Developing a novel and versatile approach to study populations of microbes on surfaces

许多微生物种群生活在表面上。为了更好地理解它们，我们需要更好的定量实验设备。本项目旨在开发这样一种设备。所涉及的技术包括建模、微流体和显微镜。目的：开发、表征和应用一种装置，在明确的条件下实验研究表面上的微生物种群。背景：许多微生物种群生活在地表，但由此产生的空间结构的生态和进化后果尚未得到很好的理解。这主要是由于缺乏合适的实验技术。在标准琼脂板上调查菌落受到有限的营养可用性和缺乏在实验过程中改变环境条件的选择的限制。为了能够进行高度定量的实验，需要空间上类似的化学调节器和微流体室，它们都可以通过不断涌入的营养物质来实现连续的、理想的无限的生长。项目：该项目旨在通过开发能够在两个维度上实现长期增长的新技术来缩小这一差距。特别是，将考虑两种设置：(i)在琼脂-空气界面生长种群，提供营养物质，并通过琼脂表面以下的流体管道系统控制环境。（二）种群在一个由塑料制成的平腔内生长，通过膜和流体网提供营养和控制环境。该项目将涉及该设备的开发、表征和应用。开发将基于理论考虑和反应扩散模型。一旦候选设备建成，它们将使用众所周知的大肠杆菌群体，使用显微镜和定量图像分析来表征。特别是，实验将需要研究菌落的生长动态。为了展示和测试该装置，它最终被用于研究细菌和噬菌体在许多天的过程中的进化。可能的例子是研究生长菌落内抗生素耐药性的进化，以及噬菌体在细菌草坪上传播时的进化。通过这种方式，该技术的发展将与它在微生物进化和生态学方面的应用和可能的新发现相结合。

Many microbial populations live on surfaces. To better understand them, we need better devices for quantitative experiments. This project aims to develop such a device. The techniques involved include modelling, microfluidics, and microscopy. Aim: Develop, characterize, and apply a device to experimentally study populations of microbes under well-defined conditions on surfaces.Background: Many microbial populations live on surfaces, but the ecological and evolutionary consequences of the resulting spatial structure are not well understood. This is not least due to the lack of suitable experimental techniques. Investigating colonies on standard agar plates is constrained by limited nutrient availability and the lack of options to change the environmental conditions over the course of the experiment. To enable highly quantitative experiments, spatial analogues of chemostats and microfluidic chambers are needed, which both enable continuous, and ideally infinite, growth by continuous influx of nutrients. Project: This project aims to close this gap by developing novel techniques enabling long-term growth in two dimensions. In particular, two setups will be considered: (i) Growth of populations at an agar-air interface with supply of nutrients and control of the environment by a system of fluidic tubing below the agar surface. (ii) Growth of populations within a flat chamber made of plastic with nutrients provided and environment controlled through a membrane and a fluidic network.The project will involve development, characterization, and application of the device. Development will be based on theoretical considerations and reaction-diffusion modelling. Once candidate devices are built, they will be characterized using populations of the well-understood bacterium E. coli, using microscopy and quantitative image analysis. In particular, experiments will entail studying the growth dynamics of colonies.To showcase and test the device, it finally be used to study evolution of bacteria and bacteriophage over the course of many days. Possible examples are the study of the evolution of antibiotic resistance within growing colonies and the evolution of bacteriophage as they spread on lawns of bacteria. In this way, development of the technique will be coupled to its application and possibly new findings in microbial evolution and ecology.