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Barbosa A, Azevedo NF, Goeres DM, Cerqueira L. Ecology of Legionella pneumophila biofilms: The link between transcriptional activity and the biphasic cycle. Biofilm 2024; 7:100196. [PMID: 38601816 PMCID: PMC11004079 DOI: 10.1016/j.bioflm.2024.100196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/10/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
There has been considerable discussion regarding the environmental life cycle of Legionella pneumophila and its virulence potential in natural and man-made water systems. On the other hand, the bacterium's morphogenetic mechanisms within host cells (amoeba and macrophages) have been well documented and are linked to its ability to transition from a non-virulent, replicative state to an infectious, transmissive state. Although the morphogenetic mechanisms associated with the formation and detachment of the L. pneumophila biofilm have also been described, the capacity of the bacteria to multiply extracellularly is not generally accepted. However, several studies have shown genetic pathways within the biofilm that resemble intracellular mechanisms. Understanding the functionality of L. pneumophila cells within a biofilm is fundamental for assessing the ecology and evaluating how the biofilm architecture influences L. pneumophila survival and persistence in water systems. This manuscript provides an overview of the biphasic cycle of L. pneumophila and its implications in associated intracellular mechanisms in amoeba. It also examines the molecular pathways and gene regulation involved in L. pneumophila biofilm formation and dissemination. A holistic analysis of the transcriptional activities in L. pneumophila biofilms is provided, combining the information of intracellular mechanisms in a comprehensive outline. Furthermore, this review discusses the techniques that can be used to study the morphogenetic states of the bacteria within biofilms, at the single cell and population levels.
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Affiliation(s)
- Ana Barbosa
- LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- ALiCE – Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- ALiCE – Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Darla M. Goeres
- LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- ALiCE – Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- The Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Laura Cerqueira
- LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- ALiCE – Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
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2
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Lee SH, Glover T, Lavey N, Fu X, Donohue M, Karunasena E. Modified in-vitro AATCC-100 procedure to measure viable bacteria from wound dressings. PLoS One 2024; 19:e0298829. [PMID: 38512908 PMCID: PMC10956864 DOI: 10.1371/journal.pone.0298829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/30/2024] [Indexed: 03/23/2024] Open
Abstract
Chronic wounds are reoccurring healthcare problems in the United States and cost up to $50 billion annually. Improper wound care results in complications such as wound debridement, surgical amputation, and increased morbidity/ mortality due to opportunistic infections. To eliminate wound infections, many antimicrobial dressings are developed and submitted to FDA for evaluation. AATCC-100 is a standard method widely used to evaluate cloth wound dressings. This method, requires enrichment, followed by culturing to measure the concentration of culturable organisms; a caveat to this method could result in neglected viable but nonculturable (VBNC) bacteria and overestimate the antimicrobial properties of wound dressings. Therefore, the objectives of this study were to assess this accepted protocol with quantitative real-time polymerase chain reaction (qRT-PCR), to measure time dependent antimicrobial efficacy of wound dressing, and to examine for potential viable bacteria but non-culturable as compared with traditional plating methods. The test organisms included opportunistic pathogens: Pseudomonas aeruginosa (ATCC 15692) and Staphylococcus aureus (ATCC 43300). To mimic a wound dressing environment, samples of commercially available wound dressings (McKesson Inc.) with silver ion (positive control) and dressings without silver ion (positive control) were assessed under sterile conditions. All samples were examined by the original protocol (the extended AATCC-100 method) and qRT-PCR. The expression of specific housekeeping genes was measured (proC for P. aeruginosa and 16s rRNA for S. aureus). Based on these tests, log reduction of experimental conditions was compared to identify time dependent and precise antimicrobial properties from wound dressing samples. These results showed antimicrobial properties of wound dressings diminished as incubation days are increased for both methods from day 1 PCR result of 4.31 ± 0.54 and day 1 plating result of 6.31 ± 3.04 to day 3 PCR result of 1.22 ± 0.97 and day 3 plating result of 5.89 ± 2.41. These results show that data from qRT-PCR generally produced lower standard deviation than that of culture methods, hence shown to be more precise. Complementary parallel analysis of samples using both methods better characterized antimicrobial properties of the tested samples.
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Affiliation(s)
- Sang Hyuk Lee
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
- US Department of Energy, Oak Ridge Institute for Science and Education, Office of Science, Oak Ridge, TN, United States of America
| | - Thomas Glover
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
- US Department of Energy, Oak Ridge Institute for Science and Education, Office of Science, Oak Ridge, TN, United States of America
| | - Nathan Lavey
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
- US Department of Energy, Oak Ridge Institute for Science and Education, Office of Science, Oak Ridge, TN, United States of America
| | - Xiao Fu
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
- US Department of Energy, Oak Ridge Institute for Science and Education, Office of Science, Oak Ridge, TN, United States of America
| | - Marc Donohue
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Enusha Karunasena
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
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Dergham Y, Le Coq D, Nicolas P, Bidnenko E, Dérozier S, Deforet M, Huillet E, Sanchez-Vizuete P, Deschamps J, Hamze K, Briandet R. Direct comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities. Nat Commun 2023; 14:7546. [PMID: 37985771 PMCID: PMC10661151 DOI: 10.1038/s41467-023-43386-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
Bacillus subtilis can form various types of spatially organised communities on surfaces, such as colonies, pellicles and submerged biofilms. These communities share similarities and differences, and phenotypic heterogeneity has been reported for each type of community. Here, we studied spatial transcriptional heterogeneity across the three types of surface-associated communities. Using RNA-seq analysis of different regions or populations for each community type, we identified genes that are specifically expressed within each selected population. We constructed fluorescent transcriptional fusions for 17 of these genes, and observed their expression in submerged biofilms using time-lapse confocal laser scanning microscopy (CLSM). We found mosaic expression patterns for some genes; in particular, we observed spatially segregated cells displaying opposite regulation of carbon metabolism genes (gapA and gapB), indicative of distinct glycolytic or gluconeogenic regimes coexisting in the same biofilm region. Overall, our study provides a direct comparison of spatial transcriptional heterogeneity, at different scales, for the three main models of B. subtilis surface-associated communities.
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Affiliation(s)
- Yasmine Dergham
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Lebanese University, Faculty of Science, Beirut, Lebanon
| | - Dominique Le Coq
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MAIAGE, Jouy-en-Josas, France
| | - Elena Bidnenko
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Sandra Dérozier
- Université Paris-Saclay, INRAE, MAIAGE, Jouy-en-Josas, France
| | - Maxime Deforet
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, Paris, France
| | - Eugénie Huillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pilar Sanchez-Vizuete
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Julien Deschamps
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Kassem Hamze
- Lebanese University, Faculty of Science, Beirut, Lebanon.
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
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4
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Evans CR, Smiley MK, Asahara Thio S, Wei M, Florek LC, Dayton H, Price-Whelan A, Min W, Dietrich LEP. Spatial heterogeneity in biofilm metabolism elicited by local control of phenazine methylation. Proc Natl Acad Sci U S A 2023; 120:e2313208120. [PMID: 37847735 PMCID: PMC10614215 DOI: 10.1073/pnas.2313208120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Within biofilms, gradients of electron acceptors such as oxygen stimulate the formation of physiological subpopulations. This heterogeneity can enable cross-feeding and promote drug resilience, features of the multicellular lifestyle that make biofilm-based infections difficult to treat. The pathogenic bacterium Pseudomonas aeruginosa produces pigments called phenazines that can support metabolic activity in hypoxic/anoxic biofilm subzones, but these compounds also include methylated derivatives that are toxic to their producer under some conditions. In this study, we uncover roles for the global regulators RpoS and Hfq/Crc in controlling the beneficial and detrimental effects of methylated phenazines in biofilms. Our results indicate that RpoS controls phenazine methylation by modulating activity of the carbon catabolite repression pathway, in which the Hfq/Crc complex inhibits translation of the phenazine methyltransferase PhzM. We find that RpoS indirectly inhibits expression of CrcZ, a small RNA that binds to and sequesters Hfq/Crc, specifically in the oxic subzone of P. aeruginosa biofilms. Deletion of rpoS or crc therefore leads to overproduction of methylated phenazines, which we show leads to increased metabolic activity-an apparent beneficial effect-in hypoxic/anoxic subpopulations within biofilms. However, we also find that under specific conditions, biofilms lacking RpoS and/or Crc show increased sensitivity to phenazines indicating that the increased metabolic activity in these mutants comes at a cost. Together, these results suggest that complex regulation of PhzM allows P. aeruginosa to simultaneously exploit the benefits and limit the toxic effects of methylated phenazines.
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Affiliation(s)
| | - Marina K. Smiley
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Sean Asahara Thio
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, NY10027
| | - Lindsey C. Florek
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY10027
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5
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Saint Martin C, Caccia N, Darsonval M, Gregoire M, Combeau A, Jubelin G, Dubois-Brissonnet F, Leroy S, Briandet R, Desvaux M. Spatially localised expression of the glutamate decarboxylase gadB in Escherichia coli O157:H7 microcolonies in hydrogel matrices. NPJ Sci Food 2023; 7:55. [PMID: 37838796 PMCID: PMC10576782 DOI: 10.1038/s41538-023-00229-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Functional diversity within isogenic spatially organised bacterial populations has been shown to trigger emergent community properties such as stress tolerance. Considering gadB gene encoding a key glutamate decarboxylase involved in E. coli tolerance to acidic conditions, we investigated its expression in hydrogels mimicking the texture of some structured food matrices (such as minced meat or soft cheese). Taking advantage of confocal laser scanning microscopy combined with a genetically-engineered dual fluorescent reporter system, it was possible to visualise the spatial patterns of bacterial gene expression from in-gel microcolonies. In E. coli O157:H7 microcolonies, gadB showed radically different expression patterns between neutral (pH 7) or acidic (pH 5) hydrogels. Differential spatial expression was determined in acidic hydrogels with a strong expression of gadB at the microcolony periphery. Strikingly, very similar spatial patterns of gadB expression were further observed for E. coli O157:H7 grown in the presence of L. lactis. Considering the ingestion of contaminated foodstuff, survival of E. coli O157:H7 to acidic stomachal stress (pH 2) was significantly increased for bacterial cells grown in microcolonies in acidic hydrogels compared to planktonic cells. These findings have significant implications for risk assessment and public health as they highlight inherent differences in bacterial physiology and virulence between liquid and structured food products. The contrasting characteristics observed underscore the need to consider the distinct challenges posed by these food types, thereby emphasising the importance of tailored risk mitigation strategies.
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Affiliation(s)
- Cédric Saint Martin
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France
- INRAE, UCA, UMR0454 MEDIS, 63000, Clermont-Ferrand, France
| | - Nelly Caccia
- INRAE, UCA, UMR0454 MEDIS, 63000, Clermont-Ferrand, France
| | - Maud Darsonval
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France
| | - Marina Gregoire
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France
| | - Arthur Combeau
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France
| | | | | | - Sabine Leroy
- INRAE, UCA, UMR0454 MEDIS, 63000, Clermont-Ferrand, France
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France.
