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Ma J, Zhuang Y, Wang Y, Zhu N, Wang T, Xiao H, Chen J. Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:93345-93362. [PMID: 37548784 DOI: 10.1007/s11356-023-28894-y] [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: 03/18/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.
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Affiliation(s)
- Jinglin Ma
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Yan Zhuang
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ning Zhu
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ting Wang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Hongbin Xiao
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China.
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Nemoto Y, Ozawa K, Mori JF, Kanaly RA. Nondesulfurizing benzothiophene biotransformation to hetero and homodimeric ortho-substituted diaryl disulfides by the model PAH-degrading Sphingobium barthaii. Biodegradation 2023; 34:215-233. [PMID: 36808269 DOI: 10.1007/s10532-023-10014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/06/2023] [Indexed: 02/21/2023]
Abstract
Understanding the biotransformation mechanisms of toxic sulfur-containing polycyclic aromatic hydrocarbon (PASH) pollutants such as benzothiophene (BT) is useful for predicting their environmental fates. In the natural environment, nondesulfurizing hydrocarbon-degrading bacteria are major active contributors to PASH biodegradation at petroleum-contaminated sites; however, BT biotransformation pathways by this group of bacteria are less explored when compared to desulfurizing organisms. When a model nondesulfurizing polycyclic aromatic hydrocarbon-degrading soil bacterium, Sphingobium barthaii KK22, was investigated for its ability to cometabolically biotransform BT by quantitative and qualitative methods, BT was depleted from culture media but was biotransformed into mostly high molar mass (HMM) hetero and homodimeric ortho-substituted diaryl disulfides (diaryl disulfanes). HMM diaryl disulfides have not been reported as biotransformation products of BT. Chemical structures were proposed for the diaryl disulfides by comprehensive mass spectrometry analyses of the chromatographically separated products and were supported by the identification of transient upstream BT biotransformation products, which included benzenethiols. Thiophenic acid products were also identified, and pathways that described BT biotransformation and novel HMM diaryl disulfide formation were constructed. This work shows that nondesulfurizing hydrocarbon-degrading organisms produce HMM diaryl disulfides from low molar mass polyaromatic sulfur heterocycles, and this may be taken into consideration when predicting the environmental fates of BT pollutants.
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Affiliation(s)
- Yuki Nemoto
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Kohei Ozawa
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Jiro F Mori
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Robert A Kanaly
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan.
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Ali SS, Jiao H, Mustafa AM, Koutra E, El-Sapagh S, Kornaros M, Elsamahy T, Khalil M, Bulgariu L, Sun J. Construction of a novel microbial consortium valued for the effective degradation and detoxification of creosote-treated sawdust along with enhanced methane production. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126091. [PMID: 34118544 DOI: 10.1016/j.jhazmat.2021.126091] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 04/29/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Lignocellulosic biomass represents an unlimited and ubiquitous energy source, which can effectively address current global challenges, including climate change, greenhouse gas emissions, and increased energy demand. However, lignocellulose recalcitrance hinders microbial degradation, especially in case of contaminated materials such as creosote (CRO)-treated wood, which necessitates appropriate processing in order to eliminate pollution. This study might be the first to explore a novel bacterial consortium SST-4, for decomposing birchwood sawdust, capable of concurrently degrading lignocellulose and CRO compounds. Afterwards, SST-4 which stands for molecularly identified bacterial strains Acinetobacter calcoaceticus BSW-11, Shewanella putrefaciens BSW-18, Bacillus cereus BSW-23, and Novosphingobium taihuense BSW-25 was evaluated in terms of biological sawdust pre-treatment, resulting in effective lignocellulose degradation and 100% removal of phenol and naphthalene. Subsequently, the maximum biogas production observed was 18.7 L/kg VS, while cumulative methane production was 162.8 L/kg VS, compared to 88.5 without microbial pre-treatment. The cumulative energy production from AD-I and AD-II through biomethanation was calculated as 3177.1 and 5843.6 KJ/kg, respectively. The pretreatment process exhibited a significant increase in the energy yield by 83.9%. Lastly, effective CRO detoxification was achieved with EC50 values exceeding 90%, showing the potential for an integrated process of effective contaminated wood management and bioenergy production.
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Affiliation(s)
- Sameh Samir Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Haixin Jiao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Ahmed M Mustafa
- State Key Laboratory of Pollution Control and Resourses Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Department of Agricultural Engineering, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - Eleni Koutra
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 1 Karatheodori Str., University Campus, Patras 26504, Greece; INVALOR: Research Infrastructure for Waste Valorization and Sustainable Management, University Campus, Patras 26504, Greece
| | - Shimaa El-Sapagh
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Michael Kornaros
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 1 Karatheodori Str., University Campus, Patras 26504, Greece; INVALOR: Research Infrastructure for Waste Valorization and Sustainable Management, University Campus, Patras 26504, Greece
| | - Tamer Elsamahy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Maha Khalil
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Laura Bulgariu
- Department of Environmental Engineering and Management, Cristofor Simionescu Faculty of Chemical Engineering and Environmental Protection, Gheorghe Asachi Technical University of Iasi, 700050 Iasi, Romania
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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Anokhina TO, Esikova TZ, Gafarov AB, Polivtseva VN, Baskunov BP, Solyanikova IP. Alternative Naphthalene Metabolic Pathway Includes Formation of ortho-Phthalic Acid and Cinnamic Acid Derivatives in the Rhodococcus opacus Strain 3D. BIOCHEMISTRY (MOSCOW) 2020; 85:355-368. [DOI: 10.1134/s0006297920030116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Heine T, Großmann C, Hofmann S, Tischler D. Indigoid dyes by group E monooxygenases: mechanism and biocatalysis. Biol Chem 2020; 400:939-950. [PMID: 30844759 DOI: 10.1515/hsz-2019-0109] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/19/2019] [Indexed: 11/15/2022]
Abstract
Since ancient times, people have been attracted by dyes and they were a symbol of power. Some of the oldest dyes are indigo and its derivative Tyrian purple, which were extracted from plants and snails, respectively. These 'indigoid dyes' were and still are used for coloration of textiles and as a food additive. Traditional Chinese medicine also knows indigoid dyes as pharmacologically active compounds and several studies support their effects. Further, they are interesting for future technologies like organic electronics. In these cases, especially the indigo derivatives are of interest but unfortunately hardly accessible by chemical synthesis. In recent decades, more and more enzymes have been discovered that are able to produce these indigoid dyes and therefore have gained attention from the scientific community. In this study, group E monooxygenases (styrene monooxygenase and indole monooxygenase) were used for the selective oxygenation of indole (derivatives). It was possible for the first time to show that the product of the enzymatic reaction is an epoxide. Further, we synthesized and extracted indigoid dyes and could show that there is only minor by-product formation (e.g. indirubin or isoindigo). Thus, group E monooxygenase can be an alternative biocatalyst for the biosynthesis of indigoid dyes.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
| | - Carolin Großmann
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
| | - Sarah Hofmann
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
| | - Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany.,Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
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6
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Baratto MC, Lipscomb DA, Larkin MJ, Basosi R, Allen CCR, Pogni R. Spectroscopic Characterisation of the Naphthalene Dioxygenase from Rhodococcus sp. Strain NCIMB12038. Int J Mol Sci 2019; 20:E3402. [PMID: 31373299 PMCID: PMC6678576 DOI: 10.3390/ijms20143402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/01/2019] [Accepted: 07/09/2019] [Indexed: 12/27/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs), such as naphthalene, are potential health risks due to their carcinogenic and mutagenic effects. Bacteria from the genus Rhodococcus are able to metabolise a wide variety of pollutants such as alkanes, aromatic compounds and halogenated hydrocarbons. A naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038 has been characterised for the first time, using electron paramagnetic resonance (EPR) spectroscopy and UV-Vis spectrophotometry. In the native state, the EPR spectrum of naphthalene 1,2-dioxygenase (NDO) is formed of the mononuclear high spin Fe(III) state contribution and the oxidised Rieske cluster is not visible as EPR-silent. In the presence of the reducing agent dithionite a signal derived from the reduction of the [2Fe-2S] unit is visible. The oxidation of the reduced NDO in the presence of O2-saturated naphthalene increased the intensity of the mononuclear contribution. A study of the "peroxide shunt", an alternative mechanism for the oxidation of substrate in the presence of H2O2, showed catalysis via the oxidation of mononuclear centre while the Rieske-type cluster is not involved in the process. Therefore, the ability of these enzymes to degrade recalcitrant aromatic compounds makes them suitable for bioremediative applications and synthetic purposes.
