Biomarker Evidence for a Major Preservation Pathway of Sedimentary Organic Carbon

Source, composition and molecular diversity of dissolved and particulate organic matter varied with riparian land use in tropical coastal headstreams

Source, composition and molecular diversity determine the reactivity and stabilization of organic matter (OM, dissolved [DOM]/particulate [POM]), affecting its behavior and fate. Here, multiple spectral and mass spectrometry techniques were applied to examine how riparian land-use shaped the source, composition and molecular diversity of POM and DOM (HDOM) in adjacent headstreams. Compared to HDOM with abundant lignins, microbially-transformed heteroatoms and carboxyl-rich alicyclic acids (CRAMs), POM exhibited higher allochthonous characteristics and more bioactive components, but lower molecular weight and diversity in different land-use-dominated streams. Compared to wetland-dominated headstreams, both POM and HDOM exhibited more terrestrial origin and condensed aromatics/tannins molecules for agriculture-impacted headstreams and bio-labile lipids, proteins and carbohydrates for forest-impacted headstreams. Structural equation mode (SEM) showed that soil-derived DOM (SDOM) showed the most prominent influence on the source, composition and molecular diversity of POM and the source of HDOM. The molecular composition and diversity of HDOM were mainly influenced by soil properties/SDOM and aquatic microorganisms, respectively. Redundancy analysis (RDA) revealed that autochthonous, bio-labile compositions of POM in forest and wetland streams were positively related to aquatic Bacteroidetes/Cyanobacteria, and carbohydrates/biogenic index of SDOM, while that of HDOM were positively linked with aquatic Bacteroidetes/Cyanobacteria, and SDOM molecular diversity. Terrestrial and aromatic POM in agricultural headstreams were associated with aquatic total nitrogen/Actinobacteria, and humification degree, aromatic/phenolic substances of SDOM, while that of HDOM were mainly regulated by aquatic nitrate/total nitrogen/Actinobacteria, and aromatic/carboxylic-containing moieties of SDOM. Noteworthily, the molecular diversity of agricultural OM increased along the soil-stream continuum due to the input of soil condensed aromatics and tannins. The opposite trend was observed in forest and wetland streams due to the input of bioactive carbohydrates and the microbial-degradation in-stream. These results are helpful to predict the behavior and fate of OM and determine effective management strategies in tropical coastal regions undergoing intense anthropogenic alterations.

Shift in the Mode of Carbon Cycling Recorded by Biomarkers and Carbon Isotopic Compositions in the Yanchang Formation, Ordos Basin: Autotrophy vs Heterotrophy

Organic-rich shales and mudstones have long been investigated regarding the control of source, environment, climate, etc. on the enrichment of organic carbon. However, little is documented about how autotrophy and heterotrophy influence organic carbon cycling/export. Here, we show molecular and carbon isotopic compositional changes of the shale or mudstone source rocks from the Chang 3 to 7 members of the Yanchang Formation. The Chang 7 member source rocks have higher quality (480-500 mg/g) and total organic carbon (TOC) (15.3% on average) than other member source rocks; the sterane/hopane ratio and the δ¹³C of organic carbon and kerogen decrease from the Chang 3 to 7 members, but Δδ ([average δ¹³C of n-C₁₇ + n-C₁₈] - [average δ¹³C of pristane + phytane]) increases, and no aryl isoprenoids and C₄₀ aromatic carotenoids (e.g., isorenieratane) were observed. These low maturity biomarker features suggest that there were no water stratification, photic zone euxinia (PZE), and no obvious change in the organic matter source, and the water column is generally anoxic. A comparison of the δ¹³C of Pr and Ph with the δ¹³C of the n-C17 and n-C18 alkanes reveals a shift in the mode of carbon cycling/export (autotrophy versus heterotrophy) in the Yanchang Formation and that there was dominant heterotrophic bacterial activity or bacterial biomass in the Chang 7 member. The TOC spike in the Chang 7 member may result from boosted carbon cycling/export that improves organic carbon preservation than other members. Possible external forcings on the shift are abundant hydrothermal- or volcanic-derived metal salts as electron acceptors in the palaeowater, which is a reasonable explanation for enhanced heterotrophic bacterial activity. This finding improves our understanding of heterotrophic bacterial activity control on organic matter (OM) preservation and may be a significant supplement for understanding the ecological or environmental forcings in the Yanchang Formation, Ordos Basin.

Sulfurized diterpenoids in amber as diagenetic indicators of sulfate-reducing processes in past depositional environments

Two novel compounds isolated from an amber sample from the Santonian of Piolenc (Vaucluse, SE France) were identified using nuclear magnetic resonance and high-resolution mass spectrometry as sulfurized analogues of diterpenic acids from the isopimaric series originating from ancient conifers possibly related to the Cupressaceae family. These two compounds are members of a diterpenoid series corresponding to early diagenetic transformation products of resin diterpenoids. They were likely formed once plant resin comes into contact with reduced sulfur species originating from bacterial sulfate reduction occurring in anaerobic settings such as mangroves or marshes. They represent the first evidence of sulfurization processes affecting plant resin prior to diagenetic transformation into amber. Given their mode of formation, these compounds may be used as indicators of sulfate-reducing processes in past depositional environments.

Analysis of Natural Organic Matter in Water from Cold and Hot Mineral Springs in South Korea Using 15T FT-ICR-MS

The natural organic matter (NOM) properties in water from cold and hot mineral springs in South Korea are not well documented. We analyzed the characteristics of NOM in water from 25 cold and hot mineral springs located across South Korea. The NOM of each sample was concentrated using solid-phase extraction and analyzed using 15T Fourier-transform ion cyclotron resonance mass spectrometry. The origin of NOM was identified using van Krevelen diagrams. This study suggests that an analytical method to evaluate the characteristics of water in each region of South Korea can be established and used as a baseline for further research.

