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Bahrami Moghadam E, Nguyen N, Wang Y, Cirino PC. Directed Evolution of Protein-Based Sensors for Anaerobic Biological Activation of Methane. BIOSENSORS 2024; 14:325. [PMID: 39056601 PMCID: PMC11275114 DOI: 10.3390/bios14070325] [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] [Received: 05/24/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]
Abstract
Microbial alkane degradation pathways provide biological routes for converting these hydrocarbons into higher-value products. We recently reported the functional expression of a methyl-alkylsuccinate synthase (Mas) system in Escherichia coli, allowing for the heterologous anaerobic activation of short-chain alkanes. However, the enzymatic activation of methane via natural or engineered alkylsuccinate synthases has yet to be reported. To address this, we employed high-throughput screening to engineer the itaconate (IA)-responsive regulatory protein ItcR (WT-ItcR) from Yersinia pseudotuberculosis to instead respond to methylsuccinate (MS, the product of methane addition to fumarate), resulting in genetically encoded biosensors for MS. Here, we describe ItcR variants that, when regulating fluorescent protein expression in E. coli, show increased sensitivity, improved overall response, and enhanced specificity toward exogenously added MS relative to the wild-type repressor. Structural modeling and analysis of the ItcR ligand binding pocket provide insights into the altered molecular recognition. In addition to serving as biosensors for screening alkylsuccinate synthases capable of methane activation, MS-responsive ItcR variants also establish a framework for the directed evolution of other molecular reporters, targeting longer-chain alkylsuccinate products or other succinate derivatives.
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Affiliation(s)
| | | | | | - Patrick C. Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204-4004, USA; (E.B.M.)
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2
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Wang Y, Nguyen N, Lee SH, Wang Q, May JA, Gonzalez R, Cirino PC. Engineering Escherichia coli for anaerobic alkane activation: Biosynthesis of (1-methylalkyl)succinates. Biotechnol Bioeng 2021; 119:315-320. [PMID: 34633065 DOI: 10.1002/bit.27956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/28/2021] [Accepted: 10/03/2021] [Indexed: 11/11/2022]
Abstract
In anoxic environments, microbial activation of alkanes for subsequent metabolism occurs most commonly through the addition of fumarate to a subterminal carbon, producing an alkylsuccinate. Alkylsuccinate synthases are complex, multi-subunit enzymes that utilize a catalytic glycyl radical and require a partner, activating enzyme for hydrogen abstraction. While many genes encoding putative alkylsuccinate synthases have been identified, primarily from nitrate- and sulfate-reducing bacteria, few have been characterized and none have been reported to be functionally expressed in a heterologous host. Here, we describe the functional expression of the (1-methylalkyl)succinate synthase (Mas) system from Azoarcus sp. strain HxN1 in recombinant Escherichia coli. Mass spectrometry confirms anaerobic biosynthesis of the expected products of fumarate addition to hexane, butane, and propane. Maximum production of (1-methylpentyl)succinate is observed when masC, masD, masE, masB, and masG are all present on the expression plasmid; omitting masC reduces production by 66% while omitting any other gene eliminates production. Meanwhile, deleting iscR (encoding the repressor of the E. coli iron-sulfur cluster operon) improves product titer, as does performing the biotransformation at reduced temperature (18°C), both suggesting alkylsuccinate biosynthesis is largely limited by functional expression of this enzyme system.
