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Luo YH, Long X, Cai Y, Zheng CW, Roldan MA, Yang S, Zhou D, Zhou C, Rittmann BE. A synergistic platform enables co-oxidation of halogenated organic pollutants without input of organic primary substrate. WATER RESEARCH 2023; 234:119801. [PMID: 36889084 DOI: 10.1016/j.watres.2023.119801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/06/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
While co-oxidation is widely used to biodegrade halogenated organic pollutants (HOPs), a considerable amount of organic primary substrate is required. Adding organic primary substrates increases the operating cost and also leads to extra carbon dioxide release. In this study, we evaluated a two-stage Reduction and Oxidation Synergistic Platform (ROSP), which integrated catalytic reductive dehalogenation with biological co-oxidation for HOPs removal. The ROSP was a combination of an H2-based membrane catalytic-film reactor (H2-MCfR) and an O2-based membrane biofilm reactor (O2-MBfR). 4-chlorophenol (4-CP) was used as a model HOP to evaluate the performance of ROSP. In the MCfR stage, zero-valent palladium nanoparticles (Pd0NPs) catalyzed reductive hydrodechlorination that converted 4-CP to phenol, with a conversion yield over 92%. In the MBfR stage, the phenol was oxidized and used as a primary substrate that supported the co-oxidation of residual 4-CP. Genomic DNA sequencing revealed that phenol produced from 4-CP reduction enriched bacteria having genes for functional enzymes for phenol biodegradation in the biofilm community. In the ROSP, over 99% of 60 mg/L 4-CP was removed and mineralized during continuous operation: Effluent 4-CP and chemical oxygen demand concentrations were below 0.1 and 3 mg/L, respectively. H2 was the only added electron donor to the ROSP, which means no extra carbon dioxide was produced by primary-substrate oxidation.
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Affiliation(s)
- Yi-Hao Luo
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Northeast Normal University, Changchun 130117, China; Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287-5306, USA; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, USA
| | - Xiangxing Long
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287-5306, USA; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, USA
| | - Yuhang Cai
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Northeast Normal University, Changchun 130117, China; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-3005, USA
| | - Chen-Wei Zheng
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287-5306, USA
| | - Manuel A Roldan
- Eyring Materials Center, Arizona State University, Tempe AZ 85287-3005, USA
| | - Shize Yang
- Eyring Materials Center, Arizona State University, Tempe AZ 85287-3005, USA
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Northeast Normal University, Changchun 130117, China; Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287-5306, USA.
| | - Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287-5306, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287-5306, USA
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2
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Sookhaki E, Namazian M. A molecular modeling of iodinated organic compounds. J Mol Graph Model 2021; 108:107985. [PMID: 34315067 DOI: 10.1016/j.jmgm.2021.107985] [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: 04/08/2021] [Revised: 06/25/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
Thermodynamic quantities of some iodinated compounds have been studied by means of ab initio and density functional theory calculations. Since there are some limitations for heavy elements in the fifth row of periodic table such as the iodine atom, a high level of ab initio theory is developed to calculate the energy of iodinated compounds. The standard enthalpies of formation for alkyl iodides and other iodinated organic compounds have been computed and compared with available experimental data. The impact of iodine atoms on the change of enthalpies for deprotonation of iodobenzenes has been studied and a mathematical model is proposed for the effect of iodine on the change of deprotonation. The acidity of diiodophenols as a model for thyroxin hormone has been successfully calculated. The barriers for nucleophilic reactions of substituted methyl iodides are investigated and the energy profiles are characterized by double-well potentials which correspond to pre-reaction and post-reaction complexes, separated by a transition state.
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Affiliation(s)
- Elham Sookhaki
- Department of Chemistry, Faculty of Science, Yazd University, Yazd, P.O. Box, 89195-741, Iran
| | - Mansoor Namazian
- Department of Chemistry, Faculty of Science, Yazd University, Yazd, P.O. Box, 89195-741, Iran.
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3
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Anthony WE, Carr RR, DeLorenzo DM, Campbell TP, Shang Z, Foston M, Moon TS, Dantas G. Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:192. [PMID: 31404385 PMCID: PMC6683499 DOI: 10.1186/s13068-019-1535-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/24/2019] [Indexed: 05/09/2023]
Abstract
The current extraction and use of fossil fuels has been linked to extensive negative health and environmental outcomes. Lignocellulosic biomass-derived biofuels and bioproducts are being actively considered as renewable alternatives to the fuels, chemicals, and materials produced from fossil fuels. A major challenge limiting large-scale, economic deployment of second-generation biorefineries is the insufficient product yield, diversity, and value that current conversion technologies can extract from lignocellulose, in particular from the underutilized lignin fraction. Rhodococcus opacus PD630 is an oleaginous gram-positive bacterium with innate catabolic pathways and tolerance mechanisms for the inhibitory aromatic compounds found in depolymerized lignin, as well as native or engineered pathways for hexose and pentose sugars found in the carbohydrate fractions of biomass. As a result, R. opacus holds potential as a biological chassis for the conversion of lignocellulosic biomass into biodiesel precursors and other value-added products. This review begins by examining the important role that lignin utilization will play in the future of biorefineries and by providing a concise survey of the current lignin conversion technologies. The genetic machinery and capabilities of R. opacus that allow the bacterium to tolerate and metabolize aromatic compounds and depolymerized lignin are also discussed, along with a synopsis of the genetic toolbox and synthetic biology methods now available for engineering this organism. Finally, we summarize the different feedstocks that R. opacus has been demonstrated to consume, and the high-value products that it has been shown to produce. Engineered R. opacus will enable lignin valorization over the coming years, leading to cost-effective conversion of lignocellulose into fuels, chemicals, and materials.
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Affiliation(s)
- Winston E. Anthony
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Rhiannon R. Carr
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Drew M. DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Tayte P. Campbell
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Zeyu Shang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Marcus Foston
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
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4
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Jiang B, Jin N, Xing Y, Su Y, Zhang D. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP). Crit Rev Biotechnol 2018; 38:1025-1048. [DOI: 10.1080/07388551.2018.1427697] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Naifu Jin
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Yuping Su
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
- School of Environment, Tsinghua University, Beijing, PR China
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5
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Vatsal AA, Zinjarde SS, RaviKumar A. Phenol Is the Initial Product Formed during Growth and Degradation of Bromobenzene by Tropical Marine Yeast, Yarrowia lipolytica NCIM 3589 via an Early Dehalogenation Step. Front Microbiol 2017; 8:1165. [PMID: 28690604 PMCID: PMC5481318 DOI: 10.3389/fmicb.2017.01165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Bromobenzene (BrB), a hydrophobic, recalcitrant organic compound, is listed by the environmental protection agencies as an environmental and marine pollutant having hepatotoxic, mutagenic, teratogenic, and carcinogenic effects. The tropical marine yeast Yarrowia lipolytica 3589 was seen to grow aerobically on BrB and displayed a maximum growth rate (μmax) of 0.04 h-1. Furthermore, we also observed an increase in cell size and sedimentation velocity for the cells grown on BrB as compared to the glucose grown cells. The cells attached to the hydrophobic bromobenzene droplets through its hydrophobic and acid-base interactions. The BrB (0.5%, 47.6 mM) was utilized by the cells with the release of a corresponding amount of bromide (12.87 mM) and yielded a cell mass of 1.86 g/L after showing 34% degradation in 96 h. Maximum dehalogenase activity of 16.16 U/mL was seen in the cell free supernatant after 24 h of growth. Identification of metabolites formed as a result of BrB degradation, namely, phenol, catechol, cis, cis muconic acid, and carbon dioxide were determined by LC-MS and GC-MS. The initial attack on bromobenzene by Y. lipolytica cells lead to the transient accumulation of phenol as an early intermediate which is being reported for the first time. Degradation of phenol led to catechol which was degraded by the ortho- cleavage pathway forming cis, cis muconic acid and then to Krebs cycle intermediates eventually leading to CO2 production. The study shows that dehalogenation via an extracellular dehalogenase occurs prior to ring cleavage with phenol as the preliminary degradative compound being produced. The yeast was also able to grow on the degradative products, i.e., phenol and catechol, to varying degrees which would be of potential relevance in the degradation and remediation of xenobiotic environmental bromoaromatic pollutants such as bromobenzene.
