Hydrocarbons of Biological Origin from a One-Billion-Year-Old Sediment

Advancing archaeological sedimentary lipid biomarker analysis: A review of recent developments and methodological guidelines

This review targets archaeological scientists and geoarchaeologists, examining the current state of lipid biomarker analysis in archaeological sediments-a growing field. Lipid compounds and their stable isotope ratios serve as valuable proxies for reconstructing past climates, vegetation, freshwater availability, human-environment interactions, diet, technology, and subsistence practices. The paper reviews experimental, archaeological, and ethnoarchaeological studies that apply lipid biomarkers to archaeological sedimentary deposits, contributing to paleoenvironmental research and insights into past human behavior. Key topics include fecal biomarkers, revealing diet and subsistence, and pyrogenic biomarkers, shedding light on fire technology and cooking traditions. Methodological guidelines are provided, covering sample collection, lipid extraction, pretreatment, and compound detection. Challenges include standardizing protocols, integrating new biomarkers, microcontextual approaches, and adopting advanced analytical techniques. Advancing lipid biomarker analysis promises to enhance interdisciplinary research and deepen our understanding of archaeological contexts and human-environment dynamics.

Microbial biosignatures in ancient deep-sea hydrothermal sulfides

Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.

What about nitrogen? Using nitrogen as a carrier gas during the analysis of petroleum biomarkers by gas chromatography mass spectrometry

Gas chromatography mass spectrometry (GC-MS) is a commonly used method for organic geochemistry for both academic research and applications such as petroleum analysis. Gas chromatography requires a carrier gas, which needs to be both volatile and stable and in most organic geochemical applications helium or hydrogen have been used, with helium predominating for gas chromatography mass spectrometry. Helium, however, is becoming an increasingly scarce resource and is not sustainable. Hydrogen is the most commonly considered alternative carrier gas to helium but has characteristics that in certain respects make its use less practical, foremost is that hydrogen is flammable and explosive. But as hydrogen is increasingly used as a fuel, higher demand may also make its use less desirable. Here we show that nitrogen can be used for the GC-MS analysis of fossil lipid biomarkers. Using nitrogen, chromatographic separation of isomers and homologues can be achieved, but sensitivity is orders of magnitude less than for helium. It is reasonable to use nitrogen as a carrier gas in applications where low levels of detection are not needed, such as the characterization of samples of crude oil or foodstuffs, or potentially as part of a gas-mixture seeking to reduce helium-demand but maintain a level of chromatographic separation sufficient to support proxy-based characterizations of petroleum.

Defining Multiple Characteristic Raman Bands of α-Amino Acids as Biomarkers for Planetary Missions Using a Statistical Method

Biomarker molecules, such as amino acids, are key to discovering whether life exists elsewhere in the Solar System. Raman spectroscopy, a technique capable of detecting biomarkers, will be on board future planetary missions including the ExoMars rover. Generally, the position of the strongest band in the spectra of amino acids is reported as the identifying band. However, for an unknown sample, it is desirable to define multiple characteristic bands for molecules to avoid any ambiguous identification. To date, there has been no definition of multiple characteristic bands for amino acids of interest to astrobiology. This study examined L-alanine, L-aspartic acid, L-cysteine, L-glutamine and glycine and defined several Raman bands per molecule for reference as characteristic identifiers. Per amino acid, 240 spectra were recorded and compared using established statistical tests including ANOVA. The number of characteristic bands defined were 10, 12, 12, 14 and 19 for L-alanine (strongest intensity band: 832 cm(-1)), L-aspartic acid (938 cm(-1)), L-cysteine (679 cm(-1)), L-glutamine (1090 cm(-1)) and glycine (875 cm(-1)), respectively. The intensity of bands differed by up to six times when several points on the crystal sample were rotated through 360 °; to reduce this effect when defining characteristic bands for other molecules, we find that spectra should be recorded at a statistically significant number of points per sample to remove the effect of sample rotation. It is crucial that sets of characteristic Raman bands are defined for biomarkers that are targets for future planetary missions to ensure a positive identification can be made.