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6
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Lichtenberg M, Coenye T, Parsek MR, Bjarnsholt T, Jakobsen TH. What's in a name? Characteristics of clinical biofilms. FEMS Microbiol Rev 2023; 47:fuad050. [PMID: 37656883 PMCID: PMC10503651 DOI: 10.1093/femsre/fuad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/06/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023] Open
Abstract
In vitro biofilms are communities of microbes with unique features compared to individual cells. Biofilms are commonly characterized by physical traits like size, adhesion, and a matrix made of extracellular substances. They display distinct phenotypic features, such as metabolic activity and antibiotic tolerance. However, the relative importance of these traits depends on the environment and bacterial species. Various mechanisms enable biofilm-associated bacteria to withstand antibiotics, including physical barriers, physiological adaptations, and changes in gene expression. Gene expression profiles in biofilms differ from individual cells but, there is little consensus among studies and so far, a 'biofilm signature transcriptome' has not been recognized. Additionally, the spatial and temporal variability within biofilms varies greatly depending on the system or environment. Despite all these variable conditions, which produce very diverse structures, they are all noted as biofilms. We discuss that clinical biofilms may differ from those grown in laboratories and found in the environment and discuss whether the characteristics that are commonly used to define and characterize biofilms have been shown in infectious biofilms. We emphasize that there is a need for a comprehensive understanding of the specific traits that are used to define bacteria in infections as clinical biofilms.
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Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Matthew R Parsek
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., WA 98195 Seattle, United States
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2100 Copenhagen, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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7
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Evans CR, Smiley MK, Thio SA, Wei M, Price-Whelan A, Min W, Dietrich LE. Spatial heterogeneity in biofilm metabolism elicited by local control of phenazine methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528762. [PMID: 36824979 PMCID: PMC9949047 DOI: 10.1101/2023.02.15.528762] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Within biofilms, gradients of electron acceptors such as oxygen stimulate the formation of physiological subpopulations. This heterogeneity can enable cross-feeding and promote drug resilience, features of the multicellular lifestyle that make biofilm-based infections difficult to treat. The pathogenic bacterium Pseudomonas aeruginosa produces pigments called phenazines that can support metabolic activity in hypoxic/anoxic biofilm subzones, but these compounds also include methylated derivatives that are toxic to their producer under some conditions. Here, we uncover roles for the global regulators RpoS and Hfq/Crc in controlling the beneficial and detrimental effects of methylated phenazines in biofilms. Our results indicate that RpoS controls phenazine methylation by modulating activity of the carbon catabolite repression pathway, in which the Hfq/Crc complex inhibits translation of the phenazine methyltransferase PhzM. We find that RpoS indirectly inhibits expression of CrcZ, a small RNA that binds to and sequesters Hfq/Crc, specifically in the oxic subzone of P. aeruginosa biofilms. Deletion of rpoS or crc therefore leads to overproduction of methylated phenazines, which we show leads to increased metabolic activity-an apparent beneficial effect-in hypoxic/anoxic subpopulations within biofilms. However, we also find that biofilms lacking Crc show increased sensitivity to an exogenously added methylated phenazine, indicating that the increased metabolic activity in this mutant comes at a cost. Together, these results suggest that complex regulation of PhzM allows P. aeruginosa to simultaneously exploit the benefits and limit the toxic effects of methylated phenazines.
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Affiliation(s)
| | - Marina K. Smiley
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Sean Asahara Thio
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, NY 10025
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY 10025
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10025
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8
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The biofilm life cycle: expanding the conceptual model of biofilm formation. Nat Rev Microbiol 2022; 20:608-620. [PMID: 35922483 PMCID: PMC9841534 DOI: 10.1038/s41579-022-00767-0] [Citation(s) in RCA: 303] [Impact Index Per Article: 151.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2022] [Indexed: 01/18/2023]
Abstract
Bacterial biofilms are often defined as communities of surface-attached bacteria and are typically depicted with a classic mushroom-shaped structure characteristic of Pseudomonas aeruginosa. However, it has become evident that this is not how all biofilms develop, especially in vivo, in clinical and industrial settings, and in the environment, where biofilms often are observed as non-surface-attached aggregates. In this Review, we describe the origin of the current five-step biofilm development model and why it fails to capture many aspects of bacterial biofilm physiology. We aim to present a simplistic developmental model for biofilm formation that is flexible enough to include all the diverse scenarios and microenvironments where biofilms are formed. With this new expanded, inclusive model, we hereby introduce a common platform for developing an understanding of biofilms and anti-biofilm strategies that can be tailored to the microenvironment under investigation.
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Borges F, Briandet R, Callon C, Champomier-Vergès MC, Christieans S, Chuzeville S, Denis C, Desmasures N, Desmonts MH, Feurer C, Leroi F, Leroy S, Mounier J, Passerini D, Pilet MF, Schlusselhuber M, Stahl V, Strub C, Talon R, Zagorec M. Contribution of omics to biopreservation: Toward food microbiome engineering. Front Microbiol 2022; 13:951182. [PMID: 35983334 PMCID: PMC9379315 DOI: 10.3389/fmicb.2022.951182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/14/2022] [Indexed: 01/12/2023] Open
Abstract
Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.
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Affiliation(s)
- Frédéric Borges
- Université de Lorraine, LIBio, Nancy, France
- *Correspondence: Frédéric Borges,
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage, Aurillac, France
| | | | | | - Sarah Chuzeville
- ACTALIA, Pôle d’Expertise Analytique, Unité Microbiologie Laitière, La Roche sur Foron, France
| | | | | | | | - Carole Feurer
- IFIP, Institut de la Filière Porcine, Le Rheu, France
| | | | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | | | | | | | | | - Caroline Strub
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Régine Talon
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
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10
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Characterization of host-pathogen-device interactions in Pseudomonas aeruginosa infection of breast implants. Plast Reconstr Surg 2022; 150:260e-271e. [PMID: 35653545 DOI: 10.1097/prs.0000000000009315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa (PA) accounts for 7%-22% of breast implant-associated infections (BIAIs), which can result in reconstructive failures and explantation. Investigating host-pathogen-device interactions in mice and patient samples will improve our understanding of colonization mechanisms, for targeted treatments and clinical guidelines. METHODS Mice with and without implants (Mentor®) were infected with PAO1 lab strain or BIP2 or BIP16 clinical strains and sacrificed at 1 day or 7 days post-infection (dpi) to evaluate for colonization of implants and underlying tissues via colony-forming unit (CFU) enumeration. Immunostaining was performed on mouse implants, human tissue expanders (TE) colonized by BIP2, and acellular dermal matrix (ADM) colonized by BIP16. RESULTS Colonization of tissues and smooth implants by P. aeruginosa was strain-dependent: at 1dpi, all strains acutely infected tissues with and without implants with colonization levels reflecting growth rates of individual strains. At 7dpi, PAO1 caused colonization of ~105 CFUs/100mg of tissue but required implant presence, while in mice infected with BIP2/BIP16, CFUs were below the limit of detection with or without implants. Immunofluorescence staining of mouse implants, however, demonstrated continued presence of BIP2 and BIP16. Staining showed co-localization of all strains with fibrinogen, collagen I and collagen III on mouse and human samples. CONCLUSIONS The trajectory of P. aeruginosa in BIAIs was strain-dependent and strains could exhibit acute symptomatic or chronic asymptomatic colonization. With strains causing clinical symptoms, the presence of an implant significantly worsened infection. For asymptomatic colonizers, further studies investigating their long-term impacts, especially during periods of immunosuppression in hosts, are needed.
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11
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Hydrodynamic Effects on Biofilm Development and Recombinant Protein Expression. Microorganisms 2022; 10:microorganisms10050931. [PMID: 35630375 PMCID: PMC9145004 DOI: 10.3390/microorganisms10050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Hydrodynamics play an important role in the rate of cell attachment and nutrient and oxygen transfer, which can affect biofilm development and the level of recombinant protein production. In the present study, the effects of different flow conditions on the development of Escherichia coli biofilms and the expression of a model recombinant protein (enhanced green fluorescent protein, eGFP) were examined. Planktonic and biofilm cells were grown at two different flow rates in a recirculating flow cell system for 7 days: 255 and 128 L h−1 (corresponding to a Reynolds number of 4600 and 2300, respectively). The fluorometric analysis showed that the specific eGFP production was higher in biofilms than in planktonic cells under both hydrodynamic conditions (3-fold higher for 255 L h−1 and 2-fold higher for 128 L h−1). In the biofilm cells, the percentage of eGFP-expressing cells was on average 52% higher at a flow rate of 255 L h−1. Furthermore, a higher plasmid copy number (PCN) was obtained for the highest flow rate for both planktonic (244 PCN/cell versus 118 PCN/cell) and biofilm cells (43 PCN/cell versus 29 PCN/cell). The results suggested that higher flow velocities promoted eGFP expression in E. coli biofilms.
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Masigol M, Radaha EL, Kannan AD, Salberg AG, Fattahi N, Parameswaran P, Hansen RR. Polymer Surface Dissection for Correlated Microscopic and Compositional Analysis of Bacterial Aggregates during Membrane Biofouling. ACS APPLIED BIO MATERIALS 2022; 5:134-145. [PMID: 35014824 DOI: 10.1021/acsabm.1c00971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multispecies biofilms are a common limitation in membrane bioreactors, causing membrane clogging, degradation, and failure. There is a poor understanding of biological fouling mechanisms in these systems due to the limited number of experimental techniques useful for probing microbial interactions at the membrane interface. Here, we develop a new experimental method, termed polymer surface dissection (PSD), to investigate multispecies assembly processes over membrane surfaces. The PSD method uses photodegradable polyethylene glycol hydrogels functionalized with bioaffinity ligands to bind and detach microscale, microbial aggregates from the membrane for microscopic observation. Subsequent exposure of the hydrogel to high resolution, patterned UV light allows for controlled release of any selected aggregate of desired size at high purity for DNA extraction. Follow-up 16S community analysis reveals aggregate composition, correlating microscopic images with the bacterial community structure. The optimized approach can isolate aggregates with microscale spatial precision and yields genomic DNA at sufficient quantity and quality for sequencing from aggregates with areas as low as 2000 μm2, without the need of culturing for sample enrichment. To demonstrate the value of the approach, PSD was used to reveal the composition of microscale aggregates of different sizes during early-stage biofouling of aerobic wastewater communities over PVDF membranes. Larger aggregates exhibited lower diversity of bacterial communities, and a shift in the community structure was found as aggregate size increased to areas between 25,000 and 45,000 μm2, below which aggregates were more enriched in Bacteroidetes and above which aggregates were more enriched with Proteobacteria. The findings demonstrate that community succession can be observed within microscale aggregates and that the PSD method is useful for identification and characterization of early colonizing bacteria that drive biofouling on membrane surfaces.
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Affiliation(s)
- Mohammadali Masigol
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Esther L Radaha
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Arvind D Kannan
- Department of Civil Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Abigail G Salberg
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Niloufar Fattahi
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Prathap Parameswaran
- Department of Civil Engineering, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ryan R Hansen
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506, United States
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Di Salle A, Viscusi G, Di Cristo F, Valentino A, Gorrasi G, Lamberti E, Vittoria V, Calarco A, Peluso G. Antimicrobial and Antibiofilm Activity of Curcumin-Loaded Electrospun Nanofibers for the Prevention of the Biofilm-Associated Infections. Molecules 2021; 26:molecules26164866. [PMID: 34443457 PMCID: PMC8400440 DOI: 10.3390/molecules26164866] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/28/2021] [Accepted: 08/08/2021] [Indexed: 12/22/2022] Open
Abstract
Curcumin extracted from the rhizome of Curcuma Longa has been used in therapeutic preparations for centuries in different parts of the world. However, its bioactivity is limited by chemical instability, water insolubility, low bioavailability, and extensive metabolism. In this study, the coaxial electrospinning technique was used to produce both poly (ε-caprolactone) (PCL)-curcumin and core-shell nanofibers composed of PCL and curcumin in the core and poly (lactic acid) (PLA) in the shell. Morphology and physical properties, as well as the release of curcumin were studied and compared with neat PCL, showing the formation of randomly oriented, defect-free cylindrical fibers with a narrow distribution of the dimensions. The antibacterial and antibiofilm potential, including the capacity to interfere with the quorum-sensing mechanism, was evaluated on Pseudomonas aeruginosa PAO1, and Streptococcus mutans, two opportunistic pathogenic bacteria frequently associated with infections. The reported results demonstrated the ability of the Curcumin-loading membranes to inhibit both PAO1 and S. mutans biofilm growth and activity, thus representing a promising solution for the prevention of biofilm-associated infections. Moreover, the high biocompatibility and the ability to control the oxidative stress of damaged tissue, make the synthesized membranes useful as scaffolds in tissue engineering regeneration, helping to accelerate the healing process.
