Table_1_A Quasi-Domesticate Relic Hybrid Population of Saccharomyces cerevisiae × S. paradoxus Adapted to Olive Brine.pdf

The adaptation of the yeast Saccharomyces cerevisiae to man-made environments for the fermentation of foodstuffs and beverages illustrates the scientific, social, and economic relevance of microbe domestication. Here we address a yet unexplored aspect of S. cerevisiae domestication, that of the emergence of lineages harboring some domestication signatures but that do not fit completely in the archetype of a domesticated yeast, by studying S. cerevisiae strains associated with processed olives, namely table olives, olive brine, olive oil, and alpechin. We confirmed earlier observations that reported that the Olives population results from a hybridization between S. cerevisiae and S. paradoxus. We concluded that the olive hybrids form a monophyletic lineage and that the S. cerevisiae progenitor belonged to the wine population of this species. We propose that homoploid hybridization gave rise to a diploid hybrid genome, which subsequently underwent the loss of most of the S. paradoxus sub-genome. Such a massive loss of heterozygosity was probably driven by adaptation to the new niche. We observed that olive strains are more fit to grow and survive in olive brine than control S. cerevisiae wine strains and that they appear to be adapted to cope with the presence of NaCl in olive brine through expansion of copy number of ENA genes. We also investigated whether the S. paradoxus HXT alleles retained by the Olives population were likely to contribute to the observed superior ability of these strains to consume sugars in brine. Our experiments indicate that sugar consumption profiles in the presence of NaCl are different between members of the Olives and Wine populations and only when cells are cultivated in nutritional conditions that support adaptation of their proteome to the high salt environment, which suggests that the observed differences are due to a better overall fitness of olives strains in the presence of high NaCl concentrations. Although relic olive hybrids exhibit several characteristics of a domesticated lineage, tangible benefits to humans cannot be associated with their phenotypes. These strains can be seen as a case of adaptation without positive or negative consequences to humans, that we define as a quasi-domestication.

酿酒酵母（Saccharomyces cerevisiae）为适配人工环境以发酵食品与饮料的驯化过程，彰显了微生物驯化在科学、社会与经济层面的重要价值。本研究聚焦酿酒酵母驯化中尚未被探索的一个维度——即那些携带部分驯化特征、但并未完全契合驯化酵母典型原型的谱系起源，通过研究与加工橄榄（包括鲜食橄榄、橄榄盐水、橄榄油及alpechin）相关的酿酒酵母菌株展开。我们证实了此前的研究结论，即橄榄种群源自酿酒酵母与帕拉酵母（Saccharomyces paradoxus）的杂交事件。研究结果表明，橄榄杂交菌株构成一个单系谱系，其酿酒酵母祖先隶属于该物种的葡萄酒发酵种群。我们提出，同倍体杂交形成了二倍体杂交基因组，随后该基因组发生了帕拉酵母亚基因组的大规模丢失。这种大规模的杂合性丢失可能是由对新生态位的适应所驱动的。我们观察到，相较于对照组的酿酒酵母葡萄酒菌株，橄榄菌株在橄榄盐水环境中更易于生长与存活，且它们似乎通过扩增ENA基因的拷贝数，以适应橄榄盐水中的氯化钠（NaCl）环境。我们还探究了橄榄种群所保留的帕拉酵母HXT等位基因，是否有助于提升这些菌株在盐水中消耗糖分的能力。实验结果显示，在氯化钠存在的条件下，橄榄种群与葡萄酒种群的糖分消耗模式存在差异；且仅当细胞在能够让蛋白质组适应高盐环境的营养条件下培养时，该差异才会显现，这表明观测到的差异源于橄榄菌株在高氯化钠浓度环境中更优异的整体适应性。尽管残存的橄榄杂交菌株展现出驯化谱系的若干特征，但其表型并未给人类带来切实的益处。这类菌株可被视为一种对人类既无正面也无负面影响的适应案例，我们将其定义为准驯化（quasi-domestication）。