Engineered bacterial swarm patterns as spatial records of environmental inputs
Engineered bacterial swarm patterns as spatial records of environmental inputs
复制标题
DOI：
10.1038/s41589-023-01325-2
复制
发表时间：
2023-05-04
影响因子：
14.8
通讯作者：
Danino，Tal
中科院分区：
文献类型：
--
作者：
Doshi，Anjali;Shaw，Marian;Danino，Tal
各种各样的细菌物种通过集群运动--一种由鞭毛提供动力的高度协调和快速的细菌运动--在固体表面自然地自组织成持久的大尺度模式。工程蜂群是一个尚未开发的机会，可以增加协调合成微生物系统的规模和健壮性。在这里，我们设计了奇异变形杆菌，它天生就形成了厘米级的牛眼群模式，将外部输入‘写入’可见的空间记录。具体地说，我们设计了与蜂群相关的基因的可调表达，以修改模式特征，并开发了解码的定量方法。接下来，我们开发了一个双输入系统，同时调节两个与集群相关的基因，并分别证明了不断增长的群体可以记录动态的环境变化。我们使用深度分类和分割模型对产生的多条件模式进行解码。最后，我们设计了一种菌株，记录了水中铜的存在。这项工作为建立大规模细菌记录器创造了一种方法，扩展了工程设计紧急微生物行为的框架。
A diverse array of bacteria species naturally self-organize into durable macroscale patterns on solid surfaces via swarming motility—a highly coordinated and rapid movement of bacteria powered by flagella. Engineering swarming is an untapped opportunity to increase the scale and robustness of coordinated synthetic microbial systems. Here we engineerProteus mirabilis, which natively forms centimeter-scale bullseye swarm patterns, to ‘write’ external inputs into visible spatial records. Specifically, we engineer tunable expression of swarming-related genes that modify pattern features, and we develop quantitative approaches to decoding. Next, we develop a dual-input system that modulates two swarming-related genes simultaneously, and we separately show that growing colonies can record dynamic environmental changes. We decode the resulting multicondition patterns with deep classification and segmentation models. Finally, we engineer a strain that records the presence of aqueous copper. This work creates an approach for building macroscale bacterial recorders, expanding the framework for engineering emergent microbial behaviors.