Microbial interactions contribute to shape ecosystems and their functions. The interplay between microorganisms also shapes the evolutionary trajectory of each species, by imposing metabolic and physiological selective pressures. The mechanisms underlying these interactions are thus of interest to improve our understanding of microbial evolution at the genetic level. Here we applied a functional genomics approach in the model yeast Saccharomyces cerevisiae to identify the fitness determinants of naive biotic interactions. We used a barcoded prototroph yeast deletion collection to perform pooled fitness competitions in co-culture with seven Pseudomonas spp natural isolates. We found that co-culture had a positive impact on fitness profiles, as in general the deleterious effects of loss of function in our nutrient-poor media were mitigated. In total, 643 genes showed a fitness difference in co-culture, most of which can be explained by a media diversification procured by bacterial metabolism. However, a large fraction (36%) of gene-microbe interactions could not be recaptured in cell-free supernatant experiments, showcasing that feedback mechanisms or physical contacts modulate these interactions. Also, the gene list of some co-cultures was enriched with homologs in other eukaryote species, suggesting a variable degree of specificity underlying the mechanisms of biotic interactions and that these interactions could also exist in other organisms. Our results illustrate how microbial interactions can contribute to shape the interplay between genomes and species interactions, and that S. cerevisiae is a powerful model to study the impact of biotic interactions.

中文翻译：

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映射基因-微生物相互作用：酿酒酵母和假单胞菌属之间的功能基因组学共培养实验的见解。

微生物相互作用有助于塑造生态系统及其功能。微生物之间的相互作用还通过施加代谢和生理选择压力来塑造每个物种的进化轨迹。因此，这些相互作用的基础机制对于提高我们在遗传水平上对微生物进化的理解是令人感兴趣的。在这里，我们在啤酒酵母模型中应用了功能基因组学方法，来确定天真的生物相互作用的适应性决定因素。我们使用带条形码的原养型酵母缺失集合与7个假单胞菌属自然分离株共培养进行合体健身比赛。我们发现，共培养对体能状况有积极影响，因为总的来说，在营养不良的培养基中，功能丧失的有害影响得到缓解。总共，643个基因在共培养中显示出适应性差异，其中大多数可以通过细菌代谢引起的培养基多样化来解释。然而，在无细胞上清液实验中无法捕获到很大一部分（36％）的基因-微生物相互作用，这表明反馈机制或物理接触调节了这些相互作用。同样，一些共培养物的基因列表中丰富了其他真核生物物种的同源物，表明生物相互作用机制的特异性程度不同，并且这些相互作用也可能存在于其他生物中。我们的研究结果说明了微生物相互作用如何促进基因组和物种相互作用之间的相互作用，而酿酒酵母是研究生物相互作用影响的强大模型。