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Karunakaran E, Battarbee R, Tait S, Brentan BM, Berney C, Grinham J, Herrero MA, Omolo R, Douterelo I. Integrating molecular microbial methods to improve faecal pollution management in rivers with designated bathing waters. Sci Total Environ 2024; 912:168565. [PMID: 37979848 DOI: 10.1016/j.scitotenv.2023.168565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/23/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Rivers are at risk from a variety of pollution sources. Faecal pollution is of particular concern since it disperses pathogenic microorganisms in the aquatic environment. Currently, faecal pollution levels in rivers is monitored using faecal indicator bacteria (FIB) that do not offer information about pollution sources and associated risks. This study used a combined molecular approach, along with measurements of water quality, to gain information on pollution sources, and risk levels, in a newly designated recreational bathing site in the River Wharfe (UK). Physico-chemical parameters were monitored in situ, with water quality multiparameter monitoring sondes installed during the 2021 bathing season. The molecular approach was based on quantitative PCR (qPCR)-aided Microbial Source Tracking (MST) and 16S rRNA gene metabarcoding to obtain a fingerprint of bacterial communities and identify potential bioindicators. The analysis from the water quality sondes showed that ammonium was the main parameter determining the distribution of FIB values. Lower faecal pollution levels were detected in the main river when compared to tributaries, except for samples in the river located downstream of a wastewater treatment plant. The faecal pollution type (anthropogenic vs. zoogenic) changed the diversity and the structure of bacterial communities, giving a distinctive fingerprint that can be used to inform source. DNA-based methods showed that the presence of human-derived bacteria was associated with Escherichia coli spikes, coinciding with higher bacterial diversity and the presence of potential pathogenic bacteria mainly of the genus Mycobacterium, Aeromonas and Clostridium. Samples collected after a heavy rainfall event were associated with an increase in Bacteroidales, which are markers of faecal pollution, including Bacteroides graminisolvens, a ruminant marker associated with surface run-off from agricultural sources. The combined use of qPCR and 16S rRNA sequencing was able to identify pollution sources, and novel bacterial indicators, thereby aiding decision-making and management strategies in recreational bathing rivers.
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Affiliation(s)
- Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Rick Battarbee
- Environmental Change Research Centre, University College London, London WC1E 6BT, UK; Addingham Environment Group, Addingham, West Yorkshire LS29 0PD, UK
| | - Simon Tait
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Bruno Melo Brentan
- Hydraulic Engineering and Water Resource Department, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil
| | - Cathal Berney
- Addingham Environment Group, Addingham, West Yorkshire LS29 0PD, UK
| | - James Grinham
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Maria Angeles Herrero
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Ronex Omolo
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Isabel Douterelo
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK.
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Cai Z, Karunakaran E, Pandhal J. Bottom-up construction and screening of algae-bacteria consortia for pollutant biodegradation. Front Microbiol 2024; 15:1349016. [PMID: 38389536 PMCID: PMC10883772 DOI: 10.3389/fmicb.2024.1349016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/17/2024] [Indexed: 02/24/2024] Open
Abstract
Microbial communities have been used as important biological tools for a variety of purposes associated with agriculture, the food industry and human health. Artificial engineering of microbial communities is an emerging field of research motivated by finding stable and efficient microbial systems. However, the successful design of microbial communities with desirable functions not only requires profound understanding of microbial activities, but also needs efficient approaches to piece together the known microbial traits to give rise to more complex systems. This study demonstrates the bottom-up integration of environmentally isolated phototrophic microalgae and chemotrophic bacteria as artificial consortia to bio-degrade selected volatile organic compounds (VOCs). A high throughput screening method based on 96-well plate format was developed for discovering consortia with bioremediation potential. Screened exemplar consortia were verified for VOCs degradation performance, among these, certain robust consortia were estimated to have achieved efficiencies of 95.72% and 92.70% and near 100% removal (7 days) of benzene, toluene, and phenol, respectively, with initial concentrations of 100 mg/L. VOCs degradation by consortia was mainly attributed to certain bacteria including Rhodococcus erythropolis, and Cupriavidus metallidurans, and directly contributed to the growth of microalgae Coelastrella terrestris (R = 0.82, p < 0.001). This work revealed the potential of converting VOCs waste into algal biomass by algae-bacteria consortia constructed through a bottom-up approach. The screening method enables rapid shortlisting of consortia combinatorial scenarios without prior knowledge about the individual strains or the need for interpreting complex microbial interactions.
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Affiliation(s)
- Zongting Cai
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
- Grantham Centre for Sustainable Futures, The University of Sheffield, Sheffield, United Kingdom
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
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3
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Ragupathi NKD, Muthuirulandi Sethuvel DP, Gopikrishnan M, Dwarakanathan HT, Murugan D, Biswas I, Bakthavachalam YD, Murugesan M, George Priya Doss C, Monk PN, Karunakaran E, Veeraraghavan B. Phage-based therapy against biofilm producers in gram-negative ESKAPE pathogens. Microb Pathog 2023; 178:106064. [PMID: 36898591 DOI: 10.1016/j.micpath.2023.106064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023]
Abstract
Persistent antibiotic use results in the rise of antimicrobial resistance with limited or no choice for multidrug-resistant (MDR) and extensively drug resistant (XDR) bacteria. This necessitates a need for alternative therapy to effectively combat clinical pathogens that are resistant to last resort antibiotics. The study investigates hospital sewage as a potential source of bacteriophages to control resistant bacterial pathogens. Eighty-one samples were screened for phages against selected clinical pathogens. Totally, 10 phages were isolated against A. baumannii, 5 phages against K. pneumoniae, and 16 phages were obtained against P. aeruginosa. The novel phages were observed to be strain-specific with complete bacterial growth inhibition of up to 6 h as monotherapy without antibiotics. Phage plus colistin combinations reduced the minimum-biofilm eradication concentration of colistin up to 16 folds. Notably, a cocktail of phages exhibited maximum efficacy with complete killing at 0.5-1 μg/ml colistin concentrations. Thus, phages specific to clinical strains have a higher edge in treating nosocomial pathogens with their proven anti-biofilm efficacy. In addition, analysis of phage genomes revealed close phylogenetic relations with phages reported from Europe, China, and other neighbouring countries. This study serves as a reference and can be extended to other antibiotics and phage types to assess optimum synergistic combinations to combat various drug resistant pathogens in the ongoing AMR crisis.