Hydrocarbons preserved in a ~2.7 Ga outcrop sample from the Fortescue Group, Pilbara Craton, Western Australia

The hydrocarbons preserved in an Archean rock were extracted, and their composition and distribution in consecutive slices from the outside to the inside of the rock were examined. The 2.7 Ga rock was collected from the Fortescue Group in the Pilbara region, Western Australia. The bitumen I (solvent-extracted rock) and bitumen II (solvent-extracted hydrochloric acid-treated rock) fractions have different hydrocarbon compositions. Bitumen I contains only trace amounts of aliphatic hydrocarbons and virtually no aromatic hydrocarbons. In contrast, bitumen II contains abundant aliphatic and aromatic hydrocarbons. The difference seems to reflect the weathering history and preservational environment of the investigated rock. Aliphatic hydrocarbons in bitumen I are considered to be mainly from later hydrocarbon inputs, after initial deposition and burial, and are therefore not indigenous. The lack of aromatic hydrocarbons in bitumen I suggests a severe weathering environment since uplift and exposure of the rock at the Earth's surface in the Cenozoic. On the other hand, the high abundance of aromatic hydrocarbons in bitumen II suggests that bitumen II hydrocarbons have been physically isolated from removal by their encapsulation within carbonate minerals. The richness of aromatic hydrocarbons and the relative scarcity of aliphatic hydrocarbons may reflect the original compositions of organic materials biosynthesised in ancient organisms in the Archean era, or the high thermal maturity of the rock. Cyanobacterial biomarkers were observed in the surficial slices of the rock, which may indicate that endolithic cyanobacteria inhabited the surface outcrop. The distribution of aliphatic and aromatic hydrocarbons implies a high thermal maturity, which is consistent with the lack of any specific biomarkers, such as hopanes and steranes, and the prehnite-pumpellyite facies metamorphic grade.

Leaf metallome preserved over 50 million years

Large-scale Synchrotron Rapid Scanning X-ray Fluorescence (SRS-XRF) elemental mapping and X-ray absorption spectroscopy are applied here to fossil leaf material from the 50 Mya Green River Formation (USA) in order to improve our understanding of the chemistry of fossilized plant remains. SRS-XRF of fossilized animals has previously shown that bioaccumulated trace metals and sulfur compounds may be preserved in their original distributions and these elements can also act as biomarkers for specific biosynthetic pathways. Similar spatially resolved chemical data for fossilized plants is sparsely represented in the literature despite the multitude of other chemical studies performed. Here, synchrotron data from multiple specimens consistently show that fossil leaves possess chemical inventories consisting of organometallic and organosulfur compounds that: (1) map discretely within the fossils, (2) resolve fine scale biological structures, and (3) are distinct from embedding sedimentary matrices. Additionally, the chemical distributions in fossil leaves are directly comparable to those of extant leaves. This evidence strongly suggests that a significant fraction of the chemical inventory of the examined fossil leaf material is derived from the living organisms and that original bioaccumulated elements have been preserved in situ for 50 million years. Chemical information of this kind has so far been unknown for fossilized plants and could for the first time allow the metallome of extinct flora to be studied.

Search for alkanes of 15 to 30 carbon atom length

A 50-gram sample of lunar fines was subjected to stepwise extraction in a mixture of benzene and methanol while intact, after being pulverized, and after being digested in hydrofluoric acid. None of these three extracts contained detectable quantities of C(15) to C(30) alkanes. No C(15) to C(30) alkane was present in this lunar sample at a concentration exceeding I part per billion by weight.

Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin

Non-destructive Fourier Transform InfraRed (FTIR) mapping of Eocene aged fossil reptile skin shows that biological control on the distribution of endogenous organic components within fossilized soft tissue can be resolved. Mapped organic functional units within this approximately 50 Myr old specimen from the Green River Formation (USA) include amide and sulphur compounds. These compounds are most probably derived from the original beta keratin present in the skin because fossil leaf- and other non-skin-derived organic matter from the same geological formation do not show intense amide or thiol absorption bands. Maps and spectra from the fossil are directly comparable to extant reptile skin. Furthermore, infrared results are corroborated by several additional quantitative methods including Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS). All results combine to clearly show that the organic compound inventory of the fossil skin is different from the embedding sedimentary matrix and fossil plant material. A new taphonomic model involving ternary complexation between keratin-derived organic molecules, divalent trace metals and silicate surfaces is presented to explain the survival of the observed compounds. X-ray diffraction shows that suitable minerals for complex formation are present. Previously, this study would only have been possible with major destructive sampling. Non-destructive FTIR imaging methods are thus shown to be a valuable tool for understanding the taphonomy of high-fidelity preservation, and furthermore, may provide insight into the biochemistry of extinct organisms.

