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You XY, Liu JH, Tian H, Ding Y, Bu QY, Zhang KX, Ren GY, Duan X. Mucilaginibacter Phenanthrenivorans sp. nov., a Novel Phenanthrene Degradation Bacterium Isolated from Wetland Soil. Curr Microbiol 2022; 79:382. [DOI: 10.1007/s00284-022-03085-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
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2
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Jiang B, Chen Y, Xing Y, Lian L, Shen Y, Zhang B, Zhang H, Sun G, Li J, Wang X, Zhang D. Negative correlations between cultivable and active-yet-uncultivable pyrene degraders explain the postponed bioaugmentation. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127189. [PMID: 34555764 DOI: 10.1016/j.jhazmat.2021.127189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Bioaugmentation is an effective approach to remediate soils contaminated by polycyclic aromatic hydrocarbons (PAHs), but suffers from unsatisfactory performance in engineering practices, which is hypothetically explained by the complicated interactions between indigenous microbes and introduced degraders. This study isolated a cultivable pyrene degrader (Sphingomonas sp. YT1005) and an active pyrene degrading consortium (Gp16, Streptomyces, Pseudonocardia, Panacagrimonas, Methylotenera and Nitrospira) by magnetic-nanoparticle mediated isolation (MMI) from soils. Pyrene biodegradation was postponed in bioaugmentation with Sphingomonas sp. YT1005, whilst increased by 30.17% by the active pyrene degrading consortium. Pyrene dioxygenase encoding genes (nidA, nidA3 and PAH-RHDα-GP) were enriched in MMI isolates and positively correlated with pyrene degradation efficiency. Pyrene degradation by Sphingomonas sp. YT1005 only followed the phthalate pathway, whereas both phthalate and salicylate pathways were observed in the active pyrene degrading consortium. The results indicated that the uncultivable pyrene degraders were suitable for bioaugmentation, rather than cultivable Sphingomonas sp. YT1005. The negative correlations between Sphingomonas sp. YT1005 and the active-yet-uncultivable pyrene degraders were the underlying mechanisms of bioaugmentation postpone in engineering practices.
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Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, PR China
| | - Yating Chen
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China
| | - Luning Lian
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China
| | - Yaoxin Shen
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, PR China; Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, PR China
| | - Baogang Zhang
- School of Water Resources and Environment, MOE Key Lab Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China
| | - Han Zhang
- School of Water Resources and Environment, MOE Key Lab Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, PR China
| | - Guangdong Sun
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Junyi Li
- Department of Research and Development, Yiqing (Suzhou) Environmental Technology Co. Ltd, Suzhou 215163, PR China
| | - Xinzi Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China.
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Liu Y, Hu H, Zanaroli G, Xu P, Tang H. A Pseudomonas sp. strain uniquely degrades PAHs and heterocyclic derivatives via lateral dioxygenation pathways. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123956. [PMID: 33265000 DOI: 10.1016/j.jhazmat.2020.123956] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/21/2020] [Accepted: 09/04/2020] [Indexed: 05/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and heterocyclic derivatives are organic pollutants that pose a serious health risk to human beings. In this study, a newly isolated Pseudomonas brassicacearum strain MPDS could effectively degrade PAHs and heterocyclic derivatives, including naphthalene, fluorene, dibenzofuran (DBF) and dibenzothiophene (DBT). Notably, strain MPDS is able to degrade fluorene, DBF and DBT uniquely via a lateral dioxygenation pathway, while most reported strains degrade fluorene, DBF and DBT via an angular dioxygenation pathway or co-metabolize them via a lateral dioxygenation pathway. Strain MPDS completely degraded 50 mg naphthalene (in 50 mL medium) in 84 h, and OD600 reached 1.0-1.1; while, it stabilized at OD600 0.5-0.6 with 5 mg fluorene or DBF or DBT. Meanwhile, 65.7% DBF and 32.1% DBT were degraded in 96 h, and 40.3% fluorene was degraded in 72 h, respectively. Through genomic and transcriptomic analyses, and comparative genomic analysis with another DBF degradation strain, relevant gene clusters were predicted, and a naphthalene-degrading gene cluster was identified. This study provides understanding of degradation of PAHs and their heterocyclic derivatives, as well as new insights into the lateral dioxygenation pathway of relevant contaminants.
