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Lipid biomarkers: molecular tools for illuminating the history of microbial life

Nature Reviews Microbiology volume 20, pages 174–185 (2022)Cite this article

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Abstract

Fossilized lipids preserved in sedimentary rocks offer singular insights into the Earth’s palaeobiology. These ‘biomarkers’ encode information pertaining to the oxygenation of the atmosphere and oceans, transitions in ocean plankton, the greening of continents, mass extinctions and climate change. Historically, biomarker interpretations relied on inventories of lipids present in extant microorganisms and counterparts in natural environments. However, progress has been impeded because only a small fraction of the Earth’s microorganisms can be cultured, many environmentally significant microorganisms from the past no longer exist and there are gaping holes in knowledge concerning lipid biosynthesis. The revolution in genomics and bioinformatics has provided new tools to expand our understanding of lipid biomarkers, their biosynthetic pathways and distributions in nature. In this Review, we explore how preserved organic molecules provide a unique perspective on the history of the Earth’s microbial life. We discuss how advances in molecular biology have helped elucidate biomarker origins and afforded more robust interpretations of fossil lipids and how the rock record provides vital calibration points for molecular clocks. Such studies are open to further exploitation with the expansion of sequenced microbial genomes in accessible databases.

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Fig. 1: Geological timescale of the Earth’s fossil record in the context of planetary oxygenation.
Fig. 2: Commonly referenced lipid biomarkers and their known sources.
Fig. 3: Phylogeny of the proteins essential for biosynthesis of aromatic carotenoids.
Fig. 4: Structural differences between archaeal and bacterial membrane phospholipids.
Fig. 5: Identification of GDGT ring synthase proteins in Sulfolobus acidocaldarius.

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Acknowledgements

This work was supported by a grant from the Simons Collaboration on the Origin of Life through an award (290361FY18) to R.E.S. and by National Science Foundation awards (1752564) to P.V.W and (2044871) to D.A.G.

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Authors and Affiliations

  1. Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA

    Roger E. Summons

  2. Department of Earth System Science, Stanford University, Stanford, CA, USA

    Paula V. Welander

  3. Department of Earth & Planetary Sciences, University of California Davis, Davis, CA, USA

    David A. Gold

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  1. Roger E. Summons
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  2. Paula V. Welander
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  3. David A. Gold
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The authors contributed equally to all aspects of the article.

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Glossary

Warrawoona Group

A geological unit in Western Australia that includes the remains of microorganisms as old as 3.46 billion years.

Pilbara Craton

An ancient fragment of continental crust in Western Australia that includes rocks as old as 3.6 billion years.

Stromatolites

Layered sedimentary structures that form when a microbial community traps and binds sediment grains.

Hopanoids

A class of molecules comprising six C5 isoprene units folded into a pentacyclic ring system.

Accessory pigment

A coloured molecule that absorbs light and works in concert with the primary pigment, typically chlorophyll a.

Sedimentary diagenesis

The processes by which sedimentary rocks and their components became modified over time during burial.

Carbonaceous chondrites

Carbon-rich meteorites composed of small mineral grains and representing some of the post-primitive material in the solar system.

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Summons, R.E., Welander, P.V. & Gold, D.A. Lipid biomarkers: molecular tools for illuminating the history of microbial life. Nat Rev Microbiol 20, 174–185 (2022). https://doi.org/10.1038/s41579-021-00636-2

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