Characterization of dissolved organic matter processing between surface sediment porewater and overlying bottom water in the Yangtze River Estuary

Dissolved organic matter (DOM) exchange in the sediment-water interface of estuaries is essential for the global elemental cycle. To clarify the interface DOM processing, this study applies optical techniques and ultrahigh-resolution mass spectrometry to assess DOM composition of surface sediment porewater and bottom (overlying) water across the Yangtze River Estuary (YRE). Results suggested that DOM exchange in the sediment-water interface mainly followed from sediment porewater to bottom water driven by a significant dissolved organic carbon concentration gradient and hydrodynamic force. We also characterized two porewater DOM sources, including microbial production and byproducts of processed sediments. High microbial activities resulted in the enrichment of protein-like fluorescent components and N-bearing compounds in porewater, potentially decreasing the oxygen concentration of bottom water due to the high lability. And the deamination of N-bearing compounds in the sediment-water interface could likely serve as a N-bearing nutrient source to bottom water. Moreover, due to sediment-specific features in different areas driven by hydrologic sorting and local phytoplankton supply, porewater DOM of muddy areas accumulated more aromatic substances from the degradation of terrestrial organic matter. The release and oxic transformation of oxygen-deficient aromatic compounds could contribute to the refractory carbon pool of estuarine water (carboxyl-rich alicyclic molecules, CRAM), modulating the quality of organic carbon mobilized from the land to the coastal ocean. Considering strong hydrodynamic force in numerous estuaries worldwide, DOM exchange and processing at the sediment-water interface has a meaningful influence on the biogeochemistry of estuarine water columns, which warrants further studies.

Comparative soft-tissue preservation in Holocene-age capelin concretions

Determining how soft tissues are preserved and persist through geologic time are continuing challenge because decay begins immediately after senescence while diagenetic transformations generally progress over days to millions of years. However, in recent years, carbonate concretions containing partially-to-fully decayed macroorganisms have proven to be remarkable windows into the diagenetic continuum revealing insights into the fossilization process. This is because most concretions are the result of biologically induced mineral precipitation caused by the localized decay of organic matter, which oftentimes preserves a greater biological signal relative to their host sediment. Here we present a comparative lipid biomarker study investigating processes associated with soft-tissue preservation within Holocene-age carbonate concretions that have encapsulated modern capelin (Mallotus villosus). We focus on samples collected from two depositional settings that have produced highly contrasting preservation end-members: (1) Kangerlussuaq, Greenland: a marine environment, which, due to isostatic rebound, has exposed strata containing concretions exhibiting exceptional soft-tissue preservation (6-7 kya), and (2) Greens Creek, Ottawa, Canada: a paleo brackish-to-freshwater marine excursion containing concretions exhibiting skeletal remains (~11 kya). Lipid biomarker analysis reveals endogenous capelin tissues and productive waters at Kangerlussuaq that are in sharp contrast to Greens Creek concretions, which lack appreciable capelin and environmental signals. Comparable distributions of bacterial fatty acids and statistical analyses suggest soft-tissue preservation within concretions is agnostic to specific heterotrophic decay communities. We, therefore, interpret preservation within carbonate concretions may represent a race between microbially induced authigenic precipitation and decay. Namely, factors resulting in exceptional preservation within concretions likely include: (1) organic matter input, (2) rate of decay, (3) carbonate saturation, (4) porewater velocity, and (5) rate of authigenic (carbonate) precipitation resulting in arrested decay/bacterial respiration due to cementing pore spaces limiting the diffusion of electron acceptors into the decay foci.

Carotenoid biomarkers in Namibian shelf sediments: Anoxygenic photosynthesis during sulfide eruptions in the Benguela Upwelling System

Aromatic carotenoid-derived hydrocarbon biomarkers are ubiquitous in ancient sediments and oils and are typically attributed to anoxygenic phototrophic green sulfur bacteria (GSB) and purple sulfur bacteria (PSB). These biomarkers serve as proxies for the environmental growth requirements of PSB and GSB, namely euxinic waters extending into the photic zone. Until now, prevailing models for environments supporting anoxygenic phototrophs include microbial mats, restricted basins and fjords with deep chemoclines, and meromictic lakes with shallow chemoclines. However, carotenoids have been reported in ancient open marine settings for which there currently are no known modern analogs that host GSB and PSB. The Benguela Upwelling System offshore Namibia, known for exceptionally high primary productivity, is prone to recurrent toxic gas eruptions whereupon hydrogen sulfide emanates from sediments into the overlying water column. These events, visible in satellite imagery as water masses clouded with elemental sulfur, suggest that the Benguela Upwelling System may be capable of supporting GSB and PSB. Here, we compare distributions of biomarkers in the free and sulfur-bound organic matter of Namibian shelf sediments. Numerous compounds-including acyclic isoprenoids, steranes, triterpanes, and carotenoids-were released from the polar lipid fractions upon Raney nickel desulfurization. The prevalence of isorenieratane and β-isorenieratane in sampling stations along the shelf verified anoxygenic photosynthesis by low-light-adapted, brown-colored GSB in this open marine setting. Renierapurpurane was also present in the sulfur-bound carotenoids and was typically accompanied by lower abundances of renieratane and β-renierapurpurane, thereby identifying cyanobacteria as an additional aromatic carotenoid source.

Geochemical and Stable Fe Isotopic Analysis of Dissimilatory Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park

Chocolate Pots hot spring (CP) is an Fe-rich, circumneutral-pH geothermal spring in Yellowstone National Park. Relic hydrothermal systems have been identified on Mars, and modern hydrothermal environments such as CP are useful for gaining insight into potential pathways for generation of biosignatures of ancient microbial life on Earth and Mars. Fe isotope fractionation is recognized as a signature of dissimilatory microbial iron oxide reduction (DIR) in both the rock record and modern sedimentary environments. Previous studies in CP have demonstrated the presence of DIR in vent pool deposits and show aqueous-/solid-phase Fe isotope variations along the hot spring flow path that may be linked to this process. In this study, we examined the geochemistry and stable Fe isotopic composition of spring water and sediment core samples collected from the vent pool and along the flow path, with the goal of evaluating whether Fe isotopes can serve as a signature of past or present DIR activity. Bulk sediment Fe redox speciation confirmed that DIR is active within the hot spring vent pool sediments (but not in more distal deposits), and the observed Fe isotope fractionation between Fe(II) and Fe(III) is consistent with previous studies of DIR-driven Fe isotope fractionation. However, modeling of sediment Fe isotope distributions indicates that DIR does not produce a unique Fe isotopic signature of DIR in the vent pool environment. Because of rapid chemical and isotopic communication between the vent pool fluid and sediment, sorption of Fe(II) to Fe(III) oxides would produce an isotopic signature similar to DIR despite DIR-driven generation of large quantities of isotopically light solid-associated Fe(II). The possibility exists, however, for preservation of specific DIR-derived Fe(II) minerals such as siderite (which is present in the vent pool deposits), whose isotopic composition could serve as a long-term signature of DIR in relic hot spring environments.