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Affiliation(s)
- Yunli Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China; Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China; Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Giulio Zanaroli
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, Bologna 40131, Italy
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China; Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China; Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
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Sakshi, Haritash AK. A comprehensive review of metabolic and genomic aspects of PAH-degradation. Arch Microbiol 2020; 202:2033-2058. [DOI: 10.1007/s00203-020-01929-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
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5
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Miyazawa D, Thanh LTH, Tani A, Shintani M, Loc NH, Hatta T, Kimbara K. Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8. Microorganisms 2019; 8:microorganisms8010044. [PMID: 31878343 PMCID: PMC7023095 DOI: 10.3390/microorganisms8010044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 11/26/2022] Open
Abstract
Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the dehydrogenase, a 10-kb DNA fragment was isolated. Upstream of nahB, a gene for dehydrogenase, there were two open reading frames which were designated as nahAc and nahAd, respectively. The products of nahAc and nahAd were predicted to be alpha and beta subunit of ring-hydroxylating dioxygenases, respectively. Phylogenetic analysis of amino acid sequences of NahB indicated that it did not belong to the cis-dihydrodiol dehydrogenase group that includes those of classical naphthalene degradation pathways. Downstream of nahB, four open reading frames were found, and their products were predicted as meta-cleavage product hydrolase, monooxygenase, dehydrogenase, and gentisate 1,2-dioxygenase, respectively. A reverse transcriptase-PCR analysis showed that transcription of nahAcAd was induced by naphthalene. These findings indicate that we successfully identified genes involved in the upper pathway of naphthalene degradation from a thermophilic bacterium.
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Affiliation(s)
- Daisuke Miyazawa
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; (D.M.); (A.T.)
| | - Le Thi Ha Thanh
- Department of Environment and Energy System, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8011, Japan;
- Institute of Bioactive Compounds, University of Sciences, Hue University, Hue, Thua Thien Hue 530000, Vietnam;
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; (D.M.); (A.T.)
| | - Masaki Shintani
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
- Correspondence: (M.S.); (K.K.); Tel.: +81-53-478-1181 (M.S.); +81-53-478-1170 (K.K.)
| | - Nguyen Hoang Loc
- Institute of Bioactive Compounds, University of Sciences, Hue University, Hue, Thua Thien Hue 530000, Vietnam;
| | - Takashi Hatta
- Department of Biomedical Engineering, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 703-8232, Japan;
| | - Kazuhide Kimbara
- Department of Environment and Energy System, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8011, Japan;
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
- Correspondence: (M.S.); (K.K.); Tel.: +81-53-478-1181 (M.S.); +81-53-478-1170 (K.K.)
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Suzuki T, Takizawa N. Purification and enzymatic characterization of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Rhodococcus opacus and enzymatic formation of α, β-unsaturated ketones. Biosci Biotechnol Biochem 2019; 83:1884-1888. [DOI: 10.1080/09168451.2019.1625262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
ABSTRACT
Trans-o-hydroxybenzylidenepyruvate (tHBPA) hydratase-aldolase (RnoE) catalyzes the conversion of tHBPA to 2-hydroxybenzaldehyde and pyruvate. We purified RnoE from Rhodococcus opacus and characterized its enzymatic properties. It exhibited maximum enzyme activity at 60°C and catalyzed the reverse reaction, converting various aromatic benzaldehydes and pyruvate to benzylidenepyruvate, indicating that this enzyme can be adapted for the enzymatic synthesis of α, β-unsaturated ketones.
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Affiliation(s)
- Toshihiro Suzuki
- Department of Fermentation Sciences, Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Noboru Takizawa
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Okayama University of Science, Okayama, Japan
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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: 94] [Impact Index Per Article: 6.7] [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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8
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Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, Tian YS, Yao QH. Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol Rev 2008; 32:927-55. [PMID: 18662317 DOI: 10.1111/j.1574-6976.2008.00127.x] [Citation(s) in RCA: 388] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites.
