Screening Microbial Interactions

Microwell Recovery Arrays for High-Throughput Screening and Discovery of Microbe-Microbe Interactions

Bacteria persistently live in soil and on plant roots and are critical in promoting plant health by aiding the plant in nutrient acquisition, producing plant hormones and protecting the plant from disease. These collections of bacteria are very diverse, and many interactions that occur between different types of bacteria are poorly understood or characterized. We are developing a new experimental tool called the microwell recovery array (MRA) to rapidly and simultaneously screen thousands of different microbial interactions, allowing for identification of those that are critical in shaping root-associated bacterial communities. We anticipate that the MRA platform will greatly accelerate the rate at which important bacterial interactions are discovered. Our current work focuses on discovering interactions that promote or inhibit the function of plant growth promoting rhizobacteria (PGPR) in crops of agricultural importance, such as corn. Uncovering these interactions will inform new microbial consortia that can be used for biofertilizer applications for sustainable food production.

(A) The microbial recovery array (MRA). (B) The MRA screens interactions between a bacterial focal species and individual members of a microbiome. Cells in wells where the focal species function is impacted are removed for genotyping to discover new microbe-microbe interactions.

Publications:

N. Barua, A. M. Herken, N. Melendez-Velador, T.G. Platt, R.R. Hansen, “Photo-addressable microwell devices for rapid functional screening and isolation of pathogen inhibitors from bacterial strain libraries”, Biomicrofluidics, 18, 014107 (2024). doi: 10.10163/5.0188270
N. Barua, K.M. Clouse, D.A. Ruiz Diaz, M.R. Wagner, T.G. Platt, R.R. Hansen, “Screening the maize rhizobiome for consortia that improve Azospirillum brasilense root colonization and plant growth outcomes”, Frontiers in Sustainable Food Systems, 7:1106528 (2023). doi: 10.3389/fsufs.2023.1106528

N. Barua, A.M. Herken, K.R. Stern, S. Reese, R.L. Powers, J.L. Morrell-Falvey, T.G. Platt, and R.R. Hansen, "Simultaneous Discovery of Positive and Negative Interactions Among Rhizosphere Bacteria Using Microwell Recovery Arrays", Frontiers in Microbiology, 11:601788 (2021). doi:10.3389/fmicb.2020.601788

M. Halsted, J.L. Wilmoth, P.A. Briggs, R.R. Hansen, D.P. Briggs, A.C. Timm, and S.T. Retterer. “Development of Transparent Microwell Arrays for Optical Monitoring and Dissection of Microbial Communities”, Journal of Vacuum Science and Technology B, 34, 06KI03 (2016). doi:10.1116/1.4962739

R. R. Hansen, A.N. Timm, C.M. Timm, A.N. Bible, J.L. Morrell-Falvey, D.A. Pelletier, M.L. Simpson, M.J. Doktycz, and S.T. Retterer, “Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development”, PLoS ONE, 11, e0155080 (2016). doi:10.1371/journal.pone.0155080