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Parveen S, Akhtar N, E-Kobon T, Burchmore R, Hussain AI, Akhtar K. Biodesulfurization of organosulfur compounds by a trehalose biosurfactant producing Gordonia sp. isolated from crude oil contaminated soil. World J Microbiol Biotechnol 2024; 40:103. [PMID: 38372854 DOI: 10.1007/s11274-024-03899-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
Certain factors hinder the commercialization of biodesulfurization process, including low substrate-specificity of the currently reported desulfurizing bacteria and restricted mass transfer of organic-sulfur compounds in biphasic systems. These obstacles must be addressed to clean organic-sulfur rich petro-fuels that pose serious environmental and health challenges. In current study, a dibenzothiophene desulfurizing strain, Gordonia rubripertincta W3S5 (source: oil contaminated soil) was systematically evaluated for its potential to remove sulfur from individual compounds and mixture of organic-sulfur compounds. Metabolic and genetic analyses confirmed that strain W3S5 desulfurized dibenzothiophene to 2-hydroxybiphenyl, suggesting that it follows the sulfur specific 4 S pathway. Furthermore, this strain demonstrated the ability to produce trehalose biosurfactants (with an EI24 of 53%) in the presence of dibenzothiophene, as confirmed by TLC and FTIR analyses. Various genome annotation tools, such as ClassicRAST, BlastKOALA, BV-BRC, and NCBI-PGAP, predicted the presence of otsA, otsB, treY, treZ, treP, and Trehalose-monomycolate lipid synthesis genes in the genomic pool of strain W3S5, confirming the existence of the OtsAB, TreYZ, and TreP pathways. Overall, these results underscore the potential of strain W3S5 as a valuable candidate for enhancing desulfurization efficiency and addressing the mass transfer challenges essential for achieving a scaled-up scenario.
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Affiliation(s)
- Sana Parveen
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad, 38000, Pakistan
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad, 38000, Pakistan.
| | - Teerasak E-Kobon
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Rd, Lat Yao, Chatuchak, Bangkok, 10900, Thailand
| | - Richard Burchmore
- School of Infection & Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Abdullah Ijaz Hussain
- Central Hi-Tech Lab, Department of Chemistry, Government College University, Faisalabad, 38000, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad, 38000, Pakistan
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Lobo CB, Correa Deza MA, Arnau GV, Ferrero MA, Juárez Tomás MS. Dibenzothiophene removal by environmental bacteria with differential accumulation of intracellular inorganic polyphosphate. BIORESOURCE TECHNOLOGY 2023; 387:129582. [PMID: 37506945 DOI: 10.1016/j.biortech.2023.129582] [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: 06/01/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Dibenzothiophene (DBT), which belongs to the group of polycyclic aromatic heterocycles of sulfur, is a model substance to study the removal of sulfur compounds from oil due to its recalcitrance to traditional and specific removal processes. The aim of this work was to evaluate DBT bioremoval by environmental bacteria and its relationship with polyphosphate (polyP) accumulation, cell surface characteristics and bioemulsifying activity. Pseudomonas sp. P26 achieved the highest DBT removal percentage (48%) after 7 days of incubation. Moreover, positive correlations were estimated between DBT removal and bioemulsifying activity and biofilm formation. A strain-dependent relationship between the content of intracellular polyP and the presence of DBT in the culture medium was also demonstrated. The study of these bacterial characteristics, which could promote DBT transformation, is a first approach to select DBT-removing bacteria, in order to develop bioformulations that are able to contribute to desulfurization processes of petroleum-derived pollutants in the future.
