Postdoctoral Fellowship: PRFB: Investigating DNA transfer-driven ecological relationships as a Rule of Life

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2024, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment, and Phenotypes. The fellowship supports research and training of the fellow that will contribute to the area of Rules of Life in innovative ways. This fellowship will explore ways in which organisms are connected to one another, across different levels of biological organization.

Species may be linked spatially by occupying the same physical area, or ecologically by interactions or competition for resources. However, it remains unknown what genome (DNA) level features facilitate these interactions or how those features are modified when organisms become ecologically linked or co-dependent. This project will investigate instances of genome-to-genome interactions and use this information to show how organisms within microbial communities have been connected to each other over time.

This research will give insights into how organisms cooperate on the ecosystem scale, how to identify and characterize these interactions, and how to apply this framework across diverse and changing environments. Research activities will be complemented by outreach efforts designed to educate the public about local biodiversity and microscopy.

DNA transfer, or the horizontal movement of genetic material from one genome to another, can serve as a record of which organisms have come in contact, directly or indirectly, throughout evolutionary history. Using this idea of “genome connectivity”, this fellowship will generate data from diverse microbial communities to identify patterns of DNA transfers and use them to uncover taxa or trophic level-specific trends to model past and present ecological relationships.

Historically, information encoded in genomes was thought to primarily travel vertically, from parent to offspring. However, it has now been well-established that organisms across all domains of life frequently exchange genetic information horizontally; when whole genes are transferred and retained within new genomes, they often encode adaptive functions.

Most research on DNA transfer has focused on individual species but this phenomenon has not yet been investigated on the community level, where transfers may be driving or driven by the ecological interactions of resident organisms or stressors they encounter. Using a combination of theoretical, multi-omics, and phylogenomic approaches, this project will build a pipeline to directly characterize microbial communities, that takes a bottom-up approach from genomes to ecology and can be used as a predictive way to characterize past and present stress responses within an environment.

The fellow will be trained in machine learning, -omics, and ecological modeling approaches and will pass on these skills to undergraduates who will be mentored as part of this project. The work will be integrated into broader impact efforts, including BioBlitz events to catalog local microbes, and to develop microscope-sharing programs to inspire a new generation of naturalists.

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.