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This project investigated the chemical changes undergone by modern organisms as they fossilize in order to understand the molecular transformation of biomolecules to geomolecules across the geologic timescale and their contribution to sedimentary organic matter (kerogen and bitumen).

Organic tissues (e.g., cuticles) may survive as organic remains.  They contribute significantly to the fossil record of a number of important groups such as graptolites, chelicerates, insects, chitinozoans, ammonite (beaks) and fishes (scales). Such fossils were assumed to be composed of a chitin-protein complex similar to cuticles in their living relatives.  Analysis of fossils using a range of mass spectrometric and spectroscopic methods, however, showed that preserved cuticles include a significant aliphatic hydrocarbon content, at times with an aromatic component, a composition very different to that of the cuticle of the living organism. Analyses of successively older fossil material revealed that the transformation to an aliphatic composition is gradual and perhaps time dependent. Chemolytic analyses of fossils revealed the presence of fatty acyl moieties in the macromolecule indicating that the aliphatic composition of the fossils was generated in situ from constituent lipids and not introduced from an external source.

Diagenetic alteration is critical to the preservation of fossil cuticles and to the formation of kerogen.  This process takes place over millions of years, but it was not known at what stage it is initiated. To investigate this, laboratory decay experiments were carried out on shrimp, scorpion and cockroach (taxa represented as fossils) to monitor early changes in the chitin-protein of the cuticle and associated lipids. The cockroach and scorpion exoskeleton remained largely unaltered, but the shrimp experienced rapid decomposition within a month. Mass spectrometry and ¹³C NMR spectroscopy revealed the association of an n-alkyl component of chain lengths up to C₂₄ with the decaying cuticle, a result of the incorporation of labile lipids such as fatty acids.  The scorpion and cockroach did not reveal additional lipid incorporation indicating that decay is an important agent in initiating in situ lipid association. This experiment showed that lipids can become associated with macromolecules during the very early stages of decay.  This is the first stage of a polymerization process that leads to the aliphatic-rich composition ubiquitous in organic fossils and in kerogens. 

The conventional view holds that the biopolymer chitin (poly-N-acetyl-D-glucosamine) is not preserved in ancient fossils as it is readily hydrolysable. The oldest chitin confirmed prior to this project occurs in a 25 My old beetle.  Synchrotron based micro X-ray Absorption Near Edge Structure (XANES) spectromicroscopy provides a new powerful tool for the analysis of remnant biopolymers in organic fossils. A clear molecular signature of chitin was detected in a Middle Pennsylvanian (~310 My) scorpion cuticle and a Silurian (~417 My) eurypterid cuticle via analysis with carbon, nitrogen and oxygen (XANES) spectromicroscopy. This indicates that chitin survives much longer in fossil material than previously supposed.  The preservation of organic arthropod cuticle likely depends on the condensation of cuticular fatty acids onto a chitin-derived molecular scaffold.

Analysis of the jaws of the living Humboldt squid (Dosidicus gigas) and Nautilus belauensis using mass spectrometric techniques revealed a chitin-protein composition. Analysis of comparable fossil material from several cephalopod taxa (Placenticeras, Nanaimoteuthis jeletzkyi, Anagaudryceras limatum, and Hoploscaphites) from Upper Cretaceous localities from North America and Japan detected no compounds from the chitin-protein biopolymer complex but showed the presence of aromatic compounds, including alkyl benzene derivatives, alkyl phenols, naphthalenes, and phenanthrene.  An n-alkyl component, ranging in carbon chain length up to C₂₄, was also detected.  Cleavage of ester bonds in the fossil macromolecules using thermally assisted methylation (THM) revealed a carboxylic acid distribution from C₆ to C₁₈. Additionally, methyl ketones were detected in the fossils, in which the n-alkyl (aliphatic) component was significant.  Methyl ketones (alkan-2-ones) have been reported in fossil algae and kerogen and are indicative of ether functional groups in macromolecules, which are probably cross-linked via oxidative reticulation. Thus, the aliphatic component is likely derived from in situ incorporation and polymerisation of labile lipid precursors, in part cross-linked via ether and ester bonds. This demonstrated the presence of ether linkages and oxidative cross-linking in animal fossils, suggesting that they may be important in the long term preservation of both animal and plant derived organic matter.

Chemical analysis of leaves of modern Metasequoia revealed the presence of the structural polyester cutin, guaiacyl lignin units and polysaccharides but no cutan. Analysis of environmentally decayed Metasequoia leaves revealed that guaiacyl lignin units and cellulose were degraded relative to the cutin, suggesting that cutin is more stable than lignin and cellulose during decay. This is paralleled by changes in the cellular structure of the decayed and fossil Metasequoia leaves. Heating modern Metasequoia needles in confined conditions generated a composition with a long chain aliphatic polymer up to C₃₂ and additional phenolic compounds similar to those present in the fossils. However, experimental maturation of cutin demonstrated that it generates an aliphatic polymer < C₂₀.  Thus the n-alkyl component > C₂₀ generated in Metasequoia is a diagenetic product of longer chain plant waxes. Tertiary Metasequoia fossils from the Eocene of Republic (Washington State) showed a significant aliphatic component without biopolymeric lignin and polysaccharides. Metasequoia fossils from the Eocene of Axel Heiberg revealed the presence of lignin and aliphatic polymer up to C₂₉ with minor amounts of cellulose, and fossils from the Miocene of Clarkia revealed lignin and an aliphatic polymer up to C₂₇ without any polysaccharides.  The resistant nature of cutin compared to lignin and polysaccharides explains the ubiquitous presence of n-alkyl component (<C₂₀) in fossil leaves even when lignin is absent and polysaccharides have decayed; cutin contributes to the presence of aliphatic components in terrestrially derived sedimentary organic matter.

Molecular maturity parameters including hopane and sterane stereochemical changes have been assessed at the lacustrine Enspel formation (around 25 Ma) for seven oil shale horizons overlain by a basalt sill. Currently, the microbial ecology of the lake is being evaluated from acquired biomarker data to complete this investigation.