Anne S. Palmer

Community fingerprinting in a sequencing world

Despite decreasing costs, generating large-scale, well-replicated and multivariate microbial ecology investigations with sequencing remains an expensive and time-consuming option. As a result, many microbial ecology investigations continue to suffer from a lack of appropriate replication. We evaluated two fingerprinting approaches - terminal restriction fragment length polymorphism (T-RFLP) and automated ribosomal intergenic spacer analysis (ARISA) against 454 pyrosequencing, by applying them to 225 polar soil samples from East Antarctica and the high Arctic. By incorporating local and global spatial scales into the dataset, our aim was to determine whether various approaches differed in their ability and hence utility, to identify ecological patterns. Through the reduction in the 454 sequencing data to the most dominant OTUs, we revealed that a surprisingly small proportion of abundant OTUs (< 0.25%) was driving the biological patterns observed. Overall, ARISA and T-RFLP had a similar capacity as sequencing to separate samples according to distance at a local scale, and to correlate environmental variables with microbial community structure. Pyrosequencing had a greater resolution at the global scale but all methods were capable of significantly differentiating the polar sites. We conclude fingerprinting remains a legitimate approach to generating large datasets as well as a cost-effective rapid method to identify samples for elucidating taxonomic information or diversity estimates with sequencing methods.

High-precision dating of volcanic events (A.D. 1301–1995) using ice cores from Law Dome, Antarctica

A record of volcanic activity over the period A.D. 1301–1995 has been extracted from three Law Dome ice cores (East Antarctica). The record dating is unambiguous at the annual level from A.D. 1807 to 1995 and has an uncertainty of ±1 year at A.D. 1301. Signals from 20 eruptions are preserved in the record, including those of two unknown eruptions with acid deposition beginning in A.D. 1810.8 and A.D. 1685.8. The beginning of the ice core signal from the A.D. 1815 Tambora eruption is observed in the austral summer of A.D. 1816/1817. The mean observed stratospheric transport and deposition time to Law Dome from the eruption site is 1.5 years (σ = 0.6 years) from 11 well-dated eruptions. The largest eruption observed in the Law Dome record has its maximum in A.D. 1460 with volcanic sulfate deposition beginning in the austral winter of A.D. 1459. This event is also observed in other ice core records and is attributed to the volcano Kuwae, with an eruption date in the range A.D. 1455.9–1459.9 if all sources of error are considered. This is at least three years later than the date previously ascribed by dendrochronological and historical studies.

A comparison of an optimised sequential extraction procedure and dilute acid leaching of elements in anoxic sediments, including the effects of oxidation on sediment metal partitioning.

The effect of oxidation of anoxic sediment upon the extraction of 13 elements (Cd, Sn, Sb, Pb, Al, Cr, Mn, Fe, Co, Ni, Cu, Zn, As) using the optimised Community Bureau of Reference of the European Commission (BCR) sequential extraction procedure and a dilute acid partial extraction procedure (4h, 1 molL(-1) HCl) was investigated. Elements commonly associated with the sulfidic phase, Cd, Cu, Pb, Zn and Fe exhibited the most significant changes under the BCR sequential extraction procedure. Cd, Cu, Zn, and to a lesser extent Pb, were redistributed into the weak acid extractable fraction upon oxidation of the anoxic sediment and Fe was redistributed into the reducible fraction as expected, but an increase was also observed in the residual Fe. For the HCl partial extraction, sediments with moderate acid volatile sulfide (AVS) levels (1-100 micromolg(-1)) showed no significant difference in element partitioning following oxidation, whilst sediments containing high AVS levels (>100 micromolg(-1)) were significantly different with elevated concentrations of Cu and Sn noted in the partial extract following oxidation of the sediment. Comparison of the labile metals released using the BCR sequential extraction procedure (SigmaSteps 1-3) to labile metals extracted using the dilute HCl partial extraction showed that no method was consistently more aggressive than the other, with the HCl partial extraction extracting more Sn and Sb from the anoxic sediment than the BCR procedure, whilst the BCR procedure extracted more Cr, Co, Cu and As than the HCl extraction.

