Mass Spectrometry and reverse phase HPLC techniques for the identification of degraded fossil pigments in lake sediments and their application in palaeolimnology

Accurate identification of fossil pigments is essential if they are to be used as biomarker compounds in palaeolimnological studies. In recent years High Performance Liquid Chromatography (HPLC) has greatly enhanced the efficiency with which fossil pigments can be characterised and quantified. Using HPLC, undegraded pigments are typically identified through retention times, absorbance spectra and co-chromatography with authentic reference standards. However, lake sediments may also contain degraded pigments for which there are often no standards, and which may be difficult to identify using HPLC alone. In this study, we submitted HPLC fractions of fossil pigments and pigment derivatives collected from a meromictic lake in south west Tasmania, to a combination of Mass Spectrometry (MS) techniques including Electron Impact (EI) and static Liquid Secondary Ion MS (LSIMS) to identify their molecular ion characteristics and organic chemical composition. Mass Spectrometry permitted the detection of specific mass ions which were used to verify the identity of pigments and their derivatives. These included five carotenoids, chlorophyll a and derivatives, three previously described bacteriochlorophyll c derivatives with molecular weights of 770, 784, and 802, and two undescribed derivatives of bacteriochlorophyll c with molecular weights of 766 and 788. With these improved identifications we speculate on the pathways and modes of pigment degradation in the lake and asses the value of the degraded pigments as biomarkers. The use of MS permitted the identification of a greater number of signature pigments of algal and bacterial communities thus increasing the palaeolimnological value of the sediments. These methods are best applied in fossil pigment studies where there are a large number of unknown pigments and pigment degradation products, and where there are no authentic standards for co-chromatography. Practical suggestions for pigment MS are included in the discussion.     

Exploring former subglacial Hodgson Lake,Antarctica. Paper II: palaeolimnology

Direct exploration of subglacial lakes buried deep under the Antarctic Ice Sheet has yet to be achieved. However, at retreating margins of the ice sheet, there are a number of locations where former subglacial lakes are emerging from under the ice but remain perennially ice covered. One of these lakes, Hodgson Lake (72°00.549′S, 068°27.708′W) has emerged from under more than 297–465 m of glacial ice during the last few thousand years. This paper presents data from a multidisciplinary investigation of the palaeolimnology of this lake through a study of a 3.8 m sediment core extracted at a depth of 93.4 m below the ice surface. The core was dated using a combination of radiocarbon, optically stimulated luminescence, and relative palaeomagnetic intensity dating incorporated into a chronological model. Stratigraphic analyses included magnetic susceptibility, clast provenance, organic content, carbonate composition, siliceous microfossils, isotope and biogeochemical markers. Based on the chronological model we provisionally assign a well-defined magnetic polarity reversal event at ca 165 cm in the lake sediments to the Mono Lake excursion (ca 30–34 ka), whilst OSL measurements suggest that material incorporated into the basal sediments might date to 93 ± 9 ka. Four stratigraphic zones (A–D) were identified in the sedimentological data. The chronological model suggests that zones A–C were deposited between Marine Isotope Stages 5–2 and zone A during Stage 1, the Holocene. The palaeolimnological record tracks changes in the subglacial depositional environment linked principally to changing glacier dynamics and mass transport and indirectly to climate change. The sediment composition in zones A–C consists of fine-grained sediments together with sands, gravels and small clasts. There is no evidence of overriding glaciers being in contact with the bed reworking the stratigraphy or removing this sediment. This suggests that the lake existed in a subglacial cavity beneath overriding LGM ice. In zone D there is a transition to finer grained sediments characteristic of lower energy delivery coupled with a minor increase in the organic content attributed either to increases in allochthonous organic material being delivered from the deglaciating catchment, a minor increase in within-lake production or to an analytical artefact associated with an increase in the clay fraction. Evidence of biological activity is sparse. Total organic carbon varies from 0.2 to 0.6%, and cannot be unequivocally linked to in situ biological activity as comparisons of δ¹³C and C/N values with local reference data suggest that much of it is derived from the incorporation of carbon in catchment soils and gravels and possibly old CO₂ in meteoric ice. We use the data from this study to provide guidelines for the study of deep continental subglacial lakes including establishing sediment geochronologies, determining the extent to which subglacial sediments might provide a record of glaciological and environmental change and a brief review of methods to use in the search for life.     

