Multifactorial Competition and Resistance in a Two-Species Bacterial System

Abstract

Microorganisms exist almost exclusively in interactive multispecies communities, but genetic determinants of the fitness of interacting bacteria, and accessible adaptive pathways, remain uncharacterized. Here, using a two-species system, we studied the antagonism of Pseudomonas aeruginosa against Escherichia coli. Our unbiased genome-scale approach enabled us to identify multiple factors that explained the entire antagonism observed. We discovered both forms of ecological competition–sequestration of iron led to exploitative competition, while phenazine exposure engendered interference competition. We used laboratory evolution to discover adaptive evolutionary trajectories in our system. In the presence of P. aeruginosa toxins, E. coli populations showed parallel molecular evolution and adaptive convergence at the gene-level. The multiple resistance pathways discovered provide novel insights into mechanisms of toxin entry and activity. Our study reveals the molecular complexity of a simple two-species interaction, an important first-step in the application of systems biology to detailed molecular dissection of interactions within native microbiomes.

Magnitude and mechanism of siderophore-mediated competition in bacterial interactions

“…Overall, our findings support the hypothesis that siderophores in environmental systems inhibit other bacteria that lack the specific siderophore receptor system, as supported by previous observational studies (Vachée et al, 1997;Gram et al, 1999;Khare and Tavazoie, 2015). We argue that inhibition is highly efficient in kinetically controlled, saturated systems, and that the competitive benefits obtained by siderophore secretion might surpass the benefit of making iron more available, e.g., if iron is not limiting growth per se.…”

“…Several mathematical models of the effects of siderophores on competitive interactions support this view (Eberl and Collinson, 2009;Fgaier and Eberl, 2010;2011). Also, inhibition of bacterial growth has been linked to the presence of siderophores in various natural and engineered environments (Vachée et al, 1997;Gram et al, 1999;Khare and Tavazoie, 2015).…”

The guanidinobutyrase GbuA is essential for the alkylquinolone‐regulated pyocyanin production during parasitic growth of Pseudomonas aeruginosa in co‐culture with Aeromonas hydrophila

“…Therefore, the co-culture represents a useful model system to screen for genes involved in virulence regulation that might also be important in infection processes. To this end, our study is another example for the value of bacterial co-cultures for studying important traits of the ecophysiology of P. aeruginosa, such as QS, biocide resistance and biofilm formation Chu et al, 2012;Jagmann et al, 2015;Khare and Tavazoie, 2015).…”

A Moving Target: The Megaplasmid pMPPla107 Sensitizes Cells to an Inhibitory Agent Conserved AcrossPseudomonas spp

“…Bacteria exist in complex ecological networks where interactions between community members range from mutualistic to antagonistic. Individual strains have therefore developed a variety of methods to interact with and/or outcompete surrounding bacterial cells including the production of secondary metabolites that can inhibit or allow growth of various microorganisms, as well as bacteriocins that kill target cells with high specificity (1)(2)(3)(4)(5)(6)(7)(8)(9). Secondary metabolites can also provide neighboring microbes a previously missing metabolic resource allowing for colonization of previously uninhabitable niches (10,11).…”