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Razia S, Hadibarata T, Lau SY. Acidophilic microorganisms in remediation of contaminants present in extremely acidic conditions. Bioprocess Biosyst Eng 2023; 46:341-358. [PMID: 36602611 DOI: 10.1007/s00449-022-02844-3] [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: 08/31/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023]
Abstract
Acidophiles are a group of microorganisms that thrive in acidic environments where pH level is far below the neutral value 7.0. They belong to a larger family called extremophiles, which is a group that thrives in various extreme environmental conditions which are normally inhospitable to other organisms. Several human activities such as mining, construction and other industrial processes release highly acidic effluents and wastes into the environment. Those acidic wastes and wastewaters contain different types of pollutants such as heavy metals, radioactive, and organic, whose have adverse effects on human being as well as on other living organisms. To protect the whole ecosystem, those pollutants containing effluents or wastes must be clean properly before releasing into environment. Physicochemical cleanup processes under extremely acidic conditions are not always successful due to high cost and release of toxic byproducts. While in case of biological methods, except acidophiles, no other microorganisms cannot survive in highly acidic conditions. Therefore, acidophiles can be a good choice for remediation of different types of contaminants present in acidic conditions. In this review article, various roles of acidophilic microorganisms responsible for removing heavy metals and radioactive pollutants from acidic environments were discussed. Bioremediation of various acidic organic pollutants by using acidophiles was also studied. Overall, this review could be helpful to extend our knowledge as well as to do further relevant novel studies in the field of acidic pollutants remediation by applying acidophilic microorganisms.
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Affiliation(s)
- Sultana Razia
- Environmental Engineering Program, Faculty of Engineering and Science, Curtin University, Miri, Malaysia
| | - Tony Hadibarata
- Environmental Engineering Program, Faculty of Engineering and Science, Curtin University, Miri, Malaysia.
| | - Sie Yon Lau
- Department of Chemical and Energy Engineering, Faculty of Engineering and Science, Curtin University, Miri, Malaysia
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2
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Wolf J, Koblitz J, Albersmeier A, Kalinowski J, Siebers B, Schomburg D, Neumann-Schaal M. Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon Saccharolobus solfataricus P2 Is Limited by Oxygen Supply and the Cellular Stress Response. Front Microbiol 2021; 11:587032. [PMID: 33488537 PMCID: PMC7820114 DOI: 10.3389/fmicb.2020.587032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/08/2020] [Indexed: 12/20/2022] Open
Abstract
Present in many industrial effluents and as common degradation product of organic matter, phenol is a widespread compound which may cause serious environmental problems, due to its toxicity to animals and humans. Degradation of phenol from the environment by mesophilic bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation at high temperatures or low pH. In this work we studied phenol degradation in the thermoacidophilic archaeon Saccharolobus solfataricus P2 (basonym: Sulfolobus solfataricus) under extreme conditions (80°C, pH 3.5). We combined metabolomics and transcriptomics together with metabolic modeling to elucidate the organism’s response to growth with phenol as sole carbon source. Although S. solfataricus is able to utilize phenol for biomass production, the carbon source induces profound stress reactions, including genome rearrangement as well as a strong intracellular accumulation of polyamines. Furthermore, computational modeling revealed a 40% higher oxygen demand for substrate oxidation, compared to growth on glucose. However, only 16.5% of oxygen is used for oxidation of phenol to catechol, resulting in a less efficient integration of carbon into the biomass. Finally, our data underlines the importance of the phenol meta-degradation pathway in S. solfataricus and enables us to predict enzyme candidates involved in the degradation processes downstream of 2-hydroxymucconic acid.
