Pseudomonas sp. Strain 273 Incorporates Organofluorine into the Lipid Bilayer during Growth with Fluorinated Alkanes

Fontimonas thermophila Alkane Monooxygenase (FtAlkB) Is an Alkyl Fluoride Dehalogenase

Purified alkane monooxygenase (AlkB) from Fontimonas thermophila (FtAlkB) catalyzes the defluorination of 1-fluorooctane, producing octanal, which is partially reduced under the reaction conditions to generate 1-octanol. This reaction occurs preferentially at the monofluorinated methyl group, with only a minor amount of oxidation at the nonfluorinated end of the molecule. The dehalogenation chemistry is specific to 1-fluorooctane, as neither 1-chlorooctane or 1-bromooctane are dehalogenated to an appreciable extent. Furthermore, P. putida cells containing the structurally related AlkB (PpAlkB) along with the full set of genes required for alkane metabolism, utilize 1-fluorooctane as their sole source of carbon with growth rates comparable to those for cells grown with octane.

Enriching fluorotelomer carboxylic acids-degrading consortia from sludges and soils

Fluorotelomer carboxylic acids (FTCAs) has drawn increasing attention due to their prevalent occurrence, high toxicity, and bioaccumulating effects. In this study, microbial consortia with sustainable FTCA removal abilities were enriched and characterized from two activated sludges and five soils when no external carbon sources were supplemented. After four generations of enrichment, stable 6:2 FTCA and 5:3 FTCA biodegradation were achieved, reaching 0.72-0.98 and 0.53-1.05 μM/day, respectively. Coupling with 6:2 FTCA biotransformation, fluoride release co-occurred, conducive to approximate 0.19 fluoride per 6:2 FTCA molecule that was biodegraded. In contrast, minimal free fluoride was detected in 5:3 FTCA-amended consortia, indicating the dominance of "non-fluoride releasing pathways". Microbial community analysis revealed the dominance of 13 genera across all consortia. Among them, 3 genera, including Hyphomicrobium, Methylorubrum, and Achromobacter, were found more enriched in consortia amended with 6:2 FTCA than those with 5:3 FTCA from an identical inoculation source, suggesting their involvement in biodefluorination. This study uncovered that microbial consortia can degrade FTCAs without the supplementation of external carbon sources, though with low biotransformation and biodefluorination rates. Further research is underscored to investigate the involved biotransformation pathways and biodefluorination mechanisms, as well as effects of external carbon sources.

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.

Discovery of Combustion-Like in-Source Oxidation of Linear Saturated Hydrocarbons Using GC-APCI-HRMS

Atmospheric pressure chemical ionization (APCI) is often used in the analysis of linear saturated hydrocarbons (LSHs) as this ionization technique commonly produces [M - H]+ ions in high abundance. However, APCI (along with other atmospheric pressure sources) is often impacted by in-source oxidation, leading to a variety of ionic products. Identifying these products and understanding their mechanisms of formation is crucial for characterizing complex mixtures with substantial hydrocarbon content, such as those found in the petrochemical industry. In this study, in-source oxidation of LSHs was observed in gas chromatography (GC) coupled to high-resolution mass spectrometry (HRMS) via a custom-built APCI interface. Studies showed that the abundance of these oxidized ions correlated positively with atmospheric water, yet occurred without the inclusion of water-based oxygen as judged by experiments with stable isotope-labeled water. The oxidation of LSHs was further influenced by the reactive species in the ionization atmosphere. Fragmentation data using stable isotope-labeled LSH standards unveiled multiple structurally unique ions with one or more oxidation sites on both primary and secondary carbons. These ionic products bear resemblance to combustion byproducts, suggesting the instrumental configuration fosters plasma-assisted combustion-like processes that encourage the radical-mediated oxidation of LSHs rather than generate [M - H]+. Through these investigative efforts, a mechanism analogous to combustion was proposed for the formation of LSH oxidation products in GC-APCI-HRMS. Data demonstrate that these ions are robustly generated in petrochemical products, allowing for proper characterization of these complex mixtures.

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.

Distinctive biotransformation and biodefluorination of 6:2 versus 5:3 fluorotelomer carboxylic acids by municipal activated sludge

Fluorotelomer carboxylic acids (FTCAs) represent an important group of per- and polyfluoroalkyl substances (PFAS) given their high toxicity, bioaccumulation potential, and frequent detection in landfill leachates and PFAS-impacted sites. In this study, we assessed the biodegradability of 6:2 FTCA and 5:3 FTCA by activated sludges from four municipal wastewater treatment plants (WWTPs) in the New York Metropolitan area. Coupling with 6:2 FTCA removal, significant fluoride release (0.56∼1.83 F-/molecule) was evident in sludge treatments during 7 days of incubation. Less-fluorinated transformation products (TPs) were formed, including 6:2 fluorotelomer unsaturated carboxylic acid (6:2 FTUCA), perfluorohexanoic acid (PFHxA), perfluoropentanoic acid (PFPeA), and perfluorobutanoic acid (PFBA). In contrast, little fluoride (0.01∼0.09 F-/molecule) was detected in 5:3 FTCA-dosed microcosms, though 25∼68% of initially dosed 5:3 FTCA was biologically removed. This implies the dominance of "non-fluoride-releasing pathways" that may contribute to the formation of CoA adducts or other conjugates over 5:3 FTCA biotransformation. The discovery of defluorinated 5:3 FTUCA revealed the possibility of microbial attacks of the C-F bond at the γ carbon to initiate the transformation. Microbial community analysis revealed the possible involvement of 9 genera, such as Hyphomicrobium and Dechloromonas, in aerobic FTCA biotransformation. This study unraveled that biotransformation pathways of 6:2 and 5:3 FTCAs can be divergent, resulting in biodefluorination at distinctive degrees. Further research is underscored to uncover the nontarget TPs and investigate the involved biotransformation and biodefluorination mechanisms and molecular basis.