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Affiliation(s)
- Constanza Belén Lobo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - María Alejandra Correa Deza
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - Gonzalo Víctor Arnau
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - Marcela Alejandra Ferrero
- YPF Tecnología (Y-TEC), Av. del Petróleo Argentino (RP10) S/N entre 129 y 143 (1923), Berisso, Buenos Aires, Argentina.
| | - María Silvina Juárez Tomás
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
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Sadare OO, Daramola MO. Bio-catalytic degradation of dibenzothiophene (DBT) in petroleum distillate (diesel) by Pseudomonas spp. Sci Rep 2023; 13:6020. [PMID: 37055435 PMCID: PMC10102322 DOI: 10.1038/s41598-023-31951-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/20/2023] [Indexed: 04/15/2023] Open
Abstract
Biodesulfurization (BDS) was employed in this study to degrade dibenzothiophene (DBT) which accounts for 70% of the sulfur compounds in diesel using a synthetic and typical South African diesel in the aqueous and biphasic medium. Two Pseudomonas sp. bacteria namely Pseudomonas aeruginosa and Pseudomonas putida were used as biocatalysts. The desulfurization pathways of DBT by the two bacteria were determined by gas chromatography (GC)/mass spectrometry (MS) and High-Performance Liquid Chromatography (HPLC). Both organisms were found to produce 2-hydroxy biphenyl, the desulfurized product of DBT. Results showed BDS performance of 67.53% and 50.02%, by Pseudomonas aeruginosa and Pseudomonas putida, respectively for 500 ppm initial DBT concentration. In order to study the desulfurization of diesel oils obtained from an oil refinery, resting cells studies by Pseudomonas aeruginosa were carried out which showed a decrease of about 30% and 70.54% DBT removal for 5200 ppm in hydrodesulfurization (HDS) feed diesel and 120 ppm in HDS outlet diesel, respectively. Pseudomonas aeruginosa and Pseudomonas putida selectively degraded DBT to form 2-HBP. Application of these bacteria for the desulfurization of diesel showed promising potential for decreasing the sulfur content of South African diesel oil.
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Affiliation(s)
- Olawumi Oluwafolakemi Sadare
- Department of Chemical Engineering, Faculty of Engineering, Built Environment and Information Technology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa.
| | - Michael Olawale Daramola
- Department of Chemical Engineering, Faculty of Engineering, Built Environment and Information Technology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa.
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Comparative Genomic Analysis of the Hydrocarbon-Oxidizing Dibenzothiophene-Desulfurizing Gordonia Strains. Microorganisms 2022; 11:microorganisms11010004. [PMID: 36677296 PMCID: PMC9861168 DOI: 10.3390/microorganisms11010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
A number of actinobacteria of the genus Gordonia are able to use dibenzothiophene (DBT) and its derivatives as the only source of sulfur, which makes them promising agents for the process of oil biodesulfurization. Actinobacteria assimilate sulfur from condensed thiophenes without breaking the carbon-carbon bonds, using the 4S pathway encoded by the dszABC operon-like structure. The genome of the new dibenzothiophene-degrading hydrocarbon-oxidizing bacterial strain Gordonia amicalis 6-1 was completely sequenced and the genes potentially involved in the pathways of DBT desulfurization, oxidation of alkanes and aromatic compounds, as well as in the osmoprotectant metabolism in strain 6-1 and other members of the genus Gordonia, were analyzed. The genome of G. amicalis strain 6-1 consists of a 5,105,798-bp circular chromosome (67.3% GC content) and an 86,621-bp circular plasmid, pCP86 (65.4% GC content). This paper presents a comparative bioinformatic analysis of complete genomes of strain 6-1 and dibenzothiophene-degrading Gordonia strains 1D and 135 that do not have the dsz operon. The assumption is made about the participation in this process of the region containing the sfnB gene. Genomic analysis supported the results of phenomenological studies of Gordonia strains and the possibility of their application in the bioremediation of oil-contaminated environments and in the purification of oil equipment from oil and asphalt-resin-paraffin deposits.