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Affiliation(s)
- Yixi Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Nam Nguyen
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Seung H Lee
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, Florida, USA.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Qinxuan Wang
- Department of Chemistry, University of Houston, Houston, Texas, USA
| | - Jeremy A May
- Department of Chemistry, University of Houston, Houston, Texas, USA
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, Florida, USA
| | - Patrick C Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
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3
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Mitschke N, Eruçar G, Fsadni MH, Roberts AR, Sadeghi MM, Golding BT, Christoffers J, Wilkes H. Enantiopure 2,9‐Dideuterodecane – Preparation and Proof of Enantiopurity. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nico Mitschke
- Institut für Chemie Carl von Ossietzky Universität Oldenburg 26111 Oldenburg Germany
- Institut für Chemie und Biologie des Meeres (ICBM) Carl von Ossietzky Universität Oldenburg 26111 Oldenburg Germany
| | - Gülsera Eruçar
- Institut für Chemie Carl von Ossietzky Universität Oldenburg 26111 Oldenburg Germany
| | - Miriam H. Fsadni
- School of Natural & Environmental Sciences, Bedson Building Newcastle University NE1 7RU Newcastle upon Tyne UK
| | - Amy R. Roberts
- School of Natural & Environmental Sciences, Bedson Building Newcastle University NE1 7RU Newcastle upon Tyne UK
| | - Majid M. Sadeghi
- School of Natural & Environmental Sciences, Bedson Building Newcastle University NE1 7RU Newcastle upon Tyne UK
| | - Bernard T. Golding
- School of Natural & Environmental Sciences, Bedson Building Newcastle University NE1 7RU Newcastle upon Tyne UK
| | - Jens Christoffers
- Institut für Chemie Carl von Ossietzky Universität Oldenburg 26111 Oldenburg Germany
| | - Heinz Wilkes
- Institut für Chemie und Biologie des Meeres (ICBM) Carl von Ossietzky Universität Oldenburg 26111 Oldenburg Germany
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4
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Rossmassler K, Snow CD, Taggart D, Brown C, De Long SK. Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium. Appl Microbiol Biotechnol 2019; 103:4177-4192. [PMID: 30968165 DOI: 10.1007/s00253-019-09762-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.
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Affiliation(s)
- Karen Rossmassler
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | | | - Casey Brown
- Microbial Insights, Inc., Knoxville, TN, USA
| | - Susan K De Long
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.
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5
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Methanogenic degradation of branched alkanes in enrichment cultures of production water from a high-temperature petroleum reservoir. Appl Microbiol Biotechnol 2019; 103:2391-2401. [DOI: 10.1007/s00253-018-09574-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 11/26/2022]
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6
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Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E, Stokke R, Bødtker G, Steen IH. Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. Microorganisms 2018; 6:E63. [PMID: 29973550 PMCID: PMC6163223 DOI: 10.3390/microorganisms6030063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.
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Affiliation(s)
- Anders Schouw
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Francesca Vulcano
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Irene Roalkvam
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - William Peter Hocking
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Eoghan Reeves
- Department of Earth Science and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Runar Stokke
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Gunhild Bødtker
- Centre for Integrated Petroleum Research (CIPR), Uni Research AS, Nygårdsgaten 112, N-5008 Bergen, Norway.
| | - Ida Helene Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
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7
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Nowak JA, Shrestha PM, Weber RJ, McKenna AM, Chen H, Coates JD, Goldstein AH. Comprehensive Analysis of Changes in Crude Oil Chemical Composition during Biosouring and Treatments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1290-1300. [PMID: 29320174 DOI: 10.1021/acs.est.7b05346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biosouring in crude oil reservoirs by sulfate-reducing microbial communities (SRCs) results in hydrogen sulfide production, precipitation of metal sulfide complexes, increased industrial costs of petroleum production, and exposure issues for personnel. Potential treatment strategies include nitrate or perchlorate injections into reservoirs. Gas chromatography with vacuum ultraviolet ionization and high-resolution time-of-flight mass spectrometry (GC-VUV-HTOF) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with electrospray ionization were applied in this study to identify hydrocarbon degradation patterns and product formations in crude oil samples from biosoured, nitrate-treated, and perchlorate-treated bioreactor column experiments. Crude oil hydrocarbons were selectively transformed based on molecular weight and compound class in the biosouring control environment. Both the nitrate and the perchlorate treatments significantly reduced sulfide production; however, the nitrate treatment enhanced crude oil biotransformation, while the perchlorate treatment inhibited crude oil biotransformation. Nitrogen- and oxygen-containing biodegradation products, particularly with chemical formulas consistent with monocarboxylic and dicarboxylic acids containing 10-60 carbon atoms, were observed in the oil samples from both the souring control and the nitrate-treated columns but were not observed in the oil samples from the perchlorate-treated column. These results demonstrate that hydrocarbon degradation and product formation of crude oil can span hydrocarbon isomers and molecular weights up to C60 and double-bond equivalent classes ranging from straight-chain alkanes to polycyclic aromatic hydrocarbons. Our results also strongly suggest that perchlorate injections may provide a preferred strategy to treat biosouring through inhibition of biotransformation.
