RUI: Collaborative Research: Genetic and ecological drivers of microbial adaptation to high-nickel serpentine soils

As Earth's geology varies across the landscape, so do the properties of soil microbial communities. Variation among these microbial communities reflect an adaptive process in which genes providing benefits in a particular soil habitat are more common in the microbes dwelling there. Grassland landscapes in California are naturally punctuated by unusual patches of toxic, nickel-rich soil. For thousands of years, these patches have been sites of microbial adaptation to toxic metals. The primary goal of this project is to discover genes that allow the nitrogen fixing soil bacteria, Mesorhizobium, to tolerate toxic metals, to understand how these genes are distributed among bacteria across a patchy landscape, and to test whether these tolerance genes impose disadvantages when toxic metals are not present. Insights from this study will assist in developing strategies for biologically based remediation of human-contaminated soils and provide insight into adaptation of microbes to toxic environments. Since rhizobial bacteria, which include the Mesorhizobium, are responsible for approximately half of the biological nitrogen fixation, this research has agricultural implications. The project will integrate an undergraduate-focused training program that provides students with authentic research experiences. In this program, students will isolate bacterial strains with extremely high tolerance to toxic metals, and investigate whether their genomes include genes known to provide heavy metal tolerance. The funded work therefore contributes to understanding how organisms adapt to extreme environments and employs the efforts of young scientists at a critical stage of their training.<br/><br/>This project explores a critical frontier in microbial evolutionary ecology: microbial local adaptation in nature, and the role of fitness trade-offs in determining genotype distributions across heterogeneous environments. In this project, mesorhizobia, nitrogen-fixing bacteria that are easily isolated from symbiotic host plants, will be isolated from serpentine and non-serpentine soils. These Mesorhizobium strains will be subjected to straightforward laboratory physiology and fitness assays under varying nickel levels. Whole genome sequencing, transcriptional profiling, as well as molecular genetic manipulations, will also be used to characterize these strains. This highly tractable system will enable the identification of genes and mechanisms of nickel adaptation, along with direct measurement of fitness trade-offs. The project will additionally link trade-offs to the distribution of specific adaptations across a landscape of serpentine patches that vary in size and level of nickel enrichment, thereby testing general evolutionary-ecological theories about the relationship between specialization and fitness trade-offs. Undergraduates will be involved in characterization of the physiology, taxonomy, genetics, and genomics of Mesorhizobia during a course based research experience. Additionally, outreach will be performed to K-12 schools to expose these students to STEM research.<br/><br/>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.