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Jeon Y, Kwon YS, Noh YJ, Lee SM, Song JW, Kim JH, Seo JS. Unraveling the mechanisms of benzo[a]pyrene degradation by Pigmentiphaga kullae strain KIT-003 using a multi-omics approach. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 281:116665. [PMID: 38964062 DOI: 10.1016/j.ecoenv.2024.116665] [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: 01/25/2024] [Revised: 05/15/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), notably benzo[a]pyrene (BaP), are environmental contaminants with multiple adverse ecological implications. Numerous studies have suggested the use of BaP biodegradation using various bacterial strains to remove BaP from the environment. This study investigates the BaP biodegradation capability of Pigmentiphaga kullae strain KIT-003, isolated from the Nak-dong River (South Korea) under specific environmental conditions. The optimum conditions of biodegradation were found to be pH 7.0, 35°C, and a salinity of 0 %. GC-MS analysis suggested alternative pathways by which KIT-003 produced catechol from BaP through several intermediate metabolites, including 4-formylchrysene-5-carboxylic acid, 5,6-dihydro-5,6-dihydroxychrysene-5-carboxylic acid (isomer: 3,4-dihydro-3,4-dihydroxychrysene-4-carboxylic acid), naphthalene-1,2-dicarboxylic acid, and 2-hydroxy-1-naphthoic acid. Proteomic profiles indicated upregulation of enzymes associated with aromatic compound degradation, such as nahAc and nahB, and of those integral to the tricarboxylic acid cycle, reflecting the strain's adaptability to and degradation of BaP. Lipidomic analysis of KIT-003 demonstrated that BaP exposure induced an accumulation of glycerolipids such as diacylglycerol and triacylglycerol, indicating their crucial role in bacterial adaptation mechanisms under BaP stress. This study provides significant scientific knowledge regarding the intricate mechanisms involved in BaP degradation by microorganisms.
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Affiliation(s)
- Yoonjeong Jeon
- Environmental Safety-Assessment Center, Korea Institute of Toxicology, Jinju 52834, Republic of Korea
| | - Young Sang Kwon
- Environmental Safety-Assessment Center, Korea Institute of Toxicology, Jinju 52834, Republic of Korea
| | - Young Ji Noh
- Environmental Safety-Assessment Center, Korea Institute of Toxicology, Jinju 52834, Republic of Korea
| | - Seung-Min Lee
- Environmental Safety-Assessment Center, Korea Institute of Toxicology, Jinju 52834, Republic of Korea
| | - Jong-Wook Song
- Environmental Safety-Assessment Center, Korea Institute of Toxicology, Jinju 52834, Republic of Korea
| | - Jong-Hwan Kim
- Environmental Safety-Assessment Center, Korea Institute of Toxicology, Jinju 52834, Republic of Korea.
| | - Jong-Su Seo
- Environmental Safety-Assessment Center, Korea Institute of Toxicology, Jinju 52834, Republic of Korea.
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Hamed MM, Sayed M, Abdel-Mohsen SA, Saddik AA, Ibrahim OA, El-Dean AMK, Tolba MS. Synthesis, biological evaluation, and molecular docking studies of novel diclofenac derivatives as antibacterial agents. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Mező E, Hartmann-Balogh F, Madarászné Horváth I, Bufa A, Marosvölgyi T, Kocsis B, Makszin L. Effect of Culture Conditions on Fatty Acid Profiles of Bacteria and Lipopolysaccharides of the Genus Pseudomonas-GC-MS Analysis on Ionic Liquid-Based Column. Molecules 2022; 27:molecules27206930. [PMID: 36296523 PMCID: PMC9610168 DOI: 10.3390/molecules27206930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 12/02/2022] Open
Abstract
The profiling of bacterial fatty acids is a well-established technique in identifying and classifying bacteria. Cultivation conditions may affect the biosynthesis, thereby, changing the fatty acid profile in bacteria. The effect of the culture conditions on the fatty acid components of Pseudomonas aeruginosa PAO1, Pseudomonas aeruginosa ATCC 27853, Pseudomonas aeruginosa polyresistant and Pseudomonas putida all are aligned to the genus Pseudomonas. The fatty acids in the lipopolysaccharides of Pseudomonas aeruginosa PAO1 were also examined. The effects of the cultivation conditions were followed by using agar and blood agar media at the characteristic temperatures, 25 °C, 37 °C and 42 °C, respectively, and an analysis was made during the 1st, 3rd and 5th day following inoculation. In addition to quantitative differences, we also experienced qualitative differences in the fatty acid profiles which detect newly appearing fatty acids, due to changes in environmental factors. The application of ionic liquid-based column unveils new possibilities for the analyses of fatty acids in GC-MS experiments for bacterial fatty acid profiling. The validation results (response linearity, limit of detection, limit of quantification, system suitability, intraday and interday repeatability and accuracy) show the high separation efficiency of the ionic liquid-based column in the analyses.
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Affiliation(s)
- Emerencia Mező
- Institute of Bioanalysis, Medical School, Szentágothai Research Center, University of Pécs, 7622 Pécs, Hungary
| | - Fruzsina Hartmann-Balogh
- Institute of Bioanalysis, Medical School, Szentágothai Research Center, University of Pécs, 7622 Pécs, Hungary
| | - Ibolya Madarászné Horváth
- Institute of Bioanalysis, Medical School, Szentágothai Research Center, University of Pécs, 7622 Pécs, Hungary
| | - Anita Bufa
- Institute of Bioanalysis, Medical School, Szentágothai Research Center, University of Pécs, 7622 Pécs, Hungary
| | - Tamás Marosvölgyi
- Institute of Bioanalysis, Medical School, Szentágothai Research Center, University of Pécs, 7622 Pécs, Hungary
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7622 Pécs, Hungary
| | - Lilla Makszin
- Institute of Bioanalysis, Medical School, Szentágothai Research Center, University of Pécs, 7622 Pécs, Hungary
- Correspondence:
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Dhamale T, Saha BK, Papade SE, Singh S, Phale PS. A unique global metabolic trait of Pseudomonas bharatica CSV86 T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35925665 DOI: 10.1099/mic.0.001206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.