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Affiliation(s)
- Anna Di Salle
- Research Institute of Terrestrial Ecosystems (IRET)—CNR, Via Castellino, 111, 80131 Naples, Italy; (A.D.S.); (A.V.); (G.P.)
| | - Gianluca Viscusi
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy;
| | | | - Anna Valentino
- Research Institute of Terrestrial Ecosystems (IRET)—CNR, Via Castellino, 111, 80131 Naples, Italy; (A.D.S.); (A.V.); (G.P.)
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale “A. Avogadro”, Largo Donegani, 2, 28100 Novara, Italy
| | - Giuliana Gorrasi
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy;
- Correspondence: (G.G.); (A.C.)
| | - Elena Lamberti
- Nice Filler s.r.l., Via Loggia dei Pisani, 25, 80133 Naples, Italy; (E.L.); (V.V.)
| | - Vittoria Vittoria
- Nice Filler s.r.l., Via Loggia dei Pisani, 25, 80133 Naples, Italy; (E.L.); (V.V.)
| | - Anna Calarco
- Research Institute of Terrestrial Ecosystems (IRET)—CNR, Via Castellino, 111, 80131 Naples, Italy; (A.D.S.); (A.V.); (G.P.)
- Correspondence: (G.G.); (A.C.)
| | - Gianfranco Peluso
- Research Institute of Terrestrial Ecosystems (IRET)—CNR, Via Castellino, 111, 80131 Naples, Italy; (A.D.S.); (A.V.); (G.P.)
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Functional Characterization of the Pseudomonas aeruginosa Ribosome Hibernation-Promoting Factor. J Bacteriol 2020; 202:JB.00280-20. [PMID: 32900865 DOI: 10.1128/jb.00280-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Hibernation-promoting factor (HPF) is a ribosomal accessory protein that inactivates ribosomes during bacterial starvation. In Pseudomonas aeruginosa, HPF protects ribosome integrity while the cells are dormant. The sequence of HPF has diverged among bacteria but contains conserved charged amino acids in its two alpha helices that interact with the rRNA. Here, we characterized the function of HPF in P. aeruginosa by performing mutagenesis of the conserved residues and then assaying mutant HPF alleles for their ability to protect ribosome integrity of starved P. aeruginosa cells. The results show that HPF functionally tolerates point mutations in charged residues and in the conserved Y71 residue as well as a C-terminal truncation. Double and triple mutations of charged residues in helix 1 in combination with a Y71F substitution reduce HPF activity. Screening for single point mutations that caused impaired HPF activity identified additional substitutions in the two HPF alpha helices. However, alanine substitutions in equivalent positions restored HPF activity, indicating that HPF is tolerant to mutations that do not disrupt the protein structure. Surprisingly, heterologous HPFs from Gram-positive bacteria that have long C-terminal domains functionally complement the P. aeruginosa Δhpf mutant, suggesting that HPF may play a similar role in ribosome protection in other bacterial species. Collectively, the results show that HPF has diverged among bacteria and is tolerant to most single amino acid substitutions. The Y71 residue in combination with helix 1 is important for the functional role of HPF in ribosome protection during bacterial starvation and resuscitation of the bacteria from dormancy.IMPORTANCE In most environments, bacteria experience conditions where nutrients may be readily abundant or where nutrients are limited. Under nutrient limitation conditions, even non-spore-forming bacteria may enter a dormant state. Dormancy is accompanied by a variety of cellular physiological changes that are required for the cells to remain viable during dormancy and to resuscitate when nutrients become available. Among the physiological changes that occur in dormant bacteria is the inactivation and preservation of ribosomes by the dormancy protein, hibernation-promoting factor (HPF). In this study, we characterized the activity of HPF of Pseudomonas aeruginosa, an opportunistic pathogen that causes persistent infections, and analyzed the role of HPF in ribosome protection and bacterial survival during dormancy.
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Soares A, Alexandre K, Etienne M. Tolerance and Persistence of Pseudomonas aeruginosa in Biofilms Exposed to Antibiotics: Molecular Mechanisms, Antibiotic Strategies and Therapeutic Perspectives. Front Microbiol 2020; 11:2057. [PMID: 32973737 PMCID: PMC7481396 DOI: 10.3389/fmicb.2020.02057] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/05/2020] [Indexed: 01/19/2023] Open
Abstract
Pseudomonas aeruginosa biofilm-related infections are difficult to treat with antibiotics. Along the different layers of the biofilm, the P. aeruginosa population is heterogeneous, exhibiting an extreme ability to adapt his metabolic activity to the local microenvironment. At the deepest layers of the biofilm is a subset of dormant cells, called persister cells. Though antimicrobial failure might be multifactorial, it is now demonstrated that these persister cells, genetically identical to a fully susceptible strain, but phenotypically divergent, are highly tolerant to antibiotics, and contribute to antimicrobial failure. By eradicating susceptible, metabolically active cells, antibiotics bring out pre-existing persister cells. The biofilm mode of growth creates microenvironment conditions that activate stringent response mechanisms, SOS response and toxin-antitoxin systems that render the bacterial population highly tolerant to antibiotics. Using diverse, not standardized, models of biofilm infection, a large panel of antibiotic regimen has been evaluated. They demonstrated that biofilm growth had an unequal impact of antibiotic activity, colistin and meropenem being the less impacted antibiotics. Different combination and sequential antimicrobial therapies were also evaluated, and could be partially efficient, but none succeeded in eradicating persister cells, so that non-antibiotic alternative strategies are currently under development. This article reviews the molecular mechanisms involved in antibiotic tolerance and persistence in P. aeruginosa biofilm infections. A review of the antimicrobial regimen evaluated for the treatment of P. aeruginosa biofilm infection is also presented. While tremendous progress has been made in the understanding of biofilm-related infections, alternative non-antibiotic strategies are now urgently needed.
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Affiliation(s)
- Anaïs Soares
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France
| | - Kévin Alexandre
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France.,Infectious Diseases Department, Rouen University Hospital, Rouen, France
| | - Manuel Etienne
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France.,Infectious Diseases Department, Rouen University Hospital, Rouen, France
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Omokhua-Uyi AG, Abdalla MA, Leonard CM, Aro A, Uyi OO, Van Staden J, McGaw LJ. Flavonoids isolated from the South African weed Chromolaena odorata (Asteraceae) have pharmacological activity against uropathogens. BMC Complement Med Ther 2020; 20:233. [PMID: 32703212 PMCID: PMC7376718 DOI: 10.1186/s12906-020-03024-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 07/10/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Urinary tract infections (UTIs) caused by opportunistic pathogens are among the leading health challenges globally. Most available treatment options are failing as a result of antibiotic resistance and adverse effects. Natural sources such as plants may serve as promising alternatives. METHODS Compounds were isolated from the South African weed Chromolaena odorata through column chromatography. Purified compounds were tested for antimicrobial activity using the p-iodonitrotetrazolium chloride (INT) colorimetric method, against uropathogenic Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Aspergillus fumigatus and Cryptococcus neoformans. Anti-biofilm, anti-adhesion and metabolic inhibition activities were investigated against selected strains. Safety of the compounds was determined against Vero monkey kidney, C3A human liver and colon (Caco2) cells. RESULTS Four compounds identified as pectolinaringenin (1), (±)-4',5,7-trimethoxy flavanone (2), 5-hydroxy-3,7,4'-trimethoxyflavone (3) and 3,5,7-trihydroxy-4'-methoxyflavone) (4) were isolated. Minimum inhibitory concentration (MIC) varied between 0.016 and 0.25 mg/mL. Compounds 2 and 3 showed promising antimicrobial activity against E. coli, S. aureus, K. pneumoniae, A. fumigatus and C. neoformans with MIC between 0.016 and 0.125 mg/mL, comparable to gentamicin, ciprofloxacin and amphotericin B used as positive controls. Compounds 2 and 3 showed good anti-biofilm and metabolic inhibition activities against E. coli and S. aureus but weak anti-adhesion activity against the organisms. Low toxicity with selectivity indexes between 1 and 12.625 were recorded with the compounds, indicating that the compounds were rather toxic to the microbial strains and not to the human and animal cells. CONCLUSION Pharmacological activities displayed by compounds 2 and 3 isolated from C. odorata and low toxicity recorded credits it as a potential lead for the development of useful prophylactic treatments and anti-infective drugs against UTIs. Although known compounds, this is the first time these compounds have been isolated from the South African weed C. odorata and tested for antimicrobial, anti-biofilm, metabolic inhibition and anti-adhesion activities.
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Affiliation(s)
- Aitebiremen G. Omokhua-Uyi
- Phytomedicine Programme, Department of Paraclinical Sciences, University of Pretoria, Private Bag X04, Onderstepoort, 0110 South Africa
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3201 South Africa
| | - Muna A. Abdalla
- Phytomedicine Programme, Department of Paraclinical Sciences, University of Pretoria, Private Bag X04, Onderstepoort, 0110 South Africa
- Deparment of Food Science and Technology, Faculty of Agriculture, University of Khartoum, 13314 Khartoum North, Sudan
| | - Carmen M. Leonard
- Department of Pharmaceutical Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001 South Africa
| | - Abimbola Aro
- Phytomedicine Programme, Department of Paraclinical Sciences, University of Pretoria, Private Bag X04, Onderstepoort, 0110 South Africa
| | - Osariyekemwen O. Uyi
- Department of Animal and Environmental Biology, University of Benin, P.M.B, Benin City, 1154 Nigeria
| | - Johannes Van Staden
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3201 South Africa
| | - Lyndy J. McGaw
- Phytomedicine Programme, Department of Paraclinical Sciences, University of Pretoria, Private Bag X04, Onderstepoort, 0110 South Africa
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Gomes L, Monteiro G, Mergulhão F. The Impact of IPTG Induction on Plasmid Stability and Heterologous Protein Expression by Escherichia coli Biofilms. Int J Mol Sci 2020; 21:ijms21020576. [PMID: 31963160 PMCID: PMC7013871 DOI: 10.3390/ijms21020576] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 11/30/2022] Open
Abstract
This work assesses the effect of chemical induction with isopropyl β-D-1-thiogalactopyranoside (IPTG) on the expression of enhanced green fluorescent protein (eGFP) by planktonic and biofilm cells of Escherichia coli JM109(DE3) transformed with a plasmid containing a T7 promoter. It was shown that induction negatively affected the growth and viability of planktonic cultures, and eGFP production did not increase. Heterologous protein production was not limited by gene dosage or by transcriptional activity. Results suggest that plasmid maintenance at high copy number imposes a metabolic burden that precludes high level expression of the heterologous protein. In biofilm cells, the inducer avoided the overall decrease in the amount of expressed eGFP, although this was not correlated with the gene dosage. Higher specific production levels were always attained with biofilm cells and it seems that while induction of biofilm cells shifts their metabolism towards the maintenance of heterologous protein concentration, in planktonic cells the cellular resources are directed towards plasmid replication and growth.