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Affiliation(s)
| | | | - Ameeta RaviKumar
- Biochemistry Research Laboratory, Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune UniversityPune, India
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Yoneda A, Henson WR, Goldner NK, Park KJ, Forsberg KJ, Kim SJ, Pesesky MW, Foston M, Dantas G, Moon TS. Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Res 2016; 44:2240-54. [PMID: 26837573 PMCID: PMC4797299 DOI: 10.1093/nar/gkw055] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/20/2016] [Indexed: 12/29/2022] Open
Abstract
Lignin-derived (e.g. phenolic) compounds can compromise the bioconversion of lignocellulosic biomass to fuels and chemicals due to their toxicity and recalcitrance. The lipid-accumulating bacterium Rhodococcus opacus PD630 has recently emerged as a promising microbial host for lignocellulose conversion to value-added products due to its natural ability to tolerate and utilize phenolics. To gain a better understanding of its phenolic tolerance and utilization mechanisms, we adaptively evolved R. opacus over 40 passages using phenol as its sole carbon source (up to 373% growth improvement over wild-type), and extensively characterized two strains from passages 33 and 40. The two adapted strains showed higher phenol consumption rates (∼20 mg/l/h) and ∼2-fold higher lipid production from phenol than the wild-type strain. Whole-genome sequencing and comparative transcriptomics identified highly-upregulated degradation pathways and putative transporters for phenol in both adapted strains, highlighting the important linkage between mechanisms of regulated phenol uptake, utilization, and evolved tolerance. Our study shows that the R. opacus mutants are likely to use their transporters to import phenol rather than export them, suggesting a new aromatic tolerance mechanism. The identified tolerance genes and pathways are promising candidates for future metabolic engineering in R. opacus for improved lignin conversion to lipid-based products.
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Affiliation(s)
- Aki Yoneda
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - William R Henson
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas K Goldner
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Kun Joo Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kevin J Forsberg
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Soo Ji Kim
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Mitchell W Pesesky
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Marcus Foston
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Gautam Dantas
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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7
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Hollinshead WD, Henson WR, Abernathy M, Moon TS, Tang YJ. Rapid metabolic analysis of
Rhodococcus opacus
PD630 via parallel
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C‐metabolite fingerprinting. Biotechnol Bioeng 2015; 113:91-100. [DOI: 10.1002/bit.25702] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/04/2015] [Accepted: 07/07/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Whitney D. Hollinshead
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
| | - William R. Henson
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
| | - Mary Abernathy
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
| | - Yinjie J. Tang
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
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9
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Solyanikova IP, Golovleva LA. Physiological and biochemical properties of actinobacteria as the basis of their high biodegradative activity (Review). APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Biodegradation of chloroaromatic pollutants by bacterial consortium immobilized in polyurethene foam and other matrices. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2014.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Solyanikova IP, Plotnikova EG, Shumkova ES, Robota IV, Prisyazhnaya NV, Golovleva LA. Chloromuconolactone dehalogenase ClcF of actinobacteria. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2014; 49:422-431. [PMID: 24762180 DOI: 10.1080/03601234.2014.894778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This work investigated the distribution of the clcF gene in actinobacteria isolated from different ecotopes. The gene encodes chloromuconolactone dehalogenase (CMLD) ClcF, the enzyme found to date in only one representative of Gram-positive bacteria, Rhodococcus opacus 1CP, adapted to 2-chlorophenol (2CP). Using primers specific to the clcF gene, from the DNA matrix of rhodococcal strains closely related to species Rhodococcus wratislaviensis (P1, P12, P13, P20, G10, KT112, KT723, BO1) we obtained PCR products whose nucleotide sequences were 100% identical to that of the clcF gene from strain R. opacus 1CP. CMLDs isolated from the biomass of strains Rhodococcus spp. G10 and P1 grown on 2CP did not differ by their subunit molecular mass deduced from the known amino acid sequence of the clcF gene from the ClcF of strain R. opacus 1CP. Matrix-assisted laser dissociation/ionization time-of-flight mass spectrometry showed the presence of a peak with m/z 11,194-11,196 Da both in whole cells and in protein solutions with a ClcF activity. Thus, we have first time shown the distribution of ClcF among actinobacteria isolated from geographically distant habitats.
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Affiliation(s)
- Inna P Solyanikova
- a Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences , Pushchino , Moscow Region , Russia
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Arif NM, Ahmad SA, Syed MA, Shukor MY. Isolation and characterization of a phenol-degradingRhodococcussp. strain AQ5NOL 2 KCTC 11961BP. J Basic Microbiol 2012; 53:9-19. [DOI: 10.1002/jobm.201100120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 11/03/2011] [Indexed: 11/09/2022]
Affiliation(s)
- N. M. Arif
- Department of Biochemistry; Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia; UPM 43400 Serdang, Selangor; Malaysia
| | - S. A. Ahmad
- Department of Biochemistry; Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia; UPM 43400 Serdang, Selangor; Malaysia
| | - M. A. Syed
- Department of Biochemistry; Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia; UPM 43400 Serdang, Selangor; Malaysia
| | - M. Y. Shukor
- Department of Biochemistry; Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia; UPM 43400 Serdang, Selangor; Malaysia
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13
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Degradation of difluorobenzenes by the wild strain Labrys portucalensis. Biodegradation 2012; 23:653-62. [DOI: 10.1007/s10532-012-9541-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 01/20/2012] [Indexed: 10/14/2022]
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14
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Solyanikova I, Golovleva L. Biochemical features of the degradation of pollutants by Rhodococcus as a basis for contaminated wastewater and soil cleanup. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711050158] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Letek M, González P, MacArthur I, Rodríguez H, Freeman TC, Valero-Rello A, Blanco M, Buckley T, Cherevach I, Fahey R, Hapeshi A, Holdstock J, Leadon D, Navas J, Ocampo A, Quail MA, Sanders M, Scortti MM, Prescott JF, Fogarty U, Meijer WG, Parkhill J, Bentley SD, Vázquez-Boland JA. The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions. PLoS Genet 2010; 6:e1001145. [PMID: 20941392 PMCID: PMC2947987 DOI: 10.1371/journal.pgen.1001145] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 08/31/2010] [Indexed: 11/29/2022] Open
Abstract
We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid–rich intestine and manure of herbivores—two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche–adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT–acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi. Rhodococcus is a prototypic genus within the Actinobacteria, one of the largest microbial groups on Earth. Many of the ubiquitous rhodococcal species are biotechnologically useful due to their metabolic versatility and biodegradative properties. We have deciphered the genome of a facultatively parasitic Rhodococcus, the animal and human pathogen R. equi. Comparative genomic analyses of related species provide a unique opportunity to increase our understanding of niche-adaptive genome evolution and specialization. The environmental rhodococci have much larger genomes, richer in metabolic and degradative pathways, due to gene duplication and acquisition, not genome contraction in R. equi. This probably reflects that the host-associated R. equi habitat is more stable and favorable than the chemically diverse but nutrient-poor environmental niches of nonpathogenic rhodococci, necessitating metabolically more complex, expanded genomes. Our work also highlights that the recruitment or cooption of core microbial traits, following the horizontal acquistion of a few critical genes that provide access to the host niche, is an important mechanism in actinobacterial virulence evolution. Gene cooption is a key evolutionary mechanism allowing rapid adaptive change and novel trait acquisition. Recognizing the contribution of cooption to virulence provides a rational framework for understanding and interpreting the emergence and evolution of microbial pathogenicity.
