Research

Metabolism mediates the global biogeochemical cycles and supplies the energy and building blocks of all cells on Earth. Reconstructing its evolution is important for many major questions across biological and geological science: How did metabolism emerge, and how has it constrained the long-term evolution of life? How does the metabolic evolution of cells shape the flow of mass and energy through ecosystems? How do metabolic innovations shape Earth’s environment and global climate, and how does global change shape ecosystems and drive biological innovations? What is the role of gradual vs punctuated change in the production of global biodiversity and Earth’s long-term biogeochemical evolution?

A metabolic tree of life: from geochemical roots and adaptive radiations, to ecosystem organization and global climate feedbacks

To help address these questions I have been developing a new approach to reconstructing metabolic evolution that produces trees of metabolic networks. Integrating phylogenetic and metabolic constraints suggests the order in which alternative pathways emerged within a given metabolic sub-network, while preserving continuity of metabolic flux (and thus life) at each node in the tree. Differences in the biochemical properties of phenotypes in turn suggests potential evolutionary driving forces.

Phylometabolomics
Phylometabolic trees reconstruct the evolution of metabolic phenotypes

I began developing this approach to trace the evolution of metabolism back to the roots of the tree of life, with a particular focus on microbes living at deep-sea hydrothermal vents. The general goals of this work are to understand how prebiotic geochemistry gave rise to biochemistry, and how this `chemical selection’ shaped the subsequent diversification of life (see Braakman & Smith 2012, 2013, 2014 and Braakman 2013).

CFixation_Tree
Phylometabolic tree of CO2-fixation (Braakman & Smith, 2012, 2013)

More recently I have been extending this approach to develop more general views of how microbial phenotypes evolve, and how new phenotypes modify the environments and ecosystems in which they emerge. Once continuity of life has been established at the level of metabolism, we can look to features of diversity at other levels (such as population ecology, growth physiology and cell biology) to develop integrative multi-level frameworks of evolution. For this work I have been mainly focusing on microbial ecosystems that dominate the world’s tropical and sub-tropical surface oceans (Braakman, Follows & Chisholm, 2017), but eventually I hope to translate the insights we have gained to other systems and environments.

Going forward another major goal is to identify feedbacks between Earth and the biosphere in their long-term co-evolution. The two main repositories of biospheric and Earth system evolution are the genomic and geologic records, and decoding the logic of the universal chart of metabolism is key in temporally and mechanistically linking them. Major opportunities exist in combining increasingly accurate molecular clock dating of microbial divergences with mechanisms of how their emergent metabolic phenotypes chemically modify their environment. This could help us identify correlations among chemical proxies in geochemical sediment record that may reflect interconnected changes in the Earth’s global elemental cycles that are in turn recorded in the genomic record.

A collaborative trans-disciplinary approach is key in this work, and I have been fortunate to be able to start building a network of wonderful and inspiring colleagues from many different backgrounds. Working together as a community, and collaboratively bridging disciplines at the interface of chemical, biological, geological and complex systems science, I believe we will increasingly be able to tackle the “big questions” of how life and our Earth are intertwined and co-evolve.

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