Atmospheric trace gases support primary production in Antarctic desert surface soil.

Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities. Given that phototroph abundance varies across these Antarctic soils, an enduring question is what supports life in those communities with low photosynthetic capacity. Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation. Soil microcosms aerobically scavenged atmospheric H2 and CO at rates sufficient to sustain their theoretical maintenance energy and mediated substantial levels of chemosynthetic but not photosynthetic CO2 fixation. We propose that atmospheric H2, CO2 and CO provide dependable sources of energy and carbon to support these communities, which suggests that atmospheric energy sources can provide an alternative basis for ecosystem function to solar or geological energy sources. Although more extensive sampling is required to verify whether this process is widespread in terrestrial Antarctica and other oligotrophic habitats, our results provide new understanding of the minimal nutritional requirements for life and open the possibility that atmospheric gases support life on other planets.

From urban municipalities to polar bioremediation: the characterisation and contribution of biogenic minerals for water treatment.

Minerals of biological origin have shown significant potential for the separation of contaminants from water worldwide. This study details the contribution of biologically derived minerals to water treatment operations, with a focus on filtration media from urban municipalities and remote cold regions. The results support biofilm-embedded iron and manganese to be the building blocks of biogenic mineral development on activated carbon and nutrient-amended zeolites. The presence of similar iron and manganese oxidising bacterial species across all filter media supports the analogous morphologies of biogenic minerals between sites and suggests that biological water treatment processes may be feasible across a range of climates. This is the first time the stages of biogenic mineral formation have been aligned with comprehensive imaging of the biofilm community and bacterial identification; especially with respect to cold regions. Where biogenic mineral formation occurs on filter media, the potential exists for enhanced adsorption for a range of organic and inorganic contaminants and improved longevity of filter media beyond the adsorption or exchange capacities of the raw material.

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.

Application of controlled nutrient release to permeable reactive barriers.

The application of controlled release nutrient (CRN) materials to permeable reactive barriers to promote biodegradation of petroleum hydrocarbons in groundwater was investigated. The longevity of release, influence of flow velocity and petroleum hydrocarbon concentration on nutrient release was assessed using soluble and ion exchange CRN materials; namely Polyon™ and Zeopro™. Both CRN materials, assessed at 4 °C and 23 °C, demonstrated continuing release of nitrogen, phosphorus and potassium (N-P-K) at 3500 bed volumes passing, with longer timeframes of N-P-K release at 4 °C. Zeopro™-activated carbon mixtures demonstrated depletion of N-P-K prior to 3500 bed volumes passing. Increased flow velocity was shown to lower nutrient concentrations in Polyon™ flow cells while nutrient release from Zeopro™ was largely unchanged. The presence of petroleum hydrocarbons, at 1.08 mmol/L and 3.25 mmol/L toluene, were not shown to alter nutrient release from Polyon™ and Zeopro™ across 14 days. These findings suggest that Polyon™ and Zeopro™ may be suitable CRN materials for application to PRBs in low nutrient environments.

Validating the scalability of soft X-ray spectromicroscopy for quantitative soil ecology and biogeochemistry research.

Synchrotron-based soft-X-ray scanning transmission X-ray microscopy (STXM) has the potential to provide nanoscale resolution of the associations among biological and geological materials. However, standard methods for how samples should be prepared, measured, and analyzed to allow the results from these nanoscale imaging and spectroscopic tools to be scaled to field scale biogeochemical results are not well established. We utilized a simple sample preparation technique that allows one to assess detailed mineral, metal, and microbe spectroscopic information at the nano- and microscale in soil colloids. We then evaluated three common approaches to collect and process nano- and micronscale information by STXM and the correspondence of these approaches to millimeter scale soil measurements. Finally, we assessed the reproducibility and spatial autocorrelation of nano- and micronscale protein, Fe(II) and Fe(III) densities in a soil sample. We demonstrate that linear combination fitting of entire spectra provides slightly different Fe(II) mineral densities compared to image resonance difference mapping but that difference mapping results are highly reproducible between among sample replicates. Further, STXM results scale to the mm scale in complex systems with an approximate geospatial range of 3 µm in these samples.

Bacterial targets as potential indicators of diesel fuel toxicity in subantarctic soils.