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Affiliation(s)
- Naveen Kumar Devanga Ragupathi
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom; Department of Clinical Microbiology, Christian Medical College, Vellore, India; Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom; Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), The University of Sheffield, Sheffield, United Kingdom
| | - Dhiviya Prabaa Muthuirulandi Sethuvel
- Department of Clinical Microbiology, Christian Medical College, Vellore, India; Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom
| | - Mohanraj Gopikrishnan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India; School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | | | - Dhivya Murugan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Indranil Biswas
- Microbiology Department, Molecular Genetics and Immunology, University of Kansas, Lawrence, KS, United States
| | | | - Malathi Murugesan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - C George Priya Doss
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Peter N Monk
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom; Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom; Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom; Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), The University of Sheffield, Sheffield, United Kingdom
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India; Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom.
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Regan HC, Taylor AF, Karunakaran E. A Novel High-Throughput <em>Ex Vivo</em> Ovine Skin Wound Model for Testing Emerging Antibiotics. J Vis Exp 2022. [DOI: 10.3791/64041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Devanga Ragupathi NK, Veeraraghavan B, Karunakaran E, Monk PN. Editorial: Biofilm-mediated nosocomial infections and its association with antimicrobial resistance: Detection, prevention, and management. Front Med (Lausanne) 2022; 9:987011. [PMID: 35979211 PMCID: PMC9376627 DOI: 10.3389/fmed.2022.987011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Naveen Kumar Devanga Ragupathi
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), The University of Sheffield, Sheffield, United Kingdom
- Division of Microbial Interactions, Bioberrys Healthcare and Research Centre, Vellore, India
- *Correspondence: Naveen Kumar Devanga Ragupathi
| | - Balaji Veeraraghavan
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), The University of Sheffield, Sheffield, United Kingdom
| | - Peter N. Monk
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries (BARCOD), The University of Sheffield, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
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Santos M, Pereira SB, Flores C, Príncipe C, Couto N, Karunakaran E, Cravo SM, Oliveira P, Tamagnini P. Absence of KpsM (Slr0977) Impairs the Secretion of Extracellular Polymeric Substances (EPS) and Impacts Carbon Fluxes in Synechocystis sp. PCC 6803. mSphere 2021; 6:e00003-21. [PMID: 33504656 PMCID: PMC7885315 DOI: 10.1128/msphere.00003-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 12/02/2022] Open
Abstract
Many cyanobacteria produce extracellular polymeric substances (EPS), composed mainly of heteropolysaccharides, that play a variety of physiological roles, being crucial for cell protection, motility, and biofilm formation. However, due to their complexity, the EPS biosynthetic pathways as well as their assembly and export mechanisms are still far from being fully understood. Here, we show that the absence of a putative EPS-related protein, KpsM (Slr0977), has a pleiotropic effect on Synechocystis sp. strain PCC 6803 physiology, with a strong impact on the export of EPS and carbon fluxes. The kpsM mutant exhibits a significant reduction of released polysaccharides and a smaller decrease of capsular polysaccharides, but it accumulates more polyhydroxybutyrate (PHB) than the wild type. In addition, this strain shows a light/cell density-dependent clumping phenotype and exhibits an altered protein secretion capacity. Furthermore, the most important structural component of pili, the protein PilA, was found to have a modified glycosylation pattern in the mutant compared to the wild type. Proteomic and transcriptomic analyses revealed significant changes in the mechanisms of energy production and conversion, namely, photosynthesis, oxidative phosphorylation, and carbon metabolism, in response to the inactivation of slr0977 Overall, this work shows for the first time that cells with impaired EPS secretion undergo transcriptomic and proteomic adjustments, highlighting the importance of EPS as a major carbon sink in cyanobacteria. The accumulation of PHB in cells of the mutant, without affecting significantly its fitness/growth rate, points to its possible use as a chassis for the production of compounds of interest.IMPORTANCE Most cyanobacteria produce extracellular polymeric substances (EPS) that fulfill different biological roles depending on the strain/environmental conditions. The interest in the cyanobacterial EPS synthesis/export pathways has been increasing, not only to optimize EPS production but also to efficiently redirect carbon flux toward the production of other compounds, allowing the implementation of industrial systems based on cyanobacterial cell factories. Here, we show that a Synechocystis kpsM (slr0977) mutant secretes less EPS than the wild type, accumulating more carbon intracellularly, as polyhydroxybutyrate. Further characterization showed a light/cell density-dependent clumping phenotype, altered protein secretion, and modified glycosylation of PilA. The proteome and transcriptome of the mutant revealed significant changes, namely, in photosynthesis and carbon metabolism. Altogether, this work provides a comprehensive overview of the impact of kpsM disruption on Synechocystis physiology, highlighting the importance of EPS as a carbon sink and showing how cells adapt when their secretion is impaired, and the redirection of the carbon fluxes.
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Affiliation(s)
- Marina Santos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Sara B Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Carlos Flores
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Catarina Príncipe
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Narciso Couto
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Sara M Cravo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Matosinhos, Portugal
- Laboratório de Química Orgânica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Paulo Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Okurowska K, Karunakaran E, Al-Farttoosy A, Couto N, Pandhal J. Adapting the algal microbiome for growth on domestic landfill leachate. Bioresour Technol 2021; 319:124246. [PMID: 33254468 DOI: 10.1016/j.biortech.2020.124246] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 06/12/2023]
Abstract
We aimed to improve algal growth rate on leachate by optimising the algal microbiome. An algal-bacterial consortium was enriched from landfill leachate and subjected to 24 months of adaptive laboratory evolution, increasing the growth rate of the dominant algal strain, Chlorella vulgaris, almost three-fold to 0.2 d-1. A dramatic reduction in nitrate production suggested a shift in biological utilisation of ammoniacal-N, supported by molecular 16S rRNA taxonomic analyses, where Nitrosomonas numbers were not detected in the adapted consortium. A PICRUSt approach predicted metagenomic functional content and revealed a high number of sequences belonging to bioremediation pathways, including degradation of aromatic compounds, benzoate and naphthalene, as well as pathways known to be involved in algal-bacterial symbiosis. This study enhances our understanding of beneficial mechanisms in algal-bacterial associations in complex effluents, and ultimately enables the bottom-up design of optimised algal microbiomes for exploitation within industry.