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Affiliation(s)
- Ri-He Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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9
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Chauhan A, Fazlurrahman, Oakeshott JG, Jain RK. Bacterial metabolism of polycyclic aromatic hydrocarbons: strategies for bioremediation. Indian J Microbiol 2008; 48:95-113. [PMID: 23100704 DOI: 10.1007/s12088-008-0010-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 01/21/2008] [Accepted: 02/04/2008] [Indexed: 10/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are compounds of intense public concern due to their persistence in the environment and potentially deleterious effects on human, environmental and ecological health. The clean up of such contaminants using invasive technologies has proven to be expensive and more importantly often damaging to the natural resource properties of the soil, sediment or aquifer. Bioremediation, which exploits the metabolic potential of microbes for the clean-up of recalcitrant xenobiotic compounds, has come up as a promising alternative. Several approaches such as improvement in PAH solubilization and entry into the cell, pathway and enzyme engineering and control of enzyme expression etc. are in development but far from complete. Successful application of the microorganisms for the bioremediation of PAH-contaminated sites therefore requires a deeper understanding of the physiology, biochemistry and molecular genetics of potential catabolic pathways. In this review, we briefly summarize important strategies adopted for PAH bioremediation and discuss the potential for their improvement.
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Affiliation(s)
- Archana Chauhan
- Institute of Microbial Technology, Sector-39A, Chandigarh, India
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10
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Kweon O, Kim SJ, Baek S, Chae JC, Adjei MD, Baek DH, Kim YC, Cerniglia CE. A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases. BMC BIOCHEMISTRY 2008; 9:11. [PMID: 18387195 PMCID: PMC2358900 DOI: 10.1186/1471-2091-9-11] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 04/03/2008] [Indexed: 11/18/2022]
Abstract
BACKGROUND Rieske non-heme iron aromatic ring-hydroxylating oxygenases (RHOs) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. Since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many RHOs have been discovered, which do not belong to any group in the previous classification. Here, we present a scheme for classification of RHOs reflecting new sequence information and interactions between RHO enzyme components. RESULT We have analyzed a total of 130 RHO enzymes in which 25 well-characterized RHO enzymes were used as standards to test our hypothesis for the proposed classification system. From the sequence analysis of electron transport chain (ETC) components of the standard RHOs, we extracted classification keys that reflect not only the phylogenetic affiliation within each component but also relationship among components. Oxygenase components of standard RHOs were phylogenetically classified into 10 groups with the classification keys derived from ETC components. This phylogenetic classification scheme was converted to a new systematic classification consisting of 5 distinct types. The new classification system was statistically examined to justify its stability. Type I represents two-component RHO systems that consist of an oxygenase and an FNRC-type reductase. Type II contains other two-component RHO systems that consist of an oxygenase and an FNRN-type reductase. Type III represents a group of three-component RHO systems that consist of an oxygenase, a [2Fe-2S]-type ferredoxin and an FNRN-type reductase. Type IV represents another three-component systems that consist of oxygenase, [2Fe-2S]-type ferredoxin and GR-type reductase. Type V represents another different three-component systems that consist of an oxygenase, a [3Fe-4S]-type ferredoxin and a GR-type reductase. CONCLUSION The new classification system provides the following features. First, the new classification system analyzes RHO enzymes as a whole. RwithSecond, the new classification system is not static but responds dynamically to the growing pool of RHO enzymes. Third, our classification can be applied reliably to the classification of incomplete RHOs. Fourth, the classification has direct applicability to experimental work. Fifth, the system provides new insights into the evolution of RHO systems based on enzyme interaction.
