Competitive behaviours in Serratia marcescens are coordinately regulated by a lifestyle switch frequently inactivated in the clinical environment

Opportunistic bacterial pathogens require effective mechanisms to compete with other bacteria and to switch between host and environment-adapted states. The Type VI secretion system (T6SS) occurs widely in Gram-negative bacteria and mediates efficient killing of neighbouring competitors. Here we describe the distribution of T6SSs across the genus Serratia and report the unexpected discovery that a highly-conserved antibacterial T6SS is differentially active between closely-related clinical isolates of Serratia marcescens. By combining genomic and experimental approaches, we identified a genus-core two-component system which controls T6SS activity and is subject to very frequent inactivating mutations, exclusively in clinically-derived isolates of S. marcescens. This regulatory system controls a number of lifestyle-related traits at transcriptional and post-translational levels, including T6SS activity, antibiotic production, motility and adhesion. Our data support a model whereby this system represents a conserved, modular switch from sessile to pioneering and aggressive behaviour, which is subject to strong selection pressure in the clinical environment. We observed that near-identical isolates of S. marcescens have different phenotypes relating to anti-bacterial antagonism, motility, and adherence, that correspond with variation in full-length/loss-of-function mutations in betR and reg2. To investigate the role of BetR and Reg2 on S. marcescens, we constructed betR and reg2 mutants from three near-identical isolates in order to compare between full-length and naturally-occuring loss-of-function mutations in these two genes, in otherwise isogenic isolates. Cells were grown for 4.5 hours in liquid LB medium at 37 degrees celcius with shaking, before total RNA was harvested. 4 independent biological replicates for each isolate were performed.