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Affiliation(s)
- Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Julia Koblitz
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology-CeBiTec, Universität Bielefeld, Bielefeld, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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3
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Anteneh YS, Franco CMM. Whole Cell Actinobacteria as Biocatalysts. Front Microbiol 2019; 10:77. [PMID: 30833932 PMCID: PMC6387938 DOI: 10.3389/fmicb.2019.00077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/15/2019] [Indexed: 12/25/2022] Open
Abstract
Production of fuels, therapeutic drugs, chemicals, and biomaterials using sustainable biological processes have received renewed attention due to increasing environmental concerns. Despite having high industrial output, most of the current chemical processes are associated with environmentally undesirable by-products which escalate the cost of downstream processing. Compared to chemical processes, whole cell biocatalysts offer several advantages including high selectivity, catalytic efficiency, milder operational conditions and low impact on the environment, making this approach the current choice for synthesis and manufacturing of different industrial products. In this review, we present the application of whole cell actinobacteria for the synthesis of biologically active compounds, biofuel production and conversion of harmful compounds to less toxic by-products. Actinobacteria alone are responsible for the production of nearly half of the documented biologically active metabolites and many enzymes; with the involvement of various species of whole cell actinobacteria such as Rhodococcus, Streptomyces, Nocardia and Corynebacterium for the production of useful industrial commodities.
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Affiliation(s)
- Yitayal Shiferaw Anteneh
- College of Medicine and Public Health, Medical Biotechnology, Flinders University, Bedford Park, SA, Australia
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
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Orellana R, Macaya C, Bravo G, Dorochesi F, Cumsille A, Valencia R, Rojas C, Seeger M. Living at the Frontiers of Life: Extremophiles in Chile and Their Potential for Bioremediation. Front Microbiol 2018; 9:2309. [PMID: 30425685 PMCID: PMC6218600 DOI: 10.3389/fmicb.2018.02309] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022] Open
Abstract
Extremophiles are organisms capable of adjust, survive or thrive in hostile habitats that were previously thought to be adverse or lethal for life. Chile gathers a wide range of extreme environments: salars, geothermal springs, and geysers located at Altiplano and Atacama Desert, salars and cold mountains in Central Chile, and ice fields, cold lakes and fjords, and geothermal sites in Patagonia and Antarctica. The aims of this review are to describe extremophiles that inhabit main extreme biotopes in Chile, and their molecular and physiological capabilities that may be advantageous for bioremediation processes. After briefly describing the main ecological niches of extremophiles along Chilean territory, this review is focused on the microbial diversity and composition of these biotopes microbiomes. Extremophiles have been isolated in diverse zones in Chile that possess extreme conditions such as Altiplano, Atacama Desert, Central Chile, Patagonia, and Antarctica. Interesting extremophiles from Chile with potential biotechnological applications include thermophiles (e.g., Methanofollis tationis from Tatio Geyser), acidophiles (e.g., Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum from Atacama Desert and Central Chile copper ores), halophiles (e.g., Shewanella sp. Asc-3 from Altiplano, Streptomyces sp. HKF-8 from Patagonia), alkaliphiles (Exiguobacterium sp. SH31 from Altiplano), xerotolerant bacteria (S. atacamensis from Atacama Desert), UV- and Gamma-resistant bacteria (Deinococcus peraridilitoris from Atacama Desert) and psychrophiles (e.g., Pseudomonas putida ATH-43 from Antarctica). The molecular and physiological properties of diverse extremophiles from Chile and their application in bioremediation or waste treatments are further discussed. Interestingly, the remarkable adaptative capabilities of extremophiles convert them into an attractive source of catalysts for bioremediation and industrial processes.
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Affiliation(s)
- Roberto Orellana
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
| | - Constanza Macaya
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Guillermo Bravo
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Flavia Dorochesi
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Andrés Cumsille
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Ricardo Valencia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Claudia Rojas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
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Krzmarzick MJ, Taylor DK, Fu X, McCutchan AL. Diversity and Niche of Archaea in Bioremediation. ARCHAEA (VANCOUVER, B.C.) 2018; 2018:3194108. [PMID: 30254509 PMCID: PMC6140281 DOI: 10.1155/2018/3194108] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 08/01/2018] [Indexed: 12/03/2022]
Abstract
Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.
