficiently degrade and catabolize natural rubber [poly(cis-1,4-isoprene)]. Recently, a pathway for the catabolism of rubber by strain VH2 was postulated based on genomic data and the analysis of mutants (Hiessl et al. in Appl Environ Microbiol 78:2874-2887, 2012). To further elucidate the degradation pathway of poly(cis-1,4-isoprene), 2-dimensional-polyacrylamide gel electrophoresis was performed. The analysis of the identified protein spots by matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry confirmed the postulated intracellular pathway suggesting a degradation of rubber via β-oxidation. In addition, other valuable information on rubber catabolism of G. polyisoprenivorans strain VH2 (e.g. oxidative stress response) was provided. Identified proteins, which were more abundant in cells grown with rubber than in cells grown with propionate, implied a putative long-chain acyl-CoA-dehydrogenase, a 3-ketoacyl-CoA-thiolase, and an aldehyde dehydrogenase. The amino acid sequence of the latter showed a high similarity towards geranial dehydrogenases. The expression of the corresponding gene was upregulated > 10-fold under poly(cis-1,4-isoprene)-degrading conditions. The putative geranial dehydrogenase and a homolog were purified and used for enzyme assays. Deletion mutants for five aldehyde dehydrogenases were generated, and growth with poly(cis-1,4-isoprene) was investigated. While none of the mutants had an altered phenotype regarding growth with poly(cis-1,4-isoprene) as sole carbon and energy source, purified aldehyde dehydrogenases were able to catalyze the oxidation of oligoisoprene aldehydes indicating an involvement in rubber degradation.

Fate of thianthrene in biological systems

1. Thianthrene is a sulfur-containing tricyclic molecule distributed widely within the macrostructure of hydrocarbon fossil fuels. Identified nearly 150 years ago, its chemistry has been widely explored leading to insights into reaction mechanisms and radical ion formation. 2. It has been claimed to have therapeutic application in the treatment of dermal infections and to interfere with enzyme and nucleic acid function, but appears to have little toxicity. 3. Following its oral administration to the rat, the majority remained within the gastrointestinal tract. After three days, about 88% was detected in the combined excreta with the remainder still within the animal. It is readily taken up into fish from the surrounding aqueous environment and has been placed within the "bioaccumulative category" to be regarded with concern. 4. Mammalian metabolism appeared to be restricted to ring carbon oxidation and subsequent glucuronic acid conjugation. Small amounts of sulfoxide and disulfoxide were also formed. No ring degradation was evident. Microorganisms similarly undertook aromatic ring hydroxylation but were able also to rupture the ring system by attacking the carbon-sulfur linkages and thereby degrading the molecule.

Draft Genome Sequence of a Thermophilic Desulfurization Bacterium, Geobacillus thermoglucosidasius Strain W-2

Geobacillus thermoglucosidasius strain W-2 is a thermophilic bacterium isolated from a deep-subsurface oil reservoir in northern China, which is capable of degrading organosulfur compounds. Here, we report the draft genome sequence of G. thermoglucosidasius strain W-2, which may help to elucidate the genetic basis of biodegradation of organosulfur pollutants under heated conditions.

Biotransformation potential of 6:2 fluorotelomer sulfonate (6:2 FTSA) in aerobic and anaerobic sediment

Aqueous film-forming foam (AFFF) products are used in industrial and military firefighting around the globe. These products contain fluoroalkylthioamido sulfonates, fluoroalkylthiobetaine, and other related substances as the major ingredients, which can be biotransformed in the environment to form 6:2 fluorotelomer sulfonate (6:2 FTSA, F(CF2)6CH2CH2SO3-) as one of the major initial biotransformation products. Limited information is available on 6:2 FTSA aerobic biotransformation in activated sludge and pure microbial culture. This is the first study to report 6:2 FTSA biotransformation in aerobic and anaerobic sediment. 6:2 FTSA was rapidly biotransformed in aerobic river sediment with a half-life less than 5 d. Major stable transformation products observed after 90 d included 5:3 Acid [F(CF2)5CH2CH2COOH), 16 mol%), PFPeA [F(CF2)4COOH, 21 mol%] and PFHxA (F(CF2)5COOH, 20 mol%). 6:2 fluorotelomer alcohol [6:2 FTOH, F(CF2)6CH2CH2OH] was readily biotransfomed whereas 6:2 FTSA biotransformation did not occur in anaerobic sediment over 100 d, indicating that the enzymatic desulfonation step limited 6:2 FTSA biotransformation in anaerobic sediment. These results suggest that 6:2 FTSA related products, after release to the aerobic environment, is likely to biodegrade forming 5:3 Acid, PFPeA and PFHxA. This study also indicates that 6:2 FTSA formed from its aforementioned precursors may be persistent in the anaerobic environment after their potential release. This work provides insight to understanding the fate and environmental loading of AFFF-related products and their major transformation products in the environment.

Draft genome sequence of Paenibacillus sp. strain A2

Paenibacillus sp. strain A2 is a Gram-negative rod-shaped bacterium isolated from a mixture of formation water and petroleum in Daqing oilfield, China. This facultative aerobic bacterium was found to have a broad capacity for metabolizing hydrocarbon and organosulfur compounds, which are the main reasons for the interest in sequencing its genome. Here we describe the features of Paenibacillus sp. strain A2, together with the genome sequence and its annotation. The 7,650,246 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 54.2 % and contains 7575 protein-coding and 49 RNA genes, including 3 rRNA genes. One putative alkane monooxygenase, one putative alkanesulfonate monooxygenase, one putative alkanesulfonate transporter and four putative sulfate transporters were found in the draft genome.

High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil

Enterobacter mori strain 5-4 is a Gram-negative, motile, rod shaped, and facultatively anaerobic bacterium, which was isolated from a mixture of formation water (also known as oil-reservior water) and crude-oil in Karamay oilfield, China. To date, there is only one E. mori genome has been sequenced and very little knowledge about the mechanism of E. mori adapted to the petroleum reservoir. Here, we report the second E. mori genome sequence and annotation, together with the description of features for this organism. The 4,621,281 bp assembly genome exhibits a G + C content of 56.24% and contains 4,317 protein-coding and 65 RNA genes, including 5 rRNA genes.

Genome sequence of Brevibacillus agri strain 5-2, isolated from the formation water of petroleum reservoir

Brevibacillus agri strain 5-2 was isolated from the formation water of a deep oil reservoir in Changqing Oilfield, China. This bacterium was found to have a capacity for degrading tetradecane, hexadecane and alkanesulfonate. To gain insights into its efficient metabolic pathway for degrading hydrocarbon and organosulfur compounds, here, we report the high quality draft genome of this strain. Two putative alkane 1-monooxygenases, one putative alkanesulfonate monooxygenase, one putative alkanesulfonate transporter, one putative sulfate permease and five putative sulfate transporters were identified in the draft genome. The genomic data of strain 5-2 may provide insights into the mechanism of microorganisms adapt to the petroleum reservoir after chemical flooding.