Microbial interactions are expected to be major determinants of microbiome structure and function. Although fungi are found in diverse microbiomes, their interactions with bacteria remain largely uncharacterized. In this work, we characterize interactions in 16 different bacterial–fungal pairs, examining the impacts of 8 different fungi isolated from cheese rind microbiomes on 2 bacteria (Escherichia coli and a cheese-isolated Pseudomonas psychrophila). Using random barcode transposon-site sequencing with an analysis pipeline that allows statistical comparisons between different conditions, we observed that fungal partners caused widespread changes in the fitness of bacterial mutants compared to growth alone. We found that all fungal species modulated the availability of iron and biotin to bacterial species, which suggests that these may be conserved drivers of bacterial–fungal interactions. Species-specific interactions were also uncovered, a subset of which suggested fungal antibiotic production. Changes in both conserved and species-specific interactions resulted from the deletion of a global regulator of fungal specialized metabolite production. This work highlights the potential for broad impacts of fungi on bacterial species within microbiomes.

微生物相互作用有望成为微生物组结构和功能的主要决定因素。尽管真菌存在于不同的微生物组中，但它们与细菌的相互作用在很大程度上仍未得到表征。在这项工作中，我们描述了 16 种不同细菌-真菌对的相互作用，检查了从奶酪外皮微生物群中分离的 8 种不同真菌对 2 种细菌（大肠杆菌和奶酪分离的嗜冷假单胞菌）的影响。）。使用随机条形码转座子位点测序和允许在不同条件之间进行统计比较的分析管道，我们观察到与单独生长相比，真菌伙伴导致细菌突变体的适应性发生广泛变化。我们发现所有真菌物种都调节了铁和生物素对细菌物种的可用性，这表明这些可能是细菌 - 真菌相互作用的保守驱动因素。还发现了物种特异性相互作用，其中一部分暗示了真菌抗生素的产生。保守和物种特异性相互作用的变化是由于缺失了一个真菌特化代谢物产生的全球调节器。这项工作强调了真菌对微生物群落中细菌种类的广泛影响的潜力。