Biomarkers and Genomics


Life in the Precambrian was dominated by bacteria and archaea, organisms that rarely leave diagnostic cellular remains in the fossil record. However, hydrocarbon biomarkers, the molecular fossils of natural products such as lipids and pigments, can yield a wealth of infor­mation about Precambrian ecosystems. Biomarkers often retain the diagnostic carbon skeleton of their biological precursors and may survive in sedimentary rocks for hundreds of millions of years. Many biomarkers are diagnostic for specific microbial groups such as methanogens, methano­trophs or photo­trophic bacteria and, thus, may give infor­mation about ancient biodiversity. Therefore, biomarkers can answer outstanding questions about Precambrian ecology and evolution, such as how ecosystems responded to the oxygenation of the atmosphere ~2.4 billion years ago, whether Earth oceans were anoxic and sulfidic during the mid-Proterozoic, or how life responded to massive glaciations in the Neoproterozoic.

The Problem

However, there is a major obstacle that hampers the application of biomarkers as paleoenvironmental proxies: the incomplete knowledge of the lipid biosynthetic capacity of living organisms. According to some estimates, less than 1 per cent of microorganisms can be isolated from the environment and grown in pure culture, and the biomarker content of these uncultivated microbes remains almost always unknown. Detecting and describing the lipids and pigments produced by those 99 per cent of microorganisms that can not yet be cultured would boost the value of biomarkers extracted from ancient rocks.

The Solution

The might be able to assign many biomarkers to organisms in the coming decade by combining lipid research with environmental genomics and microbial community proteomics. Of particular interest will be studies of communities where it is possible to reconstruct nearly complete genomes, proteomes and lipid profiles of dominant microorganisms taken directly from modern environments without cultivation. These genomes will be screened for genes involved in lipid and pigment biosynthesis and matched with corresponding enzymes and lipids detected in the same sample. In addition to defining the diversity of as yet unknown branches of the tree of life, this will contribute to new understanding of the phylogenetic distribution of potential biomarkers produced by micro­organisms, even if they evade isolation. The intricate knowledge of the lipid biosynthetic machinery of present ecosystems will then serve to elucidate new biomarkers and biomarker patterns in ancient sedimentary rocks.