Martin P. Koopmans

Evidence for gammacerane as an indicator of water column stratification.

A new route for the formation of gammacerane from tetrahymanol is proposed; in addition to dehydration and hydrogenation, sulphurisation and early C-S cleavage are shown to be important in the pathway of formation, especially in marine sediments. Evidence is twofold. First, relatively large amounts of the gammacerane skeleton are sequestered in S-rich macromolecular aggregates formed by natural sulphurisation of functionalised lipids. Selective cleavage of polysulphide linkages with MeLi/MeI led to formation of 3-methylthiogammacerane, indicating that the gammacerane skeleton is primarily bound via sulphur at position 3, consistent with the idea that tetrahymanol (or the corresponding ketone) is the precursor for gammacerane. Second, upon mild artificial maturation of two sediments using hydrous pyrolysis, gammacerane is released from S-rich macromolecular aggregates by cleavage of the relatively weak C-S bonds. The stable carbon isotopic compositions of gammacerane and lipids derived from primary producers and green sulphur bacteria in both the Miocene Gessoso-solfifera and Upper Jurassic Allgau Formations indicate that gammacerane is derived from bacterivorous ciliates which were partially feeding on green sulphur bacteria. This demonstrates that anaerobic ciliates living at or below the chemocline are important sources for gammacerane, consistent with the fact that ciliates only biosynthesize tetrahymanol if their diet is deprived of sterols. This leads to the conclusion that gammacerane is an indicator for water column stratification, which solves two current enigmas in gammacerane geochemistry. Firstly, it explains why gammacerane is often found in sediments deposited under hypersaline conditions but is not necessarily restricted to this type of deposits. Secondly, it explains why lacustrine deposits may contain abundant gammacerane since most lakes in the temperate climatic zones are stratified during summer.

Diagenetic and catagenetic products of isorenieratene: Molecular indicators for photic zone anoxia

Abstract A wide range of novel diagenetic and catagenetic products of the diaromatic carotenoid isorenieratene, a pigment of the photosynthetic green sulphur bacteria Chlorobiaceae, has been identified in a number of sedimentary rocks ranging from Ordovician to Miocene. Compound identification is based on NMR, mass spectrometry, the presence of atropisomers, and stable carbon isotopes. Atropisomers contain an axially chiral centre which, in combination with other chiral centres, results in two or more diastereomers that can be separated on a normal GC column. Chlorobiaceae use the reverse TCA cycle to fix carbon, so that their biomass is enriched in 13C. High 13C contents of isorenieratene derivatives therefore support their inferred origins. Isorenieratene derivatives include C 40, C 33, and C 32, diaryl isoprenoids and short-chain aryl isoprenoids with additional aromatic and/or S-containing rings. C 33 and C 32 compounds are diagenetic products of C 33 and C 32 “carotenoids” formed from isorenieratene during early diagenesis through expulsion of toluene and m-xylene, respectively. Cyclisation of the polyene acyclic isoprenoid chain can proceed via an intramolecular Diels-Alder reaction, followed by aromatisation of the newly formed ring. Sulphurisation is also an important process during early diagenesis, competing with expulsion and cyclisation. Sulphur-bound isorenieratane is released during progressive diagenesis, due to cleavage of relatively weak S S and C S bonds. Cleavage of C-C bonds during aromatisation of newly formed rings and during catagenesis yields short-chain compounds. The inherent presence of a conjugated double bond system in carotenoids implies that similar diagenetic and catagenetic reactions can occur with all carotenoids. Chlorobiaceae live at or below the oxic/anoxic boundary layer and require both light and H 2S. The presence of isorenieratene or its diagenetic and catagenetic products in ancient sedimentary rocks and crude oils is therefore an excellent indication for photic zone anoxia in the depositional environment. Diagenetic and catagenetic products of isorenieratene are expected to find applications in reconstruction of palaeoenvironments and in oil-oil and oil-source rock correlation studies. Their presence in several petroleum source rocks suggests that anoxia is an important environmental parameter for the preservation of organic matter.