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Affiliation(s)
- Luciana Gomes
- LEPABE—Department of Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal;
| | - Gabriel Monteiro
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - Filipe Mergulhão
- LEPABE—Department of Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal;
- Correspondence: ; Tel.: +351-225081668
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Lotlikar SR, Kayastha BB, Vullo D, Khanam SS, Braga RE, Murray AB, McKenna R, Supuran CT, Patrauchan MA. Pseudomonas aeruginosa β-carbonic anhydrase, psCA1, is required for calcium deposition and contributes to virulence. Cell Calcium 2019; 84:102080. [PMID: 31589941 DOI: 10.1016/j.ceca.2019.102080] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/16/2019] [Accepted: 09/07/2019] [Indexed: 01/07/2023]
Abstract
Calcification of soft tissue leads to serious diseases and has been associated with bacterial chronic infections. However, the origin and the molecular mechanisms of calcification remain unclear. Here we hypothesized that a human pathogen Pseudomonas aeruginosa deposits extracellular calcium, a process requiring carbonic anhydrases (CAs). Transmission electron microscopy confirmed the formation of 0.1-0.2 μm deposits by P. aeruginosa PAO1 growing at 5 mM CaCl2, and X-ray elemental analysis confirmed they contain calcium. Quantitative analysis of deposited calcium showed that PAO1 deposits 0.35 and 0.75 mM calcium/mg protein when grown at 5 mM and 10 mM CaCl2, correspondingly. Fluorescent microscopy indicated that deposition initiates at the cell surface. We have previously characterized three PAO1 β-class CAs: psCA1, psCA2, and psCA3 that hydrate CO2 to HCO3-, among which psCA1 showed the highest catalytic activity (Lotlikar et. al. 2013). According to immunoblot and RT-qPCR, growth at elevated calcium levels increases the expression of psCA1. Analyses of the deletion mutants lacking one, two or all three psCA genes, determined that psCA1 plays a major role in calcium deposition and contributes to the pathogen's virulence. In-silico modeling of the PAO1 β-class CAs identified four amino acids that differ in psCA1 compared to psCA2, and psCA3 (T59, A61A, A101, and A108), and these differences may play a role in catalytic rate and thus calcium deposition. A series of inhibitors were tested against the recombinant psCA1, among which aminobenzene sulfonamide (ABS) and acetazolamide (AAZ), which inhibited psCA1 catalytic activity with KIs of 19 nM and 37 nM, correspondingly. The addition of ABS and AAZ to growing PAO1 reduced calcium deposition by 41 and 78, respectively. Hence, for the first time, we showed that the β-CA psCA1 in P. aeruginosa contributes to virulence likely by enabling calcium salt deposition, which can be partially controlled by inhibiting its catalytic activity.
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Affiliation(s)
- Shalaka R Lotlikar
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Biraj B Kayastha
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Daniela Vullo
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sharmily S Khanam
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Reygan E Braga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Akilah B Murray
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Polo Scientifico, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA.
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Soares A, Azevedo A, Gomes LC, Mergulhão FJ. Recombinant protein expression in biofilms. AIMS Microbiol 2019; 5:232-250. [PMID: 31663059 PMCID: PMC6787351 DOI: 10.3934/microbiol.2019.3.232] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022] Open
Abstract
Biofilm research is usually focused on the prevention or control of biofilm formation. Recently, the significance of the biofilm mode of growth in biotechnological applications received increased attention. Since biofilm reactors show many advantages over suspended cell reactors, especially in their higher biomass density and operational stability, bacterial biofilms have emerged as an interesting approach for the expression of specific proteins. Despite the potential of biofilm systems, recombinant protein production using biofilms has been scarcely investigated for the past 25 years. Our group has demonstrated that E. coli biofilms were able to produce a model recombinant protein, the enhanced green fluorescent protein (eGFP), at much higher levels than their planktonic counterparts. Even without optimization of cultivation conditions, an attractive productivity was obtained, indicating that biofilm cultures can be used as an alternative form of high cell density cultivation (HCDC). E. coli remains one of the favorite hosts for recombinant protein production and it has been successfully used in metabolic engineering for the synthesis of high value products. This review presents the advantages and concerns of using biofilms for the production of recombinant proteins and summarizes the different biofilm systems which have been described for this purpose. The relative advantages and disadvantages of the four microbial hosts tested for recombinant protein production in biofilms (two bacteria and two filamentous fungi) are also discussed.
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Affiliation(s)
- Alexandra Soares
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Luciana C Gomes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Filipe J Mergulhão
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Bisht K, Wakeman CA. Discovery and Therapeutic Targeting of Differentiated Biofilm Subpopulations. Front Microbiol 2019; 10:1908. [PMID: 31507548 PMCID: PMC6718512 DOI: 10.3389/fmicb.2019.01908] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022] Open
Abstract
The association of microorganisms into biofilms produces functionally organized microbial structures that promote community survival in a wide range of environments. Much like when individual cells within a multicellular organism express different genes from the same DNA blueprint, individual microbial cells located within different regions of a biofilm structure can exhibit distinct genetic programs. These spatially defined regions of physiologically differentiated cells are reminiscent of the role of tissues in multicellular organisms, with specific subpopulations in the microbial community serving defined roles to promote the overall health of the biofilm. The functions of these subpopulations are quite diverse and can range from dormant cells that can withstand antibiotic onslaughts to cells actively producing extracellular polymeric substances providing integrity to the entire community. The purpose of this review is to discuss the diverse roles of subpopulations in the stability and function of clonal biofilms, the methods for studying these subpopulations, and the ways these subpopulations can potentially be exploited for therapeutic intervention.
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Affiliation(s)
- Karishma Bisht
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Catherine Ann Wakeman
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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Jain N, Mansuri A. Stopping the Unstoppable: Unconventional Methods to Prevent the Biofilm Growth. Curr Drug Discov Technol 2019; 17:515-522. [PMID: 31362660 DOI: 10.2174/1570163816666190726153441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/11/2019] [Accepted: 06/03/2019] [Indexed: 12/18/2022]
Abstract
Biofilms are consortia of microorganisms encased in extracellular matrix that protect cells from adverse conditions. A biofilm matrix is typically composed of extracellular DNA, cellulose and proteinaceous amyloid fibers. The matrix aids in adhesion to abiotic and biotic surface including medical devices and host tissues. The presence of biofilm makes bacteria more resilient and non-responsive to most current treatment regimes at disposal. Therefore, biofilm-associated infections are serious threat in hospital settings and pose a huge burden on economy. Inhibition of matrix components (cellulose and/or amyloid formation) has emerged as a lucrative alternative strategy to cure biofilm-related infections and combat antibiotic resistance. Here we review the current and emerging therapeutic interventions to mitigate persistent infections due to biofilms. The successful implementation of these interventions will have a huge impact on alleviating the current financial burden on healthcare services.
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Affiliation(s)
- Neha Jain
- Department of Bioscience and Bioengineering, Indian Institute of Technology (IIT) Jodhpur, NH 65, Nagaur Road, Karwar, Jodhpur (Rajasthan), India
| | - Abdulkhalik Mansuri
- Department of Bioscience and Bioengineering, Indian Institute of Technology (IIT) Jodhpur, NH 65, Nagaur Road, Karwar, Jodhpur (Rajasthan), India
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Wu S, Wu H, Button M, Konnerup D, Brix H. Impact of engineered nanoparticles on microbial transformations of carbon, nitrogen, and phosphorus in wastewater treatment processes - A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:1144-1154. [PMID: 30743910 DOI: 10.1016/j.scitotenv.2019.01.106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
Concern regarding the potential negative impacts of released engineered nanoparticles (ENPs) on pollutant removal performance of wastewater treatment systems has received booming attention in recent years. However, the conclusions drawn from different studies often lead to fragmented overall knowledge, some of which are even contradictory. This scenario shows the necessity for a comprehensive review of the interactions of ENPs in wastewater treatment systems, particularly on the impacts of ENPs on microbial processes of carbon (C), nitrogen (N), and phosphorus (P) removal in water treatment systems. This review introduced the impact of 6 often reported ENPs in 5 types of treatment systems. We found that exposure to most of the investigated ENPs at low concentrations doesn't adversely influence the growth of the heterotrophic microbes, which are responsible for organic matter removal. The impacts of ENPs on various microbial nitrogen transformation processes have been investigated. Dosing of ENPs often causes acute microbial nitrogen removal inhibition at various concentrations, but does not influence long-term operation due to microbial adaption. No significant negative effects on biological phosphorus removal in different wastewater treatment processes have been reported after both short-term and long-term exposure (except copper nanoparticles). Environmentally relevant concentrations of ENPs have been reported to enhance the photosynthetic capacity of wetland plants, whereas chronic inhibition to photosynthesis was found in exposure to high concentrations of ENPs. Inhibition effects are often overestimated in pure cultivated toxicity test assays compared to testing with artificially prepared wastewater containing various ingredients or with real wastewater. Potential ligands in real wastewater can bind with ENPs and lower their dissolution. Some challenges exist regarding detection and quantification techniques of ENPs at environmental concentrations, modeling of engineered nanomaterial release on a worldwide scale, and inhibitory mechanisms to microbial transformations.
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Affiliation(s)
- Shubiao Wu
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus 8000C, Denmark; Department of Bioscience, Aarhus University, Aarhus 8000C, Denmark.
| | - Haiming Wu
- College of Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Mark Button
- Department of Earth and Environmental Sciences, University of British Columbia - Okanagan, Kelowna, British Columbia, Canada
| | - Dennis Konnerup
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus 8000C, Denmark; Department of Bioscience, Aarhus University, Aarhus 8000C, Denmark
| | - Hans Brix
- Department of Bioscience, Aarhus University, Aarhus 8000C, Denmark
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Neale HC, Jackson RW, Preston GM, Arnold DL. Supercoiling of an excised genomic island represses effector gene expression to prevent activation of host resistance. Mol Microbiol 2018; 110:444-454. [PMID: 30152900 PMCID: PMC6220960 DOI: 10.1111/mmi.14111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 01/18/2023]
Abstract
The plant pathogen Pseudomonas syringae pv. phaseolicola, which causes halo blight disease of beans, contains a 106 kb genomic island PPHGI‐1. PPHGI‐1 carries a gene, avrPphB, which encodes an effector protein that triggers a resistance response in certain bean cultivars. Previous studies have shown that when PPHGI‐1 is excised from the bacterial chromosome, avrPphB is downregulated and therefore the pathogen avoids triggering the host’s defence mechanism. Here, we investigate whether the downregulation of avrPphB is caused by the supercoiling of PPHGI‐1. We also investigate the effect of a PPHGI‐1‐encoded type 1A topoisomerase, TopB3, on island stability and bacterial pathogenicity in the plant. Supercoiling inhibitors significantly increased the expression of avrPphB but did not affect the excision of PPHGI‐1. An insertional mutant of topB3 displayed an increase in avrPphB expression and an increase in PPHGI‐1 excision as well as reduced population growth in resistant and susceptible cultivars of bean. These results suggest an important role for topoisomerases in the maintenance and stability of a bacterial‐encoded genomic island and demonstrate that supercoiling is involved in the downregulation of an effector gene once the island has been excised, allowing the pathogen to prevent further activation of the host defence response.
