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Halsted MC, Bible AN, Morrell-Falvey JL, Retterer ST. Quantifying biofilm propagation on chemically modified surfaces. Biofilm 2022; 4:100088. [PMID: 36303845 PMCID: PMC9594113 DOI: 10.1016/j.bioflm.2022.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/26/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Conditions affecting biofilm formation differ among bacterial species and this presents a challenge to studying biofilms in the lab. This work leverages functionalized silanes to control surface chemistry in the study of early biofilm propagation, quantified with a semi-automated image processing algorithm. These methods support the study of Pantoea sp. YR343, a gram-negative bacterium isolated from the poplar rhizosphere. We found that Pantoea sp. YR343 does not readily attach to hydrophilic surfaces but will form biofilms with a “honeycomb” morphology on hydrophobic surfaces. Our image processing algorithm described here quantified the evolution of the honeycomb morphology over time, and found the propagation to display a logarithmic behavior. This methodology was repeated with a flagella-deficient fliR mutant of Pantoea sp. YR343 which resulted in reduced surface attachment. Quantifiable differences between Pantoea WT and ΔfliR biofilm morphologies were captured by the image processing algorithm, further demonstrating the insight gained from these methods.
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Affiliation(s)
| | - Amber N. Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Scott T. Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA,Center for Nanophase Materials Sciences, Oak Ridge, TN, USA,Corresponding author. Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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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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3
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Kim JJ, Reátegui E, Hopke A, Jalali F, Roushan M, Doyle PS, Irimia D. Large-scale patterning of living colloids for dynamic studies of neutrophil-microbe interactions. LAB ON A CHIP 2018; 18:1514-1520. [PMID: 29770423 PMCID: PMC5995581 DOI: 10.1039/c8lc00228b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Neutrophils are the first white blood cells to respond to microbes and to limit their invasion of the body. However, the growth of the microbes into colonies often challenges the neutrophils ability to contain them. To study the interactions between neutrophils and microbial colonies, we designed an assay for arranging microbes in clusters of controlled size (i.e. living colloids). The patterned microbes in the living colloid are mechanically trapped inside the wells and fully accessible to neutrophils. Using the assay, we studied the interactions between human neutrophils and Candida albicans and Staphylococcus aureus, two common human pathogens. We also probed the susceptibility of C. albicans colloids to caspofungin, a common antifungal drug.
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Affiliation(s)
- Jae Jung Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Huang Y, Xia A, Yang G, Jin F. Bioprinting Living Biofilms through Optogenetic Manipulation. ACS Synth Biol 2018; 7:1195-1200. [PMID: 29664610 DOI: 10.1021/acssynbio.8b00003] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this paper, we present a new strategy for microprinting dense bacterial communities with a prescribed organization on a substrate. Unlike conventional bioprinting techniques that require bioinks, through optogenetic manipulation, we directly manipulated the behaviors of Pseudomonas aeruginosa to allow these living bacteria to autonomically form patterned biofilms following prescribed illumination. The results showed that through optogenetic manipulation, patterned bacterial communities with high spatial resolution (approximately 10 μm) could be constructed in 6 h. Thus, optogenetic manipulation greatly increases the range of available bioprinting techniques.
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Affiliation(s)
- Yajia Huang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Aiguo Xia
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Guang Yang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, PR China
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Timm AC, Halsted MC, Wilmoth JL, Retterer ST. Assembly and Tracking of Microbial Community Development within a Microwell Array Platform. J Vis Exp 2017. [PMID: 28654053 DOI: 10.3791/55701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The development of microbial communities depends on a combination of complex deterministic and stochastic factors that can dramatically alter the spatial distribution and activities of community members. We have developed a microwell array platform that can be used to rapidly assemble and track thousands of bacterial communities in parallel. This protocol highlights the utility of the platform and describes its use for optically monitoring the development of simple, two-member communities within an ensemble of arrays within the platform. This demonstration uses two mutants of Pseudomonas aeruginosa, part of a series of mutants developed to study Type VI secretion pathogenicity. Chromosomal inserts of either mCherry or GFP genes facilitate the constitutive expression of fluorescent proteins with distinct emission wavelengths that can be used to monitor community member abundance and location within each microwell. This protocol describes a detailed method for assembling mixtures of bacteria into the wells of the array and using time-lapse fluorescence imaging and quantitative image analysis to measure the relative growth of each member population over time. The seeding and assembly of the microwell platform, the imaging procedures necessary for the quantitative analysis of microbial communities within the array, and the methods that can be used to reveal interactions between microbial species area all discussed.
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Affiliation(s)
| | - Michelle C Halsted
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee
| | | | - Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory; Center for Nanophase Materials Sciences, Oak Ridge National Laboratory;
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Hansen RH, Timm AC, Timm CM, Bible AN, Morrell-Falvey JL, Pelletier DA, Simpson ML, Doktycz MJ, Retterer ST. Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development. PLoS One 2016; 11:e0155080. [PMID: 27152511 PMCID: PMC4859483 DOI: 10.1371/journal.pone.0155080] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/24/2016] [Indexed: 12/26/2022] Open
Abstract
The structure and function of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment and the abundance of its community members. The complexity of this natural parameter space has made characterization of the key drivers of community development difficult. In order to facilitate these characterizations, we have developed a microwell platform designed to screen microbial growth and interactions across a wide variety of physical and initial conditions. Assembly of microbial communities into microwells was achieved using a novel biofabrication method that exploits well feature sizes for control of innoculum levels. Wells with incrementally smaller size features created populations with increasingly larger variations in inoculum levels. This allowed for reproducible growth measurement in large (20 μm diameter) wells, and screening for favorable growth conditions in small (5, 10 μm diameter) wells. We demonstrate the utility of this approach for screening and discovery using 5 μm wells to assemble P. aeruginosa colonies across a broad distribution of innoculum levels, and identify those conditions that promote the highest probability of survivial and growth under spatial confinement. Multi-member community assembly was also characterized to demonstrate the broad potential of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.
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Affiliation(s)
- Ryan H Hansen
- Kansas State University, Manhattan, Kansas, United States of America.,The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Andrea C Timm
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Collin M Timm
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Amber N Bible
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jennifer L Morrell-Falvey
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dale A Pelletier
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Michael L Simpson
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Mitchel J Doktycz
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Scott T Retterer
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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Timm CM, Hansen RR, Doktycz MJ, Retterer ST, Pelletier DA. Microstencils to generate defined, multi-species patterns of bacteria. BIOMICROFLUIDICS 2015; 9:064103. [PMID: 26594264 PMCID: PMC4644145 DOI: 10.1063/1.4935938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/05/2015] [Indexed: 05/21/2023]
Abstract
Microbial communities are complex heterogeneous systems that are influenced by physical and chemical interactions with their environment, host, and community members. Techniques that facilitate the quantitative evaluation of how microscale organization influences the morphogenesis of multispecies communities could provide valuable insights into the dynamic behavior and organization of natural communities, the design of synthetic environments for multispecies culture, and the engineering of artificial consortia. In this work, we demonstrate a method for patterning microbes into simple arrangements that allow the quantitative measurement of growth dynamics as a function of their proximity to one another. The method combines parylene-based liftoff techniques with microfluidic delivery to simultaneously pattern multiple bacterial species with high viability using low-cost, customizable methods. Quantitative measurements of bacterial growth for two competing isolates demonstrate that spatial coordination can play a critical role in multispecies growth and structure.
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Affiliation(s)
- Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, USA
| | - Ryan R Hansen
- Department of Chemical Engineering, Kansas State University , Manhattan, Kansas 66506, USA
| | | | | | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, USA
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