One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity

Abstract

Many bacteria cycle between sessile and motile forms in which they must sense and respond to internal and external signals to coordinate appropriate physiology. Maintaining fitness requires genetic networks that have been honed in variable environments to integrate these signals. The identity of the major regulators and how their control mechanisms evolved remain largely unknown in most organisms. During four different evolution experiments with the opportunist betaproteobacterium Burkholderia cenocepacia in a biofilm model, mutations were most frequently selected in the conserved gene rpfR. RpfR uniquely integrates two major signaling systems—quorum sensing and the motile–sessile switch mediated by cyclic-di-GMP—by two domains that sense, respond to, and control the synthesis of the autoinducer cis-2-dodecenoic acid (BDSF). The BDSF response in turn regulates the activity of diguanylate cyclase and phosphodiesterase domains acting on cyclic-di-GMP. Parallel adaptive substitutions evolved in each of these domains to produce unique life history strategies by regulating cyclic-di-GMP levels, global transcriptional responses, biofilm production, and polysaccharide composition. These phenotypes translated into distinct ecology and biofilm structures that enabled mutants to coexist and produce more biomass than expected from their constituents grown alone. This study shows that when bacterial populations are selected in environments challenging the limits of their plasticity, the evolved mutations not only alter genes at the nexus of signaling networks but also reveal the scope of their regulatory functions.

The BDSF quorum sensing receptor RpfR regulates Bep exopolysaccharide synthesis in Burkholderia cenocepacia via interaction with the transcriptional regulator BerB

“…2A , cepacian production was significantly reduced in the single mutants Δ bceC and Δ gtaB and completely abolished in the Δ bceC Δ gtaB double mutant, indicating that both cepacian clusters bce-I and bce-II are required for high-level cepacian production. Inactivation of rpfR had no apparent effect on cepacian production, suggesting that RpfR is not involved in the regulation of this EPS molecule, in agreement with a recent transcriptome analysis 21 . Phenotypic characterization of the strains on NYG agar plates revealed that inactivation of cepacian production (Δ rpfR Δ bceC , Δ rpfR Δ gtaB , and Δ rpfR Δ bceC Δ gtaB) did not abolish the wrinkled phenotype but led to flatter and smoother macrocolonies relative to the Δ rpfR mutant, suggesting that cepacian contributes to the architecture of microcolonies but is not the actual cause of wrinkle formation.…”

Rampant prophage movement among transient competitors drives rapid adaptation during infection

“…S1A). Here, again, the prophage-mediated adaptation was not caused by the addition of new genes but rather by the disruption of an existing regulatory gene, which is a common initial route to increased fitness in new environments ( 38 – 40 ). Furthermore, competition between strains in chronic wounds can generate eco-evolutionary dynamics, where induced prophage can not only infect and kill susceptible competitors and favor resistant types but also produce new genotypes that are adapted to the phage-laden environment.…”

Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes

“…Since the first report introducing the bead-based experiment evolution setup 25 , which primarily focused on the ecological mechanisms that sustained biofilm diversity, numerous follow-up studies have validated the robustness of this model by describing the mutational patterns 59 , genetic properties 53 , 60 – 63 , niche complementarity 64 , 65 , and antibiotic resistance 66 , 67 . Unlike other laboratory-based experimental evolution systems, this simple method is useful for modeling the complex biofilm cycle, including initial attachment, biofilm maturation, dispersal, and recolonization 68 , 69 .…”