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Glekas PD, Martzoukou O, Mastrodima ME, Zarkadoulas E, Kanakoglou DS, Kekos D, Pachnos M, Mavridis G, Mamma D, Hatzinikolaou DG. Deciphering the biodesulfurization potential of two novel Rhodococcus isolates from a unique Greek environment. AIMS Microbiol 2022; 8:484-506. [PMID: 36694580 PMCID: PMC9834085 DOI: 10.3934/microbiol.2022032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/10/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Sustainable biodesulfurization (BDS) processes require the use of microbial biocatalysts that display high activity against the recalcitrant heterocyclic sulfur compounds and can simultaneously withstand the harsh conditions of contact with petroleum products, inherent to any industrial biphasic BDS system. In this framework, the functional microbial BDS-related diversity in a naturally oil-exposed ecosystem, was examined through a 4,6-dimethyl-dibenzothiophene based enrichment process. Two new Rhodococcus sp. strains were isolated, which during a medium optimization process revealed a significantly enhanced BDS activity profile when compared to the model strain R. qingshengii IGTS8. In biocatalyst stability studies conducted in biphasic mode using partially hydrodesulfurized diesel under various process conditions, the new strains also presented an enhanced stability phenotype. In these studies, it was also demonstrated for all strains, that the BDS activity losses were decoupled from the overall cells' viability, in addition to the fact that the use of whole-broth biocatalyst positively affected BDS performance.
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Affiliation(s)
- Panayiotis D. Glekas
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Olga Martzoukou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Maria-Eleni Mastrodima
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Efstathios Zarkadoulas
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Dimitrios S. Kanakoglou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Dimitris Kekos
- Biotechnology Laboratory, Sector of Synthesis and Development of Industrial Processes (IV), School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Michalis Pachnos
- Division of European Affairs, Motor Oil Hellas, 15121 Marousi, Athens, Greece
| | - George Mavridis
- Division of European Affairs, Motor Oil Hellas, 15121 Marousi, Athens, Greece
| | - Diomi Mamma
- Biotechnology Laboratory, Sector of Synthesis and Development of Industrial Processes (IV), School of Chemical Engineering, National Technical University of Athens, Athens, Greece,* Correspondence:
| | - Dimitris G. Hatzinikolaou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece,* Correspondence: ; Tel: +306932782004
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Hokmabadi M, Khosravinia S, Mahdavi MA, Gheshlaghi R. Enhancing the biodesulphurization capacity of Rhodococcus sp. FUM94 in a biphasic system through optimization of operational factors. J Appl Microbiol 2022; 132:3461-3475. [PMID: 34995396 DOI: 10.1111/jam.15442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/13/2021] [Accepted: 01/03/2022] [Indexed: 11/28/2022]
Abstract
The biodesulfurization activity of bacteria through the 4S pathway in aqueous-oil emulsions is affected by various operational factors. These factors also demonstrate interacting effects that influence the potential for field applications of biodesulfurization technology and can solely be deciphered through multi-variable experiments. In this study, the effects of the influential factors and their interactions on the desulfurizing activity of a newly identified desulfurizing bacterium, Rhodococcus sp, FUM94 were quantitatively investigated. The capacity improvement achieved through optimized values obtained in this study is significant due to its simple implementation to large scale processes. This is the most simple and the most cost-effective way to scale-up a biodesulfurization process.Using response surface methodology (RSM). Optimum values of the factors were identified with the objective of maximizing biodesulfurization activity. Results revealed that the desulfurization activity of the biocatalyst increased from 0.323 ± 0.072 to 46.57 ± 4.556 mmol 2-Hydroxybiphenyl (kg dry cell weight)-1 h-1 at the optimized conditions of 6 h reaction time, 2 g.L-1 biocatalyst concentration, 0.54 mM (100 ppm) dibenzothiophene (DBT) concentration (sulfur source), and 25% oil phase fraction. Desirability analysis proved that the selected conditions are the most desirable combination of factors (desirability value = 0.896) to achieve the highest biodesulfurization activity of the biocatalyst. A comparison between the biodesulfurization capacity achieved in this study and the capacities reported in similar studies published in the past two decades revealed that biodesulfurization under optimized operational conditions outperforms previously proposed techniques.
