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Chen Y, Ren H, Kong X, Wu H, Lu Z. A multicomponent propane monooxygenase catalyzes the initial degradation of methyl tert-butyl ether in Mycobacterium vaccae JOB5. Appl Environ Microbiol 2023; 89:e0118723. [PMID: 37823642 PMCID: PMC10617536 DOI: 10.1128/aem.01187-23] [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: 07/10/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
Methyl tert-butyl ether (MTBE) has been recognized as a groundwater contaminant due to its widespread distribution and potential threat to human health. The limited understanding of the enzymes catalyzing MTBE degradation restricts their application in MTBE bioremediation. In this study, an MTBE-degrading soluble di-iron monooxygenase that clusters phylogenetically with a known propane monooxygenase (PRM) encoded by the prmABCD gene cluster was identified and functionally characterized, revealing their role in MTBE metabolism by Mycobacterium vaccae JOB5. Transcriptome analysis demonstrated that the expression of prmABCD was upregulated when JOB5 was induced by MTBE. Escherichia coli Rosetta heterologously expressing prmABCD from JOB5 could transform MTBE, indicating that the PRM of JOB5 is capable of the initial degradation of MTBE. The loss of the gene encoding the oxygenase α-subunit or β-subunit, the coupling protein, or the reductase disrupted MTBE transformation by the recombinant E. coli Rosetta. In addition, the catalytic capacity of PRM is likely affected by residue G95 in the active site pocket and residues I84, P165, A269, and V270 in the substrate tunnel structure. Mutation of amino acids in the active site and substrate tunnel resulted in inefficiency or inactivation of MTBE degradation, and the activity in 1,4-dioxane (1,4-D) degradation was diminished less than that in MTBE degradation.IMPORTANCEMulticomponent monooxygenases catalyzing the initial hydroxylation of MTBE are important in MTBE biodegradation. Previous studies of MTBE degradation enzymes have focused on P450s, alkane monooxygenase and MTBE monooxygenase, but the vital role of soluble di-iron monooxygenases has rarely been reported. In this study, we deciphered the essential catalytic role of a PRM and revealed the key residues of the PRM in MTBE metabolism. Our findings provide new insight into the MTBE-degrading gene cluster and enzymes in bacteria. This characterization of the PRM associated with MTBE degradation expands our understanding of MTBE-degrading gene diversity and provides a novel candidate enzyme for the bioremediation of MTBE-contaminated sites.
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Affiliation(s)
- Yiyang Chen
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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Rau J, Werner D, Beer M, Höper D, Kampen H. The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany. Parasitol Res 2022; 121:2587-2599. [PMID: 35857094 PMCID: PMC9378336 DOI: 10.1007/s00436-022-07576-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022]
Abstract
Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of numerous pathogens of medical and veterinary importance, including dengue, chikungunya and Zika viruses. Among others, the vector potential of mosquitoes is influenced by their microbiome. However, this influence is very dynamic and can vary between individuals and life stages. To obtain a rough overview on the microbiome of Ae. albopictus populations in Germany, pooled female and pooled male individuals from seven German locations were investigated by total RNA sequencing. The mosquito specimens had been collected as larvae in the field and processed immediately after adult emergence, i.e. without females having fed on blood. RNA fragments with high degrees of identity to a large number of viruses and microorganisms were identified, including, for example, Wolbachia pipientis and Acinetobacter baumannii, with differences between male and female mosquitoes. Knowledge about the natural occurrence of microorganisms in mosquitoes may be translated into new approaches to vector control, for example W. pipientis can be exploited to manipulate mosquito reproduction and vector competence. The study results show how diverse the microbiome of Ae. albopictus can be, and the more so needs to be adequately analysed and interpreted.
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Affiliation(s)
- Janine Rau
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research, Muencheberg, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
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Thornton SF, Nicholls HCG, Rolfe SA, Mallinson HEH, Spence MJ. Biodegradation and fate of ethyl tert-butyl ether (ETBE) in soil and groundwater: A review. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122046. [PMID: 32145642 DOI: 10.1016/j.jhazmat.2020.122046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/07/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
This review summarises the current state of knowledge on the biodegradation and fate of the gasoline ether oxygenate ethyl tert-butyl ether (ETBE) in soil and groundwater. Microorganisms have been identified in soil and groundwater with the ability to degrade ETBE aerobically as a carbon and energy source, or via cometabolism using alkanes as growth substrates. Aerobic biodegradation of ETBE initially occurs via hydroxylation of the ethoxy carbon by a monooxygenase enzyme, with subsequent formation of intermediates which include acetaldehyde, tert-butyl acetate (TBAc), tert-butyl alcohol (TBA), 2-hydroxy-2-methyl-1-propanol (MHP) and 2-hydroxyisobutyric acid (2-HIBA). Slow cell growth and low biomass yields on ETBE are believed to result from the ether structure and slow degradation kinetics, with potential limitations on ETBE metabolism. Genes known to facilitate transformation of ETBE include ethB (within the ethRABCD cluster), encoding a cytochrome P450 monooxygenase, and alkB-encoding alkane hydroxylases. Other genes have been identified in microorganisms but their activity and specificity towards ETBE remains poorly characterised. Microorganisms and pathways supporting anaerobic biodegradation of ETBE have not been identified, although this potential has been demonstrated in limited field and laboratory studies. The presence of co-contaminants (other ether oxygenates, hydrocarbons and organic compounds) in soil and groundwater may limit aerobic biodegradation of ETBE by preferential metabolism and consumption of available dissolved oxygen or enhance ETBE biodegradation through cometabolism. Both ETBE-degrading microorganisms and alkane-oxidising bacteria have been characterised, with potential for use in bioaugmentation and biostimulation of ETBE degradation in groundwater.
