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Medić A, Hüttmann N, Lješević M, Risha Y, Berezovski MV, Minić Z, Karadžić I. A study of the flexibility of the carbon catabolic pathways of extremophilic P. aeruginosa san ai exposed to benzoate versus glucose as sole carbon sources by multi omics analytical platform. Microbiol Res 2022; 259:126998. [PMID: 35276454 DOI: 10.1016/j.micres.2022.126998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/17/2022] [Accepted: 02/26/2022] [Indexed: 10/19/2022]
Abstract
Polyextremophilic, hydrocarbonoclastic Pseudomonas aeruginosa san ai can survive under extreme environmental challenges in the presence of a variety of pollutants such as organic solvents and hydrocarbons, particularly aromatics, heavy metals, and high pH. To date, the metabolic plasticity of the extremophilic P. aeruginosa, has not been sufficiently studied in regard to the effect of changing carbon sources. Therefore, the present study explores the carbon metabolic pathways of polyextremophilic P. aeruginosa san ai grown on sodium benzoate versus glucose and its potential for aromatic degradation. P. aeruginosa san ai removed/metabolised nearly 430 mg/L of benzoate for 48 h, demonstrating a high capacity for aromatic degradation. Comparative functional proteomics, targeted metabolomics and genomics analytical approaches were employed to study the carbon metabolism of the P. aeruginosa san ai. Functional proteomic study of selected enzymes participating in the β-ketoadipate and the Entner-Doudoroff pathways revealed a metabolic reconfiguration induced by benzoate compared to glucose. Metabolome analysis implied the existence of both catechol and protocatechuate branches of the β-ketoadipate pathway. Enzymatic study of benzoate grown cultures confirmed the activity of the ortho- catechol branch of the β-ketoadipate pathway. Even high concentrations of benzoate did not show increased stress protein synthesis, testifying to its extremophilic nature capable of surviving in harsh conditions. This ability of Pseudomonas aeruginosa san ai to efficiently degrade benzoate can provide a wide range of use of this strain in environmental and agricultural application.
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Affiliation(s)
- Ana Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
| | - Nico Hüttmann
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Marija Lješević
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, Njegoševa 12, 11000 Belgrade, Serbia
| | - Yousef Risha
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Maxim V Berezovski
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Zoran Minić
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Ivanka Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
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Degradation of 2,4,6-Trinitrotoluene (TNT): Involvement of Protocatechuate 3,4-Dioxygenase (P34O) in Buttiauxella sp. S19-1. TOXICS 2021; 9:toxics9100231. [PMID: 34678927 PMCID: PMC8540567 DOI: 10.3390/toxics9100231] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 11/22/2022]
Abstract
Extensive use and disposal of 2,4,6-trinitrotoluene (TNT), a primary constituent of explosives, pollutes the environment and causes severe damage to human health. Complete mineralization of TNT via bacterial degradation has recently gained research interest as an effective method for the restoration of contaminated sites. Here, screening for TNT degradation by six selected bacteria revealed that Buttiauxella sp. S19-1, possesses the strongest degrading ability. Moreover, BuP34O (a gene encoding for protocatechuate 3,4-dioxygenase—P34O, a key enzyme in the β-ketoadipate pathway) was upregulated during TNT degradation. A knockout of BuP34O in S19-1 to generate S-M1 mutant strain caused a marked reduction in TNT degradation efficiency compared to S19-1. Additionally, the EM1 mutant strain (Escherichia coli DH5α transfected with BuP34O) showed higher degradation efficiency than DH5α. Gas chromatography mass spectrometry (GC-MS) analysis of TNT degradation by S19-1 revealed 4-amino-2,6-dinitrotolune (ADNT) as the intermediate metabolite of TNT. Furthermore, the recombinant protein P34O (rP34O) expressed the activity of 2.46 µmol/min·mg. Our findings present the first report on the involvement of P34O in bacterial degradation of TNT and its metabolites, suggesting that P34O could catalyze downstream reactions in the TNT degradation pathway. In addition, the TNT-degrading ability of S19-1, a Gram-negative marine-derived bacterium, presents enormous potential for restoration of TNT-contaminated seas.