Suppressed ion chromatography methods for the routine determination of ultra low level anions and cations in ice cores

The concentration of trace ionic species in snow and ice samples was determined using suppressed ion chromatography (IC) with conductivity detection and ultra-clean sample preparation techniques. Trace anion species were determined in a single 24-min run by combining sample preconcentration with gradient elution using Na2B4O7 eluent. The detection limits (ranging from 0.001 to 0.006 microM) are the lowest reported in the literature. Cation species were analysed by direct injection of 0.25 ml and isocratic elution with a H2SO4 eluent. The clean preparation techniques showed no evidence of a difference (Students t-test) between Milli-Q water samples analysed directly and processed Milli-Q ice samples. These robust, ultra-clean IC methods were routinely applied to the analysis of large number of samples to produce a high-resolution trace ion ice core record from Law Dome, East Antarctica.

Ice‐core evidence for a small solar‐source of atmospheric nitrate

A precision-dated ice-core nitrate record from Law Dome, coastal East Antarctica is compared to the timing of known solar proton events and geomagnetic storms over the period 1888 to 1995. We find statistical evidence for a significant (P < 0.03) but small elevation in mean nitrate concentrations following the solar events (∼11% over the 12 months beginning 3 months post-event). While some solar events are identifiable in the nitrate record, most are not distinguishable from the background noisy signal (which has numerous large peaks), and some solar events show no nitrate elevation above even mean levels.

Lead isotopic signatures in Antarctic marine sediment cores: A comparison between 1 M HCl partial extraction and HF total digestion pre-treatments for discerning anthropogenic inputs

Sensitive analytical techniques are typically required when dealing with samples from Antarctica as even low concentrations of contaminants can have detrimental environmental effects. Magnetic Sector ICP-MS is an ideal technique for environmental assessment as it offers high sensitivity, multi-element capability and the opportunity to determine isotope ratios. Here we consider the Pb isotope record of five marine sediment cores collected from three sites in the Windmill Islands area of East Antarctica: Brown Bay adjacent to the current Australian station Casey, Wilkes near the abandoned US/Australian Station and McGrady Cove lying midway between the two. Two sediment pre-treatment approaches were considered, namely partial extraction with 1M HCl and total dissolution involving HF. Lead isotope ratio measurements made following sediment partial extraction provided a more sensitive indication of Pb contamination than either Pb concentrations alone (irrespective of sample pre-treatment method) or isotope ratios made after HF digestion, offering greater opportunity for discrimination between impacted and natural/geogenic samples and sites. Over 90% of the easily extractable Pb from sediments near Casey was anthropogenic in origin, consisting of Pb from major Australian deposits. At Wilkes impact from discarded batteries with a unique isotopic signature was found to be a key source of Pb contamination to the marine environment with ~70-80% of Pb being anthropogenic in origin. The country and source of origin of these batteries remain unknown. Little evidence was found suggesting contamination at Wilkes by Pb originating from the major US source, Missouri. No definitive assessment could be made regarding Pb impact at McGrady Cove as the collected sediment core was of insufficient depth. Although Pb isotope ratio signatures may indicate anthropogenic input, spatial concentration gradients at nearby Brown Bay suggest contamination at McGrady Cove is unlikely. We recommend Pb isotopic analysis following 1M HCl partial extraction pre-treatment as a powerful and sensitive method for tracing Pb contamination in marine sediments.