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Affiliation(s)
- Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro 2, 53100 Siena, Italy.
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - David A Lipscomb
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Michael J Larkin
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro 2, 53100 Siena, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK.
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro 2, 53100 Siena, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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Indole Degradation in a Model System and in Poultry Manure by Acinetobacter spp. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9081622] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Indole degradation in a model system and in poultry manure was studied using an enrichment culture of two Acinetobacter species; Acinetobacter toweneri NTA1-2A and Acinetobacter guillouiae TAT1-6A. Degradation of indole was quantified using reverse phase high performance liquid chromatography (HPLC). The two strains were capable of degrading initial concentrations of indole ranging from 58.58–300 mg/L. The degradation efficiency was 66.36% (NTA1-2A), 94.87% (TAT1-6A), and 96.00% (mix) in 6 days when the initial concentration <300 mg/L. The strains were tested for enzymatic activity using 120 mg/L indole. The enzyme extracts of NTA1-2A and TAT1-6A from culture medium degraded indole completely, and no appreciable change of indole concentration was witnessed in the control group. The NTA1-2A, TAT1-6A, and the mix of strains were also used for in vivo poultry manure fermentation and removed 78.67%, 83.28%, and 83.70% of indole, respectively in 8 d. The strains showed a statistically significant difference (p < 0.05) in indole removal efficiency compared with the control, but no significant difference between the two strains and the mix in indole removal capacity. We concluded that A. toweneri NTA1-2A and A. guillouiae TAT1-6A are promising strains to remove indole and its derivatives to control the notorious odor in poultry and other livestock industries.
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Ma Q, Zhang X, Qu Y. Biodegradation and Biotransformation of Indole: Advances and Perspectives. Front Microbiol 2018; 9:2625. [PMID: 30443243 PMCID: PMC6221969 DOI: 10.3389/fmicb.2018.02625] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Indole is long regarded as a typical N-heterocyclic aromatic pollutant in industrial and agricultural wastewater, and recently it has been identified as a versatile signaling molecule with wide environmental distributions. An exponentially growing number of researches have been reported on indole due to its significant roles in bacterial physiology, pathogenesis, animal behavior and human diseases. From the viewpoint of both environmental bioremediation and biological studies, the researches on metabolism and fates of indole are important to realize environmental treatment and illuminate its biological function. Indole can be produced from tryptophan by tryptophanase in many bacterial species. Meanwhile, various bacterial strains have obtained the ability to transform and degrade indole. The characteristics and pathways for indole degradation have been investigated for a century, and the functional genes for indole aerobic degradation have also been uncovered recently. Interestingly, many oxygenases have proven to be able to oxidize indole to indigo, and this historic and motivating case for biological applications has attracted intensive attention for decades. Herein, the bacteria, enzymes and pathways for indole production, biodegradation and biotransformation are systematically summarized, and the future researches on indole-microbe interactions are also prospected.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Food and Environment, Dalian University of Technology, Panjin, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
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Khara P, Roy M, Chakraborty J, Dutta A, Dutta TK. Characterization of a topologically unique oxygenase from Sphingobium sp. PNB capable of catalyzing a broad spectrum of aromatics. Enzyme Microb Technol 2018; 111:74-80. [DOI: 10.1016/j.enzmictec.2017.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/25/2017] [Accepted: 10/16/2017] [Indexed: 11/25/2022]
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Draft Genome Sequence of
Rhodococcus
sp. Strain NCIMB 12038, a Naphthalene-Degrading Bacterium. GENOME ANNOUNCEMENTS 2018; 6:6/1/e01420-17. [PMID: 29301890 PMCID: PMC5754499 DOI: 10.1128/genomea.01420-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
We report here the draft genome sequence of
Rhodococcus
sp. strain NCIMB 12038, an industrially important bacterium, possessing a large and diverse repertoire of genes involved in the biotransformation of various organic compounds, including naphthalene.
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Indole Biodegradation in Acinetobacter sp. Strain O153: Genetic and Biochemical Characterization. Appl Environ Microbiol 2017; 83:AEM.01453-17. [PMID: 28778892 DOI: 10.1128/aem.01453-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/26/2017] [Indexed: 01/30/2023] Open
Abstract
Indole is a molecule of considerable biochemical significance, acting as both an interspecies signal molecule and a building block of biological elements. Bacterial indole degradation has been demonstrated for a number of cases; however, very little is known about genes and proteins involved in this process. This study reports the cloning and initial functional characterization of genes (iif and ant cluster) responsible for indole biodegradation in Acinetobacter sp. strain O153. The catabolic cascade was reconstituted in vitro with recombinant proteins, and each protein was assigned an enzymatic function. Degradation starts with oxidation, mediated by the IifC and IifD flavin-dependent two-component oxygenase system. Formation of indigo is prevented by IifB, and the final product, anthranilic acid, is formed by IifA, an enzyme which is both structurally and functionally comparable to cofactor-independent oxygenases. Moreover, the iif cluster was identified in the genomes of a wide range of bacteria, suggesting the potential of widespread Iif-mediated indole degradation. This work provides novel insights into the genetic background of microbial indole biodegradation.IMPORTANCE The key finding of this research is identification of the genes responsible for microbial biodegradation of indole, a toxic N-heterocyclic compound. A large amount of indole is present in urban wastewater and sewage sludge, creating a demand for an efficient and eco-friendly means to eliminate this pollutant. A common strategy of oxidizing indole to indigo has the major drawback of producing insoluble material. Genes and proteins of Acinetobacter sp. strain O153 (DSM 103907) reported here pave the way for effective and indigo-free indole removal. In addition, this work suggests possible novel means of indole-mediated bacterial interactions and provides the basis for future research on indole metabolism.
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Guermouche M'rassi A, Bensalah F, Gury J, Duran R. Isolation and characterization of different bacterial strains for bioremediation of n-alkanes and polycyclic aromatic hydrocarbons. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15332-15346. [PMID: 25813636 DOI: 10.1007/s11356-015-4343-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Crude oil is a common environmental pollutant composed of a large number of both aromatic and aliphatic hydrocarbons. Biodegradation is carried out by microbial communities that are important in determining the fate of pollutants in the environment. The intrinsic biodegradability of the hydrocarbons and the distribution in the environment of competent degrading microorganisms are crucial information for the implementation of bioremediation processes. In the present study, the biodegradation capacities of various bacteria toward aliphatic and aromatic hydrocarbons were determined. The purpose of the study was to isolate and characterize hydrocarbon-degrading bacteria from contaminated soil of a refinery in Arzew, Algeria. A collection of 150 bacterial strains was obtained; the bacterial isolates were identified by 16S rRNA gene sequencing and their ability to degrade hydrocarbon compounds characterized. The isolated strains were mainly affiliated to the Gamma-Proteobacteria class. Among them, Pseudomonas spp. had the ability to metabolize high molecular weight hydrocarbon compounds such as pristane (C19) at 35.11 % by strain LGM22 and benzo[a] pyrene (C20) at 33.93 % by strain LGM11. Some strains were able to grow on all the hydrocarbons tested including octadecane, squalene, phenanthrene, and pyrene. Some strains were specialized degrading only few substrates. In contrast, the strain LGM2 designated as Pseudomonas sp. was found able to degrade both linear and branched alkanes as well as low and high poly-aromatic hydrocarbons (PAHs). The alkB gene involved in alkane degradation was detected in LGM2 and other Pseudomonas-related isolates. The capabilities of the isolated bacterial strains to degrade alkanes and PAHs should be of great practical significance in bioremediation of oil-contaminated environments.