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Affiliation(s)
- Katarzyna Okurowska
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Alaa Al-Farttoosy
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Narciso Couto
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
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8
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Devanga Ragupathi NK, Muthuirulandi Sethuvel DP, Triplicane Dwarakanathan H, Murugan D, Umashankar Y, Monk PN, Karunakaran E, Veeraraghavan B. The Influence of Biofilms on Carbapenem Susceptibility and Patient Outcome in Device Associated K. pneumoniae Infections: Insights Into Phenotype vs Genome-Wide Analysis and Correlation. Front Microbiol 2020; 11:591679. [PMID: 33381089 PMCID: PMC7767932 DOI: 10.3389/fmicb.2020.591679] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/24/2020] [Indexed: 12/18/2022] Open
Abstract
Klebsiella pneumoniae is one of the leading causes of nosocomial infections. Carbapenem-resistant K. pneumoniae are on the rise globally. The biofilm forming ability of K. pneumoniae further complicates patient management. There is still a knowledge gap on the association of biofilm formation with patient outcome and carbapenem susceptibility, which is investigated in present study. K. pneumoniae isolates from patients admitted in critical care units with catheters and ventilators were included. K. pneumoniae (n = 72) were subjected to 96-well plate biofilm formation assay followed by MBEC assay for subset of strong biofilm formers. Whole genome sequencing and a core genome phylogenetic analysis in comparison with global isolates were performed. Phenotypic analyses showed a positive correlation between biofilm formation and carbapenem resistance. Planktonic cells observed to be susceptible in vitro exhibited higher MICs in biofilm structure, hence MICs cannot be extrapolated for treatment. The biofilm forming ability had a significant association with morbidity/mortality. Infections by stronger biofilm forming pathogens significantly (p < 0.05) resulted in fewer “average days alive” for the patient (3.33 days) in comparison to those negative for biofilms (11.33 days). Phylogenetic analysis including global isolates revealed clear association of sequence types with genes for biofilm formation and carbapenem resistance. Known hypervirulent clone-ST23 with wcaG, magA, rmpA, rmpA2, and wzc with lack of mutation for hyper-capsulation might be poor biofilm formers. ST15, ST16, ST307, and ST258 (reported global high-risk clones) were wcaJ negative indicating the high potential of biofilm forming capacity. Genes wabG and treC for CPS, bcsA and pgaC for adhesins, luxS for quorum sensing were common in all clades in addition to genes for aerobactin (iutA), allantoin (allS), type I and III fimbriae (fimA, fimH, and mrkD) and pili (pilQ and ecpA). This study is the first of its kind to compare genetic features of antimicrobial resistance with a spectrum covering most of the genetic factors for K. pneumoniae biofilm. These results highlight the importance of biofilm screening to effectively manage nosocomial infections by K. pneumoniae. Further, data obtained on epidemiology and associations of biofilm and resistance genetic factors will serve to enhance our understanding on biofilm mechanisms in K. pneumoniae.
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Affiliation(s)
- Naveen Kumar Devanga Ragupathi
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), The University of Sheffield, Sheffield, United Kingdom.,Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom.,Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | | | - Dhivya Murugan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Yamini Umashankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Peter N Monk
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), The University of Sheffield, Sheffield, United Kingdom.,Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
| | - Esther Karunakaran
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), The University of Sheffield, Sheffield, United Kingdom.,Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
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9
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Urwin L, Okurowska K, Crowther G, Roy S, Garg P, Karunakaran E, MacNeil S, Partridge LJ, Green LR, Monk PN. Corneal Infection Models: Tools to Investigate the Role of Biofilms in Bacterial Keratitis. Cells 2020; 9:E2450. [PMID: 33182687 PMCID: PMC7696224 DOI: 10.3390/cells9112450] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/06/2020] [Accepted: 11/07/2020] [Indexed: 12/15/2022] Open
Abstract
Bacterial keratitis is a corneal infection which may cause visual impairment or even loss of the infected eye. It remains a major cause of blindness in the developing world. Staphylococcus aureus and Pseudomonas aeruginosa are common causative agents and these bacterial species are known to colonise the corneal surface as biofilm populations. Biofilms are complex bacterial communities encased in an extracellular polymeric matrix and are notoriously difficult to eradicate once established. Biofilm bacteria exhibit different phenotypic characteristics from their planktonic counterparts, including an increased resistance to antibiotics and the host immune response. Therefore, understanding the role of biofilms will be essential in the development of new ophthalmic antimicrobials. A brief overview of biofilm-specific resistance mechanisms is provided, but this is a highly multifactorial and rapidly expanding field that warrants further research. Progression in this field is dependent on the development of suitable biofilm models that acknowledge the complexity of the ocular environment. Abiotic models of biofilm formation (where biofilms are studied on non-living surfaces) currently dominate the literature, but co-culture infection models are beginning to emerge. In vitro, ex vivo and in vivo corneal infection models have now been reported which use a variety of different experimental techniques and animal models. In this review, we will discuss existing corneal infection models and their application in the study of biofilms and host-pathogen interactions at the corneal surface.
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Affiliation(s)
- Lucy Urwin
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2RX, UK; (L.R.G.); (P.N.M.)
| | - Katarzyna Okurowska
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK; (K.O.); (G.C.); (E.K.)
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield, Sheffield S1 3JD, UK; (S.M.); (L.J.P.)
| | - Grace Crowther
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK; (K.O.); (G.C.); (E.K.)
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield, Sheffield S1 3JD, UK; (S.M.); (L.J.P.)
| | - Sanhita Roy
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (S.R.); (P.G.)
| | - Prashant Garg
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (S.R.); (P.G.)
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK; (K.O.); (G.C.); (E.K.)
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield, Sheffield S1 3JD, UK; (S.M.); (L.J.P.)
| | - Sheila MacNeil
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield, Sheffield S1 3JD, UK; (S.M.); (L.J.P.)
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Lynda J. Partridge
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield, Sheffield S1 3JD, UK; (S.M.); (L.J.P.)
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Luke R. Green
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2RX, UK; (L.R.G.); (P.N.M.)
| | - Peter N. Monk
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2RX, UK; (L.R.G.); (P.N.M.)
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield, Sheffield S1 3JD, UK; (S.M.); (L.J.P.)
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Couto N, Newton JRA, Russo C, Karunakaran E, Achour B, Al-Majdoub ZM, Sidaway J, Rostami-Hodjegan A, Clench MR, Barber J. Label-Free Quantitative Proteomics and Substrate-Based Mass Spectrometry Imaging of Xenobiotic Metabolizing Enzymes in Ex Vivo Human Skin and a Human Living Skin Equivalent Model. Drug Metab Dispos 2020; 49:39-52. [PMID: 33139459 DOI: 10.1124/dmd.120.000168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/08/2020] [Indexed: 01/15/2023] Open
Abstract
We report for the first time label-free quantification of xenobiotic metabolizing enzymes (XME), transporters, redox enzymes, proteases, and nucleases in six human skin explants and a three-dimensional living skin equivalent model from LabSkin. We aimed to evaluate the suitability of LabSkin as an alternative to animal testing for the development of topical formulations. More than 2000 proteins were identified and quantified from total cellular protein. Alcohol dehydrogenase 1C, the most abundant phase I XME in human skin, and glutathione S-transferase pi 1, the most abundant phase II XME in human skin, were present in similar abundance in LabSkin. Several esterases were quantified and esterase activity was confirmed in LabSkin using substrate-based mass spectrometry imaging. No cytochrome P450 (P450) activity was observed for the substrates tested, in agreement with the proteomics data, where the cognate P450s were absent in both human skin and LabSkin. Label-free protein quantification allowed insights into other related processes such as redox homeostasis and proteolysis. For example, the most abundant antioxidant enzymes were thioredoxin and peroxiredoxin-1. This systematic determination of functional equivalence between human skin and LabSkin is a key step toward the construction of a representative human in vitro skin model, which can be used as an alternative to current animal-based tests for chemical safety and for predicting dosage of topically administered drugs. SIGNIFICANCE STATEMENT: The use of label-free quantitative mass spectrometry to elucidate the abundance of xenobiotic metabolizing enzymes, transporters, redox enzymes, proteases, and nucleases in human skin enhance our understanding of the skin physiology and biotransformation of topical drugs and cosmetics. This will help to develop mathematical models to predict drug metabolism in human skin and to develop more robust in vitro engineered human skin tissue as alternatives to animal testing.
