Mutualism-enhancing mutations dominate early adaptation in a microbial community

Venkataram, Sandeep; Kuo, Huan-Yu; Hom, Erik F. Y.; Kryazhimskiy, Sergey

doi:10.1101/2021.07.07.451547

Cited by 17 publications

(16 citation statements)

References 147 publications

(267 reference statements)

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“…the relative abundances of all species) after the member species evolved all together compared to them having evolved alone [152]. In contrast, Venkataram et al found that the interaction between yeast Saccharomyces cerevisiae and alga Chlamydomonas reinhardtii shifted more repeatably towards stronger mutualism when yeast evolved in the presence of the alga than alone [171]. Thus, species interactions appear to affect repeatability, but further studies will be needed to understand this effect.…”

Section: Community Evolution In the Labmentioning

confidence: 98%

“…In Box 3, we use the study by Meroz et al [158] to illustrate the potential for community evolution experiments to address some of these questions. While research in these directions is at its earliest stages, the initial results are encouraging [152,158,171]. One important potential outcome of this work would be to identify general rules for predicting a system's evolutionary repeatability based on its features.…”

Section: Which Features Of the Community Predict The Repeatability Of...mentioning

confidence: 98%

“…Identifying features of the community or the environment that predict the repeatability of community evolution is an emerging area of research (see Section 4.2 below). In particular, two recent studies tested an intriguing hypothesis that species interactions influence the repeatability of community evolution [152,171]. Researchers compared communities formed by coevolved species with those formed by the same species evolved alone in otherwise identical abiotic conditions.…”

Section: Community Evolution In the Labmentioning

confidence: 99%

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Evolutionary repeatability of emergent properties of ecological communities

Venkataram¹,

Kryazhimskiy²

2022

Preprint

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Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (1) Is the observed degree of repeatability surprising? (2) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (3) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics.

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Section: Community Evolution In the Labmentioning

confidence: 98%

Section: Which Features Of the Community Predict The Repeatability Of...mentioning

confidence: 98%

Section: Community Evolution In the Labmentioning

confidence: 99%

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Evolutionary repeatability of emergent properties of ecological communities

Venkataram¹,

Kryazhimskiy²

2022

Preprint

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“…That evolutionary and ecological changes often go together has been most clearly shown in controlled experiments on synthetic microbial communities: evolution can change the way microbes consume resources or otherwise interact with each other (11–15). This leads to environmental changes that modify selection pressures, forcing lineages into new evolutionary paths (16–21). Complex adaptive landscapes have been hypothesized to chiefly shape the feedback between ecology and evolution in microbial communities (19, 22), but it is still unclear how diversification and other ecological shifts change those landscapes.…”

Section: Introductionmentioning

confidence: 99%

Quantifying the Local Adaptive Landscape of a Nascent Bacterial Community

Ascensao

Wetmore

Good

et al. 2022

Preprint

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The fitness effects of all possible mutations available to an organism largely shapes the dynamics of evolutionary adaptation. Tremendous progress has been made in quantifying the strength and abundance of selected mutations available to single microbial species in simple environments, lacking strong ecological interactions. However, the adaptive potential of strains that are part of multi-strain communities remains largely unclear. We sought to fill this gap for a stable community of two closely related ecotypes ("L" and "S") shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE). To this end, we engineered genome-wide barcoded transposon libraries and developed a computational inference pipeline to measure the fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different conditions. We found that the fitness effect of most gene knockouts sensitively depends on the genetic background and the ecological conditions, as set by environmental perturbations and the relative frequency of both ecotypes. Despite the idiosyncratic behavior of individual knockouts, we still see consistent statistical patterns of fitness effect variation across both genetic background and community composition. The background dependence of mutational effects appears to reflect widespread changes in which gene functions are important for determining fitness, for all but the most strongly interacting genes. 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 drive adaptive potential in recently diverged, coexisting ecotypes.

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“…While application of barcoding initially focussed on adaptive evolution in single populations of model microbes, particularly yeast ( Saccharomyces cerevisiae ) (Blundell and Levy 2014; Cvijović et al 2018) and Escherichia coli (Jasinska et al 2020), strategies have since been devised for studying the evolution of cancer using barcoded lung cancer cells in mice (Rogers et al 2018) and quantification of eco-evolutionary dynamics in microbial communities (Venkataram et al 2022). The potential for extending strategies and applications is considerable, ranging from tracing object provenance (Nguyen Ba et al 2022), enhancing experimental power through mutant-multiplexing (Jackson et al 2020), extending understanding of microbiome transmission (Vasquez et al 2021), to the study of demographic changes during colonisation of new environments (Brettner et al 2022).…”

Section: Introductionmentioning

confidence: 99%

Barcoding populations ofPseudomonas fluorescensSBW25

Theodosiou

Farr

Rainey

2022

Preprint

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In recent years evolutionary biologists have developed increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.

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Mutualism-enhancing mutations dominate early adaptation in a microbial community

Cited by 17 publications

References 147 publications

Evolutionary repeatability of emergent properties of ecological communities

Evolutionary repeatability of emergent properties of ecological communities

Quantifying the Local Adaptive Landscape of a Nascent Bacterial Community

Barcoding populations ofPseudomonas fluorescensSBW25

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