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Affiliation(s)
- Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Braja Kishor Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Sandesh E Papade
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Srushti Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India.,Present address: Presently affiliated to TCR Therapeutics, Inc., 100 Binney Street, Cambridge, MA 02142, USA
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
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Borrero‐de Acuña JM, Gutierrez‐Urrutia I, Hidalgo‐Dumont C, Aravena‐Carrasco C, Orellana‐Saez M, Palominos‐Gonzalez N, van Duuren JBJH, Wagner V, Gläser L, Becker J, Kohlstedt M, Zacconi FC, Wittmann C, Poblete‐Castro I. Channelling carbon flux through the meta-cleavage route for improved poly(3-hydroxyalkanoate) production from benzoate and lignin-based aromatics in Pseudomonas putida H. Microb Biotechnol 2021; 14:2385-2402. [PMID: 33171015 PMCID: PMC8601166 DOI: 10.1111/1751-7915.13705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Lignin-based aromatics are attractive raw materials to derive medium-chain length poly(3-hydroxyalkanoates) (mcl-PHAs), biodegradable polymers of commercial value. So far, this conversion has exclusively used the ortho-cleavage route of Pseudomonas putida KT2440, which results in the secretion of toxic intermediates and limited performance. Pseudomonas putida H exhibits the ortho- and the meta-cleavage pathways where the latter appears promising because it stoichiometrically yields higher levels of acetyl-CoA. Here, we created a double-mutant H-ΔcatAΔA2 that utilizes the meta route exclusively and synthesized 30% more PHA on benzoate than the parental strain but suffered from catechol accumulation. The single deletion of the catA2 gene in the H strain provoked a slight attenuation on the enzymatic capacity of the ortho route (25%) and activation of the meta route by nearly 8-fold, producing twice as much mcl-PHAs compared to the wild type. Inline, the mutant H-ΔcatA2 showed a 2-fold increase in the intracellular malonyl-CoA abundance - the main precursor for mcl-PHAs synthesis. As inferred from flux simulation and enzyme activity assays, the superior performance of H-ΔcatA2 benefited from reduced flux through the TCA cycle and malic enzyme and diminished by-product formation. In a benzoate-based fed-batch, P. putida H-ΔcatA2 achieved a PHA titre of 6.1 g l-1 and a volumetric productivity of 1.8 g l-1 day-1 . Using Kraft lignin hydrolysate as feedstock, the engineered strain formed 1.4 g l- 1 PHA. The balancing of carbon flux between the parallel catechol-degrading routes emerges as an important strategy to prevent intermediate accumulation and elevate mcl-PHA production in P. putida H and, as shown here, sets the next level to derive this sustainable biopolymer from lignin hydrolysates and aromatics.
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Affiliation(s)
- José Manuel Borrero‐de Acuña
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
- Present address:
Institute of MicrobiologyTechnical University of BraunschweigBraunschweigGermany
| | - Izabook Gutierrez‐Urrutia
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Cristian Hidalgo‐Dumont
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
| | - Carla Aravena‐Carrasco
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
| | - Matias Orellana‐Saez
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
| | - Nestor Palominos‐Gonzalez
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
| | | | - Viktoria Wagner
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Lars Gläser
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Judith Becker
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Flavia C. Zacconi
- Facultad de Química y de FarmaciaPontificia Universidad Católica de ChileSantiagoChile
- Institute for Biological and Medical EngineeringSchools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| | | | - Ignacio Poblete‐Castro
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
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6
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Zubkov IN, Nepomnyshchiy AP, Kondratyev VD, Sorokoumov PN, Sivak KV, Ramsay ES, Shishlyannikov SM. Adaptation of Pseudomonas helmanticensis to fat hydrolysates and SDS: fatty acid response and aggregate formation. J Microbiol 2021; 59:1104-1111. [PMID: 34697784 DOI: 10.1007/s12275-021-1214-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/15/2023]
Abstract
An essential part of designing any biotechnological process is examination of the physiological state of producer cells in different phases of cultivation. The main marker of a bacterial cell's state is its fatty acid (FA) profile, reflecting membrane lipid composition. Consideration of FA composition enables assessment of bacterial responses to cultivation conditions and helps biotechnologists understand the most significant factors impacting cellular metabolism. In this work, soil SDS-degrading Pseudomonas helmanticensis was studied at the fatty acid profile level, including analysis of rearrangement between planktonic and aggregated forms. The set of substrates included fat hydrolysates, SDS, and their mixtures with glucose. Such media are useful in bioplastic production since they can help incrementally lower overall costs. Conventional gas chromatography-mass spectrometry was used for FA analysis. Acridine orange-stained aggregates were observed by epifluorescence microscopy. The bacterium was shown to change fatty acid composition in the presence of hydrolyzed fats or SDS. These changes seem to be driven by the depletion of metabolizable substrates in the culture medium. Cell aggregation has also been found to be a defense strategy, particularly with anionic surfactant (SDS) exposure. It was shown that simple fluidity indices (such as saturated/unsaturated FA ratios) do not always sufficiently characterize a cell's physiological state, and morphological examination is essential in cases where complex carbon sources are used.
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Affiliation(s)
- Ilya N Zubkov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia.