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Affiliation(s)
- Narciso Couto
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - Jillian R A Newton
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - Cristina Russo
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - Brahim Achour
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - Zubida M Al-Majdoub
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - James Sidaway
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - Amin Rostami-Hodjegan
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - Malcolm R Clench
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
| | - Jill Barber
- Department of Chemical and Biological Engineering (N.C., E.K.) and Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB) (N.C., E.K.), University of Sheffield, Sheffield, United Kingdom; Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, United Kingdom (N.C., B.A., Z.M.A.-M., A.R.-H., J.B.); Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom (J.R.A.N., C.R., M.R.C.); Phenotox Ltd., Bollington, United Kingdom (J.S.); and Certara UK Limited (Simcyp Division), Sheffield, United Kingdom (A.R.-H.)
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11
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Del Olmo G, Ahmad A, Jensen H, Karunakaran E, Rosales E, Calero Preciado C, Gaskin P, Douterelo I. Influence of phosphate dosing on biofilms development on lead in chlorinated drinking water bioreactors. NPJ Biofilms Microbiomes 2020; 6:43. [PMID: 33097725 PMCID: PMC7585443 DOI: 10.1038/s41522-020-00152-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/24/2020] [Indexed: 12/22/2022] Open
Abstract
Phosphate dosing is used by water utilities to prevent plumbosolvency in water supply networks. However, there is a lack of knowledge regarding biofilm formation on lead and plastic materials when phosphate concentrations are modified in drinking water systems. In this study, biofilms were grown over lead coupons and PVC tubes in bioreactors supplied with local drinking water treated to provide different phosphate doses (below 1, 1 and 2 mg/L) over a period of 28 days. A range of commercial iron pellets (GEH104 and WARP) were tested aiming to maintain phosphate levels below the average 1 mg/L found in drinking water. Changes in biofilm community structure in response to three different phosphate treatments were characterised by Illumina sequencing of the 16S rRNA gene for bacteria and the ITS2 gene for fungi. Scanning electron microscopy was used to visualise physical differences in biofilm development in two types of materials, lead and PVC. The experimental results from the kinetics of phosphate absorption showed that the GEH104 pellets were the best option to, in the long term, reduce phosphate levels while preventing undesirable turbidity increases in drinking water. Phosphate-enrichment promoted a reduction of bacterial diversity but increased that of fungi in biofilms. Overall, higher phosphate levels selected for microorganisms with enhanced capabilities related to phosphorus metabolism and heavy metal resistance. This research brings new insights regarding the influence of different phosphate concentrations on mixed-species biofilms formation and drinking water quality, which are relevant to inform best management practices in drinking water treatment.
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Affiliation(s)
- Gonzalo Del Olmo
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield, UK
| | - Arslan Ahmad
- KWR Water Cycle Research Institute, Groningenhaven 7, 3433, PE, Nieuwegein, The Netherlands
- KTH-International Groundwater Arsenic Research Group, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-100 44, Stockholm, Sweden
- Department of Environmental Technology, Wageningen University and Research (WUR), Droevendaalsesteeg 4, 6708, PB, Wageningen, The Netherlands
| | - Henriette Jensen
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Esther Rosales
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield, UK
| | | | | | - Isabel Douterelo
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield, UK.
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12
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Del Olmo G, Rosales E, Karunakaran E, Jensen H, Calero C, Ahmad A, Gaskin P, Douterelo I. Influence of phosphate dosing on biofilm development on Drinking Water Distribution Systems infrastructure surfaces. Access Microbiol 2020. [DOI: 10.1099/acmi.ac2020.po0309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphate is added to drinking water by UK water companies as a treatment to prevent the corrosion and metal leaching, like lead, in pipes. However, phosphate is a nutrient for microorganisms, and it can favour biofilm formation in Drinking Water Distribution Systems (DWDS), which can alter the water quality and safety. This study analyses the effect of phosphate addition on biofilm formation over different materials and its consequences for drinking water quality by i) using controlled experimental pipeline facility representative of a real-scale DWDS with high-density polyethylene coupons and ii) using a small-scale DWDS biofilm reactors with lead coupons. Biofilms developed over one month were exposed to the effect of different phosphate dosing and compare with UK normal water phosphate concentrations. During the experiment, physico-chemical analysis of water and microbial analysis of biofilms was carried out. Sequencing analysis of the 16s rRNA gene, from extracted DNA obtained from biofilms, provided information on any bacterial changes, and Scanning Electron Microscopy gave information about the biofilm organization. The results indicate that microorganisms find more difficult to establish and develop biofilms under high phosphate dosing, resulting in biofilms with less cells. Also, some physico-chemical parameter seems to be affected by phosphate dosing, like chlorine and lead. It is expected that differences in the biofilm community will be found depending on phosphate dosing. This study will provide information on the effect of phosphate on biofilm development in different pipes materials, which will facilitate to adjust an optimal phosphate dose to prevent plumbosolvency in DWDS.
