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Yang SNN, Haritos V, Kertesz MA, Coleman NV. A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli. Environ Microbiol 2024; 26:e16567. [PMID: 38233213 DOI: 10.1111/1462-2920.16567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024]
Abstract
Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.
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Affiliation(s)
- Sui Nin Nicholas Yang
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Victoria Haritos
- Department of Chemical and Biological Engineering, Monash University, Melbourne, Victoria, Australia
| | - Michael A Kertesz
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
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Characterization of 1,4-dioxane degrading microbial community enriched from uncontaminated soil. Appl Microbiol Biotechnol 2023; 107:955-969. [PMID: 36625913 DOI: 10.1007/s00253-023-12363-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/01/2022] [Accepted: 01/01/2023] [Indexed: 01/11/2023]
Abstract
1,4-Dioxane is a contaminant of emerging concern that has been commonly detected in groundwater. In this study, a stable and robust 1,4-dioxane degrading enrichment culture was obtained from uncontaminated soil. The enrichment was capable to metabolically degrade 1,4-dioxane at both high (100 mg L-1) and environmentally relevant concentrations (300 μg L-1), with a maximum specific 1,4-dioxane degradation rate (qmax) of 0.044 ± 0.001 mg dioxane h-1 mg protein-1, and 1,4-dioxane half-velocity constant (Ks) of 25 ± 1.6 mg L-1. The microbial community structure analysis suggested Pseudonocardia species, which utilize the dioxane monooxygenase for metabolic 1,4-dioxane biodegradation, were the main functional species for 1,4-dioxane degradation. The enrichment culture can adapt to both acidic (pH 5.5) and alkaline (pH 8) conditions and can recover degradation from low temperature (10°C) and anoxic (DO < 0.5 mg L-1) conditions. 1,4-Dioxane degradation of the enrichment culture was reversibly inhibited by TCE with concentrations higher than 5 mg L-1 and was completely inhibited by the presence of 1,1-DCE as low as 1 mg L-1. Collectively, these results demonstrated indigenous stable and robust 1,4-dioxane degrading enrichment culture can be obtained from uncontaminated sources and can be a potential candidate for 1,4-dioxane bioaugmentation at environmentally relevant conditions. KEY POINTS: •1,4-Dioxane degrading enrichment was obtained from uncontaminated soil. • The enrichment culture could degrade 1,4-dioxane to below 10 μg L-1. •Low Ks and low cell yield of the enrichment benefit its application in bioremediation.
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Cupples AM, Li Z, Wilson FP, Ramalingam V, Kelly A. In silico analysis of soil, sediment and groundwater microbial communities to predict biodegradation potential. J Microbiol Methods 2022; 202:106595. [DOI: 10.1016/j.mimet.2022.106595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 12/27/2022]
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Kikani M, Satasiya GV, Sahoo TP, Kumar PS, Kumar MA. Remedial strategies for abating 1,4-dioxane pollution-special emphasis on diverse biotechnological interventions. ENVIRONMENTAL RESEARCH 2022; 214:113939. [PMID: 35921903 DOI: 10.1016/j.envres.2022.113939] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
1,4-dioxane is a heterocyclic ether used as a polar industrial solvent and are released as waste discharges. 1,4-dioxane deteriorates health and quality, thereby attracts concern by the environment technologists. The need of attaining sustainable development goals have resulted in search of an eco-friendly and technically viable treatment strategy. This extensive review is aimed to emphasis on the (a) characteristics of 1,4-dioxane and their occurrence in the environment as well as their toxicity, (b) remedial strategies, such as physico-chemical treatment and advanced oxidation techniques. Special reference to bioremediation that involves diverse microbial strains and their mechanism are highlighted in this review. The role of macronutrients, stimulants and other abiotic cofactors in the biodegradation of 1,4-dioxane is discussed lucidly. We have critically discussed the inducible enzymes, enzyme-based remediation, distinct instrumental method of analyses to know the fate of intermediates produced from 1,4-dioxane biotransformation. This comprehensive survey also tries to put forth the different toxicity assessment tools used in evaluating the extent of detoxification of 1,4-dioxane achieved through biotransforming mechanism. Conclusively, the challenges, opportunities, techno-economic feasibility and future prospects of implementing 1,4-dioxane through biotechnological interventions are also discussed.