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Affiliation(s)
- Ohgew Kweon
- Microbiology Division, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA
| | - Seong-Jae Kim
- Microbiology Division, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA
| | - Songjoon Baek
- Division of Personalized Nutrition & Medicine, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA
| | - Jong-Chan Chae
- Biotechnology Center for Agriculture and the Environment, Cook College, Rutgers University, New Brunswick, NJ 08901, USA
| | - Michael D Adjei
- Department of Health Norfolk Department of Public Health Bureau of Laboratories, Norfolk, VA 23510, USA
| | - Dong-Heon Baek
- Department of Oral Microbiology and Immunology, School of Dentistry, Dankook University, Chonan 330-714, Republic of Korea
| | - Young-Chang Kim
- School of Life Science, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Carl E Cerniglia
- Microbiology Division, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA
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11
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Pagnout C, Frache G, Poupin P, Maunit B, Muller JF, Férard JF. Isolation and characterization of a gene cluster involved in PAH degradation in Mycobacterium sp. strain SNP11: Expression in Mycobacterium smegmatis mc2155. Res Microbiol 2007; 158:175-86. [PMID: 17258432 DOI: 10.1016/j.resmic.2006.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 11/22/2006] [Accepted: 11/24/2006] [Indexed: 10/23/2022]
Abstract
Mycobacterium sp. strain SNP11 is able to grow with pyrene, fluoranthene, phenanthrene and fluorene the sole carbon and energy sources. A probe based on the previously described gene pdoA2, which encodes the alpha subunit of a PAH ring-hydroxylating dioxygenase in Mycobacterium sp. strain 6PY1 [S. Krivobok et al., Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases, J. Bacteriol. 185(13) (2003) 3828-3841], was used to isolate a 14kb DNA fragment from strain SNP11. Twelve putative open reading frames (ORFs), divided into two groups by a promoter intergenic region, were detected in this DNA sequence. The first gene cluster, located upstream of the promoter region, showed low but significant deduced amino acid sequence homologies with enzymes involved in aromatic degradation. The second gene cluster, under control of the promoter, contained pdoA2 (designated phdA in this study) and several other ORFs with deduced amino acid sequences closely related to enzymes involved in the phenanthrene-degrading pathway of Nocardioides sp. strain KP7. Gene expression analysis in Mycobacterium smegmatis mc(2)155 revealed broad substrate specificity of the ring-hydroxylating dioxygenase, since transformant cells containing phdAB strongly oxidized fluoranthene, phenanthrene, anthracene, fluorine and dibenzofuran. Laser desorption/ionization time-of-flight mass spectrometry (LDI-ToF MS) analyses of culture media after PAH degradation by M. smegmatis transformants also revealed that the second gene cluster, located downstream of the promoter, takes an active share in initial phenanthrene and anthracene degradation by allowing transformation of these two PAHs in aromatic ring-cleaved metabolites.
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Affiliation(s)
- Christophe Pagnout
- Laboratoire d'Ecotoxicité, Santé Environnementale, CNRS UMR 7146, Université Paul Verlaine, rue du Général Delestraint, F-57070 Metz, France
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12
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Ono A, Miyazaki R, Sota M, Ohtsubo Y, Nagata Y, Tsuda M. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl Microbiol Biotechnol 2006; 74:501-10. [PMID: 17096121 DOI: 10.1007/s00253-006-0671-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2006] [Revised: 09/06/2006] [Accepted: 09/10/2006] [Indexed: 10/23/2022]
Abstract
Two different cultivation-independent approaches were applied to isolate genes for naphthalene dioxygenase (NDO) from oil-contaminated soil in Japan. One approach was the construction of a broad-host-range cosmid-based metagenomic DNA library, and the other was the so-called exogenous plasmid isolation technique. Our screening of NDO genes in both approaches was based on the functional complementation of Pseudomonas putida strains which contained Tn4655K, a transposon carrying the entire set of naphthalene-catabolic (nah) genes but lacking the NDO-encoding gene. We obtained in the former approach a cosmid clone (pSLX928-6) that carried an nah upper pathway operon for conversion of naphthalene to salicylate, and this operon showed a significantly high level of similarity to the corresponding operon on an IncP-9 naphthalene-catabolic plasmid, pDTG1. In the latter approach, the microbial fraction from the soil was mated with a plasmid-free P. putida strain containing a chromosomal copy of Tn4655K, and transconjugants were obtained that received either a 200- or 80-kb plasmid containing all the nah genes for the complete degradation of naphthalene. Subsequent analysis revealed that (1) both plasmids belong to the IncP-9 incompatibility group; (2) their nah upper pathway operons are significantly similar, but not completely identical, to those of pDTG1 and pSLX928-6; and (3) these plasmids carried genes for the salicylate metabolism by the meta-cleavage pathway.
