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Title: Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development

Abstract

The structure, function and evolving composition of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment. The complexity of this parameter space in naturally occurring systems has made a clear understanding of the key drivers of community development elusive. Here, we examine the role of spatial confinement on community development using a microwell platform that allows for assembly and monitoring of unique microbial communities en masse. This platform was designed to contain microwells with varied size features in order to mimic various levels of spatial confinement found in natural systems. Microbial populations assembled in wells with incrementally smaller size features showed increasingly larger variations in inoculum levels. By exploiting this size dependence, large wells were used to assemble homogenous initial populations of Pseudomonas aeruginosa, allowing for reproducible, directed growth trajectories. In contrast, smaller wells were used to assemble a heterogeneous range of initial populations, resulting in a variety of growth and decay trajectories. This allowed for parallel screening of single member communities across different levels of confinement to identify initial conditions in which P. aeruginosa colonies have dramatically higher probabilities of survival. These results demonstrate a unique approach for manipulating the distribution of initialmore » microbial populations assembled into controlled microenvironments to rapidly identify population and environmental parameters conducive or inhibitive to growth. Additionally, multi-member community assembly was characterized to demonstrate the power of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.« less

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Sciences (CNMS)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1337723
Alternate Identifier(s):
OSTI ID: 1263836
Grant/Contract Number:  
KP1601010 ERKP730 Plant-Microbe Interfaces; KC403040 ERKCZ01 Center for Nanophase Materials Sciences; LDRD 7856; AC05-00OR22725
Resource Type:
Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Name: PLoS ONE Journal Volume: 11 Journal Issue: 5; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science (PLoS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Hansen, Ryan H., Timm, Andrea C., Timm, Collin M., Bible, Amber N., Morrell-Falvey, Jennifer L., Pelletier, Dale A., Simpson, Michael L., Doktycz, Mitchel J., Retterer, Scott T., and Li, ed., Xiangzhen. Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0155080.
Hansen, Ryan H., Timm, Andrea C., Timm, Collin M., Bible, Amber N., Morrell-Falvey, Jennifer L., Pelletier, Dale A., Simpson, Michael L., Doktycz, Mitchel J., Retterer, Scott T., & Li, ed., Xiangzhen. Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development. United States. doi:10.1371/journal.pone.0155080.
Hansen, Ryan H., Timm, Andrea C., Timm, Collin M., Bible, Amber N., Morrell-Falvey, Jennifer L., Pelletier, Dale A., Simpson, Michael L., Doktycz, Mitchel J., Retterer, Scott T., and Li, ed., Xiangzhen. Fri . "Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development". United States. doi:10.1371/journal.pone.0155080.
@article{osti_1337723,
title = {Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development},
author = {Hansen, Ryan H. and Timm, Andrea C. and Timm, Collin M. and Bible, Amber N. and Morrell-Falvey, Jennifer L. and Pelletier, Dale A. and Simpson, Michael L. and Doktycz, Mitchel J. and Retterer, Scott T. and Li, ed., Xiangzhen},
abstractNote = {The structure, function and evolving composition of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment. The complexity of this parameter space in naturally occurring systems has made a clear understanding of the key drivers of community development elusive. Here, we examine the role of spatial confinement on community development using a microwell platform that allows for assembly and monitoring of unique microbial communities en masse. This platform was designed to contain microwells with varied size features in order to mimic various levels of spatial confinement found in natural systems. Microbial populations assembled in wells with incrementally smaller size features showed increasingly larger variations in inoculum levels. By exploiting this size dependence, large wells were used to assemble homogenous initial populations of Pseudomonas aeruginosa, allowing for reproducible, directed growth trajectories. In contrast, smaller wells were used to assemble a heterogeneous range of initial populations, resulting in a variety of growth and decay trajectories. This allowed for parallel screening of single member communities across different levels of confinement to identify initial conditions in which P. aeruginosa colonies have dramatically higher probabilities of survival. These results demonstrate a unique approach for manipulating the distribution of initial microbial populations assembled into controlled microenvironments to rapidly identify population and environmental parameters conducive or inhibitive to growth. Additionally, multi-member community assembly was characterized to demonstrate the power of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.},
doi = {10.1371/journal.pone.0155080},
journal = {PLoS ONE},
number = 5,
volume = 11,
place = {United States},
year = {2016},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1371/journal.pone.0155080

