Collaborative Research: MTM 2: Using successional dynamics, biogeography, and experimental communities to examine mechanisms of plant-microbiome functional interactions

Microbial communities (microbiomes) play important roles in animals, plants, and even whole ecosystems. However, microbiomes are constantly changing through time and space. These changes can have big impacts on the health of animal or plant hosts and the functioning of entire ecosystems. For this reason, uncovering rules that govern how microbiomes change across time and space is essential for understanding how they affect their hosts and ecosystems. This project builds on previous understanding of different strategies used by microbes to survive and compete for resources and applies it to studying the ecosystem that forms in the ‘pitchers’ of the carnivorous pitcher plant, Sarracenia purpurea. Through a combination of experiments and modeling, the microbiome will be studied to determine how microbial community functions change over time, how the host plant influences microbiome formation, and how the microbiome affects the host plant. The results will be compared with other aquatic, plant- and soil-associated microbiomes, to understand how S. purpurea pitchers can be relevant models for understanding roles of microbiomes in larger ecosystems. The project will train the next generation of scientists in interdisciplinary skills. The researchers will involve undergraduate and graduate students including those who are under-represented in STEM research, train students in coding to develop a Sarracenia microbiome website for public education, develop K-12 educational modules, and present interactive public lectures. This project employs interdisciplinary approaches including molecular genetics, biochemistry, ecological modeling, multivariate statistics, and biogeography to characterize microbiome succession, functions and host interactions. It builds from the Yield-Acquisition-Stress (Y-A-S) predictive framework, which characterizes microbial life history strategies based on functional traits related to cell growth yield (Y), resource acquisition (A) and stress tolerance (S), with the microbiomes changing proportions of these strategies over time. The Y-A-S framework has yet to be applied to microbiome succession or functions important for host and ecosystem health. The project will determine dynamics of functional succession across climatic gradients using field-sampling of natural communities over broad biogeographical scales, test how host factors influence microbiome succession using experimental manipulations of natural pitcher communities, and examine microbiome effects on host fitness using experimental bacterial communities. A cutting-edge approach with Latent Dirichlet Allocation (LDA) and Random Forest models will be used to identify Y-A-S life strategies based on a trait matrix derived from metagenomes, RNA transcripts, and measured biochemical nutrient transformation functions. A meta-analysis will compare succession and function of other plant- and soil-associated microbial communities to explore the generality of rules for microbiomes across ecosystems.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.