Appropriate remediation targets or universal guidelines for polar regions do not currently exist, and a comprehensive understanding of the effects of diesel fuel on the natural microbial populations in polar and subpolar soils is lacking. Our aim was to investigate the response of the bacterial community to diesel fuel and to evaluate if these responses have the potential to be used as indicators of soil toxicity thresholds. We set up short- and long-exposure tests across a soil organic carbon gradient. Utilizing broad and targeted community indices, as well as functional genes involved in the nitrogen cycle, we investigated the bacterial community structure and its potential functioning in response to special Antarctic blend (SAB) diesel fuel. We found the primary effect of diesel fuel toxicity was a reduction in species richness, evenness, and phylogenetic diversity, with the resulting community heavily dominated by a few species, principally Pseudomonas. The decline in richness and phylogenetic diversity was linked to disruption of the nitrogen cycle, with species and functional genes involved in nitrification significantly reduced. Of the 11 targets we evaluated, we found the bacterial amoA gene indicative of potential ammonium oxidation, the most suitable indicator of toxicity. Dose-response modeling for this target generated an average effective concentration responsible for 20% change (EC20) of 155 mg kg(-1), which is consistent with previous Macquarie Island ecotoxicology assays. Unlike traditional single-species tolerance testing, bacterial targets allowed us to simultaneously evaluate more than 1,700 species from 39 phyla, inclusive of rare, sensitive, and functionally relevant portions of the community.

Influence of liquid water and soil temperature on petroleum hydrocarbon toxicity in Antarctic soil.

Fuel spills in Antarctica typically occur in rare ice-free oases along the coast, which are areas of extreme seasonal freezing. Spills often occur at subzero temperatures, but little is known of ecosystem sensitivity to pollutants, in particular the influence that soil liquid water and low temperature have on toxicity of petroleum hydrocarbons (PHC) in Antarctic soil. To evaluate PHC toxicity, 32 locations at an aged diesel spill site in Antarctica were sampled nine times to encompass frozen, thaw, and refreeze periods. Toxicity was assessed using potential activities of substrate-induced respiration, basal respiration, nitrification, denitrification, and metabolic quotient as well as microbial community composition and bacterial biomass. The most sensitive indicator was community composition with a PHC concentration effecting 25% of the population (EC25) of 800 mg/kg, followed by nitrification (2,000 mg/kg), microbial biomass (2,400 mg/kg), and soil respiration (3,500 mg/kg). Despite changes in potential microbial activities and composition over the frozen, thaw, and refreeze period, the sensitivity of these endpoints to PHC did not change with liquid water or temperature. However, the variability associated with ecotoxicity data increased at low liquid water contents. As a consequence of this variability, highly replicated (n = 50) experiments are needed to quantify a 25% ecological impairment by PHCs in Antarctic soils at a 95% level of significance. Increases in biomass and respiration associated with changes in community composition suggest that PHC contamination in Antarctic soils may have irrevocable effects on the ecosystem.

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.

Soil biogeochemical toxicity end points for sub-Antarctic islands contaminated with petroleum hydrocarbons.

Sub-Antarctic islands have been subjected to petroleum hydrocarbon spills, yet no information is available regarding the toxicity of petroleum hydrocarbons to these subpolar soils. The purpose of the present study was to identify soil biogeochemical toxicity end points for petroleum hydrocarbon contamination in sub-Antarctic soil. Soil from Macquarie Island, a sub-Antarctic island south of Australia, was collected and exposed to 10 concentrations of Special Antarctic Blend (SAB) diesel fuel, ranging from 0 to 50,000 mg fuel/kg soil, for a 21-d period. The sensitivity of nitrification, denitrification, carbohydrate utilization, and total soil respiration to SAB fuel was assessed. Potential nitrification activity was the most sensitive indicator of SAB contamination assessed for nitrogen cycling, with an IC20 (concentration that results in a 20% change from the control response) of 190 mg fuel/ kg soil. Potential denitrification activity was not as sensitive to SAB contamination, with an IC20 of 950 mg fuel/kg soil for nitrous oxide production. Nitrous oxide consumption was unaffected by SAB contamination. Carbohydrate utilization (respiration caused by sucrose) was a more sensitive indicator (IC20, 16 mg fuel/kg soil) of SAB contamination than total respiration (IC20, 220 mg fuel/kg soil). However, total soil respiration was a more responsive measurement end point, increasing soil respiration over a 72-h period by 17 mg of CO2, compared to a change of only 2.1 mg of CO2 for carbohydrate utilization. Our results indicate that IC20s varied between 16 to 950 mg fuel/kg soil for Macquarie Island soil spiked with SAB diesel fuel. These results indicate that current cleanup levels derived from temperate zones may be too liberal for soil contamination in sub-Antarctic islands.

