The origin of lager-brewing yeast: tracking the wild genetic stock of a domesticated microbe

Domestication of plants and animals promoted humanity’s transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, microbe domestication remains more obscure despite the importance of microbes to the production of cheese, bread, beer, and other staples. Lager-beer was first brewed in the fifteenth century and employs an allotetraploid hybrid yeast, Saccharomyces pastorianus, a domesticated species created by the fusion of a S. cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the discovery of that species in the form of the first wild, genetically pure isolates of S. bayanus. Individuals from populations of S. bayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus Patagonian forests, but we show that they are isolated genetically through intrinsic post-zygotic barriers and ecologically through host-preference. Analyses of genetic markers and draft genome sequences conclusively demonstrate that strains previously asserted to be S. bayanus are hybrids, making the Patagonian population the only known source of a pure, natural genetic stock of S. bayanus. Comparing the wild genome sequence to brewing strains suggests that changes in sugar and sulfite metabolism were important to the domestication of S. pastorianus in the lager-brewing environment. This study illustrates a fruitful approach for the discovery and preservation of wild genetic stocks of domesticated microbes that combines microbial ecology and comparative genomics to trace their history, identify genetic changes, and suggest paths to further industrial improvement.