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Wang B, Zhang C, Li K, Huang J, Sun J. Induced domestication of humic reduction-denitrification coupled bacteria improved treatment of sediment: Performance, remediation effect, and metabolic mechanisms. ENVIRONMENTAL RESEARCH 2024; 251:118761. [PMID: 38518914 DOI: 10.1016/j.envres.2024.118761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
The high organic matter in river sediment primarily induces black and odorous rebound. Traditional humic-reducing bacteria demonstrate relatively single metabolic functions and restrain the remediation within complex sediment environments. In addition, Ca(NO3)2 is commonly utilized in synergistic with bioremediation to improve the reducing environment of sediments. In this study, a multifunctional bacterial community with humic reduction-denitrification coupled bacteria was domesticated by the step-feeding strategy in an anaerobic baffle reactor (ABR). The performance, remediation effect, and metabolic mechanisms were analyzed. The results indicated that humic-reducing bacteria (HRB) and denitrifying-humic-reducing bacteria (DF/HRB) have quinone-reduction and denitrification capabilities. The synergistic effect of DF/HRBs and Ca(NO3)2 was superior to HRBs and Ca(NO3)2 on the removal of total organic matter(TOM). Microbial community structure analysis revealed an enhanced relative abundance of denitrification and humic-reducing bacteria (e.g., Thauera, Pseudomonas, Sulfurospirillum, Desulfovibrio, Geobacter) in the DF/HRB, resulting in a superior synergistic effect of DF/HRBs with Ca(NO3)2. This work helps to present an innovative approach to domesticate humic-reducing bacteria suited for the remediation environment effectively. It also expands the application of humic-reducing bacteria for in-situ anaerobic remediation of river sediments.
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Affiliation(s)
- Bin Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
| | - Chao Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China; Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin, 300191, PR China
| | - Ketong Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
| | - Jianjun Huang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China
| | - Jingmei Sun
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, PR China.
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Khalife M, Stankovic D, Stankovic V, Danicka J, Rizzotto F, Costache V, Schwok AS, Gaudu P, Vidic J. Electrochemical biosensor based on NAD(P)H-dependent quinone reductase for rapid and efficient detection of vitamin K 3. Food Chem 2024; 433:137316. [PMID: 37690134 DOI: 10.1016/j.foodchem.2023.137316] [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: 05/12/2023] [Revised: 07/16/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Vitamin K refers to a group of vitamins that play an important role in blood coagulation and regulation of bone and vascular metabolism. However, vitamin K3 may give severe side effects in animal and humans when improperly added to food and feed due to its toxicity. Here, an electrochemical biosensor, based on the YaiB NADPH-dependent quinone reductase from Lactococcus lactis (YaiB), was developed to achieve rapid and redox probe-free detection of vitamin K3. First, the ability of the carbon electrode to distinguish between 1,4-benzoquinone and hydroquinone was demonstrated. Then, we engineered YaiB to work as a bioreceptor immobilized at the electrode and its sensitivity and specificity to reduce vitamin K3 were demonstrated. Finally, to demonstrate the practical potential of the biosensor, we tested it directly in spiked milk samples, achieving 15-minute quantification of the vitamin K3. The limit of detection was 0.87 µM and 4.1 µM in buffer and milk, respectively.
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Affiliation(s)
- Majd Khalife
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy en Josas, France
| | - Dalibor Stankovic
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Vesna Stankovic
- Institute of Chemistry, Technology and Metallurgy-National Institute of the Republic of Serbia, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
| | - Julia Danicka
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy en Josas, France; Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Francesco Rizzotto
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy en Josas, France
| | - Vlad Costache
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy en Josas, France; MIMA2 Imaging Core Facility, INRAE, Microscopie et Imagerie des Microorganismes, Animaux et Aliments, Jouy en Josas, France
| | | | - Philippe Gaudu
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy en Josas, France
| | - Jasmina Vidic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy en Josas, France.
