Dimensions: Ordering the microbial world into natural genetic, ecological, and functional units

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The vast majority of our planet's biological diversity is microbial, and this diversity is being discovered at unprecedented rates due to advances in DNA sequencing technologies. Understanding the roles of these organisms, however, has been greatly hindered by our ignorance of the extent of microbial diversity, how it is generated, maintained, and shaped by evolution, and how it functions in the Earth's ecosystems. Understanding these aspects of the microbial world are fundamental to several questions critical to society, such as "Are emerging diseases new species, or variants of existing ones?", and "How will microbial populations respond to changing climates?". This project has the ambitious goals of developing methods that will for the first time allow all microbial species to be classified in a biologically meaningful way, and it will reveal the factors that give rise to new species. The research is a collaboration between four laboratories that have complementary scientific strengths in microbial biology, genome analysis, evolutionary genetics, and statistics. In addition to advancing scientists' fundamental understanding of microbes, the project will provide an important platform for training undergraduates, graduate students, and the postdoctoral scholars that will soon become independent scientists. This research program itself involves three major aims. The first major aim is to identify bacterial species under the framework provided by the Biological Species Concept (BSC), which defines species as genetically and reproductively isolated units. Applying this framework will unify the phylogenetic organization of bacteria with that of eukaryotes, and allow the researchers to determine the functional and ecological differences among species, and to quantify the rates and amounts of genetic exchange between them. The second major aim is to distinguish "ecotypes" that represent ecologically, functionally, or geographically isolated populations within species. This aim will be based on a genetic framework called "coalescence" that is well-established in eukaryotic phylogenetics. This work will both uncover new dimensions of microbial diversity and develop new statistical tools for other scientists to use. The third major aim is to determine how the process of bacterial speciation occurs and whether it mimics the patterns observed in eukaryotes. This aim will be accomplished by examining the patterns of gene exchange in the genomes of bacteria that have co-diversified with their host species (including humans), and the results will provide the first measurement of the amount of time required for the emergence of new bacterial species.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.