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Affiliation(s)
- Mahsa Hokmabadi
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Somayeh Khosravinia
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahmood A Mahdavi
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Reza Gheshlaghi
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
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7
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Efficient biodesulfurization of diesel oil by Gordonia sp. SC-10 with highly hydrophobic cell surfaces. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Basik AA, Sanglier JJ, Yeo CT, Sudesh K. Microbial Degradation of Rubber: Actinobacteria. Polymers (Basel) 2021; 13:polym13121989. [PMID: 34204568 PMCID: PMC8235351 DOI: 10.3390/polym13121989] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/25/2023] Open
Abstract
Rubber is an essential part of our daily lives with thousands of rubber-based products being made and used. Natural rubber undergoes chemical processes and structural modifications, while synthetic rubber, mainly synthetized from petroleum by-products are difficult to degrade safely and sustainably. The most prominent group of biological rubber degraders are Actinobacteria. Rubber degrading Actinobacteria contain rubber degrading genes or rubber oxygenase known as latex clearing protein (lcp). Rubber is a polymer consisting of isoprene, each containing one double bond. The degradation of rubber first takes place when lcp enzyme cleaves the isoprene double bond, breaking them down into the sole carbon and energy source to be utilized by the bacteria. Actinobacteria grow in diverse environments, and lcp gene containing strains have been detected from various sources including soil, water, human, animal, and plant samples. This review entails the occurrence, physiology, biochemistry, and molecular characteristics of Actinobacteria with respect to its rubber degrading ability, and discusses possible technological applications based on the activity of Actinobacteria for treating rubber waste in a more environmentally responsible manner.
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Affiliation(s)
- Ann Anni Basik
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Jean-Jacques Sanglier
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Chia Tiong Yeo
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Correspondence: ; Tel.: +60-4-6534367; Fax: +60-4-6565125
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Parveen S, Akhtar N, Akram J. Genomic analysis provides insights into the Gordonia sp. W3S5 taxonomy and sulfur metabolism-related genes. 3 Biotech 2021; 11:300. [PMID: 34194893 DOI: 10.1007/s13205-021-02850-4] [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: 10/13/2020] [Accepted: 05/17/2021] [Indexed: 10/21/2022] Open
Abstract
The Gordonia sp. W3S5, isolated from oil-polluted soil samples can remove sulfur from a variety of symmetric and asymmetric thiophenic compounds and diesel oil. Its draft genome sequence was comprised of 49 contigs, total genome size 4.86 Mb, and a G + C content of 67.50%. According to the current bacterial taxonomy procedures (16S rRNA gene sequence and overall genome-related index), the W3S5 was affiliated to Gordonia rubripertincta. Rapid Annotation using Subsystem Technology (ClassicRAST) server revealed that the W3S5 contains 4435 coding sequences, 404 subsystems and 60 sulfur metabolism genes. The RAST comparative genomic analysis showed that the genes connected with organic sulfur metabolism are majorly related to ssu and dszABC operons. Moreover, the comparison of orthologous gene clusters using OrthoVenn2 web server revealed a total of 4869 clusters, 2685 core orthologs, 632 shared orthologs and 112 unique ortholog clusters among the W3S5 and other type strains of Gordonia. This is the first report describing genome-based characterization of a Gordonia rubripertincta strain desulfurizing thiophenic compounds and diesel oil. The desulfurization potential of Gordonia rubripertincta W3S5 and genomic analyses revealed it as a valuable biocatalyst for process development to desulfurize a broad range of thiophenic sulfur-containing compounds, which are a major component of organic sulfur in petroleum oil. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02850-4.
