Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand

Abstract

Yeasts are a diverse seemingly ubiquitous group of eukaryotic microbes, and many are naturally associated with fruits. Humans have harnessed yeasts since the dawn of civilisation to make wine, and thus it is surprising that we know little of the distribution of yeast communities naturally associated with fruits. Previous reports of yeast community diversity have been descriptive only. Here we present, we believe, the first robust test for the geographic delineation of yeast communities. Humans have relatively recently employed Saccharomyces cerevisiae as a model research organism, and have long harnessed its ancient adaption to ferment even in the presence of oxygen. However, as far as we are aware, there has not been a rigorous test for the presence of regional differences in natural S. cerevisiae populations before. We combined these community- and population-level questions and surveyed replicate vineyards and corresponding spontaneous ferments from different regions on New Zealand's (NZ's) North Island and analysed the resulting data with community ecology and population genetic tests. We show that there are distinct regional delineations of yeast communities, but the picture for S. cerevisiae is more complex: there is evidence for region-specific sub-populations but there are also reasonable levels of gene flow among these regions in NZ. We believe this is the first demonstration of regional delineations of yeast populations and communities worldwide.

Figure 1

Correlation between ITS-RFLP patterns and D1/D2 26s RNA sequence data. Neighbour-joining consensus tree of 1000 bootstrap replicates reconstructed from an alignment of the D1/D2 26s RNA region for 45 isolates associated with Chardonnay and Syrah fruit (see Supplementary Material). Random isolates from each of the 22 ITS-RFLP cohorts were selected. Isolates from the same cohort whose 26S sequences match to the same type species and are placed together with 100% support are shown in red. Isolates from different ITS-RFLP cohorts whose 26S sequences match to the same species in GenBank and are placed together with 100% support are shown in blue. The two examples from cohort 18 that yielded different 26s RNA sequences are in green. The >98% homology of our query sequences to type-strain deposits in GenBank allow species names to be ascribed to well-supported groups and the abundance of each group among the 2688 isolates is shown. Those species previously reported as associated with juice/wines in NZ are denoted with a superscript.

Figure 2

The average relatedness of 303 S. cerevisiae genotypes isolated from 21 spontaneous ferments among the 17 inferred sub-populations, partitioned by region. The proportion of ancestry of each genotype was inferred from five Markov Chain Monte Carlo chains with K=17 using InStruct; the grand mean for ancestry of genotypes for each region in each sub-population was calculated from the average of these five runs and is plotted, along with the s.d. Blue bars: genotypes from West Auckland; red bars: Waiheke Island; green bars: Hawkes Bay. The sum of any one isolate's ancestry across all sub-populations is one. Deviation in relatedness between regions within each sub-population was tested with a one-way analysis of variance, and those sub-populations with a significant difference in relatedness between regions are indicated (^*P<0.01; ^**P<0.001; ^***P<0.0001).