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

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, Hagan Bayley () and Kevin R. Foster ()
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Ravinash Krishna Kumar: University of Oxford
Thomas A. Meiller-Legrand: University of Oxford
Alessandro Alcinesio: University of Oxford
Diego Gonzalez: University of Oxford
Despoina A. I. Mavridou: University of Texas at Austin
Oliver J. Meacock: University of Oxford
William P. J. Smith: University of Oxford
Linna Zhou: University of Oxford
Wook Kim: University of Oxford
Gökçe Su Pulcu: University of Oxford
Hagan Bayley: University of Oxford
Kevin R. Foster: University of Oxford

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-20996-w

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