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

Abstract

Bacteria often live in diverse communities where the spatial arrangement of strains and species is considered critical for their ecology, including whether strains can coexist, which are ecologically dominant, and how productive they are as a community. However, a test of the importance of spatial structure requires manipulation at the fine scales at which this structure naturally occurs. Here we develop a droplet-based printing method to arrange different bacterial genotypes across a sub-millimetre array. We use this to test the importance of fine-scale spatial structure by printing strains of the gut bacterium Escherichia coli that naturally compete with one another using protein toxins. This reveals that the spatial arrangement of bacterial genotypes is important for ecological outcomes. Toxin-producing strains largely eliminate susceptible non-producers when genotypes are well-mixed. However, printing strains side-by-side creates an ecological refuge such that susceptible strains can coexist with toxin producers, even to the extent that a susceptible strain outnumbers the toxin producer. Head-to-head competitions between toxin producers also reveals strong effects, where spatial structure can make the difference between one strain winning and mutual destruction. Finally, we print different potential barriers between two competing strains to understand why space is so important. This reveals the importance of processes that limit the free diffusion of molecules. Specifically, we show that cells closest to a toxin producer bind to and capture toxin molecules, which creates a refuge for their clonemates. Our work provides a new method to generate customised bacterial communities with defined spatial distributions, and reveals that micron-scale changes in these distributions can drive major shifts in their ecology.

A type IVB secretion system adapted for bacterial killing, biofilm invasion and biocontrol

“…However, when the two wild type strains competed against each other, KT2442 was eliminated, presumably because it was killed before it could fire its T6SS. In accordance with a recent report 81 , we observed that on agar plates dead cells created a barrier that prevented further killing. This was not observed when the biofilms were grown in flow cells, as dead KT2442 cells detached from the glass substratum and were removed by the shear forces of the nutrient flow.…”

Suicidal chemotaxis in bacteria

“…Bacterial biofilms often experience steep antibiotic gradients when they are treated because the high cell density within these communities both attenuates diffusion and removes compounds from circulation (1)(2)(3). In addition, bacteria commonly live alongside other strains and species that themselves release antimicrobials that diffuse and can again generate chemical gradients (4)(5)(6). In order to cope with life under these conditions, bacteria have evolved a wide variety of physiological responses that detect and respond to toxic compounds.…”

Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress

“…For example, microbiologists have long reported the existence of (sometimes annoying (77)) “satellite” colonies (78), drug-sensitive populations that appear near enzyme-producing resistant colonies on agar plates, suggesting that resistance can be cooperative on scales of millimeters or more. Similarly long-range effects have been recently measured for oxygen gradients in biofilms (79), yet metabolic gradients have been shown to be relatively short-ranged (80), and droplet-based printing techniques have shown that specific microscale structure determines dynamics in interacting colicin-producing strains (81). In systems where intercellular interactions are primarily short-range–with resistance driven by intracellular drug degradation, for example (14)–recent work shows that additional physiological mechanisms, such as persistence, might be needed to drive cooperative resistance (18).…”