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Affiliation(s)
- Mark James Krzmarzick
- School of Civil and Environmental Engineering, College of Engineering, Architecture, and Technology, Oklahoma State University, Stillwater, OK 74078, USA
| | - David Kyle Taylor
- School of Civil and Environmental Engineering, College of Engineering, Architecture, and Technology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Xiang Fu
- School of Civil and Environmental Engineering, College of Engineering, Architecture, and Technology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Aubrey Lynn McCutchan
- School of Civil and Environmental Engineering, College of Engineering, Architecture, and Technology, Oklahoma State University, Stillwater, OK 74078, USA
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6
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Batista-García RA, Kumar VV, Ariste A, Tovar-Herrera OE, Savary O, Peidro-Guzmán H, González-Abradelo D, Jackson SA, Dobson ADW, Sánchez-Carbente MDR, Folch-Mallol JL, Leduc R, Cabana H. Simple screening protocol for identification of potential mycoremediation tools for the elimination of polycyclic aromatic hydrocarbons and phenols from hyperalkalophile industrial effluents. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 198:1-11. [PMID: 28499155 DOI: 10.1016/j.jenvman.2017.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 04/28/2017] [Accepted: 05/05/2017] [Indexed: 06/07/2023]
Abstract
A number of fungal strains belonging to the ascomycota, basidiomycota and zygomycota genera were subjected to an in vitro screening regime to assess their ligninolytic activity potential, with a view to their potential use in mycoremediation-based strategies to remove phenolic compounds and polycyclic aromatic hydrocarbons (PAHs) from industrial wastewaters. All six basidiomycetes completely decolorized remazol brilliant blue R (RBBR), while also testing positive in both the guaiacol and gallic acid tests indicating good levels of lignolytic activity. All the fungi were capable of tolerating phenanthrene, benzo-α- pyrene, phenol and p-chlorophenol in agar medium at levels of 10 ppm. Six of the fungal strains, Pseudogymnoascus sp., Aspergillus caesiellus, Trametes hirsuta IBB 450, Phanerochate chrysosporium ATCC 787, Pleurotus ostreatus MTCC 1804 and Cadophora sp. produced both laccase and Mn peroxidase activity in the ranges of 200-560 U/L and 6-152 U/L, respectively, in liquid media under nitrogen limiting conditions. The levels of adsorption of the phenolic and PAHs were negligible with 99% biodegradation being observed in the case of benzo-α-pyrene, phenol and p-chlorophenol. The aforementioned six fungal strains were also found to be able to effectively treat highly alkaline industrial wastewater (pH 12.4). When this wastewater was supplemented with 0.1 mM glucose, all of the tested fungi, apart from A. caesiellus, displayed the capacity to remove both the phenolic and PAH compounds. Based on their biodegradative capacity we found T. hirsuta IBB 450 and Pseudogymnoascus sp., to have the greatest potential for further use in mycoremediation based strategies to treat wastestreams containing phenolics and PAHs.
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Affiliation(s)
- Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico; Department of Civil Engineering, Université de Sherbrooke (UdeS), Sherbrooke, Quebec, J1K 2R1, Canada.
| | - Vaidyanathan Vinoth Kumar
- Department of Civil Engineering, Université de Sherbrooke (UdeS), Sherbrooke, Quebec, J1K 2R1, Canada; Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Arielle Ariste
- Department of Civil Engineering, Université de Sherbrooke (UdeS), Sherbrooke, Quebec, J1K 2R1, Canada
| | - Omar Eduardo Tovar-Herrera
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, Mexico
| | - Olivier Savary
- Department of Civil Engineering, Université de Sherbrooke (UdeS), Sherbrooke, Quebec, J1K 2R1, Canada
| | - Heidy Peidro-Guzmán
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico
| | - Deborah González-Abradelo
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico
| | | | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland
| | | | | | - Roland Leduc
- Department of Civil Engineering, Université de Sherbrooke (UdeS), Sherbrooke, Quebec, J1K 2R1, Canada
| | - Hubert Cabana
- Department of Civil Engineering, Université de Sherbrooke (UdeS), Sherbrooke, Quebec, J1K 2R1, Canada.