| | - Anatoly P Nepomnyshchiy
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia
| | - Vadim D Kondratyev
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia
| | - Pavel N Sorokoumov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia
| | - Konstantin V Sivak
- Smorodintsev Research Institute of Influenza, 15/17 Ulitsa Professora Popova, Saint Petersburg, 4197022, Russia
| | - Edward S Ramsay
- Smorodintsev Research Institute of Influenza, 15/17 Ulitsa Professora Popova, Saint Petersburg, 4197022, Russia
| | - Sergey M Shishlyannikov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia
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7
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Pal A, Bhattacharjee S, Saha J, Sarkar M, Mandal P. Bacterial survival strategies and responses under heavy metal stress: a comprehensive overview. Crit Rev Microbiol 2021; 48:327-355. [PMID: 34473592 DOI: 10.1080/1040841x.2021.1970512] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Heavy metals bring long-term hazardous consequences and pose a serious threat to all life forms. Being non-biodegradable, they can remain in the food webs for a long period of time. Metal ions are essential for life and indispensable for almost all aspects of metabolism but can be toxic beyond threshold level to all living beings including microbes. Heavy metals are generally present in the environment, but many geogenic and anthropogenic activities has led to excess metal ion accumulation in the environment. To survive in harsh metal contaminated environments, bacteria have certain resistance mechanisms to metabolize and transform heavy metals into less hazardous forms. This also gives rise to different species of heavy metal resistant bacteria. Herein, we have tried to incorporate the different aspects of heavy metal toxicity in bacteria and provide an up-to-date and across-the-board review. The various aspects of heavy metal biology of bacteria encompassed in this review includes the biological notion of heavy metals, toxic effect of heavy metals on bacteria, the factors regulating bacterial heavy metal resistance, the diverse mechanisms governing bacterial heavy metal resistance, bacterial responses to heavy metal stress, and a brief overview of gene regulation under heavy metal stress.
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Affiliation(s)
- Ayon Pal
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Sukanya Bhattacharjee
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Jayanti Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Sarkar
- Mycology and Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
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8
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Pacholak A, Burlaga N, Guzik U, Kaczorek E. Investigation of the bacterial cell envelope nanomechanical properties after long-term exposure to nitrofurans. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124352. [PMID: 33160784 DOI: 10.1016/j.jhazmat.2020.124352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic residues in the environment may negatively affect biological communities in the natural ecosystems. However, their influence on environmental bacterial strains has not been thoroughly investigated. In this study, two representatives of 5-nitrofuran antibiotics (nitrofurantoin and furaltadone) were investigated in terms of their long-term influence on the cell envelopes of newly isolated environmental bacterial strains (Sphingobacterium caeni FTD2, Achromobacter xylosoxidans NFZ2 and Pseudomonas hibiscicola FZD2). A 12-month exposure of bacterial cells to nitrofurans at a concentration of 20 mg L-1 induced changes in the cell structure and texture (bacteria under stress conditions showed a loss of their original shape and seemed to be vastly inflated, the cells increased average surface roughness after exposure to NFT and FTD, respectively). AFM observations allowed the calculation of the bacterial cell nanomechanical properties. Significant increase in adhesion energy of bacteria after prolonged contact with nitrofurantoin was demonstrated. Changes in the permeability of bacterial membrane, fatty acids' composition and bacterial cell surface hydrophobicity were determined. Despite visible bacterial adaptation to nitrofurans, prolonged presence of pharmaceuticals in the environment has led to significant alterations in the cells' structures which was particularly visible in P. hibiscicola.
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Affiliation(s)
- Amanda Pacholak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland.
| | - Natalia Burlaga
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland.
| | - Urszula Guzik
- University of Silesia in Katowice, Faculty of Natural Science, Institute of Biology, Biotechnology and Environmental Protection, Jagiellońska 28, 40 032 Katowice, Poland.
| | - Ewa Kaczorek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland.
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Sharma M, Khurana H, Singh DN, Negi RK. The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 280:111744. [PMID: 33280938 DOI: 10.1016/j.jenvman.2020.111744] [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: 07/27/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.
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Affiliation(s)
- Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Durgesh Narain Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India.
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Estepa KMO, Lamont K, Malicevic S, Paschos A, Colaruotolo L, Corradini M, Marangoni AG, Lim LT, Pensini E. Chitosan-Based biogels: A potential approach to trap and bioremediate naphthalene. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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11
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Shon JC, Noh YJ, Kwon YS, Kim JH, Wu Z, Seo JS. The impact of phenanthrene on membrane phospholipids and its biodegradation by Sphingopyxis soli. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110254. [PMID: 32007746 DOI: 10.1016/j.ecoenv.2020.110254] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
The direct interactions of bacterial membranes and polycyclic aromatic hydrocarbons (PAHs) strongly influence the biological processes, such as metabolic activity and uptake of substrates due to changes in membrane lipids. However, the elucidation of adaptation mechanisms as well as membrane phospholipid alterations in the presence of phenanthrene (PHE) from α-proteobacteria has not been fully explored. This study was conducted to define the degradation efficiency of PHE by Sphingopyxis soli strain KIT-001 in a newly isolated from Jeonju river sediments and to characterize lipid profiles in the presence of PHE in comparison to cells grown on glucose using quantitative lipidomic analysis. This strain was able to respectively utilize 1-hydroxy-2-naphthoic acid and salicylic acid as sole carbon source and approximately 90% of PHE (50 mg/L) was rapidly degraded via naphthalene route within 1 day incubation. In the cells grown on PHE, strain KIT-001 appeared to dynamically change profiles of metabolite and lipid in comparison to cells grown on glucose. The levels of primary metabolites, phosphatidylethanolamines (PE), and phosphatidic acids (PA) were significantly decreased, whereas the levels of phosphatidylcholines (PC) and phosphatidylglycerols (PG) were significantly increased. The adaptation mechanism of Sphingopyxis sp. regarded mainly the accumulation of bilayer forming lipids and anionic lipids to adapt more quickly under restricted nutrition and toxicity condition. Hence, these findings are conceivable that strain KIT-001 has a good adaptive ability and biodegradation for PHE through the alteration of phospholipids, and will be helpful for applications for effective bioremediation of PAHs-contaminated sites.
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Affiliation(s)
- Jong Cheol Shon
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Young Ji Noh
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Young Sang Kwon
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Jong-Hwan Kim
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Zhexue Wu
- Mass Spectrometry Convergence Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jong-Su Seo
- Environmental Chemistry Research Group, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea.