The controls on the composition of biodegraded oils in the deep subsurface—part 1: biodegradation rates in petroleum reservoirs

Abstract Biodegradation rates in oilfields have been assessed conservatively using whole oil-column minimum rate estimates, diffusion-controlled oil column compositional gradient modelling and mixed oil kinetic models. Biodegradation rate constants (first order) are around 10−6–10−7 yr−1 for hydrocarbons in the degradation zones these corresponding well with zero order field-wide minimum rate estimates of about 10−8 kg hydrocarbons/kg oil/year for the whole oil column. With biodegradation induction times of around 1–2 Ma to perturb an entire oil column for light oil reservoirs and 10–20 Ma for heavy oil reservoir degradation the results indicate that where we see continuous gradients in the oil columns, degradation must have been occurring episodically for many millions of years. To remove the n-alkanes from an oil (i.e. about 10% of an oil) around ca 15 Ma is needed for a heavy oil (ca 5 Ma for a light N. Sea oil). The timescales of oilfield degradation and filling are thus very similar and consequently the degree of biodegradation will be substantially controlled by oilfield charge history. Assessment of mixed degraded/non-degraded oil occurrence provides an independent confirmation that these rates are realistic and that timescales of degradation and field charging are similar. The maximum effective rate constant of degradation, ultimately controlled by the limiting effect of diffusion of alkanes to the oil water contact (OWC) (ca 10−4 yr−1 for a 130 m thick oil column first order rate constant) is well above the estimated rate constants indicating oil biodegradation rate is not limited by electron donor supply (i.e. hydrocarbons) but by supply of nutrients or oxidants. This suggests that diffusive transport of nutrients and electron acceptors in the aquifer to the site of biodegradation may be adequate to maintain the low rate biosphere.

Structural characterization, occurrence and fate of archaeal ether-bound acyclic and cyclic biphytanes and corresponding diols in sediments

Abstract Acyclic and cyclic biphytane carbon skeletons derived from planktonic archaea have been investigated in a number of marine and lacustrine sediments. With the exception of a tricyclic biphytane, the structures have been identified using authentic standards obtained from the thermophilic archaeon Sulfolobus solfataricus . The tricyclic biphytane, which is different to that biosynthesized by S. solfataricus , was tentatively identified based on mass spectral data. These acyclic and cyclic biphytanes occur ether-bound at the α and ω positions and as free and ester-bound α , ω -diols. Artificial maturation experiments show that the acyclic biphytane can endure greater thermal stress than cyclic biphytanes, in accordance with the occurrence of the acyclic biphytane in petroleum but absence of cyclic biphytanes. Compound specific isotope analysis reveals that the biphytanes all have similar 13 C-contents to each other, even among different sediments. The acyclic biphytane sometimes differs in 13 C-contents compared to the cyclic biphytanes, suggesting an additional source for this compound, possibly methanogenic archaea. Acyclic and cyclic biphytanes are sometimes the most abundant lipids in sediments compared to those biosynthesized by eukaryotes and prokaryotes, indicating that pelagic archaea can be a much more important source of sedimentary lipids than thought previously.

A thermal and chemical degradation approach to decipher pristane and phytane precursors in sedimentary organic matter

A thermal and chemical degradation approach was followed to determine the precursors of pristane (Pr) and phytane (Ph) in samples from the Gessoso-solfifera, Ghareb and Green River Formations. Hydrous pyrolysis of these samples yields large amounts of Pr and Ph carbon skeletons, indicating that their precursors are predominantly sequestered in high-molecular-weight fractions. However, chemical degradation of the polar fraction and the kerogen of the unheated samples generally does not release large amounts of Pr and Ph. Additional information on the precursors of Pr and Ph is obtained from flash pyrolysis analyses of kerogens and residues after hydrous pyrolysis and after chemical degradation. Multiple precursors for Pr and Ph are recognised in these three samples. The main increase of the Pr/Ph ratio with increasing maturation temperature, which is associated with strongly increasing amounts of Pr and Ph, is probably due to the higher amount of precursors of Pr compared to Ph, and not to the different timing of generation of Pr and Ph.

