The evolutionary advantage of haploid versus diploid microbes in nutrient-poor environments

Stable demographic ratios of haploid gametophyte to diploid sporophyte abundance in macroalgal populations

Macroalgal populations often consist of free-living haploid (gametophyte) and diploid (sporophyte) stages. Various ecological studies have been conducted to examine the demographic diversity of haploid-diploid populations with regard to the dominant stage. Here, I relaxed the assumption of classical research that the life history parameters of haploids and diploids are identical and developed a generalized haploid-diploid model that explicitly accounts for population density dependence and asexual reproduction. Analysis of this model yielded an exact solution for the abundance ratio of haploids to diploids in a population in which the ratio is determined by the balance of four demographic forces: sexual reproduction by haploids, sexual reproduction by diploids, asexual reproduction by haploids, and asexual reproduction by diploids. Furthermore, the persistence of a haploid-diploid population and its total biomass are shown to be determined by the basic reproductive number (R0), which is shown to be a function of these four demographic forces. When R0 is greater than one, the haploid-diploid population stably persists, and the ploidy ratio obtained by the analytical solution is realized.

Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism

Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here, we report an unusual recurrent ploidy reduction in replicate populations of the budding yeast Saccharomyces eubayanus experimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment-cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.

A Saccharomyces eubayanus haploid resource for research studies

Since its identification, Saccharomyces eubayanus has been recognized as the missing parent of the lager hybrid, S. pastorianus. This wild yeast has never been isolated from fermentation environments, thus representing an interesting candidate for evolutionary, ecological and genetic studies. However, it is imperative to develop additional molecular genetics tools to ease manipulation and thus facilitate future studies. With this in mind, we generated a collection of stable haploid strains representative of three main lineages described in S. eubayanus (PB-1, PB-2 and PB-3), by deleting the HO gene using CRISPR-Cas9 and tetrad micromanipulation. Phenotypic characterization under different conditions demonstrated that the haploid derivates were extremely similar to their parental strains. Genomic analysis in three strains highlighted a likely low frequency of off-targets, and sequencing of a single tetrad evidenced no structural variants in any of the haploid spores. Finally, we demonstrate the utilization of the haploid set by challenging the strains under mass-mating conditions. In this way, we found that S. eubayanus under liquid conditions has a preference to remain in a haploid state, unlike S. cerevisiae that mates rapidly. This haploid resource is a novel set of strains for future yeast molecular genetics studies.

Effects of pyruvate decarboxylase (pdc1, pdc5) gene knockout on the production of metabolites in two haploid Saccharomyces cerevisiae strains

Saccharomyces cerevisiae has good reproductive ability in both haploid and diploid forms, a pyruvate decarboxylase plays an important role in S. cerevisiae cell metabolism. In this study, pdc1 and pdc5 double knockout strains of S. cerevisiae H14-02 (MATa type) and S. cerevisiae H5-02 (MATα type) were obtained by the Cre/loxP technique. The effects of the deletion of pdc1 and pdc5 on the metabolites of the two haploid S. cerevisiae strains were consistent. In S. cerevisiae H14-02, the ethanol conversion decreased by 30.19%, the conversion of glycerol increased by 40.005%, the concentration of acetic acid decreased by 43.54%, the concentration of acetoin increased by 12.79 times, and the activity of pyruvate decarboxylase decreased by 40.91% compared to those in the original H14 strain. The original S. cerevisiae haploid strain H14 produced a small amount of acetoin but produced very little 2,3-butanediol. However, S. cerevisiae H14-02 produced 1.420 ± 0.063 g/L 2,3-BD. This study not only provides strain selection for obtaining haploid strains with a high yield of 2,3-BD but also lays a foundation for haploid S. cerevisiae to be used as a new tool for genetic research and breeding programs.

Influence of nutrients on ploidy-specific performance in an invasive, haplodiplontic red macroalga

Worldwide, macroalgae have invaded near-shore marine ecosystems. However, their haplodiplontic life cycles have complicated efforts to predict patterns of growth and spread, particularly since most theoretical predictions are derived from diplontic taxa (i.e., animals). To complete one revolution of the life cycle, two separate ploidy stages, often including separate haploid sexes, must pass through development and reproduction. In the case of the invasive, red macroalga Agarophyton vermiculophyllum, during the invasion of soft-sediment estuaries throughout the Northern Hemisphere, diploid tetrasporophytes came to dominate all free-floating populations and haploid gametophytes were consistently lost. The ecological hypothesis of nutrient limitation might contribute to an explanation of this pattern of tetrasporophytic dominance in free-floating populations. Under this hypothesis, gametophytes should outperform tetrasporophytes under nutrient limited conditions, but tetrasporophytes should be better able to exploit optimal or even abundant nutrient conditions, such as in eutrophic estuaries. We sampled tetrasporophytes, male gametophytes, and female gametophytes from two sites each located on either side of the Delmarva Peninsula that separates the Chesapeake Bay from the Atlantic Ocean. We subjected apices excised from multiple thalli from each life cycle stage to a nutrient-enriched and a nutrient-poor seawater treatment and assessed growth and survival. While nutrient addition increased growth rates, there was no significant difference among ploidies or sexes. Gametophytes did, however, suffer higher mortality than tetrasporophytes. We discuss how nutrient-dependent differences in growth and survival may contribute to observed patterns of tetrasporophytic dominance in soft-sediment A. vermiculophyllum populations.