Department of Chemistry, University of Oxford, Oxford, UK.
Department of Biochemistry, University of Oxford, Oxford, UK.
Nat Commun. 2021 Feb 8;12(1):857. doi: 10.1038/s41467-021-20996-w.
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.
细菌通常生活在多样化的群落中，其中菌株和物种的空间排列被认为对它们的生态至关重要。然而，对这一假设的检验需要在自然发生空间结构的精细尺度上进行操作。在这里，我们开发了一种基于液滴的打印方法，可将细菌基因型排列在亚毫米级的阵列上。我们使用蛋白质毒素打印出在肠道细菌大肠杆菌中自然相互竞争的菌株。我们的实验表明，当基因型充分混合时，产生毒素的菌株会在很大程度上消灭易感的非生产者。然而，将菌株并排打印会产生一个生态避难所，使易感菌株能够大量存在。转而进行毒素生产者之间的竞争，揭示了空间结构可以决定一种菌株是获胜还是相互毁灭。最后，我们在竞争菌株之间打印不同的潜在障碍，以了解生态避难所是如何形成的，这表明最接近毒素生产者的细胞会清除毒素并保护其克隆体。我们的工作提供了一种方法，可以生成具有定义空间分布的定制化细菌群落，并揭示了这些分布在微米尺度上的变化可以驱动生态的重大转变。