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3
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Quinones: More Than Electron Shuttles. Res Microbiol 2022; 173:103953. [DOI: 10.1016/j.resmic.2022.103953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 11/21/2022]
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Sharma V, Kumar R, Sharma VK, Yadav AK, Tiirola M, Sharma PK. Expression, purification, characterization and in silico analysis of newly isolated hydrocarbon degrading bleomycin resistance dioxygenase. Mol Biol Rep 2019; 47:533-544. [PMID: 31724125 DOI: 10.1007/s11033-019-05159-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/23/2019] [Indexed: 10/25/2022]
Abstract
In the present investigation, we report cloning, expression, purification and characterization of a novel Bleomycin Resistance Dioxygenase (BRPD). His-tagged fusion protein was purified to homogeneity using Ni-NTA affinity chromatography, yielding 1.2 mg of BRPD with specific activity of 6.25 U mg-1 from 600 ml of E. coli culture. Purified enzyme was a dimer with molecular weight ~ 26 kDa in SDS-PAGE and ~ 73 kDa in native PAGE analysis. The protein catalyzed breakdown of hydrocarbon substrates, including catechol and hydroquinone, in the presence of metal ions, as characterized via spectrophotometric analysis of the enzymatic reactions. Bleomycin binding was proven using the EMSA gel retardation assay, and the putative bleomycin binding site was further determined by in silico analysis. Molecular dynamic simulations revealed that BRPD attains octahedral configuration in the presence of Fe2+ ion, forming six co-ordinate complexes to degrade hydroquinone-like molecules. In contrary, in the presence of Zn2+ ion BRPD adopts tetrahedral configuration, which enables degradation of catechol-like molecules.
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Affiliation(s)
- Vinay Sharma
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Pb, India
| | - Rajender Kumar
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
| | | | | | - Marja Tiirola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014, Jyvaskyla, Finland
| | - Pushpender Kumar Sharma
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Pb, India.
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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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Żur J, Wojcieszyńska D, Hupert-Kocurek K, Marchlewicz A, Guzik U. Paracetamol - toxicity and microbial utilization. Pseudomonas moorei KB4 as a case study for exploring degradation pathway. CHEMOSPHERE 2018; 206:192-202. [PMID: 29751245 DOI: 10.1016/j.chemosphere.2018.04.179] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Paracetamol, a widely used analgesic and antipyretic drug, is currently one of the most emerging pollutants worldwide. Besides its wide prevalence in the literature only several bacterial strains able to degrade this compound have been described. In this study, we isolated six new bacterial strains able to remove paracetamol. The isolated strains were identified as the members of Pseudomonas, Bacillus, Acinetobacter and Sphingomonas genera and characterized phenotypically and biochemically using standard methods. From the isolated strains, Pseudomonas moorei KB4 was able to utilize 50 mg L-1 of paracetamol. As the main degradation products, p-aminophenol and hydroquinone were identified. Based on the measurements of specific activity of acyl amidohydrolase, deaminase and hydroquinone 1,2-dioxygenase and the results of liquid chromatography analyses, we proposed a mechanism of paracetamol degradation by KB4 strain under co-metabolic conditions with glucose. Additionally, toxicity bioassays and the influence of various environmental factors, including pH, temperature, heavy metals at no-observed-effective-concentrations, and the presence of aromatic compounds on the efficiency and mechanism of paracetamol degradation by KB4 strain were determined. This comprehensive study about paracetamol biodegradation will be helpful in designing a treatment systems of wastewaters contaminated with paracetamol.
