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Yan M, Gao Z, Xiang X, Wang Q, Song X, Wu Y, Löffler FE, Zeng J, Lin X. Defluorination of monofluorinated alkane by Rhodococcus sp. NJF-7 isolated from soil. AMB Express 2024; 14:65. [PMID: 38842638 PMCID: PMC11156826 DOI: 10.1186/s13568-024-01729-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
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.
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Affiliation(s)
- Meng Yan
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Zhaozhao Gao
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Xingjia Xiang
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
| | - Qing Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Xin Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Yucheng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Frank E Löffler
- Department of Civil and Environmental Engineering, Department of Microbiology, Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jun Zeng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China.
- Department of Biology and Biochemistry, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, People's Republic of China.
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
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2
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Stockbridge RB, Wackett LP. The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis. Nat Commun 2024; 15:4593. [PMID: 38816380 PMCID: PMC11139923 DOI: 10.1038/s41467-024-49018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
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.
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Affiliation(s)
- Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Lawrence P Wackett
- Department of Biochemistry, Biophysics & Molecular Biology and Biotechnology Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
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3
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Qian X, Huang J, Yan C, Xiao J, Cao C, Wu Y, Wang L. Evaluation of ecological impacts with ferrous iron addition in constructed wetland under perfluorooctanoic acid stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134074. [PMID: 38518702 DOI: 10.1016/j.jhazmat.2024.134074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/27/2024] [Accepted: 03/17/2024] [Indexed: 03/24/2024]
Abstract
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.
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Affiliation(s)
- Xiuwen Qian
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 211189, China
| | - Juan Huang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 211189, China.
| | - Chunni Yan
- School of Urban Planning and Municipal Engineering, Xi'an Polytechnic University, Xi'an 710048, China
| | - Jun Xiao
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Chong Cao
- Department of Municipal Engineering, College of Civil Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yufeng Wu
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 211189, China
| | - Luming Wang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 211189, China
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4
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Yan PF, Dong S, Woodcock MJ, Manz KE, Garza-Rubalcava U, Abriola LM, Pennell KD, Cápiro NL. Biotransformation of 6:2 fluorotelomer sulfonate and microbial community dynamics in water-saturated one-dimensional flow-through columns. WATER RESEARCH 2024; 252:121146. [PMID: 38306753 DOI: 10.1016/j.watres.2024.121146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 02/04/2024]
Abstract
Nearly all per- and polyfluoroalkyl substances (PFAS) biotransformation studies reported to date have been limited to laboratory-scale batch reactors. The fate and transport of PFAS in systems that more closely represent field conditions, i.e., in saturated porous media under flowing conditions, remain largely unexplored. This study investigated the biotransformation of 6:2 fluorotelomer sulfonate (6:2 FTS), a representative PFAS of widespread environmental occurrence, in one-dimensional water-saturated flow-through columns packed with soil obtained from a PFAS-contaminated site. The 305-day column experiments demonstrated that 6:2 FTS biotransformation was rate-limited, where a decrease in pore-water velocity from 3.7 to 2.4 cm/day, resulted in a 21.7-26.1 % decrease in effluent concentrations of 6:2 FTS and higher yields (1.0-1.4 mol% vs. 0.3 mol%) of late-stage biotransformation products (C4C7 perfluoroalkyl carboxylates). Flow interruptions (2 and 7 days) were found to enhance 6:2 FTS biotransformation during the 6-7 pore volumes following flow resumption. Model-fitted 6:2 FTS column biotransformation rates (0.039-0.041 cmw3/gs/d) were ∼3.5 times smaller than those observed in microcosms (0.137 cmw3/gs/d). Additionally, during column experiments, planktonic microbial communities remained relatively stable, whereas the composition of the attached microbial communities shifted along the flow path, which may have been attributed to oxygen availability and the toxicity of 6:2 FTS and associated biotransformation products. Genus Pseudomonas dominated in planktonic microbial communities, while in the attached microbial communities, Rhodococcus decreased and Pelotomaculum increased along the flow path, suggesting their potential involvement in early- and late-stage 6:2 FTS biotransformation, respectively. Overall, this study highlights the importance of incorporating realistic environmental conditions into experimental systems to obtain a more representative assessment of in-situ PFAS biotransformation.