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Affiliation(s)
- A Guermouche M'rassi
- Laboratoire de Génétique Microbienne, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 Ahmed Ben Bella, Es-Senia, Oran, 31000, Algérie, Algeria.
| | - F Bensalah
- Laboratoire de Génétique Microbienne, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 Ahmed Ben Bella, Es-Senia, Oran, 31000, Algérie, Algeria
| | - J Gury
- Equipe Environnement et Microbiologie, UMR IPREM5254, IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
| | - R Duran
- Equipe Environnement et Microbiologie, UMR IPREM5254, IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
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Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems. PLoS One 2015; 10:e0138455. [PMID: 26372223 PMCID: PMC4570806 DOI: 10.1371/journal.pone.0138455] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/31/2015] [Indexed: 12/02/2022] Open
Abstract
Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia colinagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. colinagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. colinagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0–30 days) (P < 0.001) but not in later stages (30–132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities.
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Indole: a signaling molecule or a mere metabolic byproduct that alters bacterial physiology at a high concentration? J Microbiol 2015; 53:421-8. [PMID: 26115989 DOI: 10.1007/s12275-015-5273-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
Abstract
Indole is an organic compound that is widespread in microbial communities inhabiting diverse habitats, like the soil environment and human intestines. Measurement of indole production is a traditional method for the identification of microbial species. Escherichia coli can produce millimolar concentrations of indole in the stationary growth phase under nutrient-rich conditions. Indole has received considerable attention because of its remarkable effects on various biological functions of the microbial communities, for example, biofilm formation, motility, virulence, plasmid stability, and antibiotic resistance. Indole may function as an intercellular signaling molecule, like a quorum-sensing signal. Nevertheless, a receptor system for indole and the function of this compound in coordinated behavior of a microbial population (which are requirements for a true signaling molecule) have not yet been confirmed. Recent findings suggest that a long-known quorum-sensing regulator, E. coli's SdiA, cannot recognize indole and that this compound may simply cause membrane disruption and energy reduction, which can lead to various changes in bacterial physiology including unstable folding of a quorum-sensing regulator. Indole appears to be responsible for acquisition of antibiotic resistance via the formation of persister cells and activation of an exporter. This review highlights and summarizes the current knowledge about indole as a multitrophic molecule among bacteria, together with recently identified new avenues of research.
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Meynet P, Head IM, Werner D, Davenport RJ. Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders. FEMS Microbiol Ecol 2015; 91:fiv049. [PMID: 25944871 PMCID: PMC4462182 DOI: 10.1093/femsec/fiv049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2015] [Indexed: 11/30/2022] Open
Abstract
Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reactions initiating the bacterial degradation of organic compounds, for instance aromatic hydrocarbons. The genes encoding these enzymes offer a potential target for studying aromatic hydrocarbon-degrading organisms in the environment. However, previously reported primer sets that target dioxygenase gene sequences or the common conserved Rieske centre of aromatics dioxygenases have limited specificity and/or target non-dioxygenase genes. In this work, an extensive database of dioxygenase α-subunit gene sequences was constructed, and primer sets targeting the conserved Rieske centre were developed. The high specificity of the primers was confirmed by polymerase chain reaction analysis, agarose gel electrophoresis and sequencing. Quantitative polymerase chain reaction (qPCR) assays were also developed and optimized, following MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR Experiments). Comparison of the qPCR quantification of dioxygenases in spiked sediment samples and in pure cultures demonstrated an underestimation of the Ct value, and the requirement for a correction factor at gene abundances below 108 gene copies per g of sediment. Externally validated qPCR provides a valuable tool to monitor aromatic hydrocarbon degrader population abundances at contaminated sites. Our study aimed to re-evaluate the phylogeny of Rieske non-heme iron dioxygenases using only retrieved primary nucleic acid sequences for the development of quantitative real-time PCR primers.
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Affiliation(s)
- Paola Meynet
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, England, UK
| | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, England, UK
| | - David Werner
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, England, UK
| | - Russell J Davenport
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, England, UK
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Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole. PLoS One 2015; 10:e0125732. [PMID: 25928424 PMCID: PMC4416020 DOI: 10.1371/journal.pone.0125732] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/25/2015] [Indexed: 11/24/2022] Open
Abstract
Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.
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Abstract
Indole and its derivatives, including 3-methylindole and 4-chloroindole, are environmental pollutants that are present worldwide. Microbial degradation of indole and its derivatives can occur in several aerobic and anaerobic pathways; these pathways involve different known and characterized genes. In this minireview, we summarize and explain the microbial degradation of indole, indole-3-acetic acid, 4-chloroindole, and methylindole.
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Peng R, Fu X, Tian Y, Zhao W, Zhu B, Xu J, Wang B, Wang L, Yao Q. Metabolic engineering of Arabidopsis for remediation of different polycyclic aromatic hydrocarbons using a hybrid bacterial dioxygenase complex. Metab Eng 2014; 26:100-110. [PMID: 25305469 DOI: 10.1016/j.ymben.2014.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/02/2014] [Accepted: 09/18/2014] [Indexed: 12/24/2022]
Abstract
The widespread presence of polycyclic aromatic hydrocarbons (PAHs) and their potential harm to various organisms has generated interest in efficiently eliminating these compounds from the environment. Phytoremediation is an efficient technology for cleaning up pollutants. However, unlike microorganisms, plants lack the catabolic pathway for complete degradation of these dangerous groups of compounds. One way to enhance the potential of plants for remediation of these compounds is by transferring genes involved in xenobiotic degradation from microbes to plants. In this paper, four genes, namely nidA and nidB (encoding the large and small subunits of naphthalene dioxygenase of Mycobacterium vanbaalenii PYR-1) as well as NahAa and NahAb (encoding flavoprotein reductase and ferredoxin of the electron-transport chain of the Pseudomonas putida G7 naphthalene dioxygenase system), were transferred and ectopically expressed in Arabidopsis thaliana. Transgenic Arabidopsis plants overexpressing the heterozygous naphthalene dioxygenase system exhibited enhanced tolerance toward 2-4 rings PAHs. Transgenic plants assimilated PAHs from the culture media faster and accumulated less in vivo than wild-type plants. Furthermore, examination of metabolic intermediates by gas chromatography-mass spectrometry revealed that the naphthalene metabolic pathway in transgenic plants mainly involves the dioxygenase pathway. Taken together, our findings suggest that grafting the naphthalene dioxygenase complex into plants is a possible strategy to breed PAH-tolerant plants to efficiently degrade PAHs in the environment.
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Affiliation(s)
- Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Xiaoyan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Wei Zhao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Bo Zhu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Jing Xu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China.
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Sah VR, Baier RE. Bacteria inside semiconductors as potential sensor elements: biochip progress. SENSORS 2014; 14:11225-44. [PMID: 24961215 PMCID: PMC4118370 DOI: 10.3390/s140611225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/10/2014] [Accepted: 06/19/2014] [Indexed: 11/16/2022]
Abstract
It was discovered at the beginning of this Century that living bacteria-and specifically the extremophile Pseudomonas syzgii-could be captured inside growing crystals of pure water-corroding semiconductors-specifically germanium-and thereby initiated pursuit of truly functional "biochip-based" biosensors. This observation was first made at the inside ultraviolet-illuminated walls of ultrapure water-flowing semiconductor fabrication facilities (fabs) and has since been, not as perfectly, replicated in simpler flow cell systems for chip manufacture, described here. Recognizing the potential importance of these adducts as optical switches, for example, or probes of metabolic events, the influences of the fabs and their components on the crystal nucleation and growth phenomena now identified are reviewed and discussed with regard to further research needs. For example, optical beams of current photonic circuits can be more easily modulated by integral embedded cells into electrical signals on semiconductors. Such research responds to a recently published Grand Challenge in ceramic science, designing and synthesizing oxide electronics, surfaces, interfaces and nanoscale structures that can be tuned by biological stimuli, to reveal phenomena not otherwise possible with conventional semiconductor electronics. This short review addresses only the fabrication facilities' features at the time of first production of these potential biochips.
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Affiliation(s)
- Vasu R Sah
- Harvard-MIT Health Sciences and Technology Division, Cambridge, MA 02139, USA.
| | - Robert E Baier
- Industry/University Center for Biosurfaces, State University of New York at Buffalo, Buffalo, NY 14214, USA.