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Affiliation(s)
- S F Thornton
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - H C G Nicholls
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - S A Rolfe
- Dept of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield S10 2TN, UK
| | - H E H Mallinson
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - M J Spence
- Concawe, Environmental Science for European Refining, Boulevard du Souverain 165, 1160 Brussels, Belgium
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Hashemi SH, Kaykhaii M, Mirmoghaddam M, Boczkaj G. Preconcentration and Analytical Methods for Determination of Methyl Tert-Butyl Ether and Other Fuel Oxygenates and Their Degradation Products in Environment: A Review. Crit Rev Anal Chem 2020; 51:582-608. [PMID: 32312086 DOI: 10.1080/10408347.2020.1753164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fuel oxygenates (FOs) are mainly ethers or alcohols which are added to gasoline either to boost the octane number or to make the fuel burning process more "cleaner" with increasing the oxygen content, or to obtain a combination of both effects. FOs are water soluble with high mobility in the environment which presence even at very low concentrations lower the quality of water making it unsafe or unpleasant due to their objectionable taste and/or odor. Thus, their determination at trace in environmental samples is of high importance because of their sparingly biodegradability and their biological hazards. Instruments such as gas chromatography, Fourier transform infrared spectroscopy and ion mobility spectrometry are mainly used for the determination of FOs. However, the main challenge for determination of such oxygenates relates to proper sample preparation. Dilute or complex samples often demand a specific treatment to ensure effective enrichment of FOs before their detection. The main techniques used for this purpose are purge and trap, membrane extraction, and solid phase microextraction. This review presents a comprehensive evaluation of extraction/preconcentration techniques and analytical methods for determination of FOs in environmental samples. Advantages and disadvantages of each method are discussed in details along with critical evaluation of currently available methods.
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Affiliation(s)
- Sayyed Hossein Hashemi
- Department of Marine Chemistry, Faculty of Marine Science, Chabahar Maritime University, Chabahar, Iran
| | - Massoud Kaykhaii
- Department of Chemistry, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
| | - Majid Mirmoghaddam
- Department of Chemistry, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
| | - Grzegorz Boczkaj
- Faculty of Chemistry, Department of Process Engineering and Chemical Technology, Gdansk University of Technology, Gdansk, Poland
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Nicholls HCG, Mallinson HEH, Rolfe SA, Hjort M, Spence MJ, Thornton SF. Influence of contaminant exposure on the development of aerobic ETBE biodegradation potential in microbial communities from a gasoline-impacted aquifer. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:122022. [PMID: 31962211 DOI: 10.1016/j.jhazmat.2020.122022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/14/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Aerobic biodegradation of ethyl tert butyl ether (ETBE) in a gasoline-impacted aquifer was investigated in laboratory microcosms containing groundwater and aquifer material from ETBE-impacted and non-impacted locations amended with either ETBE, or ETBE plus methyl tert butyl ether (MTBE). As sole substrate, ETBE was biodegraded (maximum rate of 0.54 day-1) without a lag in ETBE-impacted microcosms but with a lag of up to 66 days in non-impacted microcosms (maximum rate of 0.38 day-1). As co-substrate, ETBE was biodegraded preferentially (maximum rate of 0.25 and 0.99 day-1 in non-impacted and impacted microcosms, respectively) before MTBE (maximum rate of 0.24 and 0.36 day-1 in non-impacted and impacted microcosms, respectively). Further addition of ETBE and MTBE reduced lags and increased biodegradation rates. ethB gene copy numbers increased significantly (>100 fold) after exposure to ETBE, while overall cell numbers remained constant, suggesting that ethB-containing microorganisms come to dominate the microbial communities. Deep sequencing of 16S rRNA genes identified members of the Comamonadaceae family that increased in relative abundance upon exposure to ETBE. This study demonstrates the potential for ETBE biodegradation within the unsaturated and saturated zone, and that ETBE biodegrading capability is rapidly developed and maintained within the aquifer microbial community over extended timescales.
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Affiliation(s)
- H C G Nicholls
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - H E H Mallinson
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - S A Rolfe
- Dept of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - M Hjort
- Concawe, Environmental Science for European Refining, Boulevard du Souverain 165, 1160 Brussels, Belgium
| | - M J Spence
- Concawe, Environmental Science for European Refining, Boulevard du Souverain 165, 1160 Brussels, Belgium
| | - S F Thornton
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom.
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Purswani J, Guisado IM, Coello-Cabezas J, González-López J, Pozo C. Social microbial inocula confer functional stability in a methyl tert-butyl ether extractive membrane biofilm bioreactor. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 244:855-860. [PMID: 30390459 DOI: 10.1016/j.envpol.2018.10.100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/19/2018] [Accepted: 10/24/2018] [Indexed: 06/08/2023]
Abstract
Methyl tert-butyl ether (MTBE) degradation technologies based on two-phase partitioning systems such as extractive membrane biofilm reactors (EMBFR) permit separation of biological and contaminant compartments, thus allowing optimization of the biological section. In this study, we set-up an EMBFR with three MTBE-degrading and cooperating strains (termed social biofilm: Agrobacterium sp. MS2, Paenibacillus etheri SH7T and Rhodococcus ruber EE6). The removal efficiency of the social-biofilm EMBFR was 80%, and functional stability was observed in the reactor, i.e. more efficient than previous studies (single-strain inoculated EMBFR, <50% removal efficiency and unstable function). Metabolite tert-butyl alcohol was not observed, and the EC50 values were higher than those observed in single-strain EMBFRs. Comparative analysis of the MTBE enzymatic pathway and the social-biofilm was performed, where the mechanism of cooperation observed within the social-biofilm is likely due to enzymatic redundancy. Functional outcomes were equal to previous batch tests, hence 100% scalability was obtained. Overall, higher functional and stability outcomes are obtained with the use of the social-biofilm in an MTBE-EMBFR.
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Affiliation(s)
- Jessica Purswani
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain.