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Affiliation(s)
- Peng-Fei Yan
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States.
| | - Sheng Dong
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | | | - Katherine E Manz
- School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | | | - Linda M Abriola
- School of Engineering, Brown University, Providence, RI, United States
| | - Kurt D Pennell
- School of Engineering, Brown University, Providence, RI, United States
| | - Natalie L Cápiro
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States.
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5
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Tang Z, Vogel TM, Wang Q, Wei C, Ali M, Song X. Microbial defluorination of TFA, PFOA, and HFPO-DA by a native microbial consortium under anoxic conditions. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133217. [PMID: 38101019 DOI: 10.1016/j.jhazmat.2023.133217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
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.
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Affiliation(s)
- Zhiwen Tang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Timothy M Vogel
- Ecologie Microbienne, Université Claude Bernard Lyon 1, Villeurbanne F-69622, France
| | - Qing Wang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changlong Wei
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Mukhtiar Ali
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Song
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Dodge AG, Thoma CJ, O’Connor MR, Wackett LP. Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion. mBio 2024; 15:e0278523. [PMID: 38063407 PMCID: PMC10790756 DOI: 10.1128/mbio.02785-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Society uses thousands of organofluorine compounds, sometimes denoted per- and polyfluoroalkyl substances (PFAS), in hundreds of products, but recent studies have shown some to manifest human and environmental health effects. As a class, they are recalcitrant to biodegradation, partly due to the paucity of fluorinated natural products to which microbes have been exposed. Another limit to PFAS biodegradation is the intracellular toxicity of fluoride anion generated from C-F bond cleavage. The present study identified a broader substrate specificity in an enzyme originally studied for its activity on the natural product fluoroacetate. A recombinant Pseudomonas expressing this enzyme was used here as a model system to better understand the limits and effects of a high level of intracellular fluoride generation. A fluoride stress response has evolved in bacteria and has been described in Pseudomonas spp. The present study is highly relevant to organofluorine compound degradation or engineered biosynthesis in which fluoride anion is a substrate.
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Affiliation(s)
- Anthony G. Dodge
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, USA
| | - Calvin J. Thoma
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, USA
| | - Madeline R. O’Connor
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, USA
| | - Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, USA
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7
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Wackett LP. Microwell fluoride assay screening for enzymatic defluorination. Methods Enzymol 2024; 696:65-83. [PMID: 38658089 DOI: 10.1016/bs.mie.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
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.
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Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, United States.
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8
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Chetverikov S, Hkudaygulov G, Sharipov D, Starikov S, Chetverikova D. Biodegradation Potential of C 7-C 10 Perfluorocarboxylic Acids and Data from the Genome of a New Strain of Pseudomonas mosselii 5(3). TOXICS 2023; 11:1001. [PMID: 38133402 PMCID: PMC10748008 DOI: 10.3390/toxics11121001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
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.
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Affiliation(s)
| | - Gaisar Hkudaygulov
- Ufa Institute of Biology, Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia; (S.C.); (D.S.); (S.S.); (D.C.)
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9
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Xie Y, Ramirez D, Chen G, He G, Sun Y, Murdoch FK, Löffler FE. Genome-Wide Expression Analysis Unravels Fluoroalkane Metabolism in Pseudomonas sp. Strain 273. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15925-15935. [PMID: 37647029 PMCID: PMC11217894 DOI: 10.1021/acs.est.3c03855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
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.
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Affiliation(s)
- Yongchao Xie
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Diana Ramirez
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Gao Chen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Guang He
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yanchen Sun
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Fadime Kara Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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10
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Xie Y, Erşan S, Guan X, Wang J, Sha J, Xu S, Wohlschlegel JA, Park JO, Liu C. Unexpected metabolic rewiring of CO 2 fixation in H 2-mediated materials-biology hybrids. Proc Natl Acad Sci U S A 2023; 120:e2308373120. [PMID: 37816063 PMCID: PMC10589654 DOI: 10.1073/pnas.2308373120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/31/2023] [Indexed: 10/12/2023] Open
Abstract
A hybrid approach combining water-splitting electrochemistry and H2-oxidizing, CO2-fixing microorganisms offers a viable solution for producing value-added chemicals from sunlight, water, and air. The classic wisdom without thorough examination to date assumes that the electrochemistry in such a H2-mediated process is innocent of altering microbial behavior. Here, we report unexpected metabolic rewiring induced by water-splitting electrochemistry in H2-oxidizing acetogenic bacterium Sporomusa ovata that challenges such a classic view. We found that the planktonic S. ovata is more efficient in utilizing reducing equivalent for ATP generation in the materials-biology hybrids than cells grown with H2 supply, supported by our metabolomic and proteomic studies. The efficiency of utilizing reducing equivalents and fixing CO2 into acetate has increased from less than 80% of chemoautotrophy to more than 95% under electroautotrophic conditions. These observations unravel previously underappreciated materials' impact on microbial metabolism in seemingly simply H2-mediated charge transfer between biotic and abiotic components. Such a deeper understanding of the materials-biology interface will foster advanced design of hybrid systems for sustainable chemical transformation.
