A Review of Macromolecular Organic Compounds That Comprise Living Organisms and Their Role in Kerogen, Coal, and Petroleum Formation

Long-term preservation of biomolecules in lake sediments: potential importance of physical shielding by recalcitrant cell walls

Even though lake sediments are globally important organic carbon (OC) sinks, the controls on long-term OC storage in these sediments are unclear. Using a multiproxy approach, we investigate changes in diatom, green algae, and vascular plant biomolecules in sedimentary records from the past centuries across five temperate lakes with different trophic histories. Despite past increases in the input and burial of OC in sediments of eutrophic lakes, biomolecule quantities in sediments of all lakes are primarily controlled by postburial microbial degradation over the time scales studied. We, moreover, observe major differences in biomolecule degradation patterns across diatoms, green algae, and vascular plants. Degradation rates of labile diatom DNA exceed those of chemically more resistant diatom lipids, suggesting that chemical reactivity mainly controls diatom biomolecule degradation rates in the lakes studied. By contrast, degradation rates of green algal and vascular plant DNA are significantly lower than those of diatom DNA, and in a similar range as corresponding, much less reactive lipid biomarkers and structural macromolecules, including lignin. We propose that physical shielding by degradation-resistant cell wall components, such as algaenan in green algae and lignin in vascular plants, contributes to the long-term preservation of labile biomolecules in both groups and significantly influences the long-term burial of OC in lake sediments.

Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds

Methane-generating archaea drive the final step in anaerobic organic compound mineralization and dictate the carbon flow of Earth's diverse anoxic ecosystems in the absence of inorganic electron acceptors. Although such Archaea were presumed to be restricted to life on simple compounds like hydrogen (H2), acetate or methanol, an archaeon, Methermicoccus shengliensis, was recently found to convert methoxylated aromatic compounds to methane. Methoxylated aromatic compounds are important components of lignin and coal, and are present in most subsurface sediments. Despite the novelty of such a methoxydotrophic archaeon its metabolism has not yet been explored. In this study, transcriptomics and proteomics reveal that under methoxydotrophic growth M. shengliensis expresses an O-demethylation/methyltransferase system related to the one used by acetogenic bacteria. Enzymatic assays provide evidence for a two step-mechanisms in which the methyl-group from the methoxy compound is (1) transferred on cobalamin and (2) further transferred on the C1-carrier tetrahydromethanopterin, a mechanism distinct from conventional methanogenic methyl-transfer systems which use coenzyme M as final acceptor. We further hypothesize that this likely leads to an atypical use of the methanogenesis pathway that derives cellular energy from methyl transfer (Mtr) rather than electron transfer (F420H2 re-oxidation) as found for methylotrophic methanogenesis.

Access to diverse organosulfur compounds via arynes: a comprehensive review on Kobayashi's aryne precursor

Arynes are highly reactive transient intermediates having enormous applications in organic synthesis. In the last three decades aryne chemistry has shown incredible developments in carbon-carbon and carbon-heteroatom bond formation reactions. After the discovery of Kobayashi's protocol for the generation of aryne intermediates in a mild way, this field of chemistry witnessed rapid growth in synthetic organic chemistry. One aspect of development in this field involves C-S bond formation under mild conditions which has a tremendous scope for the synthesis of various important organosulfur building blocks.

Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach

Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.

Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures

Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance organic carbon oxidation via direct electron transfer. Here, we investigated the effect of various iron oxide phases with differing crystallinity (magnetite, hematite, and lepidocrocite) during microbial degradation of the aromatic model compound benzoate in methanic sediments. In slurry incubations with magnetite or hematite, concurrent iron reduction, and methanogenesis were stimulated during accelerated benzoate degradation with methanogenesis as the dominant electron sink. In contrast, with lepidocrocite, benzoate degradation, and methanogenesis were inhibited. These observations were reproducible in sediment-free enrichments, even after five successive transfers. Genes involved in the complete degradation of benzoate were identified in multiple metagenome assembled genomes. Four previously unknown benzoate degraders of the genera Thermincola (Peptococcaceae, Firmicutes), Dethiobacter (Syntrophomonadaceae, Firmicutes), Deltaproteobacteria bacteria SG8_13 (Desulfosarcinaceae, Deltaproteobacteria), and Melioribacter (Melioribacteraceae, Chlorobi) were identified from the marine sediment-derived enrichments. Scanning electron microscopy (SEM) and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) images showed the ability of microorganisms to colonize and concurrently reduce magnetite likely stimulated by the observed methanogenic benzoate degradation. These findings explain the possible contribution of organoclastic reduction of iron oxides to the elevated dissolved Fe²⁺ pool typically observed in methanic zones of rapidly accumulating coastal and continental margin sediments.