| | - Isabel M Guisado
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain
| | - Julio Coello-Cabezas
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain
| | - Jesús González-López
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain
| | - Clementina Pozo
- Environmental Microbiology Group, Institute of Water Research, University of Granada, Granada, Spain; Department of Microbiology, University of Granada, Granada, Spain
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van der Waals MJ, Plugge C, Meima-Franke M, de Waard P, Bodelier PLE, Smidt H, Gerritse J. Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater. WATER RESEARCH 2019; 148:314-323. [PMID: 30391860 DOI: 10.1016/j.watres.2018.10.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
EtBE is a fuel oxygenate that is synthesized from (bio)ethanol and fossil-based isobutylene, and replaces the fossil-based MtBE. Biodegradation of EtBE to harmless metabolites or end products can reduce the environmental and human health risks after accidental release. In this study, an algal-bacterial culture enriched from contaminated groundwater was used to (i) assess the potential for EtBE degradation, (ii) resolve the EtBE degradation pathway and (iii) characterize the phylogenetic composition of the bacterial community involved in EtBE degradation in contaminated groundwater. In an unamended microcosm, algal growth was observed after eight weeks when exposed to a day-night light cycle. In the fed-batch reactor, oxygen produced by the algae Scenedesmus and Chlorella was used by bacteria to degrade 50 μM EtBE replenishments with a cumulative total of 1250 μM in a day/night cycle (650 lux), over a period of 913 days. The microbial community in the fed-batch reactor degraded EtBE, using a P450 monooxygenase and 2-hydroxyisobutyryl-CoA mutase, to tert-butyl alcohol (TBA), ethanol and CO2 as determined using 13C nuclear magnetic resonance spectroscopy (NMR) and gas chromatography. Stable isotope probing (SIP) with 13C6 labeled EtBE in a fed-batch vessel showed no significant difference in community profiles of the 13C and 12C enriched DNA fractions, with representatives of the families Halomonadaceae, Shewanellaceae, Rhodocyclaceae, Oxalobacteraceae, Comamonadaceae, Sphingomonadaceae, Hyphomicrobiaceae, Candidatus Moranbacteria, Omnitrophica, Anaerolineaceae, Nocardiaceae, and Blastocatellaceae. This is the first study describing micro-oxic degradation of EtBE by an algal-bacterial culture. This algal-bacterial culture has advantages compared with conventional aerobic treatments: (i) a lower risk of EtBE evaporation and (ii) no need for external oxygen supply in the presence of light. This study provides novel leads towards future possibilities to implement algal-bacterial consortia in field-scale groundwater or wastewater treatment.
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Affiliation(s)
- Marcelle J van der Waals
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, the Netherlands; Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.
| | - Caroline Plugge
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Marion Meima-Franke
- The Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - Pieter de Waard
- Wageningen University & Research, BioNanoTechnology, Bornse Weilanden 9, 6700 EK, Wageningen, the Netherlands
| | - Paul L E Bodelier
- The Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Jan Gerritse
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, the Netherlands
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Suk WA, Heacock ML, Trottier BA, Amolegbe SM, Avakian MD, Henry HF, Carlin DJ, Reed LG. Assessing the Economic and Societal Benefits of SRP-Funded Research. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:065002. [PMID: 29916809 PMCID: PMC6108577 DOI: 10.1289/ehp3534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The National Institute of Environmental Health Sciences (NIEHS) Superfund Basic Research and Training Program (SRP) funds a wide range of transdisciplinary research projects spanning the biomedical and environmental sciences and engineering, supporting and promoting the application of that research to solving real-world problems. OBJECTIVES We used a case study approach to identify the economic and societal benefits of SRP-funded research, focusing on the use of potentially hazardous substance remediation and site monitoring tools. We also identified successes and challenges involved in translating SRP grantees' research findings and advances into application. DISCUSSION We identified remediation and detection research projects supported by the SRP with the most potential for economic and societal benefits and selected 36 for analysis. To examine the benefits of these applied technologies, we interviewed 28 SRP-supported researchers and 41 partners. Five case studies emerged with the most complete information on cost savings-total savings estimated at >$100 million. Our analysis identified added societal benefits such as creation of small businesses, land and water reuse, sustainable technologies, exposure reduction, and university-industry partnerships. CONCLUSIONS Research funded by the SRP has yielded significant cost savings while providing additional societal benefits. https://doi.org/10.1289/EHP3534.
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Affiliation(s)
- William A Suk
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Michelle L Heacock
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Brittany A Trottier
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | | | - Heather F Henry
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Danielle J Carlin
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
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Joshi G, Schmidt R, Scow KM, Denison MS, Hristova KR. Effect of benzene and ethylbenzene on the transcription of methyl-tert-butyl ether degradation genes of Methylibium petroleiphilum PM1. MICROBIOLOGY-SGM 2016; 162:1563-1571. [PMID: 27450417 DOI: 10.1099/mic.0.000338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes mdpA (MTBE monooxygenase), mdpJ (TBA hydroxylase) and bmoA (benzene monooxygenase) in response to MTBE, TBA and benzene, respectively. Delayed induction of mdpA and mdpJ transcription occurred with mixtures of benzene and MTBE or TBA, respectively. bmoA transcription was similar in the presence of MTBE or TBA with benzene as in their absence. Our results also indicate that ethylbenzene, previously proposed as an inhibitor of MTBE degradation in some bacteria, inhibits transcription of mdpA, mdpJ and bmoAgenes in strain PM1.
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Affiliation(s)
- Geetika Joshi
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Kate M Scow
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Michael S Denison
- Department of Environmental Toxicology, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
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Hernández-Saldaña OF, Valencia-Posadas M, de la Fuente-Salcido NM, Bideshi DK, Barboza-Corona JE. Bacteriocinogenic Bacteria Isolated from Raw Goat Milk and Goat Cheese Produced in the Center of México. Indian J Microbiol 2016; 56:301-8. [PMID: 27407294 DOI: 10.1007/s12088-016-0587-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/19/2016] [Indexed: 01/25/2023] Open
Abstract
Currently, there are few reports on the isolation of microorganisms from goat milk and goat cheese that have antibacterial activity. In particular, there are no reports on the isolation of microorganisms with antibacterial activity from these products in central Mexico. Our objective was to isolate bacteria, from goat products, that synthesized antimicrobial peptides with activity against a variety of clinically significant bacteria. We isolated and identified Lactobacillus rhamnosus, L. plantarum, L. pentosus, L. helveticus and Enterococcus faecium from goat cheese, and Aquabacterium fontiphilum, Methylibium petroleiphilum, Piscinobacter aquaticus and Staphylococcus xylosus from goat milk. These bacteria isolated from goat cheese were able to inhibit Staphylococcus aureus, Bacillus cereus, Escherichia coli, Listeria monocytogenes, L. inoccua, Pseudomona aeruginosa, Shigella flexneri, Serratia marcescens, Enterobacter cloacae and Klebsiella pneumoniae. In addition, bacteria from goat milk showed inhibitory activity against B. cereus, L. lactis, E. coli, S. flexneri, E. cloacae and K. pneumonia; S. aureus, L. innocua, S. agalactiae and S. marcescens. The bacteriocins produced by these isolates were shown to be acid stable (pH 2-6) and thermotolerant (up to 100 °C), but were susceptible to proteinases. When screened by PCR for the presence of nisin, pediocin and enterocin A genes, none was found in isolates recovered from goat milk, and only the enterocin A gene was found in isolates from goat cheese.
