Multistep diversification in spatiotemporal bacterial-phage coevolution

Abstract

The evolutionary arms race between phages and bacteria, where bacteria evolve resistance to phages and phages retaliate with resistance-countering mutations, is a major driving force of molecular innovation and genetic diversification. Yet attempting to reproduce such ongoing retaliation dynamics in the lab has been challenging; laboratory coevolution experiments of phage and bacteria are typically performed in well-mixed environments and often lead to rapid stagnation with little genetic variability. Here, co-culturing motile E. coli with the lytic bacteriophage T7 on swimming plates, we observe complex spatiotemporal dynamics with multiple genetically diversifying adaptive cycles. Systematically quantifying over 10,000 resistance-infectivity phenotypes between evolved bacteria and phage isolates, we observe diversification into multiple coexisting ecotypes showing a complex interaction network with both host-range expansion and host-switch tradeoffs. Whole-genome sequencing of these evolved phage and bacterial isolates revealed a rich set of adaptive mutations in multiple genetic pathways including in genes not previously linked with phage-bacteria interactions. Synthetically reconstructing these new mutations, we discover phage-general and phage-specific resistance phenotypes as well as a strong synergy with the more classically known phage-resistance mutations. These results highlight the importance of spatial structure and migration for driving phage-bacteria coevolution, providing a concrete system for revealing new molecular mechanisms across diverse phage-bacterial systems.

Fight not flight: parasites drive the bacterial evolution of resistance, not escape

“…This is similar to past work where more homogenous environments accelerated the coevolution of bacterial resistance with phages (Brockhurst et al 2003). Additionally, we found that evolved populations in our local phage treatment maintained phage susceptibility that could enable coexistence of bacteria and phages (Fig 3), consistent with past work that spatial structure and heterogeneity increases host-parasite coexistence (Brockhurst et al 2006;Tamar and Kishony 2022).…”

Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies

“…Changes in the Klebsiella capsule are a primary mechanism of resistance to temperate phages, as shown for virulent phages ( Hesse et al, 2020 ; Tan et al, 2020 ; Cai et al, 2019 ; Majkowska-Skrobek et al, 2021 ). More broadly, fast inactivation of the capsule confirms that alteration of the host recognition determinants frequently results in the protection of bacterial populations against phage ( Mutalik et al, 2020 ; Westra et al, 2015 ; Shaer Tamar and Kishony, 2022 ). However, after six days of co-evolution, the frequencies of both strains in MMC reached an equilibrium.…”

Rapid bacteria-phage coevolution drives the emergence of multiscale networks

“…Although we were able to characterize the molecular underpinnings of major features of the interaction network, we also note that more phenotypic and genomic variation exists which we have yet to explain, further highlighting the complexity that can evolve rapidly (i.e., within 100 to 200 generations). Although the molecular mechanisms identified in our flasks will differ across vastly different taxa and ecological communities ( 24 , 34 ), our work demonstrates how inherent coevolutionary processes can give rise to complex patterns that abound in natural ecosystems.…”

“…More broadly, previous observations of geographically isolated modules have suggested that spatial separation assists in the formation of such patterns (5,8,9,24). Although spatial structure certainly plays an important role in generating and maintaining diversity (35), it is also possible that modules may form in sympatry, and then separate in space over time.…”

“…Modules can form as a result of fluctuating selection dynamics ( 18 , 20 , 22 ) or the presence of different phage defense elements that confer specialized immunity ( 23 ). However, experiments have been unable to reproduce PBINs with multiscale structure (modular at broad scales and nested within modules) as observed in nature without artificially providing spatial isolation between evolving subpopulations ( 24 ). These findings reinforce the assumption that spatial structure and/or other external influences are a prerequisite for the evolution of intricate ecological networks.…”