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Liu X, Xia X, Liu Y, Li Z, Shi T, Zhang H, Dong Q. Recent advances on the formation, detection, resistance mechanism, and control technology of Listeria monocytogenes biofilm in food industry. Food Res Int 2024; 180:114067. [PMID: 38395584 DOI: 10.1016/j.foodres.2024.114067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
Listeria monocytogenes is an important foodborne pathogen that causes listeriosis, a severe and fatal condition. Biofilms are communities of microorganisms nested within a self-secreted extracellular polymeric substance, and they protect L. monocytogenes from environmental stresses. Biofilms, once formed, can lead to the persistence of L. monocytogenes in processing equipment and are therefore considered to be a major concern for the food industry. This paper briefly introduces the recent advancements on biofilm formation characteristics and detection methods, and focuses on analysis of the mechanism of L. monocytogenes biofilm resistance; Moreover, this paper also summarizes and discusses the existing different techniques of L. monocytogenes biofilm control according to the physical, chemical, biological, and combined strategies, to provide a theoretical reference to aid the choice of effective control technology in the food industry.
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Affiliation(s)
- Xin Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Xuejuan Xia
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Yangtai Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Zhuosi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Tianqi Shi
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China.
| | - Hongzhi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China.
| | - Qingli Dong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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2
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Copeland R, Zhang C, Hammer BK, Yunker PJ. Spatial constraints and stochastic seeding subvert microbial arms race. PLoS Comput Biol 2024; 20:e1011807. [PMID: 38277405 PMCID: PMC10849242 DOI: 10.1371/journal.pcbi.1011807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/07/2024] [Accepted: 01/08/2024] [Indexed: 01/28/2024] Open
Abstract
Surface attached communities of microbes grow in a wide variety of environments. Often, the size of these microbial community is constrained by their physical surroundings. However, little is known about how size constraints of a colony impact the outcome of microbial competitions. Here, we use individual-based models to simulate contact killing between two bacterial strains with different killing rates in a wide range of community sizes. We found that community size has a substantial impact on outcomes; in fact, in some competitions the identity of the most fit strain differs in large and small environments. Specifically, when at a numerical disadvantage, the strain with the slow killing rate is more successful in smaller environments than in large environments. The improved performance in small spaces comes from finite size effects; stochastic fluctuations in the initial relative abundance of each strain in small environments lead to dramatically different outcomes. However, when the slow killing strain has a numerical advantage, it performs better in large spaces than in small spaces, where stochastic fluctuations now aid the fast killing strain in small communities. Finally, we experimentally validate these results by confining contact killing strains of Vibrio cholerae in transmission electron microscopy grids. The outcomes of these experiments are consistent with our simulations. When rare, the slow killing strain does better in small environments; when common, the slow killing strain does better in large environments. Together, this work demonstrates that finite size effects can substantially modify antagonistic competitions, suggesting that colony size may, at least in part, subvert the microbial arms race.
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Affiliation(s)
- Raymond Copeland
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Christopher Zhang
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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3
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Cutri A, Shrout JD, Bohn PW. Metabolic and Oxidative Stress Effects on the Spectroelectrochemical Behavior of Single Pseudomonas aeruginosa Cells. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:659-666. [PMID: 37886305 PMCID: PMC10598847 DOI: 10.1021/cbmi.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen capable of causing a wide range of diseases in immunocompromised patients. In order to better understand P. aeruginosa behavior and virulence and to advance drug therapies to combat infection, it would be beneficial to understand how P. aeruginosa cells survive stressful conditions, especially environmental stressors. Here, we report on a strategy that measures potential-dependent fluorescence of individual P. aeruginosa cells, as a sentinel, for cellular response to starvation, hunger, and oxidative stress. This is accomplished using a micropore electrode array capable of trapping large numbers of isolated, vertically oriented cells at well-defined spatial positions in order to study large arrays of single cells in parallel. We find that conditions promoting either starvation or oxidative stress produce discernible changes in the fluorescence response, demonstrated by an increase in the prevalence of fluorescence transients, one of three canonical spectroelectrochemical behaviors exhibited by single P. aeruginosa cells. In contrast, more modest nutrient limitations have little to no effect on the spectroelectrochemical response when compared to healthy cells in the stationary phase. These findings demonstrate the capabilities of micropore electrode arrays for studying the behavior of single microbial cells under conditions where the intercellular spacing, orientation, and chemical environment of the cells are controlled. Realizing single-cell studies under such well-defined conditions makes it possible to study fundamental stress responses with unprecedented control.
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Affiliation(s)
- Allison
R. Cutri
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Joshua D. Shrout
- Department
of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department
of Biological Sciences, University of Notre
Dame, Notre Dame, Indiana 46556, United
States
| | - Paul W. Bohn
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
- Department
of Chemical and Biomolecular Engineering, University of Notre Dame, Notre
Dame, Indiana 46556, United States
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4
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Kragh KN, Tolker-Nielsen T, Lichtenberg M. The non-attached biofilm aggregate. Commun Biol 2023; 6:898. [PMID: 37658117 PMCID: PMC10474055 DOI: 10.1038/s42003-023-05281-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Biofilms have conventionally been perceived as dense bacterial masses on surfaces, following the five-step model of development. Initial biofilm research focused on surface-attached formations, but detached aggregates have received increasing attention in the past decade due to their pivotal role in chronic infections. Understanding their nature sparked fervent discussions in biofilm conferences and scientific literature. This review consolidates current insights on non-attached aggregates, offering examples of their occurrence in nature and diseases. We discuss their formation and dispersion mechanisms, resilience to antibiotics and immune-responses, drawing parallels to surface-attached biofilms. Moreover, we outline available in vitro models for studying non-attached aggregates.
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Affiliation(s)
- Kasper N Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
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5
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Perry EK, Tan MW. Bacterial biofilms in the human body: prevalence and impacts on health and disease. Front Cell Infect Microbiol 2023; 13:1237164. [PMID: 37712058 PMCID: PMC10499362 DOI: 10.3389/fcimb.2023.1237164] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
Bacterial biofilms can be found in most environments on our planet, and the human body is no exception. Consisting of microbial cells encased in a matrix of extracellular polymers, biofilms enable bacteria to sequester themselves in favorable niches, while also increasing their ability to resist numerous stresses and survive under hostile circumstances. In recent decades, biofilms have increasingly been recognized as a major contributor to the pathogenesis of chronic infections. However, biofilms also occur in or on certain tissues in healthy individuals, and their constituent species are not restricted to canonical pathogens. In this review, we discuss the evidence for where, when, and what types of biofilms occur in the human body, as well as the diverse ways in which they can impact host health under homeostatic and dysbiotic states.
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Affiliation(s)
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech, South San Francisco, CA, United States
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Rattray JB, Kramer PJ, Gurney J, Thomas S, Brown SP. The dynamic response of quorum sensing to density is robust to signal supplementation and individual signal synthase knockouts. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001321. [PMID: 37204848 PMCID: PMC10268839 DOI: 10.1099/mic.0.001321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/17/2023] [Indexed: 05/20/2023]
Abstract
Quorum sensing (QS) is a widespread mechanism of environment sensing and behavioural coordination in bacteria. At its core, QS is based on the production, sensing and response to small signalling molecules. Previous work with Pseudomonas aeruginosa shows that QS can be used to achieve quantitative resolution and deliver a dosed response to the bacteria's density environment, implying a sophisticated mechanism of control. To shed light on how the mechanistic signal components contribute to graded responses to density, we assess the impact of genetic (AHL signal synthase deletion) and/or signal supplementation (exogenous AHL addition) perturbations on lasB reaction-norms to changes in density. Our approach condenses data from 2000 timeseries (over 74 000 individual observations) into a comprehensive view of QS-controlled gene expression across variation in genetic, environmental and signal determinants of lasB expression. We first confirm that deleting either (∆lasI, ∆rhlI) or both (∆lasIrhlI) AHL signal synthase gene attenuates QS response to density. In the ∆rhlI background we show persistent yet attenuated density-dependent lasB expression due to native 3-oxo-C12-HSL signalling. We then test if density-independent quantities of AHL signal (3-oxo-C12-HSL, C4-HSL) added to the WT either flatten or increase responsiveness to density and find that the WT response is robust to all tested concentrations of signal, alone or in combination. We then move to progressively supplementing the genetic knockouts and find that cognate signal supplementation of a single AHL signal (∆lasI +3-oxo-C12-HSL, ∆rhlI +C4HSL) is sufficient to restore the ability to respond in a density-dependent manner to increasing density. We also find that dual signal supplementation of the double AHL synthase knockout restores the ability to produce a graded response to increasing density, despite adding a density-independent amount of signal. Only the addition of high concentrations of both AHLs and PQS can force maximal lasB expression and ablate responsiveness to density. Our results show that density-dependent control of lasB expression is robust to multiple combinations of QS gene deletion and density-independent signal supplementation. Our work develops a modular approach to query the robustness and mechanistic bases of the central environmental sensing phenotype of quorum sensing.