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Affiliation(s)
- Oscar F Hernández-Saldaña
- División de Ciencias de la Vida, Universidad de Guanajuato, Campus Irapuato-Salamanca (CIS), Ex-Hacienda El Copal km. 9, carretera Irapuato-Silao; A.P. 311, C.P. 36500 Irapuato, Guanajuato Mexico ; Graduate Program in Biosciences, Life Science Division, Universidad de Guanajuato, Ex-Hacienda El Copal km. 9, carretera Irapuato-Silao; A.P. 311, C.P. 36500 Irapuato, Guanajuato Mexico
| | - Mauricio Valencia-Posadas
- División de Ciencias de la Vida, Universidad de Guanajuato, Campus Irapuato-Salamanca (CIS), Ex-Hacienda El Copal km. 9, carretera Irapuato-Silao; A.P. 311, C.P. 36500 Irapuato, Guanajuato Mexico ; Departamento de Agronomía, Universidad de Guanajuato CIS, Ex-Hacienda El Copal km. 9, carretera Irapuato-Silao; A.P. 311, C.P. 36500 Irapuato, Guanajuato Mexico ; Graduate Program in Biosciences, Life Science Division, Universidad de Guanajuato, Ex-Hacienda El Copal km. 9, carretera Irapuato-Silao; A.P. 311, C.P. 36500 Irapuato, Guanajuato Mexico
| | - Norma M de la Fuente-Salcido
- Escuela de Ciencias Biológicas, Universidad Autónoma de Coahuila, Boulevard Torreón-Matamoros Km. 7.5, Ciudad Universitaria Campus Torreón, C.P. 27104 Torreón, Coahuila Mexico
| | - Dennis K Bideshi
- Department of Natural and Mathematical Sciences, California Baptist University, 8432 Magnolia Avenue, Riverside, CA 92504 USA ; Department of Entomology, University of California, Riverside, Riverside, CA 92521 USA
| | - José E Barboza-Corona
- División de Ciencias de la Vida, Universidad de Guanajuato, Campus Irapuato-Salamanca (CIS), Ex-Hacienda El Copal km. 9, carretera Irapuato-Silao; A.P. 311, C.P. 36500 Irapuato, Guanajuato Mexico ; Departamento de Alimentos, Universidad de Guanajuato CIS, Ex-Hacienda El Copal km. 9, carretera Irapuato-Silao; A.P. 311, C.P. 36500 Irapuato, Guanajuato Mexico ; Graduate Program in Biosciences, Life Science Division, Universidad de Guanajuato, Ex-Hacienda El Copal km. 9, carretera Irapuato-Silao; A.P. 311, C.P. 36500 Irapuato, Guanajuato Mexico
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11
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Szabó Z, Gyula P, Robotka H, Bató E, Gálik B, Pach P, Pekker P, Papp I, Bihari Z. Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary. Stand Genomic Sci 2015. [PMID: 26221420 PMCID: PMC4517660 DOI: 10.1186/s40793-015-0023-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Methylibium sp. strain T29 was isolated from a gasoline-contaminated aquifer and proved to have excellent capabilities in degrading some common fuel oxygenates like methyl tert-butyl ether, tert-amyl methyl ether and tert-butyl alcohol along with other organic compounds. Here, we report the draft genome sequence of M. sp. strain T29 together with the description of the genome properties and its annotation. The draft genome consists of 608 contigs with a total size of 4,449,424 bp and an average coverage of 150×. The genome exhibits an average G + C content of 68.7 %, and contains 4754 protein coding and 52 RNA genes, including 48 tRNA genes. 71 % of the protein coding genes could be assigned to COG (Clusters of Orthologous Groups) categories. A formerly unknown circular plasmid designated as pT29A was isolated and sequenced separately and found to be 86,856 bp long.
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Affiliation(s)
- Zsolt Szabó
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Gyula
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Hermina Robotka
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Emese Bató
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Bence Gálik
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Pach
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Pekker
- Materials Science Research Group, Hungarian Academy of Sciences-University of Miskolc, Miskolc, Hungary
| | - Ildikó Papp
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Zoltán Bihari
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
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12
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Joshi G, Schmidt R, Scow KM, Denison MS, Hristova KR. Gene mdpC plays a regulatory role in the methyl-tert-butyl ether degradation pathway of Methylibium petroleiphilum strain PM1. FEMS Microbiol Lett 2015; 362:fnv029. [PMID: 25724531 DOI: 10.1093/femsle/fnv029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC(-). We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA.
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Affiliation(s)
- Geetika Joshi
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Kate M Scow
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Michael S Denison
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA
| | - Krassimira R Hristova
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA Biological Sciences Department, Marquette University, Milwaukee, WI 53201, USA
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13
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Terrell CR, Burks EA, Whitman CP, Hoffman DW. Structural and kinetic characterization of two 4-oxalocrotonate tautomerases in Methylibium petroleiphilum strain PM1. Arch Biochem Biophys 2013; 537:113-24. [PMID: 23831510 DOI: 10.1016/j.abb.2013.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 06/25/2013] [Indexed: 11/26/2022]
Abstract
Methylibium petroleiphilum strain PM1 uses various petroleum products including the fuel additive methyl tert-butyl ether and straight chain and aromatic hydrocarbons as sole carbon and energy sources. It has two operons, dmpI and dmpII, that code for the enzymes in a pair of parallel meta-fission pathways. In order to understand the roles of the pathways, the 4-oxalocrotonate tautomerase (4-OT) isozyme from each pathway was characterized. Tautomerase I and tautomerase II have the lowest pairwise sequence identity (35%) among the isozyme pairs in the parallel pathways, and could offer insight into substrate preferences and pathway functions. The kinetic parameters of tautomerase I and tautomerase II were determined using 2-hydroxymuconate and 5-(methyl)-2-hydroxymuconate. Both tautomerase I and tautomerase II process the substrates, but with different efficiencies. Crystal structures were determined for both tautomerase I and tautomerase II, at 1.57 and 1.64Å resolution, respectively. The backbones of tautomerase I and tautomerase II are highly similar, but have distinct active site environments. The results, in combination with those for other structurally and kinetically characterized 4-OT isozymes, suggest that tautomerase I catalyzes the tautomerization of both 2-hydroxymuconate and alkyl derivatives, whereas tautomerase II might specialize in other aromatic hydrocarbon metabolites.