Several ways one goal-methanogenesis from unconventional substrates

Abstract

Methane is the second most important greenhouse gas on earth. It is produced by methanogenic archaea, which play an important role in the global carbon cycle. Three main methanogenesis pathways are known: in the hydrogenotrophic pathway H₂ and carbon dioxide are used for methane production, whereas in the methylotrophic pathway small methylated carbon compounds like methanol and methylated amines are used. In the aceticlastic pathway, acetate is disproportionated to methane and carbon dioxide. However, next to these conventional substrates, further methanogenic substrates and pathways have been discovered. Several phylogenetically distinct methanogenic lineages (Methanosphaera, Methanimicrococcus, Methanomassiliicoccus, Methanonatronarchaeum) have evolved hydrogen-dependent methylotrophic methanogenesis without the ability to perform either hydrogenotrophic or methylotrophic methanogenesis. Genome analysis of the deep branching Methanonatronarchaeum revealed an interesting membrane-bound hydrogenase complex affiliated with the hardly described class 4 g of multisubunit hydrogenases possibly providing reducing equivalents for anabolism. Furthermore, methylated sulfur compounds such as methanethiol, dimethyl sulfide, and methylmercaptopropionate were described to be converted into adapted methylotrophic methanogenesis pathways of Methanosarcinales strains. Moreover, recently it has been shown that the methanogen Methermicoccus shengliensis can use methoxylated aromatic compounds in methanogenesis. Also, tertiary amines like choline (N,N,N-trimethylethanolamine) or betaine (N,N,N-trimethylglycine) have been described as substrates for methane production in Methanococcoides and Methanolobus strains. This review article will provide in-depth information on genome-guided metabolic reconstructions, physiology, and biochemistry of these unusual methanogenesis pathways.

Key points

• Newly discovered methanogenic substrates and pathways are reviewed for the first time.

• The review provides an in-depth analysis of unusual methanogenesis pathways.

• The hydrogenase complex of the deep branching Methanonatronarchaeum is analyzed.

Microbial Diversity in Deep-Subsurface Hot Brines of Northwest Poland: from Community Structure to Isolate Characteristics

Deep-subsurface hot brines in northwest Poland, extracted through boreholes reaching 1.6 and 2.6 km below the ground surface, were microbiologically investigated using culture-independent and culture-dependent methods. The high-throughput sequencing of 16S rRNA gene amplicons showed a very low diversity of bacterial communities, which were dominated by phyla Proteobacteria and Firmicutes Bacterial genera potentially involved in sulfur oxidation and nitrate reduction (Halothiobacillus and Methylobacterium) prevailed in both waters over the sulfate reducers ("Candidatus Desulforudis" and Desulfotomaculum). Only one archaeal taxon, affiliated with the order Thermoplasmatales, was detected in analyzed samples. Bacterial isolates obtained from these deep hot brines were closely related to Bacillus paralicheniformis based on the 16S rRNA sequence similarity. However, genomic and physiological analyses made for one of the isolates, Bacillus paralicheniformis strain TS6, revealed the existence of more diverse metabolic pathways than those of its moderate-temperature counterpart. These specific traits may be associated with the ecological adaptations to the extreme habitat, which suggest that some lineages of B. paralicheniformis are halothermophilic.IMPORTANCE Deep-subsurface aquifers, buried thousands of meters down the Earth's crust, belong to the most underexplored microbial habitats. Although a few studies revealed the existence of microbial life at the depths, the knowledge about the microbial life in the deep hydrosphere is still scarce due to the limited access to such environments. Studying the subsurface microbiome provides unique information on microbial diversity, community structure, and geomicrobiological processes occurring under extreme conditions of the deep subsurface. Our study shows that low-diversity microbial assemblages in subsurface hot brines were dominated by the bacteria involved in biogeochemical cycles of sulfur and nitrogen. Based on genomic and physiological analyses, we found that the Bacillus paralicheniformis isolate obtained from the brine under study differed from the mesophilic species in the presence of specific adaptations to harsh environmental conditions. We indicate that some lineages of B. paralicheniformis are halothermophilic, which was not previously reported.