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Tomás-Gallardo L, Gómez-Álvarez H, Santero E, Floriano B. Combination of degradation pathways for naphthalene utilization in Rhodococcus sp. strain TFB. Microb Biotechnol 2013; 7:100-13. [PMID: 24325207 PMCID: PMC3937715 DOI: 10.1111/1751-7915.12096] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 11/27/2022] Open
Abstract
Rhodococcus sp. strain TFB is a metabolic versatile bacterium able to grow on naphthalene as the only carbon and energy source. Applying proteomic, genetic and biochemical approaches, we propose in this paper that, at least, three coordinated but independently regulated set of genes are combined to degrade naphthalene in TFB. First, proteins involved in tetralin degradation are also induced by naphthalene and may carry out its conversion to salicylaldehyde. This is the only part of the naphthalene degradation pathway showing glucose catabolite repression. Second, a salicylaldehyde dehydrogenase activity that converts salicylaldehyde to salicylate is detected in naphthalene-grown cells but not in tetralin-or salicylate-grown cells. Finally, we describe the chromosomally located nag genes, encoding the gentisate pathway for salicylate conversion into fumarate and pyruvate, which are only induced by salicylate and not by naphthalene. This work shows how biodegradation pathways in Rhodococcus sp. strain TFB could be assembled using elements from different pathways mainly because of the laxity of the regulatory systems and the broad specificity of the catabolic enzymes.
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Affiliation(s)
- Laura Tomás-Gallardo
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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Seo JS, Keum YS, Li QX. Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N-methylcarbamates. Biodegradation 2013; 24:795-811. [PMID: 23463356 DOI: 10.1007/s10532-013-9629-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
Burkholderia sp. C3, an efficient polycyclic aromatic hydrocarbon degrader, can utilize nine of the ten N-methylcarbamate insecticides including carbaryl as a sole source of carbon. Rapid hydrolysis of carbaryl in C3 is followed by slow catabolism of the resulting 1-naphthol. This study focused on metabolomes and proteomes in C3 cells utilizing carbaryl in comparison to those using glucose or nutrient broth. Sixty of the 867 detected proteins were involved in primary metabolism, adaptive sensing and regulation, transport, stress response, and detoxification. Among the 41 proteins expressed in response to carbaryl were formate dehydrogenase, aldehyde-alcohol dehydrogenase and ethanolamine utilization protein involved in one carbon metabolism. Acetate kinase and phasin were 2 of the 19 proteins that were not detected in carbaryl-supported C3 cells, but detected in glucose-supported C3 cells. Down-production of phasin and polyhydroxyalkanoates in carbaryl-supported C3 cells suggests insufficient carbon sources and lower levels of primary metabolites to maintain an ordinary level of metabolism. Differential metabolomes (~196 identified polar metabolites) showed up-production of metabolites in pentose phosphate pathways and metabolisms of cysteine, cystine and some other amino acids, disaccharides and nicotinate, in contract to down-production of most of the other amino acids and hexoses. The proteomic and metabolomic analyses showed that carbaryl-supported C3 cells experienced strong toxic effects, oxidative stresses, DNA/RNA damages and carbon nutrient deficiency.
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Affiliation(s)
- Jong-Su Seo
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI, 96822, USA
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23
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Wang Y, Chen Y, Zhou Q, Huang S, Ning K, Xu J, Kalin RM, Rolfe S, Huang WE. A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS One 2012; 7:e47530. [PMID: 23082176 PMCID: PMC3474725 DOI: 10.1371/journal.pone.0047530] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/12/2012] [Indexed: 01/23/2023] Open
Abstract
Most microorganisms in nature are uncultured with unknown functionality. Sequence-based metagenomics alone answers ‘who/what are there?’ but not ‘what are they doing and who is doing it and how?’. Function-based metagenomics reveals gene function but is usually limited by the specificity and sensitivity of screening strategies, especially the identification of clones whose functional gene expression has no distinguishable activity or phenotypes. A ‘biosensor-based genetic transducer’ (BGT) technique, which employs a whole-cell biosensor to quantitatively detect expression of inserted genes encoding designated functions, is able to screen for functionality of unknown genes from uncultured microorganisms. In this study, BGT was integrated with Stable isotope probing (SIP)-enabled Metagenomics to form a culture-independent SMB toolbox. The utility of this approach was demonstrated in the discovery of a novel functional gene cluster in naphthalene contaminated groundwater. Specifically, metagenomic sequencing of the 13C-DNA fraction obtained by SIP indicated that an uncultured Acidovorax sp. was the dominant key naphthalene degrader in-situ, although three culturable Pseudomonas sp. degraders were also present in the same groundwater. BGT verified the functionality of a new nag2 operon which co-existed with two other nag and two nah operons for naphthalene biodegradation in the same microbial community. Pyrosequencing analysis showed that the nag2 operon was the key functional operon in naphthalene degradation in-situ, and shared homology with both nag operons in Ralstonia sp. U2 and Polaromonas naphthalenivorans CJ2. The SMB toolbox will be useful in providing deep insights into uncultured microorganisms and unravelling their ecological roles in natural environments.
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Affiliation(s)
- Yun Wang
- Kroto Research Institute, University of Sheffield, Sheffield, England, United Kingdom
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, England, United Kingdom
| | - Qian Zhou
- BioEnergy Genome Centre, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shi Huang
- BioEnergy Genome Centre, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Kang Ning
- BioEnergy Genome Centre, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jian Xu
- BioEnergy Genome Centre, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Robert M. Kalin
- David Livingstone Centre for Sustainability, Strathclyde University, Glasgow, Scotland, United Kingdom
| | - Stephen Rolfe
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, England, United Kingdom
| | - Wei E. Huang
- Kroto Research Institute, University of Sheffield, Sheffield, England, United Kingdom
- * E-mail:
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Qu Y, Ma Q, Zhang X, Zhou H, Li X, Zhou J. Optimization of indigo production by a newly isolated Pseudomonas sp. QM. J Basic Microbiol 2012; 52:687-94. [PMID: 22359270 DOI: 10.1002/jobm.201100516] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 11/20/2011] [Indexed: 11/08/2022]
Abstract
Optimization of indigo production process from indole using a newly isolated phenol-degrading bacterial strain was performed by Plackett-Burman design and response surface methodology. The strain designated as QM was identified as Pseudomonas sp. according to 16S rDNA analysis. Spectrum analysis of indole biotransformation products revealed the presence of indigo and a by-product indirubin. To improve indigo yield, Plackett-Burman design was used to select significant factors from 8 viriables. Then response surface methodology based on a 2(3) central composite design was used to further optimize the transformation process. Under the optimal conditons, strain QM can produce 27.20 mg/l indigo after 24 h cultivation at 30 °C, which was 151.3% higher than that from the initial conversion condition. The results indicated that Pseudomonas sp. QM should be a potential candidate for indigo industial production.
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Affiliation(s)
- Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, PR China.
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Boyd DR, Sharma ND, McMurray B, Haughey SA, Allen CCR, Hamilton JTG, McRoberts WC, More O'Ferrall RA, Nikodinovic-Runic J, Coulombel LA, O'Connor KE. Bacterial dioxygenase- and monooxygenase-catalysed sulfoxidation of benzo[b]thiophenes. Org Biomol Chem 2012; 10:782-90. [DOI: 10.1039/c1ob06678a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kimura N, Sakai K, Nakamura K. Isolation and characterization of a 4-nitrotoluene-oxidizing enzyme from activated sludge by a metagenomic approach. Microbes Environ 2011; 25:133-9. [PMID: 21576864 DOI: 10.1264/jsme2.me10110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To isolate a biocatalytic enzyme, metagenomic libraries were constructed in fosmids from samples of activated sludge used to treat coke plant wastewater. Six indigo-producing clones were isolated from approximately 40,000 metagenomic clones in the search for the oxygenase responsible. In vitro mutagenesis and whole-sequencing revealed one open reading frame to be responsible for the production of indigo in the fosmid clones. The deduced sequence of the gene product showed 60% identity with 2-naphthoate monooxygenase from Burkholderia sp. JT1500. Subclones carrying this open reading frame (icpA) retained indigo production, and indigo-producing enzymes expressed from subclones catalyzed the oxidization of 4-nitrotoluene to form 4-nitrobenzyl alcohol. These results suggested that the icp product is an enzyme involved in catalyzing 4-nitrotoluene's oxygenation.