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Affiliation(s)
| | | | | | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Huan Chen
- National High Magnetic Field Laboratory, Florida State University , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
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8
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Aitken C, Head I, Jones D, Rowland S, Scarlett A, West C. Comprehensive two-dimensional gas chromatography-mass spectrometry of complex mixtures of anaerobic bacterial metabolites of petroleum hydrocarbons. J Chromatogr A 2018; 1536:96-109. [DOI: 10.1016/j.chroma.2017.06.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 04/24/2017] [Accepted: 06/11/2017] [Indexed: 01/15/2023]
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9
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Toth CRA, Gieg LM. Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition. Front Microbiol 2018; 8:2610. [PMID: 29354103 PMCID: PMC5758579 DOI: 10.3389/fmicb.2017.02610] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32) or heavy crude oil (°API = 16). Over the course of 17 months, we conducted routine analytical (GC, GC-MS) and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing) surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella), along with syntrophic bacteria (Syntrophus), methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”). Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems.
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Affiliation(s)
- Courtney R A Toth
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Lisa M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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10
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Lueders T. The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers. FEMS Microbiol Ecol 2016; 93:fiw220. [PMID: 27810873 PMCID: PMC5400083 DOI: 10.1093/femsec/fiw220] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/10/2016] [Indexed: 12/24/2022] Open
Abstract
The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. 13C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation.
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Affiliation(s)
- Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
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11
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Dvorski SEM, Gonsior M, Hertkorn N, Uhl J, Müller H, Griebler C, Schmitt-Kopplin P. Geochemistry of Dissolved Organic Matter in a Spatially Highly Resolved Groundwater Petroleum Hydrocarbon Plume Cross-Section. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5536-46. [PMID: 27152868 DOI: 10.1021/acs.est.6b00849] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
At numerous groundwater sites worldwide, natural dissolved organic matter (DOM) is quantitatively complemented with petroleum hydrocarbons. To date, research has been focused almost exclusively on the contaminants, but detailed insights of the interaction of contaminant biodegradation, dominant redox processes, and interactions with natural DOM are missing. This study linked on-site high resolution spatial sampling of groundwater with high resolution molecular characterization of DOM and its relation to groundwater geochemistry across a petroleum hydrocarbon plume cross-section. Electrospray- and atmospheric pressure photoionization (ESI, APPI) ultrahigh resolution mass spectrometry (FT-ICR-MS) revealed a strong interaction between DOM and reactive sulfur species linked to microbial sulfate reduction, i.e., the key redox process involved in contaminant biodegradation. Excitation emission matrix (EEM) fluorescence spectroscopy in combination with Parallel Factor Analysis (PARAFAC) modeling attributed DOM samples to specific contamination traits. Nuclear magnetic resonance (NMR) spectroscopy evaluated the aromatic compounds and their degradation products in samples influenced by the petroleum contamination and its biodegradation. Our orthogonal high resolution analytical approach enabled a comprehensive molecular level understanding of the DOM with respect to in situ petroleum hydrocarbon biodegradation and microbial sulfate reduction. The role of natural DOM as potential cosubstrate and detoxification reactant may improve future bioremediation strategies.
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Affiliation(s)
- Sabine E-M Dvorski
- Helmholtz Zentrum München-German Research Center for Environmental Health , Research Unit Analytical BioGeoChemistry, D-85764 Neuherberg, Germany
| | - Michael Gonsior
- University of Maryland Center for Environmental Science , Chesapeake Biological Laboratory, Solomons, Maryland 20688, United States
| | - Norbert Hertkorn
- Helmholtz Zentrum München-German Research Center for Environmental Health , Research Unit Analytical BioGeoChemistry, D-85764 Neuherberg, Germany
| | - Jenny Uhl
- Helmholtz Zentrum München-German Research Center for Environmental Health , Research Unit Analytical BioGeoChemistry, D-85764 Neuherberg, Germany
| | - Hubert Müller
- Helmholtz Zentrum München-German Research Center for Environmental Health , Institute of Groundwater Ecology, D-85764 Neuherberg, Germany
| | - Christian Griebler
- Helmholtz Zentrum München-German Research Center for Environmental Health , Institute of Groundwater Ecology, D-85764 Neuherberg, Germany
| | - Philippe Schmitt-Kopplin
- Helmholtz Zentrum München-German Research Center for Environmental Health , Research Unit Analytical BioGeoChemistry, D-85764 Neuherberg, Germany