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Cited by: 9 works
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Works referenced in this record:

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem
journal, February 2014

  • Zhou, Jizhong; Deng, Ye; Zhang, Ping
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 9
  • DOI: 10.1073/pnas.1324044111

1-Million droplet array with wide-field fluorescence imaging for digital PCR
journal, January 2011

  • Hatch, Andrew C.; Fisher, Jeffrey S.; Tovar, Armando R.
  • Lab on a Chip, Vol. 11, Issue 22
  • DOI: 10.1039/c1lc20561g

Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics
journal, January 2008

  • Boedicker, James Q.; Li, Liang; Kline, Timothy R.
  • Lab on a Chip, Vol. 8, Issue 8
  • DOI: 10.1039/b804911d

Sociomicrobiology in engineered landscapes
journal, December 2011

  • Connell, Jodi L.; Whiteley, Marvin; Shear, Jason B.
  • Nature Chemical Biology, Vol. 8, Issue 1
  • DOI: 10.1038/nchembio.749

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities
journal, April 2012

  • Leung, K.; Zahn, H.; Leaver, T.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 20
  • DOI: 10.1073/pnas.1106752109

Lectin-Functionalized Poly(glycidyl methacrylate)- block -poly(vinyldimethyl azlactone) Surface Scaffolds for High Avidity Microbial Capture
journal, September 2013

  • Hansen, Ryan R.; Hinestrosa, Juan Pablo; Shubert, Katherine R.
  • Biomacromolecules, Vol. 14, Issue 10
  • DOI: 10.1021/bm4011358

Defined spatial structure stabilizes a synthetic multispecies bacterial community
journal, November 2008

  • Kim, H. J.; Boedicker, J. Q.; Choi, J. W.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 47
  • DOI: 10.1073/pnas.0807935105

Surface Engineering and Patterning Using Parylene for Biological Applications
journal, March 2010

  • Tan, Christine P.; Craighead, Harold G.
  • Materials, Vol. 3, Issue 3
  • DOI: 10.3390/ma3031803

Psl trails guide exploration and microcolony formation in Pseudomonas aeruginosa biofilms
journal, May 2013

  • Zhao, Kun; Tseng, Boo Shan; Beckerman, Bernard
  • Nature, Vol. 497, Issue 7449
  • DOI: 10.1038/nature12155

Type VI secretion system effectors: poisons with a purpose
journal, January 2014

  • Russell, Alistair B.; Peterson, S. Brook; Mougous, Joseph D.
  • Nature Reviews Microbiology, Vol. 12, Issue 2
  • DOI: 10.1038/nrmicro3185

Mechanisms of synergy in polymicrobial infections
journal, March 2014

  • Murray, Justine L.; Connell, Jodi L.; Stacy, Apollo
  • Journal of Microbiology, Vol. 52, Issue 3
  • DOI: 10.1007/s12275-014-4067-3

Bacterial metapopulations in nanofabricated landscapes
journal, November 2006

  • Keymer, J. E.; Galajda, P.; Muldoon, C.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 46
  • DOI: 10.1073/pnas.0607971103

Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy
journal, December 2011

  • Young, Jonathan W.; Locke, James C. W.; Altinok, Alphan
  • Nature Protocols, Vol. 7, Issue 1
  • DOI: 10.1038/nprot.2011.432

Rapid screening of antibiotic toxicity in an automated microdroplet system
journal, January 2012

  • Churski, Krzysztof; Kaminski, Tomasz S.; Jakiela, Slawomir
  • Lab on a Chip, Vol. 12, Issue 9
  • DOI: 10.1039/c2lc21284f

Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator
journal, December 2012

  • Lian, Meng; Collier, C. Patrick; Doktycz, Mitchel J.
  • Biomicrofluidics, Vol. 6, Issue 4
  • DOI: 10.1063/1.4765337

Microstencils to generate defined, multi-species patterns of bacteria
journal, November 2015

  • Timm, Collin M.; Hansen, Ryan R.; Doktycz, Mitchel J.
  • Biomicrofluidics, Vol. 9, Issue 6
  • DOI: 10.1063/1.4935938

High-throughput single-cell quantification using simple microwell-based cell docking and programmable time-course live-cell imaging
journal, January 2011

  • Park, Min Cheol; Hur, Jae Young; Cho, Hye Sung
  • Lab Chip, Vol. 11, Issue 1
  • DOI: 10.1039/C0LC00114G

