Adaptations Accumulated under Prolonged Resource Exhaustion Are Highly Transient

Abstract

Many nonsporulating bacterial species can survive for years within exhausted growth media in a state termed long-term stationary phase (LTSP). We have been carrying out evolutionary experiments aimed at elucidating the dynamics of genetic adaptation under LTSP. We showed that Escherichia coli adapts to prolonged resource exhaustion through the highly convergent acquisition of mutations. In the most striking example of such convergent adaptation, we observed that across all independently evolving LTSP populations, over 90% of E. coli cells carry mutations to one of three specific sites of the RNA polymerase core enzyme (RNAPC). These LTSP adaptations reduce the ability of the cells carrying them to grow once fresh resources are again provided. Here, we examine how LTSP populations recover from costs associated with their adaptation once resources are again provided to them. We demonstrate that due to the ability of LTSP populations to maintain high levels of standing genetic variation during adaptation, costly adaptations are very rapidly purged from the population once they are provided with fresh resources. We further demonstrate that recovery from costs acquired during adaptation under LTSP occurs more rapidly than would be possible if LTSP adaptations had fixed during the time populations spent under resource exhaustion. Finally, we previously reported that under LTSP, some clones develop a mutator phenotype, greatly increasing their mutation accumulation rates. Here, we show that the mechanisms by which populations recover from costs associated with fixed adaptations may depend on mutator status. IMPORTANCE Many bacterial species can survive for decades under starvation, following the exhaustion of external growth resources. We have previously shown that bacteria genetically adapt under these conditions in a manner that reduces their ability to grow once resources again become available. Here, we study how populations that have been subject to very prolonged resource exhaustion recover from costs associated with their adaptation. We demonstrate that rapid adaptations acquired under prolonged starvation tend to be highly transient, rapidly reducing in frequency once bacteria are no longer starved. Our results shed light on the longer-term consequences of bacterial survival under prolonged starvation. More generally, these results may also be applicable to understanding longer-term consequences of rapid adaptation to additional conditions as well.

Reversion is most likely under high mutation supply, when compensatory mutations don’t fully restore fitness costs

“…In this study, we use computational approaches to dissect the population genetic particulars underlying how variation in mutation rates affects the persistence of costly adaptations and the dynamics of compensation and reversion. In agreement with the LTSP experimental results [22], we demonstrate that the likelihood for reversion in lieu of persistence through compensation increases with higher mutation rates. Yet, even at high mutation rates, reversion is unlikely if there exist compensatory mutations that fully alleviate the costs associated with the adaptations (perfect compensation).…”

“…The results of our simulations correspond well with the experimental results that were previously observed in a study of costly adaptations in the RNA polymerase core enzyme in experimental E. coli long-term stationary phase (LTSP) populations. [22] In these experiments (see supplement), 5 clones with the (previously) adaptive mutation, which was shown to carry a cost to growth within fresh rich media, were used to initiate 100 generation serial dilution experiments, to see if they would lose the (previously) adaptive mutation or not. Four of the 5 clones were mutator clones that during LTSP had acquired a mutation within a mismatch repair gene, leading to substantially higher mutation rate.…”

“…The experimental results discussed in the manuscript can be found in the original reference. [22] All code is available on github: https://github.com/pleunipennings/CompensatoryEvolution.…”

“…[3] While these mutations are adaptive under LTSP they carry a cost that manifests in poorer growth in fresh media. Intriguingly, a recent study found that the tendency of RNAPC adaptations to persist within fresh media was related to the mutation rate [22]: non-mutator lineages recovered through compensatory mutations, while mutator clones (∼ 110 − 260 fold higher mutation rates than the wild type, W T ) that were able to recover near ancestral growth rates did so through reversion. Though these specific results were not rigorously explained, the general findings are in line with a vast literature supporting the role of mutation rate in dictating the dynamics of adaptive evolution in microbes [23], [24].…”

Endurance of extremely prolonged nutrient prevention across kingdoms of life

“…This incremental diversity is achieved by a mutator effect originating from mutations or alteration in the expression in DNA damage repair factors ( Avrani et al., 2017 ; Chib et al., 2017 ), error-prone SOS-induced DNA polymerases ( Avrani et al., 2017 ; Corzett et al., 2013 ; Yeiser et al., 2002 ), oxidative stress factors such as OxyR, and upregulation of genes coding for insertion sequences and putative transposases ( Arunasri et al., 2014 ). Moreover, the appearance of the mutations is dynamic and they are highly transient ( Avrani et al., 2020 ; Katz et al., 2021 ). To conclude, it seems that a diverse culture containing many different genotypes is a key factor in EPNP phase survival.…”