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In the macroscopic world, ecological interactions between multiple species of fauna and flora are recognised as major role-players in the evolution of any particular species. By comparison, research on ecological interactions as a driver of evolutionary adaptation in microbial ecosystems has been neglected. The evolutionary history of the budding yeast Saccharomyces cerevisiae has been extensively researched, providing an unmatched foundation for exploring adaptive evolution of microorganisms. However, in most studies, the habitat is only defined by physical and chemical parameters, and little attention is paid to the impact of cohabiting species. Such ecological interactions arguably provide a more relevant evolutionary framework. Within the genomic phylogenetic tree of S. cerevisiae strains, wine associated isolates form a distinct clade, also matched by phenotypic evidence. This domestication signature in genomes and phenomes suggests that the wine fermentation environment is of significant evolutionary relevance. Data also show that the microbiological composition of wine fermentation ecosystems is dominated by the same species globally, suggesting that these species have co-evolved within this ecosystem. This system therefore presents an excellent model for investigating the origins and mechanisms of interspecific yeast interactions. This review explores the role of biotic stress in the adaptive evolution of wine yeast., (© FEMS 2019.)

System-wide "omics" approaches have been widely applied to study a limited number of laboratory strains of Saccharomyces cerevisiae. More recently, industrial S. cerevisiae strains have become the target of such analyses, mainly to improve our understanding of biotechnologically relevant phenotypes that cannot be adequately studied in laboratory strains. Most of these studies have investigated single strains in a single medium. This experimental layout cannot differentiate between generally relevant molecular responses and strain- or media-specific features. Here we analyzed the transcriptomes of two phenotypically diverging wine yeast strains in two different fermentation media at three stages of wine fermentation. The data show that the intersection of transcriptome datasets from fermentations using either synthetic MS300 (simulated wine must) or real grape must (Colombard) can help to delineate relevant from "noisy" changes in gene expression in response to experimental factors such as fermentation stage and strain identity. The differences in the expression profiles of strains in the different environments also provide relevant insights into the transcriptional responses toward specific compositional features of the media. The data also suggest that MS300 is a representative environment for conducting research on wine fermentation and industrially relevant properties of wine yeast strains.

The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. Key points: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding. [ABSTRACT FROM AUTHOR]

Organic acids are a major contributor to wine flavour and aroma. In the past, the scientific focus has mostly been on organic acids derived from grapes or on the transformation of malic acid to lactic acid by lactic acid bacteria, since these acids contribute significantly to the final total acidity of wine. However, the organic acid concentration and composition also change significantly during alcoholic fermentation, yet only limited information regarding the impact of different yeast strains on these changes has been published. Here we report on changes in organic acid (malic, tartaric, citric, succinic, acetic and pyruvic) composition during fermentation by five widely used industrial wine yeast strains in a synthetic grape must (MS300) reflecting two very different, but both wine-like, fermentation conditions. Samples were obtained from three physiological stages during fermentation, namely the exponential growth phase (day 2), early stationary phase (day 5) and late stationary phase (day 14). These different stages were selected to provide more information on acid evolution throughout fermentation, as well as on the impact of nutritional and environmental conditions during aerobic and anaerobic fermentation. Among other observations, some strains (such as VIN13 and 285) were shown to be generally higher producers of most acids in white and/ or red wine fermentation settings, while other strains (such as DV10) were generally lower acid producers. The data clearly demonstrate that different strains have different acid consumption and production patterns, and this presents a first step towards enabling winemakers to appropriately select strains for acid management during fermentation. [ABSTRACT FROM AUTHOR]