Niche expansion for phototrophic sulfur bacteria at the Proterozoic-Phanerozoic transition

Carotenoid pigments afford valuable clues about the chemistry and biology of both modern and ancient aquatic environments. This study reveals that fossil aromatic carotenoids—long considered biomarkers for anoxygenic, phototrophic sulfur bacteria and their physiological requirement for hydrogen sulfide and illumination—can also be biosynthesized by oxygen-producing cyanobacteria. Cyanobacterial aromatic carotenoids, which are distinct in their chemical structures and occurrence patterns, are the most commonly encountered compounds in Proterozoic marine settings as well as in lakes from more recent eras. In contrast, carotenoids diagnostic for green sulfur bacteria of the family Chlorobiaceae became both prevalent and abundant in marine paleoenvironments beginning in the Phanerozoic Eon. This expansion occurs as marine sulfate inventories increased toward the end of the Proterozoic Eon.

Fossilized carotenoid hydrocarbons provide a window into the physiology and biochemistry of ancient microbial phototrophic communities for which only a sparse and incomplete fossil record exists. However, accurate interpretation of carotenoid-derived biomarkers requires detailed knowledge of the carotenoid inventories of contemporary phototrophs and their physiologies. Here we report two distinct patterns of fossilized C₄₀ diaromatic carotenoids. Phanerozoic marine settings show distributions of diaromatic hydrocarbons dominated by isorenieratane, a biomarker derived from low-light-adapted phototrophic green sulfur bacteria. In contrast, isorenieratane is only a minor constituent within Neoproterozoic marine sediments and Phanerozoic lacustrine paleoenvironments, for which the major compounds detected are renierapurpurane and renieratane, together with some novel C₃₉ and C₃₈ carotenoid degradation products. This latter pattern can be traced to cyanobacteria as shown by analyses of cultured taxa and laboratory simulations of sedimentary diagenesis. The cyanobacterial carotenoid synechoxanthin, and its immediate biosynthetic precursors, contain thermally labile, aromatic carboxylic-acid functional groups, which upon hydrogenation and mild heating yield mixtures of products that closely resemble those found in the Proterozoic fossil record. The Neoproterozoic–Phanerozoic transition in fossil carotenoid patterns likely reflects a step change in the surface sulfur inventory that afforded opportunities for the expansion of phototropic sulfur bacteria in marine ecosystems. Furthermore, this expansion might have also coincided with a major change in physiology. One possibility is that the green sulfur bacteria developed the capacity to oxidize sulfide fully to sulfate, an innovation which would have significantly increased their capacity for photosynthetic carbon fixation.

Molecular differences between water column and sediment pore water SPE-DOM in ten Swedish boreal lakes

Boreal lakes are considered hot spots of dissolved organic matter (DOM) processing within the global carbon cycle. This study has used FT-ICR mass spectrometry and comprehensive data evaluation to assess the molecular differences of SPE-DOM between lake column water SPE-DOM and sedimentary pore water SPE-DOM in 10 Swedish boreal lakes of the Malingsbo area, which were selected for their large diversity of physicochemical and morphological characteristics. While lake column water is well mixed and fairly oxygenated, sedimentary pore water is subject to depletion of oxygen and to confinement of molecules. Robust trends were deduced from molecular compositions present in all compartments and in all 10 lakes ("common compositions") with recognition of relative abundance. Sedimentary pore water SPE-DOM featured higher proportions of heteroatoms N and S, higher average H/C ratios in presence of higher DBE/C ratios, and higher average oxygenation than lake column water SPE-DOM. These trends were observed in all lakes except Ljustjärn, which is a ground water fed kettle lake with an unique lake biogeochemistry. Analogous trends were also observed in case of single or a few lakes and operated also for compounds present solely in either lake column water or sedimentary pore water. Unique compounds detected in either compartments and/or in a few lakes showed higher molecular diversity than the "common compositions". Processing of DOM molecules in sediments included selective preservation for polyphenolic compounds and microbial resynthesis of selected molecules of considerable diversity.

Yellowstone Hot Springs are Organic Chemodiversity Hot Spots

Yellowstone National Park hydrothermal springs were investigated according to their organic geochemistry with a special focus on the Yellowstone hot spring dissolved organic matter (YDOM) that was solid-phase extracted. Here we show that YDOM has a unique chemodiversity that has not yet been observed anywhere else in aquatic surface environments and that Yellowstone hot springs are organic chemodiversity hot spots. Four main geochemically classified hot spring types (alkaline-chloride, mixed alkaline-chloride, acid-chloride-sulfate and travertine-precipitating) exhibited distinct organic molecular signatures that correlated remarkably well with the known inorganic geochemistry and manifested themselves in excitation emission matrix fluorescence, nuclear magnetic resonance, and ultrahigh resolution mass spectra. YDOM contained thousands of molecular formulas unique to Yellowstone of which 80% contained sulfur, even in low hydrogen sulfide containing alkaline-chloride springs. This unique YDOM reflects the extreme organic geochemistry present in the hydrothermal features of Yellowstone National Park.

Organic carbon burial during OAE2 driven by changes in the locus of organic matter sulfurization

Ocean Anoxic Event 2 (OAE2) was a period of dramatic disruption to the global carbon cycle when massive amounts of organic matter (OM) were buried in marine sediments via complex and controversial mechanisms. Here we investigate the role of OM sulfurization, which makes OM less available for microbial respiration, in driving variable OM preservation in OAE2 sedimentary strata from Pont d’Issole (France). We find correlations between the concentration, S:C ratio, S-isotope composition, and sulfur speciation of OM suggesting that sulfurization facilitated changes in carbon burial at this site as the chemocline moved in and out of the sediments during deposition. These patterns are reproduced by a simple model, suggesting that small changes in primary productivity could drive large changes in local OM burial in environments poised near a critical redox threshold. This amplifying mechanism may be central to understanding the magnitude of global carbon cycle response to environmental perturbations.