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Stylianou M, Vyrides I, Agapiou A. Oil biodesulfurization: A review of applied analytical techniques. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1171:122602. [PMID: 33744596 DOI: 10.1016/j.jchromb.2021.122602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 12/26/2022]
Abstract
The wide use of fossil fuels and their associated environmental concerns, highlighted the importance of affordable and clean energy (goal 7), as adopted by the Sustainable Development Goals of the United Nations for 2030. For years now, the detection of sulfur components in liquid fuels is performed mainly for environmental and health purposes in compliance with the respective legislations. Towards this, the aerobic and anaerobic biodesulfurization (BDS) process, which entails the use of microorganisms to limit the sulfur concentration is followed. To ensure effective BDS, several traditional analytical methods are utilized, although they require bench-top, bulky, costly, and time-consuming instruments along with skilled personnel. The currently employed analytical methods are mostly chromatographic techniques (e.g. liquid and gas) coupled with various detectors. To start with, high-performance liquid chromatography with ultraviolet detector (HPLC-UV), as well as electrospray ionization-LC-mass spectrometry (ESI-LC-MS) were mostly reported. Additionally, many detectors were coupled to gas chromatography (CG) including atomic emission detector (GC-AED), flame ionization detector (GC-FID), flame photometric detector (GC-FPD), sulfur fluorescence detector (GC-SFD), mass selective detector (GC-MS), etc. The solid-phase microextraction (SPME) technique provides extra capabilities when added to the separation techniques. Towards the continuous interest in oil supercomplex synthesis, other atmospheric and surface desorption ionization techniques, as well as the multidimensional 2D chromatographic systems (GC × GC and LC × LC) were also investigated, due to their unsurpassed resolution power. The current review ends with final remarks per applied methodology and the necessity to respect and protect the human environment and life.
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Affiliation(s)
- Marinos Stylianou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Ioannis Vyrides
- Department of Chemical Engineering, Cyprus University of Technology, 57 Anexartisias Str., P.O. BOX 50329, 3603 Limassol, Cyprus
| | - Agapios Agapiou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus.
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Delegan Y, Kocharovskaya Y, Frantsuzova E, Streletskii R, Vetrova A. Characterization and genomic analysis of Gordonia alkanivorans 135, a promising dibenzothiophene-degrading strain. ACTA ACUST UNITED AC 2021; 29:e00591. [PMID: 33532248 PMCID: PMC7823215 DOI: 10.1016/j.btre.2021.e00591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/23/2020] [Accepted: 01/11/2021] [Indexed: 11/11/2022]
Abstract
Strain 135 is first dibenzothiophene-degrading Gordonia with genome fully assembled. This is the first strain of Gordonia absorbing thiophene sulfur without dsz genes. The strain utilized 45.26 % of dibenzothiophene within 150 h of growth at 26 °C.
Sulfur is the third most abundant element in crude oil. Up to 70 % of sulfur in petroleum is found in the form of dibenzothiophene (DBT) and substituted DBTs. The aim of this work was to study the physiological, biochemical and genetical characteristics of Gordonia alkanivorans 135 capable of using DBT as the sole source of sulfur. The genome of G. alkanivorans 135 consists of a 5,039,827 bp chromosome and a 164,963 bp circular plasmid. We found the absence of dsz operon present in most DBT degrading bacteria, but discovered other genes that are presumably involved in DBT utilization by G. alkanivorans 135. The strain utilized 45.26 % of DBT within 150 h of growth at 26 °C. This is the first strain of Gordonia capable of absorbing thiophene sulfur without the aid of the dsz genes.