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Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Patrick J. Kramer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - James Gurney
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, 30303, USA
| | - Stephen Thomas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sam P. Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Effect of Limosilactobacillus fermentum 332 on physicochemical characteristics, volatile flavor components, and Quorum sensing in fermented sausage. Sci Rep 2023; 13:3942. [PMID: 36894700 PMCID: PMC9998864 DOI: 10.1038/s41598-023-31161-2] [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: 12/11/2022] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
The effects of Limosilactobacillus fermentum 332 on quality characteristics in fermented sausage were explored in terms of physicochemical characteristics, volatile flavor components, and Quorum sensing (QS). The results showed that the pH of fermented sausage decreased from 5.20 to 4.54 within 24 h with the inoculation of L. fermentum 332. Lightness and redness were significantly improved, and hardness and chewiness were significantly increased after the addition of L. fermentum 332. With the inoculation of L. fermentum 332, the thiobarbituric acid reactive substance content decreased from 0.26 to 0.19 mg/100 g and total volatile basic nitrogen content decreased from 2.16 to 1.61 mg/100 g. In total, 95 and 104 types of volatile flavor components were detected in the control and fermented sausage inoculated with starter culture, respectively. The AI-2 activity of fermented sausage inoculated with L. fermentum 332 was significantly higher than that of the control and positively correlated with viable count and quality characteristics. These results provide support for further research on the effect of microorganisms on the quality of fermented food.
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8
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Rattray JB, Brown SP. Beyond Thresholds: Quorum‐Sensing as Quantitatively Varying Reaction Norms to Multiple Environmental Dimensions. Isr J Chem 2023. [DOI: 10.1002/ijch.202200109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
| | - Sam P. Brown
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
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9
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Rattray JB, Thomas SA, Wang Y, Molotkova E, Gurney J, Varga JJ, Brown SP. Bacterial Quorum Sensing Allows Graded and Bimodal Cellular Responses to Variations in Population Density. mBio 2022; 13:e0074522. [PMID: 35583321 PMCID: PMC9239169 DOI: 10.1128/mbio.00745-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Quorum sensing (QS) is a mechanism of cell-cell communication that connects gene expression to environmental conditions (e.g., cell density) in many bacterial species, mediated by diffusible signal molecules. Current functional studies focus on qualitatively distinct QS ON/OFF states. In the context of density sensing, this view led to the adoption of a "quorum" analogy in which populations sense when they are above a sufficient density (i.e., "quorate") to efficiently turn on cooperative behaviors. This framework overlooks the potential for intermediate, graded responses to shifts in the environment. In this study, we tracked QS-regulated protease (lasB) expression and showed that Pseudomonas aeruginosa can deliver a graded behavioral response to fine-scale variation in population density, on both the population and single-cell scales. On the population scale, we saw a graded response to variation in population density (controlled by culture carrying capacity). On the single-cell scale, we saw significant bimodality at higher densities, with separate OFF and ON subpopulations that responded differentially to changes in density: a static OFF population of cells and increasing intensity of expression among the ON population of cells. Together, these results indicate that QS can tune gene expression to graded environmental change, with no critical cell mass or "quorum" at which behavioral responses are activated on either the individual-cell or population scale. In an infection context, our results indicate there is not a hard threshold separating a quorate "attack" mode from a subquorate "stealth" mode. IMPORTANCE Bacteria can be highly social, controlling collective behaviors via cell-cell communication mechanisms known as quorum sensing (QS). QS is now a large research field, yet a basic question remains unanswered: what is the environmental resolution of QS? The notion of a threshold, or "quorum," separating coordinated ON and OFF states is a central dogma in QS, but recent studies have shown heterogeneous responses at a single cell scale. Using Pseudomonas aeruginosa, we showed that populations generate graded responses to environmental variation through shifts in the proportion of cells responding and the intensity of responses. In an infection context, our results indicate that there is not a hard threshold separating a quorate "attack" mode and a subquorate "stealth" mode.
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Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephen A. Thomas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Graduate Program in Quantitative Biosciences (QBioS), Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yifei Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- The Institute for Data Engineering and Science (IDEaS), Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Evgeniya Molotkova
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - James Gurney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - John J. Varga
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sam P. Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
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10
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Pseudomonas aeruginosa Initiates a Rapid and Specific Transcriptional Response during Surface Attachment. J Bacteriol 2022; 204:e0008622. [PMID: 35467391 PMCID: PMC9112911 DOI: 10.1128/jb.00086-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chronic biofilm infections by Pseudomonas aeruginosa are a major contributor to the morbidity and mortality of patients. The formation of multicellular bacterial aggregates, called biofilms, is associated with increased resistance to antimicrobials and immune clearance and the persistence of infections. Biofilm formation is dependent on bacterial cell attachment to surfaces, and therefore, attachment plays a key role in chronic infections. We hypothesized that bacteria sense various surfaces and initiate a rapid, specific response to increase adhesion and establish biofilms. RNA sequencing (RNA-Seq) analysis identified transcriptional changes of adherent cells during initial attachment, identifying the bacterial response to an abiotic surface over a 1-h period. Subsequent screens investigating the most highly regulated genes in surface attachment identified 4 genes, pfpI, phnA, leuD, and moaE, all of which have roles in both metabolism and biofilm formation. In addition, the transcriptional responses to several different medically relevant abiotic surfaces were compared after initial attachment. Surprisingly, there was a specific transcriptional response to each surface, with very few genes being regulated in response to surfaces in general. We identified a set of 20 genes that were differentially expressed across all three surfaces, many of which have metabolic functions, including molybdopterin cofactor biosynthesis and nitrogen metabolism. This study has advanced the understanding of the kinetics and specificity of bacterial transcriptional responses to surfaces and suggests that metabolic cues are important signals during the transition from a planktonic to a biofilm lifestyle. IMPORTANCE Bacterial biofilms are a significant concern in many aspects of life, including chronic infections of airways, wounds, and indwelling medical devices; biofouling of industrial surfaces relevant for food production and marine surfaces; and nosocomial infections. The effects of understanding surface adhesion could impact many areas of life. This study utilized emerging technology in a novel approach to address a key step in bacterial biofilm development. These findings have elucidated both conserved and surface-specific responses to several disease-relevant abiotic surfaces. Future work will expand on this report to identify mechanisms of biofilm initiation with the aim of identifying bacterial factors that could be targeted to prevent biofilms.
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11
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Azimi S, Lewin GR, Whiteley M. The biogeography of infection revisited. Nat Rev Microbiol 2022; 20:579-592. [PMID: 35136217 PMCID: PMC9357866 DOI: 10.1038/s41579-022-00683-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 01/01/2023]
Abstract
Many microbial communities, including those involved in chronic human infections, are patterned at the micron scale. In this Review, we summarize recent work that has defined the spatial arrangement of microorganisms in infection and begun to demonstrate how changes in spatial patterning correlate with disease. Advances in microscopy have refined our understanding of microbial micron-scale biogeography in samples from humans. These findings then serve as a benchmark for studying the role of spatial patterning in preclinical models, which provide experimental versatility to investigate the interplay between biogeography and pathogenesis. Experimentation using preclinical models has begun to show how spatial patterning influences the interactions between cells, their ability to coexist, their virulence and their recalcitrance to treatment. Future work to study the role of biogeography in infection and the functional biogeography of microorganisms will further refine our understanding of the interplay of spatial patterning, pathogen virulence and disease outcomes.
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Affiliation(s)
- Sheyda Azimi
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gina R Lewin
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
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12
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Spatial-temporal dynamics of a microbial cooperative behavior resistant to cheating. Nat Commun 2022; 13:721. [PMID: 35132084 PMCID: PMC8821651 DOI: 10.1038/s41467-022-28321-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Much of our understanding of bacterial behavior stems from studies in liquid culture. In nature, however, bacteria frequently live in densely packed spatially-structured communities. How does spatial structure affect bacterial cooperative behaviors? In this work, we examine rhamnolipid production—a cooperative and virulent behavior of Pseudomonas aeruginosa. Here we show that, in striking contrast to well-mixed liquid culture, rhamnolipid gene expression in spatially-structured colonies is strongly associated with colony specific growth rate, and is impacted by perturbation with diffusible quorum signals. To interpret these findings, we construct a data-driven statistical inference model which captures a length-scale of bacterial interaction that develops over time. Finally, we find that perturbation of P. aeruginosa swarms with quorum signals preserves the cooperating genotype in competition, rather than creating opportunities for cheaters. Overall, our data demonstrate that the complex response to spatial localization is key to preserving bacterial cooperative behaviors. Bacteria often live in densely packed, spatially-structured communities; however, much of our understanding of their behavior stems from studies in liquid culture. Here, Monaco et al. show how spatial structure and quorum sensing modulate a cooperative behavior in colonies of Pseudomonas aeruginosa.
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13
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Davidson SL, Niepa THR. Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments. Front Microbiol 2022; 12:745835. [PMID: 35154021 PMCID: PMC8831547 DOI: 10.3389/fmicb.2021.745835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
With recent advances in microfabrication technologies, the miniaturization of traditional culturing techniques has provided ideal methods for interrogating microbial communities in a confined and finely controlled environment. Micro-technologies offer high-throughput screening and analysis, reduced experimental time and resources, and have low footprint. More importantly, they provide access to culturing microbes in situ in their natural environments and similarly, offer optical access to real-time dynamics under a microscope. Utilizing micro-technologies for the discovery, isolation and cultivation of "unculturable" species will propel many fields forward; drug discovery, point-of-care diagnostics, and fundamental studies in microbial community behaviors rely on the exploration of novel metabolic pathways. However, micro-technologies are still largely proof-of-concept, and scalability and commercialization of micro-technologies will require increased accessibility to expensive equipment and resources, as well as simpler designs for usability. Here, we discuss three different miniaturized culturing practices; including microarrays, micromachined devices, and microfluidics; advancements to the field, and perceived challenges.
