CAREER: Mechanisms of microbial adaptation in variable biotic environments

微生物可以快速进化以适应其环境。例如，在医疗和农业环境中，病原菌和真菌可以迅速产生对抗生素的抗药性。对微生物进化的大部分了解来自于对单一培养中单独生长的微生物物种的研究。但大多数微生物生活在多物种群落(微生物群)中，在那里邻近物种可能会影响它们进化的速度和方式。在实验室单一培养中观察到的微生物适应过程是否转化为复杂的现实世界微生物群仍不清楚。这项研究项目将使用两组参与奶酪生产的微生物(霉菌青霉和细菌葡萄球菌)来了解微生物物种之间的相互作用如何影响它们的进化。从这个可实验驯化的奶酪皮系统中的发现可能会告诉我们，生物相互作用如何影响微生物群落中微生物物种的适应。除了为研究生和本科生提供研究机会外，这个职业研究项目还利用奶酪模式体系的流行吸引力，拓宽了获得独立研究经验的途径，提高了科学素养。这项研究还将对美国公众产生直接的社会影响，深入了解广泛存在的微生物的生态和进化，这些微生物既能给人类和自然生态系统带来好处，又能对人类和自然生态系统造成破坏。细菌、真菌和其他微生物物种生活在多物种群落中，它们不断面临邻近微生物物种的挑战和机遇。通过共培养实验和培育的模式群落，这些生物相互作用的生态后果开始显现。微生物群内生物相互作用的长期进化后果还知之甚少。这项工作将确定控制微生物在可变生物环境中适应的机制。以野生青霉菌和葡萄球菌对奶酪环境的适应为模型系统，本研究将确定微生物相互作用的保守机制，以及这些相互作用如何影响微生物进化的速度和模式。RNA测序和代谢组学将被用来确定目标青霉菌和葡萄球菌物种与奶酪皮微生物群落中的邻居之间的相互作用机制。实验室中的实验进化将确定物种相互作用如何影响青霉菌和葡萄球菌在奶酪环境中的适应。比较基因组学和转录组学将确定驱动青霉菌和葡萄球菌适应的遗传机制。塔夫茨大学开设了一门新的本科生研究课程，随着学生完成该项目的许多研究活动，对原创研究经验的需求将会增加。为来自新英格兰各地的奶酪制造商和高中教师举办的微生物夏令营将教授微生物群和微生物进化的概念和技能。MicrobialFoods.org上的专题文章和信息图表将向全球观众传授微生物进化和多样性。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Microbes can rapidly evolve to adapt to their environment. For example, pathogenic bacteria and fungi can quickly evolve resistance to antibiotics in medical and agricultural settings. Much of the understanding of microbial evolution comes from studies of microbial species growing alone in a monoculture. But most microbes live in multispecies communities (microbiomes) where neighboring species may impact how quickly and in what ways they evolve. Whether the process of microbial adaptation observed in laboratory monocultures translates to complex real-world microbiomes remains unclear. This research project will use two groups of microbes (the mold Penicillium and the bacterium Staphylococcus) that are involved in cheese production to understand how interactions between microbial species impact their evolution. Discoveries from this experimentally tractable cheese rind system may inform how biotic interactions impact adaptation of microbial species in microbial communities. In addition to providing research opportunities for graduate students and undergraduates, this CAREER research project leverages the popular appeal of the cheese model system to broaden access to independent research experiences and improve scientific literacy. This research will also have direct societal impacts on the American public by providing an in depth understanding of the ecology and evolution of widespread microbes that can both provide benefits and wreak havoc in human and natural ecosystems.Bacterial, fungal, and other microbial species live in multispecies communities where they constantly face the challenges and opportunities of neighboring microbial species. The ecological consequences of these biotic interactions are beginning to emerge through co-culture experiments and cultivated model communities. The longer-term evolutionary consequences of biotic interactions within microbiomes are poorly understood. The work will identify the mechanisms that control microbial adaptation in variable biotic environments. Using the adaptation of wild Penicillium and Staphylococcus to the cheese environment as a model system, this research will identify conserved mechanisms of microbial interactions and how these interactions impact the rate and mode of microbial evolution. RNA-sequencing and metabolomics will be used to identify mechanisms of interactions between target Penicillium and Staphylococcus species and neighbors within the cheese rind microbial community. Experimental evolution in the lab will determine how species interactions impact the adaptation of Penicillium and Staphylococcus in the cheese environment. Comparative genomics and transcriptomics will identify the genetic mechanisms that drive adaptation of Penicillium and Staphylococcus. A new undergraduate research course at Tufts University will fulfill an increased demand for original research experiences as students complete many of the research activities of the project. A summer microbiome camp for cheesemakers and high school teachers from throughout New England will teach concepts and skills in microbiomes and microbial evolution. Feature articles and infographics on MicrobialFoods.org will teach a global audience about microbial evolution and diversity.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.