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Affiliation(s)
- Nobutada Kimura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1–1–1, Higashi, Tsukuba, Ibaraki 305–8566, Japan.
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Functional characterization of a gene cluster involved in gentisate catabolism in Rhodococcus sp. strain NCIMB 12038. Appl Microbiol Biotechnol 2010; 90:671-8. [DOI: 10.1007/s00253-010-3033-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 10/18/2022]
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Mallick S, Chakraborty J, Dutta TK. Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular-weight polycyclic aromatic hydrocarbons: a review. Crit Rev Microbiol 2010; 37:64-90. [PMID: 20846026 DOI: 10.3109/1040841x.2010.512268] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Widespread environmental pollution by polycyclic aromatic hydrocarbons (PAHs) poses an immense risk to the environment. Bacteria-mediated attenuation has a great potential for the restoration of PAH-contaminated environment in an ecologically accepted manner. Bacterial degradation of PAHs has been extensively studied and mining of biodiversity is ever expanding the biodegradative potentials with intelligent manipulation of catabolic genes and adaptive evolution to generate multiple catabolic pathways. The present review of bacterial degradation of low-molecular-weight (LMW) PAHs describes the current knowledge about the diverse metabolic pathways depicting novel metabolites, enzyme-substrate/metabolite relationships, the role of oxygenases and their distribution in phylogenetically diverse bacterial species.
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Affiliation(s)
- Somnath Mallick
- Department of Chemistry, Saldiha College, Bankura, West Bengal, India
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Qu Y, Pi W, Ma F, Zhou J, Zhang X. Influence and optimization of growth substrates on indigo formation by a novel isolate Acinetobacter sp. PP-2. BIORESOURCE TECHNOLOGY 2010; 101:4527-4532. [PMID: 20156680 DOI: 10.1016/j.biortech.2010.01.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 12/29/2009] [Accepted: 01/10/2010] [Indexed: 05/28/2023]
Abstract
In this study, a novel indigo-producing bacterial strain PP-2 was isolated from activated sludge. It was identified as Acinetobacter sp. according to phylogenetic similarity of 16S rRNA gene sequence. This isolate was able to produce indigo from indole by utilizing a wide range of aromatic hydrocarbons. The results of SDS-PAGE analysis showed that the enzyme system induced by phenol was more abundant than that induced by other aromatic hydrocarbons. And the effects of metal ions on indigo production were also investigated, which indicated that the activity of cells induced with phenol could be inhibited by 0.5mM Fe(3+). Response surface methodology (RSM) was applied to optimize the process of indigo bio-production. The results exhibited that the maximal yield was achieved with 157.92 mg L(-1) phenol and 205.32 mg L(-1) indole. Under the optimal conditions, the indigo yield and transformation efficiency of indole were 202.92 mg L(-1) and 88%, respectively.
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Affiliation(s)
- Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering, MOE, School of Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
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Identification and characterization of genes involved in naphthalene degradation in Rhodococcus opacus R7. Appl Microbiol Biotechnol 2010; 87:297-308. [PMID: 20195856 DOI: 10.1007/s00253-010-2497-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 02/05/2010] [Accepted: 02/06/2010] [Indexed: 10/19/2022]
Abstract
Rhodococcus opacus R7 is a naphthalene-degrading microorganism which is also able to grow on o-xylene. This work describes the isolation and analysis of two new genomic regions in which genes involved in naphthalene (nar gene cluster) and salicylate (gen gene cluster) degradation are located. In the nar gene cluster we found: two genes encoding the large (narAa) and the small (narAb) components of the naphthalene dioxygenase, three genes (rub1, rub2, rub1bis) encoding three rubredoxins, an orf (orf7) associated to the complex encoding a protein of unknown function, two regulatory genes (narR1, narR2), a gene (narB) encoding the naphthalene dihydrodiol dehydrogenase and six orfs (orf1, orf2, orf3, orf4, orf5, orf6) encoding proteins of unknown function. In the gen gene cluster, we found the following genes: two genes encoding the salicylate CoA ligase and the salicylate CoA synthetase (genA and genB), respectively, a gene (genC) encoding a salicylate hydroxylase, a gene (genH) encoding a gentisate 1,2-dioxygenase, a gene (genI) encoding a 3-maleylpyruvate isomerase, and a gene (genL) encoding a protein of unknown function. The transcription of some genes of R. opacus R7 strain grown on different substrates was also investigated to evaluate the expression of the two gene clusters after cDNA preparations.
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Obayori OS, Adebusoye SA, Adewale AO, Oyetibo GO, Oluyemi OO, Amokun RA, Ilori MO. Differential degradation of crude oil (Bonny Light) by four Pseudomonas strains. J Environ Sci (China) 2009; 21:243-248. [PMID: 19402429 DOI: 10.1016/s1001-0742(08)62258-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Four hydrocarbon degraders isolated from enriched oil- and asphalt-contaminated soils in Lagos, Nigeria, were tested for their petroleum degradation potentials. All the isolates were identified as species of Pseudomonas. Pseudomonas putida P11 demonstrated a strong ability to degrade kerosene, gasoline, diesel, engine oil and crude oil while P. aeruginosa BB3 exhibited fair degradative ability on crude oil, gasoline, engine oil, anthracene and pyrene but weak on kerosene, diesel and dibenzothiophene. Pseudomonas putida WL2 and P. aeruginosa MVL1 grew on crude oil and all its cuts tested with the latter possessing similar polycyclic aromatic potentials as P11. All the strains grew logarithmically with 1-2 orders of magnitude and with generation time ranging significantly between 3.07 and 8.55 d at 0.05 level of confidence. Strains WL2 and MVL1 utilized the oil substrate best with more than 70% in 6 d experimental period, whereas the same feat was achieved by P11 in 12 d period. BB3 on the other hand degraded only 46% within 6 d. Interestingly, data obtained from gas chromatographic analysis of oil recovered from the culture fluids of MVL1 confirmed near-disappearance of major peaks (including aliphatics and aromatics) in the hydrocarbon mixture.
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Affiliation(s)
- Oluwafemi S Obayori
- Department of Microbiology, Lagos State University, Ojo, Lagos 100001, Nigeria.
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Mittal M, Rockne KJ. Indole production by Pseudomonas stutzeri strain NAP-3 during anaerobic naphthalene biodegradation in the presence of dimethyl formamide. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2008; 43:1027-1034. [PMID: 18569316 DOI: 10.1080/10934520802059896] [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
We previously reported on the denitrifier Pseudomonas stutzeri strain NAP-3 that degrades naphthalene without oxygen. In our present studies, naphthalene biodegradation by NAP-3 was slow or nearly absent when acetate was not present, suggesting a stimulating effect by the non-fermentable substrate. NAP-3 was sensitive to the amount of naphthalene in the culture; with naphthalene removal and nitrate utilization rates higher when present at 20 mg L(-1) compared to 40 mg L(-1). Electron equivalents represented by transformation of electron donor could be met assuming nitrate reduction to nitrite, except for the incubation with 40 mg L(-1) naphthalene which required complete denitrification. Transient production of the nitrogen-containing bicyclic indole was found by gas chromatograph mass spectrophotometry (GC/MS). Indole production was repeatable and affected by naphthalene concentration; with the 20 mg L(-1) culture producing the most indole. The production of indole was strictly biotic and required the presence of both naphthalene and the commonly-used solubilizing agent N, N dimethyl formamide (DMF). The source of nitrogen in indole was confirmed to be DMF through a series of growth experiments with NAP-3. No indole was produced in incubations fed naphthalene plus nitrate, nitrite or ammonia, either alone or in combination, when DMF was absent. Further, no production of indole was observed when heptamethyl nonane was used as an alternative solubilizing agent. We speculate that indole production proceeds through a pathway similar to the chorismic acid pathway for indole synthesis with incorporation of nitrogen from DMF. No other potential compounds of the chorismic pathway were found by GC/MS when naphthalene was the sole carbon source. NAP-3 grew statistically significantly on anthranilate, but not using salicylate or indole as the sole carbon source.
