URoL:MTM2: Defining the ecological and genomic properties that underlie microbiome sensitivity and resilience

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The microbiome is a community of organisms that lives on and within plants and animals, playing a fundamental role in the health of their hosts. However, scientists currently have limited knowledge about the processes underlying how microbiomes respond to change and how such changes may alter the health trajectories of their hosts. This project will implement a novel conceptual and methodological framework to substantially advance discovery of these processes. To transform understanding of how disturbances impact plant and animal microbiomes, a series of experiments with three important aquatic organisms: seagrasses, corals, and zebrafish, will be performed. The central aim is to define the unifying principles and properties that define a microbiome’s sensitivity and resilience to environmental changes. Moreover, this project will determine how the microbiome’s sensitivity and resilience explains reductions or improvements in their host’s health. The identification of such universal properties holds potential to transform microbiome research and innovation, particularly as it applies to health and natural resource management. To further advance the ability of scientists to define the mechanisms that alter microbiome-host interactions, researchers working on this project will develop novel and freely available data analytic tools and software. Effective training, outreach, and assessment programs that increase participation and advance the future careers of microbiome scientists of all backgrounds will also be developed. Lastly, during this project, efforts will likely yield theoretical frameworks for predicting how host-microbiome interactions respond to environmental variation, which holds implications for how optimally wildlife, livestock, agricultural, and human health are managed.This project seeks to define universal properties of host-associated microbiomes that enable their ability to resist or recover from disturbances. To do so, experiments to formally test whether innate properties of the microbiome influence its response to and recovery from a disturbance will be conducted. To uncover such properties, microbiomes of three model and phylogenetically diverse aquatic host systems - corals, seagrass, and zebrafish – will be challenged with three exogenous and environmentally relevant stressors – antibiotics, warming waters, and pathogen infection. Modeling approaches will then be developed to resolve universal properties of the microbiome that influence stress responses, irrespective of the specific perturbation or ecological context of the community. These System Agnostic Microbiome Measures, or ‘SAMMs’, will include common ecological metrics as well as novel metrics developed using AI algorithms that contextualize microbial features in a system-independent way. Host traits will also be measured to model host-microbiome interactions before, during, and after disturbance to understand how these properties relate to host physiology. This project is distinctive in that it measures how host-microbiome systems both respond to and recover from disturbances over time, considers interactions between multiple ecologically relevant disturbances, and integrates the results across systems to uncover generalizable trends. Lastly this work is expected to develop foundational insights into how human activity impacts wildlife through their microbiomes. Ultimately, it is anticipated that these efforts will contribute to a future wherein microbiomes are managed or manipulated to buffer their hosts from the impacts of the Anthropocene.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.