Raman spectroscopy is widely used to evaluate the nature and potential origins of carbonaceous matter in Earth's oldest rocks and minerals. It is also the tool that will be used for organic detection on the next vehicles to remotely explore the surface of Mars. Here we present, for the first time, a novel quantitative method in which previously neglected Raman spectral features are correlated directly, linearly, and with excellent accuracy, to the microchemistry of carbonaceous materials through the elemental H:C ratio, regardless of contamination. We show applicability and predictive capabilities of this methodology in evaluating H:C ratios between 0.01 and 0.65 in Archean and type III kerogens. We demonstrate its application to chemical microRaman mapping by statistical analysis of a 750Ma microfossil and its encompassing sediments. Raman-derived H:C data can also be used to estimate the degree to which kerogen C-isotopic data has been shifted from its original values due to the effects of metamorphism. The new methodology directly and non-invasively affords spatially resolved assessments of organic matter preservation and microscale chemical diversity within any geologically preserved terrestrial or extraterrestrial sample, including in the use of organic matter in technological applications.

Molecular fossils (or biomarkers) are key to unraveling the deep history of eukaryotes, especially in the absence of traditional fossils. In this regard, the sterane 24-isopropylcholestane has been proposed as a molecular fossil for sponges, and could represent the oldest evidence for animal life. The sterane is found in rocks ∼650–540 million y old, and its sterol precursor (24-isopropylcholesterol, or 24-ipc) is synthesized today by certain sea sponges. However, 24-ipc is also produced in trace amounts by distantly related pelagophyte algae, whereas only a few close relatives of sponges have been assayed for sterols. In this study, we analyzed the sterol and gene repertoires of four taxa (Salpingoeca rosetta, Capsaspora owczarzaki, Sphaeroforma arctica, and Creolimax fragrantissima), which collectively represent the major living animal outgroups. We discovered that all four taxa lack C30 sterols, including 24-ipc. By building phylogenetic trees for key enzymes in 24-ipc biosynthesis, we identified a candidate gene (carbon-24/28 sterol methyltransferase, or SMT) responsible for 24-ipc production. Our results suggest that pelagophytes and sponges independently evolved C30 sterol biosynthesis through clade-specific SMT duplications. Using a molecular clock approach, we demonstrate that the relevant sponge SMT duplication event overlapped with the appearance of 24-isopropylcholestanes in the Neoproterozoic, but that the algal SMT duplication event occurred later in the Phanerozoic. Subsequently, pelagophyte algae and their relatives are an unlikely alternative to sponges as a source of Neoproterozoic 24-isopropylcholestanes, consistent with growing evidence that sponges evolved long before the Cambrian explosion ∼542 million y ago.

Highlights•We sought to extend knowledge of the sterol complement of protists.•We studied the sterols in an allogromid foraminifer grown in culture.•We identified two C30 sterols previously thought to be exclusive to pelagophyte algae.•(24E)-n-propylidenecholesterol and its 24Z isomer were confirmed by direct comparison with an authentic standard.We report a study of the sterols produced by the thecate allogromid foraminiferan, Allogromia laticollaris, grown in culture. Gas chromatographic retention time, together with mass spectrometric fragmentation patterns of trimethysilyl and acetate derivatives enabled us to assign a suite of C27–C30 sterols. Two C30 sterols were identified as (24E)-n-propylidenecholesterol and its 24Z isomer by direct comparison with an authentic standard. The C30 sterols were not detected in the two algae, Isochrysis galbana and Dunaliella tertiolecta, used as a food source for the A. laticollaris, consistent with previous analysis of these organisms. The assignment of (24E)-n-propylidenecholesterol was confirmed using 600 MHz 1H nuclear magnetic resonance (NMR) spectroscopy. The result has relevance as to how we might interpret fossil sterane distributions.

