April 2022 - Volume 18, Number 2

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Organic Biomarkers

Sebastian Naeher, Xingqian Cui, and Roger Summons Guest Editors

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Biomarkers are molecular fossils that are preserved in a wide range of environmental archives (e.g., soils, sediments, sedimentary rocks, and petroleum systems). This issue introduces biomarkers and their compound­specific stable isotope compositions to study fundamental biogeochemical processes and their application as proxies for environmental and climate reconstructions. Molecular biosignatures can be used to study the evolution of life, transitions in ocean plankton over time, the microbiota of extreme environments such as hydrothermal systems and the deep­ crustal biosphere, and to search for signs of life beyond Earth. Important new discoveries are typically the result of the development and deployment of improved instrumental techniques, multidisciplinary research  approaches, and the combination of organic biogeochemistry with the new tools of molecular biology.

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2022 Topics

Thematic Articles

Biomarkers: Molecular Tools to Study Life, Environment, and Climate

By Sebastian Naeher, Xingqian Cui, and Roger E. Summons


Life on Earth produces innumerable structurally diverse biomolecules. Biomarkers, a subset of these compounds, are sufficiently specific in the structure that they serve as tracers of organisms present in the environment or preserved in the geological record. Biomarkers can be used as proxies for organisms and the biogeochemical processes they mediate or to which they respond. They can help to document and understand processes that are other- wise difficult to study, and their fossil derivatives can be used to reconstruct past ecosystems, environmental conditions, and climate variations. Biomarker science interfaces with biology, chemistry, environmental, and Earth sciences, and provides valuable opportunities to learn more about how the Earth system has evolved over time.

Contributions of Genomics to Lipid Biomarker Research: From Paleoclimatology to Evolution

By Laura Villanueva and Marco J.L. Coolen


Lipid biomarkers can be preserved over long geological timescales. They are widely used as taxonomic markers of past and present microbial communities and as parts of organic paleoclimate proxies. However, questions remain regarding the precise biological sources and evolution of the acquisition of specific lipids, and why and how they are synthesized. In the last two decades, the use of DNA-based approaches has proven to be key in unraveling some of these questions. As methodological approaches improve, (paleo) genomics increasingly supports lipid biomarker research. Here, we provide an overview of the usefulness of DNA-based approaches over the years, including ancient sedimentary DNA research and phylogenomics, and a perspective on the upcoming challenges of this field.

Biomarkers in the Precambrian: Earth’s Ancient Sedimentary Record

By Christian Hallmann, Katherine L. French, and Jochen J. Brocks


The hydrocarbon remnants of biologically diagnostic lipids inform our understanding of Earth’s early ecosystems, particularly where morpho- logical vestiges of biology are absent or ambiguous. Yet both the analysis and interpretation of ancient biomarkers require scrutinous approaches. Here, we describe the status quo of Precambrian biomarker geochemistry with four examples that highlight current challenges and opportunities.

Biomarkers in Extreme Environments on Earth and the Search for Extraterrestrial Life in Our Solar System

By Florence Schubotz, Mark A. Sephton, and Sylvie Derenne


Our appreciation of the potential distribution of life in the Solar System has been impacted by the discovery that organisms are able to occupy the most extreme environments on Earth. The persistence of life in the deepest parts of oceans, the deep sedimentary and crustal biosphere accessed by deep drill holes, hot springs, deserts, and polar regions has led to diverse hypotheses regarding the potential for extraterrestrial life on other planets. This chapter provides an overview on how scientists explore the habitability of other planets and moons of our Solar System and far away in outer space and how future space missions aim to find evidence for extraterrestrial life.

Advancing Analytical Frontiers in Molecular Biomarker Research Through Spatial and Mass Resolution

By Amy M. McKenna, Paul D. Zander, and Lars Wörmer


Analytical developments have been crucial for the advancement of molecular biomarker research in the Earth sciences. In this chapter, we focus on two areas where recent technological developments have profoundly impacted the use and relevance of molecular organic biomarkers: (1) the increase in spatial resolution heralded by imaging techniques, which results in biomarker-based paleoenvironmental reconstruction with unprecedented temporal resolution; and (2) the accurate, simultaneous characterization of a wide range of compounds in complex matrices enabled by ultra-high- resolution mass spectrometry.

Future Outlook for Applications of Biomarkers and Isotopes in Organic Geochemistry

By John K. Volkman


Organic geochemistry continues to make important contributions to our understanding of how the biogeochemistry of our planet and its environment has changed over time and of the role of human impacts today. This article provides a brief overview of the field and a perspective on how it might develop in the near future. Particular emphasis is placed on biomarkers (compounds with a distinctive chemical structure that can be related to specific organisms) and stable isotopes of carbon, hydrogen, and nitrogen, as these are major tools used by organic geochemists. Many geochemical studies involve a mixture of disciplines and so this article also focuses on how this research area can complement work in other fields.