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Affiliation(s)
- Michal Letek
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Patricia González
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Iain MacArthur
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Héctor Rodríguez
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Tom C. Freeman
- Division of Genetics and Genomics, Roslin BioCentre, University of Edinburgh, Edinburgh, United Kingdom
| | - Ana Valero-Rello
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Mónica Blanco
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Tom Buckley
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Inna Cherevach
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Ruth Fahey
- School of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland
| | - Alexia Hapeshi
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Jolyon Holdstock
- Oxford Gene Technology, Begbroke Science Park, Oxford, United Kingdom
| | | | - Jesús Navas
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | | | - Michael A. Quail
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Mandy Sanders
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Mariela M. Scortti
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Departamento de Bioquímica y Biología Molecular IV, Universidad Complutense, Madrid, Spain
| | - John F. Prescott
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | | | - Wim G. Meijer
- School of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - José A. Vázquez-Boland
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Grupo de Patogenómica Bacteriana, Universidad de León, León, Spain
- * E-mail:
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16
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Kim EJ, Jeon JR, Kim YM, Murugesan K, Chang YS. Mineralization and transformation of monofluorophenols by Pseudonocardia benzenivorans. Appl Microbiol Biotechnol 2010; 87:1569-77. [DOI: 10.1007/s00253-010-2647-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 03/03/2010] [Accepted: 04/24/2010] [Indexed: 10/19/2022]
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17
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Yam KC, van der Geize R, Eltis LD. Catabolism of Aromatic Compounds and Steroids by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2010. [DOI: 10.1007/978-3-642-12937-7_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Fernández de las Heras L, García Fernández E, María Navarro Llorens J, Perera J, Drzyzga O. Morphological, Physiological, and Molecular Characterization of a Newly Isolated Steroid-Degrading Actinomycete, Identified as Rhodococcus ruber Strain Chol-4. Curr Microbiol 2009; 59:548-53. [DOI: 10.1007/s00284-009-9474-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 06/23/2009] [Accepted: 07/24/2009] [Indexed: 01/09/2023]
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19
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Dos Santos VL, Monteiro ADS, Braga DT, Santoro MM. Phenol degradation by Aureobasidium pullulans FE13 isolated from industrial effluents. JOURNAL OF HAZARDOUS MATERIALS 2009; 161:1413-1420. [PMID: 18541369 DOI: 10.1016/j.jhazmat.2008.04.112] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 04/28/2008] [Accepted: 04/29/2008] [Indexed: 05/26/2023]
Abstract
The degradation of phenol (2-30 mM) by free cells and by alginate-immobilized cells of Aureobasidium pullulans FE13 isolated from stainless steel effluents was studied in batch cultures with saline solution not supplemented with nutrients or yeast extract. The rate at which the immobilized cells degrade phenol was similar to the rate at which the suspended cells could degrade phenol, for a concentration of up to 16 mM of phenol. The maximum phenol volumetric degradation rate for 16 mM phenol was found to be 18.35 mg l(-1)h(-1) in the assays with free cells and 20.45 mg l(-1)h(-1) in the assays with alginate-immobilized cells, 18 mM phenol and cellular concentration of 0.176 g/l. At concentrations higher than this, an inhibitory effect was observed, resulting in the lowering of the phenol degradation rates. The immobilization was detrimental to the catechol 1,2-dioxygenase activity. However, the immobilized cells remained viable for a longer period, increasing the efficiency of phenol degradation. The yeast showed catechol 1,2-dioxygenase activity only after growth in the phenol, which was induced at phenol concentrations as low as 0.05 mM and up to 25 mM at 45 h of incubation at 30 degrees C. Phenol concentrations higher than 6mM were inhibitory to the enzyme. Addition of glucose, lactate, succinate, and benzoate reduced the rate at which phenol is consumed by cells. Our results suggest that inoculants based on immobilized cells of A. pullulans FE13 has potential application in the biodegradation of phenol and possibly in the degradation of other related aromatic compounds.
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Affiliation(s)
- Vera Lúcia Dos Santos
- Department of Microbiology, Institute of Biological Science, Federal University of Minas Gerais, Belo Horizonte-MG, C.P. 486, 31270-901, Brazil.
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20
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Martínková L, Uhnáková B, Pátek M, Nesvera J, Kren V. Biodegradation potential of the genus Rhodococcus. ENVIRONMENT INTERNATIONAL 2009; 35:162-77. [PMID: 18789530 DOI: 10.1016/j.envint.2008.07.018] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 07/02/2008] [Accepted: 07/22/2008] [Indexed: 05/24/2023]
Abstract
A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.
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Affiliation(s)
- Ludmila Martínková
- Centre of Biocatalysis and Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, CZ-142 20 Prague 4, Czech Republic.
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21
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Biodegradation kinetics of 2,4,6-trichlorophenol by Rhodococcus rhodochrous in batch culture. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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22
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Solyanikova IP, Travkin VM, Rybkina DO, Plotnikova EG, Golovleva LA. Variability of enzyme system of Nocardioform bacteria as a basis of their metabolic activity. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2008; 43:241-252. [PMID: 18368545 DOI: 10.1080/03601230701771180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The present review describes some aspects of organization of biodegradative pathways of Nocardioform microorganisms, first of all, with respect to their ability to degrade aromatic compounds, mostly methylbenzoate, chlorosubstituted phenols, and chlorinated biphenyls and the intermediates of their transformation: 4-chlorobenzoate and para-hydroxybenzoate. Various enzyme systems induced during degradation processes are defined. The ability of microorganisms to induce a few key enzymes under the influence of xenobiotics is described. This ability may increase the biodegradative potential of strains allowing them to survive in the changing environment or demonstrate to some extent the unspecific response of microorganisms to the effect of toxicants. Nocardioform microorganisms responsible for degradation of such persistent compounds as polychlorinated biphenyls, polyaromatic hydrocarbons, chlorinated benzoates and phenols and other xenobiotics are characterized. The possibility of using Nocardioform microorganisms in some aspects of biotechnology due to their ability to produce some compounds important for industry is also estimated.
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Affiliation(s)
- Inna P Solyanikova
- Skryabin' Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
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23
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Li Y, Wang C. Phenol biodegradation in hybrid hollow-fiber membrane bioreactors. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9699-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Sarand I, Osterberg S, Holmqvist S, Holmfeldt P, Skärfstad E, Parales RE, Shingler V. Metabolism-dependent taxis towards (methyl)phenols is coupled through the most abundant of three polar localized Aer-like proteins of Pseudomonas putida. Environ Microbiol 2008; 10:1320-34. [PMID: 18279347 DOI: 10.1111/j.1462-2920.2007.01546.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Comparatively little is known about directed motility of environmental bacteria to common aromatic pollutants. Here, by expressing different parts of a (methyl)phenol-degradative pathway and the use of specific mutants, we show that taxis of Pseudomonas putida towards (methyl)phenols is dictated by its ability to catabolize the aromatic compound. Thus, in contrast to previously described chemoreceptor-mediated chemotaxis mechanisms towards benzoate, naphthalene and toluene, taxis in response to (methyl)phenols is mediated by metabolism-dependent behaviour. Here we show that P. putida differentially expresses three Aer-like receptors that are all polar-localized through interactions with CheA, and that inactivation of the most abundant Aer2 protein significantly decreases taxis towards phenolics. In addition, the participation of a sensory signal transduction protein composed of a PAS, a GGDEF and an EAL domain in motility towards these compounds is demonstrated. The results are discussed in the context of the versatility of metabolism-dependent coupling and the necessity for P. putida to integrate diverse metabolic signals from its native heterogeneous soil and water environments.