The mechanisms responsible for the burial of vast quantities of organic matter during Ocean Anoxic Event remain unclear. Here, the authors combine biogeochemical analysis and modeling and show that sulfurization could play a critical role in facilitating globally elevated burial of organic matter.

Organic matter preserved in 3-billion-year-old mudstones at Gale crater, Mars

Establishing the presence and state of organic matter, including its possible biosignatures, in martian materials has been an elusive quest, despite limited reports of the existence of organic matter on Mars. We report the in situ detection of organic matter preserved in lacustrine mudstones at the base of the ~3.5-billion-year-old Murray formation at Pahrump Hills, Gale crater, by the Sample Analysis at Mars instrument suite onboard the Curiosity rover. Diverse pyrolysis products, including thiophenic, aromatic, and aliphatic compounds released at high temperatures (500° to 820°C), were directly detected by evolved gas analysis. Thiophenes were also observed by gas chromatography–mass spectrometry. Their presence suggests that sulfurization aided organic matter preservation. At least 50 nanomoles of organic carbon persists, probably as macromolecules containing 5% carbon as organic sulfur molecules.

Preservation of uropygial gland lipids in a 48-million-year-old bird

Although various kinds of organic molecules are known to occur in fossils and rocks, most soft tissue preservation in animals is attributed to melanin or porphyrins. Lipids are particularly stable over time-as diagenetically altered 'geolipids' or as major molecular constituents of kerogen or fossil 'geopolymers'-and may be expected to be preserved in certain vertebrate tissues. Here we analysed lipid residues from the uropygial gland of an early Eocene bird using pyrolysis gas chromatography mass spectroscopy. We found a pattern of aliphatic molecules in the fossil gland that was distinct from the host oil shale sediment matrix and from feathers of the same fossil. The fossil gland contained abundant n-alkenes, n-alkanes and alkylbenzenes with chain lengths greater than 20, as well as functionalized long-chain aldehydes, ketones, alkylnitriles and alkylthiophenes that were not detected in host sediment or fossil feathers. By comparison with modern bird uropygial gland wax esters, we show that these molecular fossils are likely derived from endogenous wax ester fatty alcohols and fatty acids that survived initial decay and underwent early diagenetic geopolymerization. These data demonstrate the high fidelity preservation of the uropygial gland waxes and showcase the resilience of lipids over geologic time and their potential role in the exceptional preservation of lipid-rich tissues of macrofossils.

Tracing the fate of steroids through a hypersaline microbial mat (Kiritimati, Kiribati/Central Pacific)

Eukaryotic steranes are typically absent or occur in very low concentrations in Precambrian sedimentary rocks. However, it is as yet unclear whether this may reflect low source inputs or a preservational bias. For instance, it has been proposed that eukaryotic lipids were profoundly degraded in benthic microbial mats that were ubiquitous prior to the advent of vertical bioturbation in the Cambrian ("mat-seal effect"). It is therefore important to test the microbial turnover and degradation of eukaryotic steroids in real-world microbial mats. Here we assessed steroid inventories in different layers of a microbial mat from a hypersaline lake on Kiritimati (Central Pacific). Various eukaryote-derived C₂₇ -C₃₀ steroids were detected in all mat layers. These compounds most likely entered the mat system as unsaturated sterols from the water column or the topmost mat, and were progressively altered during burial in the deeper, anoxic mat layers over c. 10³  years. This is reflected by increasing proportions of saturated sterols and sterenes, as well as the presence of thiosteranes in certain horizons. Sterol alteration can partly be assigned to microbial transformation but is also due to chemical reactions promoted by the reducing environment in the deeper mat layers. Notably, however, compounds with a sterane skeleton were similarly abundant in all mat layers and their absolute concentrations did not show any systematic decrease. The observed decrease of steroid/hopanoid ratios with depth may thus rather indicate a progressive "dilution" by lipids derived from heterotrophic bacteria. Further, pyrolysis revealed that steroids, in contrast to hopanoids, were not sequestered into non-extractable organic matter. This may lead to a preservational bias against steroids during later stages of burial. Taken together, steroid preservation in the microbial mat is not only controlled by heterotrophic degradation, but rather reflects a complex interplay of taphonomic processes.

The taphonomic fate of isorenieratene in Lower Jurassic shales-controlled by iron?

Fossil derivatives of isorenieratene, an accessory pigment in brown-colored green sulfur bacteria, are often used as tracers for photic zone anoxia through Earth's history, but their diagenetic behavior is still incompletely understood. Here, we assess the preservation of isorenieratene derivatives in organic-rich shales (1.5-8.4 wt.% TOC) from two Lower Jurassic anoxic systems (Bächental oil shale, Tyrol, Austria; Posidonia Shale, Baden-Württemberg, Germany). Bitumens and kerogens were investigated using catalytic hydropyrolysis (HyPy), closed-system hydrous pyrolysis (in gold capsules), gas chromatography-mass spectrometry (GC-MS) and gas chromatography combustion isotope ratio-mass spectrometry (GC-C-IRMS). Petrography and biomarkers indicate a syngenetic relationship between bitumens and kerogens. All bitumens contain abundant isorenieratane, diverse complex aromatized isorenieratene derivatives, and a pseudohomologous series of 2,3,6-trimethyl aryl isoprenoids. In contrast, HyPy and mild closed-system hydrous pyrolysis of the kerogens yielded only minor amounts of these compounds. Given the overall low maturity of the organic matter (below oil window), it appears that isorenieratene and its abundant derivatives from the bitumen had not been incorporated into the kerogens. Accordingly, sulfur cross-linking, the key mechanism for sequestration of functionalized lipids into kerogens in anoxic systems, was not effective in the Jurassic environments studied. We explain this by (i) early cyclization/aromatization and (ii) hydrogenation reactions that have prevented effective sulfurization. In addition, (iii) sulfide was locally removed via anoxygenic photosynthesis and efficiently trapped by the reaction with sedimentary iron, as further indicated by elevated iron contents (4.0-8.7 wt.%) and the presence of abundant pyrite aggregates in the rock matrix. Although the combined processes have hampered the kerogen incorporation of isorenieratene and its derivatives, they may have promoted the long-term preservation of these biomarkers in the bitumen fraction via early defunctionalization. This particular taphonomy of aromatic carotenoids has to be considered in studies of anoxic iron-rich environments (e.g., the Proterozoic ocean).