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7
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Enhancement of phenol biodegradation by Pseudochrobactrum sp. through ultraviolet-induced mutation. Int J Mol Sci 2015; 16:7320-33. [PMID: 25837630 PMCID: PMC4425019 DOI: 10.3390/ijms16047320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 03/16/2015] [Accepted: 03/20/2015] [Indexed: 11/21/2022] Open
Abstract
The phenol-degrading efficiency of Pseudochrobactrum sp. was enhanced by ultraviolet (UV) irradiation. First, a bacterial strain, Pseudochrobactrum sp. XF1, was isolated from the activated sludge in a coking plant. It was subjected to mutation by UV radiation for 120 s and a mutant strain with higher phenol-degrading efficiency, Pseudochrobactrum sp. XF1-UV, was selected. The mutant strain XF1-UV was capable of degrading 1800 mg/L phenol completely within 48 h and had higher tolerance to hydrogen ion concentration and temperature variation than the wild type. Haldane’s kinetic model was used to fit the exponential growth data and the following kinetic parameters were obtained: μmax = 0.092 h−1, Ks = 22.517 mg/L, and Ki = 1126.725 mg/L for XF1, whereas μmax = 0.110 h−1, Ks = 23.934 mg/L, and Ki = 1579.134 mg/L for XF1-UV. Both XF1 and XF1-UV degraded phenol through the ortho-pathway; but the phenol hydroxylase activity of XF1-UV1 was higher than that of XF1, therefore, the mutant strain biodegraded phenol faster. Taken together, our results suggest that Pseudochrobactrum sp. XF1-UV could be a promising candidate for bioremediation of phenol-containing wastewaters.
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He Z, Niu C, Lu Z. Individual or synchronous biodegradation of di-n-butyl phthalate and phenol by Rhodococcus ruber strain DP-2. JOURNAL OF HAZARDOUS MATERIALS 2014; 273:104-109. [PMID: 24727011 DOI: 10.1016/j.jhazmat.2014.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/27/2014] [Accepted: 03/16/2014] [Indexed: 06/03/2023]
Abstract
The bacterial strain DP-2, identified as Rhodococcus ruber, is able to effectively degrade di-n-butyl phthalate (DBP) and phenol. Degradation kinetics of DBP and phenol at different initial concentrations revealed DBP and phenol degradation to fit modified first-order models. The half-life of DBP degradation ranged from 15.81 to 27.75h and phenol degradation from 14.52 to 45.52h under the initial concentrations of 600-1200mg/L. When strain DP-2 was cultured with a mixture of DBP (800mg/L) and phenol (700mg/L), DBP degradation rate was found to be only slightly influenced; however, phthalic acid (PA) accumulated, and phenol degradation was clearly inhibited during synchronous degradation. Transcriptional levels of degradation genes, phenol hydroxylase (pheu) and phthalate 3,4-dioxygenase (pht), decreased significantly more during synchronous degradation than during individual degradation. Quantitative estimation of individual or synchronous degradation kinetics is essential to manage mixed hazardous compounds through biodegradation in industrial waste disposal.
