Microscopic organisms, or microbes, are fascinating creatures because they exhibit an unparalleled diversity, can be found virtually everywhere in nature, and are responsible for critical ecosystem services. Advances in DNA sequencing technology have transformed how scientists study these evolutionary and ecological aspects of microbial life by providing genetic insight into which types of microbes live in specific environments. However, less is understood about how microbes have evolved the ability to thrive in these environments. This research project uses innovative methods to integrate evolutionary and ecological information about microbes to determine how they have evolved in particular environments and to discover evolutionary groups of microbes that are essential to the ecosystem. This work is important because (1) it will provide researchers with the tools needed to understand how evolutionary and ecological forces influence microbial biodiversity, (2) it will facilitate effective preservation of microbial ecosystems and their services, and (3) is will provide a means of efficiently engineering communities of microbes that are industrially valuable. Further, this research will provide valuable, fundamental insights regarding the mechanisms by which microbes evolve within the context of their ecosystem. In terms of broader impacts, this work is valuable because the tools generated will benefit future investigators in developing more quantitative analyses and research plans. The research team will also convene an annual bioinformatics workshop intended to bring in more under-represented and first-generation students.
This project will develop a set of eco-phylogenetic methods for assessing how and why specific groups of microbes diversify. Specifically, this approach analyzes phylogenies assembled from a set of microbial communities and profiles the presence and abundance of each evolutionary group (clade) in each community. It then identifies clades whose phylogenetic and ecological distributions indicate that specific evolutionary or ecological mechanisms have influenced their diversification. This includes development of statistical and model-based procedures to assess the likelihood that non-random processes created the observed patterns in community composition, diversification and relatedness. Finally, it will apply these methods to the study of mammalian gut and plant leaf associated microbial communities to determine which microbial clades are critical to the structure of these communities, co-evolving with their host, and subject to evolutionarily conserved interactions with other microbial clades.