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Affiliation(s)
- Gonzalo Del Olmo
- University of Sheffield (Civil and Structural Engineering Department),Sheffield,United Kingdom
| | - Esther Rosales
- University of Sheffield (Civil and Structural Engineering Department),Sheffield,United Kingdom
| | - Esther Karunakaran
- University of Sheffield (Chemical and Biological Engineering Department),Sheffield,United Kingdom
| | - Henriette Jensen
- University of Sheffield (Chemical and Biological Engineering Department),Sheffield,United Kingdom
| | - Carolina Calero
- University of Sheffield (Civil and Structural Engineering Department),Sheffield,United Kingdom
| | - Arsland Ahmad
- KWR Watercycle Research Institute,Nieuwegein,Netherlands
| | - Paul Gaskin
- Dŵr Cymru Welsh Water,Cardiff,United Kingdom
| | - Isabel Douterelo
- University of Sheffield (Civil and Structural Engineering Department),Sheffield,United Kingdom
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13
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Roccuzzo S, Couto N, Karunakaran E, Kapoore RV, Butler TO, Mukherjee J, Hansson EM, Beckerman AP, Pandhal J. Metabolic Insights Into Infochemicals Induced Colony Formation and Flocculation in Scenedesmus subspicatus Unraveled by Quantitative Proteomics. Front Microbiol 2020; 11:792. [PMID: 32457714 PMCID: PMC7220994 DOI: 10.3389/fmicb.2020.00792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/02/2020] [Indexed: 01/15/2023] Open
Abstract
Microalgae can respond to natural cues from crustacean grazers, such as Daphnia, by forming colonies and aggregations called flocs. Combining microalgal biology, physiological ecology, and quantitative proteomics, we identified how infochemicals from Daphnia trigger physiological and cellular level changes in the microalga Scenedesmus subspicatus, underpinning colony formation and flocculation. We discovered that flocculation occurs at an energy-demanding ‘alarm’ phase, with an important role proposed in cysteine synthesis. Flocculation appeared to be initially stimulated by the production of an extracellular matrix where polysaccharides and fatty acids were present, and later sustained at an ‘acclimation’ stage through mitogen-activated protein kinase (MAPK) signaling cascades. Colony formation required investment into fatty acid metabolism, likely linked to separation of membranes during cell division. Higher energy demands were required at the alarm phase, which subsequently decreased at the acclimation stage, thus suggesting a trade-off between colony formation and flocculation. From an ecological and evolutionary perspective, our findings represent an improved understanding of the effect of infochemicals on microalgae-grazers interactions, and how they can therefore potentially impact on the structure of aquatic communities. Moreover, the mechanisms revealed are of interest in algal biotechnology, for exploitation in low-cost, sustainable microalgal biomass harvesting.
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Affiliation(s)
- Sebastiana Roccuzzo
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Narciso Couto
- Centre for Applied Pharmacokinetic Research, The University of Manchester, Manchester, United Kingdom
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Rahul Vijay Kapoore
- Department of Biosciences, College of Science, Swansea University, Swansea, United Kingdom
| | - Thomas O Butler
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Joy Mukherjee
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Erika M Hansson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Andrew P Beckerman
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
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14
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Okurowska K, Roy S, Thokala P, Partridge L, Garg P, MacNeil S, Monk PN, Karunakaran E. Establishing a Porcine Ex Vivo Cornea Model for Studying Drug Treatments against Bacterial Keratitis. J Vis Exp 2020. [PMID: 32478743 DOI: 10.3791/61156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
When developing novel antimicrobials, the success of animal trials is dependent on accurate extrapolation of antimicrobial efficacy from in vitro tests to animal infections in vivo. The existing in vitro tests typically overestimate antimicrobial efficacy as the presence of host tissue as a diffusion barrier is not accounted for. To overcome this bottleneck, we have developed an ex vivo porcine corneal model of bacterial keratitis using Pseudomonas aeruginosa as a prototypic organism. This article describes the preparation of the porcine cornea and protocol for establishment of the infection. Bespoke glass molds enable straightforward setup of the cornea for infection studies. The model mimics in vivo infection as bacterial proliferation is dependent on the ability of the bacterium to damage corneal tissue. Establishment of infection is verified as an increase in the number of colony forming units assessed via viable plate counts. The results demonstrate that infection can be established in a highly reproducible fashion in the ex vivo corneas using the method described here. The model can be extended in the future to mimic keratitis caused by microorganisms other than P. aeruginosa. The ultimate aim of the model is to investigate the effect of antimicrobial chemotherapy on the progress of bacterial infection in a scenario more representative of in vivo infections. In so doing, the model described here will reduce the use of animals for testing, improve success rates in clinical trials and ultimately enable rapid translation of novel antimicrobials to the clinic.
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Affiliation(s)
- Katarzyna Okurowska
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield; Department of Chemical and Biological Engineering, University of Sheffield
| | - Sanhita Roy
- Hyderabad Eye Research Foundation, L V Prasad Eye Institute
| | - Praveen Thokala
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield
| | - Lynda Partridge
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield; Department of Molecular Biology and Biotechnology, University of Sheffield
| | - Prashant Garg
- Hyderabad Eye Research Foundation, L V Prasad Eye Institute
| | - Sheila MacNeil
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield; Department of Materials Science and Engineering, University of Sheffield
| | - Peter N Monk
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield
| | - Esther Karunakaran
- Sheffield Collaboratorium for Antimicrobial Resistance and Biofilms (SCARAB), University of Sheffield; Department of Chemical and Biological Engineering, University of Sheffield;
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15
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Dave A, Samarth A, Karolia R, Sharma S, Karunakaran E, Partridge L, MacNeil S, Monk PN, Garg P, Roy S. Characterization of Ocular Clinical Isolates of Pseudomonas aeruginosa from Non-Contact Lens Related Keratitis Patients from South India. Microorganisms 2020; 8:microorganisms8020260. [PMID: 32075262 PMCID: PMC7074794 DOI: 10.3390/microorganisms8020260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/25/2022] Open
Abstract
P. aeruginosa is the most common Gram-negative organism causing bacterial keratitis. Pseudomonas utilizes various virulence mechanisms to adhere and colonize in the host tissue. In the present study, we examined virulence factors associated with thirty-four clinical P. aeruginosa isolates collected from keratitis patients seeking care at L V Prasad Eye Institute, Hyderabad. The virulence-associated genes in all the isolates were genotyped and characteristics such as antibiotic susceptibility, biofilm formation, swarming motility, pyoverdine production and cell cytotoxicity were analyzed. All the isolates showed the presence of genes related to biofilm formation, alkaline proteases and elastases; however, there was a difference in the presence of genes related to the type III secretion system (T3SS). A higher prevalence of exoU+ genotype was noted in the drug-resistant isolates. All the isolates were capable of forming biofilms and more than 70% of the isolates showed good swarming motility. Pyoverdine production was not associated with the T3SS genotype. In the cytotoxicity assay, the presence of exoS,exoU or both resulted in higher cytotoxicity compared to the absence of both the genes. Overall, our results suggest that the T3SS profile is a good indicator of P. aeruginosa virulence characteristics and the isolates lacking the effector genes may have evolved alternate mechanisms of colonization in the host.
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Affiliation(s)
- Alpana Dave
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (A.D.); (A.S.); (P.G.)
| | - Apurwa Samarth
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (A.D.); (A.S.); (P.G.)
| | - Roshni Karolia
- Jhaveri Microbiology Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (R.K.); (S.S.)
| | - Savitri Sharma
- Jhaveri Microbiology Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (R.K.); (S.S.)