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Affiliation(s)
- Inga Sarand
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
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25
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Sharma NK, Pandey J, Gupta N, Jain RK. Growth and physiological response of Arthrobacter protophormiae RKJ100 toward higher concentrations of o-nitrobenzoate and p-hydroxybenzoate. FEMS Microbiol Lett 2007; 271:65-70. [PMID: 17391368 DOI: 10.1111/j.1574-6968.2007.00697.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bioremediation of sites that are heavily contaminated with pollutant chemicals is a challenge as most of the microorganisms cannot tolerate higher concentrations of toxic compounds. Only a few strains of the genus Pseudomonas have been studied for their tolerance toward the higher concentrations of aromatic pollutant compounds, a phenomenon that is accompanied by various physiological changes. In the present study we have characterized the growth response and physiological changes (adaptations) of a Gram-positive bacterium, Arthrobacter protophormiae RKJ100, toward the higher concentrations of two aromatic compounds, viz. o-nitrobenzoate (ONB) and p-hydroxybenzoate (PHB). Arthrobacter protophormiae RKJ100 could utilize 30 mM ONB and 50 mM PHB as sole sources of carbon and energy. It was capable of growth on higher concentrations of ONB (up to 200 mM) and PHB (up to 150 mM) when the cells were pre-exposed to lower concentrations of these compounds. The adaptive responses shown by the organism during growth on higher concentrations of these compounds were evident from significant changes in cellular fatty acid profiles. In addition, Bacterial Adhesion To Hydrocarbon (BATH) assay and scanning electron microscopy showed substantial increase in cell surface hydrophobicity and decrease in cell size of A. protophormiae RKJ100 when grown on ONB and PHB as compared to succinate-grown cells.
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Affiliation(s)
- Narinder K Sharma
- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
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26
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Ziagova M, Liakopoulou-Kyriakides M. Comparison of cometabolic degradation of 1,2-dichlorobenzene by Pseudomonas sp. and Staphylococcus xylosus. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Baptista IIR, Zhou NY, Emanuelsson EAC, Peeva LG, Leak DJ, Mantalaris A, Livingston AG. Evidence of species succession during chlorobenzene biodegradation. Biotechnol Bioeng 2007; 99:68-74. [PMID: 17680678 DOI: 10.1002/bit.21576] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have previously reported the disappearance of a specific strain degrading chlorobenzene from a functionally stable bioreactor. In the present work, we investigated this species succession and isolated a new dominant strain, identified as Pandoraea pnomenusa sp. strain MCB032. A specific 16S rRNA-targeted oligonucleotide probe was designed and validated to identify strain MCB032 using fluorescence in situ hybridisation (FISH). The results confirmed the presence of strain MCB032 in samples collected over time, and showed that it was primarily located within the biofilm. Denaturing gradient gel electrophoresis (DGGE) provided evidence that the species succession occurred early in the operating period. The application of these biomolecular tools highlighted the remarkable stability of this new strain during the 15 months of reactor operation. The succession was attributed to the competitive kinetic behaviour of strain MCB032, which exhibited faster growth (micro(max) = 0.34 h(-1)) and higher substrate affinity (K(s) = 0.35 mg L(-1)) than strain JS150. Finally, this study contributed to the characterisation of the recently established Pandoraea genus, an emerging group in the biodegradation field.
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Affiliation(s)
- I I R Baptista
- Department of Chemical Engineering and Chemical Technology, Imperial College London, Prince Consort Road, SW7 2AZ London, United Kingdom
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28
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Li Y, Loh KC. Continuous phenol biodegradation at high concentrations in an immobilized-cell hollow fiber membrane bioreactor. J Appl Polym Sci 2007. [DOI: 10.1002/app.26416] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Urgun-Demirtas M, Stark BC, Pagilla KR. Comparison of 2-chlorobenzoic acid biodegradation in a membrane bioreactor by B. cepacia and B. cepacia bearing the bacterial hemoglobin gene. WATER RESEARCH 2006; 40:3123-3130. [PMID: 16876227 DOI: 10.1016/j.watres.2006.05.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 02/27/2006] [Accepted: 05/28/2006] [Indexed: 05/11/2023]
Abstract
Degradation of 2-chlorobenzoic acid (2-CBA), a model recalcitrant chlorinated organic compound, by pure cultures of Burkholderia cepacia strain DNT with (transformed B. cepacia) and without (untransformed B. cepacia) the bacterial hemoglobin (Vitreoscilla hemoglobin, VHb) gene, vgb, was investigated in parallel membrane bioreactors (MBRs). This was done aseptically to prevent contamination during the operation of the MBRs. The objective was to determine whether the degradation of 2-CBA by cometabolism, using acetate as a primary carbon source, under hypoxic conditions might be enhanced for vgb-bearing cells in MBRs. The 2-CBA removal efficiency of transformed B. cepacia (97-99%) was slightly higher than that of untransformed B. cepacia (95-99%) at all stages. The average amount of chloride released from 2-CBA by transformed cells was also higher than for untransformed cells, 92-96% compared to 64-84% of the maximum theoretical amount, the exact value depending on the operating conditions. These results indicate that 2-CBA degradation/transformation is not accompanied by the stoichiometric release of chloride for the untransformed strain. The difference between percentages of 2-CBA removal and chloride release by untransformed cells was attributed to persistence, under hypoxic conditions, of the 2-CBA chlorine atom in 2-CBA metabolites. Growth of transformed cells was also significantly enhanced under hypoxic conditions compared to untransformed cells. For varying media compositions, the transformed cells reached higher cell densities (3.2-5.4 g/L) relative to untransformed cells (2.8-4.7 g/L) at food to microorganism ratios ranging from 0.44-0.59 to 0.38-0.49 g COD/g biomass-d The observed yields thus ranged from 0.16-0.20 and 0.15-0.18 g TSS/g COD for untransformed and transformed cells, respectively. The value of the yield depended on medium composition. The MBR system using vgb-containing B. cepacia maintained a high biomass concentration without oxygen limitations and provided cell-free effluent. Hence, it may be useful for treating high volumes of water contaminated with low levels of recalcitrant organics.
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Affiliation(s)
- Meltem Urgun-Demirtas
- Illinois Institute of Technology, Department of Chemical and Environmental Engineering, 10 West, 33rd Street, Chicago, IL 60616, USA
| | - Benjamin C Stark
- Illinois Institute of Technology, Department of Biological, Chemical and Physical Sciences, 3101 S. Dearborn Street, Chicago, IL 60616, USA
| | - K R Pagilla
- Illinois Institute of Technology, Department of Chemical and Environmental Engineering, 10 West, 33rd Street, Chicago, IL 60616, USA.