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Affiliation(s)
- Shanna-Leigh Davidson
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Tagbo H. R. Niepa
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, United States
- The McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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14
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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15
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Niggli S, Wechsler T, Kümmerli R. Single-Cell Imaging Reveals That Staphylococcus aureus Is Highly Competitive Against Pseudomonas aeruginosa on Surfaces. Front Cell Infect Microbiol 2021; 11:733991. [PMID: 34513736 PMCID: PMC8426923 DOI: 10.3389/fcimb.2021.733991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa and Staphylococcus aureus frequently occur together in polymicrobial infections, and their interactions can complicate disease progression and treatment options. While interactions between P. aeruginosa and S. aureus have been extensively described using planktonic batch cultures, little is known about whether and how individual cells interact with each other on solid substrates. This is important because both species frequently colonize surfaces to form aggregates and biofilms in infections. Here, we performed single-cell time-lapse fluorescence microscopy, combined with automated image analysis, to describe interactions between P. aeruginosa PAO1 with three different S. aureus strains (Cowan I, 6850, JE2) during microcolony growth on agarose surfaces. While P. aeruginosa is usually considered the dominant species, we found that the competitive balance tips in favor of S. aureus on surfaces. We observed that all S. aureus strains accelerated the onset of microcolony growth in competition with P. aeruginosa and significantly compromised P. aeruginosa growth prior to physical contact. Upon direct contact, JE2 was the most competitive S. aureus strain, simply usurping P. aeruginosa microcolonies, while 6850 was the weakest competitor itself suppressed by P. aeruginosa. Moreover, P. aeruginosa reacted to the assault of S. aureus by showing increased directional growth and expedited expression of quorum sensing regulators controlling the synthesis of competitive traits. Altogether, our results reveal that quantitative single-cell live imaging has the potential to uncover microbial behaviors that cannot be predicted from batch culture studies, and thereby contribute to our understanding of interactions between pathogens that co-colonize host-associated surfaces during polymicrobial infections.
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Affiliation(s)
- Selina Niggli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | | | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
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16
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Subramanian S, Huiszoon RC, Chu S, Bentley WE, Ghodssi R. Microsystems for biofilm characterization and sensing - A review. Biofilm 2020; 2:100015. [PMID: 33447801 PMCID: PMC7798443 DOI: 10.1016/j.bioflm.2019.100015] [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: 09/16/2019] [Revised: 11/11/2019] [Accepted: 11/26/2019] [Indexed: 11/30/2022] Open
Abstract
Biofilms are the primary cause of clinical bacterial infections and are impervious to typical amounts of antibiotics, necessitating very high doses for elimination. Therefore, it is imperative to have suitable methods for characterization to develop novel methods of treatment that can complement or replace existing approaches using significantly lower doses of antibiotics. This review presents some of the current developments in microsystems for characterization and sensing of bacterial biofilms. Initially, we review current standards for studying biofilms that are based on invasive and destructive end-point biofilm characterization. Additionally, biofilm formation and growth is extremely sensitive to various growth and environmental parameters that cause large variability in biofilms between repeated experiments, making it very difficult to compare experimental repeats and characterize the temporal characteristics of these organisms. To address these challenges, recent developments in the field have moved toward systems and miniature devices that can aid in the non-invasive characterization of bacterial biofilms. Our review focuses on several types of microsystems for biofilm evaluation including optical, electrochemical, and mechanical systems. This review will show how these devices can lead to better understanding of the physiology and function of these communities of bacteria, which can eventually lead to the development of novel treatments that do not rely on high-dosage antibiotics.
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Affiliation(s)
- Sowmya Subramanian
- MEMS Sensors and Actuators Laboratory, University of Maryland, College Park, MD, USA
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, USA
- Institute for Systems Research, University of Maryland, College Park, MD, USA
| | - Ryan C. Huiszoon
- MEMS Sensors and Actuators Laboratory, University of Maryland, College Park, MD, USA
- Institute for Systems Research, University of Maryland, College Park, MD, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
| | - Sangwook Chu
- MEMS Sensors and Actuators Laboratory, University of Maryland, College Park, MD, USA
- Institute for Systems Research, University of Maryland, College Park, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
| | - Reza Ghodssi
- MEMS Sensors and Actuators Laboratory, University of Maryland, College Park, MD, USA
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, USA
- Institute for Systems Research, University of Maryland, College Park, MD, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
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17
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Rumpel C, Ann V, Bahri H, Calabi Floody M, Cheik S, Doan TT, Harit A, Janeau JL, Jouquet P, Mora ML, Podwojewski P, Tran TM, Ngo QA, Rossi PL, Sanaullah M. Research for development in the 21st century. GEODERMA 2020; 378:114558. [PMID: 32836329 DOI: 10.1016/j.geoderma.2020.114588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- C Rumpel
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | - V Ann
- Institute of Technology of Cambodia, Phnom Penh, Cambodia
| | - H Bahri
- Institut National de Recherches en Génie Rural, Eaux et Forêts, Université de Carthage, Tunisia
| | | | - S Cheik
- Gachamaleh, lot 18, 1095 Djibouti, Djibouti
| | - T T Doan
- Soils and Fertilizers Research Institute, Hanoi, Viet Nam
| | - A Harit
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India
| | - J L Janeau
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | - P Jouquet
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | | | - P Podwojewski
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | - T M Tran
- Soils and Fertilizers Research Institute, Hanoi, Viet Nam
| | - Q A Ngo
- Institute of Chemistry, VAST, Hanoi, Viet Nam
| | - P L Rossi
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | - M Sanaullah
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
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18
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Jung H, Meile CD. Numerical investigation of microbial quorum sensing under various flow conditions. PeerJ 2020; 8:e9942. [PMID: 32983649 PMCID: PMC7500354 DOI: 10.7717/peerj.9942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/24/2020] [Indexed: 11/22/2022] Open
Abstract
Microorganisms efficiently coordinate phenotype expressions through a decision-making process known as quorum sensing (QS). We investigated QS amongst distinct, spatially distributed microbial aggregates under various flow conditions using a process-driven numerical model. Model simulations assess the conditions suitable for QS induction and quantify the importance of advective transport of signaling molecules. In addition, advection dilutes signaling molecules so that faster flow conditions require higher microbial densities, faster signal production rates, or higher sensitivities to signaling molecules to induce QS. However, autoinduction of signal production can substantially increase the transport distance of signaling molecules in both upstream and downstream directions. We present empirical approximations to the solutions of the advection–diffusion–reaction equation that describe the concentration profiles of signaling molecules for a wide range of flow and reaction rates. These empirical relationships, which predict the distribution of dissolved solutes along pore channels, allow to quantitatively estimate the effective communication distances amongst multiple microbial aggregates without further numerical simulations.
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Tan CH, Oh HS, Sheraton VM, Mancini E, Joachim Loo SC, Kjelleberg S, Sloot PMA, Rice SA. Convection and the Extracellular Matrix Dictate Inter- and Intra-Biofilm Quorum Sensing Communication in Environmental Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:6730-6740. [PMID: 32390423 DOI: 10.1021/acs.est.0c00716] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The mechanisms and impact of bacterial quorum sensing (QS) for the coordination of population-level behaviors are well studied under laboratory conditions. However, it is unclear how, in otherwise open environmental systems, QS signals accumulate to sufficient concentration to induce QS phenotypes, especially when quorum quenching (QQ) organisms are also present. We explore the impact of QQ activity on QS signaling in spatially organized biofilms in scenarios that mimic open systems of natural and engineered environments. Using a functionally differentiated biofilm system, we show that the extracellular matrix, local flow, and QQ interact to modulate communication. In still aqueous environments, convection facilitates signal dispersal while the matrix absorbs and relays signals to the cells. This process facilitates inter-biofilm communication even at low extracellular signal concentrations. Within the biofilm, the matrix further regulates the transport of the competing QS and QQ molecules, leading to heterogenous QS behavior. Importantly, only extracellular QQ enzymes can effectively control QS signaling, suggesting that the intracellular QQ enzymes may not have evolved to degrade environmental QS signals for competition.
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Affiliation(s)
- Chuan Hao Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 637551, Singapore
| | - Hyun-Suk Oh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- Department of Environmental Engineering, Seoul National University of Science and Technology, 01811 Seoul, South Korea
| | - Vivek M Sheraton
- Complexity Institute, Nanyang Technological University, 639798, Singapore
| | - Emiliano Mancini
- Institute for Advanced Study, University of Amsterdam, 1012 GC Amsterdam, The Netherlands
| | - Say Chye Joachim Loo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 637551, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- The School of Biological Sciences, Nanyang Technological University, 639798, Singapore
- Centre for Marine Bio-Innovation, The Schools of Biotechnology and Biomolecular Sciences, and Biological, Earth and Environmental Sciences, University of New South Wales, 2031 Sydney, Australia
| | - Peter M A Sloot
- Complexity Institute, Nanyang Technological University, 639798, Singapore
- Institute for Advanced Study, University of Amsterdam, 1012 GC Amsterdam, The Netherlands
- ITMO University, 197101 St. Petersburg, Russian Federation
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- The School of Biological Sciences, Nanyang Technological University, 639798, Singapore
- The ithree Institute, University of Technology Sydney, 2007 Sydney, Australia
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20
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Wang Y, Rattray JB, Thomas SA, Gurney J, Brown SP. In silico bacteria evolve robust cooperaion via complex quorum-sensing strategies. Sci Rep 2020; 10:8628. [PMID: 32451396 PMCID: PMC7248119 DOI: 10.1038/s41598-020-65076-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 04/28/2020] [Indexed: 12/22/2022] Open
Abstract
Many species of bacteria collectively sense and respond to their social and physical environment via 'quorum sensing' (QS), a communication system controlling extracellular cooperative traits. Despite detailed understanding of the mechanisms of signal production and response, there remains considerable debate over the functional role(s) of QS: in short, what is it for? Experimental studies have found support for diverse functional roles: density sensing, mass-transfer sensing, genotype sensing, etc. While consistent with theory, these results cannot separate whether these functions were drivers of QS adaption, or simply artifacts or 'spandrels' of systems shaped by distinct ecological pressures. The challenge of separating spandrels from drivers of adaptation is particularly hard to address using extant bacterial species with poorly understood current ecologies (let alone their ecological histories). To understand the relationship between defined ecological challenges and trajectories of QS evolution, we used an agent-based simulation modeling approach. Given genetic mixing, our simulations produce behaviors that recapitulate features of diverse microbial QS systems, including coercive (high signal/low response) and generalized reciprocity (signal auto-regulation) strategists - that separately and in combination contribute to QS-dependent resilience of QS-controlled cooperation in the face of diverse cheats. We contrast our in silico results given defined ecological challenges with bacterial QS architectures that have evolved under largely unknown ecological contexts, highlighting the critical role of genetic constraints in shaping the shorter term (experimental evolution) dynamics of QS. More broadly, we see experimental evolution of digital organisms as a complementary tool in the search to understand the emergence of complex QS architectures and functions.