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Affiliation(s)
- Menka Mittal
- Department of Civil and Materials Engineering, University of Illinois at Chicago, Chicago, IL, USA
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Zeinali M, Vossoughi M, Ardestani SK. Naphthalene metabolism in Nocardia otitidiscaviarum strain TSH1, a moderately thermophilic microorganism. CHEMOSPHERE 2008; 72:905-909. [PMID: 18471862 DOI: 10.1016/j.chemosphere.2008.03.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 03/11/2008] [Accepted: 03/18/2008] [Indexed: 05/26/2023]
Abstract
The thermophilic bacterium Nocardia otitidiscaviarum strain TSH1, originally isolated in our laboratory from a petroindustrial wastewater contaminated soil in Iran, grows at 50 degrees C on a broad range of hydrocarbons. Transformation of naphthalene by strain TSH1 which is able to use this two ring-polycyclic aromatic hydrocarbon (PAH) as a sole source of carbon and energy was investigated. The metabolic pathway was elucidated by identifying metabolites, biotransformation studies and monitoring enzyme activities in cell-free extracts. The identification of metabolites suggests that strain TSH1 initiates its attack on naphthalene by dioxygenation at its C-1 and C-2 positions to give 1,2-dihydro-1,2-dihydroxynaphthalene. The intermediate 2-hydroxycinnamic acid, characteristic of the meta-cleavage of the resulting diol was identified in the acidic extract. Apart from typical metabolites of naphthalene degradation known from mesophiles, benzoic acid was identified as an intermediate for the naphthalene pathway of this Nocardia strain. Neither phthalic acid nor salicylic acid metabolites were detected in culture extracts. Enzymatic experiments with cell extract showed the catechol 1,2-dioxygenase activity while transformation of phthalic acid and protocatechuic acid was not observed. The results of enzyme activity assays and identification of benzoic acid in culture extract provide strong indications that further degradation goes through benzoate and beta-ketoadipate pathway. Our results indicate that naphthalene degradation by thermophilic N. otitidiscaviarum strain TSH1 differs from the known pathways found for the thermophilic Bacillus thermoleovorans Hamburg 2 and mesophilic bacteria.
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Affiliation(s)
- Majid Zeinali
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Doyle E, Muckian L, Hickey AM, Clipson N. Microbial PAH Degradation. ADVANCES IN APPLIED MICROBIOLOGY 2008; 65:27-66. [DOI: 10.1016/s0065-2164(08)00602-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Chadhain SMN, Moritz EM, Kim E, Zylstra GJ. Identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from Sphingobium yanoikuyae B1. J Ind Microbiol Biotechnol 2007; 34:605-13. [PMID: 17647036 DOI: 10.1007/s10295-007-0235-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 06/07/2007] [Indexed: 10/23/2022]
Abstract
Sphingobium yanoikuyae B1 utilizes both polycyclic aromatic hydrocarbons (biphenyl, naphthalene, and phenanthrene) and monocyclic aromatic hydrocarbons (toluene, m- and p-xylene) as its sole source of carbon and energy for growth. The majority of the genes for these intertwined monocyclic and polycyclic aromatic pathways are grouped together on a 39 kb fragment of chromosomal DNA. However, this gene cluster is missing several genes encoding essential enzymatic steps in the aromatic degradation pathway, most notably the genes encoding the oxygenase component of the initial polycyclic aromatic hydrocarbon (PAH) dioxygenase. Transposon mutagenesis of strain B1 yielded a mutant blocked in the initial oxidation of PAHs. The transposon insertion point was sequenced and a partial gene sequence encoding an oxygenase component of a putative PAH dioxygenase identified. A cosmid clone from a genomic library of S. yanoikuyae B1 was identified which contains the complete putative PAH oxygenase gene sequence. Separate clones expressing the genes encoding the electron transport components (ferredoxin and reductase) and the PAH dioxygenase were constructed. Incubation of cells expressing the dioxygenase enzyme system with biphenyl or naphthalene resulted in production of the corresponding cis-dihydrodiol confirming PAH dioxygenase activity. This demonstrates that a single multicomponent dioxygenase enzyme is involved in the initial oxidation of both biphenyl and naphthalene in S. yanoikuyae B1.
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Affiliation(s)
- Sinéad M Ní Chadhain
- Biotechnology Center for Agriculture and the Environment, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA.
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Berberian V, Allen C, Sharma N, Boyd D, Hardacre C. A Comparative Study of the Synthesis of 3-Substituted Catechols using an Enzymatic and a Chemoenzymatic Method. Adv Synth Catal 2007. [DOI: 10.1002/adsc.200600437] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Swetha VP, Basu A, Phale PS. Purification and characterization of 1-naphthol-2-hydroxylase from carbaryl-degrading Pseudomonas strain c4. J Bacteriol 2007; 189:2660-6. [PMID: 17237179 PMCID: PMC1855793 DOI: 10.1128/jb.01418-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas sp. strain C4 metabolizes carbaryl (1-naphthyl-N-methylcarbamate) as the sole source of carbon and energy via 1-naphthol, 1,2-dihydroxynaphthalene, and gentisate. 1-Naphthol-2-hydroxylase (1-NH) was purified 9.1-fold to homogeneity from Pseudomonas sp. strain C4. Gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that the enzyme is a homodimer with a native molecular mass of 130 kDa and a subunit molecular mass of 66 kDa. The enzyme was yellow, with absorption maxima at 274, 375, and 445 nm, indicating a flavoprotein. High-performance liquid chromatography analysis of the flavin moiety extracted from 1-NH suggested the presence of flavin adenine dinucleotide (FAD). Based on the spectral properties and the molar extinction coefficient, it was determined that the enzyme contained 1.07 mol of FAD per mol of enzyme. Although the enzyme accepts electrons from NADH, it showed maximum activity with NADPH and had a pH optimum of 8.0. The kinetic constants K(m) and V(max) for 1-naphthol and NADPH were determined to be 9.6 and 34.2 microM and 9.5 and 5.1 micromol min(-1) mg(-1), respectively. At a higher concentration of 1-naphthol, the enzyme showed less activity, indicating substrate inhibition. The K(i) for 1-naphthol was determined to be 79.8 microM. The enzyme showed maximum activity with 1-naphthol compared to 4-chloro-1-naphthol (62%) and 5-amino-1-naphthol (54%). However, it failed to act on 2-naphthol, substituted naphthalenes, and phenol derivatives. The enzyme utilized one mole of oxygen per mole of NADPH. Thin-layer chromatographic analysis showed the conversion of 1-naphthol to 1,2-dihydroxynaphthalene under aerobic conditions, but under anaerobic conditions, the enzyme failed to hydroxylate 1-naphthol. These results suggest that 1-NH belongs to the FAD-containing external flavin mono-oxygenase group of the oxidoreductase class of proteins.
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Affiliation(s)
- Vandana P Swetha
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400076, India
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Pizzul L, Sjögren A, Castillo MDP, Stenström J. Degradation of polycyclic aromatic hydrocarbons in soil by a two-step sequential treatment. Biodegradation 2007; 18:607-16. [PMID: 17216539 DOI: 10.1007/s10532-006-9093-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Accepted: 11/08/2006] [Indexed: 10/23/2022]
Abstract
The objectives of this work were to isolate the microorganisms responsible for a previously observed degradation of polycyclic aromatic hydrocarbons (PAH) in soil and to test a method for cleaning a PAH-contaminated soil. An efficient PAH degrader was isolated from an agricultural soil and designated as Mycobacterium LP1. In liquid culture, it degraded phenanthrene (58%), pyrene (24%), anthracene (21%) and benzo(a)pyrene (10%) present in mixture (initial concentration 50 microg ml(-1) each) and phenanthrene (92%) and pyrene (94%) as sole carbon sources after 14 days of incubation at 30 degrees C. In soil, Mycobacterium LP1 mineralised (14)C-phenanthrene (45%) and (14)C-pyrene (65%) after 10 days. The good ability of this Mycobacterium was combined with the benzo(a)pyrene oxidation effect obtained by 1% w/w rapeseed oil in a sequential treatment of a PAH-spiked soil (total PAH concentration 200 mg kg(-1)). The first step was incubation with the bacterium for 12 days and the second step was the addition of the rapeseed oil after this time and a further incubation of 22 days. Phenanthrene (99%), pyrene (95%) and anthracene (99%) were mainly degraded in the first 12 days and a total of 85% of benzo(a)pyrene was transformed during the whole process. The feasibility of the method is discussed.