Lipid Biomarkers in Ephemeral Acid Salt Lake Mudflat/Sandflat Sediments: Implications for Mars

Sedimentary strata on Mars often contain a mix of sulfates, iron oxides, chlorides, and phyllosilicates, a mineral assemblage that is unique on Earth to acid brine environments. To help characterize the astrobiological potential of depositional environments with similar minerals present, samples from four naturally occurring acidic salt lakes and adjacent mudflats/sandflats in the vicinity of Norseman, Western Australia, were collected and analyzed. Lipid biomarkers were extracted and quantified, revealing biomarkers from vascular plants alongside trace microbial lipids. The resilience of lipids from dead organic material in these acid saline sediments through the pervasive stages of early diagenesis lends support to the idea that sulfates, in tandem with phyllosilicates and iron oxides, could be a viable target for biomarkers on Mars. To fully understand the astrobiological potential of these depositional environments, additional investigations of organic preservation in ancient acidic saline sedimentary environments are needed.

How to Detect Life on Icy Moons

The icy moons of the outer Solar System present the possibility of subsurface water, habitable conditions, and potential abodes for life. Access to evidence that reveals the presence of life on the icy moons can be facilitated by plumes that eject material from the subsurface out into space. One instrument capable of performing life-search investigations at the icy moons is the MAss SPectrometer for Planetary EXploration/Europa (MASPEX), which constitutes a high-resolution, high-sensitivity multibounce time-of-flight mass spectrometer capable of measuring trace amounts (ppb) of organic compounds. MASPEX has been selected for the NASA Europa Clipper mission and will sample any plumes and the surface-sputtered atmosphere to assess any evidence for habitability and life. MASPEX is capable of similar investigations targeted at other icy moons. Data may be forthcoming from direct sampling but also impact dissociation because of the high speed of some analytes. Impact dissociation is analogous to the dissociation provided by modern analytical pyrolysis methods. Radiolytic dissociation on the europan surface before or during the sputtering process can also induce fragmentation similar to pyrolysis. In this study, we have compiled pyrolysis mass spectrometry data from a variety of biological and nonbiological materials to demonstrate the ability of MASPEX to recognize habitability and detect life in any plumes and atmospheres of icy moons. Key Words: Europa-Icy moons-Life detection-Mass spectrometry-Organic matter. Astrobiology 18, 843-855.

Changes of aliphatic C-H bonds in cyanobacteria during experimental thermal maturation in the presence or absence of silica as evaluated by FTIR microspectroscopy

Aliphatic C-H bonds are one of the major organic signatures detected in Proterozoic organic microfossils, and their origin is a topic of interest. To investigate the influence of the presence of silica on the thermal alteration of aliphatic C-H bonds in prokaryotic cells during diagenesis, cyanobacteria Synechocystis sp. PCC6803 were heated at temperatures of 250-450°C. Changes in the infrared (IR) signals were monitored by micro-Fourier transform infrared (FTIR) spectroscopy. Micro-FTIR shows that absorbances at 2,925 cm^-1 band (aliphatic CH₂ ) and 2,960 cm^-1 band (aliphatic CH₃ ) decrease during heating, indicating loss of the C-H bonds, which was delayed by the presence of silica. A theoretical approach using solid-state kinetics indicates that the most probable process for the aliphatic C-H decrease is three-dimensional diffusion of alteration products under both non-embedded and silica-embedded conditions. The extrapolation of the experimental results obtained at 250-450°C to lower temperatures implies that the rate constant for CH₃ (k_CH3 ) is similar to or lower than that for CH₂ (k_CH2 ; i.e., CH₃ decreases at a similar rate or more slowly than CH₂ ). The peak height ratio of 2,960 cm^-1 band (CH₃ )/2,925 cm^-1 band (CH₂ ; R_3/2 values) either increased or remained constant during the heating. These results reveal that the presence of silica does affect the decreasing rate of the aliphatic C-H bonds in cyanobacteria during thermal maturation, but that it does not significantly decrease the R_3/2 values. Meanwhile, studies of microfossils suggest that the R_3/2 values of Proterozoic prokaryotic fossils from the Bitter Springs Group and Gunflint Formation have decreased during fossilization, which is inconsistent with the prediction from our experimental results that R_3/2 values did not decrease after silicification. Some process other than thermal degradation, possibly preservation of specific classes of biomolecules with low R_3/2 values, might have occurred during fossilization.