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Affiliation(s)
- Yifei Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA.
- The Institute for Data Engineering and Science (IDEaS), Georgia Institute of Technology, Atlanta, 30332 GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA.
| | - Jennifer B Rattray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA
| | - Stephen A Thomas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA
- Graduate Program in Quantitative Biosciences (QBioS), Georgia Institute of Technology, Atlanta, 30332 GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA
| | - James Gurney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA.
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21
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Matoz-Fernandez D, Arnaouteli S, Porter M, MacPhee CE, Stanley-Wall NR, Davidson FA. Comment on "Rivalry in Bacillus subtilis colonies: enemy or family?". SOFT MATTER 2020; 16:3344-3346. [PMID: 32207471 PMCID: PMC8522905 DOI: 10.1039/c9sm02141h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
It is well known that biofilms are one of the most widespread forms of life on Earth, capable of colonising almost any environment from humans to metals.
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Affiliation(s)
- Daniel Matoz-Fernandez
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK. and Division of Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK.
| | - Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Michael Porter
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | | | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Fordyce A Davidson
- Division of Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK.
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22
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Gaines A, Ludovice M, Xu J, Zanghi M, Meinersmann RJ, Berrang M, Daley W, Britton D. The dialogue between protozoa and bacteria in a microfluidic device. PLoS One 2019; 14:e0222484. [PMID: 31596855 PMCID: PMC6784911 DOI: 10.1371/journal.pone.0222484] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/30/2019] [Indexed: 01/28/2023] Open
Abstract
In nature, protozoa play a major role in controlling bacterial populations. This paper proposes a microfluidic device for the study of protozoa behaviors change due to their chemotactic response in the presence of bacterial cells. A three-channel microfluidic device was designed using a nitrocellulose membrane into which channels were cut using a laser cutter. The membrane was sandwiched between two glass slides; a Euglena suspension was then allowed to flow through the central channel. The two side channels were filled with either, 0.1% peptone as a negative control, or a Listeria suspension respectively. The membrane design prevented direct interaction but allowed Euglena cells to detect Listeria cells as secretions diffused through the nitrocellulose membrane. A significant number of Euglena cells migrated toward the chambers near the bacterial cells, indicating a positive chemotactic response of Euglena toward chemical cues released from Listeria cells. Filtrates collected from Listeria suspension with a series of molecular weight cutoffs (3k, 10k and 100k) were examined in Euglena chemotaxis tests. Euglena cells were attracted to all filtrates collected from the membrane filtration with different molecular weight cutoffs, suggesting small molecules from Listeria might be the chemical cues to attract protozoa. Headspace volatile organic compounds (VOC) released from Listeria were collected, spiked to 0.1% peptone and tested as the chemotactic effectors. It was discovered that the Euglena cells responded quickly to Listeria VOCs including decanal, 3,5- dimethylbenzaldehyde, ethyl acetate, indicating bacterial VOCs were used by Euglena to track the location of bacteria.
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Affiliation(s)
- Anna Gaines
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Miranda Ludovice
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jie Xu
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Marc Zanghi
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Richard J. Meinersmann
- Richard B. Russell Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, United States of America
| | - Mark Berrang
- Richard B. Russell Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, United States of America
| | - Wayne Daley
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Doug Britton
- Aerospace, Transportation and Advanced Systems Laboratory, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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Garg V, Chou T, Liu A, De Marco A, Kamaliya B, Qiu S, Mote RG, Fu J. Weaving nanostructures with site-specific ion induced bidirectional bending. NANOSCALE ADVANCES 2019; 1:3067-3077. [PMID: 36133581 PMCID: PMC9418629 DOI: 10.1039/c9na00382g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 05/13/2023]
Abstract
Site-specific ion-irradiation is a promising tool fostering strain-engineering of freestanding nanostructures to realize 3D-configurations towards various functionalities. We first develop a novel approach of fabricating freestanding 3D silicon nanostructures by low dose ion-implantation followed by chemical-etching. The fabricated nanostructures can then be deformed bidirectionally by varying the local irradiation of kiloelectronvolt gallium ions. By further tuning the ion-dose and energy, various nanostructure configurations can be realized, thus extending its horizon to new functional 3D-nanostructures. It has been revealed that at higher-energies (∼30 kV), the nanostructures can exhibit two-stage bidirectional-bending in contrast to the bending towards the incident-ions at lower-energies (∼16), implying an effective transfer of kinetic-energy. Computational studies show that the spatial-distribution of implanted-ions, dislocated silicon atoms, has potentially contributed to the local development of stresses. Nanocharacterization confirms the formation of two distinguishable ion-irradiated and un-irradiated regions, while the smoothened morphology of the irradiated-surface suggested that the bending is also coupled with sputtering at higher ion-doses. The bending effects associated with local ion irradiation in contrast to global ion irradiation are presented, with the mechanism elucidated. Finally, weaving of nanostructures is demonstrated through strain-engineering for new nanoscale artefacts such as ultra-long fully-bent nanowires, nano-hooks, and nano-meshes. The aligned growth of bacterial-cells is observed on the fabricated nanowires, and a mesh based "bacterial-trap" for site-specific capture of bacterial cells is demonstrated emphasizing the versatile nature of the current approach.
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Affiliation(s)
- Vivek Garg
- IITB-Monash Research Academy, Indian Institute of Technology Bombay Powai Mumbai 400076 India
- Department of Mechanical Engineering, Indian Institute of Technology Bombay Powai Mumbai 400076 India
- Department of Mechanical and Aerospace Engineering, Monash University Wellington Road Clayton Victoria 3800 Australia
| | - Tsengming Chou
- Laboratory of Multiscale Imaging, Stevens Institute of Technology Hoboken NJ 07030 USA
| | - Amelia Liu
- Monash Centre for Electron Microscopy, Monash University Clayton VIC 3800 Australia
| | - Alex De Marco
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
| | - Bhaveshkumar Kamaliya
- IITB-Monash Research Academy, Indian Institute of Technology Bombay Powai Mumbai 400076 India
- Department of Mechanical and Aerospace Engineering, Monash University Wellington Road Clayton Victoria 3800 Australia
- Department Physics, Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Shi Qiu
- Department of Mechanical and Aerospace Engineering, Monash University Wellington Road Clayton Victoria 3800 Australia
| | - Rakesh G Mote
- Department of Mechanical Engineering, Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University Wellington Road Clayton Victoria 3800 Australia
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Gordon V, Bakhtiari L, Kovach K. From molecules to multispecies ecosystems: the roles of structure in bacterial biofilms. Phys Biol 2019; 16:041001. [PMID: 30913545 DOI: 10.1088/1478-3975/ab1384] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Biofilms are communities of sessile microbes that are bound to each other by a matrix made of biopolymers and proteins. Spatial structure is present in biofilms on many lengthscales. These range from the nanometer scale of molecular motifs to the hundred-micron scale of multicellular aggregates. Spatial structure is a physical property that impacts the biology of biofilms in many ways. The molecular structure of matrix components controls their interaction with each other (thereby impacting biofilm mechanics) and with diffusing molecules such as antibiotics and immune factors (thereby impacting antibiotic tolerance and evasion of the immune system). The size and structure of multicellular aggregates, combined with microbial consumption of growth substrate, give rise to differentiated microenvironments with different patterns of metabolism and gene expression. Spatial association of more than one species can benefit one or both species, while distances between species can both determine and result from the transport of diffusible factors between species. Thus, a widespread theme in the biological importance of spatial structure in biofilms is the effect of structure on transport. We survey what is known about this and other effects of spatial structure in biofilms, from molecules up to multispecies ecosystems. We conclude with an overview of what experimental approaches have been developed to control spatial structure in biofilms and how these and other experiments can be complemented with computational work.
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Affiliation(s)
- Vernita Gordon
- Department of Physics, University of Texas at Austin, Austin TX 78712, United States of America. Center for Nonlinear Dynamics, University of Texas at Austin, Austin TX 78712, United States of America. Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin TX 78712, United States of America. Author to whom any correspondence should be addressed
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25
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Barriuso J, Hogan DA, Keshavarz T, Martínez MJ. Role of quorum sensing and chemical communication in fungal biotechnology and pathogenesis. FEMS Microbiol Rev 2018; 42:627-638. [PMID: 29788231 DOI: 10.1093/femsre/fuy022] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/17/2018] [Indexed: 12/18/2022] Open
Abstract
Microbial cells do not live in isolation in their environment, but rather they communicate with each other using chemical signals. This sophisticated mode of cell-to-cell signalling, known as quorum sensing, was first discovered in bacteria, and coordinates the behaviour of microbial population behaviour in a cell-density-dependent manner. More recently, these mechanisms have been described in eukaryotes, particularly in fungi, where they regulate processes such as pathogenesis, morphological differentiation, secondary metabolite production and biofilm formation. In this manuscript, we review the information available to date on these processes in yeast, dimorphic fungi and filamentous fungi. We analyse the diverse chemical 'languages' used by different groups of fungi, their possible cross-talk and interkingdom interactions with other organisms. We discuss the existence of these mechanisms in multicellular organisms, the ecophysiological role of QS in fungal colonisation and the potential applications of these mechanisms in biotechnology and pathogenesis.