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30
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Krallish I, Gonta S, Savenkova L, Bergauer P, Margesin R. Phenol degradation by immobilized cold-adapted yeast strains of Cryptococcus terreus and Rhodotorula creatinivora. Extremophiles 2006; 10:441-9. [PMID: 16601913 DOI: 10.1007/s00792-006-0517-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Accepted: 01/31/2006] [Indexed: 11/28/2022]
Abstract
Three strains were isolated from hydrocarbon-polluted alpine habitats and were representatives of Cryptococcus terreus (strain PB4) and Rhodotorula creatinivora (strains PB7, PB12). All three strains synthesized and accumulated glycogen (both acid- and alkali-soluble) and trehalose during growth in complex medium containing glucose as carbon source and in minimal salt medium (MSM) with phenol as sole carbon and energy source. C. terreus strain PB4 showed a lower total accumulation level of storage compounds and a lower extracellular polysaccharides (EPS) production than the two R. creatinivora strains, PB7 and PB12. Biofilm formation and phenol degradation by yeast strains attached to solid carriers of zeolite or filter sand were studied at 10 degrees C. Phenol degradation by immobilized yeast strains was always higher on zeolite compared with filter sand under normal osmotic growth conditions. The transfer of cells immobilized on both solid supports to a high osmotic environment decreased phenol degradation activity by all strains. However, both R. creatinivora PB7 and PB12 strains maintained higher ability to degrade phenol compared with C. terreus strain PB4, which almost completely lost its phenol degradation activity. Moreover, R. creatinivora strain PB7 showed the highest ability to form biofilm on both carriers under high osmotic conditions of cultivation.
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Affiliation(s)
- Irina Krallish
- Institute of Microbiology and Biotechnology, University of Latvia, Kronvald boulv. 4, 1586 Riga, Latvia.
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31
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Rehfuss M, Urban J. Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources. Syst Appl Microbiol 2005; 28:695-701. [PMID: 16261859 DOI: 10.1016/j.syapm.2005.05.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The aerobic degradation of phenol, chlorobenzene and dichlorobenzene as a sole carbon source has been observed in bacterial Gram-positive strain G2PT isolated from a wastewater bioprocessor. Cells display branching mycelia fragmenting into rod and coccoid elements when grown on TSA. Aerial hyphae formation occurs when grown on phenol and chlorinated aromatics as the sole carbon source. Growth was observed at up to 0.75% phenol as a sole carbon source, indicating a strong tolerance for the compound. The 16S rRNA gene sequence shares the greatest similarity with members of the Rhodococcus genus, with the closest shared nucleotide identity of 98% with the aromatic toxin degrading bacteria Rhodococcus zopfii DSM 44108T. Neighbor-joining and parsimony analysis of Corynebacterineae 16S rRNA gene sequences consistently places strain G2PT in a clade shared with R. zopfii within the Rhodococcus rhodochrous subclade. Based on a unique polyphasic profile involving phenotypic, ribosomal DNA sequence analysis, DNA-DNA hybridization, mol% DNA G+C content and fatty acid composition, G2PT is proposed to represent a previously uncharacterized, novel species in the genus Rhodococcus. The name Rhodococcus phenolicus is proposed for the isolate with the type strain G2PT (= DSM 44812) (= NRRL B-24323) [corrected]
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Affiliation(s)
- Marc Rehfuss
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
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32
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Urgun-Demirtas M, Stark B, Pagilla K. 2-Chlorobenzoate biodegradation by recombinant Burkholderia cepacia under hypoxic conditions in a membrane bioreactor. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2005; 77:511-8. [PMID: 16274085 DOI: 10.2175/106143005x67421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The feasibility of applying bacterial hemoglobin technology to degrade 2-chlorobenzoate (2-CBA) through co-metabolism under hypoxic conditions in a membrane bioreactor (MBR) process has been studied in the laboratory. 2-chlorobenzoate removal and chloride release rates in the MBR system varied from 99 to 78% and 98 to 73%, respectively, depending on the operation conditions. Chemical oxygen demand (COD) removal efficiencies were more than 90% at food-to-microorganism ratios ranging from 0.32 to 0.62 g/g/d, and the observed yield was 0.13 to 0.20 g biomass/g COD. The bacterial cell-floc size-distribution analysis showed that there is a significant change in bacterial floc size due to high shear stress during operation of the MBR. To characterize growth kinetics of Burkholderia cepacia strain dinitrotoluene, a mathematical model that describes co-metabolic oxidation of 2-CBA in an MBR has been developed.
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Affiliation(s)
- Meltem Urgun-Demirtas
- Department of Chemical and Environmental Engineering, Illinois Institute of Technology, Chicago 60616, USA
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33
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Goswami M, Shivaraman N, Singh RP. Microbial metabolism of 2-chlorophenol, phenol and ρ-cresol by Rhodococcus erythropolis M1 in co-culture with Pseudomonas fluorescens P1. Microbiol Res 2005; 160:101-9. [PMID: 15881826 DOI: 10.1016/j.micres.2004.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Chlorophenolic waste most often contains phenol and rho-cresol along with chlorophenols. A Rhodococcus erythropolis strain M1 was isolated with the ability to degrade 2-chlorophenol, phenol and p-cresol (100 mgl(-1), each) in 18, 24 and 20 h, respectively, with negligible lag. However, Rhodococcus sp. characterized by low growth rate, pose a threat to be outgrown by bacteria occurring in natural habitats. In the present study, interaction of R. erythropolis M1 with another isolated bacteria generally encountered in activated sludge for water treatment like Pseudomonas fluorescens P1 was studied. 2-chlorophenol, phenol and p-cresol were selected as the substrates for the study. Viable cell counts showed competitive interaction between the species on 2-chlorophenol and phenol. Specific growth rate of pure culture of R. erythropolis M1 was higher than P. fluorescens P1 on 2-chlorophenol. However, in mixed culture, P. fluorescens P1 showed higher growth rate. Degradation of phenol showed higher growth rate of R. erythropolis M1 both in pure and in mixed culture form. Degradation of p-cresol had shown similar counts for both populations indicating neutral type of interaction. This observation was substantiated by detecting the growth rate, where both cultures had similar growth rate in pure and in the mixed culture form. Rate of 2-chlorophenol degradation was higher when R. erythropolis M1 was used as the pure culture as compared to the degradation rates observed with the P. fluorescens P1 or with the mixed culture. However, in case of phenol and p-cresol, degradation by the mixed culture had resulted in higher degradation rates as compared to the degradation of the substrates by both the axenic cultures.
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Affiliation(s)
- M Goswami
- Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India
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34
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Gürtler V, Mayall BC, Seviour R. Can whole genome analysis refine the taxonomy of the genus Rhodococcus? FEMS Microbiol Rev 2004; 28:377-403. [PMID: 15449609 DOI: 10.1016/j.femsre.2004.01.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.
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Affiliation(s)
- Volker Gürtler
- Department of Microbiology, Austin Health, Studley Road, Heidelberg, Vic. 3084, Australia.