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Affiliation(s)
- Cassidy R Terrell
- Department of Chemistry and Biochemistry, University of Texas, Austin, 78712, USA
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14
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Hicks KA, Schmidt R, Nickelsen MG, Boyle SL, Baker JM, Tornatore PM, Hristova KR, Scow KM. Successful treatment of an MTBE-impacted aquifer using a bioreactor self-colonized by native aquifer bacteria. Biodegradation 2013; 25:41-53. [PMID: 23613160 DOI: 10.1007/s10532-013-9639-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/06/2013] [Indexed: 11/26/2022]
Abstract
A field-scale fixed bed bioreactor was used to successfully treat an MTBE-contaminated aquifer in North Hollywood, CA without requiring inoculation with introduced bacteria. Native bacteria from the MTBE-impacted aquifer rapidly colonized the bioreactor, entering the bioreactor in the contaminated groundwater pumped from the site, and biodegraded MTBE with greater than 99 % removal efficiency. DNA sequencing of the 16S rRNA gene identified MTBE-degrading bacteria Methylibium petroleiphilum in the bioreactor. Quantitative PCR showed M. petroleiphilum enriched by three orders of magnitude in the bioreactor above densities pre-existing in the groundwater. Because treatment was carried out by indigenous rather than introduced organisms, regulatory approval was obtained for implementation of a full-scale bioreactor to continue treatment of the aquifer. In addition, after confirmation of MTBE removal in the bioreactor to below maximum contaminant limit levels (MCL; MTBE = 5 μg L(-1)), treated water was approved for reinjection back into the aquifer rather than requiring discharge to a water treatment system. This is the first treatment system in California to be approved for reinjection of biologically treated effluent into a drinking water aquifer. This study demonstrated the potential for using native microbial communities already present in the aquifer as an inoculum for ex-situ bioreactors, circumventing the need to establish non-native, non-acclimated and potentially costly inoculants. Understanding and harnessing the metabolic potential of native organisms circumvents some of the issues associated with introducing non-native organisms into drinking water aquifers, and can provide a low-cost and efficient remediation technology that can streamline future bioremediation approval processes.
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Affiliation(s)
- Kristin A Hicks
- Department of Land, Air and Water Resources, University of California, One Shields Ave, Davis, CA, 95616, USA
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15
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Constitutive expression of the cytochrome P450 EthABCD monooxygenase system enables degradation of synthetic dialkyl ethers in Aquincola tertiaricarbonis L108. Appl Environ Microbiol 2013; 79:2321-7. [PMID: 23354715 DOI: 10.1128/aem.03348-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Rhodococcus ruber IFP 2001, Rhodococcus zopfii IFP 2005, and Gordonia sp. strain IFP 2009, the cytochrome P450 monooxygenase EthABCD catalyzes hydroxylation of methoxy and ethoxy residues in the fuel oxygenates methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME). The expression of the IS3-type transposase-flanked eth genes is ETBE dependent and controlled by the regulator EthR (C. Malandain et al., FEMS Microbiol. Ecol. 72:289-296, 2010). In contrast, we demonstrated by reverse transcription-quantitative PCR (RT-qPCR) that the betaproteobacterium Aquincola tertiaricarbonis L108, which possesses the ethABCD genes but lacks ethR, constitutively expresses the P450 system at high levels even when growing on nonether substrates, such as glucose. The mutant strain A. tertiaricarbonis L10, which is unable to degrade dialkyl ethers, resulted from a transposition event mediated by a rolling-circle IS91-type element flanking the eth gene cluster in the wild-type strain L108. The constitutive expression of Eth monooxygenase is likely initiated by the housekeeping sigma factor σ(70), as indicated by the presence in strain L108 of characteristic -10 and -35 binding sites upstream of ethA which are lacking in strain IFP 2001. This enables efficient degradation of diethyl ether, diisopropyl ether, MTBE, ETBE, TAME, and tert-amyl ethyl ether (TAEE) without any lag phase in strain L108. However, ethers with larger residues, n-hexyl methyl ether, tetrahydrofuran, and alkyl aryl ethers, were not attacked by the Eth system at significant rates in resting-cell experiments, indicating that the residue in the ether molecule which is not hydroxylated also contributes to the determination of substrate specificity.
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16
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Hyman M. Biodegradation of gasoline ether oxygenates. Curr Opin Biotechnol 2012; 24:443-50. [PMID: 23116604 DOI: 10.1016/j.copbio.2012.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 09/17/2012] [Accepted: 10/03/2012] [Indexed: 10/27/2022]
Abstract
Ether oxygenates such as methyl tertiary butyl ether (MTBE) are added to gasoline to improve fuel combustion and decrease exhaust emissions. Ether oxygenates and their tertiary alcohol metabolites are now an important group of groundwater pollutants. This review highlights recent advances in our understanding of the microorganisms, enzymes and pathways involved in both the aerobic and anaerobic biodegradation of these compounds. This review also aims to illustrate how these microbiological and biochemical studies have guided, and have helped refine, molecular and stable isotope-based analytical approaches that are increasingly being used to detect and quantify biodegradation of these compounds in contaminated environments.
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Affiliation(s)
- Michael Hyman
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA.
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North KP, Mackay DM, Annable MD, Sublette KL, Davis G, Holland RB, Petersen D, Scow KM. An ex situ evaluation of TBA- and MTBE-baited bio-traps. WATER RESEARCH 2012; 46:3879-3888. [PMID: 22621895 PMCID: PMC3582699 DOI: 10.1016/j.watres.2012.04.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 04/13/2012] [Accepted: 04/19/2012] [Indexed: 06/01/2023]
Abstract
Aquifer microbial communities can be investigated using Bio-traps(®) ("bio-traps"), passive samplers containing Bio-Sep(®) beads ("bio-beads") that are deployed in monitoring wells to be colonized by bacteria delivered via groundwater flow through the well. When bio-beads are "baited" with organic contaminants enriched in (13)C, stable isotope probing allows assessment of the composition and activity of the microbial community. This study used an ex situ system fed by groundwater continuously extracted from an adjacent monitoring well within an experimentally-created aerobic zone treating a tert-butyl alcohol (TBA) plume. The goal was to evaluate aspects of bio-trap performance that cannot be studied quantitatively in situ. The measured groundwater flow through a bio-trap housing suggests that such traps might typically "sample" about 1.8 L per month. The desorption of TBA or methyl tert-butyl ether (MTBE) bait from bio-traps during a typical deployment duration of 6 weeks was approximately 90% and 45%, respectively, of the total initial bait load, with initially high rate of mass loss that decreased markedly after a few days. The concentration of TBA in groundwater flowing by the TBA-baited bio-beads was estimated to be as high as 3400 mg/L during the first few days, which would be expected to inhibit growth of TBA-degrading microbes. Initial inhibition was also implied for the MTBE-baited bio-trap, but at lower concentrations and for a shorter time. After a few days, concentrations in groundwater flowing through the bio-traps dropped below inhibitory concentrations but remained 4-5 orders of magnitude higher than TBA or MTBE concentrations within the aquifer at the experimental site. Desorption from the bio-beads during ex situ deployment occurred at first as predicted by prior sorption analyses of bio-beads but with apparent hysteresis thereafter, possibly due to mass transfer limitations caused by colonizing microbes. These results suggest that TBA- or MTBE-baited bio-traps could be baited at lower initial total mass loading with no detriment to trapping ability. The bio-traps were able to collect detectable amounts of microbial DNA and thus allow some insight into the sparse microbial community present in the aquifer during remediation of the low concentration plume.