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Sustainable Approaches to Remove Heavy Metals from Water. ENVIRONMENTAL AND MICROBIAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-981-15-2817-0_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Medić A, Stojanović K, Izrael-Živković L, Beškoski V, Lončarević B, Kazazić S, Karadžić I. A comprehensive study of conditions of the biodegradation of a plastic additive 2,6-di- tert-butylphenol and proteomic changes in the degrader Pseudomonas aeruginosa san ai. RSC Adv 2019; 9:23696-23710. [PMID: 35530597 PMCID: PMC9069449 DOI: 10.1039/c9ra04298a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/16/2019] [Indexed: 11/21/2022] Open
Abstract
The Pseudomonas aeruginosa san ai strain was investigated for its capability to degrade the 2,6-di-tert-butylphenol (2,6-DTBP) plastic additive, a hazardous and toxic substance for aquatic life. This investigation was performed under different parameter values: 2,6-DTBP concentration, inoculum size, pH, and temperature. The GC-MS study showed that P. aeruginosa efficiently degraded 2,6-DTBP in the pH range of 5-8 at higher temperatures. Under exposure to 2,6-DTBP concentrations of 2, 10, and 100 mg L-1, the strain degraded by 100, 100, and 85%, respectively, for 7 days. Crude enzyme preparation from the biomass of P. aeruginosa san ai showed higher efficiency in 2,6-DTBP removal than that shown by whole microbial cells. Gene encoding for the enzymes involved in the degradation of aromatic compounds in P. aeruginosa san ai was identified. To complement the genomic data, a comparative proteomic study of P. aeruginosa san ai grown on 2,6-DTBP or sunflower oil was conducted by means of nanoLC-MS/MS. The presence of aromatic substances resulted in the upregulation of aromatic ring cleavage enzymes, whose activity was confirmed by enzymatic tests; therefore, it could be concluded that 2,6-DTBP might be degraded by ortho-ring cleavage. A comparative proteomics study of P. aeruginosa san ai indicated that the core molecular responses to aromatic substances can be summarized as the upregulation of proteins responsible for amino acid metabolism with emphasized glutamate metabolism and energy production with upregulated enzymes of glyoxylate bypass. P. aeruginosa san ai has a high capacity to efficiently degrade aromatic compounds, and therefore its whole cells or enzymes could be used in the treatment of contaminated areas.
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Affiliation(s)
- Ana Medić
- Department of Chemistry, Faculty of Medicine, University of Belgrade Višegradska 26 11000 Belgrade Serbia +381113607067
| | - Ksenija Stojanović
- Faculty of Chemistry, University of Belgrade Studentski trg 12-16 11000 Belgrade Serbia
| | - Lidija Izrael-Živković
- Department of Chemistry, Faculty of Medicine, University of Belgrade Višegradska 26 11000 Belgrade Serbia +381113607067
| | - Vladimir Beškoski
- Faculty of Chemistry, University of Belgrade Studentski trg 12-16 11000 Belgrade Serbia
| | - Branka Lončarević
- Institute of Chemistry, Technology and Metallurgy, Department of Chemistry Njegoševa 12 11000 Belgrade Serbia
| | - Saša Kazazić
- Ruđer Bošković Institute Bijenička cesta 54 Zagreb Croatia
| | - Ivanka Karadžić
- Department of Chemistry, Faculty of Medicine, University of Belgrade Višegradska 26 11000 Belgrade Serbia +381113607067
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Festa S, Coppotelli BM, Madueño L, Loviso CL, Macchi M, Neme Tauil RM, Valacco MP, Morelli IS. Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches. PLoS One 2017; 12:e0184505. [PMID: 28886166 PMCID: PMC5591006 DOI: 10.1371/journal.pone.0184505] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/27/2017] [Indexed: 11/18/2022] Open
Abstract
The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31-43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).
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Affiliation(s)
- Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | - Bibiana Marina Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | - Laura Madueño
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | | | - Marianela Macchi
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | - Ricardo Martin Neme Tauil
- Centro de Estudios Químicos y Biológicos por Espectrometría de Masa- CEQUIBIEM, Facultad de Ciencias Exactas y Naturales, UBA, IQUIBICEN, CONICET
| | - María Pía Valacco
- Centro de Estudios Químicos y Biológicos por Espectrometría de Masa- CEQUIBIEM, Facultad de Ciencias Exactas y Naturales, UBA, IQUIBICEN, CONICET
| | - Irma Susana Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
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Kowalczyk A, Martin TJ, Price OR, Snape JR, van Egmond RA, Finnegan CJ, Schäfer H, Davenport RJ, Bending GD. Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 111:9-22. [PMID: 25450910 DOI: 10.1016/j.ecoenv.2014.09.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 06/04/2023]
Abstract
Society's reliance upon chemicals over the last few decades has led to their increased production, application and release into the environment. Determination of chemical persistence is crucial for risk assessment and management of chemicals. Current established OECD biodegradation guidelines enable testing of chemicals under laboratory conditions but with an incomplete consideration of factors that can impact on chemical persistence in the environment. The suite of OECD biodegradation tests do not characterise microbial inoculum and often provide little insight into pathways of degradation. The present review considers limitations with the current OECD biodegradation tests and highlights novel scientific approaches to chemical fate studies. We demonstrate how the incorporation of molecular microbial ecology methods (i.e., 'omics') may improve the underlying mechanistic understanding of biodegradation processes, and enable better extrapolation of data from laboratory based test systems to the relevant environment, which would potentially improve chemical risk assessment and decision making. We outline future challenges for relevant stakeholders to modernise OECD biodegradation tests and put the 'bio' back into biodegradation.