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S102TG, UK;
| | - Lynda Partridge
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S102TG, UK;
| | - Sheila MacNeil
- Department of Material Science and Engineering, University of Sheffield, Sheffield S102TG, UK;
| | - Peter N. Monk
- Department of Infection Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S102RX, UK;
| | - Prashant Garg
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (A.D.); (A.S.); (P.G.)
| | - Sanhita Roy
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India; (A.D.); (A.S.); (P.G.)
- Correspondence: ; Tel.: +91-40-30612529; Fax: +91-40-30612535
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16
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Raut MP, Couto N, Karunakaran E, Biggs CA, Wright PC. Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85. Sci Rep 2019; 9:16542. [PMID: 31719545 PMCID: PMC6851124 DOI: 10.1038/s41598-019-52675-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 10/22/2019] [Indexed: 02/04/2023] Open
Abstract
Fibrobacter succinogenes S85, isolated from the rumen of herbivores, is capable of robust lignocellulose degradation. However, the mechanism by which it achieves this is not fully elucidated. In this study, we have undertaken the most comprehensive quantitative proteomic analysis, to date, of the changes in the cell envelope protein profile of F. succinogenes S85 in response to growth on cellulose. Our results indicate that the cell envelope proteome undergoes extensive rearrangements to accommodate the cellulolytic degradation machinery, as well as associated proteins involved in adhesion to cellulose and transport and metabolism of cellulolytic products. Molecular features of the lignocellulolytic enzymes suggest that the Type IX secretion system is involved in the translocation of these enzymes to the cell envelope. Finally, we demonstrate, for the first time, that cyclic-di-GMP may play a role in mediating catabolite repression, thereby facilitating the expression of proteins involved in the adhesion to lignocellulose and subsequent lignocellulose degradation and utilisation. Understanding the fundamental aspects of lignocellulose degradation in F. succinogenes will aid the development of advanced lignocellulosic biofuels.
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Affiliation(s)
- Mahendra P Raut
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Narciso Couto
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.,Centre for Applied Pharmacokinetic Research, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
| | - Esther Karunakaran
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Catherine A Biggs
- School of Engineering, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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17
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Flores C, Santos M, Pereira SB, Mota R, Rossi F, De Philippis R, Couto N, Karunakaran E, Wright PC, Oliveira P, Tamagnini P. The alternative sigma factor SigF is a key player in the control of secretion mechanisms inSynechocystissp. PCC 6803. Environ Microbiol 2018; 21:343-359. [DOI: 10.1111/1462-2920.14465] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/14/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Carlos Flores
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; ICBAS - Instituto de Ciências Biomédicas Abel Salazar; Porto Portugal
| | - Marina Santos
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; ICBAS - Instituto de Ciências Biomédicas Abel Salazar; Porto Portugal
| | - Sara B. Pereira
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
| | - Rita Mota
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
| | - Federico Rossi
- Department of Agrifood Production and Environmental Sciences; University of Florence; Florence Italy
| | - Roberto De Philippis
- Department of Agrifood Production and Environmental Sciences; University of Florence; Florence Italy
| | - Narciso Couto
- Department of Chemical and Biological Engineering; ChELSI Institute, University of Sheffield; Sheffield UK
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering; ChELSI Institute, University of Sheffield; Sheffield UK
| | - Phillip C. Wright
- Department of Chemical and Biological Engineering; ChELSI Institute, University of Sheffield; Sheffield UK
| | - Paulo Oliveira
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
| | - Paula Tamagnini
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
- Faculdade de Ciências, Departamento de Biologia; Universidade do Porto; Porto Portugal
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Nguyen V, Karunakaran E, Collins G, Biggs CA. Physicochemical analysis of initial adhesion and biofilm formation of Methanosarcina barkeri on polymer support material. Colloids Surf B Biointerfaces 2016; 143:518-525. [DOI: 10.1016/j.colsurfb.2016.03.042] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 12/15/2015] [Accepted: 03/15/2016] [Indexed: 12/22/2022]
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19
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Karunakaran E, Vernon D, Biggs CA, Saul A, Crawford D, Jensen H. Enumeration of sulphate-reducing bacteria for assessing potential for hydrogen sulphide production in urban drainage systems. Water Sci Technol 2016; 73:3087-3094. [PMID: 27332857 DOI: 10.2166/wst.2016.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Urban drainage structures have increasing demands which can lead to increasing hydrogen sulphide related problems forming in places where they have not previously been prevalent. This puts pressure on the methods currently used to monitor and diagnose these problems and more sophisticated methods may be needed for identifying the origin of the problems. Molecular microbiological techniques, such as quantitative polymerase chain reaction, offer a potential alternative for identifying and quantifying bacteria likely to be causing the production of hydrogen sulphide, information that, when combined with an appropriate sampling programme, can then be used to identify the potentially most effective remediation technique. The application of these methods in urban drainage systems is, however, not always simple, but good results can be achieved. In this study bacteria producing hydrogen sulphide were quantified in three small combined sewer overflow storage tanks. Bacterial counts were compared between wastewater, biofilms and sediments. Similar numbers were found in the wastewater and biofilms, with the numbers in the sediments being lower. If remediation methods for hydrogen sulphide are deemed necessary in the tanks, methods that target both the wastewater and the biofilms should therefore be considered.
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Affiliation(s)
- Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK E-mail:
| | - Dejan Vernon
- Innovation, Thames Water, Reading STW, Reading RG2 0RP, UK
| | - Catherine A Biggs
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK E-mail:
| | - Adrian Saul
- Department of Civil and Structural Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - David Crawford
- Thames Tideway Tunnel Limited, North Wharf Road, London W2 1AF, UK
| | - Henriette Jensen
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK E-mail:
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20
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Raut MP, Karunakaran E, Mukherjee J, Biggs CA, Wright PC. Influence of Substrates on the Surface Characteristics and Membrane Proteome of Fibrobacter succinogenes S85. PLoS One 2015; 10:e0141197. [PMID: 26492413 PMCID: PMC4619616 DOI: 10.1371/journal.pone.0141197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/06/2015] [Indexed: 12/02/2022] Open
Abstract
Although Fibrobacter succinogenes S85 is one of the most proficient cellulose degrading bacteria among all mesophilic organisms in the rumen of herbivores, the molecular mechanism behind cellulose degradation by this bacterium is not fully elucidated. Previous studies have indicated that cell surface proteins might play a role in adhesion to and subsequent degradation of cellulose in this bacterium. It has also been suggested that cellulose degradation machinery on the surface may be selectively expressed in response to the presence of cellulose. Based on the genome sequence, several models of cellulose degradation have been suggested. The aim of this study is to evaluate the role of the cell envelope proteins in adhesion to cellulose and to gain a better understanding of the subsequent cellulose degradation mechanism in this bacterium. Comparative analysis of the surface (exposed outer membrane) chemistry of the cells grown in glucose, acid-swollen cellulose and microcrystalline cellulose using physico-chemical characterisation techniques such as electrophoretic mobility analysis, microbial adhesion to hydrocarbons assay and Fourier transform infra-red spectroscopy, suggest that adhesion to cellulose is a consequence of an increase in protein display and a concomitant reduction in the cell surface polysaccharides in the presence of cellulose. In order to gain further understanding of the molecular mechanism of cellulose degradation in this bacterium, the cell envelope-associated proteins were enriched using affinity purification and identified by tandem mass spectrometry. In total, 185 cell envelope-associated proteins were confidently identified. Of these, 25 proteins are predicted to be involved in cellulose adhesion and degradation, and 43 proteins are involved in solute transport and energy generation. Our results supports the model that cellulose degradation in F. succinogenes occurs at the outer membrane with active transport of cellodextrins across for further metabolism of cellodextrins to glucose in the periplasmic space and inner cytoplasmic membrane.