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Affiliation(s)
- Yanina Delegan
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russian Federation
| | - Yulia Kocharovskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russian Federation.,The Federal State Budget Educational Institution of Higher Education Pushchino State Institute of Natural Science, Pushchino, Moscow Region, 142290, Russian Federation
| | - Ekaterina Frantsuzova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russian Federation.,The Federal State Budget Educational Institution of Higher Education Pushchino State Institute of Natural Science, Pushchino, Moscow Region, 142290, Russian Federation
| | - Rostislav Streletskii
- Faculty of Soil Science, Laboratory of Ecological Soil Science, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Anna Vetrova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russian Federation
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12
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Nassar HN, Abu Amr SS, El-Gendy NS. Biodesulfurization of refractory sulfur compounds in petro-diesel by a novel hydrocarbon tolerable strain Paenibacillus glucanolyticus HN4. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:8102-8116. [PMID: 33048293 DOI: 10.1007/s11356-020-11090-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
One of the main precursors of air pollution and acid rains is the presence of the recalcitrant thiophenic compounds, for example dibenzothiophene (DBT) and its derivatives in transportation fuels. In an attempt to achieve the worldwide regulations of ultra-low sulfur transportation fuels without affecting its hydrocarbon skeleton, a biphasic medium containing 100 mg/L DBT dissolved in n-hexadecane (1/4 oil/water v/v) used for enrichment and isolation of selective biodesulfurizing bacterium from an oil-polluted sediment sample collected from Egyptian Red Sea shoreline. The isolated bacterium is facultative anaerobe, motile, spore-former, and mesophile. It is genetically identified as Paenibacillus glucanolyticus strain HN4 (NCBI Gene Bank Accession No. MT645230). HN4 desulfurized DBT as a model of the recalcitrant thiophenic compounds without affecting its hydrocarbon skeleton via the 4S-pathway producing 2-hydroxybiphenyl (2-HBP) as a dead end product. HN4 substantiated to be a hydrocarbon tolerant, biosurfactants(s) producer, and endorsed unique enzymatic system capable of desulfurizing broad range of thiophenic compounds and expressed an efficient desulfurization activity against the recalcitrant alkylated DBTs. As far our knowledge, it is the first reported BDS study using P. glucanolyticus. Statistical optimization based on One-Factor-At-A-Time (OFAT) technique and response surface methodology (RSM) applied for elucidation of mathematical model correlations describing and optimizing the effect of different physicochemical parameters on batch biphasic BDS process. That illustrated an approximate increase in BDS efficiency by 1.34 fold and recorded 94% sulfur removal in biphasic batch process at optimum operation conditions of 120 h, 0.14 wt% S-content model oil (DBT dissolved in n-hexadecane), 33.5 °C, pH7 and 1/1 oil/water phase ratio, and 147 rpm. Resting cells of HN4 in a biphasic reactor (1/1 v/v) decreased the sulfur content of a refractory thiophenic model oil (thiophene, benzothiophene, DBT, and alkylated DBT dissolved in n-hexadecane) from 0.14 to 0.027 wt%, and petro-diesel from 0.2 to 0.04 wt%, within 120 h, keeping the calorific value of the treated fuel intact. Consequently, that novel strain could be recommended as a promising candidate for BDS as complementary to hydrodesulfurization process in oil refinery.
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Affiliation(s)
- Hussein N Nassar
- Petroleum Biotechnology Lab., Department of Process Design and Development, Egyptian Petroleum Research Institute (EPRI), Nasr City, Cairo, 11727, Egypt
- Department of Microbiology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October City, Giza, 12566, Egypt
- Nanobiotechnology Program, Faculty of Nanotechnology for Postgraduate Studies, Cairo University, Sheikh Zayed Branch Campus, Sheikh Zayed City, Giza, 12588, Egypt
| | - Salem S Abu Amr
- Faculty of Engineering, Karabuk University, Demir Campus, 78050 Karabuk, Turkey
| | - Nour Sh El-Gendy
- Petroleum Biotechnology Lab., Department of Process Design and Development, Egyptian Petroleum Research Institute (EPRI), Nasr City, Cairo, 11727, Egypt.
- Nanobiotechnology Program, Faculty of Nanotechnology for Postgraduate Studies, Cairo University, Sheikh Zayed Branch Campus, Sheikh Zayed City, Giza, 12588, Egypt.
- Center of Excellence, October University for Modern Sciences and Arts (MSA), 6th of October City, Giza, 12566, Egypt.
