Leveraging natural isolates and experimental evolution to characterize biofilm-related phenotypes in Saccharomyces cerevisiae

Abstract

Biofilm formation is a protective community building behavior in which microbes participate to respond to external stress or colonize new ecological niches. It is a primary mechanism used by pathogenic yeast to persist on hospital surfaces and catheters and to invade the human body, and a useful trait in brewing and industrial fermentation. Despite the importance of understanding the phenotypic diversity and genetic basis of yeast biofilms, for reasons of experimental tractability they have typically only been examined in a subset of laboratory strains. The development of budding yeast Saccharomyces cerevisiae as model for biofilm development as well as the existence of growing collections of yeast natural isolates has created an ideal system for studying the spectrum of biofilm-related traits available to yeast and the primary adaptive routes by which they are acquired. We can observe biofilm-related phenotypes experimentally using several assays including complex colony morphology, complex mat formation, flocculation in liquid media, agar invasion, and polystyrene adhesion. We have adapted these classic assays for use with an extensive collection of yeast natural isolates, and uncovered an enormous amount of diversity as well as new findings about the correlations between phenotypes and between phenotype and ecological and geographical niches. We also demonstrate that the previous understanding from lab strains of the effect of ploidy on these traits is more complicated in the context of these natural isolates. In further work, we focus on a single biofilm-related trait, flocculation, and its repeated evolution in continuous culture evolution experiments. We demonstrate, with genomic analysis of flocculent evolved clones, that there is one primary adaptive route to flocculation through changes in the regulation of known flocculin gene FLO1. Deletion of FLO1 significantly reduces the rate of evolving the trait, and the evolution-based design methodology presented here represents a novel approach to evolutionary engineering.