Microbes and Their Environment: How Environmental Stress Reshapes Microbial Communities, Ecology, and Interactions

Microbes play central roles in a wide range of biological processes, influencing the health, morphology, and behaviors of individual plants and animals, the assembly and diversity of communities, and the functioning of global ecosystem processes (e.g., carbon cycling). The services, and the stability of services, provided by microbes is dependent on the relationship between microbes and their environments. However, these microbes are experiencing and will continue to experience ongoing increases in environmental stress at unprecedented rates in the Anthropocene thereby impacting both microbiomes and their relationships with other organisms and their consequences for ecosystems overall. While the past seven years of high-throughput, next-generation sequencing have revolutionized our ability to describe where microbes are and have begun to pare back the “black box” metaphor of microbial communities, there remains substantial knowledge gaps in our understanding of how microbial communities as a whole respond to environmental stress as well as the mechanisms underlying changes in their responses. To address these gaps, I develop three conceptual/mechanistic frameworks exploring microbial relationships with environmental stress. Specifically, I demonstrate how environmental stress destabilizes microbial networks, how prokaryotic niches are confined to two trajectories impacting what is a suitable environment, and how gene family expansions are integral to context-dependency response to stress of host-microbe interactions shaping gene expression, population genetics, and genetic underpinnings of microbial benefit. To construct these frameworks, my dissertation uses a combination of local field systems, continental datasets, and model organisms as well as a wide range of methodological approaches. Overall, my dissertation fills major knowledge gaps in our understanding of how microbes and their services respond to environmental stress which will only become increasingly more important as humans push virtually every environment to new extremes.