Analysis of Water Saturation, NAPL Content, Degradation Half-Life, and Lower Boundary Conditions on VOC Transport Modeling: Implications for Closure of Soil Venting Systems

Simulations using a one-dimensional, analytical, vadose zone, solute-transport screening code (VFLUX) were conducted to assess the effect of water saturation, NAPL saturation, degradation half-life, and boundary conditions at the vadose zone/ground water interface on model output. At high initial soil concentrations, model output was significantly affected by input parameters and lower boundary conditions yet still resulted in consistent decision-making to initiate or continue venting application. At lower soil concentrations, however, typical of what is observed after prolonged venting application, differences in model input and selection of lower boundary conditions resulted in inconsistent decision-making. Specifically, under conditions of low water saturation, use of a first-type, time-dependent lower boundary condition indicated that the primary direction of mass flux was from ground water to the vadose zone, suggesting little benefit from continued venting application. Use of a finite, zero-gradient lower boundary condition, though, indicated continued mass flux from the vadose zone to ground water, suggesting a continued need for venting application. In this situation, sensitivity analysis of input parameters, selection of boundary conditions, and consideration of overall objectives in vadose zone modeling become critical in regulatory decision-making.     

Measurements of sheet flow transport in acceleration-skewed oscillatory flow and comparison with practical formulations

Near-bed oscillatory flows with acceleration skewness are characteristic of steep and breaking waves in shallow water. In order to isolate the effects of acceleration skewness on sheet flow sand transport, new experiments are carried out in the Aberdeen Oscillatory Flow Tunnel. The experiments have produced a dataset of net transport rates for full-scale oscillatory flows with varying degrees of acceleration skewness and three sand sizes. The new data confirm previous research that net transport in acceleration-skewed flow is non-zero, is always in the direction of the largest acceleration and increases with increasing acceleration skewness. Large transport rates for the fine sand conditions suggest that phase lag effects play an important role in augmenting positive net transport. A comparison of the new experimental data with a number of practical sand transport formulations that incorporate acceleration skewness shows that none of the formulations performs well in predicting the measured net transport rates for both the fine and the coarser sands. The new experimental data can be used to further develop practical sand transport formulations to better account for acceleration skewness.     

Ancient graphite in the Eoarchean quartz-pyroxene rocks from Akilia in southern West Greenland II: Isotopic and chemical compositions and comparison with Paleoproterozoic banded iron formations