Fossilization of melanosomes via sulfurization

Fossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur-bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur-rich phaeomelanosomes. Here we use pyrolysis gas chromatography mass spectrometry (Py-GCMS), fourier transform infrared spectroscopy (FTIR) and time of flight secondary ion mass spectrometry (ToF-SIMS) to assess the mode of preservation of fossil microstructures, confirmed as melanosomes based on the presence of melanin, preserved in frogs from the Late Miocene Libros biota (NE Spain). Our results reveal a high abundance of organosulfur compounds and non-sulfurized fatty acid methyl esters in both the fossil tissues and host sediment; chemical signatures in the fossil tissues are inconsistent with preservation of phaeomelanin. Our results reflect preservation via the diagenetic incorporation of sulfur, i.e. sulfurization (natural vulcanization), and other polymerization processes. Organosulfur compounds and/or elevated concentrations of sulfur have been reported from melanosomes preserved in various invertebrate and vertebrate fossils and depositional settings, suggesting that preservation through sulfurization is likely to be widespread. Future studies of sulfur-rich fossil melanosomes require that the geochemistry of the host sediment is tested for evidence of sulfurization in order to constrain interpretations of potential phaeomelanosomes and thus of original integumentary colour in fossils.

Seeking sunlight: rapid phototactic motility of filamentous mat-forming cyanobacteria optimize photosynthesis and enhance carbon burial in Lake Huron's submerged sinkholes

We studied the motility of filamentous mat-forming cyanobacteria consisting primarily of Oscillatoria-like cells growing under low-light, low-oxygen, and high-sulfur conditions in Lake Huron's submerged sinkholes using in situ observations, in vitro measurements and time-lapse microscopy. Gliding movement of the cyanobacterial trichomes (100-10,000 μm long filaments, composed of cells ∼10 μm wide and ∼3 μm tall) revealed individual as well as group-coordinated motility. When placed in a petri dish and dispersed in ground water from the sinkhole, filaments re-aggregated into defined colonies within minutes, then dispersed again. Speed of individual filaments increased with temperature from ∼50 μm min(-1) or ∼15 body lengths min(-1) at 10°C to ∼215 μm min(-1) or ∼70 body lengths min(-1) at 35°C - rates that are rapid relative to non-flagellated/ciliated microbes. Filaments exhibited precise and coordinated positive phototaxis toward pinpoints of light and congregated under the light of foil cutouts. Such light-responsive clusters showed an increase in photosynthetic yield - suggesting phototactic motility aids in light acquisition as well as photosynthesis. Once light source was removed, filaments slowly spread out evenly and re-aggregated, demonstrating coordinated movement through inter-filament communication regardless of light. Pebbles and pieces of broken shells placed upon intact mat were quickly covered by vertically motile filaments within hours and became fully buried in the anoxic sediments over 3-4 diurnal cycles - likely facilitating the preservation of falling debris. Coordinated horizontal and vertical filament motility optimize mat cohesion and dynamics, photosynthetic efficiency and sedimentary carbon burial in modern-day sinkhole habitats that resemble the shallow seas in Earth's early history. Analogous cyanobacterial motility may have played a key role in the oxygenation of the planet by optimizing photosynthesis while favoring carbon burial.

Lipid Biomarker and Isotopic Study of Community Distribution and Biomarker Preservation in a Laminated Microbial Mat from Shark Bay, Western Australia

Modern microbial mats from Shark Bay present some structural similarities with ancient stromatolites; thus, the functionality of microbial communities and processes of diagenetic preservation of modern mats may provide an insight into ancient microbial assemblages and preservation. In this study, the vertical distribution of microbial communities was investigated in a well-laminated smooth mat from Shark Bay. Biolipid and compound-specific isotopic analyses were performed to investigate the distribution of microbial communities in four distinct layers of the mat. Biomarkers indicative of cyanobacteria were more abundant in the uppermost oxic layer. Diatom markers (e.g. C25 HBI alkene, C20:4ω6 and C20:5ω3 polar lipid fatty acids (PLFAs)) were also detected in high abundance in the uppermost layer, but also in the deepest layer under conditions of permanent darkness and anoxia, where they probably used NO3 (-) for respiration. CycC19:0, an abundant PLFA of purple sulfur bacteria (PSB), was detected in all layers and presented the most (13)C-depleted values of all PLFAs, consistent with photoautotrophic PSB. Sulfur-bound aliphatic and aromatic biomarkers were detected in all layers, highlighting the occurrence of early sulfurisation which may be an important mechanism in the sedimentary preservation of functional biolipids in living and, thus, also ancient mats.

Assessing the distribution of sedimentary C40 carotenoids through time

A comprehensive marine biomarker record of green and purple sulfur bacteria (GSB and PSB, respectively) is required to test whether anoxygenic photosynthesis represented a greater fraction of marine primary productivity during the Precambrian than the Phanerozoic, as current models of ocean redox evolution suggest. For this purpose, we analyzed marine rock extracts and oils from the Proterozoic to the Paleogene for C40 diagenetic products of carotenoid pigments using new analytical methods. Gas chromatography coupled with tandem mass spectrometry provides a new perspective on the temporal distributions of carotenoid biomarkers for phototrophic sulfur bacteria, specifically okenane, chlorobactane, and paleorenieratane. According to conventional paleoredox interpretations, this revised stratigraphic distribution of the GSB and PSB biomarkers implies that the shallow sunlit surface ocean (<24 m) became sulfidic more frequently in the geologic past than was previously thought. We reexamine whether there is evidence supporting a planktonic source of GSB and PSB pigments in marine systems or whether additional factors are required to explain the marine phototrophic sulfur bacteria record. To date, planktonic GSB and PSB and their pigments have been identified in restricted basins and lakes, but they have yet to be detected in the unrestricted, transiently sulfidic, marine systems. Based on modern observations, additional environmental factors, including basin restriction, microbial mats, or sediment transport, may be required to fully explain GSB and PSB carotenoids in the geologic record.