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30-530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments.

EIMS Fragmentation Pathways and MRM Quantification of 7α/β-Hydroxy-Dehydroabietic Acid TMS Derivatives

EI mass fragmentation pathways of TMS derivatives οf 7α/β-hydroxy-dehydroabietic acids resulting from NaBH(4)-reduction of oxidation products of dehydroabietic acid (a component of conifers) were investigated and deduced by a combination of (1) low energy CID-GC-MS/MS, (2) deuterium labeling, (3) different derivatization methods, and (4) GC-QTOF accurate mass measurements. Having identified the main fragmentation pathways, the TMS-derivatized 7α/β-hydroxy-dehydroabietic acids could be quantified in multiple reaction monitoring (MRM) mode in sea ice and sediment samples collected from the Arctic. These newly characterized transformation products of dehydroabietic acid constitute potential tracers of biotic and abiotic degradation of terrestrial higher plants in the environment.

Fourier transform infrared spectral detection of life in polar subsurface environments and its application to Mars exploration

Cryptoendolithic lichen communities of the Dry Valleys, Antarctica, survive in an extremely inhospitable environment, finding refuge in microscopic niches where conditions suitable for life exist. Such "within-rock" communities may have evolved on Mars when conditions for life on the surface deteriorated to such an extent that they could no longer survive. Fourier transform infrared spectroscopy of unprepared whole-rock Antarctic Beacon sandstones was used to vertically profile molecular vibrations of fatty acids, proteins, and carboxylic acids created by endolithic communities. Spectral biosignatures were found localized to lichen-rich areas and were absent in crustal regions and the bulk rock substrate. These cryptoendolithic profiles will aid similar spectroscopic investigations of organic biosignatures during future Martian subsurface studies and will help in the identification of similar communities in other localities across the Earth.

Differences in the chemical composition of organic-walled dinoflagellate resting cysts from phototrophic and heterotrophic dinoflagellates

Dinoflagellates constitute a large proportion of the planktonic biomass from marine to freshwater environments. Some species produce a preservable organic-walled resting cyst (dinocyst) during the sexual phase of their life cycle that is an important link between the organisms, the environment in which their parent motile theca grew, and the sedimentary record. Despite their abundance and widespread usage as proxy indicators for environmental conditions, there is a lack of knowledge regarding the dinocyst wall chemical composition. It is likely that numerous factors, including phylogeny and life strategy, determine the cyst wall chemistry. However, the extent to which this composition varies based on inherent (phylogenetic) or variable (ecological) factors has not been studied. To address this, we used micro-Fourier transform infrared spectroscopy to analyze nine cyst species produced by either phototrophic or heterotrophic dinoflagellates from the extant orders Gonyaulacales, Gymnodiniales, and Peridiniales. Based on the presence of characteristic functional groups, two significantly different cyst wall compositions are observed that correspond to the dinoflagellate's nutritional strategy. The dinocyst wall compositions analyzed appeared carbohydrate-based, but the cyst wall produced by phototrophic dinoflagellates suggested a cellulose-like glucan, while heterotrophic forms produced a nitrogen-rich glycan. This constitutes the first empirical evidence nutritional strategy is related to different dinocyst wall chemistries. Our results indicated phylogeny was less important for predicting composition than the nutritional strategy of the dinoflagellate, suggesting potential for cyst wall chemistry to infer past nutritional strategies of extinct taxa preserved in the sedimentary record.

Preservation and evolution of organic matter during experimental fossilisation of the hyperthermophilic archaea Methanocaldococcus jannaschii

Identification of the earliest traces of life is made difficult by the scarcity of the preserved microbial remains and by the alteration and potential contamination of the organic matter (OM) content of rocks. These factors can confuse interpretations of the biogenicity and syngenicity of fossilised structures and organic molecules found in ancient rocks. In order to improve our knowledge of the fossilisation processes and their effects at the molecular level, we made a preliminary study of the fate of OM during experimental fossilisation. Changes in the composition and quantity of amino acids, monosaccharides and fatty acids were followed with HPLC, GC and GC-MS analyses during 1 year of silicification of the hyperthermophilic Archaea Methanocaldococcus jannaschii. Although the cells themselves did not fossilise and the accompanying extracellular polymeric substances (EPS) did, our analyses showed that the OM initially present in both cells and EPS was uniformly preserved in the precipitated silica, with amino acids and fatty acids being the best preserved compounds. This study thus completes previous data obtained by electron microscopy investigations of simulated microbial fossilisation and can help better identification and interpretation of microbial biosignatures in both ancient rocks and in recent hydrothermal formations and sediments.