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Affiliation(s)
- Yongchao Xie
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Sevcan Erşan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA90095
| | - Xun Guan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Jingyu Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Jihui Sha
- Department of Biological Chemistry, University of California, Los Angeles, CA90095
| | - Shuangning Xu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | | | - Junyoung O. Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA90095
- California NanoSystems Institute, University of California, Los Angeles, CA90095
| | - Chong Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- California NanoSystems Institute, University of California, Los Angeles, CA90095
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11
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Xie Y, Chen G, Ramirez D, Yan J, Löffler FE. Complete Genome Sequence of Pseudomonas sp. Strain 273, a Haloalkane-Degrading Bacterium. Microbiol Resour Announc 2023; 12:e0017623. [PMID: 37289054 PMCID: PMC10353463 DOI: 10.1128/mra.00176-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023] Open
Abstract
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.
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Affiliation(s)
- Yongchao Xie
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Gao Chen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Diana Ramirez
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jun Yan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Frank E. Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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12
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Xiao J, Huang J, Wang Y, Qian X. The fate and behavior of perfluorooctanoic acid (PFOA) in constructed wetlands: Insights into potential removal and transformation pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160309. [PMID: 36403847 DOI: 10.1016/j.scitotenv.2022.160309] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
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.
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Affiliation(s)
- Jun Xiao
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
| | - Juan Huang
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China.
| | - Ying Wang
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
| | - Xiuwen Qian
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
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13
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Aukema KG, Bygd MD, Tassoulas LJ, Richman JE, Wackett LP. Fluoro-recognition: New in vivo fluorescent assay for toluene dioxygenase probing induction by and metabolism of polyfluorinated compounds. Environ Microbiol 2022; 24:5202-5216. [PMID: 36054238 PMCID: PMC9828342 DOI: 10.1111/1462-2920.16187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/30/2022] [Indexed: 01/12/2023]
Abstract
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.
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Affiliation(s)
- Kelly G. Aukema
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Madison D. Bygd
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Lambros J. Tassoulas
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Jack E. Richman
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
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14
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Xie Y, May AL, Chen G, Brown LP, Powers JB, Tague ED, Campagna SR, Löffler FE. Pseudomonas sp. Strain 273 Incorporates Organofluorine into the Lipid Bilayer during Growth with Fluorinated Alkanes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:8155-8166. [PMID: 35642897 DOI: 10.1021/acs.est.2c01454] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anthropogenic organofluorine compounds are recalcitrant, globally distributed, and a human health concern. Although rare, natural processes synthesize fluorinated compounds, and some bacteria have evolved mechanisms to metabolize organofluorine compounds. Pseudomonas sp. strain 273 grows with 1-fluorodecane (FD) and 1,10-difluorodecane (DFD) as carbon sources, but inorganic fluoride release was not stoichiometric. Metabolome studies revealed that this bacterium produces fluorinated anabolites and phospholipids. Mass spectrometric fatty acid profiling detected fluorinated long-chain (i.e., C12-C19) fatty acids in strain 273 cells grown with FD or DFD, and lipidomic profiling determined that 7.5 ± 0.2 and 82.0 ± 1.0% of the total phospholipids in strain 273 grown with FD or DFD, respectively, were fluorinated. The detection of the fluorinated metabolites and macromolecules represents a heretofore unrecognized sink for organofluorine, an observation with consequences for the environmental fate and transport of fluorinated aliphatic compounds.