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35
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Vogt C, Alfreider A, Lorbeer H, Hoffmann D, Wuensche L, Babel W. Bioremediation of chlorobenzene-contaminated ground water in an in situ reactor mediated by hydrogen peroxide. JOURNAL OF CONTAMINANT HYDROLOGY 2004; 68:121-141. [PMID: 14698874 DOI: 10.1016/s0169-7722(03)00092-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
New in situ reactive barrier technologies were tested nearby a local aquifer in Bitterfeld, Saxonia-Anhalt, Germany, which is polluted mainly by chlorobenzene (CB), in concentrations up to 450 microM. A reactor filled with original aquifer sediment was designed for the microbiological remediation of the ground water by indigenous bacterial communities. Two remediation variants were examined: (a) the degradation of CB under anoxic conditions in the presence of nitrate; (b) the degradation of CB under mixed electron acceptor conditions (oxygen+nitrate) using hydrogen peroxide as the oxygen-releasing compound. Under anoxic conditions, no definite degradation of CB was observed. Adding hydrogen peroxide (2.94 mM) and nitrate (2 mM) led to the disappearance of CB (ca. 150 microM) in the lower part of the reactor, accompanied by a strong increase of the number of cultivable aerobic CB degrading bacteria in reactor water and sediment samples, indicating that CB was degraded mainly by productive bacterial metabolism. Several aerobic CB degrading bacteria, mostly belonging to the genera Pseudomonas and Rhodococcus, were isolated from reactor water and sediments. In laboratory experiments with reactor water, oxygen was rapidly released by hydrogen peroxide, whereas biotic-induced decomposition reactions of hydrogen peroxide were almost four times faster than abiotic-induced decomposition reactions. A clear chemical degradation of CB mediated by hydrogen peroxide was not observed. CB was also completely degraded in the reactor after reducing the hydrogen peroxide concentration to 880 microM. The CB degradation completely collapsed after reducing the hydrogen peroxide concentration to 440 microM. In the following, the hydrogen peroxide concentrations were increased again (to 880 microM, 2.94 mM, and 880 microM, respectively), but the oxygen demand for CB degradation was higher than observed before, indicating a shift in the bacterial population. During the whole experiment, nitrate was uniformly reduced during the flow path in the reactor.
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Affiliation(s)
- Carsten Vogt
- Department of Environmental Microbiology, UFZ Centre for Environmental Research Leipzig-Halle, Permoserstrasse 15, D-04318, Leipzig, Germany.
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36
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Urgun-Demirtas M, Pagilla KR, Stark BC. Enhanced kinetics of genetically engineeredBurkholderia cepacia: the role ofvgb in the hypoxic metabolism of 2-CBA. Biotechnol Bioeng 2004; 87:110-8. [PMID: 15211495 DOI: 10.1002/bit.20102] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Application of Vitreoscilla hemoglobin (VHb) technology to 2-CBA degradation by Burkholderia cepacia strain DNT under hypoxic conditions was studied in continuous culture chemostats. Dechlorination abilities of both recombinant (VHb gene (vgb) containing) and untransformed cells were investigated at various dilution rates to ensure complete degradation of 2-CBA. As the dilution rate increased from 0.025 to 0.25 h(-1), the ratios of chloride release to degraded 2-CBA concentration decreased from 0.95 to 0.72 and from 0.89 to 0.39 for recombinant and untransformed cells, respectively. A nonstoichiometric relationship between chloride release and 2-CBA degradation was more pronounced for untransformed cells. Recombinant cell densities were 0.1-0.2. g L(-1) greater than untransformed cell densities for a range of dilution rates. As the dilution rate increased, the oxygen uptake rate (OUR) and the substrate utilization rate (SUR) decreased for both strains. The OUR/SUR ratio increased as the dilution rate increased for both strains but was much higher for the recombinant strain compared to untransformed cells. The specific 2-CBA degradation rate of recombinant cells was greater than that of untransformed cells (1.17 vs. 0.46 mg CBA (mg) day(-1), and half-saturation constants for recombinant cells were lower than those of untransformed cells (0.18 and 0.32 mg CBA L(-1), respectively). The pseudo-first-order degradation constants, k(1CBA) and k(1ACE), were higher for recombinant cells (6.5 L (mg cells)(-1) day(-1) and 95.6 L (mg cells)(-1) day(-1), respectively) than those of untransformed cells (1.44 L (mg cells)(-1) day(-1) and 73.7 L (mg cells)(-1) day(-1), respectively).
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Affiliation(s)
- Meltem Urgun-Demirtas
- Department of Chemical and Environmental Engineering, Illinois Institute of Technology, 10 West 33rd Street, Chicago, IL 60616, USA
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Rapp P, Gabriel-Jürgens LHE. Degradation of alkanes and highly chlorinated benzenes, and production of biosurfactants, by a psychrophilic Rhodococcus sp. and genetic characterization of its chlorobenzene dioxygenase. Microbiology (Reading) 2003; 149:2879-2890. [PMID: 14523120 DOI: 10.1099/mic.0.26188-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rhodococcus sp. strain MS11 was isolated from a mixed culture. It displays a diverse range of metabolic capabilities. During growth on 1,2,4-trichlorobenzene, 1,2,4,5-tetrachlorobenzene (1,2,4,5-TeCB) and 3-chlorobenzoate stoichiometric amounts of chloride were released. It also utilized all three isomeric dichlorobenzenes and 1,2,3-trichlorobenzene as the sole carbon and energy source. Furthermore, the bacterium grew well on a great number of n-alkanes ranging from n-heptane to n-triacontane and on the branched alkane 2,6,10,14-tetramethylpentadecane (pristane) and slowly on n-hexane and n-pentatriacontane. It was able to grow at temperatures from 5 to 30 °C, with optimal growth at 20 °C, and could tolerate 6 % NaCl in mineral salts medium. Genes encoding the initial chlorobenzene dioxygenase were detected by using a primer pair that was designed against the α-subunit (TecA1) of the chlorobenzene dioxygenase of Ralstonia (formerly Burkholderia) sp. strain PS12. The amino acid sequence of the amplified part of the α-subunit of the chlorobenzene dioxygenase of Rhodococcus sp. strain MS11 showed >99 % identity to the α-subunit of the chlorobenzene dioxygenase from Ralstonia sp. strain PS12 and the parts of both α-subunits responsible for substrate specificity were identical. The subsequent enzymes dihydrodiol dehydrogenase and chlorocatechol 1,2-dioxygenase were induced in cells grown on 1,2,4,5-TeCB. During cultivation on medium-chain-length n-alkanes ranging from n-decane to n-heptadecane, including 1-hexadecene, and on the branched alkane pristane, strain MS11 produced biosurfactants lowering the surface tension of the cultures from 72 to ⩽29 mN m−1. Glycolipids were extracted from the supernatant of a culture grown on n-hexadecane and characterized by 1H- and 13C-NMR-spectroscopy and mass spectrometry. The two major components consisted of α,α-trehalose esterified at C-2 or C-4 with a succinic acid and at C-2′ with a decanoic acid. They differed from one another in that one 2,3,4,2′-trehalosetetraester, found in higher concentration, was esterified at C-2, C-3 or C-4 with one octanoic and one decanoic acid and the other one, of lower concentration, with two octanoic acids. The results demonstrate that Rhodococcus sp. strain MS11 may be well suited for bioremediation of soils and sediments contaminated for a long time with di-, tri- and tetrachlorobenzenes as well as alkanes.
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Affiliation(s)
- Peter Rapp
- GBF-National Research Centre for Biotechnology, Division of Microbiology, Mascheroderweg 1, D-38124 Braunschweig, Germany
| | - Lotte H E Gabriel-Jürgens
- GBF-National Research Centre for Biotechnology, Division of Microbiology, Mascheroderweg 1, D-38124 Braunschweig, Germany
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Seignez C, Vuillemin A, Adler N, Peringer P. A procedure for production of adapted bacteria to degrade chlorinated aromatics. JOURNAL OF HAZARDOUS MATERIALS 2001; 84:265-277. [PMID: 11406311 DOI: 10.1016/s0304-3894(01)00235-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Production of biomass adapted to the degradation of a mixture of chlorobenzene (CB) and 1,2-dichlorobenzene (DCB) was investigated in a batch culture with substrates supplied by pulses. CB and o-DCB concentrations which gave the best adapted biomass productivity were determined and found to be 150 and 30 microl l(-1), respectively. The biomass productivity was 51 mg l(-1) h(-1). The biomass yield was 0.38 g of biomass dry weight per gram of substrate. The pulses of 200 microl CB and 40 microl o-DCB, were inhibitory to the bacterial culture. Among the metabolites, muconic acid was found in large quantities in the medium and in the cells. At a time between two pulses of 60 min, adding 150 microl CB and 30 microl o-DCB per each pulse, 7.6g l(-1) of biomass was obtained. The produced biomass served as an inoculum for the biotrickling filter which treated industrial waste gases contaminated by CBs. The method of adapted biomass production was described using CBs, but the degradation of any other toxic volatile pollutant can be improved using this technique.
