Growing Yeast into Cylindrical Colonies

Abstract

Micro-organisms often form complex multicellular assemblies such as bio-films and colonies. Understanding the interplay between assembly expansion, metabolic yield, and nutrient diffusion within a freely-growing colony remains challenging. Most data available about micro-organisms are from planktonic cultures, due to the lack of experimental tools to observe multicellular assemblies. Here, we propose a method to tackle this problem by constraining the growth of yeast colonies into simple geometric shapes such as cylinders. To this end, we designed a simple, inexpensive, versatile culture system to control the location of nutrient delivery below a growing colony. Under such culture conditions, yeast colonies grow vertically and only at the locations where nutrients are delivered. Colonies increase in height at a steady growth rate which is inversely proportional to the cylinder radius. We show that the vertical growth rate of cylindrical colonies is not defined by the single cell division rate, but rather by the colony metabolic yield. This contrasts with cells in liquid culture, in which the single cell division rate is the only parameter that defines the population growth rate. This method also provides a direct, simple method to estimate the metabolic yield of a colony. Our study further demonstrates the importance of the shape of colonies on setting their expansion. We anticipate our approach to be a starting point for elaborate studies of the population dynamics, evolution, and ecology of microbial colonies in complex landscapes.