We report a geochemical study of a composite sedimentary section that captures the Permian–Triassic (PT) transition at Kap Stosch, East Greenland. The samples were from the original paleontological collection of early PT researchers. The rocks, which include samples from four proximal outcrop localities, were deposited during the Late Permian and Early Triassic at the margin of the Boreal Sea with a depositional hiatus and erosional event of unknown duration. Bulk geochemical measurements for most of the samples show good correlation between S2 and TOC% which, combined with low Tmax values, indicate that the organic matter (OM) that formed contemporaneously with sediment deposition is of relatively low maturity. Significant changes through the PT transition include a pronounced switch in the δ13C of TOC from high values near −24‰ to lower values averaging −32‰, that is matched by a significant increase in the hydrogen index (HI) of the kerogen. The Permian samples containing 13C enriched OM also have low Rock–Eval HI values and anomalous pyrograms, indicating that the kerogen is heterogeneous in terms of source and maturity, as confirmed by microscopic analysis of the kerogen concentrates. Samples from the Permian section contain an abundance of black angular fragments of woody tissue in addition to gymnosperm pollen and spinose acritarchs of the Vittatina-Association (Balme, B., 1979. Palynology of Permian–Triassic boundary beds at Kap Stosch. Meddeleleser om Gronland 200, 1–36). In contrast, black woody tissue is rare in samples from the Early Triassic section with well preserved gymnosperm and lycopod pollen and spores of the Protohaploxypinus and Taeniaesporites associations. Biomarkers indicate moderate maturity for Permian samples, with the C27 sterane 20S/(20S + 20R), C31 homohopane 22S/(22S + 22R) ratio and Ts/(Ts + Tm) values all being higher than those for Triassic sediments. The marked switch in maturity indicators across the PT transition suggests an unconformity consistent with palynological observations. The pristane/phytane values are low and the homohopane index values high, indicating that anoxic conditions prevailed throughout deposition of the sediments. Additionally, markers of photic zone euxinia (i.e. isorenieratane, crocetane and 2,3,6-aryl isoprenoids) were present in all samples and all show maximum abundance closest to the PT transition. The C33n-alkyl cyclohexane, a potential event marker for the onset of the biotic crisis in the Late Permian, was found in samples at, and immediately following, the paleontological PT transition. Despite the distinct change in lithology across the PT transition, the redox and Chlorobi-derived biomarkers indicate that photic zone euxinic conditions prevailed throughout the deposition of the Kap Stosch sedimentary sequence.Highlights► We studied organic matter in a Permian–Triassic transition section Kap Stosch, East Greenland. ► Mixed marine and terrestrial kerogens were identified. ► Marine biomarkers dominated the extractable organics. ► Chlorobi biomarkers suggest euxinic conditions prevailed throughout the sedimentary section

The Q family of oils from Oman was previously recognized as highly unusual and distinct from the more prevalent Huqf oil family by having an extraordinarily high C27/C29 sterane ratio and δ13C values near −30‰. A re-evaluation of the hydrocarbon constituents of the Q oils using GC–MS–MS analyses resulted in identification of other useful geochemical discriminators that include gammacerane/hopane ratios between 0.5 and 0.9, C24T/C23T ⩾ 0.7 combined with C22T/C21T cheilanthane ratios <0.4. A relatively simple branched alkane, 17-methylpentatriacontane, identified on the basis of its mass spectrum is especially characteristic. A suite of C19, C20 and C26 norsteranes, characterized by a dominant 203 Da fragment in their mass spectra, were also present with an abundance pattern that distinguished the Q oils from other south Oman oil families and their source rocks. These features enabled us to establish a Q-source rock as the origin of a suite of highly mature condensates from north Oman despite them having exceptionally low concentrations of conventional biomarkers.Although we were unable to identify a source facies within the sediments of the South Oman Salt Basin that convincingly correlated with the hydrocarbons of the Q oils, the geochemistry of Q oils provided valuable clues about their origin. Sterane and terpane patterns indicated that the Q source rock is most likely a marine shale deposited under intermittently anoxic and hypersaline conditions. The absence of a carbon isotopic ordering anomaly for normal alkanes and isoprenoids points to a Cambrian age for the Q oils. Moreover, trends in the patterns of norsteranes in south Oman carbonate stringer oils suggest the Q oil source originates from one of the upper units of the Ara carbonate and evaporite sequence. More specifically, our results point to a siliciclastic source rock lying stratigraphically above the A6 carbonates from the Dhahaban Formation. The high relative abundances of 24-isopropylcholestanes in Q oils likely originate from demosponges and we hypothesize that the 17-methylpentatriacontane, which is so abundant in Q oils, is a biomarker for early arthropods that inhabited the salt basins of Oman at the very beginning of the Cambrian Period.Highlights► New geochemical analyses of the Q family of oils from Oman are described. ► Q oils are likely derived from an Early Cambrian unit of the Ara Formation. ► This was likely prevalent in North Oman but missing from the South Oman Salt Basin. ► Some high maturity condensates from North Oman have Q-like geochemistry.

