Biomarker and isotopic trends in a Permian-Triassic sedimentary section at Kap Stosch, Greenland

We report a geochemical study of a composite sedimentary section that captures the Permian-Triassic (PT) transition at Kap Stosch, East Greenland. The samples were from the original paleontological collection of early PT researchers. The rocks, which include samples from four proximal outcrop localities, were deposited during the Late Permian and Early Triassic at the margin of the Boreal Sea with a depositional hiatus and erosional event of unknown duration. Bulk geochemical measurements for most of the samples show good correlation between S2 and TOC% which, combined with low Tmax values, indicate that the organic matter (OM) that formed contemporaneously with sediment deposition is of relatively low maturity. Significant changes through the PT transition include a pronounced switch in the δ13C of TOC from high values near -24% to lower values averaging 32%, that is matched by a significant increase in the hydrogen index (HI) of the kerogen. The Permian samples containing 13C enriched OM also have low Rock-Eval HI values and anomalous pyrograms, indicating that the kerogen is heterogeneous in terms of source and maturity, as confirmed by microscopic analysis of the kerogen concentrates.Samples from the Permian section contain an abundance of black angular fragments of woody tissue in addition to gymnosperm pollen and spinose acritarchs of the Vittatina-Association (Balme, B., 1979. Palynology of Permian-Triassic boundary beds at Kap Stosch. Meddeleleser om Gronland 200, 1-36). In contrast, black woody tissue is rare in samples from the Early Triassic section with well preserved gymnosperm and lycopod pollen and spores of the Protohaploxypinus and Taeniaesporites associations. Biomarkers indicate moderate maturity for Permian samples, with the C27 sterane 20S/(20S + 20R), C31 homohopane 22S/(22S + 22R) ratio and Ts/(Ts + Tm) values all being higher than those for Triassic sediments. The marked switch in maturity indicators across the PT transition suggests an unconformity consistent with palynological observations. The pristane/phytane values are low and the homohopane index values high, indicating that anoxic conditions prevailed throughout deposition of the sediments.Additionally, markers of photic zone euxinia (i.e. isorenieratane, crocetane and 2,3,6-aryl isoprenoids) were present in all samples and all show maximum abundance closest to the PT transition. The C33 n-alkyl cyclohexane, a potential event marker for the onset of the biotic crisis in the Late Permian, was found in samples at, and immediately following, the paleontological PT transition. Despite the distinct change in lithology across the PT transition, the redox and Chlorobi-derived biomarkers indicate that photic zone euxinic conditions prevailed throughout the deposition of the Kap Stosch sedimentary sequence

2-Methylhopanoids are maximally produced in akinetes of Nostoc punctiforme: geobiological implications

2-Methylhopanes, molecular fossils of 2-methylbacteriohopanepolyol (2-MeBHP) lipids, have been proposed as biomarkers for cyanobacteria, and by extension, oxygenic photosynthesis. However, the robustness of this interpretation is unclear, as 2-methylhopanoids occur in organisms besides cyanobacteria and their physiological functions are unknown. As a first step toward understanding the role of 2-MeBHP in cyanobacteria, we examined the expression and intercellular localization of hopanoids in the three cell types of Nostoc punctiforme: vegetative cells, akinetes, and heterocysts. Cultures in which N. punctiforme had differentiated into akinetes contained approximately 10-fold higher concentrations of 2-methylhopanoids than did cultures that contained only vegetative cells. In contrast, 2-methylhopanoids were only present at very low concentrations in heterocysts. Hopanoid production initially increased threefold in cells starved of nitrogen but returned to levels consistent with vegetative cells within 2 weeks. Vegetative and akinete cell types were separated into cytoplasmic, thylakoid, and outer membrane fractions; the increase in hopanoid expression observed in akinetes was due to a 34-fold enrichment of hopanoid content in their outer membrane relative to vegetative cells. Akinetes formed in response either to low light or phosphorus limitation, exhibited the same 2-methylhopanoid localization and concentration, demonstrating that 2-methylhopanoids are associated with the akinete cell type per se. Because akinetes are resting cells that are not photosynthetically active, 2-methylhopanoids cannot be functionally linked to oxygenic photosynthesis in N. punctiforme

Oxidation of the Ediacaran Ocean

Oxygenation of the Earth's surface is increasingly thought to have occurred in two steps. The first step, which occurred ~2,300 million years (Myr) ago, involved a significant increase in atmospheric oxygen concentrations and oxygenation of the surface ocean. A further increase in atmospheric oxygen appears to have taken place during the late Neoproterozoic period (~800–542 Myr ago). This increase may have stimulated the evolution of macroscopic multicellular animals and the subsequent radiation of calcified invertebrates, and may have led to oxygenation of the deep ocean. However, the nature and timing of Neoproterozoic oxidation remain uncertain. Here we present high-resolution carbon isotope and sulphur isotope records from the Huqf Supergroup, Sultanate of Oman, that cover most of the Ediacaran period (~635 to ~548 Myr ago). These records indicate that the ocean became increasingly oxygenated after the end of the Marinoan glaciation, and they allow us to identify three distinct stages of oxidation. When considered in the context of other records from this period, our data indicate that certain groups of eukaryotic organisms appeared and diversified during the second and third stages of oxygenation. The second stage corresponds with the Shuram excursion in the carbon isotope record and seems to have involved the oxidation of a large reservoir of organic carbon suspended in the deep ocean, indicating that this event may have had a key role in the evolution of eukaryotic organisms. Our data thus provide new insights into the oxygenation of the Ediacaran ocean and the stepwise restructuring of the carbon and sulphur cycles that occurred during this significant period of Earth's history