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Affiliation(s)
- Jorge Barriuso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Tajalli Keshavarz
- Department of Life Sciences, Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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26
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Cheptsov VS, Tsypina SI, Minaev NV, Yusupov VI, Chichkov BN. New microorganism isolation techniques with emphasis on laser printing. Int J Bioprint 2018; 5:165. [PMID: 32596530 PMCID: PMC7294688 DOI: 10.18063/ijb.v5i1.165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 01/05/2023] Open
Abstract
The study of biodiversity, growth, development, and metabolism of cultivated microorganisms is an integral part of modern microbiological, biotechnological, and medical research. Such studies require the development of new methods of isolation, cultivation, manipulation, and study of individual bacterial cells and their consortia. To this end, in recent years, there has been an active development of different isolation and three-dimensional cell positioning methods. In this review, the optical tweezers, surface heterogeneous functionalization, multiphoton lithography, microfluidic techniques, and laser printing are reviewed. Laser printing is considered as one of the most promising techniques and is discussed in detail.
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Affiliation(s)
- V S Cheptsov
- Department of Soil Science, Lomonosov Moscow State University, 11999 Moscow, Russia
| | - S I Tsypina
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - N V Minaev
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - V I Yusupov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - B N Chichkov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia.,Institut für Quantenoptik, Leibniz Universität Hannover, Welfengarten, 30167, Hannover
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27
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Darch SE, Koley D. Quantifying microbial chatter: scanning electrochemical microscopy as a tool to study interactions in biofilms. Proc Math Phys Eng Sci 2018; 474:20180405. [PMID: 30602930 DOI: 10.1098/rspa.2018.0405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/09/2018] [Indexed: 12/12/2022] Open
Abstract
Bacteria are often found in their natural habitats as spatially organized biofilm communities. While it is clear from recent work that the ability to organize into precise spatial structures is important for fitness of microbial communities, a significant gap exists in our understanding regarding the mechanisms bacteria use to adopt such physical distributions. Bacteria are highly social organisms that interact, and it is these interactions that have been proposed to be critical for establishing spatially structured communities. A primary means by which bacteria interact is via small, diffusible molecules including dedicated signals and metabolic by-products; however, quantitatively monitoring the production of these molecules in time and space with the micron-scale resolution required has been challenging. In this perspective, scanning electrochemical microscopy (SECM) is discussed as a powerful tool to study microbe-microbe interactions through the detection of small redox-active molecules. We highlight SECM as a means to quantify and spatially resolve the chemical mediators of bacterial interactions and begin to elucidate the mechanisms used by bacteria to regulate the emergent properties of biofilms.
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Affiliation(s)
- Sophie E Darch
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
| | - Dipankar Koley
- Department of Chemistry, Oregon State University, Corvallis, OR, USA
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28
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Hernandez DS, Ritschdorff ET, Connell JL, Shear JB. In Situ Imprinting of Topographic Landscapes at the Cell-Substrate Interface. J Am Chem Soc 2018; 140:14064-14068. [PMID: 30350959 DOI: 10.1021/jacs.8b09226] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In their native environments, adherent cells encounter dynamic topographical cues involved in promoting differentiation, orientation, and migration. Ideally, such processes would be amenable to study in cell culture using tools capable of imposing dynamic, arbitrary, and reversible topographic features without perturbing environmental conditions or causing chemical and/or structural disruptions to the substrate surface. To address this need, we report here development of an in vitro strategy for challenging cells with dynamic topographical experiences in which protein-based hydrogel substrate surfaces are modified in real time by positioning a pulsed, near-infrared laser focus within the hydrogel, promoting chemical cross-linking which results in local contraction of the protein matrix. Scanning the laser focus through arbitrary patterns directed by a dynamic reflective mask creates an internal contraction pattern that is projected onto the hydrogel surface as features such as rings, pegs, and grooves. By subjecting substrates to a sequence of scan patterns, we show that topographic features can be created, then eliminated or even reversed. Because laser-induced shrinkage can be confined to 3D voxels isolated from the cell-substrate interface, hydrogel modifications are made without damaging cells or disrupting the chemical or structural integrity of the surface.
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Affiliation(s)
- Derek S Hernandez
- University Station, A5300, Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Eric T Ritschdorff
- University Station, A5300, Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jodi L Connell
- University Station, A5300, Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jason B Shear
- University Station, A5300, Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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29
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Keloth A, Anderson O, Risbridger D, Paterson L. Single Cell Isolation Using Optical Tweezers. MICROMACHINES 2018; 9:mi9090434. [PMID: 30424367 PMCID: PMC6187562 DOI: 10.3390/mi9090434] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/01/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022]
Abstract
Optical tweezers offer a non-contact method for selecting single cells and translocating them from one microenvironment to another. We have characterized the optical tweezing of yeast S. cerevisiae and can manipulate single cells at 0.41 ± 0.06 mm/s using a 26.8 ± 0.1 mW from a 785 nm diode laser. We have fabricated and tested three cell isolation devices; a micropipette, a PDMS chip and a laser machined fused silica chip and we have isolated yeast, single bacteria and cyanobacteria cells. The most effective isolation was achieved in PDMS chips, where single yeast cells were grown and observed for 18 h without contamination. The duration of budding in S. cerevisiae was not affected by the laser parameters used, but the time from tweezing until the first budding event began increased with increasing laser energy (laser power × time). Yeast cells tweezed using 25.0 ± 0.1 mW for 1 min were viable after isolation. We have constructed a micro-consortium of yeast cells, and a co-culture of yeast and bacteria, using optical tweezers in combination with the PDMS network of channels and isolation chambers, which may impact on both industrial biotechnology and understanding pathogen dynamics.
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Affiliation(s)
- Anusha Keloth
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK.
| | - Owen Anderson
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK.
| | - Donald Risbridger
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK.
| | - Lynn Paterson
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK.
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Retterer ST, Morrell-Falvey JL, Doktycz MJ. Nano-Enabled Approaches to Chemical Imaging in Biosystems. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:351-373. [PMID: 29490189 DOI: 10.1146/annurev-anchem-061417-125635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding and predicting how biosystems function require knowledge about the dynamic physicochemical environments with which they interact and alter by their presence. Yet, identifying specific components, tracking the dynamics of the system, and monitoring local environmental conditions without disrupting biosystem function present significant challenges for analytical measurements. Nanomaterials, by their very size and nature, can act as probes and interfaces to biosystems and offer solutions to some of these challenges. At the nanoscale, material properties emerge that can be exploited for localizing biomolecules and making chemical measurements at cellular and subcellular scales. Here, we review advances in chemical imaging enabled by nanoscale structures, in the use of nanoparticles as chemical and environmental probes, and in the development of micro- and nanoscale fluidic devices to define and manipulate local environments and facilitate chemical measurements of complex biosystems. Integration of these nano-enabled methods will lead to an unprecedented understanding of biosystem function.
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Affiliation(s)
- Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA;
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | | | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA;
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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31
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Conrad JC, Poling-Skutvik R. Confined Flow: Consequences and Implications for Bacteria and Biofilms. Annu Rev Chem Biomol Eng 2018; 9:175-200. [DOI: 10.1146/annurev-chembioeng-060817-084006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria overwhelmingly live in geometrically confined habitats that feature small pores or cavities, narrow channels, or nearby interfaces. Fluid flows through these confined habitats are ubiquitous in both natural and artificial environments colonized by bacteria. Moreover, these flows occur on time and length scales comparable to those associated with motility of bacteria and with the formation and growth of biofilms, which are surface-associated communities that house the vast majority of bacteria to protect them from host and environmental stresses. This review describes the emerging understanding of how flow near surfaces and within channels and pores alters physical processes that control how bacteria disperse, attach to surfaces, and form biofilms. This understanding will inform the development and deployment of technologies for drug delivery, water treatment, and antifouling coatings and guide the structuring of bacterial consortia for production of chemicals and pharmaceuticals.
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Affiliation(s)
- Jacinta C. Conrad
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
| | - Ryan Poling-Skutvik
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
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Abstract
Many bacteria use a cell-cell communication system called quorum sensing to coordinate population density-dependent changes in behavior. Quorum sensing involves production of and response to diffusible or secreted signals, which can vary substantially across different types of bacteria. In many species, quorum sensing modulates virulence functions and is important for pathogenesis. Over the past half-century, there has been a significant accumulation of knowledge of the molecular mechanisms, signal structures, gene regulons, and behavioral responses associated with quorum-sensing systems in diverse bacteria. More recent studies have focused on understanding quorum sensing in the context of bacterial sociality. Studies of the role of quorum sensing in cooperative and competitive microbial interactions have revealed how quorum sensing coordinates interactions both within a species and between species. Such studies of quorum sensing as a social behavior have relied on the development of "synthetic ecological" models that use nonclonal bacterial populations. In this review, we discuss some of these models and recent advances in understanding how microbes might interact with one another using quorum sensing. The knowledge gained from these lines of investigation has the potential to guide studies of microbial sociality in natural settings and the design of new medicines and therapies to treat bacterial infections.
