Microbial communities often display region-specific properties, which give rise to complex interactions and emergent behaviors that are critical to the homeostasis and stress response of the communities. However, systems-level understanding of these properties still remains elusive. In this study, we established RAINBOW-seq and profiled the transcriptome of Escherichia coli biofilm communities with high spatial resolution and high gene coverage. We uncovered three modes of community-level coordination, including cross-regional resource allocation, local cycling and feedback signaling, which were mediated by strengthened transmembrane transport and spatially specific activation of metabolism. As a consequence of such coordination, the nutrient-limited region of the community maintained an unexpectedly high level of metabolism, enabling it to express many signaling genes and functionally unknown genes with potential sociality functions. Our work provides an extended understanding of the metabolic interplay in biofilms and presents a new approach of investigating complex interactions in bacterial communities on the systems level.

微生物群落通常表现出区域特定的特性，这会引起复杂的相互作用和突发行为，这对群落的稳态和应激反应至关重要。然而，对这些属性的系统级理解仍然难以捉摸。在本研究中，我们建立了 RAINBOW-seq，并以高空间分辨率和高基因覆盖度对大肠杆菌生物膜群落的转录组进行了分析。我们发现了社区层面协调的三种模式，包括跨区域资源分配、局部循环和反馈信号，这些模式是通过加强跨膜运输和代谢的空间特异性激活来介导的。由于这种协调，群落的营养有限区域保持了意想不到的高代谢水平，使其能够表达许多信号基因和具有潜在社会功能的功能未知基因。我们的工作提供了对生物膜中代谢相互作用的扩展理解，并提出了一种在系统水平上研究细菌群落复杂相互作用的新方法。