The Neoproterozoic Era is of widespread geobiological interest because it marks the critical transition from a world of microbes to one where animals become an established feature of the landscape. Much research into this time period has focused on the ventilation of the oceans, as this is widely considered a primary factor driving the diversification of complex, multicellular life. In this study, Proterozoic to Cambrian aged oils from eastern Siberia were analyzed for their hydrocarbon biomarker contents and compound specific carbon isotopes in order to further our understanding of the prevailing environment and its microbial and metazoan communities. Geochemically, these oils are broadly comparable to those of the Ediacaran–Cambrian sedimentary rocks and oils of the South Oman Salt Basin. Organic matter in the source sedimentary rocks included significant contributions from green algae, demosponges and bacteria including cyanobacteria and methanotrophic proteobacteria. Although the ages of the Siberian oils and putative parent source rock intervals are poorly constrained, the geochemical similarities between the Ediacaran Oman Huqf and Nepa-Botuoba-Katanga family of Siberian oil samples are impressive, leading to the inference that their source rocks are coeval. On the other hand, oils from the Baykit High are distinctive, likely older and possibly of Cryogenian age.

Diagenetic alteration is critical for the preservation of fossil cuticles of plant and animal origin and to the formation of kerogen. The process takes place over millions of years, but the stage at which it is initiated is not known. Laboratory decay experiments were carried out on shrimps, scorpions and cockroaches to monitor changes in the chitin–protein of the arthropod cuticle and associated lipids. The cockroach and scorpion exoskeleton remained largely unaltered morphologically, but the shrimp experienced rapid decomposition within a month, which progressed through the 44 week duration of the experiment as revealed using electron microscopy. Mass spectrometry and 13C NMR (nuclear magnetic resonance) spectroscopy revealed the association of an n-alkyl component with labile lipids, such as fatty acids with up to 24 carbon atoms, which were incorporated into the decaying macromolecule. The scorpion and cockroach cuticle did not reveal the incorporation of additional lipids, indicating that decay is important in initiating in situ lipid association. This experiment provides evidence that lipids can become associated with carbohydrate and proteinaceous macromolecules during the very early stages of decay, representing the first stage in the transformation process that contributes to the aliphatic rich composition ubiquitous in organic fossils and kerogen.

Biodegraded bitumens associated with quartz and calcite veins in the Cambrian Fish River Subgroup sediments of the Nama Group of southern Namibia have a geochemical signature diagnostic for organic matter that was deposited in a saline lacustrine palaeoenvironment. In particular, they contain abundant gammacerane, β-carotane and 3β-methylhopanes while 24-isopropyl cholestanes and dinosteroids are not detectable. Sealed tube hydrous pyrolysis of asphaltene and polar fractions yielded saturated hydrocarbons amenable to C isotopic analysis, and these analyses show unusually low δ13C values. These combined characteristics are also present in immature bitumens from the Permian Irati Formation of Brazil and a saline lacustrine facies of the Whitehill Formation in the Karoo Basin, South Africa. We conclude that the bitumens originated from Whitehill equivalent strata of the Kalahari Basin deposited in what was an extensive saline lacustrine basin in southwestern Gondwana during the Early Permian. In southern Africa, source rocks of the Whitehill Formation are generally immature for petroleum generation and it is therefore likely that the Nama bitumens were expelled by contact metamorphism during emplacement of Karoo dolerite sills and dykes in the Jurassic.

Hydrocarbon biomarkers in highly mature Precambrian rocks have the potential to provide important information about the diversity ecology, and evolution of early life, but studying them presents special analytical challenges. Extractable hydrocarbons are present in Archean and most Paleoproterozoic sedimentary rocks in such trace concentration that even slight contamination from petroleum-derived materials in situ or during drilling, storage, sampling, handling and laboratory analysis would compromise the results and, thereby, any consequent inferences. Here we report protocols that we have developed for the analysis of cores from several recently completed deep-time scientific drilling initiatives. By paying special attention to cutting, cleaning, crushing and extraction, it is possible to significantly reduce laboratory blanks to acceptable levels. When these methods are utilized, meaningful variations in the patterns of biomarkers over stratigraphic and lithologic boundaries provide compelling evidence for syngeneity.