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Abstract
Quorum sensing is a communication system that allows bacteria to coordinate their activities, and these systems are critical for virulence in several bacteria, including Pseudomonas aeruginosa. There is a significant gap in knowledge about how quorum sensing proceeds during infection, particularly how spatial organization of the infecting microbial community impacts signaling. Using a model that recapitulates the biogeographical properties of P. aeruginosa infection of the cystic fibrosis lung, we discovered that communication primarily occurs within P. aeruginosa aggregates and that communication between aggregates is only observed for very large aggregates containing ≥5,000 cells. This study identifies a critical role for spatial distribution and bacterial phenotypic heterogeneity in bacterial signaling during infection, and provides a platform for future ecological and evolutionary studies. Quorum sensing (QS) is a bacterial communication system that involves production and sensing of extracellular signals. In laboratory models, QS allows bacteria to monitor and respond to their own cell density and is critical for fitness. However, how QS proceeds in natural, spatially structured bacterial communities is not well understood, which significantly hampers our understanding of the emergent properties of natural communities. To address this gap, we assessed QS signaling in the opportunistic pathogen Pseudomonas aeruginosa in a cystic fibrosis (CF) lung infection model that recapitulates the biogeographical aspects of the natural human infection. In this model, P. aeruginosa grows as spatially organized, highly dense aggregates similar to those observed in the human CF lung. By combining this natural aggregate system with a micro-3D–printing platform that allows for confinement and precise spatial positioning of P. aeruginosa aggregates, we assessed the impact of aggregate size and spatial positioning on both intra- and interaggregate signaling. We discovered that aggregates containing ∼2,000 signal-producing P. aeruginosa were unable to signal neighboring aggregates, while those containing ≥5,000 cells signaled aggregates as far away as 176 µm. Not all aggregates within this “calling distance” responded, indicating that aggregates have differential sensitivities to signal. Overexpression of the signal receptor increased aggregate sensitivity to signal, suggesting that the ability of aggregates to respond is defined in part by receptor levels. These studies provide quantitative benchmark data for the impact of spatial arrangement and phenotypic heterogeneity on P. aeruginosa signaling in vivo.
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Abstract
Microfluidic technology overcomes many of the limitations to traditional analytical methods in microbiology. Unlike bulk-culture methods, it offers single-cell resolution and long observation times spanning hundreds of generations; unlike agarose pad-based microscopy, it has uniform growth conditions that can be tightly controlled. Because the continuous flow of growth medium isolates the cells in a microfluidic device from unpredictable variations in the local chemical environment caused by cell growth and metabolism, authentic changes in gene expression and cell growth in response to specific stimuli can be more confidently observed. Bacillus subtilis is used here as a model bacterial species to demonstrate a "mother machine"-type method for cellular analysis. We show how to construct and plumb a microfluidic device, load it with cells, initiate microscopic imaging, and expose cells to a stimulus by switching from one growth medium to another. A stress-responsive reporter is used as an example to reveal the type of data that may be obtained by this method. We also briefly discuss further applications of this method for other types of experiments, such as analysis of bacterial sporulation.
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Affiliation(s)
- Matthew T Cabeen
- Department of Microbiology and Molecular Genetics, Oklahoma State University;
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University;
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35
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Sønderholm M, Bjarnsholt T, Alhede M, Kolpen M, Jensen PØ, Kühl M, Kragh KN. The Consequences of Being in an Infectious Biofilm: Microenvironmental Conditions Governing Antibiotic Tolerance. Int J Mol Sci 2017; 18:E2688. [PMID: 29231866 PMCID: PMC5751290 DOI: 10.3390/ijms18122688] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/27/2017] [Accepted: 12/06/2017] [Indexed: 12/22/2022] Open
Abstract
The main driver behind biofilm research is the desire to understand the mechanisms governing the antibiotic tolerance of biofilm-growing bacteria found in chronic bacterial infections. Rather than genetic traits, several physical and chemical traits of the biofilm have been shown to be attributable to antibiotic tolerance. During infection, bacteria in biofilms exhibit slow growth and a low metabolic state due to O₂ limitation imposed by intense O₂ consumption of polymorphonuclear leukocytes or metabolically active bacteria in the biofilm periphery. Due to variable O₂ availability throughout the infection, pathogen growth can involve aerobic, microaerobic and anaerobic metabolism. This has serious implications for the antibiotic treatment of infections (e.g., in chronic wounds or in the chronic lung infection of cystic fibrosis patients), as antibiotics are usually optimized for aerobic, fast-growing bacteria. This review summarizes knowledge about the links between the microenvironment of biofilms in chronic infections and their tolerance against antibiotics.
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Affiliation(s)
- Majken Sønderholm
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Thomas Bjarnsholt
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Clinical Microbiology, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
| | - Maria Alhede
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Mette Kolpen
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Clinical Microbiology, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
| | - Peter Ø Jensen
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Clinical Microbiology, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, DK-3000 Elsinore, Denmark.
- Climate Change Cluster, University of Technology Sydney, Ultimo NSW 2007, Australia.
| | - Kasper N Kragh
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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36
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Joshi VS, Sheet PS, Cullin N, Kreth J, Koley D. Real-Time Metabolic Interactions between Two Bacterial Species Using a Carbon-Based pH Microsensor as a Scanning Electrochemical Microscopy Probe. Anal Chem 2017; 89:11044-11052. [PMID: 28920437 PMCID: PMC6265524 DOI: 10.1021/acs.analchem.7b03050] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have developed a carbon-based, fast-response potentiometric pH microsensor for use as a scanning electrochemical microscopy (SECM) chemical probe to quantitatively map the microbial metabolic exchange between two bacterial species, commensal Streptococcus gordonii and pathogenic Streptococcus mutans. The 25 μm diameter H+ ion-selective microelectrode or pH microprobe showed a Nernstian slope of 59 mV/pH and high selectivity against major ions such Na+, K+, Ca2+, and Mg2+. In addition, the unique conductive membrane composition aided us in performing an amperometric approach curve to position the probe and obtain a high-resolution pH map of the microenvironment produced by the lactate-producing S. mutans biofilm. The x-directional pH scan over S. mutans also showed the influence of the pH profile on the metabolic activity of another species, H2O2-producing S. gordonii. When these bacterial species were placed in close spatial proximity, we observed an initial increase in the local H2O2 concentration of approximately 12 ± 5 μM above S. gordonii, followed by a gradual decrease in H2O2 concentration (>30 min) to almost zero as lactate was produced, and a subsequent decrease in pH with a more pronounced metabolic output of S. mutans. These results were supported by gene expression and confocal fluorescence microscopic studies. Our findings illustrate that H2O2-producing S. gordonii is dominant while the buffering capacity of saliva is valid (∼pH 6.0) but is gradually taken over by S. mutans as the latter species slowly starts decreasing the local pH to 5.0 or less by producing lactic acid. Our observations demonstrate the unique capability of our SECM chemical probes for studying real-time metabolic interactions between two bacterial species, which would not otherwise be achievable in traditional assays.
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Affiliation(s)
- Vrushali S Joshi
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | - Partha S Sheet
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | - Nyssa Cullin
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104
- Department of Restorative Dentistry, Oregon Health & Science University, Portland, OR USA 97239
| | - Jens Kreth
- Department of Restorative Dentistry, Oregon Health & Science University, Portland, OR USA 97239
| | - Dipankar Koley
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
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37
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Kim M, Bae J, Kim T. Long-Term and Programmable Bacterial Subculture in Completely Automated Microchemostats. Anal Chem 2017; 89:9676-9684. [DOI: 10.1021/acs.analchem.7b01076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Minseok Kim
- Department
of Mechanical Engineering, and ‡Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Juyeol Bae
- Department
of Mechanical Engineering, and ‡Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Taesung Kim
- Department
of Mechanical Engineering, and ‡Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
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38
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Sadiq FA, Flint S, Li Y, Ou K, Yuan L, He GQ. Phenotypic and genetic heterogeneity within biofilms with particular emphasis on persistence and antimicrobial tolerance. Future Microbiol 2017; 12:1087-1107. [DOI: 10.2217/fmb-2017-0042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Phenotypic changes or phase variation within biofilms is an important feature of bacterial dormant life. Enhanced resistance to antimicrobials is one of the distinct features displayed by a fraction of cells within biofilms. It is believed that persisters are mainly responsible for this phenotypic heterogeneity. However, there is still an unresolved debate on the formation of persisters. In this short review, we highlight all known genomic and proteomic changes encountered by bacterial cells within biofilms. We have also described all phenotypic changes displayed by bacterial cells within biofilms with particular emphasis on enhanced antimicrobial tolerance of biofilms with particular reference to persisters. In addition, all currently known models of persistence have been succinctly discussed.
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Affiliation(s)
- Faizan A Sadiq
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
| | - Steve Flint
- School of Food & Nutrition, Massey University, Private Bag 11 222, Palmerston North 4474, New Zealand
| | - YanJun Li
- Research Institute of Food Science, Hangzhou Wahaha Group Co, Ltd, Hangzhou 310018, China
| | - Kai Ou
- Research Institute of Food Science, Hangzhou Wahaha Group Co, Ltd, Hangzhou 310018, China
| | - Lei Yuan
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
| | - Guo Qing He
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
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39
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Abstract
Polymicrobial interactions are complex and can influence the course of an infection, as is the case when two or more species exhibit a synergism that produces a disease state not seen with any of the individual species alone. Cell-to-cell signaling is key to many of these interactions, but little is understood about how the host environment influences polymicrobial interactions or signaling between bacteria. Chronic wounds are typically polymicrobial, with Staphylococcus aureus and Pseudomonas aeruginosa being the two most commonly isolated species. While P. aeruginosa readily kills S. aureusin vitro, the two species can coexist for long periods together in chronic wound infections. In this study, we investigated the ability of components of the wound environment to modulate interactions between P. aeruginosa and S. aureus We demonstrate that P. aeruginosa quorum sensing is inhibited by physiological levels of serum albumin, which appears to bind and sequester some homoserine lactone quorum signals, resulting in the inability of P. aeruginosa to produce virulence factors that kill S. aureus These data could provide important clues regarding the virulence of P. aeruginosa in albumin-depleted versus albumin-rich infection sites and an understanding of the nature of friendly versus antagonistic interactions between P. aeruginosa and S. aureus.