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Affiliation(s)
- Helen C Neale
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, The University of the West of England, Frenchay Campus, Bristol, BS16 1QY, UK
| | - Robert W Jackson
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Dawn L Arnold
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, The University of the West of England, Frenchay Campus, Bristol, BS16 1QY, UK
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25
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Ben Hamed S, Tavares Ranzani-Paiva MJ, Tachibana L, de Carla Dias D, Ishikawa CM, Esteban MA. Fish pathogen bacteria: Adhesion, parameters influencing virulence and interaction with host cells. FISH & SHELLFISH IMMUNOLOGY 2018; 80:550-562. [PMID: 29966687 DOI: 10.1016/j.fsi.2018.06.053] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/04/2018] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
Wild fisheries are declining due to over-fishing, climate change, pollution and marine habitat destructions among other factors, and, concomitantly, aquaculture is increasing significantly around the world. Fish infections caused by pathogenic bacteria are quite common in aquaculture, although their seriousness depends on the season. Drug-supplemented feeds are often used to keep farmed fish free from the diseases caused by such bacteria. However, given that bacteria can survive well in aquatic environments independently of their hosts, bacterial diseases have become major impediments to aquaculture development. On the other hand, the indiscriminate uses of antimicrobial agents has led to resistant strains and the need to switch to other antibiotics, although it seems that an integrated approach that considers not only the pathogen but also the host and the environment will be the most effective method in the long-term to improve aquatic animal health. This review covers the mechanisms of bacterial pathogenicity and details the foundations underlying the interactions occurring between pathogenic bacteria and the fish host in the aquatic environment, as well as the factors that influence virulence. Understanding and linking the different phenomena that occur from adhesion to colonization of the host will offer novel and useful means to help design suitable therapeutic strategies for disease prevention and treatment.
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Affiliation(s)
- Said Ben Hamed
- Fishery Institute-APTA - SAA, Research Center of Aquaculture, Av. Francisco Matarazzo, 455, CEP. 05001-900, Sao Paulo, SP, Brazil
| | - Maria José Tavares Ranzani-Paiva
- Fishery Institute-APTA - SAA, Research Center of Aquaculture, Av. Francisco Matarazzo, 455, CEP. 05001-900, Sao Paulo, SP, Brazil
| | - Leonardo Tachibana
- Fishery Institute-APTA - SAA, Research Center of Aquaculture, Av. Francisco Matarazzo, 455, CEP. 05001-900, Sao Paulo, SP, Brazil
| | - Danielle de Carla Dias
- Fishery Institute-APTA - SAA, Research Center of Aquaculture, Av. Francisco Matarazzo, 455, CEP. 05001-900, Sao Paulo, SP, Brazil
| | - Carlos Massatoshi Ishikawa
- Fishery Institute-APTA - SAA, Research Center of Aquaculture, Av. Francisco Matarazzo, 455, CEP. 05001-900, Sao Paulo, SP, Brazil
| | - María Angeles Esteban
- Fish Innate Immune System Group, Department of Cell Biology & Histology, Faculty of Biology, Regional Campus of International Excellence, ''Campus Mare Nostrum'', University of Murcia, 30100, Murcia, Spain.
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26
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Klauck G, Serra DO, Possling A, Hengge R. Spatial organization of different sigma factor activities and c-di-GMP signalling within the three-dimensional landscape of a bacterial biofilm. Open Biol 2018; 8:180066. [PMID: 30135237 PMCID: PMC6119863 DOI: 10.1098/rsob.180066] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/18/2018] [Indexed: 12/25/2022] Open
Abstract
Bacterial biofilms are large aggregates of cells embedded in an extracellular matrix of self-produced polymers. In macrocolony biofilms of Escherichia coli, this matrix is generated in the upper biofilm layer only and shows a surprisingly complex supracellular architecture. Stratified matrix production follows the vertical nutrient gradient and requires the stationary phase σS (RpoS) subunit of RNA polymerase and the second messenger c-di-GMP. By visualizing global gene expression patterns with a newly designed fingerprint set of Gfp reporter fusions, our study reveals the spatial order of differential sigma factor activities, stringent control of ribosomal gene expression and c-di-GMP signalling in vertically cryosectioned macrocolony biofilms. Long-range physiological stratification shows a duplication of the growth-to-stationary phase pattern that integrates nutrient and oxygen gradients. In addition, distinct short-range heterogeneity occurs within specific biofilm strata and correlates with visually different zones of the refined matrix architecture. These results introduce a new conceptual framework for the control of biofilm formation and demonstrate that the intriguing extracellular matrix architecture, which determines the emergent physiological and biomechanical properties of biofilms, results from the spatial interplay of global gene regulation and microenvironmental conditions. Overall, mature bacterial macrocolony biofilms thus resemble the highly organized tissues of multicellular organisms.
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Affiliation(s)
- Gisela Klauck
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Diego O Serra
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Alexandra Possling
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin 10115, Germany
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Lo YL, Chen CL, Shen L, Chen YC, Wang YH, Lee CC, Wang LC, Chuang CH, Janapatla RP, Chiu CH, Chang HY. Characterization of the role of global regulator FliA in the pathophysiology of Pseudomonas aeruginosa infection. Res Microbiol 2018; 169:135-144. [PMID: 29432810 DOI: 10.1016/j.resmic.2018.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 12/29/2022]
Abstract
FliA is known to be a sigma factor that regulates bacterial flagella gene expression. Accumulating evidence suggests that FliA is involved in bacterial behavior other than motility. To elucidate the contribution of FliA to Pseudomonas aeruginosa pathophysiology, we analyzed the biological properties and gene expression profiles of a ΔfliA mutant. Transcriptome analysis results demonstrated that the expression levels of flagella biogenesis genes decreased dramatically in the mutant; consequently, the ΔfliA mutant failed to synthesize flagella and exhibited reduced motility. The ΔfliA mutant displayed stronger hemolytic and caseinolytic activities, as well as pyocyanin production. The expression of type 6 secretion system-II genes and interbacterial competition activity was decreased in the ΔfliA mutant. Direct evidence of fliA participation in virulence was obtained from analysis of hypervirulent strain B136-33. Adhesion to and cytotoxicity toward mammalian cells and penetration through cell layers were noted; furthermore, the colonization ability of the fliA::Tn5 mutant in the intestines of laboratory mice was compromised. Notably, the fliA-overexpressing strain displayed phenotypes similar to that of the fliA-defective strain, indicating that optimal FliA levels are critical to bacterial physiology. Our findings indicate that FliA plays diverse roles in P. aeruginosa, not only in flagella biosynthesis, but also in pathophysiology.
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Affiliation(s)
- Yi-Ling Lo
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Lunda Shen
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Ying-Ching Chen
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Hsin Wang
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chung-Chan Lee
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Lian-Chen Wang
- Division of Parasitology, Chang Gung University, Taoyuan, Taiwan
| | | | - Rajendra Prasad Janapatla
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Hwan-You Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan.
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28
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Hall CW, Mah TF. Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria. FEMS Microbiol Rev 2018; 41:276-301. [PMID: 28369412 DOI: 10.1093/femsre/fux010] [Citation(s) in RCA: 849] [Impact Index Per Article: 141.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/22/2017] [Indexed: 02/06/2023] Open
Abstract
Biofilms are surface-attached groups of microbial cells encased in an extracellular matrix that are significantly less susceptible to antimicrobial agents than non-adherent, planktonic cells. Biofilm-based infections are, as a result, extremely difficult to cure. A wide range of molecular mechanisms contribute to the high degree of recalcitrance that is characteristic of biofilm communities. These mechanisms include, among others, interaction of antimicrobials with biofilm matrix components, reduced growth rates and the various actions of specific genetic determinants of antibiotic resistance and tolerance. Alone, each of these mechanisms only partially accounts for the increased antimicrobial recalcitrance observed in biofilms. Acting in concert, however, these defences help to ensure the survival of biofilm cells in the face of even the most aggressive antimicrobial treatment regimens. This review summarises both historical and recent scientific data in support of the known biofilm resistance and tolerance mechanisms. Additionally, suggestions for future work in the field are provided.
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29
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Abstract
One common feature of biofilm development is the active dispersal of cells from the mature biofilm, which completes the biofilm life cycle and allows for the subsequent colonization of new habitats. Dispersal is likely to be critical for species survival and appears to be a precisely regulated process that involves a complex network of genes and signal transduction systems. Sophisticated molecular mechanisms control the transition of sessile biofilm cells into dispersal cells and their coordinated detachment and release in the bulk liquid. Dispersal cells appear to be specialized and exhibit a unique phenotype different from biofilm or planktonic bacteria. Further, the dispersal population is characterized by a high level of heterogeneity, reminiscent of, but distinct from, that in the biofilm, which could potentially allow for improved colonization under various environmental conditions. Here we review recent advances in characterizing the molecular mechanisms that regulate biofilm dispersal events and the impact of dispersal in a broader ecological context. Several strategies that exploit the mechanisms controlling biofilm dispersal to develop as applications for biofilm control are also presented.
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30
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Valentini M, Gonzalez D, Mavridou DA, Filloux A. Lifestyle transitions and adaptive pathogenesis of Pseudomonas aeruginosa. Curr Opin Microbiol 2017; 41:15-20. [PMID: 29166621 DOI: 10.1016/j.mib.2017.11.006] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 02/06/2023]
Abstract
Pseudomonas aeruginosa acute and chronic infections are of great concern to human health, especially in hospital settings. It is currently assumed that P. aeruginosa has two antagonistic pathogenic strategies that parallel two different lifestyles; free-living cells are predominantly cytotoxic and induce an acute inflammatory reaction, while biofilm-forming communities cause refractory chronic infections. Recent findings suggest that the planktonic-to-sessile transition is a complex, reversible and overall dynamic differentiation process. Here, we examine how the Gac/Rsm regulatory cascade, a key player in this lifestyle switch, endows P. aeruginosa with both a permissive lifecycle in nature and flexible virulence strategy during infection.
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Affiliation(s)
- Martina Valentini
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom.
| | - Diego Gonzalez
- Département de Microbiologie Fondamentale, Université de Lausanne, CH-1015 Lausanne, Switzerland
| | - Despoina Ai Mavridou
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom.
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31
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Wilson C, Lukowicz R, Merchant S, Valquier-Flynn H, Caballero J, Sandoval J, Okuom M, Huber C, Brooks TD, Wilson E, Clement B, Wentworth CD, Holmes AE. Quantitative and Qualitative Assessment Methods for Biofilm Growth: A Mini-review. RESEARCH & REVIEWS. JOURNAL OF ENGINEERING AND TECHNOLOGY 2017; 6:http://www.rroij.com/open-access/quantitative-and-qualitative-assessment-methods-for-biofilm-growth-a-minireview-.pdf. [PMID: 30214915 PMCID: PMC6133255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biofilms are microbial communities attached to a surface and embedded in an extracellular polymeric substance which provides for the protection, stability and nutrients of the various bacterial species indwelling. These communities can build up in a variety of different environments from industrial equipment to medical devices resulting in damage, loss of productivity and disease. They also have great potential for economic and societal benefits as bioremediation agents and renewable energy sources. The great potential benefits and threats of biofilms has encouraged researchers across disciplines to study biofilm characteristics and antibiofilm strategies resulting in chemists, physicists, material scientists, and engineers, to develop beneficial biofilm applications and prevention methods. The ultimate outcome is a wealth of knowledge and innovative technology. However, without extensive formal training in microbes and biofilm research, these scientists find a daunting array of established techniques for growing, quantifying and characterizing biofilms while trying to design experiments and develop innovative laboratory protocols. This mini-review focuses on enriching interdisciplinary efforts and understanding by overviewing a variety of quantitative and qualitative biofilm characterization methods to assist the novice researcher in assay selection. This review consists of four parts. Part 1 is a brief overview of biofilms and the unique properties that demand a highly interdisciplinary approach. Part 2 describes the classical quantification techniques including colony forming unit (CFU) counting and crystal violet staining, but also introduces some modern methods including ATP bioluminescence and quartz crystal microbalance. Part 3 focuses on the characterization of biofilm morphology and chemistry including scanning electron microscopy and spectroscopic methods. Finally, Part 4 illustrates the use of software, including ImageJ and predictive modeling platforms, for biofilm analysis. Each section highlights the most common methods, including literature references, to help novice biofilm researchers make choices which commensurate with their study goals, budget and available equipment.