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Affiliation(s)
- C Seignez
- Laboratory for Environmental Biotechnology Swiss Federal Institute - EPFL, Ecublens, 1015, Lausanne, Switzerland.
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Sarand I, Skärfstad E, Forsman M, Romantschuk M, Shingler V. Role of the DmpR-mediated regulatory circuit in bacterial biodegradation properties in methylphenol-amended soils. Appl Environ Microbiol 2001; 67:162-71. [PMID: 11133441 PMCID: PMC92538 DOI: 10.1128/aem.67.1.162-171.2001] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2000] [Accepted: 10/17/2000] [Indexed: 11/20/2022] Open
Abstract
Pathway substrates and some structural analogues directly activate the regulatory protein DmpR to promote transcription of the dmp operon genes encoding the (methyl)phenol degradative pathway of Pseudomonas sp. strain CF600. While a wide range of phenols can activate DmpR, the location and nature of substituents on the basic phenolic ring can limit the level of activation and thus utilization of some compounds as assessed by growth on plates. Here we address the role of the aromatic effector response of DmpR in determining degradative properties in two soil matrices that provide different nutritional conditions. Using the wild-type system and an isogenic counterpart containing a DmpR mutant with enhanced ability to respond to para-substituted phenols, we demonstrate (i) that the enhanced in vitro biodegradative capacity of the regulator mutant strain is manifested in the two different soil types and (ii) that exposure of the wild-type strain to 4-methylphenol-contaminated soil led to rapid selection of a subpopulation exhibiting enhanced capacities to degrade the compound. Genetic and functional analyses of 10 of these derivatives demonstrated that all harbored a single mutation in the sensory domain of DmpR that mediated the phenotype in each case. These findings establish a dominating role for the aromatic effector response of DmpR in determining degradation properties. Moreover, the results indicate that the ability to rapidly adapt regulator properties to different profiles of polluting compounds may underlie the evolutionary success of DmpR-like regulators in controlling aromatic catabolic pathways.
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Affiliation(s)
- I Sarand
- Department of Cell and Molecular Biology, Umeå University, S-901 87 Umeå, Sweden
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Zaitsev GM, Surovtseva EG. Growth ofRhodococcus opacus on mixtures of monohalogenated benzenes and phenols. Microbiology (Reading) 2000. [DOI: 10.1007/bf02756763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Sarand I, Haario H, Jørgensen KS, Romantschuk M. Effect of inoculation of a TOL plasmid containing mycorrhizosphere bacterium on development of Scots pine seedlings, their mycorrhizosphere and the microbial flora in m-toluate-amended soil. FEMS Microbiol Ecol 2000; 31:127-141. [PMID: 10640666 DOI: 10.1111/j.1574-6941.2000.tb00678.x] [Citation(s) in RCA: 39] [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 purpose of this study was to evaluate the influence of introduced bacteria containing a contaminant degrading plasmid on the growth and survival of pine seedlings and mycorrhizosphere microbial flora in contaminated soil. The Pseudomonas fluorescens strain OS81, originally isolated from fungal hyphae in contaminated soil, was supplied with the TOL plasmid pWW0::Km (to generate OS81(pWW0::Km)) and inoculated in humus-soil microcosms with and without pine seedlings mycorrhized with Suillus bovinus. After 3 months of regular treatment with m-toluate (mTA) solutions, the introduced catabolic plasmid was found to be disseminated in the indigenous bacterial population of both mycorrhizosphere and soil uncolonized by the fungus. Transconjugants were represented by bacteria of the genera Pseudomonas and Burkholderia and their number correlated positively with the concentration of mTA applied. Indigenous mTA degrading bacteria with low similarity to Burkholderia species were also enriched in microcosms. They were mostly associated with mycorrhizal soil or fungal structures and virtually absent in microcosms without pines. The total number of Tol(+) bacteria was higher in mycorrhizospheric soil compared with bulk soil. Inoculation with P. fluorescens OS81(pWW0::Km) had a positive effect on the development of roots and fungus in contaminated soil. Both inoculation with the P. fluorescens OS81(pWW0::Km) and mTA contamination as well as the presence of mycorrhized pine roots and fungal hyphae had an effect on the microbial community structure of soil as measured by carbon source oxidation patterns. However, the impact of mTA on the microbial community was more prominent. The study indicates that an effect on plant and fungal development can be obtained by manipulating the mycorrhizosphere. Both introduction of the bacterium carrying the degradative plasmid and the plasmid itself are likely to have a positive effect not only on the organisms involved, but also on bioremediation of contaminated soil, a factor that was not directly monitored here.
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Affiliation(s)
- I Sarand
- Department of Biosciences, Division of General Microbiology, Viikki Biocenter, P.O. Box 56 (Viikinkaari 9), University of Helsinki, FIN-00014, Helsinki, Finland
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42
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Rapp P, Timmis KN. Degradation of chlorobenzenes at nanomolar concentrations by Burkholderia sp. strain PS14 in liquid cultures and in soil. Appl Environ Microbiol 1999; 65:2547-52. [PMID: 10347041 PMCID: PMC91376 DOI: 10.1128/aem.65.6.2547-2552.1999] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/1998] [Accepted: 04/09/1999] [Indexed: 11/20/2022] Open
Abstract
The utilization of 1,2,4,5-tetrachloro-, 1,2,4-trichloro-, the three isomeric dichlorobenzenes and fructose as the sole carbon and energy sources at nanomolar concentrations was studied in batch experiments with Burkholderia sp. strain PS14. In liquid culture, all chlorobenzenes were metabolized within 1 h from their initial concentration of 500 nM to below their detection limits of 0.5 nM for 1,2,4,5-tetrachloro- and 1,2,4-trichlorobenzene and 7.5 nM for the three dichlorobenzene isomers, with 63% mineralization of the tetra- and trichloroisomers. Fructose at the same initial concentration was, in contrast, metabolized over a 4-h incubation period down to a residual concentration of approximately 125 nM with 38% mineralization during this time. In soil microcosms, Burkholderia sp. strain PS14 metabolized tetrachlorobenzene present at 64.8 ppb and trichlorobenzene present at 54.4 ppb over a 72-h incubation period to below the detection limits of 0.108 and 0.09 ppb, respectively, with approximately 80% mineralization. A high sorptive capacity of Burkholderia sp. strain PS14 for 1,2,4, 5-tetrachlorobenzene was found at very low cell density. The results demonstrate that Burkholderia sp. strain PS14 exhibits a very high affinity for chlorobenzenes at nanomolar concentrations.
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Affiliation(s)
- P Rapp
- Division of Microbiology, GBF-National Research Centre for Biotechnology, Braunschweig, Germany.