Biodegradation of petroleum products in experimental plots in Antarctic marine sediments is location dependent.

Clean sediment collected from O'Brien Bay, East Antarctica, was artificially contaminated with a mix of Special Antarctic Blend diesel fuel and lubricating oil and deployed in two uncontaminated locations (O'Brien and Sparkes Bays) and a previously contaminated bay (Brown Bay) to evaluate whether a history of prior contamination would influence the biodegradation process. Detailed analysis of the hydrocarbon composition in the sediment after 11 weeks revealed different patterns of degradation in each bay. Biodegradation indices showed that hydrocarbon biodegradation occurred in all three bays but was most extensive in Brown Bay. This study shows that even within a relatively small geographical area, the longevity of hydrocarbons in Antarctic marine sediments can be variable. Our results are consistent with faster natural attenuation of spilt oil at sites with previous exposure to oil but further work is needed to confirm this. Such information would be useful when evaluating the true risk and longevity of oils spills.

Permeable bio-reactive barriers to address petroleum hydrocarbon contamination at subantarctic Macquarie Island.

A reliance on diesel generated power and a history of imperfect fuel management have created a legacy of petroleum hydrocarbon contamination at subantarctic Macquarie Island. Increasing environmental awareness and advances in contaminant characterisation and remediation technology have fostered an impetus to reduce the environmental risk associated with legacy sites. A funnel and gate permeable bio-reactive barrier (PRB) was installed in 2014 to address the migration of Special Antarctic Blend diesel from a spill that occurred in 2002, as well as older spills and residual contaminants in the soil at the Main Power House. The PRB gate comprised of granular activated carbon and natural clinoptilolite zeolite. Petroleum hydrocarbons migrating in the soil water were successfully captured on the reactive materials, with concentrations at the outflow of the barrier recorded as being below reporting limits. The nutrient and iron concentrations delivered to the barrier demonstrated high temporal variability with significant iron precipitation observed across the bed. The surface of the granular activated carbon was largely free from cell attachment while natural zeolite demonstrated patchy biofilm formation after 15 months following PRB installation. This study illustrates the importance of informed material selection at field scale to ensure that adsorption and biodegradation processes are utilised to manage the environmental risk associated with petroleum hydrocarbon spills. This study reports the first installation of a permeable bio-reactive barrier in the subantarctic.

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.

Evaluation of diffusive gradients in thin film (DGT) samplers for measuring contaminants in the Antarctic marine environment.

This work has been the first application of DGT samplers for measuring metals in water and sediment porewater in the Antarctic environment, and whilst DGT water sampling was restricted to quantification of Cd, Fe and Ni, preconcentration using Empore chelating disks provided results for an additional nine elements (Sn, Pb, Al, Cr, Mn, Co, Cu, Zn, As). Although higher concentrations were measured for some metals (Cd, Ni, Pb) using the Empore technique, most likely due to particulate-bound or colloidal species becoming entrapped in the Empore chelating disks, heavy metal concentrations in the impacted Brown Bay were found to be comparable with the non-impacted O'Brien Bay. Sediment porewater sampling using DGT also indicated little difference between Brown Bay and O'Brien Bay for many metals (Cd, Al, Cr, Co, Ni, Cu), however, greater amounts of Pb, Mn, Fe and As were accumulated in DGT probes deployed in Brown Bay compared with O'Brien Bay, and a higher accumulation of Sn was observed in Brown Bay inner than any of the other three sites sampled. Comparison of DGT derived porewater concentrations with actual porewater concentrations showed limited resupply of Cd, Pb, Al, Cr, Mn, Co, Ni, Cu, Zn and As from the solid phase to porewater, with these metals appearing to be strongly bound to the sediment, however, resupply of Fe and Sn was apparent. Based upon our observations here, we suggest that Sn, and to a lesser extent Pb, are critical contaminants.

Investigation of evaporation and biodegradation of fuel spills in Antarctica: II-extent of natural attenuation at Casey Station.