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Affiliation(s)
- Christina Wilson
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Rachel Lukowicz
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Stefan Merchant
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Helena Valquier-Flynn
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Jeniffer Caballero
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Jasmin Sandoval
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Macduff Okuom
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Christopher Huber
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Tessa Durham Brooks
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | - Erin Wilson
- Department of Chemistry, Westminster College, New Wilmington, Pennsylvania
| | - Barbara Clement
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
| | | | - Andrea E Holmes
- Department of Chemistry, Biology, Physics & Engineering, Doane University, Crete, Nebraska
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32
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Heacock-Kang Y, Sun Z, Zarzycki-Siek J, McMillan IA, Norris MH, Bluhm AP, Cabanas D, Fogen D, Vo H, Donachie SP, Borlee BR, Sibley CD, Lewenza S, Schurr MJ, Schweizer HP, Hoang TT. Spatial transcriptomes within the Pseudomonas aeruginosa biofilm architecture. Mol Microbiol 2017; 106:976-985. [PMID: 29030956 PMCID: PMC5720903 DOI: 10.1111/mmi.13863] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 01/24/2023]
Abstract
Bacterial cooperative associations and dynamics in biofilm microenvironments are of special interest in recent years. Knowledge of localized gene‐expression and corresponding bacterial behaviors within the biofilm architecture at a global scale has been limited, due to a lack of robust technology to study limited number of cells in stratified layers of biofilms. With our recent pioneering developments in single bacterial cell transcriptomic analysis technology, we generated herein an unprecedented spatial transcriptome map of the mature in vitro Pseudomonas aeruginosa biofilm model, revealing contemporaneous yet altered bacterial behaviors at different layers within the biofilm architecture (i.e., surface, middle and interior of the biofilm). Many genes encoding unknown functions were highly expressed at the biofilm‐solid interphase, exposing a critical gap in the knowledge of their activities that may be unique to this interior niche. Several genes of unknown functions are critical for biofilm formation. The in vivo importance of these unknown proteins was validated in invertebrate (fruit fly) and vertebrate (mouse) models. We envisage the future value of this report to the community, in aiding the further pathophysiological understanding of P. aeruginosa biofilms. Our approach will open doors to the study of bacterial functional genomics of different species in numerous settings.
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Affiliation(s)
- Yun Heacock-Kang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Zhenxin Sun
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jan Zarzycki-Siek
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Ian A McMillan
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA.,Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Michael H Norris
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Andrew P Bluhm
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Darlene Cabanas
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dawson Fogen
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Hung Vo
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Stuart P Donachie
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Bradley R Borlee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Christopher D Sibley
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Shawn Lewenza
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Michael J Schurr
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, USA
| | - Herbert P Schweizer
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Tung T Hoang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, USA.,Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
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Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms. mBio 2017; 8:mBio.01593-17. [PMID: 29066549 PMCID: PMC5654934 DOI: 10.1128/mbio.01593-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Biofilm infections exhibit high tolerance against antibiotic treatment. The study of biofilms is complicated by phenotypic heterogeneity; biofilm subpopulations differ in their metabolic activities and their responses to antibiotics. Here, we describe the use of the bio-orthogonal noncanonical amino acid tagging (BONCAT) method to enable selective proteomic analysis of a Pseudomonas aeruginosa biofilm subpopulation. Through controlled expression of a mutant methionyl-tRNA synthetase, we targeted BONCAT labeling to cells in the regions of biofilm microcolonies that showed increased tolerance to antibiotics. We enriched and identified proteins synthesized by cells in these regions. Compared to the entire biofilm proteome, the labeled subpopulation was characterized by a lower abundance of ribosomal proteins and was enriched in proteins of unknown function. We performed a pulse-labeling experiment to determine the dynamic proteomic response of the tolerant subpopulation to supra-MIC treatment with the fluoroquinolone antibiotic ciprofloxacin. The adaptive response included the upregulation of proteins required for sensing and repairing DNA damage and substantial changes in the expression of enzymes involved in central carbon metabolism. We differentiated the immediate proteomic response, characterized by an increase in flagellar motility, from the long-term adaptive strategy, which included the upregulation of purine synthesis. This targeted, selective analysis of a bacterial subpopulation demonstrates how the study of proteome dynamics can enhance our understanding of biofilm heterogeneity and antibiotic tolerance. Bacterial growth is frequently characterized by behavioral heterogeneity at the single-cell level. Heterogeneity is especially evident in the physiology of biofilms, in which distinct cellular subpopulations can respond differently to stresses, including subpopulations of pathogenic biofilms that are more tolerant to antibiotics. Global proteomic analysis affords insights into cellular physiology but cannot identify proteins expressed in a particular subpopulation of interest. Here, we report a chemical biology method to selectively label, enrich, and identify proteins expressed by cells within distinct regions of biofilm microcolonies. We used this approach to study changes in protein synthesis by the subpopulation of antibiotic-tolerant cells throughout a course of treatment. We found substantial differences between the initial response and the long-term adaptive strategy that biofilm cells use to cope with antibiotic stress. The method we describe is readily applicable to investigations of bacterial heterogeneity in diverse contexts.
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34
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Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms. mBio 2017. [PMID: 29066549 DOI: 10.1128/mbio.01593‐17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilm infections exhibit high tolerance against antibiotic treatment. The study of biofilms is complicated by phenotypic heterogeneity; biofilm subpopulations differ in their metabolic activities and their responses to antibiotics. Here, we describe the use of the bio-orthogonal noncanonical amino acid tagging (BONCAT) method to enable selective proteomic analysis of a Pseudomonas aeruginosa biofilm subpopulation. Through controlled expression of a mutant methionyl-tRNA synthetase, we targeted BONCAT labeling to cells in the regions of biofilm microcolonies that showed increased tolerance to antibiotics. We enriched and identified proteins synthesized by cells in these regions. Compared to the entire biofilm proteome, the labeled subpopulation was characterized by a lower abundance of ribosomal proteins and was enriched in proteins of unknown function. We performed a pulse-labeling experiment to determine the dynamic proteomic response of the tolerant subpopulation to supra-MIC treatment with the fluoroquinolone antibiotic ciprofloxacin. The adaptive response included the upregulation of proteins required for sensing and repairing DNA damage and substantial changes in the expression of enzymes involved in central carbon metabolism. We differentiated the immediate proteomic response, characterized by an increase in flagellar motility, from the long-term adaptive strategy, which included the upregulation of purine synthesis. This targeted, selective analysis of a bacterial subpopulation demonstrates how the study of proteome dynamics can enhance our understanding of biofilm heterogeneity and antibiotic tolerance.IMPORTANCE Bacterial growth is frequently characterized by behavioral heterogeneity at the single-cell level. Heterogeneity is especially evident in the physiology of biofilms, in which distinct cellular subpopulations can respond differently to stresses, including subpopulations of pathogenic biofilms that are more tolerant to antibiotics. Global proteomic analysis affords insights into cellular physiology but cannot identify proteins expressed in a particular subpopulation of interest. Here, we report a chemical biology method to selectively label, enrich, and identify proteins expressed by cells within distinct regions of biofilm microcolonies. We used this approach to study changes in protein synthesis by the subpopulation of antibiotic-tolerant cells throughout a course of treatment. We found substantial differences between the initial response and the long-term adaptive strategy that biofilm cells use to cope with antibiotic stress. The method we describe is readily applicable to investigations of bacterial heterogeneity in diverse contexts.
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35
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Costa AM, Mergulhão FJ, Briandet R, Azevedo NF. It is all about location: how to pinpoint microorganisms and their functions in multispecies biofilms. Future Microbiol 2017; 12:987-999. [PMID: 28745517 DOI: 10.2217/fmb-2017-0053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multispecies biofilms represent the dominant mode of life for the vast majority of microorganisms. Bacterial spatial localization in such biostructures governs ecological interactions between different populations and triggers the overall community functions. Here, we discuss the pros and cons of fluorescence-based techniques used to decipher bacterial species patterns in biofilms at single cell level, including fluorescence in situ hybridization and the use of genetically modified bacteria that express fluorescent proteins, reporting the significant improvements of those techniques. The development of tools for spatial and temporal study of multispecies biofilms will allow live imaging and spatial localization of cells in naturally occurring biofilms coupled with metabolic information, increasing insight of microbial community and the relation between its structure and functions.
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Affiliation(s)
- Angela M Costa
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal.,INEB - Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Filipe J Mergulhão
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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Bridier A, Piard JC, Pandin C, Labarthe S, Dubois-Brissonnet F, Briandet R. Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities. Front Microbiol 2017; 8:1364. [PMID: 28775718 PMCID: PMC5517491 DOI: 10.3389/fmicb.2017.01364] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Biofilms are dynamic habitats which constantly evolve in response to environmental fluctuations and thereby constitute remarkable survival strategies for microorganisms. The modulation of biofilm functional properties is largely governed by the active remodeling of their three-dimensional structure and involves an arsenal of microbial self-produced components and interconnected mechanisms. The production of matrix components, the spatial reorganization of ecological interactions, the generation of physiological heterogeneity, the regulation of motility, the production of actives enzymes are for instance some of the processes enabling such spatial organization plasticity. In this contribution, we discussed the foundations of architectural plasticity as an adaptive driver of biofilms through the review of the different microbial strategies involved. Moreover, the possibility to harness such characteristics to sculpt biofilm structure as an attractive approach to control their functional properties, whether beneficial or deleterious, is also discussed.
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Affiliation(s)
- Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, ANSESFougères, France
| | - Jean-Christophe Piard
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Caroline Pandin
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Simon Labarthe
- MaIAGE, INRA, Université Paris-SaclayJouy-en-Josas, France
| | | | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
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Podgorny OV, Lazarev VN. Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts. J Microbiol Methods 2017; 138:82-92. [PMID: 26775287 DOI: 10.1016/j.mimet.2016.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/11/2015] [Accepted: 01/01/2016] [Indexed: 12/14/2022]
Abstract
Laser microdissection is a method that allows for the isolation of homogenous cell populations from their native niches in tissues for downstream molecular assays. This method is widely used for genomic analysis, gene expression profiling and proteomic and metabolite assays in various fields of biology, but it remains an uncommon approach in microbiological research. In spite of the limited number of publications, laser microdissection was shown to be an extremely useful method for studying host-microorganism interactions in animals and plants, investigating bacteria within biofilms, identifying uncultivated bacteria and performing single prokaryotic cell analysis. The current paper describes the methodological aspects of commercially available laser microdissection instruments and representative examples that demonstrate the advantages of this method for resolving a variety of issues in microbiology.