Microorganisms three billion years old from the precambrian of South Africa

A minute, bacterium-like, rod-shaped organism, Eobacterium isolatum, has been found organically and structurally preserved in black chert from the Fig Tree Series (3.1 x 10(9) years old) of South Africa. Filamentous organic structures of probable biological origin, and complex alkanes, which apparently contain small amounts of the isoprenoid hydrocarbons pristane and phytane, are also indigenous to this Early Precambrian sediment. These organic remnants comprise the oldest known evidence of biological organization in the geologic record.

Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph

Sedimentary 2-methyhopanes have been used as biomarker proxies for cyanobacteria, the only known bacterial clade capable of oxygenic photosynthesis and the only group of organisms found thus far to produce abundant 2-methylbacteriohopanepolyols (2-MeBHPs). Here, we report the identification of significant quantities of 2-MeBHP in two strains of the anoxygenic phototroph Rhodopseudomonas palustris. Biosynthesis of 2-MeBHP can occur in the absence of O(2), deriving the C-2 methyl group from methionine. The relative abundance of 2-MeBHP varies considerably with culture conditions, ranging from 13.3% of total bacteriohopanepolyol (BHP) to trace levels of methylation. Analysis of intact BHPs reveals the presence of methylated bacteriohopane-32,33,34,35-tetrol but no detectable methylation of 35-aminobacteriohopane-32,33,34-triol. Our results demonstrate that an anoxygenic photoautotroph is capable of generating 2-MeBHPs and show that the potential origins of sedimentary 2-methylhopanoids are more diverse than previously thought.

The Bakerian Lecture, 1965 - Chemical evolution

How did life come to be on the surface of the Earth? Darwin himself recognized that his basic idea of evolution by variation and natural selection must be a continuous process extending backward in time through that period in which the first living things arose and into the period of ‘chemical evolution´ which preceded it. We are approaching the examination of these events by two routes. One is to seek for evidence in the ancient rocks of the Earth which were laid down before the time in which organisms capable of leaving their skeletons in the rocks to be fossilized were in existence. This period is somewhat more than ca. 600 My ago. The Earth is believed to have taken its present form approximately 4700 My ago. We have found in rocks whose age is about 1000 My certain organic molecules which are closely related to the green pigments of plants, chlorophyll. This seems to establish that green plants were already flourishing before that time. We have now found in rocks of still greater age, namely, 2500 My, the same kinds of molecules mentioned above which can be attributed to the presence of living organisms. If these molecules are as old as the rocks, we have thus shortened the time available for the generation of the complex biosynthetic sequences which give rise to these specific hydro- ­ carbons (polyisoprenoids) to less than 2000 My. The second approach is to attempt to reproduce in the laboratory those chemical processes induced by energy of various kinds— radiation from the sun, from radioactivity, from electrical storm, etc.— which could give rise to simple organic molecules and polymeric combinations of them, ultimately leading to systems which could be called alive. This attempt has also succeeded along a variety of lines, and many of the present-day biologically important molecules have been constructed abiogenically from the primeval atmosphere, thus providing laboratory evidence for the hypothetical processes. The latest step in this approach has been to demonstrate the formation of polypeptides in dilute aqueous solutions through the agency of molecules formed in the primitive atmosphere of the Earth. Finally we must seek evidence for the same processes in material found elsewhere than on the Earth, such as other parts of our solar system , e.g. the Moon and Mars. We can expect to know whether such materials exist at all in the rocks of the Moon within this decade. We may even know something more definite about the botany of Mars during this same period.

