PAPM EAGER: Microwell array platform for high-throughput screening and discovery of microbial interactions

Kansas State University, Manhattan KS

Investigators

Abstract

This project aims to develop a new tool for the discovery of interactions occurring within root-associated bacterial communities. Thousands of different bacteria persistently live on plant roots where bacterial interactions help shape these communities and are a critical factor in determining plant health. Traditional approaches test only a few interactions at a time, leaving many bacterial communities poorly characterized. By simultaneously testing thousands of different bacterial interactions, our approach will greatly accelerate the pace of discovery. Uncovering these interactions will aid efforts to manipulate bacterial communities to improve food production and environmental decontamination efforts. Our method will be highly adaptable, allowing for examination of any microbial community and for use in any microbiology laboratory. The project involves an interdisciplinary team of engineers and microbiologists that will apply recent advances in microfabrication with concepts from microbial ecology and genetics, thereby providing interdisciplinary training for a post-doctoral researcher and a graduate student. In addition, the project will support an interactive public outreach program at the Flint Hills Discovery Center illustrating the impact of land use management practices on microbiome diversity in the Flint Hills ecoregion, as well as how micro- and nanotechnologies can be used to improve our understanding of microbes. Microbe-microbe interactions influence microbial community dynamics, composition, and impact on the host. This project aims to develop a high-throughput screening approach for identifying bacterial species that impact a focal bacterial species. The screening platform will use a microwell array to create thousands of unique pairings between the focal species and different bacterial species within a microbiome. Cell pairs will be trapped within their respective wells using a polymer membrane and then monitored with a fluorescent microscope for effects on the focal species. Wells showing enhancement or suppression of focal species function will be extracted and the antagonizing or promoting species will be sequenced for identification. We will validate this technology platform with two screens of Helianthus annuus microbiomes sampled from sites under different land use management regimes at the Konza Long-Term Ecological Research (LTER) site. The first screen will identify bacteria that antagonize or promote the growth of the generalist plant pathogen Agrobacterium tumefaciens. To target specific mechanisms of microbial interaction, the second screen will identify microbiome members that either positively or negatively influence induction of A. tumefaciens' quorum sensing system. The established platform will be low-cost, simple to operate, and applicable for discovery in any microbiome.