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Affiliation(s)
- Leticia Pizzul
- Department of Microbiology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
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Larkin MJ, Kulakov LA, Allen CCR. Biodegradation by members of the genus Rhodococcus: biochemistry, physiology, and genetic adaptation. ADVANCES IN APPLIED MICROBIOLOGY 2006; 59:1-29. [PMID: 16829254 DOI: 10.1016/s0065-2164(06)59001-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Michael J Larkin
- The QUESTOR Centre, The Queen's University of Belfast, Belfast BT9 5AG, Northern Ireland, United Kingdom
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Ní Chadhain SM, Norman RS, Pesce KV, Kukor JJ, Zylstra GJ. Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microbiol 2006; 72:4078-87. [PMID: 16751518 PMCID: PMC1489606 DOI: 10.1128/aem.02969-05] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria has been widely studied. While many pure cultures have been isolated and characterized for their ability to grow on PAHs, limited information is available on the diversity of microbes involved in PAH degradation in the environment. We have designed generic PCR primers targeting the gene fragment encoding the Rieske iron sulfur center common to all PAH dioxygenase enzymes. These Rieske primers were employed to track dioxygenase gene population shifts in soil enrichment cultures following exposure to naphthalene, phenanthrene, or pyrene. PAH degradation was monitored by gas chromatograph with flame ionization detection. DNA was extracted from the enrichment cultures following PAH degradation. 16S rRNA and Rieske gene fragments were PCR amplified from DNA extracted from each enrichment culture and an unamended treatment. The PCR products were cloned and sequenced. Molecular monitoring of the enrichment cultures before and after PAH degradation using denaturing gradient gel electrophoresis and 16S rRNA gene libraries suggests that specific phylotypes of bacteria were associated with the degradation of each PAH. Sequencing of the cloned Rieske gene fragments showed that different suites of genes were present in soil microbe populations under each enrichment culture condition. Many of the Rieske gene fragment sequences fell into clades which are distinct from the reference dioxygenase gene sequences used to design the PCR primers. The ability to profile not only the bacterial community but also the dioxygenases which they encode provides a powerful tool for both assessing bioremediation potential in the environment and for the discovery of novel dioxygenase genes.
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Affiliation(s)
- Sinéad M Ní Chadhain
- Biotechnology Center for Agriculture and the Environment, Rutgers University, 59 Dudley Rd., New Brunswick, NJ 08901-8520, USA
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Augustin T, Schlosser D, Baumbach R, Schmidt J, Grancharov K, Krauss G, Krauss GJ. Biotransformation of 1-naphthol by a strictly aquatic fungus. Curr Microbiol 2006; 52:216-20. [PMID: 16479357 DOI: 10.1007/s00284-005-0239-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 11/07/2005] [Indexed: 10/25/2022]
Abstract
The aquatic hyphomycete Heliscus lugdunensis belongs to a group of exclusively aquatic mitosporic fungi with an only scarcely explored potential to oxidatively attack xenobiotic compounds, and was used to study the biotransformation of the environmental pollutant metabolite 1-naphthol. H. lugdunensis metabolized approximately 74% of 1-naphthol within 5 days. The identification and quantification of degradation products using gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, and high performance liquid chromatography revealed that approximately 12% of the parent compound was converted into 1-naphthylsulfate, 3% was transformed into 1-methoxy-naphthalene, and less than 1% was converted into 1,4-naphthoquinone. A further metabolite, most likely 4-hydroxy-1-naphthylsulfate, was also detected. In contrast to sulfate conjugate metabolites, no glucuronide and glucoside conjugates of 1-naphthol were found, and neither UDP-glucuronyltransferase nor UDP-glucosyltransferase present in H. lugdunensis showed activity towards 1-naphthol. These results support a role of fungi adapted to aquatic environments in affecting the environmental fate of pollutants in aquatic ecosystems.
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Affiliation(s)
- Torsten Augustin
- Department of Biochemistry/Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120, Halle/Saale, Germany
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Dunn HD, Curtin T, O'riordan MA, Coen P, Kieran PM, Malone DM, O'Connor KE. Aromatic and aliphatic hydrocarbon consumption and transformation by the styrene degrading strain Pseudomonas putida CA-3. FEMS Microbiol Lett 2005; 249:267-73. [PMID: 16002236 DOI: 10.1016/j.femsle.2005.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Revised: 04/22/2005] [Accepted: 06/10/2005] [Indexed: 11/25/2022] Open
Abstract
Pseudomonas putida CA-3 is capable of consuming a number of aromatic and aliphatic hydrocarbons. With the exception of styrene none of the alkenes tested are capable of supporting the growth of P. putida CA-3 as sole sources of carbon and energy. The highest rate of alkene consumption was observed with styrene as the substrate. A 6.5- and 15.5-fold lower rate of substrate consumption was observed with indene and indole with the concomitant formation of 2-indanone and indigo, respectively. The presence of a sulphur (benzothiopene) or oxygen (benzofuran) in the cyclopentene ring resulted in further decreases in the rate of substrate consumption by whole cells of P. putida CA-3. P. putida CA-3 is incapable of consuming benzene and consumes toluene at a low rate. No detectable products were observed in supernatants of cultures incubated with benzothiopene, benzofuran or toluene. The aliphatic alkenes 1-octene and 1,7-octadiene were both consumed by whole cells of P. putida CA-3 at a rate equivalent to indene consumption. The consumption of (R) styrene oxide was 1.7- and 1.25-fold higher than that of the S isomer and the racemic mix, respectively. The rate of racemic indene oxide, 1,2-epoxyoctane and 1,2-epoxy-7-octene consumption was lower than their equivalent alkene and 55-, 11.8-, and 27.5-fold lower than the rate of racemic styrene oxide consumption. A transposon mutant incapable of growth with styrene or styrene oxide failed to transform indole to indigo. The ratio of styrene utilisation relative to other substrates changes in the mutant strain compared to the wild-type strain, e.g., Indene biotransformation by mutant AF5 is 1.9-fold higher than styrene consumption compared to the wild-type strain CA-3 where the rate of styrene consumption is 6.7-fold higher than indene consumption. This trend is also observed for other alkenes and epoxides.
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Affiliation(s)
- Helen D Dunn
- Department of Industrial Microbiology, Centre for Synthesis and Chemical Biology, Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Republic of Ireland
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Maruyama T, Ishikura M, Taki H, Shindo K, Kasai H, Haga M, Inomata Y, Misawa N. Isolation and characterization of o-xylene oxygenase genes from Rhodococcus opacus TKN14. Appl Environ Microbiol 2005; 71:7705-15. [PMID: 16332743 PMCID: PMC1317363 DOI: 10.1128/aem.71.12.7705-7715.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Accepted: 07/27/2005] [Indexed: 11/20/2022] Open
Abstract
o-Xylene is one of the most difficult-to-degrade environmental pollutants. We report here Rhodococcus genes mediating oxygenation in the first step of o-xylene degradation. Rhodococcus opacus TKN14, isolated from soil contaminated with o-xylene, was able to utilize o-xylene as the sole carbon source and to metabolize it to o-methylbenzoic acid. A cosmid library from the genome of this strain was constructed in Escherichia coli. A bioconversion analysis revealed that a cosmid clone incorporating a 15-kb NotI fragment had the ability to convert o-xylene into o-methylbenzyl alcohol. The sequence analysis of this 15-kb region indicated the presence of a gene cluster significantly homologous to the naphthalene-inducible dioxygenase gene clusters (nidABCD) that had been isolated from Rhodococcus sp. strain I24. Complementation studies, using E. coli expressing various combinations of individual open reading frames, revealed that a gene (named nidE) for rubredoxin (Rd) and a novel gene (named nidF) encoding an auxiliary protein, which had no overall homology with any other proteins, were indispensable for the methyl oxidation reaction of o-xylene, in addition to the dioxygenase iron-sulfur protein genes (nidAB). Regardless of the presence of NidF, the enzyme composed of NidABE was found to function as a typical naphthalene dioxygenase for converting naphthalene and various (di)methylnaphthalenes into their corresponding cis-dihydrodiols. All the nidABEF genes were transcriptionally induced in R. opacus TKN14 by the addition of o-xylene to a mineral salt medium. It is very likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by Rhodococcus species as the first key enzyme.