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Affiliation(s)
- Joanna Żur
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Danuta Wojcieszyńska
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Katarzyna Hupert-Kocurek
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Ariel Marchlewicz
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Urszula Guzik
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
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Solioz M. Copper Homeostasis in Gram-Positive Bacteria. SPRINGERBRIEFS IN MOLECULAR SCIENCE 2018. [DOI: 10.1007/978-3-319-94439-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Almeida CMR, Oliveira T, Reis I, Gomes CR, Mucha AP. Bacterial community dynamic associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt-marsh sediments. MARINE ENVIRONMENTAL RESEARCH 2017; 132:68-78. [PMID: 29122290 DOI: 10.1016/j.marenvres.2017.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 10/09/2017] [Accepted: 10/13/2017] [Indexed: 05/12/2023]
Abstract
Autochthonous bioaugmentation for metal phytoremediation is still little explored, particularly its application to estuarine salt marshes, but results obtained so far are promising. Nevertheless, understanding the behaviour of the microbial communities in the process of bioaugmentation and their role in improving metal phytoremediation is very important to fully validate the application of this biological technology. This study aimed to characterize the bacterial community dynamic associated with the application of autochthonous bioaugmentation in an experimentation which showed that Phragmites australis rhizosphere microorganisms could increase this salt marsh plant potential to phytoremediate Cu contaminated sediments. Bacterial communities present in the autochthonous microbial consortium resistant to Cu added to the medium and in the sediment at the beginning and at the end of the experiment were characterized by ARISA. Complementarily, the consortium and the sediment used for its production were characterized by next generation sequencing using the pyrosequencing platform 454. The microbial consortium resistant to Cu obtained from non-vegetated sediment was dominated by the genus Lactococcus (46%), Raoultella (25%), Bacillus (12%) and Acinetobacter (11%), whereas the one obtained form rhizosediment was dominated by the genus Gluconacetobacter (77%), Bacillus (17%) and Dyella (3%). Results clearly showed that, after two months of experiment, Cu caused a shift in the bacterial community structure of sediments, an effect that was observed either with or without addition of the metal resistant microbial consortium. Therefore, bioaugmentation application improved the process of phytoremediation (metal translocation by the plant was increased) without inducing long term changes in the bacterial community structure of the sediments. So, phytoremediation combined with autochthonous bioaugmentation can be a suitable technology for the recovery of estuarine areas, contributing for an efficient risk management strategy of these coastal zones.
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Affiliation(s)
- C Marisa R Almeida
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Tânia Oliveira
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Izabela Reis
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Carlos R Gomes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Ana P Mucha
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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Mechanism of Attenuation of Uranyl Toxicity by Glutathione in Lactococcus lactis. Appl Environ Microbiol 2016; 82:3563-3571. [PMID: 27060118 DOI: 10.1128/aem.00538-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Both prokaryotic and eukaryotic organisms possess mechanisms for the detoxification of heavy metals, and these mechanisms are found among distantly related species. We investigated the role of intracellular glutathione (GSH), which, in a large number of taxa, plays a role in protection against the toxicity of common heavy metals. Anaerobically grown Lactococcus lactis containing an inducible GSH synthesis pathway was used as a model organism. Its physiological condition allowed study of putative GSH-dependent uranyl detoxification mechanisms without interference from additional reactive oxygen species. By microcalorimetric measurements of metabolic heat during cultivation, it was shown that intracellular GSH attenuates the toxicity of uranium at a concentration in the range of 10 to 150 μM. In this concentration range, no effect was observed with copper, which was used as a reference for redox metal toxicity. At higher copper concentrations, GSH aggravated metal toxicity. Isothermal titration calorimetry revealed the endothermic binding of U(VI) to the carboxyl group(s) of GSH rather than to the reducing thiol group involved in copper interactions. The data indicate that the primary detoxifying mechanism is the intracellular sequestration of carboxyl-coordinated U(VI) into an insoluble complex with GSH. The opposite effects on uranyl and on copper toxicity can be related to the difference in coordination chemistry of the respective metal-GSH complexes, which cause distinct growth phase-specific effects on enzyme-metal interactions. IMPORTANCE Understanding microbial metal resistance is of particular importance for bioremediation, where microorganisms are employed for the removal of heavy metals from the environment. This strategy is increasingly being considered for uranium. However, little is known about the molecular mechanisms of uranyl detoxification. Existing studies of different taxa show little systematics but hint at a role of glutathione (GSH). Previous work could not unequivocally demonstrate a GSH function in decreasing the presumed uranyl-induced oxidative stress, nor could a redox-independent detoxifying action of GSH be identified. Combining metabolic calorimetry with cell number-based assays and genetics analysis enables a novel and general approach to quantify toxicity and relate it to molecular mechanisms. The results show that GSH-expressing microorganisms appear advantageous for uranyl bioremediation.
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