Data from: The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus, are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high-throughput environmental sequencing to show that S. paradoxus is a very rare member of the oak bark microbial community. We find that S. paradoxus can grow well on sterile medium made from oak bark, but that its growth is strongly suppressed when the other members of the community are present. We purified a set of twelve common fungal and bacterial species from the oak bark community, and tested how each affected the growth of S. paradoxus in direct competition on oak bark medium at summer and winter temperatures, identifying both positive and negative interactions. One Pseudomonas species produces a diffusible toxin that suppresses S. paradoxus almost as effectively as either the whole set of twelve species together, or the complete community present in non-sterilized oak medium. Conversely, one of the twelve species, Mucilaginibacter sp., had the opposite effect and promoted S. paradoxus growth at low temperatures. We conclude that, in its natural oak tree habitat, S. paradoxus is a rare species whose success depends on the much more abundant microbial species surrounding it.模式酵母酿酒酵母（Saccharomyces cerevisiae）的自然史尚不明晰，且其驯化背景进一步混淆了相关研究认知。在自然环境中，酿酒酵母及其未驯化近缘种帕氏酿酒酵母（Saccharomyces paradoxus）通常栖息于橡树树皮之上，该栖息环境与葡萄酒酿造或其他人类发酵场景截然不同。目前尚不清楚橡树树皮是否为野生酵母的核心原生栖息地，亦或是这种看似紧密的关联仅源于采样偏差。本研究通过微生物培养与高通量环境测序技术证实，帕氏酿酒酵母（S. paradoxus）仅是橡树树皮微生物群落中极为稀有的成员。研究发现，帕氏酿酒酵母可在经灭菌处理的橡树树皮培养基上良好生长，但当群落中其他微生物存在时，其生长会受到显著抑制。本研究从橡树树皮微生物群落中分离得到12种常见真菌与细菌，并分别测试了这些物种在夏季、冬季温度条件下，于橡树树皮培养基中与帕氏酿酒酵母直接竞争时对其生长的影响，明确了二者间存在正负两种相互作用。其中一种假单胞菌属（Pseudomonas sp.）物种可分泌可扩散毒素，其对帕氏酿酒酵母的抑制效果几乎等同于12种物种的混合群落，或是未灭菌橡树树皮培养基中的完整微生物群落。与之相反，12种分离物种中的黏杆菌属（Mucilaginibacter sp.）则呈现相反作用，可在低温环境下促进帕氏酿酒酵母的生长。综上，在自然栖息的橡树树皮环境中，帕氏酿酒酵母实为稀有物种，其生存繁衍依赖于周遭更为丰富的其他微生物群落。