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Affiliation(s)
- Mahendra P. Raut
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Esther Karunakaran
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Joy Mukherjee
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Catherine A. Biggs
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C. Wright
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
- * E-mail:
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21
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Abdul-Majeed WS, Karunakaran E, Biggs CA, Zimmerman WB. Development of wastewater treatment system based on cascade dielectric barrier discharge plasma atomizers. J Environ Sci Health A Tox Hazard Subst Environ Eng 2015; 50:1249-1258. [PMID: 26301851 DOI: 10.1080/10934529.2015.1055150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A novel design for a cascade dielectric barrier discharge (DBD) atomizer was applied for treating samples of water containing biological and organic contaminants. Several experimental investigations were conducted on artificial samples and real sample (digested sludge collected from a wastewater treatment plant, WWTP). The artificial water samples were prepared by using different concentrations of E. coli for biological samples, whereas acetic acid was used to prepare the organic samples. The biological samples were subjected to the plasma effect for different treatment periods, and the growth curves of E. coli were generated for 24 h after treatment. Moreover, the viable cells were counted after each treatment period and the change in E. coli morphology was monitored. The results showed that a significant reduction in the viable cell number, by 3 orders of magnitude, occurred for an artificial biological sample after only 5-min treatment. The treatment of organic samples for 10 min showed a significant reduction in the concentration of acetic acid by 50%. In consequence, treatment of real wastewater sample for 10 min resulted in more than 70% reduction in BOD5 and 30% reduction in COD.
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Affiliation(s)
- Wameath S Abdul-Majeed
- a Department of Chemical and Petrochemical Engineering, University of Nizwa , Nizwa , Oman
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22
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Honsbein A, Madsen MA, Amezaga JM, Biggs CA, Bond T, Gandy CJ, Karunakaran E, Lawton L, Minas K, Templeton MR, Amtmann A. ’Biodesalination’: a synthetic biology approach for the use of photosynthetic bacteria in water treatment. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.1962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Amezaga JM, Amtmann A, Biggs CA, Bond T, Gandy CJ, Honsbein A, Karunakaran E, Lawton L, Madsen MA, Minas K, Templeton MR. Biodesalination: a case study for applications of photosynthetic bacteria in water treatment. Plant Physiol 2014; 164:1661-76. [PMID: 24610748 PMCID: PMC3982732 DOI: 10.1104/pp.113.233973] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/05/2014] [Indexed: 05/07/2023]
Abstract
Shortage of freshwater is a serious problem in many regions worldwide, and is expected to become even more urgent over the next decades as a result of increased demand for food production and adverse effects of climate change. Vast water resources in the oceans can only be tapped into if sustainable, energy-efficient technologies for desalination are developed. Energization of desalination by sunlight through photosynthetic organisms offers a potential opportunity to exploit biological processes for this purpose. Cyanobacterial cultures in particular can generate a large biomass in brackish and seawater, thereby forming a low-salt reservoir within the saline water. The latter could be used as an ion exchanger through manipulation of transport proteins in the cell membrane. In this article, we use the example of biodesalination as a vehicle to review the availability of tools and methods for the exploitation of cyanobacteria in water biotechnology. Issues discussed relate to strain selection, environmental factors, genetic manipulation, ion transport, cell-water separation, process design, safety, and public acceptance.
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Affiliation(s)
- Jaime M. Amezaga
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | | | - Catherine A. Biggs
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | - Tom Bond
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | - Catherine J. Gandy
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | - Annegret Honsbein
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | - Esther Karunakaran
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | - Linda Lawton
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | - Mary Ann Madsen
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | - Konstantinos Minas
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
| | - Michael R. Templeton
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (J.M.A., C.J.G.)
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom (A.A., A.H., M.A.M.)
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom (C.A.B., E.K.)
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United Kingdom (T.B., M.R.T.); and
- Institute for Innovation, Design and Sustainability, Robert Gordon University, Aberdeen AB10 7AQ, United Kingdom (L.L., K.M.)
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Deepika G, Karunakaran E, Hurley CR, Biggs CA, Charalampopoulos D. Influence of fermentation conditions on the surface properties and adhesion of Lactobacillus rhamnosus GG. Microb Cell Fact 2012; 11:116. [PMID: 22931558 PMCID: PMC3441878 DOI: 10.1186/1475-2859-11-116] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 08/07/2012] [Indexed: 12/19/2022] Open
Abstract
Background The surface properties of probiotic bacteria influence to a large extent their interactions within the gut ecosystem. There is limited amount of information on the effect of the production process on the surface properties of probiotic lactobacilli in relation to the mechanisms of their adhesion to the gastrointestinal mucosa. The aim of this work was to investigate the effect of the fermentation pH and temperature on the surface properties and adhesion ability to Caco-2 cells of the probiotic strain Lactobacillus rhamnosus GG. Results The cells were grown at pH 5, 5.5, 6 (temperature 37°C) and at pH 6.5 (temperature 25°C, 30°C and 37°C), and their surfaces analysed by X-ray photoelectron spectrometry (XPS), Fourier transform infrared spectroscopy (FT-IR) and gel-based proteomics. The results indicated that for all the fermentation conditions, with the exception of pH 5, a higher nitrogen to carbon ratio and a lower phosphate content was observed at the surface of the bacteria, which resulted in a lower surface hydrophobicity and reduced adhesion levels to Caco-2 cells as compared to the control fermentation (pH 6.5, 37°C). A number of adhesive proteins, which have been suggested in previous published works to take part in the adhesion of bacteria to the human gastrointestinal tract, were identified by proteomic analysis, with no significant differences between samples however. Conclusions The temperature and the pH of the fermentation influenced the surface composition, hydrophobicity and the levels of adhesion of L. rhamnosus GG to Caco-2 cells. It was deduced from the data that a protein rich surface reduced the adhesion ability of the cells.
