Bacteria-phage coevolution with a seed bank

Abstract

Dormancy is an adaptation to living in fluctuating environments. It allows individuals to enter a reversible state of reduced metabolic activity when challenged by unfavorable conditions. Dormancy can also influence species interactions by providing organisms with a refuge from predators and parasites. Here we test the hypothesis that, by generating a seed bank of protected individuals, dormancy can modify the patterns and processes of antagonistic coevolution. We conducted a factorially designed experiment where we passaged a bacterial host (Bacillus subtilis) and its phage (SPO1) in the presence versus absence of a seed bank consisting of dormant endospores. Owing in part to the inability of phages to attach to spores, seed banks stabilized population dynamics and resulted in minimum host densities that were 30-fold higher compared to bacteria that were unable to engage in dormancy. By supplying a refuge to phage-sensitive strains, we show that seed banks retained phenotypic diversity that was otherwise lost to selection. Dormancy also stored genetic diversity. After characterizing allelic variation with pooled population sequencing, we found that seed banks retained twice as many host genes with mutations, whether phages were present or not. Based on mutational trajectories over the course of the experiment, we demonstrate that seed banks can dampen bacteria-phage coevolution. Not only does dormancy create structure and memory that buffers populations against environmental fluctuations, it also modifies species interactions in ways that can feed back onto the eco-evolutionary dynamics of microbial communities.

Phage-Defense Systems Are Unlikely to Cause Cell Suicide

“…Instead, it is far more likely that rather than causing cell death, which, in general, has not been shown, cells reduce metabolism during phage attack, and a subpopulation of cells enters the dormant (persister) state. The benefits of dormancy include (i) providing increased time for host-encoded phage-defense systems to function; (ii) slowing viral replication by depriving the phage of its requisite nucleotides and proteins; (iii) providing time for spacer accumulation for CRISPR–Cas [ 28 ]; (iv) increasing genetic diversity [ 29 ]; and (v) reducing bacteria–phage coevolution [ 29 ].…”

“…Similarly, growth-inhibited cells have more spacers [ 32 ]. The fourth and fifth points have been established for bacteria that form spores during phage attack [ 29 ], and since persister cells are dormant [ 33 ], it should hold for them as well.…”

“…Viruses 2023, 15, x FOR PEER REVIEW 3 of 5 time for spacer accumulation for CRISPR-Cas [28]; (iv) increasing genetic diversity [29]; and (v) reducing bacteria-phage coevolution [29]. Evidence of the first point for the advantages of dormancy includes the fact that CRISPR-Cas has been shown to act first in phage defense, followed by restriction/modification systems in Listeria spp.…”

Phages produce persisters

“…Becoming persistent (i.e. dormant) is advantageous for bacteria to combat phages since slow growth/dormancy (i) increases time for phage‐defence systems to function, (ii) slows production of phage‐dependent proteins and nucleic acids, (iii) increases time for spacer acquisition for CRISPR‐Cas (van Beljouw et al., 2022 ), (iv) enhances genetic diversity (Schwartz et al., 2023 ), and (v) reduces bacteria‐phage coevolution (Schwartz et al., 2023 ). For example, activation of the MqsR/MqsA/MqsC tripartite toxin/antitoxin system in E. coli by phage T2 attack results in cells entering the persister state, which enables the EcoK McrBC restriction system to eliminate T2 phages (Fernández‐García et al., 2024 ).…”