PurSUiT: Uncovering bacterial and archaeal diversity in Great Basin hot springs

University Of Oregon Eugene, Eugene OR

Investigators

Abstract

Microbes are the most ubiquitous, most ancient and most resilient form of life, exhibiting several unique metabolic capabilities and remarkable adaptations to extreme environments. These properties have led to the use of microbes in a variety of industrial processes, ranging from biofuel production and wastewater treatment to bioremediation of oil spills and drug production. Despite their ubiquity and importance, only a minuscule fraction of microbes has been characterized and taxonomically classified so far, resulting in a large underutilization of their industrial potential and a major gap in our understanding of life. This project aims to reduce this gap by exploring previously undiscovered microbial diversity in hot springs across the US Great Basin, which are some of Earth's most extreme and least understood environments. Our rationale for targeting Great Basin hot springs is four-fold. First, hot springs exert strong selective pressures on organisms, thus increasing the potential for discovering novel species. Second, hot springs likely resemble some of the earliest life-harboring environments on Earth, thus yielding insight into the origins of life. Third, prokaryotes found in hot springs are known to exhibit strong degrees of endemism, and hence hot springs can be considered "isolated islands" from a microbial perspective, each with unique diversity. This "island"-nature is expected to be particularly pronounced in the largely arid desert-like Great Basin. Fourth, the Great Basin is rich in geothermal features that nevertheless remain poorly studied. Our data will be made publicly available, thus serving as a valuable resource to society. The discovery of new species from a large number of poorly studied taxonomic groups will assist in the future cultivation of new microorganisms and their physiological characterization, based on predicted nutrient requirements. Increasing the coverage of the microbial tree of life will also facilitate reconstruction of the timing and order of various evolutionary events believed to have shaped our planet's surface chemistry and climate. The project will provide hands-on training to students in field work, lab work and bioinformatics, through participation in the research activities as well as through a microbiology summer course. The project aims to recover novel microbial (bacterial and archaeal) diversity in 40 hot springs across the US Great Basin at whole-genome resolution, using culture-independent genome-resolved metagenomics. The hot springs have been chosen such that the potential for discovery of new microbial diversity is maximized. Recovered genomes will be taxonomically classified and functionally annotated through comparison to reference databases. In addition, material from each sample will be archived via cryopreservation as well as lyophilization, to facilitate follow-up investigations of the recovered microbial diversity. The project is expected to lead to the discovery of 1000-1500 new prokaryotic species, many of which from new classes and even phyla. The project will also collect rich geochemical metadata, such as ion concentrations, pH and temperatures, to provide environmental context for the recovered genomes. 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.