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Affiliation(s)
- Mansi Kikani
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar-364 002 (Gujarat), India
| | - Gopi Vijaybhai Satasiya
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar-364 002 (Gujarat), India
| | - Tarini Prasad Sahoo
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar-364 002 (Gujarat), India; Academy of Scientific and Innovative Research, Ghaziabad-201 002 (Uttar Pradesh), India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai-603 110 (Tamil Nadu), India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai-603 110 (Tamil Nadu), India
| | - Madhava Anil Kumar
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar-364 002 (Gujarat), India; Academy of Scientific and Innovative Research, Ghaziabad-201 002 (Uttar Pradesh), India.
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Horizontal Gene Transfer of Genes Encoding Copper-Containing Membrane-Bound Monooxygenase (CuMMO) and Soluble Di-iron Monooxygenase (SDIMO) in Ethane- and Propane-Oxidizing Rhodococcus Bacteria. Appl Environ Microbiol 2021; 87:e0022721. [PMID: 33962978 DOI: 10.1128/aem.00227-21] [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: 12/20/2022] Open
Abstract
The families of copper-containing membrane-bound monooxygenases (CuMMOs) and soluble di-iron monooxygenases (SDIMOs) are involved not only in methane oxidation but also in short-chain alkane oxidation. Here, we describe Rhodococcus sp. strain ZPP, a bacterium able to grow with ethane or propane as the sole carbon and energy source, and report on the horizontal gene transfer (HGT) of actinobacterial hydrocarbon monooxygenases (HMOs) of the CuMMO family and the sMMO (soluble methane monooxygenase)-like SDIMO in the genus Rhodococcus. The key function of HMO in strain ZPP for propane oxidation was verified by allylthiourea inhibition. The HMO genes (designated hmoCAB) and those encoding sMMO-like SDIMO (designated smoXYB1C1Z) are located on a linear megaplasmid (pRZP1) of strain ZPP. Comparative genomic analysis of similar plasmids indicated the mobility of these plasmids within the genus Rhodococcus. The plasmid pRZP1 in strain ZPP could be conjugatively transferred to a recipient Rhodococcus erythropolis strain in a mating experiment and showed similar ethane- and propane-consuming activities. Finally, our findings demonstrate that the horizontal transfer of plasmid-based CuMMO and SDIMO genes confers the ability to use ethane and propane on the recipient. IMPORTANCE CuMMOs and SDIMOs initiate the aerobic oxidation of alkanes in bacteria. Here, the supposition that horizontally transferred plasmid-based CuMMO and SDIMO genes confer on the recipient similar abilities to use ethane and propane was proposed and confirmed in Rhodococcus. This study is a living example of HGT of CuMMOs and SDIMOs and outlines the plasmid-borne properties responsible for gaseous alkane degradation. Our results indicate that plasmids can support the rapid evolution of enzyme-mediated biogeochemical processes.