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Affiliation(s)
- Katharine P. North
- Department of Land, Air and Water Resources, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Douglas M. Mackay
- Department of Land, Air and Water Resources, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Michael D. Annable
- Department of Environmental Engineering Sciences, University of Florida, 1600 SW Archer Rd, Gainesville, FL 32611, USA
| | - Kerry L. Sublette
- Center for Applied Biogeosciences, University of Tulsa, 800 South Tucker Dr, Tulsa, OK 74104, USA
| | - Greg Davis
- Microbial Insights, Inc., 2340 Stock Creek Blvd, Rockford, TN 37853, USA
| | - Reef B. Holland
- Department of Microbiology, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Daniel Petersen
- Department of Land, Air and Water Resources, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Kate M. Scow
- Department of Land, Air and Water Resources, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
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18
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Rosell M, Gonzalez-Olmos R, Rohwerder T, Rusevova K, Georgi A, Kopinke FD, Richnow HH. Critical evaluation of the 2D-CSIA scheme for distinguishing fuel oxygenate degradation reaction mechanisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:4757-4766. [PMID: 22455373 DOI: 10.1021/es2036543] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Although the uniform initial hydroxylation of methyl tert-butyl ether (MTBE) and other oxygenates during aerobic biodegradation has already been proven by molecular tools, variations in carbon and hydrogen enrichment factors (ε(C) and ε(H)) have still been associated with different reaction mechanisms (McKelvie et al. Environ. Sci. Technol. 2009, 43, 2793-2799). Here, we present new laboratory-derived ε(C) and ε(H) data on the initial degradation mechanisms of MTBE, ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME) by chemical oxidation (permanganate, Fenton reagents), acid hydrolysis, and aerobic bacteria cultures (species of Aquincola, Methylibium, Gordonia, Mycobacterium, Pseudomonas, and Rhodococcus). Plotting of Δδ(2)H/ Δδ(13)C data from chemical oxidation and hydrolysis of ethers resulted in slopes (Λ values) of 22 ± 4 and between 6 and 12, respectively. With A. tertiaricarbonis L108, R. zopfii IFP 2005, and Gordonia sp. IFP 2009, ε(C) was low (<|-1|‰) and ε(H) was insignificant. Fractionation obtained with P. putida GPo1 was similar to acid hydrolysis and M. austroafricanum JOB5 and R. ruber DSM 7511 displayed Λ values previously only ascribed to anaerobic attack. The fractionation patterns rather correlate with the employment of different P450, AlkB, and other monooxygenases, likely catalyzing ether hydroxylation via different transition states. Our data questions the value of 2D-CSIA for a simple distinguishing of oxygenate biotransformation mechanisms, therefore caution and complementary tools are needed for proper interpretation of groundwater plumes at field sites.
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Affiliation(s)
- Mònica Rosell
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany.
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19
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Bacterial degradation of tert-amyl alcohol proceeds via hemiterpene 2-methyl-3-buten-2-ol by employing the tertiary alcohol desaturase function of the Rieske nonheme mononuclear iron oxygenase MdpJ. J Bacteriol 2011; 194:972-81. [PMID: 22194447 DOI: 10.1128/jb.06384-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tertiary alcohols, such as tert-butyl alcohol (TBA) and tert-amyl alcohol (TAA) and higher homologues, are only slowly degraded microbially. The conversion of TBA seems to proceed via hydroxylation to 2-methylpropan-1,2-diol, which is further oxidized to 2-hydroxyisobutyric acid. By analogy, a branched pathway is expected for the degradation of TAA, as this molecule possesses several potential hydroxylation sites. In Aquincola tertiaricarbonis L108 and Methylibium petroleiphilum PM1, a likely candidate catalyst for hydroxylations is the putative tertiary alcohol monooxygenase MdpJ. However, by comparing metabolite accumulations in wild-type strains of L108 and PM1 and in two mdpJ knockout mutants of strain L108, we could clearly show that MdpJ is not hydroxylating TAA to diols but functions as a desaturase, resulting in the formation of the hemiterpene 2-methyl-3-buten-2-ol. The latter is further processed via the hemiterpenes prenol, prenal, and 3-methylcrotonic acid. Likewise, 3-methyl-3-pentanol is degraded via 3-methyl-1-penten-3-ol. Wild-type strain L108 and mdpJ knockout mutants formed isoamylene and isoprene from TAA and 2-methyl-3-buten-2-ol, respectively. It is likely that this dehydratase activity is catalyzed by a not-yet-characterized enzyme postulated for the isomerization of 2-methyl-3-buten-2-ol and prenol. The vitamin requirements of strain L108 growing on TAA and the occurrence of 3-methylcrotonic acid as a metabolite indicate that TAA and hemiterpene degradation are linked with the catabolic route of the amino acid leucine, including an involvement of the biotin-dependent 3-methylcrotonyl coenzyme A (3-methylcrotonyl-CoA) carboxylase LiuBD. Evolutionary aspects of favored desaturase versus hydroxylation pathways for TAA conversion and the possible role of MdpJ in the degradation of higher tertiary alcohols are discussed.
