Description:

Microbiome Stability: What Can We Learn From Extreme Environments?

My research team and I investigate the causes and consequences of microbiome stability, with an emphasis on understanding the key feature of resilience. Resilience is the ability of a community to recover in structure or function after a disturbance. We are especially interested in quantifying the contributions of microbial diversity reservoirs, like rare and dormant members, to resilience. As a model for our research, we work in the Centralia, Pennsylvania soil ecosystem. Centralia is the site of a slow-burning coal seam fire that presents a severe disturbance to the surface soil communities. The fire ignited in 1962 and advances along the coal seams at a rate of 3-7 m/yr. The heat from the fire vents through overlying soils, causing surface soil temperatures to reach as high as > 400°C, but more recently in the range of 40 - 75°C. The fire-impact gradient at Centralia provides a unique opportunity to investigate eco-evolutionary microbiome dynamics in response to a severe press disturbance. I will discuss our recent results about the response and recovery of soil microbial communities to the Centralia fire, including overarching community responses and traits of members that flourish in the extreme environment. We anticipate that the results of our research will provide insights into microbiome stability, and will broadly inform management or manipulation of microbiomes towards desired functions.

Biography
Dr. Ashley Shade received her Ph.D. from the University of Wisconsin Microbiology Doctoral Training Program in 2010, and afterwards was a Gordon and Betty Moore Foundation postdoctoral fellow of the Life Sciences Research Foundation at Yale University. In 2014, she started her position in the Department of Microbiology and Molecular Genetics at Michigan State University. Her research interests concern the microbial ecology of environmental systems, including plants, soils, and their feedbacks. She applies an ecological approach to understand how microbial communities respond to stressors, and what determines their resilience as a system. Her lab employs ‘omics tools (metagenomics, metatranscriptomics, exometabolomics) with both field and laboratory studies. ShadeLab phytobiome research is focused on common dry bean, a legume important for human and livestock nutrition, and switchgrass, a biofuel feedstock.  Shade is an advocate of reproducible research and open science, and her lab’s analysis workflows are on GitHub (https://github.com/ShadeLab). In addition, Shade has developed a popular workshop on microbial metagenome analysis (edamamecourse.org). She is member of the Earth Microbiome Project (http://www.earthmicrobiome.org/) and the International Society for Microbial Ecology, and serves as an editor at the American Society for Microbiology journal mSystems and the Society for Applied Microbiology journal Environmental Microbiology.