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Affiliation(s)
- Yongchao Xie
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Amanda L May
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Gao Chen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Lindsay P Brown
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Joshua B Powers
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Eric D Tague
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, Tennessee 37996, United States
- University of Tennessee - Oak Ridge Innovation Institute, Knoxville, Tennessee 37996, United States
| | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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15
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Microwell Fluoride Screen for Chemical, Enzymatic, and Cellular Reactions Reveals Latent Microbial Defluorination Capacity for -CF 3 Groups. Appl Environ Microbiol 2022; 88:e0028822. [PMID: 35435713 DOI: 10.1128/aem.00288-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
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.
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16
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Wackett LP. Pseudomonas: Versatile Biocatalysts for PFAS. Environ Microbiol 2022; 24:2882-2889. [PMID: 35384226 DOI: 10.1111/1462-2920.15990] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Lawrence P Wackett
- Microbial Engineering, University of Minnesota.,Biotechnology Institute, University of Minnesota.,Biochemistry, Molecular Biology and Biophysics, University of Minnesota
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Bygd MD, Aukema KG, Richman JE, Wackett LP. Unexpected Mechanism of Biodegradation and Defluorination of 2,2-Difluoro-1,3-Benzodioxole by Pseudomonas putida F1. mBio 2021; 12:e0300121. [PMID: 34781746 PMCID: PMC8593668 DOI: 10.1128/mbio.03001-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Perfluorinated carbon atoms in a diether linkage are common in commercial anesthetics, drugs, fungicides, and insecticides. An important chemical group comprising perfluorodiethers is the 2,2-fluoro-1,3-benzodioxole (DFBD) moiety. The fluorine atoms stabilize the molecule by mitigating against metabolism by humans and microbes, as used in drugs and pesticides, respectively. Pseudomonas putida F1 catalyzed defluorination of DFBD at an initial rate of 2,100 nmol/h per mg cellular protein. This is orders of magnitude higher than previously reported microbial defluorination rates with multiply fluorinated carbon atoms. Defluorination rates declined after several hours, and the medium darkened. Significant defluorination activity was observed with cells grown on toluene but not l-arginine. Defluorination required only toluene dioxygenase. Pseudomonas and recombinant Escherichia coli cells expressing toluene dioxygenase oxidized DFBD to DFBD-4,5-dihydrodiol. The dihydrodiol could be oxidized to 4,5-dihydroxy-DFBD via the dihydrodiol dehydrogenase from P. putida F1. The dihydrodiol dehydrated with acid to yield a mixture of 4-hydroxy-DFBD and 5-hydroxy-DFBD. All those metabolites retained the difluoromethylene group; no fluoride or dark color was observed. The major route of DFBD-4,5-dihydrodiol decomposition produced fluoride and 1,2,3-trihydroxybenzene, or pyrogallol, and that was shown to be the source of the dark colors in the medium. A mechanism for DFBD-4,5-dihydrodiol transformation to two fluoride ions and pyrogallol is proposed. The Pseudomonas genome database and other databases revealed hundreds of bacteria with enzymes sharing high amino acid sequence identity to toluene dioxygenase from P. putida F1, suggesting the mechanism revealed here may apply to the defluorination of DFBD-containing compounds in the environment. IMPORTANCE There are more than 9,000 polyfluorinated compounds developed for commercial use, some negatively impacting human health, and they are generally considered to be resistant to biodegradation. Only a limited number of studies have identified microbes with enzymes sufficiently reactive to defluorinate difluoromethylene carbon groups. The present study examined one important group of commercial fluorinated chemicals and showed its rapid defluorination by a bacterium and its key enzyme, a Rieske dioxygenase. Rieske dioxygenases are common in environmental bacteria, and those closely resembling toluene dioxygenase from Pseudomonas putida F1 are candidates for biodegradative defluorination of the common 2,2-fluoro-1,3-benzodioxole (DFBD) moiety.
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Affiliation(s)
- Madison D. Bygd
- Microbial Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Kelly G. Aukema
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Jack E. Richman
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Lawrence P. Wackett
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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18
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Wackett LP. Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances. Microb Biotechnol 2021; 15:773-792. [PMID: 34570953 PMCID: PMC8913905 DOI: 10.1111/1751-7915.13928] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
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.
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Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, 55108, USA
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