Physicochemical regulation of biofilm formation
journal, May 2011


Encapsulating Bacteria in Agarose Microparticles Using Microfluidics for High-Throughput Cell Analysis and Isolation
journal, December 2010

  • Eun, Ye-Jin; Utada, Andrew S.; Copeland, Matthew F.
  • ACS Chemical Biology, Vol. 6, Issue 3
  • DOI: 10.1021/cb100336p

The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms
journal, November 2007

  • Ingham, C. J.; Sprenkels, A.; Bomer, J.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 46
  • DOI: 10.1073/pnas.0701693104

Bio-Inspired Antifouling Strategies
journal, August 2012


Microdroplet-Enabled Highly Parallel Co-Cultivation of Microbial Communities
journal, February 2011


Protein adsorption on solid–liquid interfaces monitored by laser-ellipsometry
journal, September 2005


Microfluidic Confinement of Single Cells of Bacteria in Small Volumes Initiates High-Density Behavior of Quorum Sensing and Growth and Reveals Its Variability
journal, July 2009

  • Boedicker, James Q.; Vincent, Meghan E.; Ismagilov, Rustem F.
  • Angewandte Chemie International Edition, Vol. 48, Issue 32
  • DOI: 10.1002/anie.200901550

Polybacterial human disease: the ills of social networking
journal, September 2014

  • Short, Francesca L.; Murdoch, Sarah L.; Ryan, Robert P.
  • Trends in Microbiology, Vol. 22, Issue 9
  • DOI: 10.1016/j.tim.2014.05.007

A programmable microenvironment for cellular studies via microfluidics-generated double emulsions
journal, June 2013


High Content Evaluation of Shear Dependent Platelet Function in a Microfluidic Flow Assay
journal, September 2012

  • Hansen, Ryan R.; Wufsus, Adam R.; Barton, Steven T.
  • Annals of Biomedical Engineering, Vol. 41, Issue 2
  • DOI: 10.1007/s10439-012-0658-5

Cellular self-organization on micro-structured surfaces
journal, January 2014

  • Röttgermann, Peter J. F.; Alberola, Alicia Piera; Rädler, Joachim O.
  • Soft Matter, Vol. 10, Issue 14
  • DOI: 10.1039/c3sm52419a

3D printing of microscopic bacterial communities
journal, October 2013

  • Connell, J. L.; Ritschdorff, E. T.; Whiteley, M.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 46
  • DOI: 10.1073/pnas.1309729110

Quantitative single-cell characterization of bacterial interactions reveals type VI secretion is a double-edged sword
journal, November 2012

  • LeRoux, M.; De Leon, J. A.; Kuwada, N. J.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 48
  • DOI: 10.1073/pnas.1213963109

Bacterial flagella explore microscale hummocks and hollows to increase adhesion
journal, March 2013

  • Friedlander, R. S.; Vlamakis, H.; Kim, P.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 14
  • DOI: 10.1073/pnas.1219662110

Cooperation and conflict in microbial biofilms
journal, January 2007

  • Xavier, Joao B.; Foster, Kevin R.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 3
  • DOI: 10.1073/pnas.0607651104

Microstructured Block Copolymer Surfaces for Control of Microbe Adhesion and Aggregation
journal, March 2014

  • Hansen, Ryan; Shubert, Katherine; Morrell-Falvey, Jennifer
  • Biosensors, Vol. 4, Issue 1
  • DOI: 10.3390/bios4010063

Combinatorial quorum sensing allows bacteria to resolve their social and physical environment
journal, March 2014

  • Cornforth, D. M.; Popat, R.; McNally, L.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 11
  • DOI: 10.1073/pnas.1319175111

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments
journal, September 2011


Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems
journal, February 2013

  • Drescher, Knut; Shen, Yi; Bassler, Bonnie L.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 11
  • DOI: 10.1073/pnas.1300321110

Creating Biological Membranes on the Micron Scale: Forming Patterned Lipid Bilayers Using a Polymer Lift-Off Technique
journal, November 2003


An introduction to micro-ecology patches
journal, January 2010

  • Austin, Robert H.; Tung, Chih-kuan; Lambert, Guillaume
  • Chemical Society Reviews, Vol. 39, Issue 3
  • DOI: 10.1039/b911230h

Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities
journal, October 2008