CAREER: Mechanisms of microbial adaptation in variable biotic environments

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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.