Department of Bioengineering, Stanford University School of Medicine, Stanford, United States
Yangbo Xiao
Department of Bioengineering, Stanford University School of Medicine, Stanford, United States
Jason Peters
Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, United States; Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, United States; Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States
Department of Bioengineering, Stanford University School of Medicine, Stanford, United States; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, United States; Chan Zuckerberg Biohub, San Francisco, United States
Life in a three-dimensional biofilm is typical for many bacteria, yet little is known about how strains interact in this context. Here, we created essential gene CRISPR interference knockdown libraries in biofilm-forming Bacillus subtilis and measured competitive fitness during colony co-culture with wild type. Partial knockdown of some translation-related genes reduced growth rates and led to out-competition. Media composition led some knockdowns to compete differentially as biofilm versus non-biofilm colonies. Cells depleted for the alanine racemase AlrA died in monoculture but survived in a biofilm colony co-culture via nutrient sharing. Rescue was enhanced in biofilm colony co-culture with a matrix-deficient parent due to a mutualism involving nutrient and matrix sharing. We identified several examples of mutualism involving matrix sharing that occurred in three-dimensional biofilm colonies but not when cultured in two dimensions. Thus, growth in a three-dimensional colony can promote genetic diversity through sharing of secreted factors and may drive evolution of mutualistic behavior.