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13
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Ung KL, Kremer L, Blaise M. Structural analysis of the N-acetyltransferase Eis1 from Mycobacterium abscessus reveals the molecular determinants of its incapacity to modify aminoglycosides. Proteins 2021; 89:94-106. [PMID: 32860271 DOI: 10.1002/prot.25997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/30/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
Enhanced intracellular survival (Eis) proteins belonging to the superfamily of the GCN5-related N-acetyltransferases play important functions in mycobacterial pathogenesis. In Mycobacterium tuberculosis, Eis enhances the intracellular survival of the bacilli in macrophages by modulating the host immune response and is capable to chemically modify and inactivate aminoglycosides. In nontuberculous mycobacteria (NTM), Eis shares similar functions. However, Mycobacterium abscessus, a multidrug resistant NTM, possesses two functionally distinct Eis homologues, Eis1Mab and Eis2Mab . While Eis2Mab participates in virulence and aminoglycosides resistance, this is not the case for Eis1Mab, whose exact biological function remains to be determined. Herein, we show that overexpression of Eis1Mab in M. abscessus fails to induce resistance to aminoglycosides. To clarify why Eis1Mab is unable to modify this class of antibiotics, we solved its crystal structure bound to its cofactor, acetyl-CoA. The structure revealed that Eis1Mab has a typical homohexameric Eis-like organization. The structural analysis supported by biochemical approaches demonstrated that while Eis1Mab can acetylate small substrates, its active site is too narrow to accommodate aminoglycosides. Comparison with other Eis structures showed that an extended loop between strands 9 and 10 is blocking the access of large substrates to the active site and movement of helices 4 and 5 reduces the volume of the substrate-binding pocket to these compounds in Eis1Mab . Overall, this study underscores the molecular determinants explaining functional differences between Eis1Mab and Eis2Mab, especially those inherent to their capacity to modify aminoglycosides.
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Affiliation(s)
- Kien Lam Ung
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR, Montpellier, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR, Montpellier, France.,INSERM, IRIM, Montpellier, France
| | - Mickaël Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR, Montpellier, France
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14
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Kotelnikov VI, Saryglar CA, Chysyma RB. Microorganisms in Coal Desulfurization (Review). APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820050105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Parveen S, Akhtar N, Ghauri MA, Akhtar K. Conventional genetic manipulation of desulfurizing bacteria and prospects of using CRISPR-Cas systems for enhanced desulfurization activity. Crit Rev Microbiol 2020; 46:300-320. [PMID: 32530374 DOI: 10.1080/1040841x.2020.1772195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Highly active and stable biocatalysts are the prerequisite for industrial scale application of the biodesulfurization process. Scientists are making efforts for increasing the desulfurizing activity of native strains by employing various genetic engineering approaches. Nevertheless, the achieved desulfurization rate is lower than the industrial requirements. Thus, there is a dire need to use efficient genetic tools for precise genome editing of desulfurizing bacteria for enhanced efficiency. In comparison to the previously used genetic engineering tools the newly developed CRISPR-Cas is a more efficient and simple genetic tool that has been successfully applied for targeted genome modification of eukaryotes as well as prokaryotes. In this paper, we have reviewed the approaches, previously used to enhance the biodesulfurization rates of the sulfur metabolizing microorganisms and have discussed the potential of CRISPR-Cas systems in engineering desulfurizing biocatalysts. We have also proposed a model to construct competent desulfurizing recombinants involving use of CRISPR-Cas technology. The model can be used to over-express the dsz genes under a constitutive promoter in a suitable heterologous host, to get a steady expression of desulfurization pathway. This may serve as an inducement to develop better performing desulfurizing recombinant strains using CRISPR-Cas systems, which can be helpful in increasing the rate of biodesulfurization in future.