Diagenesis of Metals Chemically Complexed to Bacteria: Laboratory Formation of Metal Phosphates, Sulfides, and Organic Condensates in Artificial Sediments

Cells of Bacillus subtilis , when suspended in a 5mM metal solution, bind metals tenaciously to their cell walls. These metal-loaded cells, when mixed with a synthetic sediment and put under laboratory conditions to simulate low-temperature sediment diagenesis, nucleate the formation of a mixed assemblage of crystalline metal phosphates, metal sulfides, and polymeric, metal-complexed, organic residues. The sequential series of diagenetic events leading to the formation of authigenic mineral phases was followed by transmission electron microscopy and energy-dispersive X-ray analysis. The minerals quartz (SiO 2 ) and calcite (CaCO 3 ) were employed in the synthetic sediment. Crystalline magnetite (Fe 2 O 3 ) and elemental sulfur were added as redox buffering agents to ensure anoxic conditions. Quartz and magnetite appeared unreactive throughout the experimental conditions. Elemental sulfur interacted with the metal-loaded cells, affected both the eventual chemistry and crystal habit of the metal phosphates, and formed a variety of crystalline metal sulfides. Calcite raised the pH of the fluid phase of the sediment, which influenced phosphate mineralization and inhibited metal sulfide genesis.

Binding of metals to cell envelopes of Escherichia coli K-12

As representative of gram-negative bacteria, the isolated and purified envelopes of an Escherichia coli K-12 strain were used to determine metal-binding capacity. The envelopes were suspended in 5 mM metal solutions for 10 min and 23 degrees C, separated and washed by centrifugation, and analyzed for metal by either atomic absorption or X-ray fluorescence spectroscopy. Of 32 metals tested, large amounts (> 0.9 mumol/mg [dry weight]) of Hf and Os, intermediate amounts (0.1 to 0.4 mumol/mg [dry weight]) of Pb, Zn, Zr, Fe III, Mn, Mo, Mg, Co, and Ce IV, and small amounts (< 0.1 mumol/mg [dry weight]) of Na, K, Rb, Ca, Sr, Cu, Sc, La, Pr, Sm, U, Fe II, Ru, Ni, Hg, Pt, Pd, Au, and In were detected Li and V were not bound to the envelopes. Electron microscopy of unstained, thin-sectioned material provided an electron-scattering profile for localizing the bound metal within the envelope. Energy-dispersive X-ray analysis of thin sections detected all metals in single envelope vesicles. These data suggest that most metal deposition occurred at the polar head group regions of the constituent membranes or along the peptidoglycan layer. No leaching of envelope components was detected by monitoring radioactive probes within the lipopolysaccharide and peptidoglycan layers during metal uptake experiments, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins from metal-loaded envelopes, or protein and carbohydrate determinations on the wash fluids. These results suggest that membrane integrity was not disturbed under these ionic conditions.

Uptake and retention of metals by cell walls of Bacillus subtilis

Isolated walls of Bacillus subtilis Marburg, prepared in a manner which avoided metal contamination other than by the growth medium, were incubated in dilute metal solutions, separated by membrane filtration (0.22 mum), and monitored by atomic absorption to give uptake data for 18 metals. Substantial amounts of Mg2+, Fe3+, Cu2+, Na+, and K+ (amounts which were often visible as Au3+, and Ni2+ (the higher atomic-numbered elements also visible as electron scattering), and small amounts of Hg2+, Sr2+, Pb2+, and Ag+ were taken into the wall. Some (Li+, Ba2+, Co2+, and Al3+) were not absorbed. Most metals which had atomic numbers greater than 11 and which could be detected by electron microscopy appeared to diffusely stain thin sections of the wall. Magnesium, on the other hand, partitioned into the central region, and these sections of walls resisted ruthenium red staining, which was not true for the other metals. Areas of the walls also acted as nucleation sites for the growth of microscopic elemental gold crystals when incubated in solutions of auric chloride. Retention or displacement of the metals was estimated by a "chromatographic" method using the walls cross-linked by the carbodiimide reaction to adipic hydrazide agarose beads (which did not take up metal but reduced the metal binding capacity of the walls by ca. 1%) packed in a column. When a series of 12 metal solutions was passed through the column, it became evident that Mg2+, Ca2+, Fe3+, and Ni2+ were strongly bound to the walls and could be detected by both atomic absorption and by their electron-scattering power in thin sections, qhereas the other metals were fisplaced or replaced. Partial lysozyme digestion of the walls (causing a 28% loss of a [3H]diaminopimelic acid label) greatly diminished the Mg2+ retention but not that of Ca2+, Fe3+, or Ni2+, indicating that there are select sites for various cations.

