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      Evaluation of Saccharomyces cerevisiae Wine Yeast Competitive Fitness in Enologically Relevant Environments by Barcode Sequencing

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          Abstract

          When a wine yeast is inoculated into grape juice the potential variation in juice composition that confronts it is huge. Assessing the performance characteristics of the many commercially available wine yeasts in the many possible grape juice compositions is a daunting task. To this end we have developed a barcoded Saccharomyces cerevisiae wine yeast collection to facilitate the task of performance assessment that will contribute to a broader understanding of genotype-phenotype relations. Barcode sequencing of mixed populations is used to monitor strain abundance in different grape juices and grape juice-like environments. Choice of DNA extraction method is shown to affect strain-specific barcode count in this highly related set of S. cerevisiae strains; however, the analytical approach is shown to be robust toward strain dependent variation in DNA extraction efficiency. Of the 38 unique compositional variables assessed, resistance to copper and SO 2 are found to be dominant discriminatory factors in wine yeast performance. Finally, a comparison of competitive fitness profile with performance in single inoculum fermentations reveal strain dependent correspondence of yeast performance using these two different approaches.

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          Most cited references 75

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          Improved method for high efficiency transformation of intact yeast cells.

           A Jean,  John Woods,  R Gietz (1992)
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            A new efficient gene disruption cassette for repeated use in budding yeast.

            The dominant kanr marker gene plays an important role in gene disruption experiments in budding yeast, as this marker can be used in a variety of yeast strains lacking the conventional yeast markers. We have developed a loxP-kanMX-loxP gene disruption cassette, which combines the advantages of the heterologous kanr marker with those from the Cre-lox P recombination system. This disruption cassette integrates with high efficiency via homologous integration at the correct genomic locus (routinely 70%). Upon expression of the Cre recombinase the kanMX module is excised by an efficient recombination between the loxP sites, leaving behind a single loxP site at the chromosomal locus. This system allows repeated use of the kanr marker gene and will be of great advantage for the functional analysis of gene families.
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              Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.

              Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.
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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                02 December 2019
                February 2020
                : 10
                : 2
                : 591-603
                Affiliations
                [* ]The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, Australia, 5064 and
                []Department of Genetics and Evolution, University of Adelaide, South Australia, Australia, 5000
                Author notes
                [1 ]Corresponding author: The Australian Wine Research Institute, PO Box 197, Glen Osmond, SA 5064. E-mail: simon.schmidt@ 123456awri.com.au .
                Article
                GGG_400743
                10.1534/g3.119.400743
                7003103
                31792006
                Copyright © 2020 Schmidt et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 5, Tables: 0, Equations: 0, References: 92, Pages: 13
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                Investigations

                Genetics

                competitive growth, barcode sequencing, bar-seq, copper tolerance, sulfite tolerance

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