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12
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Liu C, Zhou Z, Qin J, Li F, Yu C, Liu G, Huang H, Wu W. Influence of Titanium Species on the Ordered Mesoporous Structure of V‐Zr Catalysts for Naphthalene Oxidation with Hydrogen Peroxide. ChemistrySelect 2020. [DOI: 10.1002/slct.201904071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chuanfa Liu
- College of Chemical Engineering Nanjing Tech University Nanjing 210009 P. R. China
| | - Zhiwei Zhou
- College of Chemical Engineering Nanjing Tech University Nanjing 210009 P. R. China
| | - Juan Qin
- Productivity Center of Jiangsu Province Technology and Finance Service Center of Jiangsu Province Nanjing 210042 P. R. China
| | - Fanqing Li
- College of Chemical Engineering Nanjing Tech University Nanjing 210009 P. R. China
| | - Chaojie Yu
- College of Chemical Engineering Nanjing Tech University Nanjing 210009 P. R. China
| | - Guang Liu
- College of Chemical Engineering Nanjing Tech University Nanjing 210009 P. R. China
| | - Hao Huang
- College of Chemical Engineering Nanjing Tech University Nanjing 210009 P. R. China
| | - Wenliang Wu
- College of Chemical Engineering Nanjing Tech University Nanjing 210009 P. R. China
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Abd Alamer IS, Tomah AA, Li B, Zhang JZ. Isolation, Identification and Characterization of Rhizobacteria Strains for Biological Control of Bacterial Wilt (Ralstonia solanacearum) of Eggplant in China. AGRICULTURE 2020; 10:37. [DOI: 10.3390/agriculture10020037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Bacterial wilt of eggplant is the most destructive disease caused by Ralstonia solanacearum throughout the world. Eleven bacterial strains with high antagonistic activity were obtained from 245 rhizobacteria. Based on analysis of morphology, 16S rRNA sequences, fatty acid profiles, gyrA and rpoB genes, they were identified as Pseudomonas putida (IMA3), Paenibacillus polymyxa (IMA5), Bacillus cereus (IMA4, IMA7 and IMA11) and the “operational group Bacillus amyloliquefaciens” (IMA1, IMA2, IMA6, IMA8, IMA9 and IMA10). The lipopeptide compounds produced by each strain also were determined. The biocontrol tests demonstrated that co-inoculation by strain IMA5 and the pathogen gave the greatest biocontrol efficiency of 87.0% and 69.2% 30 and 40 days after co-inoculation, respectively. Plant growth promotion tests revealed that IMA5 markedly promoted eggplant growth, enhancing aboveground seedling length and biomass by 60.8% and by 107.6% and underground root length and biomass by 33.0% and 69.2%, respectively. Hence, strain IMA5 could be considered for developing potential biocontrol agents and for promoting plant growth characteristics, to aid the management of the pathogen R. solanacearum in eggplants.
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14
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Santos IC, Chaumette A, Smuts J, Hildenbrand ZL, Schug KA. Analysis of bacteria stress responses to contaminants derived from shale energy extraction. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:269-278. [PMID: 30444232 DOI: 10.1039/c8em00338f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In order to survive environmental changes, bacteria have stress responses, which protect them from adverse and variable conditions. Contamination can be a source of stress and bacterial responses can serve as an indicator of environmental abnormality. In this work, the biochemical effects of toxic compounds that stem from hydraulic fracturing were measured on the whole cell-derived fatty acid and protein compositions of Escherichia coli, Klebsiella oxytoca, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas stutzeri, Aeromonas hydrophila, Bacillus cereus, and Bacillus subtilis. These microorganisms were exposed to elevated levels of benzene, ethanol, propanol, toluene, and salt. These were chosen to represent significant subsurface contamination or a surface spill. The fatty acid and protein profiles for the bacteria were analyzed using gas chromatography - vacuum ultraviolet spectroscopy and matrix-assisted laser desorption ionization time-of-flight mass spectrometry, respectively. Overall, different fatty acid and protein profiles were observed when the microorganisms were grown in the presence of the toxic compounds. The cells exhibited an increase in the saturated/unsaturated ratio and displayed the presence of branched and cyclopropane fatty acids when in the presence of common fracture fluid constituents to decrease membrane permeability which was confirmed by the analysis of produced water. This approach provides a potentially useful tool for environmental diagnosis, since proteins and fatty acids can act as a harbinger of ecological health.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Pl.; Box 19065, Arlington, TX 76019-0065, USA.
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Ma Z, Liu J, Dick RP, Li H, Shen D, Gao Y, Waigi MG, Ling W. Rhamnolipid influences biosorption and biodegradation of phenanthrene by phenanthrene-degrading strain Pseudomonas sp. Ph6. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 240:359-367. [PMID: 29751332 DOI: 10.1016/j.envpol.2018.04.125] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/04/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Given the sub-lethal risks of synthetic surfactants, rhamnolipid is a promising class of biosurfactants with the potential to promote the bioavailability of polycyclic aromatic hydrocarbons (PAHs), to provide a favorable substitute for synthetic surfactants. However, few previous studies have integrated the behavior and mechanism behind rhamnolipid-influenced PAH biosorption and biodegradation. This is, to our knowledge, the first report of a bacterial envelope regulated link between phenanthrene (PHE) biosorption and biodegradation by rhamnolipid-induced PHE-degrading strain Pseudomonas sp. Ph6. Rhamnolipid (0─400 mg L-1) can change the cell-surface zeta potential, cell surface hydrophobicity (CSH), cell ultra-microstructure and functional groups, and then alter PHE biosorption and biodegradation of Ph6. Greater amounts of PHE sorbed on cell envelopes results in more PHE diffusing into cytochylema, thus favoring PHE intracellular biodegradation of Ph6. Rhamnolipid (≤100 mg L-1) could change the microstructures and functional groups of cell envelopes of Ph6, enhance the cell-surface zeta potential and CSH, thus consequently favor PHE biosorption and biodegradation by strain Ph6. By contrast, rhamnolipid at higher concentrations (≥200 mg L-1) hindered PHE biosorption and biodegradation. Rhamnolipid, as a biosurfactant, can be successfully utilized as an additive to improve the microbial biodegradation of PAHs in the environments.
