The Macroevolutionary Consequences of Niche Construction in Microbial Metabolism

Djordje Bajić; María Rebolleda-Gómez; Martha M Muñoz; Álvaro Sánchez

doi:10.3389/fmicb.2021.718082

The Macroevolutionary Consequences of Niche Construction in Microbial Metabolism

Front Microbiol. 2021 Oct 4:12:718082. doi: 10.3389/fmicb.2021.718082. eCollection 2021.

Authors

Djordje Bajić^{1

2}, María Rebolleda-Gómez^{1

2

3}, Martha M Muñoz¹, Álvaro Sánchez^{1

2}

Affiliations

¹ Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.
² Microbial Sciences Institute, Yale University, West Haven, CT, United States.
³ Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.

Abstract

Microorganisms display a stunning metabolic diversity. Understanding the origin of this diversity requires understanding how macroevolutionary processes such as innovation and diversification play out in the microbial world. Metabolic networks, which govern microbial resource use, can evolve through different mechanisms, e.g., horizontal gene transfer or de novo evolution of enzymes and pathways. This process is governed by a combination of environmental factors, selective pressures, and the constraints imposed by the genetic architecture of metabolic networks. In addition, many independent results hint that the process of niche construction, by which organisms actively modify their own and each other's niches and selective pressures, could play a major role in microbial innovation and diversification. Yet, the general principles by which niche construction shapes microbial macroevolutionary patterns remain largely unexplored. Here, we discuss several new hypotheses and directions, and suggest metabolic modeling methods that could allow us to explore large-scale empirical genotype-phenotype-(G-P)-environment spaces in order to study the macroevolutionary effects of niche construction. We hope that this short piece will further stimulate a systematic and quantitative characterization of macroevolutionary patterns and processes in microbial metabolism.

Keywords: diversification; genotype-by-environment (G×E) interaction; genotype-phenotype (G-P) map; innovation; macroevolution; metabolism; niche construction; non-commutative epistasis.