MTM2: Drivers of functional redundancy across microbiomes

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Microbes are essential components of all ecosystems. Human activity has impacted microbes across a wide range of natural ecosystems, including oceans, soils, and human guts. In most cases, humans simplify these environments, resulting in a decrease in the number of different microbial species present and a corresponding decrease in the number of different functions that these microbes can perform. Both losses have been linked to decreases in ecosystem health. What is not well understood is whether human-mediated ecosystem simplification causes losses in microbial ‘functional redundancy’ – the number of different microbial species that can perform any given function. Functional redundancy is important, because it provides ecosystem insurance – in a redundant system, when one microbial species goes extinct, there is another waiting to take its place. If human activity is driving large losses in functional redundancy, then microbial ecosystems will become more and more fragile, and more and more prone to collapse. This project is characterizing the functional redundancy of microbes in a variety of ecosystems that range in habitat complexity by using experimental research, theoretical modelling, and novel computational methods. The end goals of this project are to identify rules that govern the relationship between complexity, functional redundancy and health of microbial ecosystems as well as train graduate students and postdoctoral scientists in interdisciplinary research. This project is also helping to educate undergraduate students and the public about the importance of science through social media outlets, videos, and the development of interdisciplinary curricula for first year college students. A decrease in habitat complexity has been linked to decreases in microbiome taxonomic and functional diversity. By contrast, effects on functional redundancy – that is, the extent of duplicity of function across taxa – are poorly known. Functional redundancy, however, is a key predictor of ecosystem stability and resilience. Thus, understanding the extent to which functional redundancy is being lost is critical for predicting how microbial ecosystems will respond to future change. The overall goal of this project is to identify the ecological rules relating habitat complexity to functional redundancy in both host-associated (human, mouse, plants), and environmental (bulk soils, estuarine and marine) microbiomes. Specifically, this project is: 1. Determining how fundamental functional redundancy (gene encoded) and realized functional redundancy (actively expressed) vary with habitat complexity. 2. Developing deep learning algorithms to identify and link functional redundancy in metagenomes and metatranscriptomes, and then comparing these algorithms to more traditional techniques. 3. Characterizing the partitioning of redundancy within genomes (core vs. accessory) and among taxa (e.g. based on genome size, dormancy, growth rate), determining how this partitioning facilitates maintenance of redundancy, and predicting how the impacts of habitat complexity differ with distinct partitioning schemes. 4. Developing theoretical models linking functional redundancy to habitat complexity via effects on taxonomic diversity and mechanisms like environmental filtering and niche partitioning.This project is funded by the Understanding the Rules of Life: Microbiome Theory and Mechanisms Program, administered as part of NSF's Ten Big Ideas through the Division of Emerging Frontiers in the Directorate for Biological Sciences.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.