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20
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Rasa E, Chapman SW, Bekins BA, Fogg GE, Scow KM, Mackay DM. Role of back diffusion and biodegradation reactions in sustaining an MTBE/TBA plume in alluvial media. JOURNAL OF CONTAMINANT HYDROLOGY 2011; 126:235-47. [PMID: 22115089 PMCID: PMC3267905 DOI: 10.1016/j.jconhyd.2011.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 07/27/2011] [Accepted: 08/18/2011] [Indexed: 05/19/2023]
Abstract
A methyl tert-butyl ether (MTBE) / tert-butyl alcohol (TBA) plume originating from a gasoline spill in late 1994 at Vandenberg Air Force Base (VAFB) persisted for over 15 years within 200 feet of the original spill source. The plume persisted until 2010 despite excavation of the tanks and piping within months after the spill and excavations of additional contaminated sediments from the source area in 2007 and 2008. The probable history of MTBE concentrations along the plume centerline at its source was estimated using a wide variety of available information, including published details about the original spill, excavations and monitoring by VAFB consultants, and our own research data. Two-dimensional reactive transport simulations of MTBE along the plume centerline were conducted for a 20-year period following the spill. These analyses suggest that MTBE diffused from the thin anaerobic aquifer into the adjacent anaerobic silts and transformed to TBA in both aquifer and silt layers. The model reproduces the observation that after 2004 TBA was the dominant solute, diffusing back out of the silts into the aquifer and sustaining plume concentrations much longer than would have been the case in the absence of such diffusive exchange. Simulations also suggest that aerobic degradation of MTBE or TBA at the water table in the overlying silt layer significantly affected concentrations of MTBE and TBA by limiting the chemical mass available for back diffusion to the aquifer.
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Affiliation(s)
- Ehsan Rasa
- Department of Civil and Environmental Engineering, University of California-Davis, One Shields Avenue, Davis, California, 95616, USA
- Tel.: +1 530 574 8193; fax: +1 530 752 1552.
| | - Steven W. Chapman
- School of Engineering, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Barbara A. Bekins
- U.S. Geological Survey, 345 Middlefield Rd, Menlo Park, California 94025, USA.
| | - Graham E. Fogg
- Department of Land, Air, and Water Resources, University of California-Davis, One Shields Avenue, Davis, California, 95616, USA.
| | - Kate M. Scow
- Department of Land, Air, and Water Resources, University of California-Davis, One Shields Avenue, Davis, California, 95616, USA.
| | - Douglas M. Mackay
- Department of Land, Air, and Water Resources, University of California-Davis, One Shields Avenue, Davis, California, 95616, USA.
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A novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by Variovorax sp. strain SRS16. Appl Environ Microbiol 2011; 77:8754-64. [PMID: 22003008 DOI: 10.1128/aem.06162-11] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The soil bacterial isolate Variovorax sp. strain SRS16 mineralizes the phenylurea herbicide linuron. The proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (DCA) and N,O-dimethylhydroxylamine, followed by conversion of DCA to Krebs cycle intermediates. Differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (LibA), a multicomponent chloroaniline dioxygenase, and enzymes associated with a modified chlorocatechol ortho-cleavage pathway. Purified LibA is a monomeric linuron hydrolase of ∼55 kDa with a K(m) and a V(max) for linuron of 5.8 μM and 0.16 nmol min⁻¹, respectively. This novel member of the amidase signature family is unrelated to phenylurea-hydrolyzing enzymes from Gram-positive bacteria and lacks activity toward other tested phenylurea herbicides. Orthologues of libA are present in all other tested linuron-degrading Variovorax strains with the exception of Variovorax strains WDL1 and PBS-H4, suggesting divergent evolution of the linuron catabolic pathway in different Variovorax strains. The organization of the linuron degradation genes identified in the draft SRS16 genome sequence indicates that gene patchwork assembly is at the origin of the pathway. Transcription analysis suggests that a catabolic intermediate, rather than linuron itself, acts as effector in activation of the pathway. Our study provides the first report on the genetic organization of a bacterial pathway for complete mineralization of a phenylurea herbicide and the first report on a linuron hydrolase in Gram-negative bacteria.
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Purswani J, Juárez B, Rodelas B, Gónzalez-López J, Pozo C. Biofilm formation and microbial activity in a biofilter system in the presence of MTBE, ETBE and TAME. CHEMOSPHERE 2011; 85:616-624. [PMID: 21774959 DOI: 10.1016/j.chemosphere.2011.06.106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 06/22/2011] [Accepted: 06/26/2011] [Indexed: 05/31/2023]
Abstract
Emerging water contaminants derived from unleaded gasoline such as methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE) and tert-amyl methyl ether (TAME), are in need of effective bioremediation technologies for restoring water resources. In order to design the conditions of a future groundwater bioremediating biofilter, this work assesses the potential use of Acinetobacter calcoaceticus M10, Rhodococcus ruber E10 and Gordonia amicalis T3 for the removal of MTBE, ETBE and TAME in consortia or as individual strains. Biofilm formation on an inert polyethylene support material was assessed with scanning electron microscopy, and consortia were also analysed with fluorescent in situ hybridisation to examine the relation between the strains. A. calcoaceticus M10 was the best coloniser, followed by G. amicalis T3, however, biofilm formation of pair consortia favoured consortium M10-E10 both in formation and activity. However, degradation batch studies determined that neither consortium exhibited higher degradation than individual strain degradation. The physiological state of the three strains was also determined through flow cytometry using propidium iodide and 3'-dihexylocarbocyanine iodide thus gathering information on their viability and activity with the three oxygenates since previous microbial counts revealed slow growth. Strain E10 was observed to have the highest physiological activity in the presence of MTBE, and strain M10 activity with TAME was only maintained for 24 h, thus we believe that biotransformation of MTBE occurs within the active periods established by the cytometry analyses. Viable cell counts and oxygenate removal were determined in the presence of the metabolites tert-butyl alcohol (TBA) and tert-amyl alcohol (TAA), resulting in TBA biotransformation by M10 and E10, and TAA by M10. Our results show that A. calcoaceticus M10 and the consortium M10-E10 could be adequate inocula in MTBE and TAME bioremediating technologies.