Post-depositional movement of methanesulphonic acid at Law Dome, Antarctica, and the influence of accumulation rate

Abstract A series of ice cores from sites with different snow-accumulation rates across Law Dome, East Antarctica, was investigated for methanesulphonic acid (MSA) movement. the precipitation at these sites (up to 35 km apart) is influenced by the same air masses, the principal difference being the accumulation rate. At the low-accumulation-rate W20k site (0.17m ice equivalent), MSAwas completely relocated from the summer to winter layer. Moderate movement was observed at the intermediate-accumulation-rate site (0.7m ice equivalent), Dome Summit South (DSS), while there was no evidence of movement at the high-accumulation-rate DE08 site (1.4m ice equivalent). the main DSS record of MSA covered the epoch AD 1727–2000 and was used to investigate temporal post-depositional changes. Co-deposition of MSA and sea-salt ions was observed in the surface layers, outside of the main summer MSA peak,which complicates interpretation of these peaks as evidence of movement in deeper layers. A seasonal study of the 273 year DSS record revealed MSA migration predominantly from summer into autumn (in the up-core direction), but this migration was suppressed during the Tambora (1815) and unknown (1809) volcanic eruption period, and enhanced during an epoch (1770–1800) with high summer nitrate levels. A complex interaction between the gradients in nss-sulphate, nitrate and sea salts (which are influenced by accumulation rate) is believed to control the rate and extent of movement of MSA.

A method to reconstruct past accumulation rates in alpine firn regions: A study on Fiescherhorn, Swiss Alps

Annual snow layers in the accumulation zone of glaciers become thinner by viscous deformation while moving to greater depth. The reconstruction of the accumulation rate history requires the correction of the thickness of annual layers. We apply a novel method to determine the vertical velocity by repeated survey with a caliper probe of grooves scratched into the wall of a borehole. With this information and the assumptions of steady state velocity and density fields, the correction of layer thicknesses can be determined without knowledge of the ice density profile and thus can be applied to boreholes without ice cores. The method is applied to a borehole on Fiescherhorn, Swiss Alps, resulting in a substantially larger correction than with the simpler method of Nye (1963). Copyright 2006 by the American Geophysical Union.

Antarctic volcanic flux ratios from Law Dome ice cores

Abstract Explosive volcanic eruptions can inject large quantities of sulphur dioxide into the stratosphere. the aerosols that result from oxidation of the sulphur dioxide can produce significant cooling of the troposphere by reflecting or absorbing solar radiation. It is possible to obtain an estimate of the relative stratospheric sulphur aerosol concentration produced by different volcanoes by comparing sulphuric acid fluxes determined by analysis of polar ice cores. Here,we use a non-sea-salt sulphate time series derived from three well-dated Law Dome ice cores to investigate sulphuric acid flux ratios for major eruptions over the period AD 1301–1995. We use additional data from other cores to investigate systematic spatial variability in the ratios. Only for the Kuwae eruption (Law Dome ice date AD 1459.5) was the H2SO4 flux larger than that deposited by Tambora (Law Dome ice date AD 1816.7).

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems

Landscape heterogeneity impacts community assembly in animals and plants, but it is not clear if this ecological concept extends to microbes. To examine this question, we chose to investigate polar soil environments from the Antarctic and Arctic, where microbes often form the major component of biomass. We examined soil environments that ranged in connectivity from relatively well-connected slopes to patchy, fragmented landforms that comprised isolated frost boils. We found landscape connectedness to have a significant correlation with microbial community structure and connectivity, as measured by co-occurrence networks. Soils from within fragmented landforms appeared to exhibit less local environmental heterogeneity, harboured more similar communities, but fewer biological associations than connected landforms. This effect was observed at both poles, despite the geographical distances and ecological differences between them. We suggest that microbial communities inhabiting well-connected landscape elements respond consistently to regional-scale gradients in biotic and edaphic factors. Conversely, the repeated freeze thaw cycles that characterize fragmented landscapes create barriers within the landscape and act to homogenize the soil environment within individual frost boils and consequently the microbial communities. We propose that lower microbial connectivity in the fragmented landforms is a function of smaller patch size and continual disturbances following soil mixing.