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Affiliation(s)
- Akira Ono
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
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13
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Molecular cloning of genenahH encoding extradiol-type dioxygenase from the NAH plasmid ofPseudomonas stutzeri NA1. ANN MICROBIOL 2006. [DOI: 10.1007/bf03174987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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14
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Polymenakou PN, Stephanou EG. Effect of temperature and additional carbon sources on phenol degradation by an indigenous soil Pseudomonad. Biodegradation 2005; 16:403-13. [PMID: 15865154 DOI: 10.1007/s10532-004-3333-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A new indigenous soil bacterium Pseudomonas sp. growing on phenol and on a mixture of phenol, toluene, o-cresol, naphthalene and 1,2,3-trimethylbenzene (1,2,3-TMB) was isolated and characterized. Phylogenetic analysis suggested its classification to Pseudomonadaceae family and showed 99.8% DNA sequence identity to Pseudomonas pseudoalcaligenes species. The isolate was psychrotroph, with growth temperatures ranging from ca. 0 to 40 degrees C. The GC-MS structural analysis of metabolic products of phenol degradation by this microorganism indicated a possible ortho cleavage pathway for high concentrations (over 200 mg L(-1)) of phenol. Biodegradation rates by this species were found to be three times more effective than those previously reported by other Pseudomonas strains. The effect of temperature on phenol degradation was studied in batch cultures at temperatures ranging from 10 to 40 degrees C and different initial phenol concentrations (up to 500 mg L(-1)). Above 300 mg L(-1) of initial phenol concentration no considerable depletion was recorded at both 10 and 40 degrees C. Maximum degradation rates for phenol were recorded at 30 degrees C. The biodegradation rate of phenol was studied also in the presence of additional carbon sources (o-cresol, toluene, naphthalene, 1,2,3-TMB) at the optimum growth temperature and was found significantly lower by a factor of eight in respect to the strong competitive inhibition between the substrates and the more available sources of carbon and energy. The Haldane equation mu = mum S/(Ks + S + S2/K1) was found to best fit the experimental data at the optimum temperature of 30 degrees C than the Monod equation with kinetic constants mum = 0.27 h(-1), KS = 56.70 mg L(-1), KI = 249.08 mg L(-1).
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Affiliation(s)
- Paraskevi N Polymenakou
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Knossos Avenue PO Box 1470, 714 09 Heraklion, Greece
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Vacca DJ, Bleam WF, Hickey WJ. Isolation of soil bacteria adapted to degrade humic acid-sorbed phenanthrene. Appl Environ Microbiol 2005; 71:3797-805. [PMID: 16000791 PMCID: PMC1169045 DOI: 10.1128/aem.71.7.3797-3805.2005] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (PAHs) to PAH-degrading microbes. Micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model PAH. Enrichments from PAH-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. In contrast, only three strains of Burkholderia spp. and one strain each of Delftia sp. and Sphingomonas sp. were isolated from enrichments with humic acid-sorbed phenanthrene (HASP). Using [14C]phenanthrene as a radiotracer, we verified that only HASP isolates were capable of mineralizing HASP, a phenotype hence termed "competence." Competence was an all-or-nothing phenotype: noncompetent strains showed no detectable phenanthrene mineralization in HASP cultures, but levels of phenanthrene mineralization effected by competent strains in HASP and NSP cultures were not significantly different. Levels and rates of phenanthrene mineralization exceeded those predicted to be supported solely by the metabolism of phenanthrene in the aqueous phase of HASP cultures. Thus, competent strains were able to directly access phenanthrene sorbed by the humic acids and did not rely on desorption for substrate uptake. To the best of our knowledge, this is the first report of (i) a selective interaction between aerobic bacteria and humic acid molecules and (ii) differential bioavailability to bacteria of PAHs sorbed to a natural biogeopolymer.
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Affiliation(s)
- D J Vacca
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI 53706-1299, USA.