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Affiliation(s)
- Jessica Purswani
- Environmental Microbiology Group, Institute of Water Research, Department of Microbiology, University of Granada, C/Ramón y Cajal no. 4, 18071 Granada, Spain
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Formation of alkenes via degradation of tert-alkyl ethers and alcohols by Aquincola tertiaricarbonis L108 and Methylibium spp. Appl Environ Microbiol 2011; 77:5981-7. [PMID: 21742915 DOI: 10.1128/aem.00093-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial degradation pathways of fuel oxygenates such as methyl tert-butyl and tert-amyl methyl ether (MTBE and TAME, respectively) have already been studied in some detail. However, many of the involved enzymes are still unknown, and possible side reactions have not yet been considered. In Aquincola tertiaricarbonis L108, Methylibium petroleiphilum PM1, and Methylibium sp. strain R8, we have now detected volatile hydrocarbons as by-products of the degradation of the tert-alkyl ether metabolites tert-butyl and tert-amyl alcohol (TBA and TAA, respectively). The alkene isobutene was formed only during TBA catabolism, while the beta and gamma isomers of isoamylene were produced only during TAA conversion. Both tert-alkyl alcohol degradation and alkene production were strictly oxygen dependent. However, the relative contribution of the dehydration reaction to total alcohol conversion increased with decreasing oxygen concentrations. In resting-cell experiments where the headspace oxygen content was adjusted to less than 2%, more than 50% of the TAA was converted to isoamylene. Isobutene formation from TBA was about 20-fold lower, reaching up to 4% alcohol turnover at low oxygen concentrations. It is likely that the putative tert-alkyl alcohol monooxygenase MdpJ, belonging to the Rieske nonheme mononuclear iron enzymes and found in all three strains tested, or an associated enzymatic step catalyzed the unusual elimination reaction. This was also supported by the detection of mdpJK genes in MTBE-degrading and isobutene-emitting enrichment cultures obtained from two treatment ponds operating at Leuna, Germany. The possible use of alkene formation as an easy-to-measure indicator of aerobic fuel oxygenate biodegradation in contaminated aquifers is discussed.
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Linking low-level stable isotope fractionation to expression of the cytochrome P450 monooxygenase-encoding ethB gene for elucidation of methyl tert-butyl ether biodegradation in aerated treatment pond systems. Appl Environ Microbiol 2010; 77:1086-96. [PMID: 21148686 DOI: 10.1128/aem.01698-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidimensional compound-specific stable isotope analysis (CSIA) was applied in combination with RNA-based molecular tools to characterize methyl tertiary (tert-) butyl ether (MTBE) degradation mechanisms occurring in biofilms in an aerated treatment pond used for remediation of MTBE-contaminated groundwater. The main pathway for MTBE oxidation was elucidated by linking the low-level stable isotope fractionation (mean carbon isotopic enrichment factor [ε(C)] of -0.37‰ ± 0.05‰ and no significant hydrogen isotopic enrichment factor [ε(H)]) observed in microcosm experiments to expression of the ethB gene encoding a cytochrome P450 monooxygenase able to catalyze the oxidation of MTBE in biofilm samples both from the microcosms and directly from the ponds. 16S rRNA-specific primers revealed the presence of a sequence 100% identical to that of Methylibium petroleiphilum PM1, a well-characterized MTBE degrader. However, neither expression of the mdpA genes encoding the alkane hydroxylase-like enzyme responsible for MTBE oxidation in this strain nor the related MTBE isotope fractionation pattern produced by PM1 could be detected, suggesting that this enzyme was not active in this system. Additionally, observed low inverse fractionation of carbon (ε(C) of +0.11‰ ± 0.03‰) and low fractionation of hydrogen (ε(H) of -5‰ ± 1‰) in laboratory experiments simulating MTBE stripping from an open surface water body suggest that the application of CSIA in field investigations to detect biodegradation may lead to false-negative results when volatilization effects coincide with the activity of low-fractionating enzymes. As shown in this study, complementary examination of expression of specific catabolic genes can be used as additional direct evidence for microbial degradation activity and may overcome this problem.
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Assessment of MTBE biodegradation pathways by two-dimensional isotope analysis in mixed bacterial consortia under different redox conditions. Appl Microbiol Biotechnol 2010; 88:309-17. [DOI: 10.1007/s00253-010-2730-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/02/2010] [Accepted: 06/12/2010] [Indexed: 11/27/2022]
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Rosell M, Finsterbusch S, Jechalke S, Hübschmann T, Vogt C, Richnow HH. Evaluation of the effects of low oxygen concentration on stable isotope fractionation during aerobic MTBE biodegradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:309-315. [PMID: 19928956 DOI: 10.1021/es902491d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Laboratory experiments were performed with two aerobic MTBE degrading strains ( Methylibium sp. PM1 and Aquincola tertiaricarbonaris L108) in order to determine whether conditions of low oxygen availability, typically found in fuel-contaminated aquifers, can influence stable isotope fractionation of MTBE. Although single carbon and hydrogen enrichment factors of the two strains were not significantly or were only slightly (L108) affected by low oxygen concentrations (fully oxic incubation with initial 21% O2 in the headspace tested versus hypoxic conditions always <2% O2), the experiments showed indirect effects caused by competition interactions in mixed cultures. In a mixed culture of PM1 and L108 under oxic and even more so under hypoxic conditions, the total observed carbon isotope enrichment factor was significantly reduced, while hydrogen fractionation was not detectable. This indicates that the low fractionating model strain L108 is more competitive in degrading MTBE compared to strain PM1. Consistently, higher oxygen affinities during MTBE degradation were observed for strain L108. These first studies, conducted with resting cells, may explain the low isotope fractionation observed in some field studies that are not necessarily related to a lack of biodegradation.
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Affiliation(s)
- Mònica Rosell
- Department of Isotope Biogeochemistry, Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany.
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House AJ, Hyman MR. Effects of gasoline components on MTBE and TBA cometabolism by Mycobacterium austroafricanum JOB5. Biodegradation 2009; 21:525-41. [DOI: 10.1007/s10532-009-9321-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 11/26/2009] [Indexed: 11/28/2022]
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Sørensen SR, Simonsen A, Aamand J. Constitutive mineralization of low concentrations of the herbicide linuron by a Variovorax sp. strain. FEMS Microbiol Lett 2009; 292:291-6. [PMID: 19187207 DOI: 10.1111/j.1574-6968.2009.01501.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The mineralization of the herbicide linuron at concentrations of microg and mg L(-1) was studied in liquid batch experiments with Variovorax sp. strain SRS16. The strain was highly efficient at mineralizing a range of linuron concentrations (0.002-10 mg L(-1)) with 20-60% of the added (14)C-ring-labeled linuron metabolized to (14)CO(2) within hours to days depending on the initial linuron concentration and incubation period. At mg L(-1) linuron concentrations the mineralization activity by SRS16 was inducible and a shift to constitutive mineralization activity was apparent with a reduction in the linuron concentration to microg L(-1) levels. This study revealed that strain SRS16 is a promising candidate for bioaugmentation of water or soil resources contaminated with low linuron concentrations.
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Affiliation(s)
- Sebastian R Sørensen
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen K, Denmark.
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