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Miao Y, Heintz MB, Bell CH, Johnson NW, Polasko AL, Favero D, Mahendra S. Profiling microbial community structures and functions in bioremediation strategies for treating 1,4-dioxane-contaminated groundwater. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124457. [PMID: 33189472 DOI: 10.1016/j.jhazmat.2020.124457] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/28/2020] [Accepted: 10/30/2020] [Indexed: 06/11/2023]
Abstract
Microbial community compositions and functional profiles were analyzed in microcosms established using aquifer materials from a former automobile factory site, where 1,4-dioxane was identified as the primary contaminant of concern. Propane or oxygen biostimulation resulted in limited 1,4-dioxane degradation, which was markedly enhanced with the addition of nutrients, resulting in abundant Mycobacterium and Methyloversatilis taxa and high expressions of propane monooxygenase gene, prmA. In bioaugmented treatments, Pseudonocardia dioxanivorans CB1190 or Rhodococcus ruber ENV425 strains dominated immediately after augmentation and degraded 1,4-dioxane rapidly which was consistent with increased representation of xenobiotic and lipid metabolism-related functions. Although the bioaugmented microbes decreased due to insufficient growth substrates and microbial competition, they did continue to degrade 1,4-dioxane, presumably by indigenous propanotrophic and heterotrophic bacteria, inducing similar community structures across bioaugmentation conditions. In various treatments, functional redundancy acted as buffer capacity to ensure a stable microbiome, drove the restoration of the structure and microbial functions to original levels, and induced the decoupling between basic metabolic functions and taxonomy. The results of this study provided valuable information for design and decision-making for ex-situ bioreactors and in-situ bioremediation applications. A metagenomics-based understanding of the treatment process will enable efficient and accurate adjustments when encountering unexpected issues in bioremediation.
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Affiliation(s)
- Yu Miao
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Monica B Heintz
- Arcadis North America, Highlands Ranch, CO 80129, United States
| | | | - Nicholas W Johnson
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Alexandra LaPat Polasko
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - David Favero
- Revitalizing Auto Communities Environmental Response (RACER) Trust, Detroit, MI 48226, United States
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States.
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Discovery of an Inducible Toluene Monooxygenase That Cooxidizes 1,4-Dioxane and 1,1-Dichloroethylene in Propanotrophic Azoarcus sp. Strain DD4. Appl Environ Microbiol 2020; 86:AEM.01163-20. [PMID: 32591384 DOI: 10.1128/aem.01163-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/21/2020] [Indexed: 11/20/2022] Open
Abstract
Cometabolic degradation plays a prominent role in bioremediation of commingled groundwater contamination (e.g., chlorinated solvents and the solvent stabilizer 1,4-dioxane [dioxane]). In this study, we untangled the diversity and catalytic functions of multicomponent monooxygenases in Azoarcus sp. strain DD4, a Gram-negative propanotroph that is effective in degrading dioxane and 1,1-dichloroethylene (1,1-DCE). Using a combination of knockout mutagenesis and heterologous expression, a toluene monooxygenase (MO) encoded by the tmoABCDEF gene cluster was unequivocally proved to be the key enzyme responsible for the cometabolism of both dioxane and 1,1-DCE. Interestingly, in addition to utilizing toluene as a primary substrate, this toluene MO can also oxidize propane into 1-propanol. Expression of this toluene MO in DD4 appears inducible by both substrates (toluene and propane) and their primary hydroxylation products (m-cresol, p-cresol, and 1-propanol). These findings coherently explain why DD4 can grow on propane and express toluene MO for active cooxidation of dioxane and 1,1-DCE. Furthermore, upregulation of tmo transcription by 1-propanol underlines the implication potential of using 1-propanol as an alternative auxiliary substrate for DD4 bioaugmentation. The discovery of this toluene MO in DD4 and its degradation and induction versatility can lead to broad applications, spanning from environmental remediation and water treatment to biocatalysis in green chemistry.IMPORTANCE Toluene MOs have been well recognized given their robust abilities to degrade a variety of environmental pollutants. Built upon previous research efforts, this study ascertained the untapped capability of a toluene MO in DD4 for effective cooxidation of dioxane and 1,1-DCE, two of the most prevailing yet challenging groundwater contaminants. This report also aligns the induction of a toluene MO with nontoxic and commercially accessible chemicals (e.g., propane and 1-propanol), extending its implications in the field of environmental microbiology and beyond.
