Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods.

Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic "k-selected" bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea, and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in an increase in diversity from 14 to 57 microfungi OTUs compared to standard cultivation. Furthermore, the SSMS offers the opportunity to retrieve a greater diversity of bacterial and fungal taxa for future exploitation.

The Roles of Sea-Ice, Light and Sedimentation in Structuring Shallow Antarctic Benthic Communities.

On polar coasts, seasonal sea-ice duration strongly influences shallow marine environments by affecting environmental conditions, such as light, sedimentation, and physical disturbance. Sea-ice dynamics are changing in response to climate, but there is limited understanding of how this might affect shallow marine environments and benthos. Here we present a unique set of physical and biological data from a single region of Antarctic coast, and use it to gain insights into factors shaping polar benthic communities. At sites encompassing a gradient of sea-ice duration, we measured temporal and spatial variation in light and sedimentation and hard-substrate communities at different depths and substrate orientations. Biological trends were highly correlated with sea-ice duration, and appear to be driven by opposing gradients in light and sedimentation. As sea-ice duration decreased, there was increased light and reduced sedimentation, and concurrent shifts in community structure from invertebrate to algal dominance. Trends were strongest on shallower, horizontal surfaces, which are most exposed to light and sedimentation. Depth and substrate orientation appear to mediate exposure of benthos to these factors, thereby tempering effects of sea-ice and increasing biological heterogeneity. However, while light and sedimentation both varied spatially with sea-ice, their dynamics differed temporally. Light was sensitive to the site-specific date of sea-ice breakout, whereas sedimentation fluctuated at a regional scale coincident with the summer phytoplankton bloom. Sea-ice duration is clearly the overarching force structuring these shallow Antarctic benthic communities, but direct effects are imposed via light and sedimentation, and mediated by habitat characteristics.

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.

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.

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.

A study of metal and metalloid contaminant availability in Antarctic marine sediments.

Previous studies of impacted sites near Casey Station, Antarctica, have revealed elevated concentrations of metals and metalloids, particularly Cd, Cu, Fe, Pb, Sn and Zn in marine sediments. However, attempts to understand the availability and mobility of contaminant elements have not provided a true understanding of speciation. The current work shows, for the first time, that sediments in Brown Bay, an embayment adjacent to the Thala Valley waste disposal site, have elevated concentrations of sulfide, well in excess of that required to bind contaminant metals such as Cd, Cu, Pb and Zn. Furthermore, sediment characterisation using the BCR sequential extraction scheme has shown metal partitioning consistent with sulfides being the controlling factor in metal availability, thus explaining the low porewater concentrations of these metals. The speciation of Sn in Brown Bay, however, is still unclear with the BCR sequential extraction scheme partitioning Sn predominantly into the residual fraction despite Sn being readily extracted by dilute HCl.

Monitoring the remediation of a near shore waste disposal site in Antarctica using the amphipod Paramoera walkeri and diffusive gradients in thin films (DGTs).

The water quality of a marine embayment (Brown Bay) was monitored during the remediation of an abandoned waste disposal site at Casey Station, East Antarctica, using a combination of biomonitoring and chemical methods. The Antarctic amphipod Paramoera walkeri, in field mesocosms suspended in the water column, was deployed adjacent to the site and at two reference sites for periods of 14 days, repeated three times during the remediation period (December to February). Diffusive gradients in thin film (DGT) samplers were deployed for the same periods to provide estimates of dissolved metals. No difference in mortality of amphipods was observed between Brown Bay and reference sites. There were significant differences, however, in accumulated metal concentrations between amphipods from Brown Bay and reference sites, with greater concentrations of antimony, copper, cadmium, lead, iron and tin at Brown Bay. The melt water/runoff treatment strategy employed for the remediation was successful in preventing acute toxic effects, but water quality was reduced at Brown Bay, where increased metal bioavailability may have been high enough to induce chronic effects in some biota. DGT samplers were less sensitive than amphipods in detecting differences in metal concentrations between sites, indicating that metals bound to suspended particulates were a potentially significant source of contamination.

Baseline metal concentrations in Paramoera walkeri from East Antarctica.

Remediation of the Thala Valley waste disposal site near Casey Station, East Antarctica was conducted in the austral summer of 2003/2004. Biomonitoring of the adjacent marine environment was undertaken using the gammaridean amphipod Paramoera walkeri as a sentinel species [Stark, J.S., Johnstone, G.J., Palmer, A.S., Snape, I., Larner, B.L., Riddle, M.J., in press, . Monitoring the remediation of a near shore waste disposal site in Antarctica using the amphipod Paramoera walkeri and diffusive gradients in thin films (DGTs). Marine Pollution Bulletin and references therein]. Determination of uptake of metals and hypothesis testing for differences that could be attributed to contamination required the establishment of baseline metal concentrations in P. walkeri. Baseline metal concentrations from two reference locations in the Windmill Islands are presented here. P. walkeri was a found to be a sensitive bioaccumulating organism that recorded spatial and temporal variability at the reference sites. Measurement of metals in P. walkeri required the development of a simple digestion procedure that used concentrated nitric acid. For the first time, rare earth metals were determined with additional clean procedures required to measure ultra low concentrations using magnetic sector ICP-MS. Certified and in-house reference materials were employed to ensure method reliability.

Ice core evidence for Antarctic sea ice decline since the 1950s.

The instrumental record of Antarctic sea ice in recent decades does not reveal a clear signature of warming despite observational evidence from coastal Antarctica. Here we report a significant correlation (P < 0.002) between methanesulphonic acid (MSA) concentrations from a Law Dome ice core and 22 years of satellite-derived sea ice extent (SIE) for the 80 degrees E to 140 degrees E sector. Applying this instrumental calibration to longer term MSA data (1841 to 1995 A.D.) suggests that there has been a 20% decline in SIE since about 1950. The decline is not uniform, showing large cyclical variations, with periods of about 11 years, that confuse trend detection over the relatively short satellite era.

On-column ion-exchange preconcentration of inorganic anions in open tubular capillary electrochromatography with elution using transient-isotachophoretic gradients. 3. Implementation and method development.

A solid-phase extraction method based on an ion-exchange retention mechanism has been used for in-line preconcentration of inorganic anions prior to their separation by capillary electrophoresis (CE). A single capillary containing a preconcentration and a separation zone has been used in a commercial CE instrument without instrumental modification. Analyte anions were retained on a preconcentration zone comprising an adsorbed layer of cationic latex particles, while separation was achieved in a separation zone comprising fused silica modified by adsorption of a cationic polymer. Elution of the adsorbed analytes was achieved using an eluotropic gradient formed by a transient isotachophoretic boundary between a fluoride electrolyte and a naphthalenedisulfonate electrolyte. Optimization of the electrolyte concentrations, sample injection times, and back-flushing times allowed the successful separation of sub-ppb levels of inorganic anions using a 100-min injection at 2 bar pressure, introducing over 40 capillary volumes of sample. A method based on a 10-min injection allowed a 100-fold increase in sensitivity over conventional hydrodynamic injection for Br-, I-, NO3-, CrO4(2-), and MoO4(2-) with a total analysis time of 25 min. Detection limits were dependent on the injection time but were in the range 2.2-11.6 ppb for a 10-min injection time. This approach was used to determine NO3- in Antarctic ice cores where the analysis could be performed using a sample volume 100 times less than that used for ion chromatography.