Restricted utility of aryl isoprenoids as indicators for photic zone anoxia

In a North Sea oil, the carotenoid derivatives -carotene, -isorenieratane, and isorenieratane were identified, together with a series of aryl isoprenoids with a 2,3,6-trimethyl substitution pattern for the aromatic ring. The 13C values of -carotene and -isorenieratane are similar, whereas isorenieratane is ca. 15% heavier. This suggests that -isorenieratane is not derived from -isorenieratane biosynthesised by Chlorobiaceae, but from aromatisation of -carotene. This was confirmed by laboratory aromatisation of partially hydrogenated -carotene, which yielded -isorenieratane as the main product. The aryl isoprenoids, which can be formed by C---C bond cleavage of both isorenieratane and -isorenieratane, have a mixed isotopic signature in the oil. These results indicate that mere identification of aryl isoprenoids, without determination of their 13C values, cannot be used to assess the presence of Chlorobiaceae, and, thus, photic zone anoxia in the depositional environment.

Impact of dia- and catagenesis on sulphur and oxygen sequestration of biomarkers as revealed by artificial maturation of an immature sedimentary rock

Hydrous pyrolysis of an immature (Ro ≈ 0.25%) sulphur-rich marl from the Gessoso-solfifera Formation (Messinian) in the Vena del Gesso Basin was carried out at 160°C ≤ T ≤330°C for 72 h, to study the effect of progressive diagenesis and early catagenesis on the abundance and distribution of sulphur-containing and sulphur- and oxygen-linked carbon skeletons in low-molecular-weight and high-molecular-weight fractions (e.g. kerogen). To this end, compounds in the saturated hydrocarbon fraction, monoaromatic hydrocarbon fraction, polyaromatic hydrocarbon fraction, alkylsulphide fraction and ketone fraction were quantified, as well as compounds released after desulphurisation of the polar fraction and HILiAlH4 treatment of the desulphurised polar fraction. Sulphur-bound phytane and (20R)-5α,14α,17α(H) and (20R)-5β,14α,17α(H) C27–C29 steranes in the polar fraction become less abundant with increasing maturation temperature, whereas the amount of their corresponding hydrocarbons increases in the saturated hydrocarbon fraction. Carbon skeletons that are bound in the kerogen by multiple bonds (e.g. C38n-alkane and isorenieratane) are first released into the polar fraction, and then as free hydrocarbons. These changes occur at relatively low levels of thermal maturity (Ro <0.6%), as evidenced by the “immature” values of biomarker maturity parameters such as the ββ/(ββ + αβ + βα) C35 hopane ratio and the 22S/(22S + 22R)−17α,21β(H) C35 hopane ratio. Sulphur- and oxygen-bound moieties, present in the polar fraction, are not stable with increasing thermal maturation. However, alkylthiophenes, ketones, 1,2-di-n-alkylbenzenes and free n-alkanes seem to be stable thermal degradation products of these sulphur- and oxygen-bound moieties. Thus, apart from free n-alkanes, which are abundantly present in more mature sedimentary rocks and crude oils, alkylthiophenes, 1,2-di-n-alkylbenzenes and ketones can also be expected to occur. The positions of the thiophene moiety and the carbonyl group coincide with the original positions of the functional groups of their precursors. Thus, important information about palaeobiochemicals is retained throughout the sequestration/degradation process.