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Enrichment of novel Actinomycetales and the detection of monooxygenases during aerobic 1,4-dioxane biodegradation with uncontaminated and contaminated inocula. Appl Microbiol Biotechnol 2020; 104:2255-2269. [DOI: 10.1007/s00253-020-10376-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/22/2019] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
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Tupa PR, Masuda H. Genomic Analysis of Propane Metabolism in Methyl Tert-Butyl Ether-Degrading Mycobacterium Sp. Strain ENV421. J Genomics 2018; 6:24-29. [PMID: 29576806 PMCID: PMC5865082 DOI: 10.7150/jgen.24929] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 02/21/2018] [Indexed: 11/05/2022] Open
Abstract
Methyl tert-butyl ether (MTBE) is a ground water contaminant with plausible carcinogenic properties. Mycobacterium sp. strain ENV421 cometabolically degrades MTBE and other ethers during the growth on propane as a carbon source. In this study, the 6.2 Mb genome of strain ENV421 was deciphered. The genome sequence revealed the presence of numerous putative propane catabolic genes including genes encoding hydrocarbon oxygenases and short chain alcohol dehydrogenases. These data provide the basis for the elucidation of propane metabolic pathways in strain ENV421 and its application for the remediation of ground water contaminated with toxic ethers.
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Affiliation(s)
- Peter Robert Tupa
- School of Sciences, Indiana University Kokomo, Kokomo, Indiana, 46902, United States of America
| | - Hisako Masuda
- School of Sciences, Indiana University Kokomo, Kokomo, Indiana, 46902, United States of America
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Draft Genome Sequence of a Propanotroph, Rhodococcus sp. Strain ENV425, Capable of Degrading Methyl tert-Butyl Ether and N-Nitrosodimethylamine. GENOME ANNOUNCEMENTS 2018; 6:6/8/e00051-18. [PMID: 29472328 PMCID: PMC5824016 DOI: 10.1128/genomea.00051-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, the draft genome of Rhodococcus sp. strain ENV425 was determined. The propane-grown strain ENV425 cometabolically degrades environmental contaminants such as methyl tert-butyl ether and N-nitrosodimethylamine. The sequence revealed the presence of multiple hydrocarbon metabolic genes that could play pivotal roles in the biodegradation of pollutants.
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He Y, Mathieu J, da Silva MLB, Li M, Alvarez PJJ. 1,4-Dioxane-degrading consortia can be enriched from uncontaminated soils: prevalence of Mycobacterium and soluble di-iron monooxygenase genes. Microb Biotechnol 2017; 11:189-198. [PMID: 28984418 PMCID: PMC5743803 DOI: 10.1111/1751-7915.12850] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 12/22/2022] Open
Abstract
Two bacterial consortia were enriched from uncontaminated soil by virtue of their ability to grow on 1,4‐dioxane (dioxane) as a sole carbon and energy source. Their specific dioxane degradation rates at 30°C, pH = 7 (i.e. 5.7 to 7.1 g‐dioxane per g‐protein per day) were comparable to those of two dioxane‐metabolizing archetypes: Pseudonocardia dioxanivoransCB1190 and Mycobacterium dioxanotrophicusPH‐06. Based on 16S rRNA sequencing, Mycobacterium was the dominant genus. Acetylene inhibition tests suggest that dioxane degradation was mediated by monooxygenases. However, qPCR analyses targeting the tetrahydrofuran/dioxane monooxygenase gene (thmA/dxmA) (which is, to date, the only sequenced dioxane monooxygenase gene) were negative, indicating that other (as yet unknown) catabolic gene(s) were responsible. DNA sequence analyses also showed threefold to sevenfold enrichment of group 5 and group 6 soluble di‐iron monooxygenase (SDIMO) genes relative to the original soil samples. Whereas biodegradation of trace levels of dioxane is a common challenge at contaminated sites, both consortia degraded dioxane at low initial concentrations (300 μg l−1) below detectable levels (5 μg l−1) in bioaugmented microcosms prepared with impacted groundwater. Overall, this work shows that dioxane‐degrading bacteria (and the associated natural attenuation potential) exist even in some uncontaminated soils, and may be enriched to broaden bioaugmentation options for sites experiencing insufficient dioxane catabolic capacity.
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Affiliation(s)
- Ya He
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
| | - Marcio L B da Silva
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
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