Host responses of a marine bacterium, Roseobacter denitrificans OCh114, to phage infection

RDJLΦ1 is a marine siphophage infecting Roseobacter denitrificans OCh114. In this study, host responses of R. denitrificans OCh114 to phage infection were investigated through in situ real-time atomic force microscopy (AFM) and proteomics approaches. As seen from the AFM observations, during phage infection processes, depression areas appeared on the host cell surface in a few minutes after infection and expanded in both diameter and depth over time and finally led to the collapse of host cells within 30 min. The two-dimensional polyacrylamide gel electrophoresis revealed significant changes in the proteomic composition of the host cells during infection. The expression of 91 proteins, including some involved in DNA transcription regulation and substrate transportation, was changed with at least twofold up- or downregulation as compared to the control without phage infection. This observed rapid lysis of host cells and the great changes in protein expression caused by phage infection added more perspectives to the documented important roles of viruses in mediating carbon cycling in the ocean.

The microbial carbon pump: from genes to ecosystems

The majority of marine dissolved organic carbon (DOC) is resistant to biological degradation and thus can remain in the water column for thousands of years, constituting carbon sequestration in the ocean. To date the origin of such recalcitrant DOC (RDOC) is unclear. A recently proposed conceptual framework, the microbial carbon pump (MCP), emphasizes the microbial transformation of organic carbon from labile to recalcitrant states. The MCP is concerned with both microbial uptakes and outputs of DOC compounds, covering a wide range from gene to ecosystem levels. In this minireview, the ATP binding cassette (ABC) transporter is used as an example for the microbial processing of DOC at the genetic level. The compositions of the ABC transporter genes of the two major marine bacterial clades Roseobacter and SAR11 demonstrate that they have distinct patterns in DOC utilization: Roseobacter strains have the advantage of taking up carbohydrate DOC, while SAR11 bacteria prefer nitrogen-containing DOC. At the ecosystem level, bacterially derived RDOC based on d-amino acid biomarkers is reported to be responsible for about a quarter of the total marine RDOC pool. Under future global warming scenarios, partitioning of primary production into DOC could be enhanced, and thus the MCP could play an even more important role in carbon sequestration by the ocean. Joint efforts to study the MCP from multiple disciplines are required to obtain a better understanding of ocean carbon cycle and its coupling with global change.

An organic geochemical perspective on terrestrialization

The colonization of land required new strategies for safe gamete/diaspore dispersal, and to cope with desiccation, harmful radiation, fire and gravity. Accordingly, the morphology, behaviour and physiology of the organisms changed. Here, we explore to what extent physiological adaptations, reflected in the molecular content of the sediments, add to our understanding of the terrestrialization. Many compounds considered characteristic of land organisms do not provide valuable information from the fossil record since (1) they were not preserved; (2) they occur or correspond to substances that evolved prior to the terrestrialization (e.g. cutan vs. algaenan, cellulose); or (3) they have been changed diagenetically and/or catagenetically. The latter leads to geo(macro)molecules without a chemical fingerprint relating them to their original bio(macro)molecules despite, sometimes, excellent morphological preservation of the organic remains. Nevertheless, some molecular markers and their stable isotopes provide independent information on the terrestrialization process. The odd predominance of n-alkane surface waxes is a feature already apparent in early land plants and could, with caution, be used as such. Furthermore, fossil terpenoids and their derivatives are valuable for reconstructing the evolution of major plant groups. The radiation of the phenylpropanoid pathway with for example, sporopollenin and lignin seems to be closely related to the evolution of land plants.

Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment

This study has utilized the tools of lipid biomarker chemistry and molecular phylogenetic analyses to assess the archaeal contribution to diversity and abundance within a microbial mat and underlying sediment from a hypersaline lagoon in Baja California. Based on abundance of ether-linked isoprenoids, archaea made up from 1 to 4% of the cell numbers throughout the upper 100 mm of mat and sediment core. Below this depth archaeal lipid was two times more abundant than bacterial. Archaeol was the primary archaeal lipid in all layers. Relatively small amounts of caldarchaeol (dibiphytanyl glyceroltetraether) were present at most depths with phytanyl to biphytanyl molar ratios lowest (approximately 10 : 1) in the 4-17 mm and 100-130 mm horizons, and highest (132 : 1) in the surface 0-2 mm. Lipids with cyclic biphytanyl cores were only detected below 100 mm. A novel polar lipid containing a C(30) isoprenoid (squalane) moiety was isolated from the upper anoxic portion of the core and partially characterized. Hydrocarbon biomarker lipids included pentamethylicosane (2-10 mm) and crocetane (primarily below 10 mm). Archaeal molecular diversity varied somewhat with depth. With the exception of samples at 0-2 mm and 35-65 mm, Thermoplasmatales of marine benthic group D dominated clone libraries. A significant number of phylotypes representing the Crenarchaeota from marine benthic group B were generally present below 17 mm and dominated the 35-65 mm sample. Halobacteriaceae family made up 80% of the clone library of the surface 2 mm, and consisted primarily of sequences affiliated with the haloalkaliphilic Natronomonas pharaonis.

Levoglucosan and other cellulose markers in pyrolysates of Miocene lignites: geochemical and environmental implications

Using the pyrolysis-gas chromatography-mass spectrometry and off-line pyrolysis/silylation methods for lignites from three Miocene brown coal basins of Poland resulted in the characterization of many organic compounds, including dominant cellulose degradation products such as levoglucosan, 1,6-anhydro-beta-D-glucofuranose, and 1,4:3,6-dianhydroglucopyranose. Levoglucosan is a general source-specific tracer for wood smoke in the atmosphere and recent sediments. The presence of unusually high levels of this compound in brown coal pyrolysates suggests that a portion of this compound concentration in some airsheds may originate from lignite combustion. On the other hand, nonglucose anhydrosaccharides, in particular, mannosan and galactosan, typical of hemicellulose, are not detected in those lignite pyrolysates investigated. This indicates that mannosan and galactosan are better specific tracers for combustion of contemporary biomass in those regions were the utilization of brown coals containing fossilized cellulose is important.

An overview of developments related to the characterization and significance of high molecular weight paraffins/hydrocarbons (>C40) in crude oils

Over the past 10 years, investigations into the characteristics of the high molecular weight hydrocarbon (HMWHC) fraction in crude oils and, to a lesser extent, source rock extracts have continued to reveal novel information concerning the distribution of hydrocarbons >C40. The major impetus for this work has come from the fact that HMWHCs can cause significant production problems in certain geographical regions and particularly deepwater frontier areas. Since these HMWHCs appear to be ubiquitous in crude oils, the primary questions that need to be addressed are: what are these compounds, where do they come from, and how do they affect physical properties of oils? Here, we review our work over the past decade and discuss the significance of these results and their potential application to reservoir and production problems involving paraffins and asphaltenes.

It was commonly believed for many years that only oils derived from source rocks containing higher plant source material would have a high paraffin content. However, it is now abundantly clear that oils derived from lacustrine and marine source rocks also contain relatively high concentrations of higher molecular weight hydrocarbons. In addition to developing methods for the qualitative and quantitative separation of HMWHCs from asphaltenes, progress has been made in identifying individual components of the high molecular weight fraction. This fraction is not a simple mixture of n-alkanes but a complex mixture of seven or eight homologous hydrocarbon series, each with significantly different physical properties. A knowledge of these structures is important in predicting crude oil properties such as cloud point and pour point. Series identified to date include alkylcyclopentanes, alkylcyclohexanes, alkylbenzenes and various branched hydrocarbons.

In summary, since the 1970s most of the geochemical research emphasis has been placed on compounds below C40. Whilst compounds above C40 may not have the same degree of structural specificity as the traditional biomarkers, the amount of information available from these compounds could be extremely beneficial in the long term, particularly for reservoir characterization and production purposes and other problems involving high molecular weight hydrocarbons.