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Affiliation(s)
- Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Richard P Dick
- School of Environment & Natural Resources, Ohio State University, Columbus, OH 43210, United States
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Di Shen
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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16
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Jeong D, Yan JJ, Noh H, Hedman B, Hodgson KO, Solomon EI, Cho J. Oxidation of Naphthalene with a Manganese(IV) Bis(hydroxo) Complex in the Presence of Acid. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Donghyun Jeong
- Department of Emerging Materials Science DGIST Daegu 42988 Korea
| | - James J. Yan
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Hyeonju Noh
- Department of Emerging Materials Science DGIST Daegu 42988 Korea
| | - Britt Hedman
- Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center Menlo Park CA 94025 USA
| | - Keith O. Hodgson
- Department of Chemistry Stanford University Stanford CA 94305 USA
- Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center Menlo Park CA 94025 USA
| | - Edward I. Solomon
- Department of Chemistry Stanford University Stanford CA 94305 USA
- Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center Menlo Park CA 94025 USA
| | - Jaeheung Cho
- Department of Emerging Materials Science DGIST Daegu 42988 Korea
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17
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Jeong D, Yan JJ, Noh H, Hedman B, Hodgson KO, Solomon EI, Cho J. Oxidation of Naphthalene with a Manganese(IV) Bis(hydroxo) Complex in the Presence of Acid. Angew Chem Int Ed Engl 2018; 57:7764-7768. [PMID: 29701293 PMCID: PMC6013404 DOI: 10.1002/anie.201802641] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/05/2018] [Indexed: 11/06/2022]
Abstract
Naphthalene oxidation with metal-oxygen intermediates is a difficult reaction in environmental and biological chemistry. Herein, we report that a MnIV bis(hydroxo) complex, which was fully characterized by various physicochemical methods, such as ESI-MS, UV/Vis, and EPR analysis, X-ray diffraction, and XAS, can be employed for the oxidation of naphthalene in the presence of acid to afford 1,4-naphthoquinone. Redox titration of the MnIV bis(hydroxo) complex gave a one-electron reduction potential of 1.09 V, which is the most positive potential for all reported nonheme MnIV bis(hydroxo) species as well as MnIV oxo analogues. Kinetic studies, including kinetic isotope effect analysis, suggest that the naphthalene oxidation occurs through a rate-determining electron transfer process.
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Affiliation(s)
- Donghyun Jeong
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Korea
| | - James J Yan
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Hyeonju Noh
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Korea
| | - Britt Hedman
- Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Menlo Park, CA, 94025, USA
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Menlo Park, CA, 94025, USA
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Menlo Park, CA, 94025, USA
| | - Jaeheung Cho
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Korea
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18
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Xu J, Zhu D, Ibrahim AD, Allen CCR, Gibson CM, Fowler PW, Song Y, Huang WE. Raman Deuterium Isotope Probing Reveals Microbial Metabolism at the Single-Cell Level. Anal Chem 2017; 89:13305-13312. [DOI: 10.1021/acs.analchem.7b03461] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jiabao Xu
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Di Zhu
- Kroto
Research Institute, University of Sheffield, Sheffield S3 7HQ, United Kingdom
| | - Aliyu D. Ibrahim
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 7BL, United Kingdom
| | - Christopher C. R. Allen
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 7BL, United Kingdom
| | | | - Patrick W. Fowler
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Yizhi Song
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Wei E. Huang
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
- Kroto
Research Institute, University of Sheffield, Sheffield S3 7HQ, United Kingdom
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Wei K, Yin H, Peng H, Liu Z, Lu G, Dang Z. Characteristics and proteomic analysis of pyrene degradation by Brevibacillus brevis in liquid medium. CHEMOSPHERE 2017; 178:80-87. [PMID: 28319745 DOI: 10.1016/j.chemosphere.2017.03.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/07/2017] [Accepted: 03/11/2017] [Indexed: 06/06/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely spread in various ecosystems and are of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Bioremediation has been proposed as an effective approach to remove PAHs. In this study, the physiological responses and proteome of Brevibacillus brevis under exposure to pyrene, a four-ring compound from PAHs family, were investigated. The changes of cell viability of B. brevis were observed during the degradation of pyrene by means of flow cytometry. The results indicated that pyrene stimulated superoxide dismutase (SOD) activity from 93.9 to 100.6 U mg-1 prot, whereas inhibited catalase (CAT) activity from 29.1 to 20.3 U mg-1 prot. The main compositions of B. brevis changed during pyrene degradation, with the proportion of unsaturated fatty acids increased by 13.4%. In addition, we performed a proteomic approach (two-dimensional gel electrophoresis and MALDI-TOF/TOF-MS) in order to explore how B. brevis survived upon treatment with pyrene. It was showed that the expression of 13 proteins increased whereas 10 other decreased after pyrene-treatment. The differentially expressed proteins were identified and the results indicated that they were involved in multiple biological processes including energy metabolism, biosynthesis, transmembrane transport and oxidative stress. Overall, these findings offered a new insights into the cellular response strategy developed by B. brevis to overcome the pyrene stress.
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Affiliation(s)
- Kun Wei
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Hua Yin
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China.
| | - Hui Peng
- Department of Chemistry, Jinan University, Guangzhou 510632, Guangdong, China
| | - Zehua Liu
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Guining Lu
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Zhi Dang
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
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Changes in fatty acid composition of Stenotrophomonas maltophilia KB2 during co-metabolic degradation of monochlorophenols. World J Microbiol Biotechnol 2016; 32:198. [PMID: 27757793 PMCID: PMC5069324 DOI: 10.1007/s11274-016-2160-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/14/2016] [Indexed: 11/14/2022]
Abstract
The changes in the cellular fatty acid composition of Stenotrophomonas maltophilia KB2 during co-metabolic degradation of monochlorophenols in the presence of phenol as well as its adaptive mechanisms to these compounds were studied. It was found that bacteria were capable of degrading 4-chlorophenol (4-CP) completely in the presence of phenol, while 2-chlorophenol (2-CP) and 3-chlorophenol (3-CP) they degraded partially. The analysis of the fatty acid profiles indicated that adaptive mechanisms of bacteria depended on earlier exposure to phenol, which isomer they degraded, and on incubation time. In bacteria unexposed to phenol the permeability and structure of their membranes could be modified through the increase of hydroxylated and cyclopropane fatty acids, and straight-chain and hydroxylated fatty acids under 2-CP, 3-CP and 4-CP exposure, respectively. In the exposed cells, regardless of the isomer they degraded, the most important changes were connected with the increase of the contribution of branched fatty acid on day 4 and the content of hydroxylated fatty acids on day 7. The changes, particularly in the proportion of branched fatty acids, could be a good indicator for assessing the progress of the degradation of monochlorophenols by S. maltophilia KB2. In comparison, in phenol-degrading cells the increase of cyclopropane and straight-chain fatty acid content was established. These findings indicated the degradative potential of the tested strain towards the co-metabolic degradation of persistent chlorophenols, and extended the current knowledge about the adaptive mechanisms of these bacteria to such chemicals.