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Bodour AA, Wang JM, Brusseau ML, Maier RM. Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system. Environ Microbiol 2004; 5:888-95. [PMID: 14510842 DOI: 10.1046/j.1462-2920.2003.00481.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Widespread environmental contamination by polycyclic aromatic hydrocarbons (PAH) has led to increased interest in the use of natural attenuation as a clean-up strategy. However, few bioremediation studies have investigated the behaviour of the indigenous PAH-degrading community after long-term exposure to a PAH. In this study, a column packed with sandy loam soil was exposed to a solution saturated with phenanthrene ( approximately 1.2 mg l-1) for a 6-month period to examine the temporal response of the indigenous phenanthrene-degrading community. Initial soil, effluent, and final soil samples were collected and analysed for phenanthrene concentration and culturable phenanthrene degraders. Phenanthrene-degrading isolates were grouped by colony morphology. For each unique group, 16S rDNA polymerase chain reaction was performed, and then sequencing analysis was used to identify the isolate at the genus level. Twenty-five phenanthrene-degrading isolates, potentially representing 19 genera, were obtained from this analysis. Of these, eight genera have not been reported previously to degrade phenanthrene, including Afipia, Janthinobacterium, Leptothrix, Massilia, Methylobacterium, Rhizobium, Sinorhizobium and Thiobacillus. Results indicate that the dominant phenanthrene-degrading population changed over the course of this 6-month experiment. Specifically, the isolates obtained initially from the soil were not subsequently found in either effluent samples or the soil at the end of the experiment. Furthermore, several isolates that were found in the soil at the end of the experiment were not observed in the soil initially or in the effluent samples. This study confirms earlier findings indicating that a diverse community participates in phenanthrene degradation in the environment, and also suggests that the composition of this community is temporally variable.
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Affiliation(s)
- Adria A Bodour
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
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Samanta SK, Singh OV, Jain RK. Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation. Trends Biotechnol 2002; 20:243-8. [PMID: 12007492 DOI: 10.1016/s0167-7799(02)01943-1] [Citation(s) in RCA: 569] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely distributed and relocated in the environment as a result of the incomplete combustion of organic matter. Many PAHs and their epoxides are highly toxic, mutagenic and/or carcinogenic to microorganisms as well as to higher systems including humans. Although various physicochemical methods have been used to remove these compounds from our environment, they have many limitations. Xenobiotic-degrading microorganisms have tremendous potential for bioremediation but new modifications are required to make such microorganisms effective and efficient in removing these compounds, which were once thought to be recalcitrant. Metabolic engineering might help to improve the efficiency of degradation of toxic compounds by microorganisms. However, efficiency of naturally occurring microorganisms for field bioremediation could be significantly improved by optimizing certain factors such as bioavailability, adsorption and mass transfer. Chemotaxis could also have an important role in enhancing biodegradation of pollutants. Here, we discuss the problems of PAH pollution and PAH degradation, and relevant bioremediation efforts.
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Affiliation(s)
- Sudip K Samanta
- Institute of Microbial Technology, Sector-39A, -160036, Chandigarh, India
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Shimura M, Mukerjee-Dhar G, Kimbara K, Nagato H, Kiyohara H, Hatta T. Isolation and characterization of a thermophilic Bacillus sp. JF8 capable of degrading polychlorinated biphenyls and naphthalene. FEMS Microbiol Lett 1999; 178:87-93. [PMID: 10483727 DOI: 10.1111/j.1574-6968.1999.tb13763.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bacillus sp. strain JF8, which was isolated from compost, utilizes naphthalene and biphenyl as carbon sources at 60 degrees C. Biphenyl grown cells of strain JF8 barely degraded naphthalene while naphthalene grown cells did not degrade p-chlorobiphenyl, suggesting the existince of two independent degradation pathways. Isolation of JF8N, a mutant strain which can not utilize biphenyl as a carbon source while retaining the ability to utilize naphthalene, supports this hypothesis. Biphenyl grown cells of strain JF8 can degrade several polychlorinated biphenyl congeners including tetra- and pentachlorobiphenyl. bph and nah probes from mesophilic organisms failed to hybridize to strain JF8 DNA.
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Affiliation(s)
- M Shimura
- Environmental Biotechnology Laboratory, Railway Technical Research Institute, Tokyo, Japan.
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