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Affiliation(s)
- Oleg V Podgorny
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str., Moscow 119435, Russia; Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 26 Vavilov Str., Moscow 119334, Russia.
| | - Vassili N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str., Moscow 119435, Russia
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Camps J, Iftimie S, García-Heredia A, Castro A, Joven J. Paraoxonases and infectious diseases. Clin Biochem 2017; 50:804-811. [PMID: 28433610 DOI: 10.1016/j.clinbiochem.2017.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/18/2017] [Accepted: 04/18/2017] [Indexed: 12/14/2022]
Abstract
The paraoxonases (PON1, PON2 and PON3) are an enzyme family with a high structural homology. All of them have lactonase activity and degrade lipid peroxides in lipoproteins and cells. As such, they play a role in protection against oxidation and inflammation. Infectious diseases are often associated with oxidative stress and an inflammatory response. Infection and inflammation trigger a cascade of reactions in the host, known as the acute-phase response. This response is associated with dramatic changes in serum proteins and lipoproteins, including a decrease in serum PON1 activity. These alterations have clinical consequences for the infected patient, including an increased risk for cardiovascular diseases, and an impaired protection against the formation of antibiotic-resistant bacterial biofilms. Several studies have investigated the value of serum PON1 measurement as a biomarker of the infection process. Low serum PON1 activities are associated with poor survival in patients with severe sepsis. In addition, preliminary studies suggest that serum PON1 concentration and/or enzyme activity may be useful as markers of acute concomitant infection in patients with an indwelling central venous catheter. Investigating the associations between paraoxonases and infectious diseases is a recent, and productive, line of research.
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Affiliation(s)
- Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, C. Sant Joan, s/n, 43201 Reus, Catalonia, Spain.
| | - Simona Iftimie
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Av. del Dr. Josep Laporte, 2, 43204 Reus, Catalonia, Spain
| | - Anabel García-Heredia
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, C. Sant Joan, s/n, 43201 Reus, Catalonia, Spain
| | - Antoni Castro
- Department of Internal Medicine, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Av. del Dr. Josep Laporte, 2, 43204 Reus, Catalonia, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, C. Sant Joan, s/n, 43201 Reus, Catalonia, Spain
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Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, Kačániová M, Knøchel S, Lourenço A, Mergulhão F, Meyer RL, Nychas G, Simões M, Tresse O, Sternberg C. Critical review on biofilm methods. Crit Rev Microbiol 2016; 43:313-351. [PMID: 27868469 DOI: 10.1080/1040841x.2016.1208146] [Citation(s) in RCA: 541] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.
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Affiliation(s)
- Joana Azeredo
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Nuno F Azevedo
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Romain Briandet
- c Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| | - Nuno Cerca
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Tom Coenye
- d Laboratory of Pharmaceutical Microbiology , Ghent University , Ghent , Belgium
| | - Ana Rita Costa
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Mickaël Desvaux
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Giovanni Di Bonaventura
- f Department of Medical, Oral, and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine (CeSI-MeT) , "G. d'Annunzio" University of Chieti-Pescara , Chieti , Italy
| | - Michel Hébraud
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Zoran Jaglic
- g Department of Food and Feed Safety, Laboratory of Food Bacteriology , Veterinary Research Institute , Brno , Czech Republic
| | - Miroslava Kačániová
- h Department of Microbiology, Faculty of Biotechnology and Food Sciences , Slovak University of Agriculture in Nitra , Nitra , Slovakia
| | - Susanne Knøchel
- i Department of Food Science (FOOD) , University of Copenhagen , Frederiksberg C , Denmark
| | - Anália Lourenço
- j Department of Computer Science , University of Vigo , Ourense , Spain
| | - Filipe Mergulhão
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Rikke Louise Meyer
- k Aarhus University, Interdisciplinary Nanoscience Center (iNANO) , Aarhus , Denmark
| | - George Nychas
- l Agricultural University of Athens, Lab of Microbiology and Biotechnology of Foods , Athens , Greece
| | - Manuel Simões
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Odile Tresse
- m LUNAM Université, Oniris, SECALIM UMR1024 INRA , Université de Nantes , Nantes , France
| | - Claus Sternberg
- n Department of Biotechnology and Biomedicine , Technical University of Denmark , Lyngby, Denmark
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Khanam S, Guragain M, Lenaburg DL, Kubat R, Patrauchan MA. Calcium induces tobramycin resistance in Pseudomonas aeruginosa by regulating RND efflux pumps. Cell Calcium 2016; 61:32-43. [PMID: 28034459 DOI: 10.1016/j.ceca.2016.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/27/2016] [Accepted: 11/17/2016] [Indexed: 11/24/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic multidrug resistant pathogen causing severe chronic infections. Our previous studies showed that elevated calcium (Ca2+) enhances production of several virulence factors and plant infectivity of the pathogen. Here we show that Ca2+ increases resistance of P. aeruginosa PAO1 to tobramycin, antibiotic commonly used to treat Pseudomonas infections. LC-MS/MS-based comparative analysis of the membrane proteomes of P aeruginosa grown at elevated versus not added Ca2+, determined that the abundances of two RND (resistance-nodulation-cell division) efflux pumps, MexAB-OprM and MexVW-OprM, were increased in the presence of elevated Ca2+. Analysis of twelve transposon mutants with disrupted RND efflux pumps showed that six of them (mexB, muxC, mexY, mexJ, czcB, and mexE) contribute to Ca2+-induced tobramycin resistance. Transcriptional analyses by promoter activity and RT-qPCR showed that the expression of mexAB, muxABC, mexXY, mexJK, czcCBA, and mexVW is increased by elevated Ca2+. Disruption of mexJ, mexC, mexI, and triA significantly decreased Ca2+-induced plant infectivity of the pathogen. Earlier, our group showed that PAO1 maintains intracellular Ca2+ (Ca2+in) homeostasis, which mediates Ca2+ regulation of P. aeruginosa virulence, and identified four putative Ca2+ transporters involved in this process (Guragain et al., 2013). Here we show that three of these transporters (PA2435, PA2092, PA4614) play role in Ca2+-induced tobramycin resistance and one of them (PA2435) contributes to Ca2+ regulation of mexAB-oprM promoter activity. Furthermore, mexJ, czcB, and mexE contribute to the maintenance of Ca2+in homeostasis. This provides the first evidence that Ca2+in homeostasis mediates Ca2+ regulation of RND transport systems, which contribute to Ca2+-enhanced tobramycin resistance and plant infectivity in P. aeruginosa.
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Affiliation(s)
- Sharmily Khanam
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Manita Guragain
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Dirk L Lenaburg
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Ryan Kubat
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States.
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41
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Hwang G, Liu Y, Kim D, Sun V, Aviles-Reyes A, Kajfasz JK, Lemos JA, Koo H. Simultaneous spatiotemporal mapping of in situ pH and bacterial activity within an intact 3D microcolony structure. Sci Rep 2016; 6:32841. [PMID: 27604325 PMCID: PMC5015094 DOI: 10.1038/srep32841] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
Biofilms are comprised of bacterial-clusters (microcolonies) enmeshed in an extracellular matrix. Streptococcus mutans can produce exopolysaccharides (EPS)-matrix and assemble microcolonies with acidic microenvironments that can cause tooth-decay despite the surrounding neutral-pH found in oral cavity. How the matrix influences the pH and bacterial activity locally remains unclear. Here, we simultaneously analyzed in situ pH and gene expression within intact biofilms and measured the impact of damage to the surrounding EPS-matrix. The spatiotemporal changes of these properties were characterized at a single-microcolony level following incubation in neutral-pH buffer. The middle and bottom-regions as well as inner-section within the microcolony 3D structure were resistant to neutralization (vs. upper and peripheral-region), forming an acidic core. Concomitantly, we used a green fluorescent protein (GFP) reporter to monitor expression of the pH-responsive atpB (PatpB::gfp) by S. mutans within microcolonies. The atpB expression was induced in the acidic core, but sharply decreased at peripheral/upper microcolony regions, congruent with local pH microenvironment. Enzymatic digestion of the surrounding matrix resulted in nearly complete neutralization of microcolony interior and down-regulation of atpB. Altogether, our data reveal that biofilm matrix facilitates formation of an acidic core within microcolonies which in turn activates S. mutans acid-stress response, mediating both the local environment and bacterial activity in situ.
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Affiliation(s)
- Geelsu Hwang
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuan Liu
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dongyeop Kim
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Victor Sun
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandro Aviles-Reyes
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Jessica K Kajfasz
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Jose A Lemos
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Hyun Koo
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
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42
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Gomes L, Carvalho D, Briandet R, Mergulhão F. Temporal variation of recombinant protein expression in Escherichia coli biofilms analysed at single-cell level. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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43
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Lawrence JR, Swerhone GDW, Kuhlicke U, Neu TR. In situevidence for metabolic and chemical microdomains in the structured polymer matrix of bacterial microcolonies. FEMS Microbiol Ecol 2016; 92:fiw183. [DOI: 10.1093/femsec/fiw183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2016] [Indexed: 11/13/2022] Open
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Minh Tran T, MacIntyre A, Khokhani D, Hawes M, Allen C. Extracellular DNases of Ralstonia solanacearum modulate biofilms and facilitate bacterial wilt virulence. Environ Microbiol 2016; 18:4103-4117. [PMID: 27387368 DOI: 10.1111/1462-2920.13446] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/01/2016] [Indexed: 12/21/2022]
Abstract
Ralstonia solanacearum is a soil-borne vascular pathogen that colonizes plant xylem vessels, a flowing, low-nutrient habitat where biofilms could be adaptive. Ralstonia solanacearum forms biofilm in vitro, but it was not known if the pathogen benefits from biofilms during infection. Scanning electron microscopy revealed that during tomato infection, R. solanacearum forms biofilm-like masses in xylem vessels. These aggregates contain bacteria embedded in a matrix including chromatin-like fibres commonly observed in other bacterial biofilms. Chemical and enzymatic assays demonstrated that the bacterium releases extracellular DNA in culture and that DNA is an integral component of the biofilm matrix. An R. solanacearum mutant lacking the pathogen's two extracellular nucleases (exDNases) formed non-spreading colonies and abnormally thick biofilms in vitro. The biofilms formed by the exDNase mutant in planta contained more and thicker fibres. This mutant was also reduced in virulence on tomato plants and did not spread in tomato stems as well as the wild-type strain, suggesting that these exDNases facilitate biofilm maturation and bacterial dispersal. To our knowledge, this is the first demonstration that R. solanacearum forms biofilms in plant xylem vessels, and the first documentation that plant pathogens use DNases to modulate their biofilm structure for systemic spread and virulence.
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Affiliation(s)
- Tuan Minh Tran
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - April MacIntyre
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Devanshi Khokhani
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Martha Hawes
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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Rice SA, Wuertz S, Kjelleberg S. Next-generation studies of microbial biofilm communities. Microb Biotechnol 2016; 9:677-80. [PMID: 27471123 PMCID: PMC4993187 DOI: 10.1111/1751-7915.12390] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 07/09/2016] [Indexed: 11/30/2022] Open
Abstract
As we look into the future of microbial biofilm research, there is clearly an emerging focus on communities rather than populations. This represents an essential change in direction to more accurately understand how and why microorganisms assemble into communities, as well as the functional implications for such a life style. For example, current research studies shows that communities display emergent properties or functions that are not predicted from the individual single species populations, including elevated stress tolerance and resistance to antibiotics. Models for mixed species biofilms can be very simple, comprised only a handful of species or can be extremely species rich, with hundreds or thousands of species present. The future holds much promise for this area of research, where investigators will increasingly be able to resolve, at the molecular and biochemical levels, interspecies relationships and mechanisms of interaction. The outcome of these studies will greatly enhance our understanding of the ecological and evolutionary factors that drive community function in natural and engineered systems.