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43
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Fritsche K, Auling G, Andreesen JR, Lechner U. Defluvibacter lusatiae gen. nov., sp. nov., a new chlorohenol-degrading member of the alpha-2 subgroup of proteobacteria. Syst Appl Microbiol 1999; 22:197-204. [PMID: 10390870 DOI: 10.1016/s0723-2020(99)80066-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The two Gram-negative bacterial strains S1 and S4 were isolated from activated sludge of an industrial waste water treatment plant and exhibited a stable capability to degrade 2,4-dichlorophenol, 4-chloro-2-methylphenol, 4-chlorophenol and phenol. The cells were short rods with a polar flagellum, being mesophilic, strictly aerobic, oxidase-positive, and chemoorganotrophic. They utilized a range of amino acids, but only a restricted number of carbohydrates. Reassociation experiments with DNA from strains S1 and S4 revealed high interstrain similarity, indicating, that both strains belong to the same species. The phylogenetic position was determined by comparison of the almost complete 16S rDNA sequence of strain S1 with sequences of related bacteria. Strain S1 clustered with members of the alpha-2 subgroup of the Proteobacteria by forming a separate lineage within the radiation of Mesorhizobium, Phyllobacterium and Sinorhizobium. Both strains can be differentiated from members of related taxa by a set of physiological and chemotaxonomic properties including the ability to grow with norvaline, L-tryptophan, putrescine, glutarate and malonate, and by the presence of spermidine as major polyamine and of 12:0 3OH as fatty acid. Strain S1 is described as type strain of a new species and assigned to a new genus with the proposed name Defluvibacter lusatiae.
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Affiliation(s)
- K Fritsche
- Institut für Mikrobiologie, Martin-Luther-Universität, Halle/Saale, Germany
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44
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Tsitko IV, Zaitsev GM, Lobanok AG, Salkinoja-Salonen MS. Effect of aromatic compounds on cellular fatty acid composition of Rhodococcus opacus. Appl Environ Microbiol 1999; 65:853-5. [PMID: 9925629 PMCID: PMC91108 DOI: 10.1128/aem.65.2.853-855.1999] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In cells of Rhodococcus opacus GM-14, GM-29, and 1CP, the contents of branched (10-methyl) fatty acids increased from 3% to 15 to 34% of the total fatty acids when the cells were grown on benzene, phenol, 4-chlorophenol, chlorobenzene, or toluene as the sole source of carbon and energy, in comparison with cells grown on fructose. In addition, the content of trans-hexadecenoic acid increased from 5% to 8 to 18% with phenol or chlorophenol as the carbon source. The 10-methyl branched fatty acid content of R. opacus GM-14 cells increased in a dose-related manner following exposure to phenol or toluene when toluene was not utilized as the growth substrate. The results suggest that 10-methyl branched fatty acids may participate in the adaptation of R. opacus to lipophilic aromatic compounds.
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Affiliation(s)
- I V Tsitko
- Department of Applied Chemistry and Microbiology, University of Helsinki, FIN-00014, Helsinki, Finland.
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Angelova B, Schmauder HP. Lipophilic compounds in biotechnology--interactions with cells and technological problems. J Biotechnol 1999; 67:13-32. [PMID: 9987845 DOI: 10.1016/s0168-1656(98)00139-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Lipophilic compounds are of significant importance in modern biotechnology. Centerly of interest are the biodegradation as well as the biotransformation of such lipophilic and often water-immiscible substances. Both whole cells and/or enzymes are used for these processes. It is obvious that a wide range of problems arise in an application of such complex systems consisting of biocatalysts substrate(s), product(s), water, (in some cases water-immiscible organic solvents): (i) interactions between lipophilic compounds and the membranes resulting in the change of some physiological characteristics of the living system; (ii) problems in the transport of these compounds (substrates and/or products) within the complex structured reaction systems; (iii) the problem of increasing the solubility of the lipophilic and mostly water-immiscible compounds with a minimum of inhibition effects on the processes; (iv) the presence of lipophilic components may also cause changes of the transport processes within the system (e.g. immobilized cells) resulting in changed yield or activity of the biological system. These problems are critically discussed in this review in relation to the known modes of interaction of lipophilic compounds with membranes, the bioavailability of the substrates, and the cases of steroid biotransformations. An outlook of future aspects in research, development and application of such processes is given.
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Affiliation(s)
- B Angelova
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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46
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Tondo E, Andretta C, Souza C, Monteiro A, Henriques J, Ayub M. High biodegradation levels of 4,5,6-trichloroguaiacol by Bacillus sp. isolated from cellulose pulp mill effluent. ACTA ACUST UNITED AC 1998. [DOI: 10.1590/s0001-37141998000400006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aerobic Gram positive spore-forming bacterium was isolated from cellulose pulp mill effluent. This microorganism, identified as Bacillus sp. and named IS13, was able to rapidly degrade the organic chlorinated compound 4,5,6-trichloroguaiacol (4,5,6-TCG) from a culture containing 50 mg/l, which corresponds to about 3x104 times the concentration found in the original effluent. The biodegradation of this compound, usually found in cellulose pulp mill effluents, was evaluated by spectrophotometry and gas chromatography analysis. During 4,5,6-TCG decreasing, the lack of by-products had shown by such analysis lead to verify the possibility of either adsorption or absorption of 4,5,6-TCG by the cells, instead of real biodegradation. There were no traces of 4,5,6-TCG after lysozyme and SDS cell disruption. Vigorous extraction was applied before spectrophotometry analysis and there was no release of residual 4,5,6-TCG. Plasmid isolation was attempted by using different protocols. The best results were reached by CTAB method, but no plasmid DNA was found in Bacillus sp. IS13. The results suggest that genes located at the bacterial chromosome might mediate the high decrease of 4,5,6-TCG. The importance of this work is that, in being a natural ocurring microorganism, Bacillus sp. IS13, can be used as inoculum in plant effluents to best organochlorinated compounds biodegradation.
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Affiliation(s)
- E.C. Tondo
- Universidade Federal do Rio Grande do Sul
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47
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Paje MLF, Neilan BA, Couperwhite L. A Rhodococcus species that thrives on medium saturated with liquid benzene. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 9):2975-2981. [PMID: 9308180 DOI: 10.1099/00221287-143-9-2975] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A bacterium isolated from a contaminated site in Sydney, Australia, utilized benzene in the liquid phase as a sole carbon source at levels toxic to other micro-organisms. The organism was a short Gram-positive rod which grew at 6% NaCl, 0-37 degrees C and pH 2-10. Biochemical tests, fatty acid analysis, and 16S rDNA sequencing identified the organism as a member of the genus Rhodococcus. Vapour-phase addition of benzene to the medium in batch and continuous systems resulted in initial concentrations averaging 200 p.p.m. Under these conditions, 95% of the benzene was degraded. In separate experiments, medium spiked with liquid benzene resulted in concentrations of up to 2789 p.p.m. and supported good growth of the organism. To confirm utilization of benzene at levels known to be toxic to other micro-organisms, continuous cultures were used; benzene added at 2% (v/v) per day resulted in growth and 89% degradation, which was maintained for more than 30 d. Rhodococcus sp. strain 33 appears to be the only organism known that can grow at these levels of benzene.
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Affiliation(s)
- M Luz F Paje
- School of Microbiology and Immunology, The University of New South Wales, Sydney NSW 2052, Australia
| | - Brett A Neilan
- School of Microbiology and Immunology, The University of New South Wales, Sydney NSW 2052, Australia
| | - Lain Couperwhite
- School of Microbiology and Immunology, The University of New South Wales, Sydney NSW 2052, Australia
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Luz Paje M, Couperwhite I. Short communication: Benzene metabolism via the intradiol cleavage in a Rhodococcus sp. World J Microbiol Biotechnol 1996; 12:653-4. [DOI: 10.1007/bf00327733] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/03/1996] [Accepted: 05/05/1996] [Indexed: 10/26/2022]
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