Microbial defluorination of TFA, PFOA, and HFPO-DA by a native microbial consortium under anoxic conditions

In this study, the biodegradability of trifluoroacetate (TFA), perfluorooctanoic acid (PFOA), and perfluoro-2-methyl-3-oxahexanoic acid (HFPO-DA) by a native microbial community was evaluated over a 10-month incubation period. The observed microbial defluorination ratios and removal efficiency were 3.46 ( ± 2.73) % and 8.03 ( ± 3.03) %, 8.44 ( ± 1.88) % and 13.52 ( ± 4.96) %, 3.02 ( ± 0.62) % and 5.45 ( ± 2.99) % for TFA, PFOA and HFPO-DA, respectively. The biodegradation intermediate products, TFA and pentafluoropropionic acid (PFA), of PFOA and HFPO-DA were detected in their biodegradation treatment groups. Furthermore, the concentrations of the PFOA metabolites, perfluorohexanoic acid (PFHxA) and perfluoroheptanoic acid (PFHpA), in the aqueous solutions after incubation were quantified to be 0.21 and 4.14 µg/L. TFA, PFOA and HFPO-DA significantly reduced the microbial diversity and changed the structure of the community. The co-occurrence network analysis showed that low abundance species, such as Flexilinea flocculi, Bacteriovorax stolpii, and g_Sphingomonas, are positively correlated with the generation of fluoride ion, implying their potential collaborative functions contributing to the observed biodefluorination. The findings in this study can provide insights for the biodegradation of perfluoroalkyl carboxylic acids and their emerging alternatives by indigenous microorganisms in the environment.

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.

Developmental toxicity in Daphnia magna induced by environmentally relevant concentrations of carbon black: From the perspective of metabolomics and symbiotic bacteria composition

The level of carbon black (CB) pollution in the environment is rapidly increasing, owing to the increase in natural and industrial emissions. The water environment has become an important sink for CB. However, studies on CB mainly focused on its impact on air pollution and phytoremediation applications, and the toxicity mechanism of CB in aquatic organisms is relatively limited. Thus, Daphnia magna was used as a model organism to explore the developmental toxicity of environmentally relevant concentrations of CB under a full life-cycle exposure. The toxicity mechanism of CB in aquatic organisms was investigated based on metabolomic and symbiotic microbial analyses. It was found that compared with the control group, the body length of exposed D. magna decreased, while the mortality and intestinal inflammation increased with increasing concentration of CB. The normal reproductive regularity of D. magna was disturbed, and the deformity and body length of the offspring increased and decreased, respectively, after CB exposure. Metabolomic analysis showed that the urea cycle metabolic pathway of exposed D. magna was increased significantly, suggesting a perturbation of N metabolism. In addition, two eicosanoids were increased, suggesting possible inflammation in D. magna. The levels of seven phospholipid metabolites decreased that might be responsible for offspring malformations. Microbiological analysis showed that the composition of the symbiotic microbial community of D. magna was disturbed, including microorganisms involved in carbon cycling, nitrogen cycling, and biodegradation of pollutants, as well as pathogenic microorganisms. Overall, this study found that the inflammatory related metabolites and symbiotic bacterial, as well as reproductive related metabolites, were disrupted after D. magna exposed to different concentrations of CB, which revealed a possible developmental toxicity mechanism of CB in D. magna. These findings provide a scientific basis for analyzing the risks of CB in aquatic environments.

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.

Complete Genome Sequence of Pseudomonas sp. Strain 273, a Haloalkane-Degrading Bacterium

Pseudomonas sp. strain 273 utilizes terminally mono- and bis-halogenated alkanes (C7 to C16) as carbon and energy sources under oxic conditions. During metabolism of fluorinated alkanes, strain 273 releases inorganic fluoride and synthesizes fluorinated phospholipids. The complete genome sequence consists of a circular 7.48-Mb chromosome with a G+C content of 67.5%, containing 6,890 genes.

Roles of various enzymes in the biotransformation of 6:2 fluorotelomer alcohol (6:2 FTOH) by a white-rot fungus

Six-carbon-chained polyfluoroalkyl substances, such as 6:2 fluorotelomer alcohol (6:2 FTOH), are being used to replace longer chained compounds in the manufacture of various commercial products. This study examined the effects of growth substrates and nutrients on specific intracellular and extracellular enzymes mediating 6:2 FTOH aerobic biotransformation by the white-rot fungus, Phanerochaete chrysosporium. Cellulolytic conditions with limited glucose were a suitable composition, resulting in high 5:3 FTCA yield (37 mol%), which is a key intermediate in 6:2 FTOH degradation without forming significant amounts of terminal perfluorocarboxylic acids (PFCAs). Sulfate and ethylenediaminetetraacetic acid (EDTA) were also essential for 5:3 FTCA production, but, at lower levels, resulted in the buildup of 5:2 sFTOH (52 mol%) and 6:2 FTUCA (20 mol%), respectively. In non-ligninolytic nutrient-rich medium, 45 mol% 6:2 FTOH was transformed but produced only 12.7 mol% 5:3 FTCA. Enzyme activity studies imply that cellulolytic conditions induce the intracellular cytochrome P450 system. In contrast, extracellular peroxidase synthesis is independent of 6:2 FTOH exposure. Gene expression studies further verified that peroxidases were relevant in catalyzing the downstream transformations from 5:3 FTCA. Collectively, the identification of nutrients and enzymatic systems will help elucidate underlying mechanisms and biogeochemical conditions favorable for fungal transformation of PFCA precursors in the environment.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.