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Scholarly Works (3 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2023)

A central problem of evolutionary biology lies in understanding how organisms adapt and evolve in response to environmental and ecological challenges. This thesis delves into the dynamics of evolutionary adaptation and ecology within microbial communities, focusing on Escherichia coli as a model organism. Through a series of three interconnected studies, this thesis illuminates the complex interplay between genetic mutations, environmental pressures, and adaptive strategies that govern microbial evolution.

The first chapter sets the foundation by exploring the genetics of adaptation in a simple E. coli community. Using controlled experimental settings, it examines how specific genetic variations confer survival advantages under varying environmental conditions. This chapter underscores the significance of genetic diversity as a reservoir for adaptive potential, illustrating how even minor genetic changes can lead to significant evolutionary shifts in microbial populations.

Building on the genetic insights from the first chapter, the second chapter shifts focus to ecological interactions and their impact on evolutionary outcomes. Here, the study investigates how E. coli strains can diversify to exploit different ecological niches and the resulting impact on their adaptive trajectories. This chapter reveals the importance of ecological factors in shaping evolutionary pathways, highlighting how microbial communities dynamically respond to ecological constraints and opportunities.

The final chapter extends the discussion to focus on the evolutionary effects of non-adaptive population fluctuations. Using the same E. coli communities, it shows how population fluctuations can arise from differences in offspring number correlations between individuals. These fluctuations are distinct from the classical source of population fluctuations, genetic drift, and can have significant impacts on the trajectory of evolution.

Together, these findings emphasizes the multifaceted nature of evolutionary adaptation in microbial communities. They highlight the critical role of genetic diversity in providing the raw material for evolution, the influence of ecological interactions in directing adaptive pathways, and the effect of non-adaptive processes.

Future research can continue to explore the complex dynamics of microbial evolution, particularly focusing on the interplay between genetic and ecological factors over varying temporal scales. This would not only enhance our understanding of microbial adaptation but also provide insights applicable to broader evolutionary contexts, including those of higher organisms.

    Cover page: The Dynamics of Ecology and Evolution in Simple Experimental Microbial Communities
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2023)
    The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes ("L" and "S") shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE). We engineered genome-wide barcoded transposon libraries to measure the invasion fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different, ecologically relevant conditions. We find consistent statistical patterns of fitness effect variation across both genetic background and community composition, despite the idiosyncratic behavior of individual knockouts. Additionally, fitness effects are correlated with evolutionary outcomes for a number of conditions, possibly revealing shifting patterns of adaptation. Together, our results reveal how ecological and epistatic effects combine to shape the adaptive landscape in a nascent ecological community.
      Cover page: Quantifying the local adaptive landscape of a nascent bacterial community.Creative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2024)
      Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about whether communities can regenerate ecological diversity following ecotype removal or extinction and how the rediversified communities would compare to the original ones. Here, we show that simple two-ecotype communities from the E. coli long-term evolution experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different from the original community in ways relevant to the mechanism of ecotype coexistence-for example, in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, although the rediversified community showed unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species where there are even more potential niches, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.
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