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Affiliation(s)
- Zhixing He
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Chengzhen Niu
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Zhenmei Lu
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
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9
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Comte A, Christen P, Davidson S, Pophillat M, Lorquin J, Auria R, Simon G, Casalot L. Biochemical, transcriptional and translational evidences of the phenol-meta-degradation pathway by the hyperthermophilic Sulfolobus solfataricus 98/2. PLoS One 2013; 8:e82397. [PMID: 24349276 PMCID: PMC3859572 DOI: 10.1371/journal.pone.0082397] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022] Open
Abstract
Phenol is a widespread pollutant and a model molecule to study the biodegradation of monoaromatic compounds. After a first oxidation step leading to catechol in mesophilic and thermophilic microorganisms, two main routes have been identified depending on the cleavage of the aromatic ring: ortho involving a catechol 1,2 dioxygenase (C12D) and meta involving a catechol 2,3 dioxygenase (C23D). Our work aimed at elucidating the phenol-degradation pathway in the hyperthermophilic archaea Sulfolobus solfataricus 98/2. For this purpose, the strain was cultivated in a fermentor under different substrate and oxygenation conditions. Indeed, reducing dissolved-oxygen concentration allowed slowing down phenol catabolism (specific growth and phenol-consumption rates dropped 55% and 39%, respectively) and thus, evidencing intermediate accumulations in the broth. HPLC/Diode Array Detector and LC-MS analyses on culture samples at low dissolved-oxygen concentration (DOC = 0.06 mg x L(-1)) suggested, apart for catechol, the presence of 2-hydroxymuconic acid, 4-oxalocrotonate and 4-hydroxy-2-oxovalerate, three intermediates of the meta route. RT-PCR analysis on oxygenase-coding genes of S. solfataricus 98/2 showed that the gene coding for the C23D was expressed only on phenol. In 2D-DIGE/MALDI-TOF analysis, the C23D was found and identified only on phenol. This set of results allowed us concluding that S. solfataricus 98/2 degrade phenol through the meta route.
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Affiliation(s)
- Alexia Comte
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Pierre Christen
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Sylvain Davidson
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Matthieu Pophillat
- Institut Paoli-Calmettes, Aix Marseille Université, CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Jean Lorquin
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Richard Auria
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Gwenola Simon
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Laurence Casalot
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
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Moscoso F, Teijiz I, Sanromán MA, Deive FJ. On the Suitability of a Bacterial Consortium To Implement a Continuous PAHs Biodegradation Process in a Stirred Tank Bioreactor. Ind Eng Chem Res 2012. [DOI: 10.1021/ie3021736] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Moscoso
- Department
of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
| | - I. Teijiz
- Department
of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
| | - M. A. Sanromán
- Department
of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
| | - F. J. Deive
- Department
of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
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11
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Abstract
Extremely thermophilic microorganisms have been sources of thermostable and thermoactive enzymes for over 30 years. However, information and insights gained from genome sequences, in conjunction with new tools for molecular genetics, have opened up exciting new possibilities for biotechnological opportunities based on extreme thermophiles that go beyond single-step biotransformations. Although the pace for discovering novel microorganisms has slowed over the past two decades, genome sequence data have provided clues to novel biomolecules and metabolic pathways, which can be mined for a range of new applications. Furthermore, recent advances in molecular genetics for extreme thermophiles have made metabolic engineering for high temperature applications a reality.
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Affiliation(s)
- Andrew D Frock
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905
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12
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Ulas T, Riemer SA, Zaparty M, Siebers B, Schomburg D. Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One 2012; 7:e43401. [PMID: 22952675 PMCID: PMC3432047 DOI: 10.1371/journal.pone.0043401] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/20/2012] [Indexed: 12/21/2022] Open
Abstract
We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2–4 (optimum 3.5) and a temperature of 75–80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism.
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Affiliation(s)
- Thomas Ulas
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - S. Alexander Riemer
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melanie Zaparty
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
| | - Bettina Siebers
- Faculty of Chemistry, Biofilm Centre, Molecular Enzyme Technology and Biochemistry, University of Duisburg-Essen, Essen, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail:
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Kinetics of aerobic phenol biodegradation by the acidophilic and hyperthermophilic archaeon Sulfolobus solfataricus 98/2. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2011.12.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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