We present detailed petrographic surveys of apatite grains in association with carbonaceous material (CM) in two banded iron formations (BIFs) from the Paleoproterozoic of Uruguay and Michigan for comparison with similar mineral associations in the highly debated Akilia Quartz-pyroxene (Qp) rock. Petrographic and Raman spectroscopic surveys of these Paleoproterozoic BIFs show that apatite grains typically occur in bands parallel to bedding and are more often associated with CM when concentrations of organic matter are high. Carbonaceous material in the Vichadero BIF from Uruguay is generally well-crystallized graphite and occurs in concentrations around 0.01 wt% with an average δ¹³C_gra value of −28.6 ± 4.4‰ (1σ). In this BIF, only about 5% of apatite grains are associated with graphite. In comparison, CM in the Bijiki BIF from Michigan is also graphitic, but occurs in concentrations around 2.4 wt% with δ¹³C_gra values around −24.0 ± 0.3‰ (1σ). In the Bijiki BIF, more than 78% of apatite grains are associated with CM. Given the geologic context and high levels of CM in the Bijiki BIF, the significantly higher proportion of apatite grains associated with CM in this rock is interpreted to represent diagenetically altered biomass and shows that such diagenetic mineral associations can survive metamorphism up to the amphibolite facies.Isotope compositions of CM in muffled acidified whole-rock powders from the Akilia Qp rock have average δ¹³C_gra values of −17.5 ± 2.5‰ (1σ), while δ¹³C_carb values in whole-rock powders average −4.0 ± 1.0‰ (1σ). Carbon isotope compositions of graphite associated with apatite and other minerals in the Akilia Qp rock were also measured with the NanoSIMS to have similar ranges of δ¹³C_gra values averaging −13.8 ± 5.6‰ (1σ). The NanoSIMS was also used to semi-quantitatively map the distributions of H, N, O, P, and S in graphite from the Akilia Qp rock, and relative abundances were found to be similar for graphite associated with apatite or with hornblende, calcite, and sulfides. These analyses revealed generally lower abundances of trace elements in the Akilia graphite compared to graphite associated with apatite from Paleoproterozoic BIFs.Graphite associated with hornblende, calcite, and sulfides in the Akilia Qp rock was fluid-deposited at high-temperature from carbon-bearing fluids, and since this graphite has similar ranges of δ¹³C_gra values and of trace elements compared to graphite associated with apatite, we conclude that the Akilia graphite in different mineral associations formed from the same source(s) of CM. Collectively our results do not exclude a biogenic origin of the carbon in the Akilia graphite, but because some observations can not exclude graphitization of abiogenic carbon from CO₂- and CH₄-bearing mantle fluids, there remain ambiguities with respect to the exact origin of carbon in this ancient metasedimentary rock. Accordingly, there may have been several generations of graphite formation along with possibly varying mixtures of CO₂- and CH₄-bearing fluids that may have resulted in large ranges of δ¹³C_gra values. The possibility of fluid-deposited graphite associated with apatite should be a focus of future investigations as this may prove to be an alternative pathway of graphitization from phosphate-bearing fluids. Correlated micro-analytical approaches tested on terrestrial rocks in this work provide insights into the origin of carbon in ancient graphite and will pave the way for the search for life on other ancient planetary surfaces.     

Geological constraints on glacio-isostatic adjustment models of relative sea-level change during deglaciation of Prince Gustav Channel,Antarctic Peninsula

The recent disintegration of Antarctic Peninsula ice shelves, and the associated accelerated discharge and retreat of continental glaciers, has highlighted the necessity of quantifying the current rate of Antarctic ice mass loss and the regional contributions to future sea-level rise. Observations of present day ice mass change need to be corrected for ongoing glacial isostatic adjustment, a process which must be constrained by geological data. However, there are relatively little geological data on the geometry, volume and melt history of the Antarctic Peninsula Ice Sheet (APIS) after Termination 1, and during the Holocene so the glacial isostatic correction remains poorly constrained. To address this we provide field constraints on the timing and rate of APIS deglaciation, and changes in relative sea-level (RSL) for the north-eastern Antarctic Peninsula based on geomorphological evidence of former marine limits, and radiocarbon-dated marine-freshwater transitions from a series of isolation basins at different altitudes on Beak Island. Relative sea-level fell from a maximum of c. 15 m above present at c. 8000 cal yr BP, at a rate of 3.91 mm yr^?1 declining to c. 2.11 mm yr^?1 between c. 6900–2900 cal yr BP, 1.63 mm yr^?1 between c. 2900–1800 cal yr BP, and finally to 0.29 mm yr^?1 during the last c. 1800 years. The new Beak Island RSL curve improves the spatial coverage of RSL data in the Antarctic. It is in broad agreement with some glacio-isostatic adjustment models applied to this location, and with work undertaken elsewhere on the Antarctic Peninsula. These geological and RSL constraints from Beak Island imply significant thinning of the north-eastern APIS by the early Holocene. Further, they provide key data for the glacial isostatic correction required by satellite-derived gravity measurements of contemporary ice mass loss, which can be used to better assess the future contribution of the APIS to rising sea-levels.     

