Substrate, temperature, and geographical patterns among nearly 2,000 natural yeast isolates

Abstract

Yeasts have broad importance as industrially and clinically relevant microbes and as powerful models for fundamental research, but we are only beginning to understand the roles yeasts play in natural ecosystems. Yeast ecology is often more difficult to study compared to other, more abundant microbes, but growing collections of natural yeast isolates are beginning to shed light on fundamental ecological questions. Here we used environmental sampling and isolation to assemble a dataset of 1,962 isolates collected from throughout the contiguous United States of America (USA) and Alaska, which were then used to uncover geographic patterns, along with substrate and temperature associations among yeast taxa. We found some taxa, including the common yeasts Torulaspora delbrueckii and Saccharomyces paradoxus, to be repeatedly isolated from multiple sampled regions of the US, and we classify these as broadly distributed cosmopolitan yeasts. A number of yeast taxon - substrate associations were identified, some of which were novel and some of which support previously reported associations. Further, we found a strong effect of isolation temperature on the phyla of yeasts recovered, as well as for many species. We speculate that substrate and isolation temperature associations reflect the ecological diversity of and niche partitioning by yeast taxa.

Genomic and ecological factors shaping specialism and generalism across an entire subphylum

“…Cultures were sent from the culture collections as frozen stocks in glycerol yeast extract peptone dextrose (YPD), on YPD slants, or as lyophilized cultures that were revived in YPD upon arrival and cultured onto YPD plates for single colonies to be grown to saturation in YPD to be frozen down in 15% glycerol at -80 o C. For 55 yeast species where we could not obtain the taxonomic type strain, we used instead another available strain with a preference toward authentic or widely used reference strains (table S1A). In addition to the named yeast species, 62 taxa included in our dataset are candidates for novel species that await formal taxonomic description; 28 were isolated in the Hittinger Lab at the University of Wisconsin -Madison using standard protocols (76,77), while the remaining 34 were obtained from the ARS NRRL Culture Collection. Species names were up-to date as of May 2023.…”