Isoprenoid and Dicarboxylic Acids Isolated from Colorado Green River Shale (Eocene)

Isolation of the C(9) and C(10) isoprenoid carboxylic acids, the C(12) to C(18)alpha,omega-dicarboxylic acids, and the 2-methyl 1,n-dicarboxylic acids (n is 13, 15, and 16) from organic extract of the Colorado Green River shale (Eocene) is reported. Separation was achieved by column and gas-liquid chromatographic techniques and structural identification of individual components, by mass spectrometry.

Perhydro-β-Carotene in the Green River Shale

Several triterpenes and the tetraterpene perhydro-beta-carotene have been identified in the branched-cyclic hydrocarbon fraction of this Eocene shale. The analytical procedure included thiourea adduction followed by combined gas chromatography and mass spectrometry.

Alga-like fossils from the early precambrian of South Africa

Micropaleontological studies of carbonaceouis chert from the Fig Tree Series of South Africa (> 3.1 x 10(9) years old) revealed the presence of spheroidal microfossils, here designated Archaeosphaeroides barbertonensis, interpreted as probably representing the remnants of unicellular alga-like organisms. The presumed photosynthetic nature of these primitive microorganisms seems corroborated by organic geochemical and carbon isotopic studies of the Fig Tree organic matter, and is consistent with the geologically and mineralogically indicated Early Precambrian environment. These alga-like spheroids, together with a bacterium-like organism previously described from the Fig Tree chert, are the oldest fossil orgisms now known.

Occurrence of Isoprenoid Fatty Acids in the Green River Shale

The most abundant free fatty acids present in a sample of shale from the Green River Formation (Eocene, about 60 x 10(6) years) from Sulfur Creek are the acylic C(19) and C(20) isoprenoid acids. The dominance of these acids parallels the abundance of the corresponding hydrocarbons pristane and phytane.

Isoprenoid Hydrocarbons in Recent Sediments: Presence of Pristane and Probable Absence of Phytane

Pristane (2,6,10,14-tetramethylpentadecane) has been isolated from two recent marine sediments. Unlike their ancient counterparts, these sediments contain no detectable phytane. These two facts suggest a biochemical origin for at least a fraction of the sedimentary pristane and a later, geochemical formation of phytane. Commercial reagent-grade solvents (pentane, isooctane, methanol) contain appreciable quantities of fossil pristane and probably phytane.

Soudan Formation: Organic Extracts of Early Precambrian Rocks

Biological-type alkanes are present in rocks of the Soudan formation that are more than 2.7 x 10(9) years old, but evidence of life in Soudan times is marginal. The distributional patterns of the alkanes from various regions in the Soudan indicate an indigenous origin of these compounds. Isotopic analyses do not confirm the compositional analyses.

Microorganisms from the Late Precambrian of Central Australia

An assemblage of structurally and organically well preserved microorganisms, interpreted as both green and blue-green algae, has been found in chert facies of the Bitter Springs limestone from the upper Precambrian of central Australia. This appears to be the earliest known occurrence of green algae in the fossil record. These organisms are among the oldest known multicellular and unicellular fossils exhibiting distinct histological preservation.

Paleobiology of a Precambrian Shale: Geology, organic geochemistry, and paleontology are applied to the problem of detection of ancient life

Investigations have been made of crude oil, pristane, phytane, steranetype and optically active alkanes, porphyrins, microfossils, and the stable isotopes of carbon and of sulfur found in the Nonesuch shale of Precambrian age from Northern Michigan. These sediments are approximately 1 billion years old. Geologic evidence indicates that they were deposited in a nearshore deltaic environment. Porphyrins are found in the siltstones but not in the crude oils of the Nonesuch formation-evidence that these chemical fossils are adsorbed or absorbed and immobile. This immobility makes it highly unlikely that these porphyrins could have moved from younger formations into the Nonesuch sediments, and the widely disseminated particulate organic matters and fossils in this Precambrian shale are certainly indigenous.