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Droplet printing reveals the importance of micron-scale structure for bacterial ecology

Author

Listed:
  • Ravinash Krishna Kumar

    (University of Oxford)

  • Thomas A. Meiller-Legrand

    (University of Oxford
    University of Oxford)

  • Alessandro Alcinesio

    (University of Oxford)

  • Diego Gonzalez

    (University of Oxford
    Université de Neuchâtel)

  • Despoina A. I. Mavridou

    (University of Texas at Austin)

  • Oliver J. Meacock

    (University of Oxford
    University of Oxford
    University of Sheffield)

  • William P. J. Smith

    (University of Oxford
    University of Oxford)

  • Linna Zhou

    (University of Oxford)

  • Wook Kim

    (University of Oxford
    Duquesne University)

  • Gökçe Su Pulcu

    (University of Oxford)

  • Hagan Bayley

    (University of Oxford)

  • Kevin R. Foster

    (University of Oxford
    University of Oxford)

Abstract

Bacteria often live in diverse communities where the spatial arrangement of strains and species is considered critical for their ecology. However, a test of this hypothesis requires manipulation at the fine scales at which spatial structure naturally occurs. Here we develop a droplet-based printing method to arrange bacterial genotypes across a sub-millimetre array. We print strains of the gut bacterium Escherichia coli that naturally compete with one another using protein toxins. Our experiments reveal that toxin-producing strains largely eliminate susceptible non-producers when genotypes are well-mixed. However, printing strains side-by-side creates an ecological refuge where susceptible strains can persist in large numbers. Moving to competitions between toxin producers reveals that spatial structure can make the difference between one strain winning and mutual destruction. Finally, we print different potential barriers between competing strains to understand how ecological refuges form, which shows that cells closest to a toxin producer mop up the toxin and protect their clonemates. Our work provides a method to generate customised bacterial communities with defined spatial distributions, and reveals that micron-scale changes in these distributions can drive major shifts in ecology.

Suggested Citation

  • Ravinash Krishna Kumar & Thomas A. Meiller-Legrand & Alessandro Alcinesio & Diego Gonzalez & Despoina A. I. Mavridou & Oliver J. Meacock & William P. J. Smith & Linna Zhou & Wook Kim & Gökçe Su Pulcu , 2021. "Droplet printing reveals the importance of micron-scale structure for bacterial ecology," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-20996-w
    DOI: 10.1038/s41467-021-20996-w
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    Cited by:

    1. Yangteng Ou & Shixiang Cao & Yang Zhang & Hongjia Zhu & Chengzhi Guo & Wei Yan & Fengxue Xin & Weiliang Dong & Yanli Zhang & Masashi Narita & Ziyi Yu & Tuomas P. J. Knowles, 2023. "Bioprinting microporous functional living materials from protein-based core-shell microgels," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Yongcheng Jin & Ellina Mikhailova & Ming Lei & Sally A. Cowley & Tianyi Sun & Xingyun Yang & Yujia Zhang & Kaili Liu & Daniel Catarino da Silva & Luana Campos Soares & Sara Bandiera & Francis G. Szele, 2023. "Integration of 3D-printed cerebral cortical tissue into an ex vivo lesioned brain slice," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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