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Felczak A, Bernat P, Różalska S, Lisowska K. Quinoline biodegradation by filamentous fungus Cunninghamella elegans and adaptive modifications of the fungal membrane composition. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:8872-8880. [PMID: 26810790 PMCID: PMC4850185 DOI: 10.1007/s11356-016-6116-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
Quinoline, which belongs to N-heterocyclic compounds, occurs naturally in the environment and is used in numerous industrial processes. The structures of various chemicals, such as dyes and medicines, are based on this compound. Due to that fact, quinoline and its derivatives are widely distributed in environment and can exert toxic effects on organisms from different trophic levels. The ability of the filamentous fungus Cunninghamella elegans IM 1785/21Gp to degrade quinoline and modulate the membrane composition in response to the pollutant was studied. C. elegans IM 1785/21Gp removes quinoline with high efficiency and transforms the pollutant into two novel hydroxylated derivatives, 2-hydroxyquinoline and 3-hydroxyquinoline. Moreover, due to the disruption in the membrane stability by quinoline, C. elegans IM 1785/21Gp modulates the fatty acid composition and phospholipid profile.
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Affiliation(s)
- Aleksandra Felczak
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237, Lodz, Poland
| | - Przemysław Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237, Lodz, Poland
| | - Sylwia Różalska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237, Lodz, Poland
| | - Katarzyna Lisowska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237, Lodz, Poland.
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Nowak A, Mrozik A. Facilitation of Co-Metabolic Transformation and Degradation of Monochlorophenols by Pseudomonas sp. CF600 and Changes in Its Fatty Acid Composition. WATER, AIR, AND SOIL POLLUTION 2016; 227:83. [PMID: 26917860 PMCID: PMC4752961 DOI: 10.1007/s11270-016-2775-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/31/2016] [Indexed: 06/05/2023]
Abstract
In this study, co-metabolic degradation of monochlorophenols (2-CP, 3-CP, and 4-CP) by the Pseudomonas sp. CF600 strain in the presence of phenol, sodium benzoate, and 4-hydroxybenzoic acid as an additional carbon source as well as the survival of bacteria were investigated. Moreover, the changes in cellular fatty acid profiles of bacteria depending on co-metabolic conditions were analyzed. It was found that bacteria were capable of degrading 4-CP completely in the presence of phenol, and in the presence of all substrates, they degraded 2-CP and 3-CP partially. The highest 2-CP and 3-CP removal was observed in the presence of sodium benzoate. Bacteria exhibited three various dioxygenases depending on the type of growth substrate. It was also demonstrated that bacteria exposed to aromatic growth substrates earlier degraded monochlorophenols more effectively than unexposed cells. The analysis of fatty acid profiles of bacteria indicated the essential changes in their composition, involving alterations in fatty acid saturation, hydroxylation, and cyclopropane ring formation. The most significant change in bacteria exposed to sodium benzoate and degrading monochlophenols was the appearance of branched fatty acids. The knowledge from this study indicates that Pseudomonas sp. CF600 could be a suitable candidate for the bioaugmentation of environments contaminated with phenolic compounds.
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Affiliation(s)
- Agnieszka Nowak
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
| | - Agnieszka Mrozik
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
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Membrane fluidity-related adaptive response mechanisms of foodborne bacterial pathogens under environmental stresses. Food Res Int 2015. [DOI: 10.1016/j.foodres.2015.03.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Murínová S, Dercová K. Response mechanisms of bacterial degraders to environmental contaminants on the level of cell walls and cytoplasmic membrane. Int J Microbiol 2014; 2014:873081. [PMID: 25057269 PMCID: PMC4099092 DOI: 10.1155/2014/873081] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/12/2014] [Accepted: 05/27/2014] [Indexed: 11/18/2022] Open
Abstract
Bacterial strains living in the environment must cope with the toxic compounds originating from humans production. Surface bacterial structures, cell wall and cytoplasmic membrane, surround each bacterial cell and create selective barriers between the cell interior and the outside world. They are a first site of contact between the cell and toxic compounds. Organic pollutants are able to penetrate into cytoplasmic membrane and affect membrane physiological functions. Bacteria had to evolve adaptation mechanisms to counteract the damage originated from toxic contaminants and to prevent their accumulation in cell. This review deals with various adaptation mechanisms of bacterial cell concerning primarily the changes in cytoplasmic membrane and cell wall. Cell adaptation maintains the membrane fluidity status and ratio between bilayer/nonbilayer phospholipids as well as the efflux of toxic compounds, protein repair mechanisms, and degradation of contaminants. Low energy consumption of cell adaptation is required to provide other physiological functions. Bacteria able to survive in toxic environment could help us to clean contaminated areas when they are used in bioremediation technologies.