The conversion of grape sugar to ethanol and carbon dioxide is the primary biochemical reaction in alcoholic wine fermentation, but microbial interactions, as well as complex secondary metabolic reactions, are equally relevant in terms of the composition of the final wine produced. The chemical composition of a wine determines the taste, flavour and aroma of the product, and is determined by many factors such as grape variety, geographical and viticultural conditions, microbial ecology of the grapes and of the fermentation processes, and the winemaking practices. Through the years, major advances have been made in understanding the biochemistry, ecology, physiology and molecular biology of the various yeast strains involved in wine production, and how these yeasts affect wine chemistry and wine sensory properties. However, many important aspects of the impact of yeast on specific wine-relevant sensory parameters remain little understood. One of these areas of limited knowledge is the contribution of individual wine yeast strains to the total organic acid profile of wine. Wine quality is indeed very directly linked to what wine tasters frequently refer to as the sugar-acid balance. The total acidity of a wine is therefore of prime sensory importance, and acidity adjustments are a frequent and legal practice in many wineries. However, the total acidity is the result of the sum of all the individual organic acids that are present in wine. Importantly, each of these acids has its own sensory attributes, with descriptors ranging from fresh to sour to metallic. It is therefore important not only to consider total acidity, but also the contribution of each individual acid to the overall acid profile of the wine. This review will summarise the current knowledge about the origin, synthesis and analysis of organic acids in wine, as well as on the management of wine acidity. [ABSTRACT FROM AUTHOR]

Acidity is one of the primary sensory elements in wine, and the balance of sugar and acidity is probably the strongest element affecting wine appreciation. However, little is known about how yeast strains and fermentation conditions will affect the production of fermentation-derived acids, including acetic, succinic and pyruvic acid. This study employs a multifactorial experimental design to provide a better understanding of how individual or simultaneous changes in environmental parameters such as pH, sugar and temperature influence the production of individual organic acids during fermentation in several yeast strains in synthetic must. Certain changes in environmental factors led to conserved trends between strains and treatments. Strains produced higher succinic acid levels when temperature was increased. Significant strain-dependent differences were observed when sugar concentrations were varied for both strains: the combinatorial impact of high initial sugars and fermentation temperature was more pronounced when increased pyruvic acid production was observed in yeast strain VIN13. On the other hand, while combinatorial influences are evident, higher sugar fermentation settings were largely characterised by high acetic acid concentrations for both strains. It is clear that simultaneous changes in sugar, pH and temperature affect organic acid trends in a variable manner, depending on the particular combination of environmental parameters and yeast strain. The study provides valuable information regarding the manner in which initial must parameters and environmental conditions throughout fermentation may affect wine acidity. Since many of these parameters can be controlled at least in part during the winemaking process, the data provide important background information for oenological strategies that aim to optimise the acid balance of wines. [ABSTRACT FROM AUTHOR]

The outcome of co- or sequential inoculation of Lachancea thermotolerans in winemaking remains unpredictable due to a lack of integrated data regarding the impact of grape juice composition on L. thermotolerans fermentation behaviour. Here, we investigate the impact of nitrogen composition on fermentation characteristics and aroma compound production in grape juice sequentially inoculated with commercial L. thermotolerans and S. cerevisiae strains. Subsequently, all treatments were subjected to malolactic fermentation (MLF) using two commercial strains of Oenococcus oeni. Addition of amino acids led to faster growth for S. cerevisiae fermentations, compared to the nitrogen-equivalent addition of diammonium phosphate (DAP). L. thermotolerans persistence in the mixed fermentations was significantly higher following DAP addition, with higher glycerol and lactic acid production. Interestingly, the lower total Nitrogen content in DAP-treated musts compared to other treatments did not alter the subsequent growth of S. cerevisiae. MLF was more similar between musts fermented with L. thermotolerans , regardless of nutrient regime, whereas significant differences in MLF completion times were observed for different nitrogen treatments in S. cerevisiae fermentations. Collectively, the data present an integrated view of the impact of nitrogen treatment on multispecies co-inoculation (growth kinetics and aromatic outcomes) and the downstream impact on MLF. • Integrated analysis of the co-inoculation of two yeast species and of nitrogen sources on fermentation and wine composition. • L. thermotolerans reduces total nitrogen levels without affecting growth of sequentially inoculated S. cerevisiae. • Volatile aroma production in response to addition of branched chain amino acids is similar in both yeast species. • Amino acids that are preferred nitrogen sources lead to significantly higher acetic acid production in both yeast species. • L. thermotolerans fermentations resulted in reduced overall medium chain fatty acids and ethyl esters. [ABSTRACT FROM AUTHOR]