Biota and biomolecules in extreme environments on Earth: implications for life detection on Mars

The three main requirements for life as we know it are the presence of organic compounds, liquid water, and free energy. Several groups of organic compounds (e.g., amino acids, nucleobases, lipids) occur in all life forms on Earth and are used as diagnostic molecules, i.e., biomarkers, for the characterization of extant or extinct life. Due to their indispensability for life on Earth, these biomarkers are also prime targets in the search for life on Mars. Biomarkers degrade over time; in situ environmental conditions influence the preservation of those molecules. Nonetheless, upon shielding (e.g., by mineral surfaces), particular biomarkers can persist for billions of years, making them of vital importance in answering questions about the origins and limits of life on early Earth and Mars. The search for organic material and biosignatures on Mars is particularly challenging due to the hostile environment and its effect on organic compounds near the surface. In support of life detection on Mars, it is crucial to investigate analogue environments on Earth that resemble best past and present Mars conditions. Terrestrial extreme environments offer a rich source of information allowing us to determine how extreme conditions affect life and molecules associated with it. Extremophilic organisms have adapted to the most stunning conditions on Earth in environments with often unique geological and chemical features. One challenge in detecting biomarkers is to optimize extraction, since organic molecules can be low in abundance and can strongly adsorb to mineral surfaces. Methods and analytical tools in the field of life science are continuously improving. Amplification methods are very useful for the detection of low concentrations of genomic material but most other organic molecules are not prone to amplification methods. Therefore, a great deal depends on the extraction efficiency. The questions “what to look for”, “where to look”, and “how to look for it” require more of our attention to ensure the success of future life detection missions on Mars.

Development and Initial Biogeochemical Applications of Compound-Specific Sulfur Isotope Analysis

Compound-specific isotope analysis (CSIA) has been extended to the 32S and 34S stable isotopes of sulfur (δ34S) through the combination of gas chromatography (GC) and multi-collector inductively coupled mass spectrometry (ICPMS). The molecular level resolution of sulfur-CSIA is greatly expanding the biogeochemical applications ofexisting sulfur isotope methods, particularly with respect to organic sulfur compounds. Sulfur participates in a variety of important biogeochemical and redox processes, with distinctive isotopic fractionations accompanying many of these. For example, hydrogen sulfideproduced duringmicrobial sulfate reduction can be strongly depleted in 34S (up to 66‰ in δ34S) compared to the source sulfate. An improved understanding of sulfur biogeochemistry at the molecular level will assist in the interpretation of studies of sulfur cycling associated with the modern and paleo-environments. A comparison of δ34S values between organic and inorganic sulfurspecies mayhelp to illuminate the complex role of sulfur in sedimentary organic diagenesis and the pathways of organic sulfurformation. The δ34S values of individual organic sulfur compounds from natural settings can be currently measured by GC-ICPMS with impressive accuracy, precision (&lt;0.5‰) and sensitivity (≥20 pmol S) over a broad range of analyte volatility. The new sulfur-CSIA capability has already been used to study pathways of early diagenetic organic sulfurisation, volatile sulfur emission from the oceans, oil correlations, thermochemical sulfate reduction of petroleum hydrocarbons, and the relationship between OSCs and mineralising sulfides of large metal deposits.

Exceptional preservation of Palaeozoic steroids in a diagenetic continuum

The occurrence of intact sterols has been restricted to immature Cretaceous (~125 Ma) sediments with one report from the Late Jurassic (~165 Ma). Here we report the oldest occurrence of intact sterols in a Crustacean fossil preserved for ca. 380 Ma within a Devonian concretion. The exceptional preservation of the biomass is attributed to microbially induced carbonate encapsulation, preventing full decomposition and transformation thus extending sterol occurrences in the geosphere by 250 Ma. A suite of diagenetic transformation products of sterols was also identified in the concretion, demonstrating the remarkable coexistence of biomolecules and geomolecules in the same sample. Most importantly the original biolipids were found to be the most abundant steroids in the sample. We attribute the coexistence of steroids in a diagenetic continuum -ranging from stenols to triaromatic steroids- to microbially mediated eogenetic processes.

Diatom microfossils from cretaceous and eocene sediments contain native silica precipitating long-chain polyamines

Organic molecules from known biological sources (biomarkers) that are preserved over geological time are critical tools in the study of past conditions and events on earth. Polar molecules are typically recycled rapidly in marine environments and do not survive burial within aquatic sediments in unambiguously recognizable form. As such, geological biomarkers are formed almost exclusively from precursor biomolecules that have been altered, limiting their utility as paleoproxies. Here, we report that nitrogen-rich aliphatic long-chain polyamines (LCPAs), biosynthesized by diatoms in species-specific assemblages for the precipitation of nanopatterned siliceous cell walls (frustules), are preserved unaltered in the oldest available diatom fossils dating to the Lower Cretaceous (early Albian, 115-110 Ma). We further show that the cumulative LCPA pool accounts for 60% of the total C and 80% of the total N preserved in the Cretaceous age sediments. We suggest that silica glass formation by diatoms constitutes an important preservation mechanism for source-specific, polar biomolecules, protecting them indefinitely by encapsulation within the silicified frustule. LCPAs are a unique, source-specific carbon and nitrogen archive of diatom biomass, offering a promising tool for reconstruction of global cycles of carbon and nitrogen over geological timescales.