In many temperate regions, fuel and oil spills are sometimes managed simply by allowing natural degradation to occur, while monitoring soils and groundwater to ensure that there is no off-site migration or on-site impact. To critically assess whether this approach is suitable for coastal Antarctic sites, we investigated the extent of evaporation and biodegradation at three old fuel spills at Casey Station. Where the contaminants migrated across frozen ground, probably beneath snow, approximately half the fuel evaporated in the first few months prior to infiltration at the beginning of summer. Once in the ground, however, evaporation rates were negligible. In contrast, minor spills from fuel drums buried in an abandoned waste disposal site did not evaporate to the same extent. Biodegradation within all three spill sites is generally very minor. We conclude that natural attenuation is not a suitable management strategy for fuel-contaminated soils in Antarctic coastal regions.

Evaluation of geochemical methods for discrimination of metal contamination in Antarctic marine sediments: a case study from Casey Station.

Detecting anthropogenic metal contamination in regional surveys can be particularly difficult when there is a lack of pre-disturbance data, especially when trying to differentiate low to moderate levels of contamination from background values. Furthermore, comparisons with other regional studies are confounded by differing analytical methods used and variations in sediment properties such as grainsize. Several types of geochemical technique, including weak acid partial extraction, strong acid extractions and total digestion have been used. Attempts have been made to overcome the influence that grainsize has on chemical concentrations in heterogeneous environments by analysing the fines, typically the mud fraction (<63 microm), in an attempt to improve the detection of anthropogenic contamination. Here we compare a weak acid partial extraction using 1M HCl and total digestion methods for a regional survey of reference and impacted sites in Antarctica using both whole sediment (<2 mm) and mud (<63 microm) fractions. The 1M partial extraction on whole sediment (<2 mm) most closely distinguished weakly, or moderately, impacted sites from reference locations. It also identified small scale within-location spatial variation in metal contamination that the total digest did not detect. Compared with total digests or analysis of the <63 microm fraction alone, this method minimised the possibility of a Type II statistical error in the regional survey - that is, failing to identify a site as being contaminated when it has elevated metal concentrations. To allow inter-regional comparison of sediment chemistry data from elsewhere in Antarctica, and also more generally, we recommend a 1M HCl partial extraction on whole sediment (<2 mm).

In situ lubricant degradation in Antarctic marine sediments. 1. Short-term changes.

A large-scale, in situ experiment was set up near the Bailey Peninsula area (Casey Station, East Antarctica) to monitor the natural attenuation of synthetic lubricants in marine sediments over five years. Here, we report the short-term changes after 5 and 56 weeks. The lubricants tested were an unused and used Mobil lubricant (0W/40; Exxon Mobil, Irving, TX, USA) and a biodegradable alternative (0W/20; Fuchs Lubricants, Harvey, IL, USA). Clean sediment was collected, contaminated with the lubricants, and deployed by divers onto the seabed in a randomized block design. The sampled sediments were analyzed by gas chromatography-flame-ionization detector and gas chromatography-mass spectrometry with selective ion monitoring. The base fluid of all lubricant treatments did not decrease significantly after 56 weeks in situ. Alkanoate esters of 1,1,1-tris(hydroxymethyl)propane in the biodegradable and unused lubricants were degraded extensively in situ; however, these esters constituted only a minor proportion of the lubricant volume. The additives, alkylated naphthalenes and substituted diphenylamines, were fairly resistant to degradation, which is of environmental concern because of their toxicity. The biodegradable lubricant did not break down to recognized biodegradable thresholds and, as such, should not be classified as biodegradable under Antarctic marine conditions. A separate experiment was conducted to determine the influence of sediment preparation and deployment on compound ratios within the lubricants, and we found that preparation and deployment of the contaminated sediments had only a minor effect on compound recovery. Further monitoring of this in situ experiment will provide much needed information about the long-term natural attenuation of lubricants.

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.

The performance of ammonium exchanged zeolite for the biodegradation of petroleum hydrocarbons migrating in soil water.

Nitrogen deficiency has been identified as the main inhibiting factor for biodegradation of petroleum hydrocarbons in low nutrient environments. This study examines the performance of ammonium exchanged zeolite to enhance biodegradation of petroleum hydrocarbons migrating in soil water within laboratory scale flow cells. Biofilm formation and biodegradation were accelerated by the exchange of cations in soil water with ammonium in the pores of the exchanged zeolite when compared with natural zeolite flow cells. These results have implications for sequenced permeable reactive barrier design and the longevity of media performance within such barriers at petroleum hydrocarbon contaminated sites deficient in essential soil nutrients.