Organic geochemistry of the early Toarcian oceanic anoxic event in Hawsker Bottoms, Yorkshire, England

A comprehensive organic geochemical investigation of the Hawsker Bottoms outcrop section in Yorkshire, England has provided new insights about environmental conditions leading into and during the Toarcian oceanic anoxic event (T-OAE; ~183 Ma). Rock-Eval and molecular analyses demonstrate that the section is uniformly within the early oil window. Hydrogen index (HI), organic petrography, polycyclic aromatic hydrocarbon (PAH) distributions, and tricyclic terpane ratios mark a shift to a lower relative abundance of terrigenous organic matter supplied to the sampling locality during the onset of the T-OAE and across a lithological transition. Unlike other ancient intervals of anoxia and extinction, biomarker indices of planktonic community structure do not display major changes or anomalous values. Depositional environment and redox indicators support a shift towards more reducing conditions in the sediment porewaters and the development of a seasonally stratified water column during the T-OAE. In addition to carotenoid biomarkers for green sulfur bacteria (GSB), we report the first occurrence of okenane, a marker of purple sulfur bacteria (PSB), in marine samples younger than ~1.64 Ga. Based on modern observations, a planktonic source of okenane's precursor, okenone, would require extremely shallow photic zone euxinia (PZE) and a highly restricted depositional environment. However, due to coastal vertical mixing, the lack of planktonic okenone production in modern marine sulfidic environments, and building evidence of okenone production in mat-dwelling Chromatiaceae, we propose a sedimentary source of okenone as an alternative. Lastly, we report the first parallel compound-specific δ[superscript 13]C record in marine- and terrestrial-derived biomarkers across the T-OAE. The δ[superscript 13]C records of short-chain n-alkanes, acyclic isoprenoids, and long-chain n -alkanes all encode negative carbon isotope excursions (CIEs), and together, they support an injection of isotopically light carbon that impacted both the atmospheric and marine carbon reservoirs. To date, molecular δ[superscript 13]C records of the T-OAE display a negative CIE that is smaller in magnitude compared to the bulk organic δ[superscript 13]C excursion. Although multiple mechanisms could explain this observation, our molecular, petrographic, and Rock-Eval data suggest that variable mixing of terrigenous and marine organic matter is an important factor affecting the bulk organic δ[superscript 13]C records of the T-OAE.NASA Astrobiology InstituteExobiology Program (U.S.)National Science Foundation (U.S.). Graduate Research Fellowshi

Design Strategy for a Scalable Virtual Pharmacy Patient

This paper reports on the completion of the first stage of research of a pilot study undertaken in collaboration by 3 Australian universities. The pilot involves the development of a virtual pharmacy patient (VPP) as a study of its effects on student learning when it is used as a formative assessment tool for pharmacy students in interviewing and diagnosing a patient. The design criteria that have been incorporated into the virtual patient system are described. The novelty of this system is in its ability to track and report on the style and appropriateness of student questioning of a virtual pharmacy patient. One of the main problems in this type of system is recognition of free-text student questions. An overview of the pragmatic solution to this and the systems potential as a tool to generate a lexicon for more complex question recognition is presented

Identification and characterization of Rhodopseudomonas palustris TIE-1 hopanoid biosynthesis mutants

Hopanes preserved in both modern and ancient sediments are recognized as the molecular fossils of bacteriohopanepolyols, pentacyclic hopanoid lipids. Based on the phylogenetic distribution of hopanoid production by extant bacteria, hopanes have been used as indicators of specific bacterial groups and/or their metabolisms. However, our ability to interpret them ultimately depends on understanding the physiological roles of hopanoids in modern bacteria. Toward this end, we set out to identify genes required for hopanoid biosynthesis in the anoxygenic phototroph Rhodopseudomonas palustris TIE-1 to enable selective control of hopanoid production. We attempted to delete 17 genes within a putative hopanoid biosynthetic gene cluster to determine their role, if any, in hopanoid biosynthesis. Two genes, hpnH and hpnG, are required to produce both bacteriohopanetetrol and aminobacteriohopanetriol, whereas a third gene, hpnO, is required only for aminobacteriohopanetriol production. None of the genes in this cluster are required to exclusively synthesize bacteriohopanetetrol, indicating that at least one other hopanoid biosynthesis gene is located elsewhere on the chromosome. Physiological studies with the different deletion mutants demonstrated that unmethylated and C_30 hopanoids are sufficient to maintain cytoplasmic but not outer membrane integrity. These results imply that hopanoid modifications, including methylation of the A-ring and the addition of a polar head group, may have biologic functions beyond playing a role in membrane permeability

Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes

The rise of atmospheric oxygen has driven environmental change and biological evolution throughout much of Earth’s history and was enabled by the evolution of oxygenic photosynthesis in the cyanobacteria. Dating this metabolic innovation using inorganic proxies from sedimentary rocks has been difficult and one important approach has been to study the distributions of fossil lipids, such as steranes and 2-methylhopanes, as biomarkers for this process. 2-methylhopanes arise from degradation of 2-methylbacteriohopanepolyols (2-MeBHPs), lipids thought to be synthesized primarily by cyanobacteria. The discovery that 2-MeBHPs are produced by an anoxygenic phototroph, however, challenged both their taxonomic link with cyanobacteria and their functional link with oxygenic photosynthesis. Here, we identify a radical SAM methylase encoded by the hpnP gene that is required for methylation at the C-2 position in hopanoids. This gene is found in several, but not all, cyanobacteria and also in α -proteobacteria and acidobacteria. Thus, one cannot extrapolate from the presence of 2-methylhopanes alone, in modern environments or ancient sedimentary rocks, to a particular taxonomic group or metabolism. To understand the origin of this gene, we reconstructed the evolutionary history of HpnP. HpnP proteins from cyanobacteria, Methylobacterium species, and other α-proteobacteria form distinct phylogenetic clusters, but the branching order of these clades could not be confidently resolved. Hence,it is unclear whether HpnP, and 2-methylhopanoids, originated first in the cyanobacteria. In summary, existing evidence does not support the use of 2-methylhopanes as biomarkers for oxygenic photosynthesis

Carbon Isotope and Lipid Biomarker Stratigraphy from Organic-Rich Strata Through the Neoproterozoic Shuram Excursion in South Oman

The regulation of oxygen levels in Earth’s atmosphere and oceans is inextricably linked to the carbon cycle. Carbon isotope ratios of carbonate and sedimentary organic matter provide first order insights into the operation of the carbon cycle in the geologic past. During the Ediacaran period, the ~580 Ma ‘Shuram Excursion’ (SE) records a dramatic, systematic shift in δ^(13)C_(carbonate) values to as low as cɑ. -12‰, lasting potentially millions to tens of millions of years in duration and constitutes the largest carbon isotope excursion known in the record [1]. The extremely negative carbon isotope values in carbonate challenges our understanding of the ancient carbon cycle and is difficult to rationalise via uniform carbon cycle principles. Several hypotheses have been developed to explain this behaviour, all of which make different predictions for the abundance, structure, and isotopic composition of organic carbon through the excursion. For a direct test of these ideas, we report paired organic and inorganic stable carbon isotope ratios in addition to detailed lipid biomarker stratigraphic records from a subsurface well drilled on the eastern flank of the South Oman Salt Basin, Sultanate of Oman. This well captures thermally immature and organic-rich Nafun Group strata traversing the SE, yielding variable but primary biomarker characteristics typical of Neoproterozoic rocks from this region. Despite the high organic matter contents, the carbon isotopic compositions of carbonates do not covary with those of organic phases. Furthermore, lipid biomarker data reveal that organic matter composition and source inputs varied stratigraphically, reflecting biological community shifts in non-migrated, syngenetic organic matter deposited during this interval. Together these observations imply that carbonateorganic isotopic decoupling during the SE is not a result of mixing of fossil or exogenous carbon sources (either DOC, detrital, or migrated) with syngenetic organic matter

Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche

Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (P-value<10^−6); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche

The RND-family transporter, HpnN, is required for hopanoid localization to the outer membrane of Rhodopseudomonas palustris TIE-1

Rhodopseudomonas palustris TIE-1 is a Gram-negative bacterium that produces structurally diverse hopanoid lipids that are similar to eukaryotic steroids. Its genome encodes several homologues to proteins involved in eukaryotic steroid trafficking. In this study, we explored the possibility that two of these proteins are involved in intracellular hopanoid transport. R. palustris has a sophisticated membrane system comprising outer, cytoplasmic, and inner cytoplasmic membranes. It also divides asymmetrically, producing a mother and swarmer cell. We deleted genes encoding two putative hopanoid transporters that belong to the resistance–nodulation– cell division superfamily. Phenotypic analyses revealed that one of these putative transporters (HpnN) is essential for the movement of hopanoids from the cytoplasmic to the outer membrane, whereas the other (Rpal_4267) plays a minor role. C30 hopanoids, such as diploptene, are evenly distributed between mother and swarmer cells, whereas hpnN is required for the C35 hopanoid, bacteriohopanetetrol, to remain localized to the mother cell type. Mutant cells lacking HpnN grow like the WT at 30 °C but slower at 38 °C. Following cell division at 38 °C, the ΔhpnN cells remain connected by their cell wall, forming long filaments. This phenotype may be attributed to hopanoid mislocalization because a double mutant deficient in both hopanoid biosynthesis and transport does not form filaments. However, the lack of hopanoids severely compromises cell growth at higher temperatures more generally. Because hopanoid mutants only manifest a strong phenotype under certain conditions, R. palustris is an attractive model organism in which to study their transport and function