Systematic Identification of Antimicrobial Proteins Secreted by the Plant Microbiome

The plant environment is teeming with microbes that are attracted to the rich nutrients exuded by the plant host. In order to colonize the highly occupied niche of the rhizosphere, bacteria have ostensibly evolved various mechanisms to hinder microbial competitors. These mechanisms play a role in microbial community assembly at the plant environment and can also be harnessed to control pathogens. However, there is a little understanding of the identity of these molecular mechanisms and their target cells. We study two bacterial secretion systems that are commonly employed by members of the plant microbiome named the Type 6 Secretion System (T6SS) and the extracellular contractile injection system (eCIS). We developed computational algorithms to predict novel antibacterial proteins (effectors) secreted by each of the secretion systems. We scanned genomes of plant-associated bacteria to predict the genes encoding for these antibacterial proteins. We then validated the antimicrobial activity of putative effectors through heterologous expression in bacteria and yeast. This approach has uncovered seven novel antimicrobial proteins families, including the first antibacterial proteins secreted by eCIS. Our results shed light on new mechanisms using which bacteria gain a selective advantage in the plant environment. Harnessing these mechanisms in different agricultural settings can lead to efficient, sustainable biocontrol strategies.