Effects of Recurring Resource Limitation on Present and Future Evolutionary Responses
Abstract
In nature, microbes commonly inhabit fluctuating environments, since nutrient availability and exposure to other stressors is rarely constant. While experimental evolution approaches have been previously utilized to describe how microbes evolve across a gradient of sustained stress, how this evolution proceeds in response to fluctuating stress is less known. A more thorough understanding of how microbes persist and eventually evolve resistance to fluctuating stress Ð allowing them to thrive in these environments Ð is imperative. Such understanding will aid in overcoming the substantial public-health challenge that resistant microbes pose and enable the harnessing of this adaptive potential to engineer stress-resistant microbes for agriculture and industry. The objective of the proposed research is to characterize specific evolutionary outcomes to a classical example of fluctuating stress in microbial populationsÑfeast and famine. Prior analysis of Escherichia coli populations which have experimentally evolved in response to cycles of either 1-, 10-, or 100-days between nutrient resource replenishment has revealed distinct mutational and phenotypic outcomes. These outcomes range from complex co-dependent interactions and the evolution of extreme trait values in intermediately-starved, 10-day resourcelimited populations, to highly-parallel mutations in global regulators of gene expression in extremely-starved, 100-day resource-limited populations. The proposed aims of this project include the following methods and goals: 1) Utilizing a novel low-cost sequencing technique combined with time-series exometabolomic profiling to resolve the key genes and nutrients underlying evolved cooperative interactions in repeatedly-starved E. coli populations (YIP); 2) Engineering genetic reconstructions of mutations that affect conserved global regulators and conducting RNA-seq to determine how these mutations affect the expression of known and novel transcripts during extreme starvation (YIP). We will additionally engineer Ôcombination mutantsÕ and conduct competition assays to quantify any resulting epistatic interactions that may exist between these mutations (PECASE); 3) Identifying how historical contingency alters the trajectory of adaptation to resource availability by culturing previously evolved E. coli populations in a reciprocal transplant framework and tracking their evolution through whole-population metagenomic sequencing (YIP); and 4) Replaying evolution to distinguish if generalizable patterns exist in how E. coli evolve across a fine-scaled gradient of fluctuating stress. Populations will be cultured in seven different resource-replenishment intervals and their evolution will be tracked through whole-population metagenomic sequencing and extensive phenotyping assays (PECASE). The stated aims are relevant to the mission of the ARO Microbiology Program under the ÔProkaryotic Survival Mechanisms in Challenging and Extreme EnvironmentsÕ thrust. The knowledge gained will shed light on the survival strategies of microbes in the presence of fluctuating stress beyond persistence and the general stress response, and will describe how microbes evolve to eventually thrive under extreme and highly-changeable conditions. Further, as these strategies involve the evolution of intraspecific cooperation and mutation of highlyconserved global regulators, these results are expected to be broadly applicable across the bacterial tree of life.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Jun 25, 2021
- Source ID
- W911NF2110161
Entities
People
- Megan Behringer
Organizations
- Army Contracting Command
- United States Army
- Vanderbilt University