Comparative analysis of partial structures of a peat humic and fulvic acid using one- and two-dimensional nuclear magnetic resonance spectroscopy

Nuclear magnetic resonance (NMR) resonance integrals obtained from one-dimensional NMR spectra provide semiquantitative contents of humic constituents with limited resolution in structural detail. When supplemented by connectivity information available from homo- and heteronuclear two-dimensional NMR spectra a more reliable assignment of humic substructures becomes available. This is demonstrated with a comparative one- and two-dimensional NMR analysis of a fulvic and a humic acid obtained from Eriophorum peat. An example of a detailed analysis of the proton chemical shift region normally attributed to carbohydrates shows substantial contributions from amino acids, amino and desoxy sugars, and highly oxidized aliphatic chains of intermediate length. The very good resolution of structural detail by a combined analysis of all NMR spectra shows that the effect of the fractionation procedure on the composition and chemical structure of humic materials is very significant. The comparison of the partial structures comprising humic acid (HA) and fulvic acid (FA) of the peat humic materials studied indicates that FA is diagenetically downstream of HA, favoring the biopolymer degradation (BD) model of humification.

Evidence for non-selective preservation of organic matter in sinking marine particles

The sinking of particulate organic matter from ocean surface waters transports carbon to the ocean interior, where almost all is then recycled. The unrecycled fraction of this organic matter can become buried in ocean sediments, thus sequestering carbon and so influencing atmospheric carbon dioxide concentrations. The processes controlling the extensive biodegradation of sinking particles remain unclear, partly because of the difficulty in resolving the composition of the residual organic matter at depth with existing chromatographic techniques. Here, using solid-state 13C NMR spectroscopy, we characterize the chemical structure of organic carbon in both surface plankton and sinking particulate matter from the Pacific Ocean and the Arabian Sea. We found that minimal changes occur in bulk organic composition, despite extensive (>98%) biodegradation, and that amino-acid-like material predominates throughout the water column in both regions. The compositional similarity between phytoplankton biomass and the small remnant of organic matter reaching the ocean interior indicates that the formation of unusual biochemicals, either by chemical recombination or microbial biosynthesis, is not the main process controlling the preservation of particulate organic carbon within the water column at these two sites. We suggest instead that organic matter might be protected from degradation by the inorganic matrix of sinking particles.

Molecular taphonomy of animal and plant cuticles: selective preservation and diagenesis

The nature of organic material and the environment in which it is deposited exert a major influence on the extent to which biomacromolecules are preserved in the fossil record. The role of these factors is explored with a particular focus on the cuticle of arthropods and leaves. Preservation of the original chemistry of arthropod cuticles is favoured by their thickness and degree of sclerotization, and the presence of biominerals. Decay and burial in terrestrial as opposed to marine, and anoxic rather than oxygenated conditions, likewise appear to enhance preservation. The most important factor in the long–term preservation of the chemistry of both animal and plant cuticles, however, is diagenetic alteration to an aliphatic composition. This occurs even in amber, which encapsulates the fossil, eliminating almost all external factors. Some plants contain an original decay–resistant macromolecular aliphatic component but this is not the case in arthropods. It appears that the aliphatic components of many plant as well as animal fossils may be the result of diagenetic polymerization. Selective preservation as a result of decay resistance may explain the initial survival of organic materials in sediments, but in many cases longer–term preservation relies on chemical changes. Selective preservation is only a partial explanation for the origin of kerogen.

Terminal Proterozoic reorganization of biogeochemical cycles

The Proterozoic aeon (2,500-540 million years ago) saw episodic increases in atmospheric oxygen content, the evolution of multicellular life and, at its close, an enormous radiation of animal diversity. These profound biological and environmental changes must have been linked, but the underlying mechanisms have been obscure. Here we show that hydrocarbons extracted from Proterozoic sediments in several locations worldwide are derived mainly from bacteria or other heterotrophs rather than from photosynthetic organisms. Biodegradation of algal products in sedimenting matter was therefore unusually complete, indicating that organic material was extensively reworked as it sank slowly through the water column. We propose that a significant proportion of this reworking will have been mediated by sulphate-reducing bacteria, forming sulphide. The production of sulphide and consumption of oxygen near the ocean surface will have inhibited transport of O2 to the deep ocean. We find that preservation of algal-lipid skeletons improves at the beginning of the Cambrian, reflecting the increase in transport by rapidly sinking faecal pellets. We suggest that this rapid removal of organic matter will have increased oxygenation of surface waters, leading to a descent of the O2-sulphide interface to the sea floor and to marked changes in the marine environment, ultimately contributing to the Cambrian radiation.