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Affiliation(s)
- Slavomíra Murínová
- Department of Biochemical Technology, Faculty of Chemical and Food Technology, Institute of Biotechnology and Food Science, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
- Water Research Institute, Nábrežie arm. gen. L. Svobodu 5, 812 49 Bratislava, Slovakia
| | - Katarína Dercová
- Department of Biochemical Technology, Faculty of Chemical and Food Technology, Institute of Biotechnology and Food Science, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
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Biodegradation of octyltin compounds by Cochliobolus lunatus and influence of xenobiotics on fungal fatty acid composition. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Hadibarata T, Teh ZC, Rubiyatno, Zubir MMFA, Khudhair AB, Yusoff ARM, Salim MR, Hidayat T. Identification of naphthalene metabolism by white rot fungus Pleurotus eryngii. Bioprocess Biosyst Eng 2013; 36:1455-61. [PMID: 23334282 DOI: 10.1007/s00449-013-0884-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/05/2013] [Indexed: 11/28/2022]
Abstract
The use of biomaterials or microorganisms in PAHs degradation had presented an eye-catching performance. Pleurotus eryngii is a white rot fungus, which is easily isolated from the decayed woods in the tropical rain forest, used to determine the capability to utilize naphthalene, a two-ring polycyclic aromatic hydrocarbon as source of carbon and energy. In the meantime, biotransformation of naphthalene to intermediates and other by-products during degradation was investigated in this study. Pleurotus eryngii had been incubated in liquid medium formulated with naphthalene for 14 days. The presence of metabolites of naphthalene suggests that Pleurotus eryngii begin the ring cleavage by dioxygenation on C1 and C4 position to give 1,4-naphthaquinone. 1,4-Naphthaquinone was further degraded to benzoic acid, where the proposed terepthalic acid is absent in the cultured extract. Further degradation of benzoic acid by Pleurotus eryngii shows the existence of catechol as a result of the combination of decarboxylation and hydroxylation process. Unfortunately, phthalic acid was not detected in this study. Several enzymes, including manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase are enzymes responsible for naphthalene degradation. Reduction of naphthalene and the presence of metabolites in liquid medium showed the ability of Pleurotus eryngii to utilize naphthalene as carbon source instead of a limited glucose amount.
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Affiliation(s)
- Tony Hadibarata
- Faculty of Civil Engineering, Institute of Environmental and Water Resource Management, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia,
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Zorádová-Murínová S, Dudášová H, Lukáčová L, Certík M, Silharová K, Vrana B, Dercová K. Adaptation mechanisms of bacteria during the degradation of polychlorinated biphenyls in the presence of natural and synthetic terpenes as potential degradation inducers. Appl Microbiol Biotechnol 2011; 94:1375-85. [PMID: 22159613 DOI: 10.1007/s00253-011-3763-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/13/2011] [Accepted: 11/14/2011] [Indexed: 11/29/2022]
Abstract
In this study, we examined the effect of polychlorinated biphenyls (PCBs) in the presence of natural and synthetic terpenes and biphenyl on biomass production, lipid accumulation, and membrane adaptation mechanisms of two PCB-degrading bacterial strains Pseudomonas stutzeri and Burkholderia xenovorans LB400. According to the results obtained, it could be concluded that natural terpenes, mainly those contained in ivy leaves and pine needles, decreased adaptation responses induced by PCBs in these strains. The adaptation processes under investigation included growth inhibition, lipid accumulation, composition of fatty acids, cis/trans isomerization, and membrane saturation. Growth inhibition effect decreased upon addition of these natural compounds to the medium. The amount of unsaturated fatty acids that can lead to elevated membrane fluidity increased in both strains after the addition of the two natural terpene sources. The cells adaptation changes were more prominent in the presence of carvone, limonene, and biphenyl than in the presence of natural terpenes, as indicated by growth inhibition, lipid accumulation, and cis/trans isomerization. Addition of biphenyl and carvone simultaneously with PCBs increased the trans/cis ratio of fatty acids in membrane fractions probably as a result of fluidizing effects of PCBs. This stimulation is more pronounced in the presence of PCBs as a sole carbon source. This suggests that PCBs alone have a stronger effect on bacterial membrane adaptation mechanisms than when added together with biphenyl or natural or synthetic terpenes.
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Affiliation(s)
- Slavomíra Zorádová-Murínová
- Institute of Biotechnology and Food Science, Department of Biochemical Technology, Slovak University of Technology, Faculty of Chemical and Food Technology, Bratislava, Slovakia.
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Shao S, Zhou T, McGarvey BD. Comparative metabolomic analysis of Saccharomyces cerevisiae during the degradation of patulin using gas chromatography-mass spectrometry. Appl Microbiol Biotechnol 2011; 94:789-97. [PMID: 22159606 DOI: 10.1007/s00253-011-3739-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 11/01/2011] [Accepted: 11/15/2011] [Indexed: 11/29/2022]
Abstract
A comparative metabolomic analysis was conducted on Saccharomyces cerevisiae cells with and without patulin treatment using gas chromatography-mass spectrometry-based approach. A total of 72 metabolites were detected and compared, including 16 amino acids, 29 organic acids and alcohols, 19 sugars and sugar alcohols, 2 nucleotides, and 6 miscellaneous compounds. Principle component analysis showed a clear separation of metabolome between the cells with and without patulin treatment, and most of the identified metabolites contributed to the separation. A close examination of the identified metabolites showed an increased level of most of the free amino acids, an increased level of the intermediates in the tricarboxylic acid cycle, a higher amount of glycerol, a changed fatty acid composition, and a decreased level of cysteine and glutathione in the cells with patulin treatment. This finding indicated a slower protein synthesis rate and induced oxidative stress in the cells with patulin treatment, and provided new insights into the effect of toxic chemicals on the metabolism of organisms.
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Affiliation(s)
- Suqin Shao
- Guelph Food Research Centre, Agriculture & Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9
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29
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Fonseca P, Moreno R, Rojo F. Growth of Pseudomonas putida at low temperature: global transcriptomic and proteomic analyses. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:329-339. [PMID: 23761279 DOI: 10.1111/j.1758-2229.2010.00229.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In its natural habitats (soil, water and rhizosphere), Pseudomonas putida can suffer frequent and long-term changes in temperature that affect its growth and survival. Pseudomonas putida KT2440, a well-characterized model strain, grows optimally at 30°C but can proliferate at temperatures as low as 4°C. However, little information is available on the physiological changes that occur when P. putida grows at low temperatures. To investigate this area, the transcriptome and proteome profiles of cells exponentially growing in a complex medium at 10°C were compared with those of cells exponentially growing at 30°C. Low temperature modified the expression of at least 266 genes (some 5% of the genome). Many of the genes showing differential expression were involved in energy metabolism or in the transport and binding of substrates, although genes implicated in other cellular functions were also affected. Several changes seemed directed towards neutralizing problems created by low temperature, such as increased protein misfolding, the increased stability of DNA/RNA secondary structures, reduced membrane fluidity and a reduced growth rate. The present results improve our understanding of the P. putida lifestyle at low temperature, which may be relevant for its applications in bioremediation and in promotion of plant growth.