SULPHURISATION OF HOMOHOPANOIDS : EFFECTS ON CARBON NUMBER DISTRIBUTION, SPECIATION, AND 22S/22R EPIMER RATIOS

Abstract Sulphurisation has been recognised as the most important diagenetic pathway acting on hopanoids in the organic-rich limestones, marlstone, and dolomite investigated. The qualitative and quantitative analysis of free and S-bound hopanoid moieties revealed that the incorporation of sulphur has a major impact on the carbon number distribution, the speciation and on the 22 S (22S+22 R ) ratio of the hopanoids. C35 carbon skeletons are preferentially preserved by sulphur incorporation at the end of the side chain. Hopanoid sulphides, with the sulphur atom attached to one carbon atom of ring D or E and to one carbon atom of the side chain (condensed-type), are predominantly formed from precursors with a partially degraded side chain. In all samples the degree of sulphurisation of hopanoids increases with increasing carbon number. The carbon skeleton speciation changes with maturation in favour of hopanoid thiophenes, which are evidently the most stable hopanoid sulphur compounds, and hopanes. Hopanes are mainly formed via a sulphurisation/desulphurisation pathway and increase in concentration with maturity. Their original carbon number distribution is strongly shifted towards the lower homologues. With increasing maturity only a slight dominance of the C35 members emerges. The most abundant series of condensed-type hopanoid sulphides have a 22R homohopane carbon skeleton that is not isomerised during maturation. The generation of hopanes from these condensed-type hopanoid sulphides during maturation leads to 22 S (22S+22 R ) ratios which increase with carbon number (e.g., from about 0.2 for C31 to 0.5 for C35 homologues). Data acquired from the sedimentary rock samples are supported by those obtained from artificial maturation experiments of a limestone by hydrous pyrolysis at different temperatures. The data show that generally accepted molecular maturation parameters have to be applied with caution.

Sulphur and oxygen sequestration of n-C37 and n-C38 unsaturated ketones in an immature kerogen and the release of their carbon skeletons during early stages of thermal maturation

Sedimentary rock from the Gessoso-solfifera Formation (Messinian) in the Vena del Gesso Basin (northern Italy) containing immature (Ro = 0.25%) S-rich organic matter was artificially matured by hydrous pyrolysis at temperatures from 160 to 330°C for 72 h to study the diagenetic fate of n-C37 and n-C38 di- and tri-unsaturated methyl and ethyl ketones (alkenones) biosynthesised by several prymnesiophyte algae. During early diagenesis, the alkenones are incorporated into the kerogen by both sulphur and oxygen cross-linking as indicated by chemical degradation experiments with the kerogen of the unheated sample. Heating at temperatures between 160 and 260°C, which still represents early stages of thermal maturation, produces large amounts (up to 1 mg/g TOC) of S-bound, O-bound, and both S- and O-bound n-C37 and n-C38 skeletons, saturated n-C37 and n-C38 methyl, ethyl, and mid-chain ketones, C37 and C38 mid-chain 2,5-di-n-alkylthiophenes, C37 and C38 1,2-di-n-alkylbenzenes, and C37 and C38 n-alkanes. With increasing thermal maturation, three forms of the n-C37 and n-C38 skeletons are relatively stable (saturated hydrocarbons, 1,2-di-n-alkylbenzenes and saturated ketones), whereas the S- and O-bound skeletons are relatively labile. These results suggest that in natural situations saturated ketones with an n-C37 and n-C38 skeleton can be expected as well as the corresponding hydrocarbons.

Thermal stability of thiophene biomarkers as studied by hydrous pyrolysis

Abstract An immature ( R o = 0.25%) sulphur-rich calcareous shale from the Gessoso-solfifera Formation (Messinian) in the Vena del Gesso Basin (northern Italy) was artificially matured by hydrous pyrolysis at constant temperatures ranging from 160 to 330°C for 72 h to study the applicability of alkylthiophenes as molecular indicators during progressive diagenesis and early catagenesis. Artificial maturation at temperatures up to 330°C generated large amounts of alkylthiophenes from the thermal degradation of kerogen. The importance of the kerogen in the production of alkylthiophenes is supported by the observation that the isomer distributions of alkylthiophenes at high temperatures coincide with the isomer distributions of alkylthiophenes in the Curie-point pyrolysate of the isolated kerogen of the original sample. The generation profiles of the thiophenes with a phytane carbon skeleton and the 3,4-di- n -alkylthiophenes suggest that continuous degradation of alkylthiophenes is also taking place, so that the overall effect is alkylthiophene concentrations with intermediate values. The structural isomer distribution of linear alkylthiophenes does not change significantly when these compounds are generated at different temperatures. This implies that important information regarding the original positions of functionalities in the precursor molecules is retained and, thus, that alkylthiophenes are useful biomarkers at relatively high levels of thermal maturity (up to R o ≈ 0.95–1.1%).