D/H ratios of terrestrially-sourced whole oils and their respective saturated, aromatic, and polar fractions, individual n-alkanes, formation waters and non-exchangeable hydrogen in kerogen were measured in potential source rocks from seven Australian petroleum basins. Data for 75 oils and condensates, their sub-fractions and 52 kerogens indicate that oil sub-fractions have δD values comparable to δDoil, with a ΔδD offset (δDkerogen−δDoil) averaging ca. 23‰. The weighted-average δD of individual n-alkanes is usually identical to δDoil and δDsaturate. A trend of increasing δD with n-alkane chain length in most oils causes individual n-alkanes from an oil to vary in δD by 30‰ or more. A modest correlation between δD for aromatic sub-fractions and formation waters indicates that about 50% of aromatic C-bound H has exchanged with water. In contrast, δDoil and δDsaturated show no evidence for H-exchange with formation water under reservoir conditions at temperatures up to 150 °C. Acyclic isoprenoids and n-alkanes show essentially indistinguishable δD, indicating that primary isotopic differences from biosynthesis have been erased. Overall, extensive exchange of C-bound H in petroleum with other hydrogen is apparent, but seems to have affected most hydrocarbons only during their chemical genesis from precursor molecules. Our isotopic findings from terrestrially-sourced oils should be qualitatively relevant for marine oils as well.

The occurrence of the archaeal biomarkers crocetane and pentamethylicosane (PMI) in sediments and crude oils was investigated using GC–MS and GC–MS–MS. Selected ion monitoring (SIM) and multiple reaction monitoring (MRM) protocols designed to detect the C20 and C25 irregular isoprenoids were evaluated. A method for the preferential detection of crocetane over phytane, its more abundant isomer, was refined using authentic compounds. Crocetane was found to be present in modern sediments from both aerobic and anaerobic water columns and in sediment from the 1640 Ma Barney Creek Formation, providing evidence for the antiquity of its biosynthesis. Crocetane was also detected in several Perth Basin crude oils and in the Kockatea shale, their putative source rock, and in Canning Basin oils, although MRM analysis could only verify its occurrence in Canning oils of Devonian age. Equivocal data from Ordovician and Carboniferous Canning Basin oils highlight the need for extreme caution when attempting to distinguish between acyclic isoprenoid isomers. PMI was identified by MRM in a Miocene Monterey sediment and in a modern Antarctica sediment. On the other hand, the C25 isoprenoid hydrocarbon peak detected in Triassic and older sediments was consistently identified as the regular isomer (I25 reg) whenever it was sufficiently abundant for MRM to be applied.

A novel hydrocarbon 3,7,18,22-tetramethylsqualane has been identified in extracts from the Maniguin-2 well on Maniguin Island, Philippines, the Duri oil from Sumatra, Indonesia and the Maoming Oil Shale from China. A related hydrocarbon, tentatively assigned the structure 3,7,11,14-tetramethylsqualane, occurs in the Maniguin samples. Like C34 botryococcane, the tetramethylsqualanes are unusually enriched in 13C compared to co-occuring n-alkanes and C16–20 acyclic isoprenoids. Polymethylsqualanes extend the range of distinctive hydrocarbons produced by Botryococcus braunii and its fossil counterparts.

A combination of sequence stratigraphic and conodont biostratigraphic analyses of sediment cores from five petroleum exploration wells, together with reference to nearby outcrops, has allowed us to construct a composite geological section through the Permian–Triassic transition in the Peace River Basin of Western Canada. The cores contain significant contents of organic matter comprising kerogen and bitumen of low to moderate thermal maturity. Extraction and analysis of the bitumens has revealed patterns of biomarker hydrocarbons consistent with marine deposition and photic zone euxinia. In particular isorenieratane and aryl isoprenoids, derived from the carotenoid pigments of green sulfur bacteria (Chlorobiaceae), are abundant and pervasive throughout the section and indicate that hydrogen sulfide must have been present in the photic zone for significant periods of time. These findings mirror the geochemical results obtained for other Permian–Triassic boundary sections of the Tethys realm (e.g. Western Australia, East Greenland and South China) and suggest that euxinic conditions prevailed widely, though perhaps periodically, and that hydrogen sulfide toxicity could have been an important factor in the extinction of marine invertebrates.