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Affiliation(s)
- Agnieszka Kowalczyk
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
| | - Timothy James Martin
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Oliver Richard Price
- Unilever, Safety & Environmental Assurance Centre, Colworth Science Park, Sharnbrook MK441LQ, United Kingdom
| | | | - Roger Albert van Egmond
- Unilever, Safety & Environmental Assurance Centre, Colworth Science Park, Sharnbrook MK441LQ, United Kingdom
| | - Christopher James Finnegan
- Unilever, Safety & Environmental Assurance Centre, Colworth Science Park, Sharnbrook MK441LQ, United Kingdom
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Russell James Davenport
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Gary Douglas Bending
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Wells T, Ragauskas AJ. Biotechnological opportunities with the β-ketoadipate pathway. Trends Biotechnol 2012; 30:627-37. [DOI: 10.1016/j.tibtech.2012.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 01/18/2023]
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Chambon JC, Bjerg PL, Scheutz C, Baelum J, Jakobsen R, Binning PJ. Review of reactive kinetic models describing reductive dechlorination of chlorinated ethenes in soil and groundwater. Biotechnol Bioeng 2012; 110:1-23. [DOI: 10.1002/bit.24714] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/13/2012] [Accepted: 08/16/2012] [Indexed: 11/08/2022]
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Paliwal V, Puranik S, Purohit HJ. Integrated perspective for effective bioremediation. Appl Biochem Biotechnol 2011; 166:903-24. [PMID: 22198863 DOI: 10.1007/s12010-011-9479-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 11/29/2011] [Indexed: 10/14/2022]
Abstract
Identification of factors which can influence the natural attenuation process with available microbial genetic capacities can support the bioremediation which has been viewed as the safest procedure to combat with anthropogenic compounds in ecosystems. With the advent of molecular techniques, assimilatory capacity of an ecosystem can be defined with changing community dynamics, and if required, the essential genetic potential can be met through bioaugmentation. At the same time, intensification of microbial processes with nutrient balancing, expressing and enhancing the degradative capacities, could reduce the time frame of restoration of the ecosystem. The new concept of ecosystems biology has added greatly to conceptualize the networking of the evolving microbiota of the niche that helps in effective application of bioremediation tools to manage pollutants as additional carbon source.
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Affiliation(s)
- Vasundhara Paliwal
- Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR, Nehru Marg, Nagpur 440020, India
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Qasemian L, Guiral D, Belghazi M, Ferré E, Gros R, Farnet AM. Identification of various laccases induced by anthracene and contribution to its degradation in a Mediterranean coastal pine litter. CHEMOSPHERE 2011; 84:1321-8. [PMID: 21663935 DOI: 10.1016/j.chemosphere.2011.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 05/03/2011] [Accepted: 05/07/2011] [Indexed: 05/24/2023]
Abstract
Mediterranean coastal ecosystems are known to be highly subject to natural and anthropic environmental stress. In this study, we examine the effects of anthracene as a common pollutant on the total microbial communities from a Pinus halepensis litter of a typical Mediterranean coastal site (Les Calanques, Marseille). The main objective was to identify the microbial factors leading the resilience of this ecosystem. Two questions were addressed: (i) how lignin-degrading enzymes (Laccase, Lignin-peroxidase and Mn-peroxidase) are affected by the presence of this molecule, (ii) whether the indigenous consortia are involved in its degradation in mesocosms under favorable incubation conditions (25 °C, 60% WHC) and after different time intervals (1 and 3 month(s)). We found a strong increase in laccase production in the presence of anthracene after 3 months, together with anthracene degradation (28%±5). Moreover 9,10-anthraquinone is detected as the product of anthracene oxidation after 3 months. However neither lignin-peroxidase activity nor Mn-peroxidase activity is detected. Laccase proteins directly extracted from litter were sequenced via Nano-LC-MS/MS and reveal twelve different peptide sequences induced by the presence of anthracene in the mesocoms. Our study confirms the major detoxification role of this enzymatic system and highlights the high degradation potential of fungal species inhabiting P. halepensis litter, a factor in the resilience of Mediterranean ecosystems.
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Affiliation(s)
- Leila Qasemian
- Equipe Ecologie Microbienne et Biotechnologies, UMR CNRS IRD 6116, Institut Méditerranéen d'Ecologie et de Paléoécologie, Faculté des Sciences et Techniques de St. Jérôme, Université Paul Cézanne, 13397 Marseille, France.
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