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40
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Pompano RR, Chiang AH, Kastrup CJ, Ismagilov RF. Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching. Annu Rev Biochem 2017; 86:333-356. [PMID: 28654324 PMCID: PMC10852032 DOI: 10.1146/annurev-biochem-060815-014207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many biochemical systems are spatially heterogeneous and exhibit nonlinear behaviors, such as state switching in response to small changes in the local concentration of diffusible molecules. Systems as varied as blood clotting, intracellular calcium signaling, and tissue inflammation are all heavily influenced by the balance of rates of reaction and mass transport phenomena including flow and diffusion. Transport of signaling molecules is also affected by geometry and chemoselective confinement via matrix binding. In this review, we use a phenomenon referred to as patchy switching to illustrate the interplay of nonlinearities, transport phenomena, and spatial effects. Patchy switching describes a change in the state of a network when the local concentration of a diffusible molecule surpasses a critical threshold. Using patchy switching as an example, we describe conceptual tools from nonlinear dynamics and chemical engineering that make testable predictions and provide a unifying description of the myriad possible experimental observations. We describe experimental microfluidic and biochemical tools emerging to test conceptual predictions by controlling transport phenomena and spatial distribution of diffusible signals, and we highlight the unmet need for in vivo tools.
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Affiliation(s)
- Rebecca R Pompano
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904;
| | - Andrew H Chiang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637;
| | - Christian J Kastrup
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125;
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41
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Costa-Orlandi CB, Sardi JCO, Pitangui NS, de Oliveira HC, Scorzoni L, Galeane MC, Medina-Alarcón KP, Melo WCMA, Marcelino MY, Braz JD, Fusco-Almeida AM, Mendes-Giannini MJS. Fungal Biofilms and Polymicrobial Diseases. J Fungi (Basel) 2017; 3:jof3020022. [PMID: 29371540 PMCID: PMC5715925 DOI: 10.3390/jof3020022] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/19/2017] [Accepted: 05/04/2017] [Indexed: 12/29/2022] Open
Abstract
Biofilm formation is an important virulence factor for pathogenic fungi. Both yeasts and filamentous fungi can adhere to biotic and abiotic surfaces, developing into highly organized communities that are resistant to antimicrobials and environmental conditions. In recent years, new genera of fungi have been correlated with biofilm formation. However, Candida biofilms remain the most widely studied from the morphological and molecular perspectives. Biofilms formed by yeast and filamentous fungi present differences, and studies of polymicrobial communities have become increasingly important. A key feature of resistance is the extracellular matrix, which covers and protects biofilm cells from the surrounding environment. Furthermore, to achieve cell–cell communication, microorganisms secrete quorum-sensing molecules that control their biological activities and behaviors and play a role in fungal resistance and pathogenicity. Several in vitro techniques have been developed to study fungal biofilms, from colorimetric methods to omics approaches that aim to identify new therapeutic strategies by developing new compounds to combat these microbial communities as well as new diagnostic tools to identify these complex formations in vivo. In this review, recent advances related to pathogenic fungal biofilms are addressed.
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Affiliation(s)
- Caroline B Costa-Orlandi
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Janaina C O Sardi
- Department of Physiological Sciences, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba SP 13414-018, Brazil.
| | - Nayla S Pitangui
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Haroldo C de Oliveira
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Liliana Scorzoni
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Mariana C Galeane
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Kaila P Medina-Alarcón
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Wanessa C M A Melo
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Mônica Y Marcelino
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Jaqueline D Braz
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Ana Marisa Fusco-Almeida
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Maria José S Mendes-Giannini
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
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42
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Zhao X, Liu X, Xu X, Fu YV. Microbe social skill: the cell-to-cell communication between microorganisms. Sci Bull (Beijing) 2017; 62:516-524. [PMID: 36659262 DOI: 10.1016/j.scib.2017.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 01/21/2023]
Abstract
Although microbes primarily are single-cell organisms, they are not isolated individuals. Microbes use various means to communicate with one another. Based on the communication, microbes establish a social interaction with their neighbors in a specific ecological niche, and cooperative behaviors are normally performed to provide benefits on the population and species levels. In the microbiome era, in order to better understand the behaviors of microbes, deep understanding of the social communication between microbes hence becomes a key to interpret microbe behaviors. Here we summarize the molecular mechanisms that underlie the cell-to-cell communication in prokaryotic and eukaryotic microorganisms, the recent discoveries and novel technologies in understanding the interspecies and interkingdom communication, and discuss new concepts of the sociomicrobiology.
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Affiliation(s)
- Xi Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu V Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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43
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Phage Inhibit Pathogen Dissemination by Targeting Bacterial Migrants in a Chronic Infection Model. mBio 2017; 8:mBio.00240-17. [PMID: 28377527 PMCID: PMC5380840 DOI: 10.1128/mbio.00240-17] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The microbial communities inhabiting chronic infections are often composed of spatially organized micrometer-sized, highly dense aggregates. It has recently been hypothesized that aggregates are responsible for the high tolerance of chronic infections to host immune functions and antimicrobial therapies. Little is currently known regarding the mechanisms controlling aggregate formation and antimicrobial tolerance primarily because of the lack of robust, biologically relevant experimental systems that promote natural aggregate formation. Here, we developed an in vitro model based on chronic Pseudomonas aeruginosa infection of the cystic fibrosis (CF) lung. This model utilizes a synthetic sputum medium that readily promotes the formation of P. aeruginosa aggregates with sizes similar to those observed in human CF lung tissue. Using high-resolution imaging, we exploited this model to elucidate the life history of P. aeruginosa and the mechanisms that this bacterium utilizes to tolerate antimicrobials, specifically, bacteriophage. In the early stages of growth in synthetic sputum, planktonic cells form aggregates that increase in size over time by expansion. In later growth, migrant cells disperse from aggregates and colonize new areas, seeding new aggregates. When added simultaneously with phage, P. aeruginosa was readily killed and aggregates were unable to form. When added after initial aggregate formation, phage were unable to eliminate all of the aggregates because of exopolysaccharide production; however, seeding of new aggregates by dispersed migrants was inhibited. We propose a model in which aggregates provide a mechanism that allows P. aeruginosa to tolerate phage therapy during chronic infection without the need for genetic mutation.IMPORTANCE Bacteria in chronic infections often reside in communities composed of micrometer-sized, highly dense aggregates. A primary challenge for studying aggregates has been the lack of laboratory systems that promote natural aggregate formation in relevant environments. Here, we developed a growth medium that mimics chronic lung infection and promotes natural aggregate formation by the bacterium Pseudomonas aeruginosa High-resolution, single-cell microscopy allowed us to characterize P. aeruginosa's life history-seeding, aggregate formation, and dispersal-in this medium. Our results reveal that this bacterium readily forms aggregates that release migrants to colonize new areas. We also show that aggregates allow P. aeruginosa to tolerate therapeutic bacteriophage addition, although this treatment limits P. aeruginosa dissemination by targeting migrants.
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44
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Yu FB, Willis L, Chau RMW, Zambon A, Horowitz M, Bhaya D, Huang KC, Quake SR. Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing. BMC Biol 2017; 15:11. [PMID: 28196492 PMCID: PMC5310064 DOI: 10.1186/s12915-016-0344-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 12/10/2016] [Indexed: 01/25/2023] Open
Abstract
Background Cyanobacteria are important agents in global carbon and nitrogen cycling and hold great promise for biotechnological applications. Model organisms such as Synechocystis sp. and Synechococcus sp. have advanced our understanding of photosynthetic capacity and circadian behavior, mostly using population-level measurements in which the behavior of individuals cannot be monitored. Synechocystis sp. cells are small and divide slowly, requiring long-term experiments to track single cells. Thus, the cumulative effects of drift over long periods can cause difficulties in monitoring and quantifying cell growth and division dynamics. Results To overcome this challenge, we enhanced a microfluidic cell-culture device and developed an image analysis pipeline for robust lineage reconstruction. This allowed simultaneous tracking of many cells over multiple generations, and revealed that cells expand exponentially throughout their cell cycle. Generation times were highly correlated for sister cells, but not between mother and daughter cells. Relationships between birth size, division size, and generation time indicated that cell-size control was inconsistent with the “sizer” rule, where division timing is based on cell size, or the “timer” rule, where division occurs after a fixed time interval. Instead, single cell growth statistics were most consistent with the “adder” rule, in which division occurs after a constant increment in cell volume. Cells exposed to light-dark cycles exhibited growth and division only during the light period; dark phases pause but do not disrupt cell-cycle control. Conclusions Our analyses revealed that the “adder” model can explain both the growth-related statistics of single Synechocystis cells and the correlation between sister cell generation times. We also observed rapid phenotypic response to light-dark transitions at the single cell level, highlighting the critical role of light in cyanobacterial cell-cycle control. Our findings suggest that by monitoring the growth kinetics of individual cells we can build testable models of circadian control of the cell cycle in cyanobacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0344-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Feiqiao Brian Yu
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lisa Willis
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Sainsbury Laboratory, Cambridge University, Cambridge, CB2 1LR, UK
| | | | - Alessandro Zambon
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Department of Industrial Engineering, University of Padova, Padova, 35131, Italy
| | - Mark Horowitz
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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45
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Abstract
Quorum sensing (QS) is a form of chemical communication used by certain bacteria that regulates a wide range of biogeochemically important bacterial behaviors. Although QS was first observed in a marine bacterium nearly four decades ago, only in the past decade has there been a rise in interest in the role that QS plays in the ocean. It has become clear that QS, regulated by signals such as acylated homoserine lactones (AHLs) or furanosyl-borate diesters [autoinducer-2 (AI-2) molecules], is involved in important processes within the marine carbon cycle, in the health of coral reef ecosystems, and in trophic interactions between a range of eukaryotes and their bacterial associates. The most well-studied QS systems in the ocean occur in surface-attached (biofilm) communities and rely on AHL signaling. AHL-QS is highly sensitive to the chemical and biological makeup of the environment and may respond to anthropogenic change, including ocean acidification and rising sea surface temperatures.