Late Holocene changes in cyanobacterial community structure in maritime Antarctic lakes

Despite the dominance of cyanobacteria in polar freshwater aquatic ecosystems, little is known about their past biodiversity and response to climate and environmental changes. We explored the use of light microscopy of microfossils, high performance liquid chromatography of the fossil pigment composition and denaturing gradient gel electrophoresis of fossil 16S rRNA genes to study past and present-day differences in cyanobacterial community structure in response to climate changes in two adjacent maritime Antarctic lakes with contrasting depths (4 and 26 m) and light climates. Light microscopy was of limited use because of degradation of cell structures. Fossil cyanobacterial pigment concentrations were below the detection limits of our method in several sediment samples in the deep lake, but abundant and diverse in the sediment core from the shallow pond, probably as a consequence of increased light availability and/or a more diverse and abundant benthic cyanobacterial flora. Total carotenoid and chlorophyll concentrations were highest in both lakes between ca. 2,950 and 1,800 cal yr BP, which coincides with the late Holocene climate optimum recognised elsewhere in maritime Antarctica. Cyanobacterial molecular diversity was higher in the top few centimeters of the sediments in both lakes. In deeper sediments, the taxonomic turnover of cyanobacteria appeared to be relatively small in response to past climate anomalies in both lakes, underscoring the broad tolerance of cyanobacteria to environmental variability. This, however, may in part be explained by the low taxonomic resolution obtained with the relatively conserved 16S rRNA gene and/or the preferential preservation of particular taxa. Our results highlight the potential of fossil DNA in lake sediments to study colonization and succession dynamics of lacustrine cyanobacteria and warrant further investigation of the factors that affect preservation of cyanobacterial DNA.     

Tectonic controls on Miocene sedimentation in the Southern Taranaki Basin and implications for New Zealand plate boundary deformation

Miocene strata in the southern Taranaki Basin (STB), up to 3 km thick, provide a distal record of erosion associated with plate boundary deformation in New Zealand. 2D and 3D seismic reflection data tied to drillhole stratigraphy have been used to constrain four main phases of basin development. These are: (a) Early Miocene (22–19 Ma) subsidence, dominantly bathyal water depths and deposition of minor submarine fans along the eastern basin margin. (b) Middle Miocene (19–14 Ma) widespread submarine fan deposition on a bathyal basin floor in the central STB. (c) Rapid Middle–Late Miocene (14–7 Ma) progradation of the shelf break northwards across the STB. (d) Widespread uplift and erosion of the STB during the latest Miocene–Pliocene (7–4.5 Ma). Bathyal water depths and fan deposition in the Early Miocene were influenced by vertical motions on major reverse faults and regional subsidence produced by subduction of the Pacific plate beneath northern New Zealand. Subsequent submarine fan deposition and northward shelf‐break progradation reflect increasing input of terrigenous material, primarily eroded from an uplifting region to the south of the STB. Sedimentation patterns in the STB are consistent with the age and locations of conglomerates deposited in onshore West Coast basins, related to this uplift and erosion. Sediment transport in the West Coast region was mainly parallel to NNE trending active reverse faults, and in the STB was perpendicular to the NE‐SW orientated shelf break, especially from ca. 14–7 Ma, when sedimentation rates exceeded fault‐displacement rates. Increases in sedimentation rates in the STB coincide with regional increases in the rates of shortening that appear to reflect plate boundary‐wide events and have been attributed to, or correlated with, increases in the plate convergence rate. Miocene sedimentation patterns in the STB thus reflect both intra‐basinal deformation and tectonic signals from the wider developing New Zealand plate boundary.     

Alkoxyquinoline O-dealkylation: A new fluorimetric assay for hydrocarbon-induced cytochrome P450 in fish

The O-dealkylation of a new series of substrates, the alkoxyquinolines, provides a new easy fluorimetric assay for measuring the induction of cytochrome P450 by polycyclic aromatic hydrocarbons and drilling mud oil in fish. Expression of the results as a ratio between the inducible butyloxyquinoline O-dealkylation (BuQOD) activity and the non-inducible benzyloxyquinoline O-dealkylation (BeQOD) activity (i.e. the ‘BuQOD:-BeQOD quotient’) maximises the degree of induction measured and minimises the degree of inter-animal variation.