Spatially resolved genomic, stable isotopic, and lipid analyses of a modern freshwater microbialite from Cuatro Ciénegas, Mexico

Microbialites are biologically mediated carbonate deposits found in diverse environments worldwide. To explore the organisms and processes involved in microbialite formation, this study integrated genomic, lipid, and both organic and inorganic stable isotopic analyses to examine five discrete depth horizons spanning the surface 25 mm of a modern freshwater microbialite from Cuatro Ciénegas, Mexico. Distinct bacterial communities and geochemical signatures were observed in each microbialite layer. Photoautotrophic organisms accounted for approximately 65% of the sequences in the surface community and produced biomass with distinctive lipid biomarker and isotopic (δ(13)C) signatures. This photoautotrophic biomass was efficiently degraded in the deeper layers by heterotrophic organisms, primarily sulfate-reducing proteobacteria. Two spatially distinct zones of carbonate precipitation were observed within the microbialite, with the first zone corresponding to the phototroph-dominated portion of the microbialite and the second zone associated with the presence of sulfate-reducing heterotrophs. The coupling of photoautotrophic production, heterotrophic decomposition, and remineralization of organic matter led to the incorporation of a characteristic biogenic signature into the inorganic CaCO(3) matrix. Overall, spatially resolved multidisciplinary analyses of the microbialite enabled correlations to be made between the distribution of specific organisms, precipitation of carbonate, and preservation of unique lipid and isotopic geochemical signatures. These findings are critical for understanding the formation of modern microbialites and have implications for the interpretation of ancient microbialite records.

Biosynthesis of the biomarker okenone: χ-ring formation

Purple sulfur bacteria (PSB) mainly occur in anoxic aquatic and benthic environments, where they play important roles in cycling carbon and sulfur. Many PSB characteristically produce the unique keto-carotenoid, okenone, which is important not only for its light absorption and photoprotection properties but also because of its diagenesis product, okenane, which is a biomarker for ancient sediments derived from anoxic environments. The specific methylation pattern of the χ-ring of okenane is unlikely to be formed by diagenetic processes and should therefore reflect an enzymatic activity from okenone biosynthesis. This study describes two enzymes that produce the χ-ring of okenone, the only structural element of okenone preserved in okenane. Genes encoding enzymes of carotenogenesis were identified in the draft genome sequence of an okenone-producing PSB, Thiodictyon sp. strain CAD16. Two divergently transcribed genes encoded a CrtY-type lycopene cyclase and a CrtU/CruE-type γ-carotene desaturase/methyltransferase. Expression of crtY in Escherichia coli showed that this gene encoded a lycopene cyclase that produced γ-carotene as the only product. Although the sequence of the γ-carotene desaturase/methyltransferase was more similar to CrtU sequences of green sulfur bacteria than to CruE sequences of cyanobacteria, expression of the crtU gene in Chlorobaculum tepidum showed that the enzyme produced carotenoids with χ-rings rather than φ-rings. Phylogenetic analysis of the carotene desaturase/methyltransferases revealed that enzymes capable of converting β-rings to χ-rings have independently evolved at least two times. These results indicate that it probably will not be possible to deduce the activity of carotene desaturase/methyltransferases solely from sequence data.

Reductive coupling of aldehydes by h(2) s in aqueous solutions, a C--C bond forming reaction of prebiotic interest

We report here a novel reductive coupling reaction of conjugated, non- or poorly enolizable aldehydes induced by H(2) S and operative in aqueous solutions under prebiotically relevant conditions. This reaction leads from retinal to β-carotene, and from benzylic aldehydes to the corresponding diarylethylenes. This novel reaction also opens a new potentially prebiotic pathway leading from glyoxylic acid to various compounds that are involved in the reductive tricarboxylic acid cycle. This C--C bond forming reaction of prebiotic interest might have been operative, notably, in the sulfide-rich environments of hydrothermal vents, which have been postulated as possible sites for the first steps of organic chemical evolution.

Carotenoid biomarkers as an imperfect reflection of the anoxygenic phototrophic community in meromictic Fayetteville Green Lake

Organic biomarkers in marine sedimentary rocks hold important clues about the early history of Earth's surface environment. The chemical relicts of carotenoids from anoxygenic sulfur bacteria are of particular interest to geoscientists because of their potential to signal episodes of marine photic-zone euxinia such as those proposed for extended periods in the Proterozoic as well as brief intervals during the Phanerozoic. It is therefore critical to constrain the environmental and physiological factors that influence carotenoid production and preservation in modern environments. Here, we present the results of coupled pigment and nucleic acid clone library analyses from planktonic and benthic samples collected from a microbially dominated meromictic lake, Fayetteville Green Lake (New York). Purple sulfur bacteria (PSB) are abundant and diverse both in the water column at the chemocline and in benthic mats below oxygenated shallow waters, with different PSB species inhabiting the two environments. Okenone (from PSB) is an abundant carotenoid in both the chemocline waters and in benthic mats. Green sulfur bacteria and their primary pigment Bchl e are also represented in and below the chemocline. However, the water column and sediments are devoid of the green sulfur bacteria carotenoid isorenieratene. The unexpected absence of isorenieratene and apparent benthic production of okenone provide strong rationale for continued exploration of the microbial ecology of biomarker production in modern euxinic environments.

Inverse carbon isotope patterns of lipids and kerogen record heterogeneous primary biomass

Throughout the Proterozoic δ(13)C values for preserved n-alkyl lipids are more positive than for syngenetic kerogen. This pattern is the inverse of biosynthetic expectations. It has been suggested that this isotopic inversion results from selective preservation of lipids from (13)C-enriched heterotrophic populations, while the bulk of kerogen derives from primary producers. Here, we formulate a degradation model to calculate the (13)C content of sedimentary total organic carbon and lipid. The model addresses two scenarios. The first scenario explores preferential preservation of heterotrophic lipid, thereby quantifying the existing hypothesis. In the second, we suggest that an inverse signature could be the result of prokaryotic phytoplankton contributing the majority of the total ecosystem biomass. Photosynthetic prokaryotes bearing a relative (13)C enrichment would contribute much of the resulting preserved lipids, while primary eukaryotic biomass would dominate the total organic carbon. We find that our hypothesis of a mixed primary producer community generates inverse isotopic patterns while placing far fewer requirements on specific degradation conditions. It also provides a possible explanation as to why there are large variations in the (13)C content of the isoprenoid lipids pristane and phytane relative to n-alkyl lipid, while the difference between n-alkyl lipid and kerogen is more constant. Our results suggest that the disappearance of the inverse (13)C signature in the late Ediacaran is a natural consequence of the fundamental shift to oceans in which export production has a higher ratio of eukaryotic biomass.