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Affiliation(s)
- Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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46
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Abstract
Bacteria have traditionally been studied as single-cell organisms. In laboratory settings, aerobic bacteria are usually cultured in aerated flasks, where the cells are considered essentially homogenous. However, in many natural environments, bacteria and other microorganisms grow in mixed communities, often associated with surfaces. Biofilms are comprised of surface-associated microorganisms, their extracellular matrix material, and environmental chemicals that have adsorbed to the bacteria or their matrix material. While this definition of a biofilm is fairly simple, biofilms are complex and dynamic. Our understanding of the activities of individual biofilm cells and whole biofilm systems has developed rapidly, due in part to advances in molecular, analytical, and imaging tools and the miniaturization of tools designed to characterize biofilms at the enzyme level, cellular level, and systems level.
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47
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McDaniel C, Su S, Panmanee W, Lau GW, Browne T, Cox K, Paul AT, Ko SHB, Mortensen JE, Lam JS, Muruve DA, Hassett DJ. A Putative ABC Transporter Permease Is Necessary for Resistance to Acidified Nitrite and EDTA in Pseudomonas aeruginosa under Aerobic and Anaerobic Planktonic and Biofilm Conditions. Front Microbiol 2016; 7:291. [PMID: 27064218 PMCID: PMC4817314 DOI: 10.3389/fmicb.2016.00291] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/23/2016] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa (PA) is an important airway pathogen of cystic fibrosis and chronic obstructive disease patients. Multiply drug resistant PA is becoming increasing prevalent and new strategies are needed to combat such insidious organisms. We have previously shown that a mucoid, mucA22 mutant PA is exquisitely sensitive to acidified nitrite (A-NO2−, pH 6.5) at concentrations that are well tolerated in humans. Here, we used a transposon mutagenesis approach to identify PA mutants that are hypersensitive to A-NO2−. Among greater than 10,000 mutants screened, we focused on PA4455, in which the transposon was found to disrupt the production of a putative cytoplasmic membrane-spanning ABC transporter permease. The PA4455 mutant was not only highly sensitive to A-NO2−, but also the membrane perturbing agent, EDTA and the antibiotics doxycycline, tigecycline, colistin, and chloramphenicol, respectively. Treatment of bacteria with A-NO2− plus EDTA, however, had the most dramatic and synergistic effect, with virtually all bacteria killed by 10 mM A-NO2−, and EDTA (1 mM, aerobic, anaerobic). Most importantly, the PA4455 mutant was also sensitive to A-NO2− in biofilms. A-NO2− sensitivity and an anaerobic growth defect was also noted in two mutants (rmlC and wbpM) that are defective in B-band LPS synthesis, potentially indicating a membrane defect in the PA4455 mutant. Finally, this study describes a gene, PA4455, that when mutated, allows for dramatic sensitivity to the potential therapeutic agent, A-NO2− as well as EDTA. Furthermore, the synergy between the two compounds could offer future benefits against antibiotic resistant PA strains.
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Affiliation(s)
- Cameron McDaniel
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Shengchang Su
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Warunya Panmanee
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Gee W Lau
- College of Veterinary Medicine, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Tristan Browne
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Kevin Cox
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Andrew T Paul
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Seung-Hyun B Ko
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Joel E Mortensen
- Diagnostic and Infectious Diseases Testing Laboratory, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Daniel A Muruve
- Department of Medicine, University of Calgary Calgary, AB, Canada
| | - Daniel J Hassett
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of MedicineCincinnati, OH, USA; Department of Research Services, Cincinnati Veteran's Association Medical CenterCincinnati, OH, USA
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Kragh KN, Hutchison JB, Melaugh G, Rodesney C, Roberts AEL, Irie Y, Jensen PØ, Diggle SP, Allen RJ, Gordon V, Bjarnsholt T. Role of Multicellular Aggregates in Biofilm Formation. mBio 2016; 7:e00237. [PMID: 27006463 PMCID: PMC4807362 DOI: 10.1128/mbio.00237-16] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 11/25/2022] Open
Abstract
UNLABELLED In traditional models ofin vitrobiofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development ofPseudomonas aeruginosabiofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation. IMPORTANCE During the past decades, there has been a consensus around the model of development of a biofilm, involving attachment of single planktonic bacterial cells to a surface and the subsequent development of a mature biofilm. This study presents results that call for a modification of this rigorous model. We show how free floating biofilm aggregates can have a profound local effect on biofilm development when attaching to a surface. Our findings show that an aggregate landing on a surface will eventually outcompete the biofilm population arising from single cells attached around the aggregate and dominate the local biofilm development. These results point to a regime where preformed biofilm aggregates may have a fitness advantage over planktonic cells when it comes to accessing nutrients. Our findings add to the increasingly prominent comprehension that biofilm lifestyle is the default for bacteria and that planktonic single cells may be only a transition state at the most.
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Affiliation(s)
- Kasper N Kragh
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jaime B Hutchison
- Center for Nonlinear Dynamics and Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Gavin Melaugh
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris Rodesney
- Center for Nonlinear Dynamics and Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Aled E L Roberts
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Yasuhiko Irie
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Peter Ø Jensen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Stephen P Diggle
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rosalind J Allen
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Vernita Gordon
- Center for Nonlinear Dynamics and Department of Physics, The University of Texas at Austin, Austin, Texas, USA Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
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Tata M, Wolfinger MT, Amman F, Roschanski N, Dötsch A, Sonnleitner E, Häussler S, Bläsi U. RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium. PLoS One 2016; 11:e0147811. [PMID: 26821182 PMCID: PMC4731081 DOI: 10.1371/journal.pone.0147811] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/08/2016] [Indexed: 01/22/2023] Open
Abstract
The opportunistic human pathogen Pseudomonas aeruginosa can thrive under microaerophilic to anaerobic conditions in the lungs of cystic fibrosis patients. RNASeq based comparative RNA profiling of the clinical isolate PA14 cultured in synthetic cystic fibrosis medium was performed after planktonic growth (OD600 = 2.0; P), 30 min after shift to anaerobiosis (A-30) and after anaerobic biofilm growth for 96h (B-96) with the aim to reveal differentially regulated functions impacting on sustained anoxic biofilm formation as well as on tolerance towards different antibiotics. Most notably, functions involved in sulfur metabolism were found to be up-regulated in B-96 cells when compared to A-30 cells. Based on the transcriptome studies a set of transposon mutants were screened, which revealed novel functions involved in anoxic biofilm growth.In addition, these studies revealed a decreased and an increased abundance of the oprD and the mexCD-oprJ operon transcripts, respectively, in B-96 cells, which may explain their increased tolerance towards meropenem and to antibiotics that are expelled by the MexCD-OprD efflux pump. The OprI protein has been implicated as a target for cationic antimicrobial peptides, such as SMAP-29. The transcriptome and subsequent Northern-blot analyses showed that the abundance of the oprI transcript encoding the OprI protein is strongly decreased in B-96 cells. However, follow up studies revealed that the susceptibility of a constructed PA14ΔoprI mutant towards SMAP-29 was indistinguishable from the parental wild-type strain, which questions OprI as a target for this antimicrobial peptide in strain PA14.
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Affiliation(s)
- Muralidhar Tata
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Michael T. Wolfinger
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
- Institute for Theoretical Chemistry, University of Vienna Währinger Straße 17, 1090 Vienna, Austria
| | - Fabian Amman
- Department of Chromosome Biology, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
- Institute for Theoretical Chemistry, University of Vienna Währinger Straße 17, 1090 Vienna, Austria
| | - Nicole Roschanski
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
- Free University Berlin, Institute of Animal Hygiene and Environmental Health, Robert-von-Ostertag-Str. 7–13, 14163 Berlin, Germany
| | - Andreas Dötsch
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute of Molecular Bacteriology, Twincore, Center for Experimental and Clinical Infection Research, Feodor-Lynen-Straße 7, 30625 Hannover, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
- * E-mail:
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50
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The Pseudomonas aeruginosa PAO1 Two-Component Regulator CarSR Regulates Calcium Homeostasis and Calcium-Induced Virulence Factor Production through Its Regulatory Targets CarO and CarP. J Bacteriol 2016; 198:951-63. [PMID: 26755627 DOI: 10.1128/jb.00963-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 12/31/2015] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED Pseudomonas aeruginosa is an opportunistic human pathogen that causes severe, life-threatening infections in patients with cystic fibrosis (CF), endocarditis, wounds, or artificial implants. During CF pulmonary infections, P. aeruginosa often encounters environments where the levels of calcium (Ca(2+)) are elevated. Previously, we showed that P. aeruginosa responds to externally added Ca(2+) through enhanced biofilm formation, increased production of several secreted virulence factors, and by developing a transient increase in the intracellular Ca(2+) level, followed by its removal to the basal submicromolar level. However, the molecular mechanisms responsible for regulating Ca(2+)-induced virulence factor production and Ca(2+) homeostasis are not known. Here, we characterized the genome-wide transcriptional response of P. aeruginosa to elevated [Ca(2+)] in both planktonic cultures and biofilms. Among the genes induced by CaCl2 in strain PAO1 was an operon containing the two-component regulator PA2656-PA2657 (here called carS and carR), while the closely related two-component regulators phoPQ and pmrAB were repressed by CaCl2 addition. To identify the regulatory targets of CarSR, we constructed a deletion mutant of carR and performed transcriptome analysis of the mutant strain at low and high [Ca(2+)]. Among the genes regulated by CarSR in response to CaCl2 are the predicted periplasmic OB-fold protein, PA0320 (here called carO), and the inner membrane-anchored five-bladed β-propeller protein, PA0327 (here called carP). Mutations in both carO and carP affected Ca(2+) homeostasis, reducing the ability of P. aeruginosa to export excess Ca(2+). In addition, a mutation in carP had a pleotropic effect in a Ca(2+)-dependent manner, altering swarming motility, pyocyanin production, and tobramycin sensitivity. Overall, the results indicate that the two-component system CarSR is responsible for sensing high levels of external Ca(2+) and responding through its regulatory targets that modulate Ca(2+) homeostasis, surface-associated motility, and the production of the virulence factor pyocyanin. IMPORTANCE During infectious disease, Pseudomonas aeruginosa encounters environments with high calcium (Ca(2+)) concentrations, yet the cells maintain intracellular Ca(2+) at levels that are orders of magnitude less than that of the external environment. In addition, Ca(2+) signals P. aeruginosa to induce the production of several virulence factors. Compared to eukaryotes, little is known about how bacteria maintain Ca(2+) homeostasis or how Ca(2+) acts as a signal. In this study, we identified a two-component regulatory system in P. aeruginosa PAO1, termed CarRS, that is induced at elevated Ca(2+) levels. CarRS modulates Ca(2+) signaling and Ca(2+) homeostasis through its regulatory targets, CarO and CarP. The results demonstrate that P. aeruginosa uses a two-component regulatory system to sense external Ca(2+) and relays that information for Ca(2+)-dependent cellular processes.
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