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Affiliation(s)
- Pilar Fonseca
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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Saborido Basconcillo L, Zaheer R, Finan TM, McCarry BE. Cyclopropane fatty acyl synthase in Sinorhizobium meliloti. Microbiology (Reading) 2009; 155:373-385. [DOI: 10.1099/mic.0.022608-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclopropane fatty acyl synthases (CFA synthases) are enzymes that catalyse the addition of a methylene group acrosscisdouble bonds of monounsaturated fatty acyl chains in lipids. We have investigated the function of two putative genes,cfa1andcfa2,proposed to code for CFA synthases inSinorhizobium meliloti. Total fatty acid composition and fatty acid distributions within lipid classes for wild-type andcfa1andcfa2mutant strains grown under Pistarvation and in acidic culture conditions were obtained by GC/MS and by infusion ESI/MS/MS, respectively. For wild-type cells and thecfa1mutant, total cyclopropane fatty acids (CFAs) increased by 10 % and 15 % under Pistarvation and acidic conditions, respectively; whereas in thecfa2mutant, CFAs were less than 0.1 % of wild-type under both growth conditions. Reporter gene fusion experiments revealed thatcfa1andcfa2were expressed at similar levels in free-living cells. Thus under the conditions we examined,cfa2was required for the cyclopropanation of lipids inS. melilotiwhereas the role ofcfa1remains to be determined. Analysis of intact lipids revealed that cyclopropanation occurred oncis-11-octadecenoic acid located in either thesn-1 or thesn-2 position in phospholipids and that cyclopropanation in thesn-2 position occurred to a greater extent in phosphatidylcholines and sulfoquinovosyldiacylglycerols under acidic conditions than under Pistarvation. Thecfa2gene was also required for cyclopropanation of non-phosphorus-containing lipids. Principal components analysis revealed no differences in the cyclopropanation of four lipid classes. We concluded that cyclopropanation occurred independently of the polar head group. Neithercfa1norcfa2was required for symbiotic nitrogen fixation.
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Affiliation(s)
| | - Rahat Zaheer
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Turlough M. Finan
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Brian E. McCarry
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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Keum YS, Seo JS, Li QX, Kim JH. Comparative metabolomic analysis of Sinorhizobium sp. C4 during the degradation of phenanthrene. Appl Microbiol Biotechnol 2008; 80:863-72. [PMID: 18668240 PMCID: PMC7419452 DOI: 10.1007/s00253-008-1581-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/16/2008] [Accepted: 06/18/2008] [Indexed: 11/30/2022]
Abstract
Comparative metabolic responses of Sinorhizobium sp. C4 were investigated. Comprehensive metabolites profiles, including polar metabolites, fatty acids, and polyhydroxyalkanoates were evaluated through untargeted metabolome analyses. Intracellular metabolomes during the degradation of phenanthrene were compared with those from natural carbon sources. Principal component analysis showed a clear separation of metabolomes of phenanthrene degradation from other carbon sources. Shift to more hydrophobic fatty acid was observed from the analysis of fatty acid methyl ester. Polyhydroxyalkanoate from strain C4 was composed mainly with 3-hydroxybutyric acid and small amount of 3-hydroxypentanoic acid, while the monomeric composition was independent on carbon sources. However, the amount of polyhydroxyalkanoates during degradation of phenanthrene was 50–210% less than those from other carbon sources. Among 207 gas chromatography–mass spectrometry peaks from the polar metabolite fraction, 60% of the peaks were identified and compared. Several intermediates in tricarboxylic acid cycles and glycolysis were increased during phenanthrene degradation. Accumulation of trehalose was also evident in the phenanthrene-treated bacterium. Some amino acid, including branched amino acids, glycine, homoserine, and valine, were also increased, while more than 70% of identified metabolites were decreased during the phenanthrene metabolism. Accumulation of sulfur amino acids and nicotinic acid suggested the possible oxidative stress conditions during phenanthrene metabolism.
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Affiliation(s)
- Young Soo Keum
- Department of Agricultural Biotechnology, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
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Kallimanis A, Frillingos S, Drainas C, Koukkou AI. Taxonomic identification, phenanthrene uptake activity, and membrane lipid alterations of the PAH degrading Arthrobacter sp. strain Sphe3. Appl Microbiol Biotechnol 2007; 76:709-17. [PMID: 17583808 DOI: 10.1007/s00253-007-1036-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 05/22/2007] [Accepted: 05/23/2007] [Indexed: 11/24/2022]
Abstract
This report describes phenanthrene uptake as well as the effect of phenanthrene on the membrane phospholipid and fatty acid composition in a newly isolated bacterial strain, Sphe3, that we taxonomically identified as Arthrobacter sp. Strain Sphe3 is able to utilize phenanthrene as a carbon source at high rates and appears to internalize phenanthrene with two mechanisms: a passive diffusion when cells are grown on glucose, and an inducible active transport system when cells are grown on phenanthrene as a sole carbon source. Active transport followed Michaelis-Menten kinetics, and it was amenable to inhibition by 2,4-dinitrophenol and sodium azide. Evidence provided here indicates that apart from inducing an active PAH uptake, the presence of phenanthrene elicits significant changes in membrane fluidity.
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Affiliation(s)
- Aristeidis Kallimanis
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110, Ioannina, Greece
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Lalucat J, Bennasar A, Bosch R, García-Valdés E, Palleroni NJ. Biology of Pseudomonas stutzeri. Microbiol Mol Biol Rev 2006; 70:510-47. [PMID: 16760312 PMCID: PMC1489536 DOI: 10.1128/mmbr.00047-05] [Citation(s) in RCA: 325] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.
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Affiliation(s)
- Jorge Lalucat
- Department de Biologia, Microbiologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.
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Cellular fatty acid patterns inPseudomonas sp. CF600 during catechol and phenol degradation in media supplemented with glucose as an additional carbon source. ANN MICROBIOL 2006. [DOI: 10.1007/bf03174971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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