Building the Biomarker Tree of Life

Abstract

the molecular fossils of plants and other non-microscopic eukaryotes. We highlight biomarker research using outstanding recent examples with a pedagogic emphasis on concepts but with no claim for completeness. More encyclopedic reviews were given by Peters et al. (2004) and Brocks and Summons (2004). For readers who desire more background in organic geochemistry, excellent introductions to the nomenclature, chemistry, and biology of lipids can be found in textbooks by Killops and Killops (2005) and Madigan and Martinko (2005). The biomarker principle The origin of biomarkers. In lakes and oceans, the organic matter from dead organisms usually is almost quantitatively (> 99.9%) recycled back into carbon dioxide and water (Hedges and Keil 1995). The biological degradation of most proteins, nucleic acids and carbohydrates proceeds rapidly as dead biomass sinks through the water column, and it continues in the surface layers of the sediments. However, a small fraction of organic matter escapes the remineralization process and accumulates. Molecules that are especially recalcitrant, such as pigments, lipids and many structural macromolecules, will become concentrated (Tegelaar et al. 1989). With the onset of reducing conditions, the remaining sedimentary organic matter is degraded further by anaerobic heterotrophic organisms such as sulfate reducers, fermenters and methanogens (Megonigal et al. 2004); the chemical structure of the remains is altered by biological and chemical processes (Hedges and Keil 1995; Hedges et al. 1997; Rullkötter 1999). These alterations are referred to collectively as diagenesis. Smaller molecular units and degradation-resistant macromolecules are cross-linked and form kerogen, an amorphous and exceedingly complex structural network of biochemical subunits (e.g., Derenne et al. 1991; de Leeuw and Largeau 1993). During the formation of kerogen, vulcanization reactions mediated by sulfur and polysulphides often play an important role in connecting smaller molecular units, such as lipids, to the macromolecular aggregate, thus protecting them against further structural alterations (Sinninghe Damsté and de Leeuw 1990). Over millions of years, and with increasing burial depth and geothermal heat, most lipids will undergo structural rearrangement via cracking and isomerization reactions. These processes create a vast range of homologues and stereo-and structural isomers. Through reduction, elimination and aromatization the biomarkers typically lose all of their functional groups. The resultant products are geologically-stable hydrocarbon skeletons. Structures 1 and 2; 3 and 4; and 5 and 6 show examples of biolipids and their diagenetic hydrocarbon products.

Anaerobic ammonium-oxidising bacteria: A biological source of the bacteriohopanetetrol stereoisomer in marine sediments

“…Understanding the biological origin of specific BHPs and their associated environmental setting is crucial for deciphering the geohopanoid record and for reconstructing paleoenvironmental conditions (Zundel and Rohmer, 1985;Summons et al, 1999;Brocks and Pearson, 2005).…”

Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche

“…In this context, organic biomarkers have received attention due to their potential to provide more specific information about the composition of ancient microbial communities (Brocks and Pearson, 2005). Hopanes and steranes are among the more prominent classes of these biomarkers (Rohmer, 2010).…”

Glycerol ether biomarkers and their carbon isotopic compositions in a cold seep carbonate chimney from the Shenhu area, northern South China Sea

“…Lipid biomarkers are constituents of the cytoplasmic membrane surrounding each cell, which allow the identification of dominant microbes and, if combined with a compound specific stable carbon isotope analysis, their carbon fixation pathways [13][14][15]. The identification of AOM communities was achieved using independent molecular techniques, i.e.…”