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Affiliation(s)
- Gurjot Deepika
- Food and Nutritional Sciences, University of Reading, PO Box 226, Reading, UK, RG6 6AP
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25
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Evans C, Noirel J, Ow SY, Salim M, Pereira-Medrano AG, Couto N, Pandhal J, Smith D, Pham TK, Karunakaran E, Zou X, Biggs CA, Wright PC. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012; 404:1011-27. [PMID: 22451173 DOI: 10.1007/s00216-012-5918-6] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 01/09/2023]
Abstract
The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ's attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground.
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Affiliation(s)
- Caroline Evans
- The ChELSI Institute, Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
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Mukherjee J, Karunakaran E, Biggs CA. Using a multi-faceted approach to determine the changes in bacterial cell surface properties influenced by a biofilm lifestyle. Biofouling 2012; 28:1-14. [PMID: 22150164 DOI: 10.1080/08927014.2011.639067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biofilm formation is a developmental process in which initial reversible adhesion is governed by physico-chemical forces, whilst irreversible adhesion is mediated by biological changes within a cell, such as the production of extracellular polymeric substances. Using two bacteria, E. coli MG1655 and B. cereus ATCC 10987, this study establishes that the surface of the bacterial cell also undergoes specific modifications, which result in biofilm formation and maintenance. Using various surface characterisation techniques and proteomics, an increase in the surface exposed proteins on E. coli cells during biofilm formation was demonstrated, along with an increase in hydrophobicity and a decrease in surface charge. For B. cereus, an increase in the surface polysaccharides during biofilm formation was found as well as a decrease in hydrophobicity and surface charge. This work therefore shows that surface modifications during biofilm formation occur and understanding these specific changes may lead to the formulation of effective biofilm control strategies in the future.
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Affiliation(s)
- Joy Mukherjee
- Department of Chemical and Biological Engineering, The ChELSI Institute, The University of Sheffield, Sheffield S1 3JD, UK
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27
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Koerdt A, Orell A, Pham TK, Mukherjee J, Wlodkowski A, Karunakaran E, Biggs CA, Wright PC, Albers SV. Macromolecular fingerprinting of sulfolobus species in biofilm: a transcriptomic and proteomic approach combined with spectroscopic analysis. J Proteome Res 2011; 10:4105-19. [PMID: 21761944 PMCID: PMC3166137 DOI: 10.1021/pr2003006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Microorganisms in nature often live in surface-associated sessile communities, encased in a self-produced matrix, referred to as biofilms. Biofilms have been well studied in bacteria but in a limited way for archaea. We have recently characterized biofilm formation in three closely related hyperthermophilic crenarchaeotes: Sulfolobus acidocaldarius, S. solfataricus, and S. tokodaii. These strains form different communities ranging from simple carpet structures in S. solfataricus to high density tower-like structures in S. acidocaldarius under static condition. Here, we combine spectroscopic, proteomic, and transcriptomic analyses to describe physiological and regulatory features associated with biofilms. Spectroscopic analysis reveals that in comparison to planktonic life-style, biofilm life-style has distinctive influence on the physiology of each Sulfolobus spp. Proteomic and transcriptomic data show that biofilm-forming life-style is strain specific (eg ca. 15% of the S. acidocaldarius genes were differently expressed, S. solfataricus and S. tokodaii had ∼3.4 and ∼1%, respectively). The -omic data showed that regulated ORFs were widely distributed in basic cellular functions, including surface modifications. Several regulated genes are common to biofilm-forming cells in all three species. One of the most striking common response genes include putative Lrs14-like transcriptional regulators, indicating their possible roles as a key regulatory factor in biofilm development. S. acidocaldarius, S. solfataricus, and S. tokodaii strains were grown independently as biofilms. Comparison between planktonic and biofilm cell popupations of all three strains was performed by spectroscopic analysis (FTIR and XPS), iTRAQ proteomics, and RNA microarrays. To highlight common features in biofilm formation among the Sulfolobus strains, the data is presented as a comparative analysis. One of the most striking common response genes include putative Lrs14-like transcriptional regulators, suggesting their roles as key regulatory factor in biofilm development.
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Affiliation(s)
- Andrea Koerdt
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany
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Karunakaran E, Mukherjee J, Ramalingam B, Biggs CA. "Biofilmology": a multidisciplinary review of the study of microbial biofilms. Appl Microbiol Biotechnol 2011; 90:1869-81. [PMID: 21538113 DOI: 10.1007/s00253-011-3293-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 03/26/2011] [Accepted: 03/27/2011] [Indexed: 11/29/2022]
Abstract
The observation of biofilm formation is not a new phenomenon. The prevalence and significance of biofilm and aggregate formation in various processes have encouraged extensive research in this field for more than 40 years. In this review, we highlight techniques from different disciplines that have been used to successfully describe the extracellular, surface and intracellular elements that are predominant in understanding biofilm formation. To reduce the complexities involved in studying biofilms, researchers in the past have generally taken a parts-based, disciplinary specific approach to understand the different components of biofilms in isolation from one another. Recently, a few studies have looked into combining the different techniques to achieve a more holistic understanding of biofilms, yet this approach is still in its infancy. In order to attain a global understanding of the processes involved in the formation of biofilms and to formulate effective biofilm control strategies, researchers in the next decade should recognise that the study of biofilms, i.e. biofilmology, has evolved into a discipline in its own right and that mutual cooperation between the various disciplines towards a multidisciplinary research vision is vital in this field.
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Affiliation(s)
- Esther Karunakaran
- Department of Chemical and Biological Engineering, ChELSI Institute, The University of Sheffield, Sheffield, UK
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29
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Karunakaran E, Biggs CA. Mechanisms of Bacillus cereus biofilm formation: an investigation of the physicochemical characteristics of cell surfaces and extracellular proteins. Appl Microbiol Biotechnol 2010; 89:1161-75. [PMID: 20936277 DOI: 10.1007/s00253-010-2919-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/11/2010] [Accepted: 09/11/2010] [Indexed: 10/19/2022]
Abstract
Microbial biofilms contribute to biofouling in a wide range of processes from medical implants to processed food. The extracellular polymeric substances (EPS) are implicated in imparting biofilms with structural stability and resistance to cleaning products. Still, very little is known about the structural role of the EPS in Gram-positive systems. Here, we have compared the cell surface and EPS of surface-attached (biofilm) and free-floating (planktonic) cells of Bacillus cereus, an organism routinely isolated from within biofilms on different surfaces. Our results indicate that the surface properties of cells change during biofilm formation and that the EPS proteins function as non-specific adhesions during biofilm formation. The physicochemical traits of the cell surface and the EPS proteins give us an insight into the forces that drive biofilm formation and maintenance in B. cereus.
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Affiliation(s)
- Esther Karunakaran
- ChELSI Institute Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
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