Elucidation of an iterative process of carbon-carbon bond formation of prebiotic significance

Laboratory experiments carried out under plausible prebiotic conditions (under conditions that might have occurred at primitive deep-sea hydrothermal vents) in water and involving constituents that occur in the vicinity of submarine hydrothermal vents (e.g., CO, H(2)S, NiS) have disclosed an iterative Ni-catalyzed pathway of C-C bond formation. This pathway leads from CO to various organic molecules that comprise, notably, thiols, alkylmono- and disulfides, carboxylic acids, and related thioesters containing up to four carbon atoms. Furthermore, similar experiments with organic compounds containing various functionalities, such as thiols, carboxylic acids, thioesters, and alcohols, gave clues to the mechanisms of this novel synthetic process in which reduced metal species, in particular Ni(0), appear to be the key catalysts. Moreover, the formation of aldehydes (and ketones) as labile intermediates via a hydroformylation-related process proved to be at the core of the chain elongation process. Since this process can potentially lead to organic compounds with any chain length, it could have played a significant role in the prebiotic formation of lipidic amphiphilic molecules such as fatty acids, potential precursors of membrane constituents.

Lipids modulate H(2)S/HS(-) induced NO release from S-nitrosoglutathione

Recently we observed that a gas messenger H(2)S/HS(-) released NO from S-nitrosoglutathione (Ondrias et al., Pflugers Arch. 457 (2008) 271-279). However, the effect of biological compounds on the release is not known. Measuring the NO oxidation product, which is nitrite, by the Griess reaction, we report that unsaturated fatty acid-linoleic acid and lipids having unsaturated fatty acids: asolectin, dioleoylphosphocholine and dioleoylphosphoserine depressed the H(2)S/HS(-) induced NO release from S-nitrosoglutathione. On the other hand, a depression effect of the saturated fatty acid-myristic acid and lipids having saturated fatty acids, dilauroylphosphatidylcholine, dimyristoylphosphatidylcholine, dipalmitoylphosphatidylcholine and distearoylphosphatidylcholine was less pronounced. The inhibition effect increased with the decreasing gel-to-liquid phase transitions temperature of the fatty acids and lipids. We suggest that lipid composition of biological membranes modulates NO release from nitrosoglutathione induced by H(2)S/HS(-), assuming that a reaction of H(2)S/HS(-) with unsaturated bonds of fatty acids may be partially responsible for the effect.

Unravelling ancient microbial history with community proteogenomics and lipid geochemistry

Our window into the Earth's ancient microbial past is narrow and obscured by missing data. However, we can glean information about ancient microbial ecosystems using fossil lipids (biomarkers) that are extracted from billion-year-old sedimentary rocks. In this Opinion article, we describe how environmental genomics and related methodologies will give molecular fossil research a boost, by increasing our knowledge about how evolutionary innovations in microorganisms have changed the surface of planet Earth.

Synechoxanthin, an aromatic C40 xanthophyll that is a major carotenoid in the cyanobacterium Synechococcus sp. PCC 7002

A major aromatic, dicarboxylate carotenoid (>15% of total) was isolated from the euryhaline cyanobacterium Synechococcus sp. PCC 7002. This compound, which was given the common name synechoxanthin (1), has been assigned the structure (all-E) chi,chi-caroten-18,18'-dioic acid by a combination of spectroscopic (UV-vis, FT-IR, (1)H and (13)C NMR, LC-MS) and chemical methods. This discovery conclusively establishes that some cyanobacteria are capable of synthesizing aromatic carotenoids.

Major structural components in freshwater dissolved organic matter

Dissolved organic matter (DOM) contains a complex array of chemical components that are intimately linked to many environmental processes, including the global carbon cycle, and the fate and transport of chemical pollutants. Despite its importance, fundamental aspects, such as the structural components in DOM remain elusive, due in part to the molecular complexity of the material. Here, we utilize multidimensional nuclear magnetic resonance spectroscopy to demonstrate the major structural components in Lake Ontario DOM. These include carboxyl-rich alicyclic molecules (CRAM), heteropolysaccharides, and aromatic compounds, which are consistent with components recently identified in marine dissolved organic matter. In addition, long-range proton-carbon correlations are obtained for DOM, which support the existence of material derived from linear terpenoids (MDLT). It is tentatively suggested that the bulk of freshwater dissolved organic matter is aliphatic in nature, with CRAM derived from cyclic terpenoids, and MDLT derived from linear terpenoids. This is in agreement with previous reports which indicate terpenoids as major precursors of DOM. At this time it is not clear in Lake Ontario whether these precursors are of terrestrial or aquatic origin or whether transformations proceed via biological and/ or photochemical processes.

Searching for life on Mars: selection of molecular targets for ESA's aurora ExoMars mission

The European Space Agency's ExoMars mission will seek evidence of organic compounds of biological and non-biological origin at the martian surface. One of the instruments in the Pasteur payload may be a Life Marker Chip that utilizes an immunoassay approach to detect specific organic molecules or classes of molecules. Therefore, it is necessary to define and prioritize specific molecular targets for antibody development. Target compounds have been selected to represent meteoritic input, fossil organic matter, extant (living, recently dead) organic matter, and contamination. Once organic molecules are detected on Mars, further information is likely to derive from the detailed distribution of compounds rather than from single molecular identification. This will include concentration gradients beneath the surface and gradients from generic to specific compounds. The choice of biomarkers is informed by terrestrial biology but is wide ranging, and nonterrestrial biology may be evident from unexpected molecular distributions. One of the most important requirements is to sample where irradiation and oxidation are minimized, either by drilling or by using naturally excavated exposures. Analyzing regolith samples will allow for the search of both extant and fossil biomarkers, but sequential extraction would be required to optimize the analysis of each of these in turn.

Gas chromatography coupled to mass spectrometry for analyses of organic compounds and biomarkers as tracers for geological, environmental, and forensic research

Gas chromatography, especially when coupled with mass spectrometry, is the analytical method of choice for elucidation of biomarker compounds present in organic mixtures extracted from geological, environmental, and biological samples. This review describes the biomarker concept, i. e., the precursor natural products to the geological/environmental derivatives, and their application as multi-tracers in the geosphere and ambient environment. The mass spectrometric methods currently utilized for such analyses are reviewed with a general key to the literature, and typical examples of applications using GC-MS are also described.