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Affiliation(s)
- Takahiro Maruyama
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
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Ferraro DJ, Gakhar L, Ramaswamy S. Rieske business: structure-function of Rieske non-heme oxygenases. Biochem Biophys Res Commun 2005; 338:175-90. [PMID: 16168954 DOI: 10.1016/j.bbrc.2005.08.222] [Citation(s) in RCA: 249] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2005] [Accepted: 08/30/2005] [Indexed: 11/20/2022]
Abstract
Rieske non-heme iron oxygenases (RO) catalyze stereo- and regiospecific reactions. Recently, an explosion of structural information on this class of enzymes has occurred in the literature. ROs are two/three component systems: a reductase component that obtains electrons from NAD(P)H, often a Rieske ferredoxin component that shuttles the electrons and an oxygenase component that performs catalysis. The oxygenase component structures have all shown to be of the alpha3 or alpha3beta3 types. The transfer of electrons happens from the Rieske center to the mononuclear iron of the neighboring subunit via a conserved aspartate, which is shown to be involved in gating electron transport. Molecular oxygen has been shown to bind side-on in naphthalene dioxygenase and a concerted mechanism of oxygen activation and hydroxylation of the ring has been proposed. The orientation of binding of the substrate to the enzyme is hypothesized to control the substrate selectivity and regio-specificity of product formation.
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Affiliation(s)
- Daniel J Ferraro
- Department of Biochemistry, University of Iowa Roy J. and Lucille A. Carver College of Medicine, 51 Newton Road, 4-403 BSB, Iowa City, IA 52242, USA
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Sallam KI, Mitani Y, Tamura T. Construction of random transposition mutagenesis system in Rhodococcuserythropolis using IS1415. J Biotechnol 2005; 121:13-22. [PMID: 16107286 DOI: 10.1016/j.jbiotec.2005.07.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 06/23/2005] [Accepted: 07/04/2005] [Indexed: 11/19/2022]
Abstract
Recent studies on the metabolic activities of genus Rhodococcus have shown rhodococci to be of important use in industrial, pharmaceutical and environmental biotechnology. The increasing economic significance of Rhodococcus encourages renewed efforts to characterize their genetic systems, as Rhodococcus genetics are still poorly understood. The goal of this study is to adapt a transposon system for use in creating random mutagenesis in Rhodococcus erythropolis. A plasmid carrying IS1415, a member of IS21 family identified from Rerythropolis, has been constructed and designated as pTNR. pTNR is a non-replicating transposon tool introduced into target cells by electroporation. During its transposition, the transposable-marker gene is separated from the open reading frames (istAB) of IS1415, which should avoid secondary transposition. Transposition of pTNR into wild-type R. erythropolis created mutagenesis with a high efficiency of 1.23x10(6)mutants per microgram plasmid DNA. However, it could also be transposed into other Rhodococcus spp. at lower frequencies in comparison with that of R. erythropolis. It has been indicated by Southern hybridization that the generated kanamycin-resistant mutants were resulted from single transposition event of pTNR. The results also revealed that the transposable-marker gene of pTNR was randomly inserted into the chromosomal DNA of R. erythropolis. The affected DNA regions carrying the transposed DNA element could be conveniently recovered for further characterization using a plasmid rescue procedure. Sequence data of the insertion sites of 40 random mutants analyzed indicated that transposition of pTNR generated 6-bp direct target duplications in 36 cases, while in the remaining four mutants; it generated 5- or 7-bp target duplications (two cases each). This study concluded that pTNR could be served as an efficient genetic tool for construction of random mutagenesis system in Rhodococcus species.
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Affiliation(s)
- Khalid Ibrahim Sallam
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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Kulakov LA, Chen S, Allen CCR, Larkin MJ. Web-type evolution of rhodococcus gene clusters associated with utilization of naphthalene. Appl Environ Microbiol 2005; 71:1754-64. [PMID: 15811998 PMCID: PMC1082552 DOI: 10.1128/aem.71.4.1754-1764.2005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clusters of genes which include determinants for the catalytic subunits of naphthalene dioxygenase (narAa and narAb) were analyzed in naphthalene-degrading Rhodococcus strains. We demonstrated (i) that in the region analyzed homologous gene clusters are separated from each other by nonhomologous DNA, (ii) that there are various degrees of homology between related genes, and (iii) that nar genes are located on plasmids in strains NCIMB12038 and P400 and on a chromosome in P200. These observations suggest that genetic exchange and reshuffling of genetic modules, as well as vertical descent of the genetic information, were the main routes in the evolution of naphthalene degradation in Rhodococcus. These conclusions were supported by studies of transcription patterns in the region analyzed. It was found that the nar region is not organized into a single operon but there are several transcription units which differ in the strains investigated. The narA and narB genes were found to be transcribed as a single unit in all strains analyzed, and their transcription was induced by naphthalene. The putative aldolase gene (narC) was found on the same transcript only in strains P200 and P400. In NCIMB12038 transcription of two more gene clusters was induced by growth on naphthalene. Transcription start sites for narA and narB were found to be different in all of the strains studied. Putative regulatory genes (narR1 and narR2) were transcribed as a single mRNA in naphthalene-induced cells. At the same time, a number of the genes known to be essential for naphthalene catabolism in gram-negative bacteria were not found in the region analyzed.
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Affiliation(s)
- Leonid A Kulakov
- The Questor Centre and School of Biology and Biochemistry, The Queen's University of Belfast, Belfast, United Kingdom.
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Mrozik A, Labuzek S, Piotrowska-Seget Z. Changes in fatty acid composition in Pseudomonas putida and Pseudomonas stutzeri during naphthalene degradation. Microbiol Res 2005; 160:149-57. [PMID: 15881832 DOI: 10.1016/j.micres.2004.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The effects of naphthalene on the whole cell-derived fatty acid composition of Pseudomonas putida and Pseudomonas stutzeri during naphthalene degradation were investigated. These strains differed in their abilities to degrade naphthalene and in 1,2-catechol dioxygenase activities. The cells of both strains reacted to the addition of naphthalene with an increase in the saturated/unsaturated ratio. The dynamic changes comprised also alterations in the percentage of hydroxy, cyclopropane and branched fatty acids. Upon the exposure of naphthalene, new fatty acids were detected.
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Affiliation(s)
- Agnieszka Mrozik
- Department of Biochemistry, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland.
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Foght J. Chapter 5 Whole-cell bio-processing of aromatic compounds in crude oil and fuels. STUDIES IN SURFACE SCIENCE AND CATALYSIS 2004. [DOI: 10.1016/s0167-2991(04)80146-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Abstract
Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and extents of desulfurization. Bacterial processes are being commercialized for removal of H(2)S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.
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Affiliation(s)
- Jonathan D Van Hamme
- Department of Biological Sciences, The University College of the Cariboo, Kamloops, British Columbia V2C 5N3
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Abstract
A purified microbial isolate, identified as a strain of Rhodococcus sp., metabolized indene primarily to iso quinoline and lesser amounts of indandiol and indanone. Isoquinoline production was dependent on the presence of microbial culture, indene, and ammonium ions as the source of nitrogen in the molecule. The ability to produce iso quin oline was induced by growth on benzene or naphthalene and by the presence of indene itself. The culture produced compounds tentatively identified as 3-methylisoquinoline and 3-ethylisoquinoline from 2-methylindene and from 2-ethylindene, respectively. Deuterated indene was converted to deuterated isoquinoline, deuterated indanone, and deuterated indandiol. Experiments with [15N]ammonium nitrate and ammonium [15N]nitrate confirmed ammonium as the source of nitrogen in the isoquinoline products.Key words: biotransformation, metabolism, methylisoquinoline, ethylindene.
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