Synthetic microbial ecology and the dynamic interplay between microbial genotypes

Abstract

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

The rate of environmental fluctuations shapes ecological dynamics in a two‐species microbial system

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Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

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Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists

“…Microbes are ubiquitous; they are therefore an object of interest for research ranging from detailed organ-specific physiology to large-scale ecological issues. Microbiology also harbors a proven potential to direct and propel technical and conceptual proceedings in a variety of contexts (biomedical, agricultural, and industrial, among others) and has been central to the development of many of the most essential experimental tools in modern biology (from PCR [1] to CRISPR [2][3][4]), and for constructing miniature models of ecological and evolutionary processes [5][6][7][8][9][10][11][12]. Microbiology was among the first biological disciplines to embrace an interdisciplinary approach through the research by Esty and Meyer on Clostridium botulinum, in 1922 [13].…”