- Technische Universität München , Chair of Analytical Food Chemistry, D-85354 Freising-Weihenstephan, Germany
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12
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Bellagamba M, Cruz Viggi C, Ademollo N, Rossetti S, Aulenta F. Electrolysis-driven bioremediation of crude oil-contaminated marine sediments. N Biotechnol 2016; 38:84-90. [PMID: 27079861 DOI: 10.1016/j.nbt.2016.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 01/02/2023]
Abstract
Bioremediation is an effective technology to tackle crude oil spill disasters, which takes advantage of the capacity of naturally occurring microorganisms to degrade petroleum hydrocarbons under a range of environmental conditions. The enzymatic process of breaking down oil is usually more rapid in the presence of oxygen. However, in contaminated sediments, oxygen levels are typically too low to sustain the rapid and complete biodegradation of buried hydrocarbons. Here, we explored the possibility to electrochemically manipulate the redox potential of a crude oil-contaminated marine sediment in order to establish, in situ, conditions that are conducive to contaminants biodegradation by autochthonous microbial communities. The proposed approach is based on the exploitation of low-voltage (2V) seawater electrolysis to drive oxygen generation (while minimizing chlorine evolution) on Dimensionally Stable Anodes (DSA) placed within the contaminated sediment. Results, based on a laboratory scale setup with chronically polluted sediments spiked with crude oil, showed an increased redox potential and a decreased pH in the vicinity of the anode of 'electrified' treatments, consistent with the occurrence of oxygen generation. Accordingly, hydrocarbons biodegradation was substantially accelerated (up to 3-times) compared to 'non-electrified' controls, while sulfate reduction was severely inhibited. Intermittent application of electrolysis proved to be an effective strategy to minimize the energy requirements of the process, without adversely affecting degradation performance. Taken as a whole, this study suggests that electrolysis-driven bioremediation could be a sustainable technology for the management of contaminated sediments.
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Affiliation(s)
- Marco Bellagamba
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29,300, 00015 Monterotondo (RM), Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29,300, 00015 Monterotondo (RM), Italy
| | - Nicoletta Ademollo
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29,300, 00015 Monterotondo (RM), Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29,300, 00015 Monterotondo (RM), Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29,300, 00015 Monterotondo (RM), Italy.
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13
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Wilkes H, Buckel W, Golding BT, Rabus R. Metabolism of Hydrocarbons in n-Alkane-Utilizing Anaerobic Bacteria. J Mol Microbiol Biotechnol 2016; 26:138-51. [PMID: 26959725 DOI: 10.1159/000442160] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The glycyl radical enzyme-catalyzed addition of n-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations of the two diastereoisomers of the product resulting from n-hexane activation by the n-alkane-utilizing denitrifying bacterium strain HxN1, i.e. (1-methylpentyl)succinate, were assigned as (2S,1'R) and (2R,1'R). Experiments with stereospecifically deuterated n-(2,5-2H2)hexanes revealed that exclusively the pro-S hydrogen atom is abstracted from C2 of the n-alkane by the enzyme and later transferred back to C3 of the alkylsuccinate formed. These results indicate that the alkylsuccinate-forming reaction proceeds with an inversion of configuration at the carbon atom (C2) of the n-alkane forming the new C-C-bond, and thus stereochemically resembles a SN2-type reaction. Therefore, the reaction may occur in a concerted manner, which may avoid the highly energetic hex-2-yl radical as an intermediate. The reaction is associated with a significant primary kinetic isotope effect (kH/kD ≥3) for hydrogen, indicating that the homolytic C-H-bond cleavage is involved in the first irreversible step of the reaction mechanism. The (1-methylalkyl)succinate synthases of n-alkane-utilizing anaerobic bacteria apparently have very broad substrate ranges enabling them to activate not only aliphatic but also alkyl-aromatic hydrocarbons. Thus, two denitrifiers and one sulfate reducer were shown to convert the nongrowth substrate toluene to benzylsuccinate and further to the dead-end product benzoyl-CoA. For this purpose, however, the modified β-oxidation pathway known from alkylbenzene-utilizing bacteria was not employed, but rather the pathway used for n-alkane degradation involving CoA ligation, carbon skeleton rearrangement and decarboxylation. Furthermore, various n-alkane- and alkylbenzene-utilizing denitrifiers and sulfate reducers were found to be capable of forming benzyl alcohols from diverse alkylbenzenes, putatively via dehydrogenases. The thermophilic sulfate reducer strain TD3 forms n-alkylsuccinates during growth with n-alkanes or crude oil, which, based on the observed patterns of homologs, do not derive from a terminal activation of n-alkanes.
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Affiliation(s)
- Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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