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Affiliation(s)
- Sana Parveen
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad A Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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16
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Fenibo EO, Ijoma GN, Selvarajan R, Chikere CB. Microbial Surfactants: The Next Generation Multifunctional Biomolecules for Applications in the Petroleum Industry and Its Associated Environmental Remediation. Microorganisms 2019; 7:E581. [PMID: 31752381 PMCID: PMC6920868 DOI: 10.3390/microorganisms7110581] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 11/30/2022] Open
Abstract
Surfactants are a broad category of tensio-active biomolecules with multifunctional properties applications in diverse industrial sectors and processes. Surfactants are produced synthetically and biologically. The biologically derived surfactants (biosurfactants) are produced from microorganisms, with Pseudomonas aeruginosa, Bacillus subtilis Candida albicans, and Acinetobacter calcoaceticus as dominant species. Rhamnolipids, sophorolipids, mannosylerithritol lipids, surfactin, and emulsan are well known in terms of their biotechnological applications. Biosurfactants can compete with synthetic surfactants in terms of performance, with established advantages over synthetic ones, including eco-friendliness, biodegradability, low toxicity, and stability over a wide variability of environmental factors. However, at present, synthetic surfactants are a preferred option in different industrial applications because of their availability in commercial quantities, unlike biosurfactants. The usage of synthetic surfactants introduces new species of recalcitrant pollutants into the environment and leads to undesired results when a wrong selection of surfactants is made. Substituting synthetic surfactants with biosurfactants resolves these drawbacks, thus interest has been intensified in biosurfactant applications in a wide range of industries hitherto considered as experimental fields. This review, therefore, intends to offer an overview of diverse applications in which biosurfactants have been found to be useful, with emphases on petroleum biotechnology, environmental remediation, and the agriculture sector. The application of biosurfactants in these settings would lead to industrial growth and environmental sustainability.
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Affiliation(s)
- Emmanuel O. Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Grace N. Ijoma
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa;
| | - Ramganesh Selvarajan
- Department of Environmental Science, University of South Africa, Florida Campus, Rooderpoort 1709, South Africa
| | - Chioma B. Chikere
- Department of Microbiology, Faculty of Science, University of Port Harcourt, Port Harcourt 500272, Nigeria;
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17
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Li L, Liao Y, Luo Y, Zhang G, Liao X, Zhang W, Zheng S, Han S, Lin Y, Liang S. Improved Efficiency of the Desulfurization of Oil Sulfur Compounds in Escherichia coli Using a Combination of Desensitization Engineering and DszC Overexpression. ACS Synth Biol 2019; 8:1441-1451. [PMID: 31132321 DOI: 10.1021/acssynbio.9b00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 4S pathway of biodesulfurization, which can specifically desulfurize aromatic S-heterocyclic compounds without destroying their combustion value, is a low-cost and environmentally friendly technology that is complementary to hydrodesulfurization. The four Dsz enzymes convert the model compound dibenzothiophene (DBT) into the sulfur-free compound 2-hydroxybiphenyl (HBP). Of these four enzymes, DszC, the first enzyme in the 4S pathway, is the most severely affected by the feedback inhibition caused by HBP. This study is the first attempt to directly modify DszC to decrease its inhibition by HBP, with the results showing that the modified protein is insensitive to HBP. On the basis of the principle that the final HBP product could show a blue color with Gibbs reagent, a high-throughput screening method for its rapid detection was established. The screening method and the combinatorial mutagenesis generated the mutant AKWC (A101K/W327C) of DszC. After the IC50 was calculated, the feedback inhibition of the AKWC mutant was observed to have been substantially reduced. Interestingly, the substrate inhibition of DszC had also been reduced as a result of directed evolution. Finally, the recombinant BL21(DE3)/BADC*+C* (C* represents AKWC) strain exhibited a specific conversion rate of 214.84 μmolHBP/gDCW/h, which was 13.8-fold greater than that of the wild-type strain. Desensitization engineering and the overexpression of the desensitized DszC protein resulted in the elimination of the feedback inhibition bottleneck in the 4S pathway, which is practical and effective progress toward the production of sulfur-free fuel oil. The results of this study demonstrate the utility of desensitization of feedback inhibition regulation in metabolic pathways by protein engineering.
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Affiliation(s)
- Lu Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yibo Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yifan Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Guangming Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xihao Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wei Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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18
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Enzymatic Desulfurization of Crude Oil and Its Fractions: A Mini Review on the Recent Progresses and Challenges. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2019. [DOI: 10.1007/s13369-019-03800-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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19
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Correction: Differential desulfurization of dibenzothiophene by newly identified MTCC strains: Influence of Operon Array. PLoS One 2018; 13:e0196374. [PMID: 29672615 PMCID: PMC5909621 DOI: 10.1371/journal.pone.0196374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0192536.].
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