Metabolic variation in natural populations of wild yeast

Abstract

Ecological diversification depends on the extent of genetic variation and on the pattern of covariation with respect to ecological opportunities. We investigated the pattern of utilization of carbon substrates in wild populations of budding yeast Saccharomyces paradoxus. All isolates grew well on a core diet of about 10 substrates, and most were also able to grow on a much larger ancillary diet comprising most of the 190 substrates we tested. There was substantial genetic variation within each population for some substrates. We found geographical variation of substrate use at continental, regional, and local scales. Isolates from Europe and North America could be distinguished on the basis of the pattern of yield across substrates. Two geographical races at the North American sites also differed in the pattern of substrate utilization. Substrate utilization patterns were also geographically correlated at local spatial scales. Pairwise genetic correlations between substrates were predominantly positive, reflecting overall variation in metabolic performance, but there was a consistent negative correlation between categories of substrates in two cases: between the core diet and the ancillary diet, and between pentose and hexose sugars. Such negative correlations in the utilization of substrate from different categories may indicate either intrinsic physiological trade-offs for the uptake and utilization of substrates from different categories, or the accumulation of conditionally neutral mutations. Divergence in substrate use accompanies genetic divergence at all spatial scales in S. paradoxus and may contribute to race formation and speciation.

Phenotyping Microarrays for the Characterization of Environmental Microorganisms

“…The medium must not contain a reducing agent that could interact with the redox dye. For bacteria, the Biolog™ BUG medium is commonly used [2]; yeast nitrogen base with no carbon source (modified YNB) has been used for yeast [16] and Bold's Basal Medium (BBM) for the growth of heterotrophic algae (but see Note 2.1). Biolog™ provides a variety of inoculation fluids (IF) depending on the nature of the individual species or community being tested: media are available for gram-positive and gram-negative bacteria, filamentous fungus, anaerobic bacterium, yeast, and generalized communities.…”

“…For organisms, the following roots were used for the search: bacteria: bacter*, fungi:fung*, phytoplankton:phytopl*, protozoan:protozo*. Search for soil was with the roots soil*, sand*, clay*, rhizosphere; for aquatic with marine, lake*, river*, pond*, stream*, groundwater*; for human with human*, clinic* In addition to allowing the characterization of strains and communities based on their substrate metabolism or growth condition preferences and capacities, microtiter plate-based phenotype arrays can help establish intrinsic physiological trade-offs in microorganism [16] and help characterize metabolic pathways [17]. Furthermore, using Biolog™ plates could help discover ecotypes that can have specific biodegradation capacities, within microorganism species [18].…”

“…A wavelength around 660 nm is correlated with cell counts in yeast [16]. A wavelength of 700 nm was used for the measurement of fungal hyphae [8].…”

A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology

“…The lineages perform differently at high temperature and do not survive equally to freeze–thaw cycles, with southern populations outperforming northern ones. They also appear to diverge in terms of performance when grown on limiting nutrient media with different carbon or nitrogen sources (Leducq et al, ; Samani et al, ). The molecular basis of this ecological specialization has been examined and candidate genes have been identified as potential key players (Eberlein et al, ).…”

Harnessing the power of digital droplet PCR to conduct real‐world microbial competitions

“…; Miller & Greig ; Murphy & Zeyl ; Samani et al . ). The link between what occurs out in the real world and what is measured in the laboratory has not yet been made, as so much is still unknown about the natural history of these yeasts.…”