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Affiliation(s)
- Laura R Hmelo
- School of Oceanography, University of Washington, Seattle, Washington 98195;
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46
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Ribbe J, Maier B. Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems. Biophys J 2016; 110:1648-1660. [PMID: 27074689 DOI: 10.1016/j.bpj.2016.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 02/09/2016] [Accepted: 03/08/2016] [Indexed: 10/21/2022] Open
Abstract
Bacterial quorum sensing is usually studied in well-mixed populations residing within closed systems. The latter do not exchange mass with their surroundings; however, in their natural environment, such as the rhizosphere, bacteria live in spatially structured open systems. Here, we tested the hypothesis that trapping of bacteria within microscopic pockets of an open system triggers density-dependent differentiation. We designed a microfluidic device that trapped swimming bacteria within microscopic compartments. The geometry of the traps controlled their diffusive coupling to fluid flow that played a dual role as nutrient source and autoinducer sink. Bacillus subtilis differentiates into a state of competence in response to quorum sensing and nutrient limitation. Using a mutant strain with a high differentiation rate and fluorescent reporters for competence, we found that the cell density required for differentiation was 100-fold higher than that required in closed systems. A direct comparison of strongly and moderately coupled reservoirs showed that strong coupling supported early differentiation but required a higher number of bacteria for its initiation. Weak coupling resulted in retardation of growth and differentiation. We conclude that spatial heterogeneity can promote density-dependent differentiation in open systems, and propose that the minimal quorum is determined by diffusive coupling to the environment through a trade-off between retaining autoinducers and accessing nutrients.
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Affiliation(s)
- Jan Ribbe
- Department of Physics, University of Cologne, Cologne, Germany
| | - Berenike Maier
- Department of Physics, University of Cologne, Cologne, Germany.
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47
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Connell JL, Ritschdorff ET, Shear JB. Three-Dimensional Printing of Photoresponsive Biomaterials for Control of Bacterial Microenvironments. Anal Chem 2016; 88:12264-12271. [PMID: 27782402 DOI: 10.1021/acs.analchem.6b03440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Advances in microscopic three-dimensional (μ3D) printing provide a means to microfabricate an almost limitless range of arbitrary geometries, offering new opportunities to rapidly prototype complex architectures for microfluidic and cellular applications. Such 3D lithographic capabilities present a tantalizing prospect for engineering micromechanical components, for example, pumps and valves, for cellular environments composed of smart materials whose size, shape, permeability, stiffness, and other attributes might be modified in real time to precisely manipulate ultralow-volume samples. Unfortunately, most materials produced using μ3D printing are synthetic polymers that are inert to biologically tolerated chemical and light-based triggers and provide low compatibility as materials for cell culture and encapsulation applications. We previously demonstrated feasibility for μ3D printing environmentally sensitive, microstructured protein hydrogels that undergo volume changes in response to pH, ionic strength, and thermal triggers, cues that may be incompatible with sensitive chemical and biological systems. Here, we report the systematic investigation of photoillumination as a minimally invasive and remotely applied means to trigger morphological change in protein-based μ3D-printed smart materials. Detailed knowledge of material responsiveness is exploited to develop individually addressable "smart" valves that can be used to capture, "farm", and then dilute motile bacteria at specified times in multichamber picoliter edifices, capabilities that offer new opportunities for studying cell-cell interactions in ultralow-volume environments.
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Affiliation(s)
- Jodi L Connell
- Department of Chemistry, University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States
| | - Eric T Ritschdorff
- Department of Chemistry, University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States
| | - Jason B Shear
- Department of Chemistry, University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States
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48
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Gao M, Zheng H, Ren Y, Lou R, Wu F, Yu W, Liu X, Ma X. A crucial role for spatial distribution in bacterial quorum sensing. Sci Rep 2016; 6:34695. [PMID: 27698391 PMCID: PMC5048177 DOI: 10.1038/srep34695] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/19/2016] [Indexed: 01/19/2023] Open
Abstract
Quorum sensing (QS) is a process that enables bacteria to communicate using secreted signaling molecules, and then makes a population of bacteria to regulate gene expression collectively and control behavior on a community-wide scale. Theoretical studies of efficiency sensing have suggested that both mass-transfer performance in the local environment and the spatial distribution of cells are key factors affecting QS. Here, an experimental model based on hydrogel microcapsules with a three-dimensional structure was established to investigate the influence of the spatial distribution of cells on bacterial QS. Vibrio harveyi cells formed different spatial distributions in the microcapsules, i.e., they formed cell aggregates with different structures and sizes. The cell aggregates displayed stronger QS than did unaggregated cells even when equal numbers of cells were present. Large aggregates (LA) of cells, with a size of approximately 25 μm, restricted many more autoinducers (AIs) than did small aggregates (SA), with a size of approximately 10 μm, thus demonstrating that aggregate size significantly affects QS. These findings provide a powerful demonstration of the fact that the spatial distribution of cells plays a crucial role in bacterial QS.
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Affiliation(s)
- Meng Gao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Huizhen Zheng
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Ying Ren
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Ruyun Lou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Fan Wu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Weiting Yu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
| | - Xiudong Liu
- College of Environment and Chemical Engineering, Dalian University, Dalian Economic Technological Development Zone, Dalian 116622, P.R. China
| | - Xiaojun Ma
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P.R. China
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49
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Hann SD, Niepa THR, Stebe KJ, Lee D. One-Step Generation of Cell-Encapsulating Compartments via Polyelectrolyte Complexation in an Aqueous Two Phase System. ACS APPLIED MATERIALS & INTERFACES 2016; 8:25603-11. [PMID: 27580225 DOI: 10.1021/acsami.6b07939] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Diverse fields including drug and gene delivery and live cell encapsulation require biologically compatible encapsulation systems. One widely adopted means of forming capsules exploits cargo-filled microdroplets in an external, immiscible liquid phase that are encapsulated by a membrane that forms by trapping of molecules or particles at the drop surface, facilitated by the interfacial tension. To eliminate the potentially deleterious oil phase often present in such processes, we exploit the aqueous two phase system of poly(ethylene glycol) (PEG) and dextran. We form capsules by placing dextran-rich microdroplets in an external PEG-rich phase. Strong polyelectrolytes present in either phase form complexes at the drop interface, thereby forming a membrane encapsulating the fluid interior. This process requires considerable finesse as both polyelectrolytes are soluble in either the drop or external phase, and the extremely low interfacial tension is too weak to provide a strong adsorption site for these molecules. The key to obtaining microcapsules is to tune the relative fluxes of the two polyelectrolytes so that they meet and complex at the interface. We identify conditions for which complexation can occur inside or outside of the drop phase, resulting in microparticles or poor encapsulation, respectively, or when properly balanced, at the interface, resulting in microcapsules. The resulting microcapsules respond to the stimuli of added salts or changes in osmotic pressure, allowing perturbation of capsule permeability or triggered release of capsule contents. We demonstrate that living cells can be sequestered and interrogated by encapsulating Pseudomonas aeruginosa PAO1 and using a Live/Dead assay to assess their viability. This method paves the way to the formation of a broad variety of versatile functional membranes around all aqueous capsules; by tuning the fluxes of complexing species to interact at the interface, membranes comprising other complexing functional moieties can be formed.
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Affiliation(s)
- Sarah D Hann
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Tagbo H R Niepa
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Kathleen J Stebe
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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50
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Dufour YS, Gillet S, Frankel NW, Weibel DB, Emonet T. Direct Correlation between Motile Behavior and Protein Abundance in Single Cells. PLoS Comput Biol 2016; 12:e1005041. [PMID: 27599206 PMCID: PMC5012591 DOI: 10.1371/journal.pcbi.1005041] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/29/2016] [Indexed: 01/26/2023] Open
Abstract
Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage. Cell-to-cell variations in protein numbers due to random fluctuations at the molecular level lead to cell-to-cell variations in behavior. To maintain predictable responses, signaling networks have evolved robustness against noise, but in some situations phenotypic diversity in a clonal population can be beneficial as a bet hedging or division of labor strategy. Investigating of how random molecular fluctuations affect cell behavior requires to measure biological parameters at different scales. Here, we report a new experiment that allows the measure of both protein numbers and behavior in cells that are free to move in their environment. Using Escherichia coli, a model system for the study of cellular behavior, we investigated the effects variations in the numbers of the chemo-receptor modification enzymes on single-cell swimming behavior. We found that the mean and variance of the behavior can be adjusted independently in the population by adjusting protein expression. This mechanism allows for the genetic selection of phenotypic diversity without disrupting correlations in protein expression that are important for the overall robustness of the chemotaxis system.
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Affiliation(s)
- Yann S Dufour
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Sébastien Gillet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Nicholas W Frankel
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Douglas B Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Physics, Yale University, New Haven, Connecticut, United States of America
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