Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences

Abstract

Generalist bacterial predators are likely to strongly shape many important ecological and evolutionary features of microbial communities, for example by altering the character and pace of molecular evolution, but investigations of such effects are scarce. Here we report how predator-prey interactions alter the evolution of fitness, genomes and phenotypic diversity in coevolving bacterial communities composed of Myxococcus xanthus as predator and Escherichia coli as prey, relative to single-species controls. We show evidence of reciprocal adaptation and demonstrate accelerated genomic evolution specific to coevolving communities, including the rapid appearance of mutator genotypes. Strong parallel evolution unique to the predator-prey communities occurs in both parties, with predators driving adaptation at two prey traits associated with virulence in bacterial pathogens—mucoidy and the outer-membrane protease OmpT. Our results suggest that generalist predatory bacteria are important determinants of how complex microbial communities and their interaction networks evolve in natural habitats.

The Predation Strategy of Myxococcus xanthus

“…However, it has not been reported, whether the T6SS and MXAN_0050 contribute to killing of other species for biomass acquisition during predation. A recent study reports that the survival of E. coli in prolonged co-culture with M. xanthus correlates with mutation of the E. coli outer membrane protease, OmpT (Nair et al, 2019). This led to the intriguing suggestion that pre-lytic factors secreted by M. xanthus might be activated by the prey itself, indicating a putative mechanism to limit lysis to the prey cells.…”

“…Also, biofilm-forming E. coli with a matrix of curli are less sensitive to predation by M. xanthus than non-biofilm producing mutants (DePas et al, 2014). Recently, co-evolution experiments with E. coli and M. xanthus demonstrated that predation, in fact, selects toward a mucoid prey phenotype (Nair et al, 2019). Similarly, a galactoglucane-producing Sinorhizobium meliloti strain is more resistant toward M. xanthus predation compared to the non-mucoid mutant (Pérez et al, 2014).…”

Hidden paths to endless forms most wonderful: Complexity of bacterial motility shapes diversification of latent phenotypes

“…The shared features of all MyxoEE-3 treatments have been described previously [ 46 – 48 ] and a list of distinct treatments can be found in Additional file 1 , Table S3 of [ 46 ]. Other MyxoEEs from which studies have already been published are hereby correspondingly named MyxoEE-1 [ 80 ], MyxoEE-2 [ 81 , 82 ], MyxoEE-4 [ 83 ], MyxoEE-5 [ 84 ] and MyxoEE-6 [ 85 ].…”

Copper and Melanin Play a Role in Myxococcus xanthus Predation on Sinorhizobium meliloti

“…Bacterial predation is increasingly being postulated as a crucial factor in biodiversity due to its potential role in controlling and shaping bacterial populations in the environment (Chase et al, 2002;Gallet et al, 2007;Nair et al, 2019). In bacterial predatory processes, it is not only the predator that plays an active role in attacking and killing the prey, the characteristics of the prey are also decisive.…”

“…In the case of Streptomyces coelicolor, cells respond with antibiotic overproduction and by altering multicellular development (Pérez et al, 2011). The presence of galactoglucan protects Sinorhizobium meliloti from being killed by M. xanthus (Pérez et al, 2014), and co-evolution experiments with M. xanthus and Escherichia coli as its prey have demonstrated that the predator induces changes to prey traits such as the production of mucus and the outer membrane protease OmpT (Nair et al, 2019). In the case of Bacillus, B. subtilis produces bacillaene and spore-filled megastructures in response to predation (Müller et al, 2014(Müller et al, , 2015, while B. licheniformis escapes from M. xanthus predation by deactivating the antibiotic myxovirescin (Wang et al, 2019).…”