Competition and coevolution drive the evolution and the diversification of CRISPR immunity

Abstract

The diversity of resistance challenges the ability of pathogens to spread and to exploit host populations [1][2][3]. Yet, how this host diversity evolves over time remains unclear because it depends on the interplay between intraspecific competition among host genotypes and coevolution with pathogens. Here we study experimentally the effect of coevolving phage populations on the diversification of bacterial CRISPR immunity across space and time. We demonstrate that the negative-frequency-dependent selection generated by coevolution is a powerful force that maintains host resistance diversity and selects for new resistance mutations in the host. We also find that host evolution is driven by asymmetries in competitive abilities among different host genotypes. Even if the fittest host genotypes are targeted preferentially by the evolving phages they often escape extinctions through the acquisition of new CRISPR immunity. Together, these fluctuating selective pressures maintain diversity, but not by preserving the pre-existing host composition. Instead, we repeatedly observe the introduction of new resistance genotypes stemming from the fittest hosts in each population. These results highlight the importance of competition on the transient dynamics of host-pathogen coevolution.

Dynamics of immune memory and learning in bacterial communities

“…We observed several features that suggest the presence of negative frequency-dependent selection in our model: 1) decreased clone growth rates as clone size increased, 2) cyclic clone size dynamics as immune pairs oscillate in size, and 3) continual turnover in spacer types over time. This is consistent with recent experimental observations of negative frequency-dependent selection in host-pathogen systems [86,31]. Our model also contains the base assumption that phages that can successfully infect dominant bacterial strains will experience positive selection, generating 'kill-the-winner' dynamics that lead to negative frequency-dependent selection for bacteria [35].…”

“…We saw two qualitatively different time shift curves in the experimental data we analyzed: in the long-term laboratory coevolution data, bacteria were more immune to all past phages and less immune to all future phages, while in the wastewater treatment plant data, bacteria were most immune to phages in their present context and less immune to phages in both the past and future. The time shift pattern of the laboratory coevolution data was consistent with experimental time-shift data that is typically said to be indicative of arms-race dynamics [81,82,83,111,86,27], while the wastewater data may be consistent with a "zoomed-out" view of the eventual decline in immunity in both the distant past and distant future [18,31]. Indeed, the distinction between arms race dynamics and fluctuating selection dynamics in time shift experiments may be a question of the timescale being investigated [112,111,87].…”

“…What determines clonal diversity? Many factors that correlate with transient diversity have been experimentally identified, such as phage extinction and slower phage evolution at high bacterial spacer diversity [25, 28] and maintenance of a diverse bacterial population when exposed to diverse phages [24, 27, 31, 75], but a conceptual framework to understand emergent diversity has remained elusive. For instance, while initial high spacer diversity puts low-diversity phage populations under intense pressure to the point of driving them extinct [25, 28], is the same true for emergent bacterial diversity after an extended period of coexistence?…”

“…This discrepancy occurs because bacteria and phage diversity is decoupled in these experiments. Experimental manipulations of CRISPR diversity have focused on changing the number of bacterial spacers present in the population [25,33,28] while keeping phage diversity fixed (and low), with the exception of Guillemet et al [31] who also explored high vs. low phage diversity. In contrast, emergent phage and bacterial diversity were tightly coupled in our model: if bacterial diversity was high, phage diversity was also high.…”

“…The kinetics and interactions of phages and bacteria with CRISPR systems have been the subject of numerous experiments [25, 27, 28, 29, 30, 31]. Some themes have emerged from experimental studies of CRISPR immunity: (a) high spacer diversity relative to phage diversity increases the likelihood of phage extinction [25, 28, 31], (b) bacteria become more immune to phages over time [32, 33, 27, 34], and (c) phages readily gain mutations [35, 23, 36, 37, 38, 34, 31, 39] and sometimes genome rearrangements [24] to escape CRISPR targeting. Explorations of CRISPR immunity in natural environments have also documented ongoing spacer acquisition and phage escape mutations [35, 39].…”